Molecular	O
Dissection	O
of	O
Xyloglucan	B-chemical
Recognition	O
in	O
a	O
Prominent	O
Human	B-species
Gut	O
Symbiont	O

Polysaccharide	B-gene
utilization	I-gene
loci	I-gene
(	O
PUL	B-gene
)	O
within	O
the	O
genomes	O
of	O
resident	O
human	B-species
gut	O
Bacteroidetes	B-taxonomy_domain
are	O
central	O
to	O
the	O
metabolism	O
of	O
the	O
otherwise	O
indigestible	O
complex	O
carbohydrates	B-chemical
known	O
as	O
“	O
dietary	O
fiber	O
.”	O
However	O
,	O
functional	O
characterization	O
of	O
PUL	B-gene
lags	O
significantly	O
behind	O
sequencing	O
efforts	O
,	O
which	O
limits	O
physiological	O
understanding	O
of	O
the	O
human	B-species
-	O
bacterial	B-taxonomy_domain
symbiosis	O
.	O

In	O
particular	O
,	O
the	O
molecular	O
basis	O
of	O
complex	B-chemical
polysaccharide	I-chemical
recognition	O
,	O
an	O
essential	O
prerequisite	O
to	O
hydrolysis	O
by	O
cell	O
surface	O
glycosidases	B-protein_type
and	O
subsequent	O
metabolism	O
,	O
is	O
generally	O
poorly	O
understood	O
.	O

Here	O
,	O
we	O
present	O
the	O
biochemical	B-experimental_method
,	I-experimental_method
structural	I-experimental_method
,	I-experimental_method
and	I-experimental_method
reverse	I-experimental_method
genetic	I-experimental_method
characterization	I-experimental_method
of	O
two	O
unique	O
cell	B-protein_type
surface	I-protein_type
glycan	I-protein_type
-	I-protein_type
binding	I-protein_type
proteins	I-protein_type
(	O
SGBPs	B-protein_type
)	O
encoded	O
by	O
a	O
xyloglucan	B-gene
utilization	I-gene
locus	I-gene
(	O
XyGUL	B-gene
)	O
from	O
Bacteroides	B-species
ovatus	I-species
,	O
which	O
are	O
integral	O
to	O
growth	O
on	O
this	O
key	O
dietary	O
vegetable	B-taxonomy_domain
polysaccharide	B-chemical
.	O

Biochemical	B-experimental_method
analysis	I-experimental_method
reveals	O
that	O
these	O
outer	B-protein_type
membrane	I-protein_type
-	I-protein_type
anchored	I-protein_type
proteins	I-protein_type
are	O
in	O
fact	O
exquisitely	O
specific	O
for	O
the	O
highly	O
branched	O
xyloglucan	B-chemical
(	O
XyG	B-chemical
)	O
polysaccharide	B-chemical
.	O

The	O
crystal	B-evidence
structure	I-evidence
of	O
SGBP	B-protein
-	I-protein
A	I-protein
,	O
a	O
SusD	B-protein
homolog	O
,	O
with	O
a	O
bound	B-protein_state
XyG	B-chemical
tetradecasaccharide	B-chemical
reveals	O
an	O
extended	O
carbohydrate	B-site
-	I-site
binding	I-site
platform	I-site
that	O
primarily	O
relies	O
on	O
recognition	O
of	O
the	O
β	B-chemical
-	I-chemical
glucan	I-chemical
backbone	O
.	O

The	O
unique	O
,	O
tetra	B-structure_element
-	I-structure_element
modular	I-structure_element
structure	B-evidence
of	O
SGBP	B-protein
-	I-protein
B	I-protein
is	O
comprised	O
of	O
tandem	B-structure_element
Ig	I-structure_element
-	I-structure_element
like	I-structure_element
folds	I-structure_element
,	O
with	O
XyG	B-chemical
binding	O
mediated	O
at	O
the	O
distal	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
.	O

Despite	O
displaying	O
similar	O
affinities	B-evidence
for	O
XyG	B-chemical
,	O
reverse	B-experimental_method
-	I-experimental_method
genetic	I-experimental_method
analysis	I-experimental_method
reveals	O
that	O
SGBP	B-protein
-	I-protein
B	I-protein
is	O
only	O
required	O
for	O
the	O
efficient	O
capture	O
of	O
smaller	O
oligosaccharides	B-chemical
,	O
whereas	O
the	O
presence	O
of	O
SGBP	B-protein
-	I-protein
A	I-protein
is	O
more	O
critical	O
than	O
its	O
carbohydrate	B-chemical
-	O
binding	O
ability	O
for	O
growth	O
on	O
XyG	B-chemical
.	O
Together	O
,	O
these	O
data	O
demonstrate	O
that	O
SGBP	B-protein
-	I-protein
A	I-protein
and	O
SGBP	B-protein
-	I-protein
B	I-protein
play	O
complementary	O
,	O
specialized	O
roles	O
in	O
carbohydrate	B-chemical
capture	O
by	O
B	B-species
.	I-species
ovatus	I-species
and	O
elaborate	O
a	O
model	O
of	O
how	O
vegetable	B-taxonomy_domain
xyloglucans	B-chemical
are	O
accessed	O
by	O
the	O
Bacteroidetes	B-taxonomy_domain
.	O

The	O
Bacteroidetes	B-taxonomy_domain
are	O
dominant	O
bacteria	B-taxonomy_domain
in	O
the	O
human	B-species
gut	O
that	O
are	O
responsible	O
for	O
the	O
digestion	O
of	O
the	O
complex	B-chemical
polysaccharides	I-chemical
that	O
constitute	O
“	O
dietary	O
fiber	O
.”	O
Although	O
this	O
symbiotic	O
relationship	O
has	O
been	O
appreciated	O
for	O
decades	O
,	O
little	O
is	O
currently	O
known	O
about	O
how	O
Bacteroidetes	B-taxonomy_domain
seek	O
out	O
and	O
bind	O
plant	B-taxonomy_domain
cell	O
wall	O
polysaccharides	B-chemical
as	O
a	O
necessary	O
first	O
step	O
in	O
their	O
metabolism	O
.	O

Here	O
,	O
we	O
provide	O
the	O
first	O
biochemical	B-experimental_method
,	I-experimental_method
crystallographic	I-experimental_method
,	I-experimental_method
and	I-experimental_method
genetic	I-experimental_method
insight	I-experimental_method
into	O
how	O
two	O
surface	B-protein_type
glycan	I-protein_type
-	I-protein_type
binding	I-protein_type
proteins	I-protein_type
from	O
the	O
complex	O
Bacteroides	B-species
ovatus	I-species
xyloglucan	B-gene
utilization	I-gene
locus	I-gene
(	O
XyGUL	B-gene
)	O
enable	O
recognition	O
and	O
uptake	O
of	O
this	O
ubiquitous	O
vegetable	B-taxonomy_domain
polysaccharide	B-chemical
.	O

Our	O
combined	O
analysis	O
illuminates	O
new	O
fundamental	O
aspects	O
of	O
complex	B-chemical
polysaccharide	I-chemical
recognition	O
,	O
cleavage	O
,	O
and	O
import	O
at	O
the	O
Bacteroidetes	B-taxonomy_domain
cell	O
surface	O
that	O
may	O
facilitate	O
the	O
development	O
of	O
prebiotics	O
to	O
target	O
this	O
phylum	O
of	O
gut	O
bacteria	B-taxonomy_domain
.	O

The	O
human	B-species
gut	O
microbiota	B-taxonomy_domain
influences	O
the	O
course	O
of	O
human	B-species
development	O
and	O
health	O
,	O
playing	O
key	O
roles	O
in	O
immune	O
stimulation	O
,	O
intestinal	O
cell	O
proliferation	O
,	O
and	O
metabolic	O
balance	O
.	O

This	O
microbial	B-taxonomy_domain
community	O
is	O
largely	O
bacterial	B-taxonomy_domain
,	O
with	O
the	O
Bacteroidetes	B-taxonomy_domain
,	O
Firmicutes	B-taxonomy_domain
,	O
and	O
Actinobacteria	B-taxonomy_domain
comprising	O
the	O
dominant	O
phyla	O
.	O

The	O
ability	O
to	O
acquire	O
energy	O
from	O
carbohydrates	B-chemical
of	O
dietary	O
or	O
host	O
origin	O
is	O
central	O
to	O
the	O
adaptation	O
of	O
human	B-species
gut	O
bacterial	B-taxonomy_domain
species	O
to	O
their	O
niche	O
.	O

More	O
importantly	O
,	O
this	O
makes	O
diet	O
a	O
tractable	O
way	O
to	O
manipulate	O
the	O
abundance	O
and	O
metabolic	O
output	O
of	O
the	O
microbiota	B-taxonomy_domain
toward	O
improved	O
human	B-species
health	O
.	O

However	O
,	O
there	O
is	O
a	O
paucity	O
of	O
data	O
regarding	O
how	O
the	O
vast	O
array	O
of	O
complex	B-chemical
carbohydrate	I-chemical
structures	O
are	O
selectively	O
recognized	O
and	O
imported	O
by	O
members	O
of	O
the	O
microbiota	B-taxonomy_domain
,	O
a	O
critical	O
process	O
that	O
enables	O
these	O
organisms	O
to	O
thrive	O
in	O
the	O
competitive	O
gut	O
environment	O
.	O

The	O
human	B-species
gut	O
bacteria	B-taxonomy_domain
Bacteroidetes	B-taxonomy_domain
share	O
a	O
profound	O
capacity	O
for	O
dietary	O
glycan	B-chemical
degradation	O
,	O
with	O
many	O
species	O
containing	O
>	O
250	O
predicted	O
carbohydrate	O
-	O
active	O
enzymes	O
(	O
CAZymes	O
),	O
compared	O
to	O
50	O
to	O
100	O
within	O
many	O
Firmicutes	B-taxonomy_domain
and	O
only	O
17	O
in	O
the	O
human	B-species
genome	O
devoted	O
toward	O
carbohydrate	O
utilization	O
.	O

A	O
remarkable	O
feature	O
of	O
the	O
Bacteroidetes	B-taxonomy_domain
is	O
the	O
packaging	O
of	O
genes	O
for	O
carbohydrate	O
catabolism	O
into	O
discrete	O
polysaccharide	B-gene
utilization	I-gene
loci	I-gene
(	O
PUL	B-gene
),	O
which	O
are	O
transcriptionally	O
regulated	O
by	O
specific	O
substrate	O
signatures	O
.	O

The	O
archetypal	O
PUL	B-gene
-	O
encoded	O
system	O
is	O
the	O
starch	B-complex_assembly
utilization	I-complex_assembly
system	I-complex_assembly
(	O
Sus	B-complex_assembly
)	O
(	O
Fig	O
.	O
1B	O
)	O
of	O
Bacteroides	B-species
thetaiotaomicron	I-species
.	O

The	O
Sus	B-complex_assembly
includes	O
a	O
lipid	B-protein_state
-	I-protein_state
anchored	I-protein_state
,	O
outer	O
membrane	O
endo	B-protein_type
-	I-protein_type
amylase	I-protein_type
,	O
SusG	B-protein
;	O
a	O
TonB	B-protein_type
-	I-protein_type
dependent	I-protein_type
transporter	I-protein_type
(	O
TBDT	B-protein_type
),	O
SusC	B-protein
,	O
which	O
imports	O
oligosaccharides	B-chemical
with	O
the	O
help	O
of	O
an	O
associated	O
starch	B-protein_type
-	I-protein_type
binding	I-protein_type
protein	I-protein_type
,	O
SusD	B-protein
;	O
two	O
additional	O
carbohydrate	B-protein_type
-	I-protein_type
binding	I-protein_type
lipoproteins	I-protein_type
,	O
SusE	B-protein
and	O
SusF	B-protein
;	O
and	O
two	O
periplasmic	O
exo	B-protein_type
-	I-protein_type
glucosidases	I-protein_type
,	O
SusA	B-protein
and	O
SusB	B-protein
,	O
which	O
generate	O
glucose	B-chemical
for	O
transport	O
into	O
the	O
cytoplasm	O
.	O

The	O
importance	O
of	O
PUL	B-gene
as	O
a	O
successful	O
evolutionary	O
strategy	O
is	O
underscored	O
by	O
the	O
observation	O
that	O
Bacteroidetes	B-taxonomy_domain
such	O
as	O
B	B-species
.	I-species
thetaiotaomicron	I-species
and	O
Bacteroides	B-species
ovatus	I-species
devote	O
~	O
18	O
%	O
of	O
their	O
genomes	O
to	O
these	O
systems	O
.	O

Moving	O
beyond	O
seminal	O
genomic	O
and	O
transcriptomic	O
analyses	O
,	O
the	O
current	O
state	O
-	O
of	O
-	O
the	O
-	O
art	O
PUL	B-gene
characterization	O
involves	O
combined	O
reverse	B-experimental_method
-	I-experimental_method
genetic	I-experimental_method
,	I-experimental_method
biochemical	I-experimental_method
,	I-experimental_method
and	I-experimental_method
structural	I-experimental_method
studies	I-experimental_method
to	O
illuminate	O
the	O
molecular	O
details	O
of	O
PUL	B-gene
function	O
.	O

Xyloglucan	B-chemical
and	O
the	O
Bacteroides	B-species
ovatus	I-species
xyloglucan	B-gene
utilization	I-gene
locus	I-gene
(	O
XyGUL	B-gene
).	O
(	O
A	O
)	O
Representative	O
structures	B-evidence
of	O
common	O
xyloglucans	B-chemical
using	O
the	O
Consortium	O
for	O
Functional	O
Glycomics	O
Symbol	O
Nomenclature	O
(	O
http	O
://	O
www	O
.	O
functionalglycomics	O
.	O
org	O
/	O
static	O
/	O
consortium	O
/	O
Nomenclature	O
.	O
shtml	O
).	O

Cleavage	O
sites	O
for	O
BoXyGUL	B-gene
glycosidases	B-protein_type
(	O
GHs	B-protein_type
)	O
are	O
indicated	O
for	O
solanaceous	B-taxonomy_domain
xyloglucan	B-chemical
.	O
(	O
B	O
)	O
BtSus	B-gene
and	O
BoXyGUL	B-gene
.	O
(	O
C	O
)	O
Localization	O
of	O
BoXyGUL	B-gene
-	O
encoded	O
proteins	O
in	O
cellular	O
membranes	O
and	O
concerted	O
modes	O
of	O
action	O
in	O
the	O
degradation	O
of	O
xyloglucans	B-chemical
to	O
monosaccharides	O
.	O

The	O
location	O
of	O
SGBP	B-protein
-	I-protein
A	I-protein
/	O
B	B-protein
is	O
presented	O
in	O
this	O
work	O
;	O
the	O
location	O
of	O
GH5	B-protein
has	O
been	O
empirically	O
determined	O
,	O
and	O
the	O
enzymes	O
have	O
been	O
placed	O
based	O
upon	O
their	O
predicted	O
cellular	O
location	O
.	O

We	O
recently	O
reported	O
the	O
detailed	O
molecular	O
characterization	O
of	O
a	O
PUL	B-gene
that	O
confers	O
the	O
ability	O
of	O
the	O
human	B-species
gut	O
commensal	O
B	B-species
.	I-species
ovatus	I-species
ATCC	I-species
8483	I-species
to	O
grow	O
on	O
a	O
prominent	O
family	O
of	O
plant	B-taxonomy_domain
cell	O
wall	O
glycans	B-chemical
,	O
the	O
xyloglucans	B-chemical
(	O
XyG	B-chemical
).	O

XyG	B-chemical
variants	O
(	O
Fig	O
.	O
1A	O
)	O
constitute	O
up	O
to	O
25	O
%	O
of	O
the	O
dry	O
weight	O
of	O
common	O
vegetables	B-taxonomy_domain
.	O

Analogous	O
to	O
the	O
Sus	B-gene
locus	I-gene
,	O
the	O
xyloglucan	B-gene
utilization	I-gene
locus	I-gene
(	O
XyGUL	B-gene
)	O
encodes	O
a	O
cohort	O
of	O
carbohydrate	B-protein_type
-	I-protein_type
binding	I-protein_type
,	I-protein_type
-	I-protein_type
hydrolyzing	I-protein_type
,	I-protein_type
and	I-protein_type
-	I-protein_type
importing	I-protein_type
proteins	I-protein_type
(	O
Fig	O
.	O
1B	O
and	O
C	O
).	O

The	O
number	O
of	O
glycoside	B-protein_type
hydrolases	I-protein_type
(	O
GHs	B-protein_type
)	O
encoded	O
by	O
the	O
XyGUL	B-gene
is	O
,	O
however	O
,	O
more	O
expansive	O
than	O
that	O
by	O
the	O
Sus	B-gene
locus	I-gene
(	O
Fig	O
.	O
1B	O
),	O
which	O
reflects	O
the	O
greater	O
complexity	O
of	O
glycosidic	O
linkages	O
found	O
in	O
XyG	B-chemical
vis	O
-	O
à	O
-	O
vis	O
starch	B-chemical
.	O

Whereas	O
our	O
previous	O
study	O
focused	O
on	O
the	O
characterization	O
of	O
the	O
linkage	O
specificity	O
of	O
these	O
GHs	B-protein_type
,	O
a	O
key	O
outstanding	O
question	O
regarding	O
this	O
locus	O
is	O
how	O
XyG	B-chemical
recognition	O
is	O
mediated	O
at	O
the	O
cell	O
surface	O
.	O

In	O
the	O
archetypal	O
starch	B-complex_assembly
utilization	I-complex_assembly
system	I-complex_assembly
of	O
B	B-species
.	I-species
thetaiotaomicron	I-species
,	O
starch	O
binding	O
to	O
the	O
cell	O
surface	O
is	O
mediated	O
at	O
eight	O
distinct	O
starch	B-site
-	I-site
binding	I-site
sites	I-site
distributed	O
among	O
four	O
surface	B-protein_type
glycan	I-protein_type
-	I-protein_type
binding	I-protein_type
proteins	I-protein_type
(	O
SGBPs	B-protein_type
):	O
two	O
within	O
the	O
amylase	B-protein_type
SusG	B-protein
,	O
one	O
within	O
SusD	B-protein
,	O
two	O
within	O
SusE	B-protein
,	O
and	O
three	O
within	O
SusF	B-protein
.	O
The	O
functional	O
redundancy	O
of	O
many	O
of	O
these	O
sites	O
is	O
high	O
:	O
whereas	O
SusD	B-protein
is	O
essential	O
for	O
growth	O
on	O
starch	B-chemical
,	O
combined	O
mutations	O
of	O
the	O
SusE	B-protein
,	O
SusF	B-protein
,	O
and	O
SusG	B-protein
binding	B-site
sites	I-site
are	O
required	O
to	O
impair	O
growth	O
on	O
the	O
polysaccharide	B-chemical
.	O

Bacteroidetes	B-taxonomy_domain
PUL	B-gene
ubiquitously	O
encode	O
homologs	O
of	O
SusC	B-protein
and	O
SusD	B-protein
,	O
as	O
well	O
as	O
proteins	O
whose	O
genes	O
are	O
immediately	O
downstream	O
of	O
susD	B-gene
,	O
akin	O
to	O
susE	B-gene
/	I-gene
F	I-gene
,	O
and	O
these	O
are	O
typically	O
annotated	O
as	O
“	O
putative	B-protein_state
lipoproteins	B-protein_type
”.	O

The	O
genes	O
coding	O
for	O
these	O
proteins	O
,	O
sometimes	O
referred	O
to	O
as	O
“	O
susE	B-gene
/	I-gene
F	I-gene
positioned	O
,”	O
display	O
products	O
with	O
a	O
wide	O
variation	O
in	O
amino	O
acid	O
sequence	O
and	O
which	O
have	O
little	O
or	O
no	O
homology	O
to	O
other	O
PUL	B-gene
-	O
encoded	O
proteins	O
or	O
known	O
carbohydrate	B-protein_type
-	I-protein_type
binding	I-protein_type
proteins	I-protein_type
.	O

As	O
the	O
Sus	B-complex_assembly
SGBPs	B-protein_type
remain	O
the	O
only	O
structurally	O
characterized	O
cohort	O
to	O
date	O
,	O
we	O
therefore	O
wondered	O
whether	O
such	O
glycan	B-chemical
binding	O
and	O
function	O
are	O
extended	O
to	O
other	O
PUL	B-gene
that	O
target	O
more	O
complex	O
and	O
heterogeneous	O
polysaccharides	B-chemical
,	O
such	O
as	O
XyG	B-chemical
.	O

We	O
describe	O
here	O
the	O
detailed	O
functional	B-experimental_method
and	I-experimental_method
structural	I-experimental_method
characterization	I-experimental_method
of	O
the	O
noncatalytic	B-protein_state
SGBPs	B-protein_type
encoded	O
by	O
Bacova_02651	B-gene
and	O
Bacova_02650	B-gene
of	O
the	O
XyGUL	B-gene
,	O
here	O
referred	O
to	O
as	O
SGBP	B-protein
-	I-protein
A	I-protein
and	O
SGBP	B-protein
-	I-protein
B	I-protein
,	O
to	O
elucidate	O
their	O
molecular	O
roles	O
in	O
carbohydrate	O
acquisition	O
in	O
vivo	O
.	O

Combined	O
biochemical	B-experimental_method
,	I-experimental_method
structural	I-experimental_method
,	I-experimental_method
and	I-experimental_method
reverse	I-experimental_method
-	I-experimental_method
genetic	I-experimental_method
approaches	I-experimental_method
clearly	O
illuminate	O
the	O
distinct	O
,	O
yet	O
complementary	O
,	O
functions	O
that	O
these	O
two	O
proteins	O
play	O
in	O
XyG	B-chemical
recognition	O
as	O
it	O
impacts	O
the	O
physiology	O
of	O
B	B-species
.	I-species
ovatus	I-species
.	O

These	O
data	O
extend	O
our	O
current	O
understanding	O
of	O
the	O
Sus	O
-	O
like	O
glycan	B-chemical
uptake	O
paradigm	O
within	O
the	O
Bacteroidetes	B-taxonomy_domain
and	O
reveals	O
how	O
the	O
complex	O
dietary	O
polysaccharide	B-chemical
xyloglucan	B-chemical
is	O
recognized	O
at	O
the	O
cell	O
surface	O
.	O

SGBP	B-protein
-	I-protein
A	I-protein
and	O
SGBP	B-protein
-	I-protein
B	I-protein
are	O
cell	B-protein_type
-	I-protein_type
surface	I-protein_type
-	I-protein_type
localized	I-protein_type
,	I-protein_type
xyloglucan	I-protein_type
-	I-protein_type
specific	I-protein_type
binding	I-protein_type
proteins	I-protein_type
.	O

SGBP	B-protein
-	I-protein
A	I-protein
,	O
encoded	O
by	O
the	O
XyGUL	B-gene
locus	O
tag	O
Bacova_02651	B-gene
(	O
Fig	O
.	O
1B	O
),	O
shares	O
26	O
%	O
amino	O
acid	O
sequence	O
identity	O
(	O
40	O
%	O
similarity	O
)	O
with	O
its	O
homolog	O
,	O
B	B-species
.	I-species
thetaiotaomicron	I-species
SusD	B-protein
,	O
and	O
similar	O
homology	O
with	O
the	O
SusD	B-protein_type
-	I-protein_type
like	I-protein_type
proteins	I-protein_type
encoded	O
within	O
syntenic	O
XyGUL	B-gene
identified	O
in	O
our	O
earlier	O
work	O
.	O

In	O
contrast	O
,	O
SGBP	B-protein
-	I-protein
B	I-protein
,	O
encoded	O
by	O
locus	O
tag	O
Bacova_02650	B-gene
,	O
displays	O
little	O
sequence	O
similarity	O
to	O
the	O
products	O
of	O
similarly	O
positioned	O
genes	O
in	O
syntenic	O
XyGUL	B-gene
nor	O
to	O
any	O
other	O
gene	O
product	O
among	O
the	O
diversity	O
of	O
Bacteroidetes	B-taxonomy_domain
PUL	B-gene
.	O

Whereas	O
sequence	O
similarity	O
among	O
SusC	B-protein
/	O
SusD	B-protein
homolog	O
pairs	O
often	O
serves	O
as	O
a	O
hallmark	O
for	O
PUL	B-gene
identification	O
,	O
the	O
sequence	O
similarities	O
of	O
downstream	O
genes	O
encoding	O
SGBPs	B-protein_type
are	O
generally	O
too	O
low	O
to	O
allow	O
reliable	O
bioinformatic	O
classification	O
of	O
their	O
products	O
into	O
protein	O
families	O
,	O
let	O
alone	O
prediction	O
of	O
function	O
.	O

Hence	O
,	O
there	O
is	O
a	O
critical	O
need	O
for	O
the	O
elucidation	O
of	O
detailed	O
structure	O
-	O
function	O
relationships	O
among	O
PUL	B-gene
SGBPs	B-protein_type
,	O
in	O
light	O
of	O
the	O
manifold	O
glycan	B-chemical
structures	O
in	O
nature	O
.	O

Immunofluorescence	B-experimental_method
of	O
formaldehyde	O
-	O
fixed	O
,	O
nonpermeabilized	O
cells	O
grown	O
in	O
minimal	O
medium	O
with	O
XyG	B-chemical
as	O
the	O
sole	O
carbon	O
source	O
to	O
induce	O
XyGUL	B-gene
expression	O
,	O
reveals	O
that	O
both	O
SGBP	B-protein
-	I-protein
A	I-protein
and	O
SGBP	B-protein
-	I-protein
B	I-protein
are	O
presented	O
on	O
the	O
cell	O
surface	O
by	O
N	O
-	O
terminal	O
lipidation	B-ptm
,	O
as	O
predicted	O
by	O
signal	O
peptide	O
analysis	O
with	O
SignalP	O
(	O
Fig	O
.	O
2	O
).	O

Here	O
,	O
the	O
SGBPs	B-protein_type
very	O
likely	O
work	O
in	O
concert	O
with	O
the	O
cell	B-protein_type
-	I-protein_type
surface	I-protein_type
-	I-protein_type
localized	I-protein_type
endo	I-protein_type
-	I-protein_type
xyloglucanase	I-protein_type
B	B-species
.	I-species
ovatus	I-species
GH5	B-protein
(	O
BoGH5	B-protein
)	O
to	O
recruit	O
and	O
cleave	O
XyG	B-chemical
for	O
subsequent	O
periplasmic	O
import	O
via	O
the	O
SusC	B-protein_type
-	I-protein_type
like	I-protein_type
TBDT	I-protein_type
of	O
the	O
XyGUL	B-gene
(	O
Fig	O
.	O
1B	O
and	O
C	O
).	O

SGBP	B-protein
-	I-protein
A	I-protein
and	O
SGBP	B-protein
-	I-protein
B	I-protein
visualized	O
by	O
immunofluorescence	B-experimental_method
.	O

Formalin	O
-	O
fixed	O
,	O
nonpermeabilized	O
B	B-species
.	I-species
ovatus	I-species
cells	O
were	O
grown	O
in	O
minimal	O
medium	O
plus	O
XyG	B-chemical
,	O
probed	O
with	O
custom	O
rabbit	O
antibodies	O
to	O
SGBP	B-protein
-	I-protein
A	I-protein
or	O
SGBP	B-protein
-	I-protein
B	I-protein
,	O
and	O
then	O
stained	O
with	O
Alexa	O
Fluor	O
488	O
goat	O
anti	O
-	O
rabbit	O
IgG	O
.	O
(	O
A	O
)	O
Overlay	B-experimental_method
of	O
bright	B-evidence
-	I-evidence
field	I-evidence
and	I-evidence
FITC	I-evidence
images	I-evidence
of	O
B	B-species
.	I-species
ovatus	I-species
cells	O
labeled	O
with	O
anti	O
-	O
SGBP	O
-	O
A	O
.	O
(	O
B	O
)	O
Overlay	B-experimental_method
of	O
bright	B-evidence
-	I-evidence
field	I-evidence
and	I-evidence
FITC	I-evidence
images	I-evidence
of	O
B	B-species
.	I-species
ovatus	I-species
cells	O
labeled	O
with	O
anti	O
-	O
SGBP	O
-	O
B	O
.	O
(	O
C	O
)	O
Bright	B-evidence
-	I-evidence
field	I-evidence
image	I-evidence
of	O
ΔSGBP	B-mutant
-	I-mutant
B	I-mutant
cells	O
labeled	O
with	O
anti	O
-	O
SGBP	O
-	O
B	O
antibodies	O
.	O

(	O
D	O
)	O
FITC	B-evidence
images	I-evidence
of	O
ΔSGBP	B-mutant
-	I-mutant
B	I-mutant
cells	O
labeled	O
with	O
anti	O
-	O
SGBP	O
-	O
B	O
antibodies	O
.	O

Cells	O
lacking	B-protein_state
SGBP	B-protein
-	I-protein
A	I-protein
(	O
ΔSGBP	B-mutant
-	I-mutant
A	I-mutant
)	O
do	O
not	O
grow	O
on	O
XyG	B-chemical
and	O
therefore	O
could	O
not	O
be	O
tested	O
in	O
parallel	O
.	O

In	O
our	O
initial	O
study	O
focused	O
on	O
the	O
functional	O
characterization	O
of	O
the	O
glycoside	B-protein_type
hydrolases	I-protein_type
of	O
the	O
XyGUL	B-gene
,	O
we	O
reported	O
preliminary	O
affinity	B-experimental_method
PAGE	I-experimental_method
and	O
isothermal	B-experimental_method
titration	I-experimental_method
calorimetry	I-experimental_method
(	O
ITC	B-experimental_method
)	O
data	O
indicating	O
that	O
both	O
SGBP	B-protein
-	I-protein
A	I-protein
and	O
SGBP	B-protein
-	I-protein
B	I-protein
are	O
competent	O
xyloglucan	B-protein_type
-	I-protein_type
binding	I-protein_type
proteins	I-protein_type
(	O
affinity	B-evidence
constant	I-evidence
[	O
Ka	B-evidence
]	O
values	O
of	O
3	O
.	O
74	O
×	O
105	O
M	O
−	O
1	O
and	O
4	O
.	O
98	O
×	O
104	O
M	O
−	O
1	O
,	O
respectively	O
[	O
23	O
]).	O

Additional	O
affinity	B-experimental_method
PAGE	I-experimental_method
analysis	O
(	O
Fig	O
.	O
3	O
)	O
demonstrates	O
that	O
SGBP	B-protein
-	I-protein
A	I-protein
also	O
has	O
moderate	O
affinity	O
for	O
the	O
artificial	O
soluble	O
cellulose	O
derivative	O
hydroxyethyl	B-chemical
cellulose	I-chemical
[	O
HEC	B-chemical
;	O
a	O
β	B-chemical
(	I-chemical
1	I-chemical
→	I-chemical
4	I-chemical
)-	I-chemical
glucan	I-chemical
]	O
and	O
limited	O
affinity	O
for	O
mixed	B-chemical
-	I-chemical
linkage	I-chemical
β	I-chemical
(	I-chemical
1	I-chemical
→	I-chemical
3	I-chemical
)/	I-chemical
β	I-chemical
(	I-chemical
1	I-chemical
→	I-chemical
4	I-chemical
)-	I-chemical
glucan	I-chemical
(	O
MLG	B-chemical
)	O
and	O
glucomannan	B-chemical
(	O
GM	B-chemical
;	O
mixed	O
glucosyl	B-chemical
and	O
mannosyl	B-chemical
backbone	O
),	O
which	O
together	O
indicate	O
general	O
binding	O
to	O
polysaccharide	B-chemical
backbone	O
residues	O
and	O
major	O
contributions	O
from	O
side	O
-	O
chain	O
recognition	O
.	O

In	O
contrast	O
,	O
SGBP	B-protein
-	I-protein
B	I-protein
bound	O
to	O
HEC	B-chemical
more	O
weakly	O
than	O
SGBP	B-protein
-	I-protein
A	I-protein
and	O
did	O
not	O
bind	O
to	O
MLG	B-chemical
or	O
GM	B-chemical
.	O

Neither	O
SGBP	B-protein_type
recognized	O
galactomannan	B-chemical
(	O
GGM	B-chemical
),	O
starch	B-chemical
,	O
carboxymethylcellulose	B-chemical
,	O
or	O
mucin	B-chemical
(	O
see	O
Fig	O
.	O
S1	O
in	O
the	O
supplemental	O
material	O
).	O

Together	O
,	O
these	O
results	O
highlight	O
the	O
high	O
specificities	O
of	O
SGBP	B-protein
-	I-protein
A	I-protein
and	O
SGBP	B-protein
-	I-protein
B	I-protein
for	O
XyG	B-chemical
,	O
which	O
is	O
concordant	O
with	O
their	O
association	O
with	O
XyG	B-protein_type
-	I-protein_type
specific	I-protein_type
GHs	I-protein_type
in	O
the	O
XyGUL	B-gene
,	O
as	O
well	O
as	O
transcriptomic	O
analysis	O
indicating	O
that	O
B	B-species
.	I-species
ovatus	I-species
has	O
discrete	O
PUL	B-gene
for	O
MLG	B-chemical
,	O
GM	B-chemical
,	O
and	O
GGM	B-chemical
(	O
11	O
).	O

Notably	O
,	O
the	O
absence	O
of	O
carbohydrate	B-site
-	I-site
binding	I-site
modules	I-site
in	O
the	O
GHs	B-protein_type
encoded	O
by	O
the	O
XyGUL	B-gene
implies	O
that	O
noncatalytic	O
recognition	O
of	O
xyloglucan	B-chemical
is	O
mediated	O
entirely	O
by	O
SGBP	B-protein
-	I-protein
A	I-protein
and	O
-	B-protein
B	I-protein
.	O

SGBP	B-protein
-	I-protein
A	I-protein
and	O
SGBP	B-protein
-	I-protein
B	I-protein
preferentially	O
bind	O
xyloglucan	B-chemical
.	O

Affinity	B-experimental_method
electrophoresis	I-experimental_method
(	O
10	O
%	O
acrylamide	O
)	O
of	O
SGBP	B-protein
-	I-protein
A	I-protein
and	O
SGBP	B-protein
-	I-protein
B	I-protein
with	O
BSA	B-protein
as	O
a	O
control	O
protein	O
.	O

All	O
samples	O
were	O
loaded	O
on	O
the	O
same	O
gel	O
next	O
to	O
the	O
BSA	B-protein
controls	O
;	O
thin	O
black	O
lines	O
indicate	O
where	O
intervening	O
lanes	O
were	O
removed	O
from	O
the	O
final	O
image	O
for	O
both	O
space	O
and	O
clarity	O
.	O

The	O
percentage	O
of	O
polysaccharide	B-chemical
incorporated	O
into	O
each	O
native	O
gel	O
is	O
displayed	O
.	O

The	O
vanguard	O
endo	B-protein_type
-	I-protein_type
xyloglucanase	I-protein_type
of	O
the	O
XyGUL	B-gene
,	O
BoGH5	B-protein
,	O
preferentially	O
cleaves	O
the	O
polysaccharide	B-chemical
at	O
unbranched	O
glucosyl	B-chemical
residues	O
to	O
generate	O
xylogluco	B-chemical
-	I-chemical
oligosaccharides	I-chemical
(	O
XyGOs	B-chemical
)	O
comprising	O
a	O
Glc4	B-structure_element
backbone	I-structure_element
with	O
variable	B-structure_element
side	I-structure_element
-	I-structure_element
chain	I-structure_element
galactosylation	I-structure_element
(	O
XyGO1	B-chemical
)	O
(	O
Fig	O
.	O
1A	O
;	O
n	O
=	O
1	O
)	O
as	O
the	O
limit	O
of	O
digestion	O
products	O
in	O
vitro	O
;	O
controlled	B-experimental_method
digestion	I-experimental_method
and	I-experimental_method
fractionation	I-experimental_method
by	O
size	B-experimental_method
exclusion	I-experimental_method
chromatography	I-experimental_method
allow	O
the	O
production	O
of	O
higher	O
-	O
order	O
oligosaccharides	B-chemical
(	O
e	O
.	O
g	O
.,	O
XyGO2	B-chemical
)	O
(	O
Fig	O
.	O
1A	O
;	O
n	O
=	O
2	O
).	O

ITC	B-experimental_method
demonstrates	O
that	O
SGBP	B-protein
-	I-protein
A	I-protein
binds	O
to	O
XyG	B-chemical
polysaccharide	B-chemical
and	O
XyGO2	B-chemical
(	O
based	O
on	O
a	O
Glc8	B-structure_element
backbone	I-structure_element
)	O
with	O
essentially	O
equal	O
affinities	B-evidence
,	O
while	O
no	O
binding	O
of	O
XyGO1	B-chemical
(	O
Glc4	B-structure_element
backbone	I-structure_element
)	O
was	O
detectable	O
(	O
Table	O
1	O
;	O
see	O
Fig	O
.	O
S2	O
and	O
S3	O
in	O
the	O
supplemental	O
material	O
).	O

Similarly	O
,	O
SGBP	B-protein
-	I-protein
B	I-protein
also	O
bound	B-protein_state
to	I-protein_state
XyG	B-chemical
and	O
XyGO2	B-chemical
with	O
approximately	O
equal	O
affinities	B-evidence
,	O
although	O
in	O
both	O
cases	O
,	O
Ka	B-evidence
values	O
were	O
nearly	O
10	O
-	O
fold	O
lower	O
than	O
those	O
for	O
SGBP	B-protein
-	I-protein
A	I-protein
.	O
Also	O
in	O
contrast	O
to	O
SGBP	B-protein
-	I-protein
A	I-protein
,	O
SGBP	B-protein
-	I-protein
B	I-protein
also	O
bound	B-protein_state
to	I-protein_state
XyGO1	B-chemical
,	O
yet	O
the	O
affinity	B-evidence
for	O
this	O
minimal	B-structure_element
repeating	I-structure_element
unit	I-structure_element
was	O
poor	O
,	O
with	O
a	O
Ka	B-evidence
value	O
of	O
ca	O
.	O
1	O
order	O
of	O
magnitude	O
lower	O
than	O
for	O
XyG	B-chemical
and	O
XyGO2	B-chemical
.	O

Together	O
,	O
these	O
data	O
clearly	O
suggest	O
that	O
polysaccharide	B-chemical
binding	O
of	O
both	O
SGBPs	B-protein_type
is	O
fulfilled	O
by	O
a	O
dimer	B-oligomeric_state
of	O
the	O
minimal	B-structure_element
repeat	I-structure_element
,	O
corresponding	O
to	O
XyGO2	B-chemical
(	O
cf	O
.	O

The	O
observation	O
by	O
affinity	B-experimental_method
PAGE	I-experimental_method
that	O
these	O
proteins	O
specifically	O
recognize	O
XyG	B-chemical
is	O
further	O
substantiated	O
by	O
their	O
lack	O
of	O
binding	O
for	O
the	O
undecorated	O
oligosaccharide	B-chemical
cellotetraose	B-chemical
(	O
Table	O
1	O
;	O
see	O
Fig	O
.	O
S3	O
).	O

Furthermore	O
,	O
SGBP	B-protein
-	I-protein
A	I-protein
binds	O
cellohexaose	B-chemical
with	O
~	O
770	O
-	O
fold	O
weaker	O
affinity	B-evidence
than	O
XyG	B-chemical
,	O
while	O
SGBP	B-protein
-	I-protein
B	I-protein
displays	O
no	O
detectable	O
binding	O
to	O
this	O
linear	O
hexasaccharide	B-chemical
.	O

To	O
provide	O
molecular	O
-	O
level	O
insight	O
into	O
how	O
the	O
XyGUL	B-gene
SGBPs	B-protein_type
equip	O
B	B-species
.	I-species
ovatus	I-species
to	O
specifically	O
harvest	O
XyG	B-chemical
from	O
the	O
gut	O
environment	O
,	O
we	O
performed	O
X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
analysis	O
of	O
both	O
SGBP	B-protein
-	I-protein
A	I-protein
and	O
SGPB	B-protein
-	I-protein
B	I-protein
in	O
oligosaccharide	B-complex_assembly
-	I-complex_assembly
complex	I-complex_assembly
forms	I-complex_assembly
.	O

Summary	O
of	O
thermodynamic	O
parameters	O
for	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
SGBP	B-protein
-	I-protein
A	I-protein
and	O
SGBP	B-protein
-	I-protein
B	I-protein
obtained	O
by	O
isothermal	B-experimental_method
titration	I-experimental_method
calorimetry	I-experimental_method
at	O
25	O
°	O
Ca	O

SGBP	B-protein
-	I-protein
A	I-protein
is	O
a	O
SusD	B-protein
homolog	O
with	O
an	O
extensive	O
glycan	B-site
-	I-site
binding	I-site
platform	I-site
.	O

As	O
anticipated	O
by	O
sequence	O
similarity	O
,	O
the	O
high	O
-	O
resolution	O
tertiary	O
structure	B-evidence
of	O
apo	B-protein_state
-	O
SGBP	B-protein
-	I-protein
A	I-protein
(	O
1	O
.	O
36	O
Å	O
,	O
Rwork	B-evidence
=	O
14	O
.	O
7	O
%,	O
Rfree	B-evidence
=	O
17	O
.	O
4	O
%,	O
residues	O
28	B-residue_range
to	I-residue_range
546	I-residue_range
)	O
(	O
Table	O
2	O
)	O
displays	O
the	O
canonical	O
“	B-structure_element
SusD	I-structure_element
-	I-structure_element
like	I-structure_element
”	I-structure_element
protein	I-structure_element
fold	I-structure_element
dominated	O
by	O
four	O
tetratrico	B-structure_element
-	I-structure_element
peptide	I-structure_element
repeat	I-structure_element
(	O
TPR	B-structure_element
)	O
motifs	O
that	O
cradle	O
the	O
rest	O
of	O
the	O
structure	B-evidence
(	O
Fig	O
.	O
4A	O
).	O

Specifically	O
,	O
SGBP	B-protein
-	I-protein
A	I-protein
overlays	B-experimental_method
B	B-species
.	I-species
thetaiotaomicron	I-species
SusD	B-protein
(	O
BtSusD	B-protein
)	O
with	O
a	O
root	B-evidence
mean	I-evidence
square	I-evidence
deviation	I-evidence
(	O
RMSD	B-evidence
)	O
value	O
of	O
2	O
.	O
2	O
Å	O
for	O
363	O
Cα	O
pairs	O
,	O
which	O
is	O
notable	O
given	O
the	O
26	O
%	O
amino	O
acid	O
identity	O
(	O
40	O
%	O
similarity	O
)	O
between	O
these	O
homologs	O
(	O
Fig	O
.	O
4C	O
).	O

Cocrystallization	B-experimental_method
of	O
SGBP	B-protein
-	I-protein
A	I-protein
with	O
XyGO2	B-chemical
generated	O
a	O
substrate	B-complex_assembly
complex	I-complex_assembly
structure	B-evidence
(	O
2	O
.	O
3	O
Å	O
,	O
Rwork	B-evidence
=	O
21	O
.	O
8	O
%,	O
Rfree	B-evidence
=	O
24	O
.	O
8	O
%,	O
residues	O
36	B-residue_range
to	I-residue_range
546	I-residue_range
)	O
(	O
Fig	O
.	O
4A	O
and	O
B	O
;	O
Table	O
2	O
)	O
that	O
revealed	O
the	O
distinct	O
binding	B-site
-	I-site
site	I-site
architecture	O
of	O
the	O
XyG	B-protein_type
binding	I-protein_type
protein	I-protein_type
.	O

The	O
SGBP	B-complex_assembly
-	I-complex_assembly
A	I-complex_assembly
:	I-complex_assembly
XyGO2	I-complex_assembly
complex	O
superimposes	B-experimental_method
closely	O
with	O
the	O
apo	B-protein_state
structure	B-evidence
(	O
RMSD	B-evidence
of	O
0	O
.	O
6	O
Å	O
)	O
and	O
demonstrates	O
that	O
no	O
major	O
conformational	O
change	O
occurs	O
upon	O
substrate	O
binding	O
;	O
small	O
deviations	O
in	O
the	O
orientation	O
of	O
several	O
surface	O
loops	O
are	O
likely	O
the	O
result	O
of	O
differential	O
crystal	O
packing	O
.	O

It	O
is	O
particularly	O
notable	O
that	O
although	O
the	O
location	O
of	O
the	O
ligand	B-site
-	I-site
binding	I-site
site	I-site
is	O
conserved	B-protein_state
between	O
SGBP	B-protein
-	I-protein
A	I-protein
and	O
SusD	B-protein
,	O
that	O
of	O
SGBP	B-protein
-	I-protein
A	I-protein
displays	O
an	O
~	O
29	O
-	O
Å	O
-	O
long	O
aromatic	B-site
platform	I-site
to	O
accommodate	O
the	O
extended	O
,	O
linear	O
XyG	B-chemical
chain	O
(	O
see	O
reference	O
for	O
a	O
review	O
of	O
XyG	B-chemical
secondary	O
structure	O
),	O
versus	O
the	O
shorter	O
,	O
~	O
18	O
-	O
Å	O
-	O
long	O
,	O
site	B-site
within	O
SusD	B-protein
that	O
complements	O
the	O
helical	O
conformation	O
of	O
amylose	B-chemical
(	O
Fig	O
.	O
4C	O
and	O
D	O
).	O

Molecular	O
structure	B-evidence
of	O
SGBP	B-protein
-	I-protein
A	I-protein
(	O
Bacova_02651	B-gene
).	O
(	O
A	O
)	O
Overlay	B-experimental_method
of	O
SGBP	B-protein
-	I-protein
A	I-protein
from	O
the	O
apo	B-protein_state
(	O
rainbow	O
)	O
and	O
XyGO2	B-chemical
(	O
gray	O
)	O
structures	B-evidence
.	O

The	O
apo	B-protein_state
structure	B-evidence
is	O
color	O
ramped	O
from	O
blue	O
to	O
red	O
.	O

An	O
omit	B-evidence
map	I-evidence
(	O
2σ	O
)	O
for	O
XyGO2	B-chemical
(	O
orange	O
and	O
red	O
sticks	O
)	O
is	O
displayed	O
.	O

(	O
B	O
)	O
Close	O
-	O
up	O
view	O
of	O
the	O
omit	B-evidence
map	I-evidence
as	O
in	O
panel	O
A	O
,	O
rotated	O
90	O
°	O
clockwise	O
.	O

(	O
C	O
)	O
Overlay	B-experimental_method
of	O
the	O
Cα	O
backbones	O
of	O
SGBP	B-protein
-	I-protein
A	I-protein
(	O
black	O
)	O
with	O
XyGO2	B-chemical
(	O
orange	O
and	O
red	O
spheres	O
)	O
and	O
BtSusD	B-protein
(	O
blue	O
)	O
with	O
maltoheptaose	B-chemical
(	O
pink	O
and	O
red	O
spheres	O
),	O
highlighting	O
the	O
conservation	O
of	O
the	O
glycan	B-site
-	I-site
binding	I-site
site	I-site
location	O
.	O

(	O
D	O
)	O
Close	O
-	O
up	O
of	O
the	O
SGBP	B-protein
-	I-protein
A	I-protein
(	O
black	O
and	O
orange	O
)	O
and	O
SusD	B-protein
(	O
blue	O
and	O
pink	O
)	O
glycan	B-site
-	I-site
binding	I-site
sites	I-site
.	O

The	O
approximate	O
length	O
of	O
each	O
glycan	B-site
-	I-site
binding	I-site
site	I-site
is	O
displayed	O
,	O
colored	O
to	O
match	O
the	O
protein	B-evidence
structures	I-evidence
.	O
(	O
E	O
)	O
Stereo	O
view	O
of	O
the	O
xyloglucan	B-site
-	I-site
binding	I-site
site	I-site
of	O
SGBP	B-protein
-	I-protein
A	I-protein
,	O
displaying	O
all	O
residues	O
within	O
4	O
Å	O
of	O
the	O
ligand	O
.	O

The	O
backbone	O
glucose	B-chemical
residues	O
are	O
numbered	O
from	O
the	O
nonreducing	O
end	O
;	O
xylose	B-chemical
residues	O
are	O
labeled	O
X1	B-residue_name_number
and	O
X2	B-residue_name_number
.	O

Seven	O
of	O
the	O
eight	O
backbone	O
glucosyl	B-chemical
residues	O
of	O
XyGO2	B-chemical
could	O
be	O
convincingly	O
modeled	O
in	O
the	O
ligand	B-evidence
electron	I-evidence
density	I-evidence
,	O
and	O
only	O
two	O
α	B-chemical
(	I-chemical
1	I-chemical
→	I-chemical
6	I-chemical
)-	I-chemical
linked	I-chemical
xylosyl	I-chemical
residues	O
were	O
observed	O
(	O
Fig	O
.	O
4B	O
;	O
cf	O
.	O

Indeed	O
,	O
the	O
electron	B-evidence
density	I-evidence
for	O
the	O
ligand	O
suggests	O
some	O
disorder	O
,	O
which	O
may	O
arise	O
from	O
multiple	O
oligosaccharide	B-chemical
orientations	O
along	O
the	O
binding	B-site
site	I-site
.	O

Three	O
aromatic	O
residues	O
—	O
W82	B-residue_name_number
,	O
W283	B-residue_name_number
,	O
W306	B-residue_name_number
—	O
comprise	O
the	O
flat	B-site
platform	I-site
that	O
stacks	O
along	O
the	O
naturally	O
twisted	O
β	B-chemical
-	I-chemical
glucan	I-chemical
backbone	O
(	O
Fig	O
.	O
4E	O
).	O

The	O
functional	O
importance	O
of	O
this	O
platform	B-site
is	O
underscored	O
by	O
the	O
observation	O
that	O
the	O
W82A	B-mutant
W283A	B-mutant
W306A	B-mutant
mutant	B-protein_state
of	O
SGBP	B-protein
-	I-protein
A	I-protein
,	O
designated	O
SGBP	B-mutant
-	I-mutant
A	I-mutant
*,	I-mutant
is	O
completely	B-protein_state
devoid	I-protein_state
of	I-protein_state
XyG	I-protein_state
affinity	I-protein_state
(	O
Table	O
3	O
;	O
see	O
Fig	O
.	O
S4	O
in	O
the	O
supplemental	O
material	O
).	O

Dissection	O
of	O
the	O
individual	O
contribution	O
of	O
these	O
residues	O
reveals	O
that	O
the	O
W82A	B-mutant
mutant	B-protein_state
displays	O
a	O
significant	O
4	O
.	O
9	O
-	O
fold	O
decrease	O
in	O
the	O
Ka	B-evidence
value	O
for	O
XyG	B-chemical
,	O
while	O
the	O
W306A	B-mutant
substitution	B-experimental_method
completely	O
abolishes	B-protein_state
XyG	I-protein_state
binding	I-protein_state
.	O

Contrasting	O
with	O
the	O
clear	O
importance	O
of	O
these	O
hydrophobic	O
interactions	O
,	O
there	O
are	O
remarkably	O
few	O
hydrogen	O
-	O
bonding	O
interactions	O
with	O
the	O
ligand	B-chemical
,	O
which	O
are	O
provided	O
by	O
R65	B-residue_name_number
,	O
N83	B-residue_name_number
,	O
and	O
S308	B-residue_name_number
,	O
which	O
are	O
proximal	O
to	O
Glc5	B-residue_name_number
and	O
Glc3	B-residue_name_number
.	O

Most	O
surprising	O
in	O
light	O
of	O
the	O
saccharide	B-evidence
-	I-evidence
binding	I-evidence
data	I-evidence
,	O
however	O
,	O
was	O
a	O
lack	O
of	O
extensive	O
recognition	O
of	O
the	O
XyG	B-chemical
side	O
chains	O
;	O
only	O
Y84	B-residue_name_number
appeared	O
to	O
provide	O
a	O
hydrophobic	B-site
interface	I-site
for	O
a	O
xylosyl	B-chemical
residue	O
(	O
Xyl1	B-residue_name_number
).	O

Summary	O
of	O
thermodynamic	O
parameters	O
for	O
site	O
-	O
directed	O
mutants	O
of	O
SGBP	B-protein
-	I-protein
A	I-protein
and	O
SGBP	B-protein
-	I-protein
B	I-protein
obtained	O
by	O
ITC	B-experimental_method
with	O
XyG	B-chemical
at	O
25	O
°	O
Ca	O

Protein	O
name	O
Ka	B-evidence
ΔG	O
(	O
kcal	O
⋅	O
mol	O
−	O
1	O
)	O
ΔH	B-evidence
(	O
kcal	O
⋅	O
mol	O
−	O
1	O
)	O
TΔS	B-evidence
(	O
kcal	O
⋅	O
mol	O
−	O
1	O
)	O
Fold	O
changeb	O
M	O
−	O
1	O
SGBP	B-protein
-	I-protein
A	I-protein
(	O
W82A	B-mutant
W283A	B-mutant
W306A	B-mutant
)	O
ND	O
NB	O
NB	O
NB	O
NB	O
SGBP	B-protein
-	I-protein
A	I-protein
(	O
W82A	B-mutant
)	O
c	O
4	O
.	O
9	O
9	O
.	O
1	O
×	O
104	O
−	O
6	O
.	O
8	O
−	O
6	O
.	O
3	O
0	O
.	O
5	O
SGBP	B-protein
-	I-protein
A	I-protein
(	O
W306	B-residue_name_number
)	O
ND	O
NB	O
NB	O
NB	O
NB	O
SGBP	B-protein
-	I-protein
B	I-protein
(	O
230	B-residue_range
–	I-residue_range
489	I-residue_range
)	O
0	O
.	O
7	O
(	O
8	O
.	O
6	O
±	O
0	O
.	O
20	O
)	O
×	O
104	O
−	O
6	O
.	O
7	O
−	O
14	O
.	O
9	O
±	O
0	O
.	O
1	O
−	O
8	O
.	O
2	O
SGBP	B-protein
-	I-protein
B	I-protein
(	O
Y363A	B-mutant
)	O
19	O
.	O
7	O
(	O
2	O
.	O
9	O
±	O
0	O
.	O
10	O
)	O
×	O
103	O
−	O
4	O
.	O
7	O
−	O
18	O
.	O
1	O
±	O
0	O
.	O
1	O
−	O
13	O
.	O
3	O
SGBP	B-protein
-	I-protein
B	I-protein
(	O
W364A	B-mutant
)	O
ND	O
Weak	O
Weak	O
Weak	O
Weak	O
SGBP	B-protein
-	I-protein
B	I-protein
(	O
F414A	B-mutant
)	O
3	O
.	O
2	O
(	O
1	O
.	O
80	O
±	O
0	O
.	O
03	O
)	O
×	O
104	O
−	O
5	O
.	O
8	O
−	O
11	O
.	O
4	O
±	O
0	O
.	O
1	O
−	O
5	O
.	O
6	O

Binding	O
thermodynamics	O
are	O
based	O
on	O
the	O
concentration	O
of	O
the	O
binding	O
unit	O
,	O
XyGO2	B-chemical
.	O

Weak	O
binding	O
represents	O
a	O
Ka	B-evidence
of	O
<	O
500	O
M	O
−	O
1	O
.	O

Ka	B-evidence
fold	O
change	O
=	O
Ka	B-evidence
of	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
protein	O
/	O
Ka	B-evidence
of	O
mutant	O
protein	O
for	O
xyloglucan	B-chemical
binding	O
.	O

SGBP	B-protein
-	I-protein
B	I-protein
has	O
a	O
multimodular	O
structure	O
with	O
a	O
single	O
,	O
C	O
-	O
terminal	O
glycan	B-structure_element
-	I-structure_element
binding	I-structure_element
domain	I-structure_element
.	O

The	O
crystal	B-evidence
structure	I-evidence
of	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
SGBP	B-protein
-	I-protein
B	I-protein
in	B-protein_state
complex	I-protein_state
with	I-protein_state
XyGO2	B-chemical
(	O
2	O
.	O
37	O
Å	O
,	O
Rwork	B-evidence
=	O
19	O
.	O
9	O
%,	O
Rfree	B-evidence
=	O
23	O
.	O
9	O
%,	O
residues	O
34	B-residue_range
to	I-residue_range
489	I-residue_range
)	O
(	O
Table	O
2	O
)	O
revealed	O
an	O
extended	O
structure	B-evidence
composed	O
of	O
three	O
tandem	B-structure_element
immunoglobulin	I-structure_element
(	I-structure_element
Ig	I-structure_element
)-	I-structure_element
like	I-structure_element
domains	I-structure_element
(	O
domains	O
A	B-structure_element
,	O
B	B-structure_element
,	O
and	O
C	B-structure_element
)	O
followed	O
at	O
the	O
C	O
terminus	O
by	O
a	O
novel	O
xyloglucan	B-structure_element
-	I-structure_element
binding	I-structure_element
domain	I-structure_element
(	O
domain	O
D	B-structure_element
)	O
(	O
Fig	O
.	O
5A	O
).	O

Domains	O
A	B-structure_element
,	O
B	B-structure_element
,	O
and	O
C	B-structure_element
display	O
similar	O
β	B-structure_element
-	I-structure_element
sandwich	I-structure_element
folds	I-structure_element
;	O
domains	O
B	B-structure_element
(	O
residues	O
134	B-residue_range
to	I-residue_range
230	I-residue_range
)	O
and	O
C	B-structure_element
(	O
residues	O
231	B-residue_range
to	I-residue_range
313	I-residue_range
)	O
can	O
be	O
superimposed	B-experimental_method
onto	O
domain	O
A	B-structure_element
(	O
residues	O
34	B-residue_range
to	I-residue_range
133	I-residue_range
)	O
with	O
RMSDs	B-evidence
of	O
1	O
.	O
1	O
and	O
1	O
.	O
2	O
Å	O
,	O
respectively	O
,	O
for	O
47	O
atom	O
pairs	O
(	O
23	O
%	O
and	O
16	O
%	O
sequence	O
identity	O
,	O
respectively	O
).	O

These	B-structure_element
domains	I-structure_element
also	O
display	O
similarity	O
to	O
the	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
sandwich	I-structure_element
domains	I-structure_element
of	O
many	O
GH13	B-protein_type
enzymes	I-protein_type
,	O
including	O
the	O
cyclodextrin	B-protein_type
glucanotransferase	I-protein_type
of	O
Geobacillus	B-species
stearothermophilus	I-species
(	O
Fig	O
.	O
5B	O
).	O

Such	B-structure_element
domains	I-structure_element
are	O
not	O
typically	O
involved	O
in	O
carbohydrate	B-chemical
binding	O
.	O

Indeed	O
,	O
visual	B-experimental_method
inspection	I-experimental_method
of	O
the	O
SGBP	B-protein
-	I-protein
B	I-protein
structure	B-evidence
,	O
as	O
well	O
as	O
individual	O
production	O
of	O
the	O
A	B-structure_element
and	O
B	B-structure_element
domains	O
and	O
affinity	B-experimental_method
PAGE	I-experimental_method
analysis	O
(	O
see	O
Fig	O
.	O
S5	O
in	O
the	O
supplemental	O
material	O
),	O
indicates	O
that	O
these	O
domains	O
do	O
not	O
contribute	O
to	O
XyG	B-chemical
capture	O
.	O

On	O
the	O
other	O
hand	O
,	O
production	B-experimental_method
of	O
the	O
fused	B-mutant
domains	I-mutant
C	I-mutant
and	I-mutant
D	I-mutant
in	O
tandem	O
(	O
SGBP	B-protein
-	I-protein
B	I-protein
residues	O
230	B-residue_range
to	I-residue_range
489	I-residue_range
)	O
retains	O
complete	O
binding	O
of	O
xyloglucan	B-chemical
in	O
vitro	O
,	O
with	O
the	O
observed	O
slight	O
increase	O
in	O
affinity	O
likely	O
arising	O
from	O
a	O
reduced	O
potential	O
for	O
steric	O
hindrance	O
of	O
the	O
smaller	O
protein	O
construct	O
during	O
polysaccharide	B-chemical
interactions	O
(	O
Table	O
3	O
).	O

While	O
neither	O
the	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
protein	O
nor	O
domain	O
D	B-structure_element
displays	O
structural	O
homology	O
to	O
known	O
XyG	B-protein_type
-	I-protein_type
binding	I-protein_type
proteins	I-protein_type
,	O
the	O
topology	O
of	O
SGBP	B-protein
-	I-protein
B	I-protein
resembles	O
the	O
xylan	B-protein_type
-	I-protein_type
binding	I-protein_type
protein	I-protein_type
Bacova_04391	B-protein
(	O
PDB	O
3ORJ	O
)	O
encoded	O
within	O
a	O
xylan	B-chemical
-	O
targeting	O
PUL	B-gene
of	O
B	B-species
.	I-species
ovatus	I-species
(	O
Fig	O
.	O
5C	O
).	O

The	O
structure	B-experimental_method
-	I-experimental_method
based	I-experimental_method
alignment	I-experimental_method
of	O
these	O
proteins	O
reveals	O
17	O
%	O
sequence	O
identity	O
,	O
with	O
a	O
core	O
RMSD	B-evidence
of	O
3	O
.	O
6	O
Å	O
for	O
253	O
aligned	O
residues	O
.	O

While	O
there	O
is	O
no	O
substrate	O
-	O
complexed	O
structure	O
of	O
Bacova_04391	B-protein
available	O
,	O
the	O
binding	B-site
site	I-site
is	O
predicted	O
to	O
include	O
W241	B-residue_name_number
and	O
Y404	B-residue_name_number
,	O
which	O
are	O
proximal	O
to	O
the	O
XyGO	B-site
binding	I-site
site	I-site
in	O
SGBP	B-protein
-	I-protein
B	I-protein
.	O
However	O
,	O
the	O
opposing	B-protein_state
,	I-protein_state
clamp	I-protein_state
-	I-protein_state
like	I-protein_state
arrangement	I-protein_state
of	O
these	B-structure_element
residues	I-structure_element
in	O
Bacova_04391	B-protein
is	O
clearly	O
distinct	O
from	O
the	O
planar	B-site
surface	I-site
arrangement	I-site
of	O
the	O
residues	B-structure_element
that	O
interact	O
with	O
XyG	B-chemical
in	O
SGBP	B-protein
-	I-protein
B	I-protein
(	O
described	O
below	O
).	O

Multimodular	O
structure	O
of	O
SGBP	B-protein
-	I-protein
B	I-protein
(	O
Bacova_02650	B-gene
).	O
(	O
A	O
)	O
Full	B-protein_state
-	I-protein_state
length	I-protein_state
structure	B-evidence
of	O
SGBP	B-protein
-	I-protein
B	I-protein
,	O
color	O
coded	O
by	O
domain	O
as	O
indicated	O
.	O

Prolines	B-residue_name
between	O
domains	O
are	O
indicated	O
as	O
spheres	O
.	O

An	O
omit	B-evidence
map	I-evidence
(	O
2σ	O
)	O
for	O
XyGO2	B-chemical
is	O
displayed	O
to	O
highlight	O
the	O
location	O
of	O
the	O
glycan	B-site
-	I-site
binding	I-site
site	I-site
.	O

(	O
B	O
)	O
Overlay	O
of	O
SGBP	B-protein
-	I-protein
B	I-protein
domains	O
A	B-structure_element
,	O
B	B-structure_element
,	O
and	O
C	B-structure_element
(	O
colored	O
as	O
in	O
panel	O
A	O
),	O
with	O
a	O
C	O
-	O
terminal	O
Ig	B-structure_element
-	I-structure_element
like	I-structure_element
domain	I-structure_element
of	O
the	O
G	B-species
.	I-species
stearothermophilus	I-species
cyclodextrin	B-protein_type
glucanotransferase	I-protein_type
(	O
PDB	O
1CYG	O
[	O
residues	O
375	B-residue_range
to	I-residue_range
493	I-residue_range
])	O
in	O
green	O
.	O
(	O
C	O
)	O
Cα	O
overlay	B-experimental_method
of	O
SGBP	B-protein
-	I-protein
B	I-protein
(	O
gray	O
)	O
and	O
Bacova_04391	B-protein
(	O
PDB	O
3ORJ	O
)	O
(	O
pink	O
).	O

(	O
D	O
)	O
Close	O
-	O
up	O
omit	B-evidence
map	I-evidence
for	O
the	O
XyGO2	B-chemical
ligand	O
,	O
contoured	O
at	O
2σ	O
.	O
(	O
E	O
)	O
Stereo	O
view	O
of	O
the	O
xyloglucan	B-site
-	I-site
binding	I-site
site	I-site
of	O
SGBP	B-protein
-	I-protein
B	I-protein
,	O
displaying	O
all	O
residues	O
within	O
4	O
Å	O
of	O
the	O
ligand	O
.	O

The	O
backbone	O
glucose	B-chemical
residues	O
are	O
numbered	O
from	O
the	O
nonreducing	O
end	O
,	O
xylose	B-chemical
residues	O
are	O
shown	O
as	O
X1	B-residue_name_number
,	O
X2	B-residue_name_number
,	O
and	O
X3	B-residue_name_number
,	O
potential	O
hydrogen	O
-	O
bonding	O
interactions	O
are	O
shown	O
as	O
dashed	O
lines	O
,	O
and	O
the	O
distance	O
is	O
shown	O
in	O
angstroms	O
.	O

Inspection	O
of	O
the	O
tertiary	O
structure	B-evidence
indicates	O
that	O
domains	O
C	B-structure_element
and	O
D	B-structure_element
are	O
effectively	O
inseparable	O
,	O
with	O
a	O
contact	O
interface	O
of	O
396	O
Å2	O
.	O

Domains	O
A	B-structure_element
,	O
B	B-structure_element
,	O
and	O
C	B-structure_element
do	O
not	O
pack	O
against	O
each	O
other	O
.	O

Moreover	O
,	O
the	O
five	B-structure_element
-	I-structure_element
residue	I-structure_element
linkers	I-structure_element
between	O
these	O
first	O
three	O
domains	O
all	O
feature	O
a	O
proline	B-residue_name
as	O
the	O
middle	B-structure_element
residue	I-structure_element
,	O
suggesting	O
significant	O
conformational	O
rigidity	O
(	O
Fig	O
.	O
5A	O
).	O

Despite	O
the	O
lack	O
of	O
sequence	O
and	O
structural	O
conservation	O
,	O
a	O
similarly	O
positioned	O
proline	B-residue_name
joins	O
the	O
Ig	B-structure_element
-	I-structure_element
like	I-structure_element
domains	I-structure_element
of	O
the	O
xylan	O
-	O
binding	O
Bacova_04391	B-protein
and	O
the	O
starch	B-protein_type
-	I-protein_type
binding	I-protein_type
proteins	I-protein_type
SusE	B-protein
and	O
SusF	B-protein
.	O
We	O
speculate	O
that	O
this	O
is	O
a	O
biologically	O
important	O
adaptation	O
that	O
serves	O
to	O
project	O
the	O
glycan	B-site
binding	I-site
site	I-site
of	O
these	O
proteins	O
far	O
from	O
the	O
membrane	O
surface	O
.	O

Any	O
mobility	O
of	O
SGBP	B-protein
-	I-protein
B	I-protein
on	O
the	O
surface	O
of	O
the	O
cell	O
(	O
beyond	O
lateral	O
diffusion	O
within	O
the	O
membrane	O
)	O
is	O
likely	O
imparted	O
by	O
the	O
eight	B-structure_element
-	I-structure_element
residue	I-structure_element
linker	I-structure_element
that	O
spans	O
the	O
predicted	O
lipidated	B-protein_state
Cys	B-residue_name
(	O
C28	B-residue_name_number
)	O
and	O
the	O
first	B-structure_element
β	I-structure_element
-	I-structure_element
strand	I-structure_element
of	O
domain	O
A	B-structure_element
.	O
Other	O
outer	B-protein_type
membrane	I-protein_type
proteins	I-protein_type
from	O
various	O
Sus	B-complex_assembly
-	I-complex_assembly
like	I-complex_assembly
systems	I-complex_assembly
possess	O
a	O
similar	O
10	B-structure_element
-	I-structure_element
to	I-structure_element
20	I-structure_element
-	I-structure_element
amino	I-structure_element
-	I-structure_element
acid	I-structure_element
flexible	I-structure_element
linker	I-structure_element
between	O
the	O
lipidated	B-protein_state
Cys	B-residue_name
that	O
tethers	O
the	O
protein	O
to	O
the	O
outside	O
the	O
cell	O
and	O
the	O
first	O
secondary	O
structure	O
element	O
.	O

Analogously	O
,	O
the	O
outer	B-protein_state
membrane	I-protein_state
-	I-protein_state
anchored	I-protein_state
endo	B-protein_type
-	I-protein_type
xyloglucanase	I-protein_type
BoGH5	B-protein
of	O
the	O
XyGUL	B-gene
contains	O
a	O
100	B-structure_element
-	I-structure_element
amino	I-structure_element
-	I-structure_element
acid	I-structure_element
,	I-structure_element
all	I-structure_element
-	I-structure_element
β	I-structure_element
-	I-structure_element
strand	I-structure_element
,	O
N	B-structure_element
-	I-structure_element
terminal	I-structure_element
module	I-structure_element
and	O
flexible	B-structure_element
linker	I-structure_element
that	O
imparts	O
conformational	O
flexibility	O
and	O
distances	O
the	O
catalytic	B-structure_element
module	I-structure_element
from	O
the	O
cell	O
surface	O
.	O

XyG	B-chemical
binds	B-protein_state
to	I-protein_state
domain	O
D	B-structure_element
of	O
SGBP	B-protein
-	I-protein
B	I-protein
at	O
the	O
concave	B-site
interface	I-site
of	O
the	O
top	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
,	O
with	O
binding	O
mediated	O
by	O
loops	B-structure_element
connecting	O
the	O
β	B-structure_element
-	I-structure_element
strands	I-structure_element
.	O

Six	O
glucosyl	B-chemical
residues	O
,	O
comprising	O
the	O
main	O
chain	O
,	O
and	O
three	O
branching	O
xylosyl	B-chemical
residues	O
of	O
XyGO2	B-chemical
can	O
be	O
modeled	O
in	O
the	O
density	B-evidence
(	O
Fig	O
.	O
5D	O
;	O
cf	O
.	O

The	O
backbone	O
is	O
flat	O
,	O
with	O
less	O
of	O
the	O
“	O
twisted	O
-	O
ribbon	O
”	O
geometry	O
observed	O
in	O
some	O
cello	B-chemical
-	I-chemical
and	I-chemical
xylogluco	I-chemical
-	I-chemical
oligosaccharides	I-chemical
.	O

The	O
aromatic	B-site
platform	I-site
created	O
by	O
W330	B-residue_name_number
,	O
W364	B-residue_name_number
,	O
and	O
Y363	B-residue_name_number
spans	O
four	O
glucosyl	B-chemical
residues	O
,	O
compared	O
to	O
the	O
longer	B-protein_state
platform	B-site
of	O
SGBP	B-protein
-	I-protein
A	I-protein
,	O
which	O
supports	O
six	O
glucosyl	B-chemical
residues	O
(	O
Fig	O
.	O
5E	O
).	O

The	O
Y363A	B-mutant
site	B-experimental_method
-	I-experimental_method
directed	I-experimental_method
mutant	I-experimental_method
of	O
SGBP	B-protein
-	I-protein
B	I-protein
displays	O
a	O
20	O
-	O
fold	O
decrease	O
in	O
the	O
Ka	B-evidence
for	O
XyG	B-chemical
,	O
while	O
the	O
W364A	B-mutant
mutant	B-protein_state
lacks	B-protein_state
XyG	I-protein_state
binding	I-protein_state
(	O
Table	O
3	O
;	O
see	O
Fig	O
.	O
S6	O
in	O
the	O
supplemental	O
material	O
).	O

There	O
are	O
no	O
additional	O
contacts	O
between	O
the	O
protein	O
and	O
the	O
β	B-chemical
-	I-chemical
glucan	I-chemical
backbone	O
and	O
surprisingly	O
few	O
interactions	O
with	O
the	O
side	O
-	O
chain	O
xylosyl	B-chemical
residues	O
,	O
despite	O
that	O
fact	O
that	O
ITC	B-experimental_method
data	O
demonstrate	O
that	O
SGBP	B-protein
-	I-protein
B	I-protein
does	O
not	O
measurably	O
bind	O
the	O
cellohexaose	B-chemical
(	O
Table	O
1	O
).	O

F414	B-residue_name_number
stacks	O
with	O
the	O
xylosyl	B-chemical
residue	O
of	O
Glc3	B-residue_name_number
,	O
while	O
Q407	B-residue_name_number
is	O
positioned	O
for	O
hydrogen	O
bonding	O
with	O
the	O
O4	O
of	O
xylosyl	B-chemical
residue	O
Xyl1	B-residue_name_number
.	O

Surprisingly	O
,	O
an	O
F414A	B-mutant
mutant	B-protein_state
of	O
SGBP	B-protein
-	I-protein
B	I-protein
displays	O
only	O
a	O
mild	O
3	O
-	O
fold	O
decrease	O
in	O
the	O
Ka	B-evidence
value	O
for	O
XyG	B-chemical
,	O
again	O
suggesting	O
that	O
glycan	B-chemical
recognition	O
is	O
primarily	O
mediated	O
via	O
contact	O
with	O
the	O
β	O
-	O
glucan	O
backbone	O
(	O
Table	O
3	O
;	O
see	O
Fig	O
.	O
S6	O
).	O

Additional	O
residues	B-structure_element
surrounding	O
the	O
binding	B-site
site	I-site
,	O
including	O
Y369	B-residue_name_number
and	O
E412	B-residue_name_number
,	O
may	O
contribute	O
to	O
the	O
recognition	O
of	O
more	O
highly	O
decorated	O
XyG	B-chemical
,	O
but	O
precisely	O
how	O
this	O
is	O
mediated	O
is	O
presently	O
unclear	O
.	O

Hoping	O
to	O
achieve	O
a	O
higher	O
-	O
resolution	O
view	O
of	O
the	O
SGBP	B-protein
-	I-protein
B	I-protein
–	O
xyloglucan	B-chemical
interaction	O
,	O
we	O
solved	B-experimental_method
the	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
fused	B-mutant
CD	I-mutant
domains	I-mutant
in	B-protein_state
complex	I-protein_state
with	I-protein_state
XyGO2	B-chemical
(	O
1	O
.	O
57	O
Å	O
,	O
Rwork	B-evidence
=	O
15	O
.	O
6	O
%,	O
Rfree	B-evidence
=	O
17	O
.	O
1	O
%,	O
residues	O
230	B-residue_range
to	I-residue_range
489	I-residue_range
)	O
(	O
Table	O
2	O
).	O

The	O
CD	B-structure_element
domains	I-structure_element
of	O
the	O
truncated	B-protein_state
and	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
proteins	O
superimpose	B-experimental_method
with	O
a	O
0	O
.	O
4	O
-	O
Å	O
RMSD	B-evidence
of	O
the	O
Cα	O
backbone	O
,	O
with	O
no	O
differences	O
in	O
the	O
position	O
of	O
any	O
of	O
the	O
glycan	B-site
-	I-site
binding	I-site
residues	I-site
(	O
see	O
Fig	O
.	O
S7A	O
in	O
the	O
supplemental	O
material	O
).	O

While	O
density	B-evidence
is	O
observed	O
for	O
XyGO2	B-chemical
,	O
the	O
ligand	O
could	O
not	O
be	O
unambiguously	O
modeled	O
into	O
this	O
density	B-evidence
to	O
achieve	O
a	O
reasonable	O
fit	O
between	O
the	O
X	B-evidence
-	I-evidence
ray	I-evidence
data	I-evidence
and	O
the	O
known	O
stereochemistry	O
of	O
the	O
sugar	O
(	O
see	O
Fig	O
.	O
S7B	O
and	O
C	O
).	O

While	O
this	O
may	O
occur	O
for	O
a	O
number	O
of	O
reasons	O
in	O
crystal	B-evidence
structures	I-evidence
,	O
it	O
is	O
likely	O
that	O
the	O
poor	O
ligand	O
density	O
even	O
at	O
higher	O
resolution	O
is	O
due	O
to	O
movement	O
or	O
multiple	O
orientations	O
of	O
the	O
sugar	B-chemical
averaged	O
throughout	O
the	O
lattice	O
.	O

SGBP	B-protein
-	I-protein
A	I-protein
and	O
SGBP	B-protein
-	I-protein
B	I-protein
have	O
distinct	O
,	O
coordinated	O
functions	O
in	O
vivo	O
.	O

The	O
similarity	O
of	O
the	O
glycan	B-chemical
specificity	O
of	O
SGBP	B-protein
-	I-protein
A	I-protein
and	O
SGBP	B-protein
-	I-protein
B	I-protein
presents	O
an	O
intriguing	O
conundrum	O
regarding	O
their	O
individual	O
roles	O
in	O
XyG	B-chemical
utilization	O
by	O
B	B-species
.	I-species
ovatus	I-species
.	O

To	O
disentangle	O
the	O
functions	O
of	O
SGBP	B-protein
-	I-protein
A	I-protein
and	O
SGBP	B-protein
-	I-protein
B	I-protein
in	O
XyG	B-chemical
recognition	O
and	O
uptake	O
,	O
we	O
created	O
individual	O
in	B-experimental_method
-	I-experimental_method
frame	I-experimental_method
deletion	I-experimental_method
and	I-experimental_method
complementation	I-experimental_method
mutant	I-experimental_method
strains	O
of	O
B	B-species
.	I-species
ovatus	I-species
.	O

In	O
these	O
growth	B-experimental_method
experiments	I-experimental_method
,	O
overnight	O
cultures	O
of	O
strains	O
grown	O
on	O
minimal	O
medium	O
plus	O
glucose	B-chemical
were	O
back	O
-	O
diluted	O
1	O
:	O
100	O
-	O
fold	O
into	O
minimal	O
medium	O
containing	O
5	O
mg	O
/	O
ml	O
of	O
the	O
reported	O
carbohydrate	B-chemical
.	O

Growth	O
on	O
glucose	B-chemical
displayed	O
the	O
shortest	O
lag	B-evidence
time	I-evidence
for	O
each	O
strain	O
,	O
and	O
so	O
lag	B-evidence
times	I-evidence
were	O
normalized	O
for	O
each	O
carbohydrate	B-chemical
by	O
subtracting	O
the	O
lag	B-evidence
time	I-evidence
of	O
that	O
strain	O
in	O
glucose	B-chemical
(	O
Fig	O
.	O
6	O
;	O
see	O
Fig	O
.	O
S8	O
in	O
the	O
supplemental	O
material	O
).	O

A	O
strain	O
in	O
which	O
the	O
entire	O
XyGUL	B-gene
is	O
deleted	B-experimental_method
displays	O
a	O
lag	B-evidence
of	O
24	O
.	O
5	O
h	O
during	O
growth	O
on	O
glucose	B-chemical
compared	O
to	O
the	O
isogenic	O
parental	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
(	O
WT	B-protein_state
)	O
Δtdk	B-mutant
strain	O
,	O
for	O
which	O
exponential	O
growth	O
lags	B-evidence
for	O
19	O
.	O
8	O
h	O
(	O
see	O
Fig	O
.	O
S8D	O
).	O

It	O
is	O
unknown	O
whether	O
this	O
is	O
because	O
cultures	O
were	O
not	O
normalized	O
by	O
the	O
starting	O
optical	O
density	O
(	O
OD	O
)	O
or	O
viable	O
cells	O
or	O
reflects	O
a	O
minor	O
defect	O
for	O
glucose	B-chemical
utilization	O
.	O

The	O
former	O
seems	O
more	O
likely	O
as	O
the	O
growth	O
rates	O
are	O
nearly	O
identical	O
for	O
these	O
strains	O
on	O
glucose	B-chemical
and	O
xylose	B-chemical
.	O

The	O
ΔXyGUL	B-mutant
and	O
WT	B-protein_state
Δtdk	B-mutant
strains	O
display	O
normalized	O
lag	B-evidence
times	I-evidence
on	O
xylose	B-chemical
within	O
experimental	O
error	O
,	O
and	O
curiously	O
some	O
of	O
the	O
mutant	O
and	O
complemented	O
strains	O
display	O
a	O
nominally	O
shorter	O
lag	B-evidence
time	I-evidence
on	O
xylose	B-chemical
than	O
the	O
WT	B-protein_state
Δtdk	B-mutant
strain	O
.	O

Complementation	B-experimental_method
of	O
the	O
ΔSGBP	B-mutant
-	I-mutant
A	I-mutant
strain	O
(	O
ΔSGBP	B-mutant
-	I-mutant
A	I-mutant
::	O
SGBP	B-protein
-	I-protein
A	I-protein
)	O
restores	O
growth	O
to	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
rates	O
on	O
xyloglucan	B-chemical
and	O
XyGO1	B-chemical
,	O
yet	O
the	O
calculated	O
rate	O
of	O
the	O
complemented	O
strain	O
is	O
~	O
72	O
%	O
that	O
of	O
the	O
WT	B-protein_state
Δtdk	B-mutant
strain	O
on	O
XyGO2	B-chemical
;	O
similar	O
results	O
were	O
obtained	O
for	O
the	O
SGBP	B-protein
-	I-protein
B	I-protein
complemented	O
strain	O
despite	O
the	O
fact	O
that	O
the	O
growth	O
curves	O
do	O
not	O
appear	O
much	O
different	O
(	O
see	O
Fig	O
.	O
S8C	O
and	O
F	O
).	O

The	O
reason	O
for	O
this	O
observation	O
on	O
XyGO2	B-chemical
is	O
unclear	O
,	O
as	O
the	O
ΔSGBP	B-mutant
-	I-mutant
B	I-mutant
mutant	B-protein_state
does	O
not	O
have	O
a	O
significantly	O
different	O
growth	O
rate	O
from	O
the	O
WT	B-protein_state
on	O
XyGO2	B-chemical
.	O

Growth	O
of	O
select	O
XyGUL	B-gene
mutants	O
on	O
xyloglucan	B-chemical
and	O
oligosaccharides	B-chemical
.	O

B	B-species
.	I-species
ovatus	I-species
mutants	O
were	O
created	O
in	O
a	O
thymidine	B-mutant
kinase	I-mutant
deletion	I-mutant
(	O
Δtdk	B-mutant
)	O
mutant	O
as	O
described	O
previously	O
.	O

SGBP	B-mutant
-	I-mutant
A	I-mutant
*	I-mutant
denotes	O
the	O
Bacova_02651	B-gene
(	O
W82A	B-mutant
W283A	B-mutant
W306A	B-mutant
)	O
allele	O
,	O
and	O
the	O
GH9	B-protein
gene	O
is	O
Bacova_02649	B-gene
.	O

Growth	O
was	O
measured	O
over	O
time	O
in	O
minimal	O
medium	O
containing	O
(	O
A	O
)	O
XyG	B-chemical
,	O
(	O
B	O
)	O
XyGO2	B-chemical
,	O
(	O
C	O
)	O
XyGO1	B-chemical
,	O
(	O
D	O
)	O
glucose	B-chemical
,	O
and	O
(	O
E	O
)	O
xylose	B-chemical
.	O

In	O
panel	O
F	O
,	O
the	O
growth	O
rate	O
of	O
each	O
strain	O
on	O
the	O
five	O
carbon	O
sources	O
is	O
displayed	O
,	O
and	O
in	O
panel	O
G	O
,	O
the	O
normalized	O
lag	B-evidence
time	I-evidence
of	O
each	O
culture	O
,	O
relative	O
to	O
its	O
growth	O
on	O
glucose	B-chemical
,	O
is	O
displayed	O
.	O

Solid	O
bars	O
indicate	O
conditions	O
that	O
are	O
not	O
statistically	O
significant	O
from	O
the	O
WT	B-protein_state
Δtdk	B-mutant
cultures	O
grown	O
on	O
the	O
indicated	O
carbohydrate	B-chemical
,	O
while	O
open	O
bars	O
indicate	O
a	O
P	O
value	O
of	O
<	O
0	O
.	O
005	O
compared	O
to	O
the	O
WT	B-protein_state
Δtdk	B-mutant
strain	O
.	O

Conditions	O
denoted	O
by	O
the	O
same	O
letter	O
(	O
b	O
,	O
c	O
,	O
or	O
d	O
)	O
are	O
not	O
statistically	O
significant	O
from	O
each	O
other	O
but	O
are	O
significantly	O
different	O
from	O
the	O
condition	O
labeled	O
“	O
a	O
.”	O
Complementation	O
of	O
ΔSGBP	B-mutant
-	I-mutant
A	I-mutant
and	O
ΔSBGP	B-mutant
-	I-mutant
B	I-mutant
was	O
performed	O
by	O
allelic	O
exchange	O
of	O
the	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
genes	O
back	O
into	O
the	O
genome	O
for	O
expression	O
via	O
the	O
native	O
promoter	O
:	O
these	O
growth	O
curves	O
,	O
quantified	O
rates	O
and	O
lag	B-evidence
times	I-evidence
are	O
displayed	O
in	O
Fig	O
.	O
S8	O
in	O
the	O
supplemental	O
material	O
.	O

The	O
ΔSGBP	B-mutant
-	I-mutant
A	I-mutant
(	O
ΔBacova_02651	B-mutant
)	O
strain	O
(	O
cf	O
.	O

Fig	O
.	O
1B	O
)	O
was	O
completely	O
incapable	O
of	O
growth	O
on	O
XyG	B-chemical
,	O
XyGO1	B-chemical
,	O
and	O
XyGO2	B-chemical
,	O
indicating	O
that	O
SGBP	B-protein
-	I-protein
A	I-protein
is	O
essential	O
for	O
XyG	B-chemical
utilization	O
(	O
Fig	O
.	O
6	O
).	O

This	O
result	O
mirrors	O
our	O
previous	O
data	O
for	O
the	O
canonical	O
Sus	B-complex_assembly
of	O
B	B-species
.	I-species
thetaiotaomicron	I-species
,	O
which	O
revealed	O
that	O
a	O
homologous	O
ΔsusD	B-mutant
mutant	B-protein_state
is	O
unable	O
to	O
grow	O
on	O
starch	B-chemical
or	O
malto	B-chemical
-	I-chemical
oligosaccharides	I-chemical
,	O
despite	O
normal	O
cell	O
surface	O
expression	O
of	O
all	O
other	O
PUL	B-gene
-	O
encoded	O
proteins	O
.	O

More	O
recently	O
,	O
we	O
demonstrated	O
that	O
this	O
phenotype	O
is	O
due	O
to	O
the	O
loss	O
of	O
the	O
physical	O
presence	O
of	O
SusD	B-protein
;	O
complementation	B-experimental_method
of	O
ΔsusD	B-mutant
with	O
SusD	B-mutant
*,	I-mutant
a	O
triple	B-protein_state
site	I-protein_state
-	I-protein_state
directed	I-protein_state
mutant	I-protein_state
(	O
W96A	B-mutant
W320A	B-mutant
Y296A	B-mutant
)	O
that	O
ablates	B-protein_state
glycan	I-protein_state
binding	I-protein_state
,	O
restores	O
B	B-species
.	I-species
thetaiotaomicron	I-species
growth	O
on	O
malto	B-chemical
-	I-chemical
oligosaccharides	I-chemical
and	O
starch	B-chemical
when	O
sus	B-gene
transcription	O
is	O
induced	O
by	O
maltose	B-chemical
addition	O
.	O

Similarly	O
,	O
the	O
function	O
of	O
SGBP	B-protein
-	I-protein
A	I-protein
extends	O
beyond	O
glycan	B-chemical
binding	O
.	O

Complementation	B-experimental_method
of	O
ΔSGBP	B-mutant
-	I-mutant
A	I-mutant
with	O
the	O
SGBP	B-mutant
-	I-mutant
A	I-mutant
*	I-mutant
(	O
W82A	B-mutant
W283A	B-mutant
W306A	B-mutant
)	O
variant	O
,	O
which	O
does	O
not	B-protein_state
bind	I-protein_state
XyG	B-chemical
,	O
supports	O
growth	O
on	O
XyG	B-chemical
and	O
XyGOs	B-chemical
(	O
Fig	O
.	O
6	O
;	O
ΔSGBP	B-mutant
-	I-mutant
A	I-mutant
::	O
SGBP	B-mutant
-	I-mutant
A	I-mutant
*),	I-mutant
with	O
growth	O
rates	O
that	O
are	O
~	O
70	O
%	O
that	O
of	O
the	O
WT	B-protein_state
.	O

In	O
previous	O
studies	O
,	O
we	O
observed	O
that	O
carbohydrate	B-chemical
binding	O
by	O
SusD	B-protein
enhanced	O
the	O
sensitivity	O
of	O
the	O
cells	O
to	O
limiting	O
concentrations	O
of	O
malto	O
-	O
oligosaccharides	O
by	O
several	O
orders	O
of	O
magnitude	O
,	O
such	O
that	O
the	O
addition	O
of	O
0	O
.	O
5	O
g	O
/	O
liter	O
maltose	B-chemical
was	O
required	O
to	O
restore	O
growth	O
of	O
the	O
ΔsusD	B-mutant
::	O
SusD	B-mutant
*	I-mutant
strain	O
on	O
starch	B-chemical
,	O
which	O
nonetheless	O
occurred	O
following	O
an	O
extended	O
lag	B-evidence
phase	I-evidence
.	O

In	O
contrast	O
,	O
the	O
ΔSGBP	B-mutant
-	I-mutant
A	I-mutant
::	O
SGBP	B-mutant
-	I-mutant
A	I-mutant
*	I-mutant
strain	O
does	O
not	O
display	O
an	O
extended	O
lag	B-evidence
time	I-evidence
on	O
any	O
of	O
the	O
xyloglucan	B-chemical
substrates	O
compared	O
to	O
the	O
WT	B-protein_state
(	O
Fig	O
.	O
6	O
).	O

The	O
specific	O
glycan	B-chemical
signal	O
that	O
upregulates	O
BoXyGUL	B-gene
is	O
currently	O
unknown	O
.	O

From	O
our	O
present	O
data	O
,	O
we	O
cannot	O
eliminate	O
the	O
possibility	O
that	O
the	O
glycan	B-chemical
binding	O
by	O
SGBP	B-protein
-	I-protein
A	I-protein
enhances	O
transcriptional	O
activation	O
of	O
the	O
XyGUL	B-gene
.	O

However	O
,	O
the	O
modest	O
rate	O
defect	O
displayed	O
by	O
the	O
SGBP	B-protein
-	I-protein
A	I-protein
::	O
SGBP	B-mutant
-	I-mutant
A	I-mutant
*	I-mutant
strain	O
suggests	O
that	O
recognition	O
of	O
XyG	B-chemical
and	O
product	O
import	O
is	O
somewhat	O
less	O
efficient	O
in	O
these	O
cells	O
.	O

Intriguingly	O
,	O
the	O
ΔSGBP	B-mutant
-	I-mutant
B	I-mutant
strain	O
(	O
ΔBacova_02650	B-mutant
)	O
(	O
cf	O
.	O

Fig	O
.	O
1B	O
)	O
exhibited	O
a	O
minor	O
growth	O
defect	O
on	O
both	O
XyG	B-chemical
and	O
XyGO2	B-chemical
,	O
with	O
rates	O
84	O
.	O
6	O
%	O
and	O
93	O
.	O
9	O
%	O
that	O
of	O
the	O
WT	B-protein_state
Δtdk	B-mutant
strain	O
.	O

However	O
,	O
growth	O
of	O
the	O
ΔSGBP	B-mutant
-	I-mutant
B	I-mutant
strain	O
on	O
XyGO1	B-chemical
was	O
54	O
.	O
2	O
%	O
the	O
rate	O
of	O
the	O
parental	O
strain	O
,	O
despite	O
the	O
fact	O
that	O
SGBP	B-protein
-	I-protein
B	I-protein
binds	O
this	O
substrate	O
ca	O
.	O

10	O
-	O
fold	O
more	O
weakly	O
than	O
XyGO2	B-chemical
and	O
XyG	B-chemical
(	O
Fig	O
.	O
6	O
;	O
Table	O
1	O
).	O

As	O
such	O
,	O
the	O
data	O
suggest	O
that	O
SGBP	B-protein
-	I-protein
A	I-protein
can	O
compensate	O
for	O
the	O
loss	O
of	O
function	O
of	O
SGBP	B-protein
-	I-protein
B	I-protein
on	O
longer	O
oligo	B-chemical
-	I-chemical
and	I-chemical
polysaccharides	I-chemical
,	O
while	O
SGBP	B-protein
-	I-protein
B	I-protein
may	O
adapt	O
the	O
cell	O
to	O
recognize	O
smaller	O
oligosaccharides	B-chemical
efficiently	O
.	O

Indeed	O
,	O
a	O
double	B-protein_state
mutant	I-protein_state
,	O
consisting	O
of	O
a	O
crippled	B-protein_state
SGBP	B-protein
-	I-protein
A	I-protein
and	O
a	O
deletion	B-experimental_method
of	I-experimental_method
SGBP	B-protein
-	I-protein
B	I-protein
(	O
ΔSGBP	B-mutant
-	I-mutant
A	I-mutant
::	O
SGBP	B-mutant
-	I-mutant
A	I-mutant
*/	I-mutant
ΔSGBP	B-mutant
-	I-mutant
B	I-mutant
),	O
exhibits	O
an	O
extended	O
lag	B-evidence
time	I-evidence
on	O
both	O
XyG	B-chemical
and	O
XyGO2	B-chemical
,	O
as	O
well	O
as	O
XyGO1	B-chemical
.	O

Taken	O
together	O
,	O
the	O
data	O
indicate	O
that	O
SGBP	B-protein
-	I-protein
A	I-protein
and	O
SGBP	B-protein
-	I-protein
B	I-protein
functionally	O
complement	O
each	O
other	O
in	O
the	O
capture	O
of	O
XyG	B-chemical
polysaccharide	B-chemical
,	O
while	O
SGBP	B-protein
-	I-protein
B	I-protein
may	O
allow	O
B	B-species
.	I-species
ovatus	I-species
to	O
scavenge	O
smaller	O
XyGOs	B-chemical
liberated	O
by	O
other	O
gut	O
commensals	O
.	O

This	O
additional	O
role	O
of	O
SGBP	B-protein
-	I-protein
B	I-protein
is	O
especially	O
notable	O
in	O
the	O
context	O
of	O
studies	O
on	O
BtSusE	B-protein
and	O
BtSusF	B-protein
(	O
positioned	O
similarly	O
in	O
the	O
archetypal	O
Sus	B-gene
locus	I-gene
)	O
(	O
Fig	O
.	O
1B	O
),	O
for	O
which	O
growth	O
defects	O
on	O
starch	B-chemical
or	O
malto	B-chemical
-	I-chemical
oligosaccharides	I-chemical
have	O
never	O
been	O
observed	O
.	O

Beyond	O
SGBP	B-protein
-	I-protein
A	I-protein
and	O
SGBP	B-protein
-	I-protein
B	I-protein
,	O
we	O
speculated	O
that	O
the	O
catalytically	B-protein_state
feeble	I-protein_state
endo	B-protein_type
-	I-protein_type
xyloglucanase	I-protein_type
GH9	B-protein
,	O
which	O
is	O
expendable	O
for	O
growth	O
in	O
the	O
presence	O
of	O
GH5	B-protein
,	O
might	O
also	O
play	O
a	O
role	O
in	O
glycan	B-chemical
binding	O
to	O
the	O
cell	O
surface	O
.	O

However	O
,	O
combined	B-experimental_method
deletion	I-experimental_method
of	I-experimental_method
the	I-experimental_method
genes	I-experimental_method
encoding	I-experimental_method
GH9	B-protein
(	O
encoded	O
by	O
Bacova_02649	B-gene
)	O
and	O
SGBP	B-protein
-	I-protein
B	I-protein
does	O
not	O
exacerbate	O
the	O
growth	O
defect	O
on	O
XyGO1	B-chemical
(	O
Fig	O
.	O
6	O
;	O
ΔSGBP	B-mutant
-	I-mutant
B	I-mutant
/	O
ΔGH9	B-mutant
).	O

The	O
necessity	O
of	O
SGBP	B-protein
-	I-protein
B	I-protein
is	O
elevated	O
in	O
the	O
SGBP	B-mutant
-	I-mutant
A	I-mutant
*	I-mutant
strain	O
,	O
as	O
the	O
ΔSGBP	B-mutant
-	I-mutant
A	I-mutant
::	O
SGBP	B-mutant
-	I-mutant
A	I-mutant
*/	I-mutant
ΔSGBP	B-mutant
-	I-mutant
B	I-mutant
mutant	B-protein_state
displays	O
an	O
extended	O
lag	B-evidence
during	O
growth	O
on	O
XyG	B-chemical
and	O
xylogluco	B-chemical
-	I-chemical
oligosaccharides	I-chemical
,	O
while	O
growth	O
rate	O
differences	O
are	O
more	O
subtle	O
.	O

The	O
precise	O
reason	O
for	O
this	O
lag	B-evidence
is	O
unclear	O
,	O
but	O
recapitulating	O
our	O
findings	O
on	O
the	O
role	O
of	O
SusD	B-protein
in	O
malto	B-chemical
-	I-chemical
oligosaccharide	I-chemical
sensing	O
in	O
B	B-species
.	I-species
thetaiotaomicron	I-species
,	O
this	O
extended	O
lag	B-evidence
may	O
be	O
due	O
to	O
inefficient	O
import	O
and	O
thus	O
sensing	O
of	O
xyloglucan	B-chemical
in	O
the	O
environment	O
in	O
the	O
absence	O
of	O
glycan	B-chemical
binding	O
by	O
essential	O
SGBPs	B-protein_type
.	O

Our	O
previous	O
work	O
demonstrates	O
that	O
B	B-species
.	I-species
ovatus	I-species
cells	O
grown	O
in	O
minimal	O
medium	O
plus	O
glucose	B-chemical
express	O
low	O
levels	O
of	O
the	O
XyGUL	B-gene
transcript	O
.	O

Thus	O
,	O
in	O
our	O
experiments	O
,	O
we	O
presume	O
that	O
each	O
strain	O
,	O
initially	O
grown	O
in	O
glucose	B-chemical
,	O
expresses	O
low	O
levels	O
of	O
the	O
XyGUL	B-gene
transcript	O
and	O
thus	O
low	O
levels	O
of	O
the	O
XyGUL	B-gene
-	O
encoded	O
surface	O
proteins	O
,	O
including	O
the	O
vanguard	O
GH5	B-protein
.	O

Presumably	O
without	O
glycan	B-chemical
binding	O
by	O
the	O
SGBPs	B-protein_type
,	O
the	O
GH5	B-protein
protein	O
cannot	O
efficiently	O
process	O
xyloglucan	B-chemical
,	O
and	O
/	O
or	O
the	O
lack	O
of	O
SGBP	B-protein_type
function	O
prevents	O
efficient	O
capture	O
and	O
import	O
of	O
the	O
processed	O
oligosaccharides	B-chemical
.	O

It	O
may	O
then	O
be	O
that	O
only	O
after	O
a	O
sufficient	O
amount	O
of	O
glycan	B-chemical
is	O
processed	O
and	O
imported	O
by	O
the	O
cell	O
is	O
XyGUL	B-gene
upregulated	O
and	O
exponential	O
growth	O
on	O
the	O
glycan	B-chemical
can	O
begin	O
.	O

We	O
hypothesize	O
that	O
during	O
exponential	O
growth	O
the	O
essential	O
role	O
of	O
SGBP	B-protein
-	I-protein
A	I-protein
extends	O
beyond	O
glycan	B-chemical
recognition	O
,	O
perhaps	O
due	O
to	O
a	O
critical	O
interaction	O
with	O
the	O
TBDT	B-protein_type
.	O

In	O
the	O
BtSus	B-gene
,	O
SusD	B-protein
and	O
the	O
TBDT	B-protein_type
SusC	B-protein
interact	O
,	O
and	O
we	O
speculate	O
that	O
this	O
interaction	O
is	O
necessary	O
for	O
glycan	B-chemical
uptake	O
,	O
as	O
suggested	O
by	O
the	O
fact	O
that	O
a	O
ΔsusD	B-mutant
mutant	B-protein_state
cannot	O
grow	O
on	O
starch	B-chemical
,	O
but	O
a	O
ΔsusD	B-mutant
::	O
SusD	B-mutant
*	I-mutant
strain	O
regains	O
this	O
ability	O
if	O
a	O
transcriptional	B-protein_type
activator	I-protein_type
of	O
the	O
sus	B-gene
operon	I-gene
is	O
supplied	O
.	O

Likewise	O
,	O
such	O
cognate	O
interactions	O
between	O
homologous	O
protein	O
pairs	O
such	O
as	O
SGBP	B-protein
-	I-protein
A	I-protein
and	O
its	O
TBDT	B-protein_type
may	O
underlie	O
our	O
observation	O
that	O
a	O
ΔSGBP	B-mutant
-	I-mutant
A	I-mutant
mutant	B-protein_state
cannot	O
grow	O
on	O
xyloglucan	B-chemical
.	O

However	O
,	O
unlike	O
the	O
Sus	B-complex_assembly
,	O
in	O
which	O
elimination	B-experimental_method
of	I-experimental_method
SusE	B-protein
and	O
SusF	B-protein
does	O
not	O
affect	O
growth	O
on	O
starch	B-chemical
,	O
SGBP	B-protein
-	I-protein
B	I-protein
appears	O
to	O
have	O
a	O
dedicated	O
role	O
in	O
growth	O
on	O
small	O
xylogluco	B-chemical
-	I-chemical
oligosaccharides	I-chemical
.	O

The	O
ability	O
of	O
gut	O
-	O
adapted	O
microorganisms	B-taxonomy_domain
to	O
thrive	O
in	O
the	O
gastrointestinal	O
tract	O
is	O
critically	O
dependent	O
upon	O
their	O
ability	O
to	O
efficiently	O
recognize	O
,	O
cleave	O
,	O
and	O
import	O
glycans	B-chemical
.	O

The	O
human	B-species
gut	O
,	O
in	O
particular	O
,	O
is	O
a	O
densely	O
packed	O
ecosystem	O
with	O
hundreds	O
of	O
species	O
,	O
in	O
which	O
there	O
is	O
potential	O
for	O
both	O
competition	O
and	O
synergy	O
in	O
the	O
utilization	O
of	O
different	O
substrates	O
.	O

Recent	O
work	O
has	O
elucidated	O
that	O
Bacteroidetes	B-taxonomy_domain
cross	O
-	O
feed	O
during	O
growth	O
on	O
many	O
glycans	B-chemical
;	O
the	O
glycoside	B-protein_type
hydrolases	I-protein_type
expressed	O
by	O
one	O
species	O
liberate	O
oligosaccharides	B-chemical
for	O
consumption	O
by	O
other	O
members	O
of	O
the	O
community	O
.	O

Thus	O
,	O
understanding	O
glycan	B-chemical
capture	O
at	O
the	O
cell	O
surface	O
is	O
fundamental	O
to	O
explaining	O
,	O
and	O
eventually	O
predicting	O
,	O
how	O
the	O
carbohydrate	O
content	O
of	O
the	O
diet	O
shapes	O
the	O
gut	O
community	O
structure	O
as	O
well	O
as	O
its	O
causative	O
health	O
effects	O
.	O

Here	O
,	O
we	O
demonstrate	O
that	O
the	O
surface	B-protein_type
glycan	I-protein_type
binding	I-protein_type
proteins	I-protein_type
encoded	O
within	O
the	O
BoXyGUL	B-gene
play	O
unique	O
and	O
essential	O
roles	O
in	O
the	O
acquisition	O
of	O
the	O
ubiquitous	O
and	O
abundant	O
vegetable	B-taxonomy_domain
polysaccharide	B-chemical
xyloglucan	B-chemical
.	O

Yet	O
,	O
a	O
number	O
of	O
questions	O
remain	O
regarding	O
the	O
molecular	O
interplay	O
of	O
SGBPs	B-protein_type
with	O
their	O
cotranscribed	O
cohort	O
of	O
glycoside	B-protein_type
hydrolases	I-protein_type
and	O
TonB	B-protein_type
-	I-protein_type
dependent	I-protein_type
transporters	I-protein_type
.	O

A	O
particularly	O
understudied	O
aspect	O
of	O
glycan	B-chemical
utilization	O
is	O
the	O
mechanism	O
of	O
import	O
via	O
TBDTs	B-protein_type
(	O
SusC	B-protein
homologs	O
)	O
(	O
Fig	O
.	O
1	O
),	O
which	O
are	O
ubiquitous	O
and	O
defining	O
components	O
of	O
all	O
PUL	B-gene
.	O

PUL	B-gene
-	O
encoded	O
TBDTs	B-protein_type
in	O
Bacteroidetes	B-taxonomy_domain
are	O
larger	O
than	O
the	O
well	O
-	O
characterized	O
iron	B-protein_type
-	I-protein_type
targeting	I-protein_type
TBDTs	I-protein_type
from	O
many	O
Proteobacteria	B-taxonomy_domain
and	O
are	O
further	O
distinguished	O
as	O
the	O
only	O
known	O
glycan	B-protein_type
-	I-protein_type
importing	I-protein_type
TBDTs	I-protein_type
coexpressed	O
with	O
an	O
SGBP	B-protein_type
.	O

A	O
direct	O
interaction	O
between	O
the	O
BtSusC	B-protein
TBDT	B-protein_type
and	O
the	O
SusD	B-protein
SGBP	B-protein_type
has	O
been	O
previously	O
demonstrated	O
,	O
as	O
has	O
an	O
interaction	O
between	O
the	O
homologous	O
components	O
encoded	O
by	O
an	O
N	O
-	O
glycan	B-chemical
-	O
scavenging	O
PUL	B-gene
of	O
Capnocytophaga	B-species
canimorsus	I-species
.	O

Our	O
observation	O
here	O
that	O
the	O
physical	O
presence	O
of	O
the	O
SusD	B-protein
homolog	O
SGBP	B-protein
-	I-protein
A	I-protein
,	O
independent	O
of	O
XyG	B-chemical
-	O
binding	O
ability	O
,	O
is	O
both	O
necessary	O
and	O
sufficient	O
for	O
XyG	B-chemical
utilization	O
further	O
supports	O
a	O
model	O
of	O
glycan	B-chemical
import	O
whereby	O
the	O
SusC	B-protein_type
-	I-protein_type
like	I-protein_type
TBDTs	I-protein_type
and	O
the	O
SusD	B-protein_type
-	I-protein_type
like	I-protein_type
SGBPs	I-protein_type
must	O
be	O
intimately	O
associated	O
to	O
support	O
glycan	B-chemical
uptake	O
(	O
Fig	O
.	O
1C	O
).	O

It	O
is	O
yet	O
presently	O
unclear	O
whether	O
this	O
interaction	O
is	O
static	O
or	O
dynamic	O
and	O
to	O
what	O
extent	O
the	O
association	O
of	O
cognate	O
TBDT	B-protein_type
/	O
SGBPs	B-protein_type
is	O
dependent	O
upon	O
the	O
structure	O
of	O
the	O
carbohydrate	B-chemical
to	O
be	O
imported	O
.	O

On	O
the	O
other	O
hand	O
,	O
there	O
is	O
clear	O
evidence	O
for	O
independent	O
TBDTs	B-protein_type
in	O
Bacteroidetes	B-taxonomy_domain
that	O
do	O
not	O
require	O
SGBP	B-protein_type
association	O
for	O
activity	O
.	O

For	O
example	O
,	O
it	O
was	O
recently	O
demonstrated	O
that	O
expression	O
of	O
nanO	B-gene
,	O
which	O
encodes	O
a	O
SusC	B-protein_type
-	I-protein_type
like	I-protein_type
TBDT	I-protein_type
as	O
part	O
of	O
a	O
sialic	O
-	O
acid	O
-	O
targeting	O
PUL	B-gene
from	O
B	B-species
.	I-species
fragilis	I-species
,	O
restored	O
growth	O
on	O
this	O
monosaccharide	B-chemical
in	O
a	O
mutant	O
strain	O
of	O
E	B-species
.	I-species
coli	I-species
.	O

In	O
this	O
instance	O
,	O
coexpression	O
of	O
the	O
susD	B-gene
-	O
like	O
gene	O
nanU	B-gene
was	O
not	O
required	O
,	O
nor	O
did	O
the	O
expression	O
of	O
the	O
nanU	B-gene
gene	O
enhance	O
growth	O
kinetics	O
.	O

Similarly	O
,	O
the	O
deletion	O
of	O
BT1762	B-gene
encoding	O
a	O
fructan	B-protein_type
-	I-protein_type
targeting	I-protein_type
SusD	I-protein_type
-	I-protein_type
like	I-protein_type
protein	I-protein_type
in	O
B	B-species
.	I-species
thetaiotaomicron	I-species
did	O
not	O
result	O
in	O
a	O
dramatic	O
loss	O
of	O
growth	O
on	O
fructans	B-chemical
.	O

Thus	O
,	O
the	O
strict	O
dependence	O
on	O
a	O
SusD	B-protein_type
-	I-protein_type
like	I-protein_type
SGBP	I-protein_type
for	O
glycan	B-chemical
uptake	O
in	O
the	O
Bacteroidetes	B-taxonomy_domain
may	O
be	O
variable	O
and	O
substrate	O
dependent	O
.	O

Furthermore	O
,	O
considering	O
the	O
broader	O
distribution	O
of	O
TBDTs	B-protein_type
in	O
PUL	B-gene
lacking	O
SGBPs	B-protein_type
(	O
sometimes	O
known	O
as	O
carbohydrate	B-gene
utilization	I-gene
containing	I-gene
TBDT	I-gene
[	I-gene
CUT	I-gene
]	I-gene
loci	I-gene
;	O
see	O
reference	O
and	O
reviewed	O
in	O
reference	O
)	O
across	O
bacterial	B-taxonomy_domain
phyla	O
,	O
it	O
appears	O
that	O
the	O
intimate	O
biophysical	O
association	O
of	O
these	O
substrate	O
-	O
transport	O
and	O
-	O
binding	O
proteins	O
is	O
the	O
result	O
of	O
specific	O
evolution	O
within	O
the	O
Bacteroidetes	B-taxonomy_domain
.	O

Equally	O
intriguing	O
is	O
the	O
observation	O
that	O
while	O
SusD	B-protein_type
-	I-protein_type
like	I-protein_type
proteins	I-protein_type
such	O
as	O
SGBP	B-protein
-	I-protein
A	I-protein
share	O
moderate	O
primary	O
and	O
high	O
tertiary	O
structural	O
conservation	O
,	O
the	O
genes	O
for	O
the	O
SGBPs	B-protein_type
encoded	O
immediately	O
downstream	O
(	O
Fig	O
.	O
1B	O
[	O
sometimes	O
referred	O
to	O
as	O
“	O
susE	O
positioned	O
”])	O
encode	O
glycan	B-protein_type
-	I-protein_type
binding	I-protein_type
lipoproteins	I-protein_type
with	O
little	O
or	O
no	O
sequence	O
or	O
structural	O
conservation	O
,	O
even	O
among	O
syntenic	O
PUL	B-gene
that	O
target	O
the	O
same	O
polysaccharide	B-chemical
.	O

Such	O
is	O
the	O
case	O
for	O
XyGUL	B-gene
from	O
related	O
Bacteroides	B-taxonomy_domain
species	O
,	O
which	O
may	O
encode	O
either	O
one	O
or	O
two	O
of	O
these	O
predicted	O
SGBPs	B-protein_type
,	O
and	O
these	O
proteins	O
vary	O
considerably	O
in	O
length	O
.	O

The	O
extremely	O
low	O
similarity	O
of	O
these	O
SGBPs	B-protein_type
is	O
striking	O
in	O
light	O
of	O
the	O
moderate	O
sequence	O
conservation	O
observed	O
among	O
homologous	O
GHs	B-protein_type
in	O
syntenic	O
PUL	B-gene
.	O

This	O
,	O
together	O
with	O
the	O
observation	O
that	O
these	O
SGBPs	B-protein_type
,	O
as	O
exemplified	O
by	O
BtSusE	B-protein
and	O
BtSusF	B-protein
and	O
the	O
XyGUL	B-gene
SGBP	B-protein
-	I-protein
B	I-protein
of	O
the	O
present	O
study	O
,	O
are	O
expendable	O
for	O
polysaccharide	B-chemical
growth	O
,	O
implies	O
a	O
high	O
degree	O
of	O
evolutionary	O
flexibility	O
to	O
enhance	O
glycan	B-chemical
capture	O
at	O
the	O
cell	O
surface	O
.	O

Because	O
the	O
intestinal	O
ecosystem	O
is	O
a	O
dense	O
consortium	O
of	O
bacteria	B-taxonomy_domain
that	O
must	O
compete	O
for	O
their	O
nutrients	O
,	O
these	O
multimodular	O
SGBPs	B-protein_type
may	O
reflect	O
ongoing	O
evolutionary	O
experiments	O
to	O
enhance	O
glycan	B-chemical
uptake	O
efficiency	O
.	O

Whether	O
organisms	O
that	O
express	O
longer	O
SGBPs	B-protein_type
,	O
extending	O
further	O
above	O
the	O
cell	O
surface	O
toward	O
the	O
extracellular	O
environment	O
,	O
are	O
better	O
equipped	O
to	O
compete	O
for	O
available	O
carbohydrates	B-chemical
is	O
presently	O
unknown	O
.	O

However	O
,	O
the	O
natural	O
diversity	O
of	O
these	O
proteins	O
represents	O
a	O
rich	O
source	O
for	O
the	O
discovery	O
of	O
unique	O
carbohydrate	B-structure_element
-	I-structure_element
binding	I-structure_element
motifs	I-structure_element
to	O
both	O
inform	O
gut	O
microbiology	O
and	O
generate	O
new	O
,	O
specific	O
carbohydrate	B-chemical
analytical	O
reagents	O
.	O

In	O
conclusion	O
,	O
the	O
present	O
study	O
further	O
illuminates	O
the	O
essential	O
role	O
that	O
surface	B-protein_type
-	I-protein_type
glycan	I-protein_type
binding	I-protein_type
proteins	I-protein_type
play	O
in	O
facilitating	O
the	O
catabolism	O
of	O
complex	O
dietary	O
carbohydrates	B-chemical
by	O
Bacteroidetes	B-taxonomy_domain
.	O

The	O
ability	O
of	O
our	O
resident	O
gut	O
bacteria	B-taxonomy_domain
to	O
recognize	O
polysaccharides	B-chemical
is	O
the	O
first	O
committed	O
step	O
of	O
glycan	B-chemical
consumption	O
by	O
these	O
organisms	O
,	O
a	O
critical	O
process	O
that	O
influences	O
the	O
community	O
structure	O
and	O
thus	O
the	O
metabolic	O
output	O
(	O
i	O
.	O
e	O
.,	O
short	O
-	O
chain	O
fatty	O
acid	O
and	O
metabolite	O
profile	O
)	O
of	O
these	O
organisms	O
.	O

A	O
molecular	O
understanding	O
of	O
glycan	B-chemical
uptake	O
by	O
human	B-species
gut	O
bacteria	B-taxonomy_domain
is	O
therefore	O
central	O
to	O
the	O
development	O
of	O
strategies	O
to	O
improve	O
human	B-species
health	O
through	O
manipulation	O
of	O
the	O
microbiota	B-taxonomy_domain
.	O

Mucosal	O
glycan	B-chemical
foraging	O
enhances	O
fitness	O
and	O
transmission	O
of	O
a	O
saccharolytic	O
human	O
gut	O
bacterial	O
symbiont	O

Molecular	O
Basis	O
of	O
Ligand	O
-	O
Dependent	O
Regulation	O
of	O
NadR	B-protein
,	O
the	O
Transcriptional	B-protein_type
Repressor	I-protein_type
of	O
Meningococcal	B-taxonomy_domain
Virulence	O
Factor	O
NadA	B-protein

Neisseria	B-protein
adhesin	I-protein
A	I-protein
(	O
NadA	B-protein
)	O
is	O
present	O
on	O
the	O
meningococcal	B-taxonomy_domain
surface	O
and	O
contributes	O
to	O
adhesion	O
to	O
and	O
invasion	O
of	O
human	B-species
cells	O
.	O

NadA	B-protein
is	O
also	O
one	O
of	O
three	O
recombinant	O
antigens	O
in	O
the	O
recently	O
-	O
approved	O
Bexsero	O
vaccine	O
,	O
which	O
protects	O
against	O
serogroup	B-taxonomy_domain
B	I-taxonomy_domain
meningococcus	I-taxonomy_domain
.	O

The	O
amount	O
of	O
NadA	B-protein
on	O
the	O
bacterial	B-taxonomy_domain
surface	O
is	O
of	O
direct	O
relevance	O
in	O
the	O
constant	O
battle	O
of	O
host	O
-	O
pathogen	O
interactions	O
:	O
it	O
influences	O
the	O
ability	O
of	O
the	O
pathogen	O
to	O
engage	O
human	B-species
cell	O
surface	O
-	O
exposed	O
receptors	O
and	O
,	O
conversely	O
,	O
the	O
bacterial	B-taxonomy_domain
susceptibility	O
to	O
the	O
antibody	O
-	O
mediated	O
immune	O
response	O
.	O

It	O
is	O
therefore	O
important	O
to	O
understand	O
the	O
mechanisms	O
which	O
regulate	O
nadA	B-gene
expression	O
levels	O
,	O
which	O
are	O
predominantly	O
controlled	O
by	O
the	O
transcriptional	B-protein_type
regulator	I-protein_type
NadR	B-protein
(	O
Neisseria	B-protein
adhesin	I-protein
A	I-protein
Regulator	I-protein
)	O
both	O
in	O
vitro	O
and	O
in	O
vivo	O
.	O

NadR	B-protein
binds	O
the	O
nadA	B-gene
promoter	O
and	O
represses	O
gene	O
transcription	O
.	O

In	O
the	O
presence	B-protein_state
of	I-protein_state
4	B-chemical
-	I-chemical
hydroxyphenylacetate	I-chemical
(	O
4	B-chemical
-	I-chemical
HPA	I-chemical
),	O
a	O
catabolite	O
present	O
in	O
human	B-species
saliva	O
both	O
under	O
physiological	O
conditions	O
and	O
during	O
bacterial	B-taxonomy_domain
infection	O
,	O
the	O
binding	O
of	O
NadR	B-protein
to	O
the	O
nadA	B-gene
promoter	O
is	O
attenuated	O
and	O
nadA	B-gene
expression	O
is	O
induced	O
.	O

NadR	B-protein
also	O
mediates	O
ligand	O
-	O
dependent	O
regulation	O
of	O
many	O
other	O
meningococcal	B-taxonomy_domain
genes	O
,	O
for	O
example	O
the	O
highly	O
-	O
conserved	O
multiple	O
adhesin	O
family	O
(	O
maf	O
)	O
genes	O
,	O
which	O
encode	O
proteins	O
emerging	O
with	O
important	O
roles	O
in	O
host	O
-	O
pathogen	O
interactions	O
,	O
immune	O
evasion	O
and	O
niche	O
adaptation	O
.	O

To	O
gain	O
insights	O
into	O
the	O
regulation	O
of	O
NadR	B-protein
mediated	O
by	O
4	B-chemical
-	I-chemical
HPA	I-chemical
,	O
we	O
combined	O
structural	B-experimental_method
,	I-experimental_method
biochemical	I-experimental_method
,	I-experimental_method
and	I-experimental_method
mutagenesis	I-experimental_method
studies	I-experimental_method
.	O

In	O
particular	O
,	O
two	O
new	O
crystal	B-evidence
structures	I-evidence
of	O
ligand	B-protein_state
-	I-protein_state
free	I-protein_state
and	O
ligand	B-protein_state
-	I-protein_state
bound	I-protein_state
NadR	B-protein
revealed	O
(	O
i	O
)	O
the	O
molecular	O
basis	O
of	O
‘	O
conformational	O
selection	O
’	O
by	O
which	O
a	O
single	O
molecule	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
binds	O
and	O
stabilizes	O
dimeric	B-oligomeric_state
NadR	B-protein
in	O
a	O
conformation	O
unsuitable	O
for	O
DNA	O
-	O
binding	O
,	O
(	O
ii	O
)	O
molecular	O
explanations	O
for	O
the	O
binding	O
specificities	O
of	O
different	O
hydroxyphenylacetate	B-chemical
ligands	O
,	O
including	O
3Cl	B-chemical
,	I-chemical
4	I-chemical
-	I-chemical
HPA	I-chemical
which	O
is	O
produced	O
during	O
inflammation	O
,	O
(	O
iii	O
)	O
the	O
presence	O
of	O
a	O
leucine	B-residue_name
residue	O
essential	O
for	O
dimerization	O
and	O
conserved	B-protein_state
in	O
many	O
MarR	B-protein_type
family	O
proteins	O
,	O
and	O
(	O
iv	O
)	O
four	O
residues	O
(	O
His7	B-residue_name_number
,	O
Ser9	B-residue_name_number
,	O
Asn11	B-residue_name_number
and	O
Phe25	B-residue_name_number
),	O
which	O
are	O
involved	O
in	O
binding	O
4	B-chemical
-	I-chemical
HPA	I-chemical
,	O
and	O
were	O
confirmed	O
in	O
vitro	O
to	O
have	O
key	O
roles	O
in	O
the	O
regulatory	O
mechanism	O
in	O
bacteria	B-taxonomy_domain
.	O

Overall	O
,	O
this	O
study	O
deepens	O
our	O
molecular	O
understanding	O
of	O
the	O
sophisticated	O
regulatory	O
mechanisms	O
of	O
the	O
expression	O
of	O
nadA	B-gene
and	O
other	O
genes	O
governed	O
by	O
NadR	B-protein
,	O
dependent	O
on	O
interactions	O
with	O
niche	O
-	O
specific	O
signal	O
molecules	O
that	O
may	O
play	O
important	O
roles	O
during	O
meningococcal	B-taxonomy_domain
pathogenesis	O
.	O

Serogroup	B-taxonomy_domain
B	I-taxonomy_domain
meningococcus	I-taxonomy_domain
(	O
MenB	B-species
)	O
causes	O
fatal	O
sepsis	O
and	O
invasive	O
meningococcal	B-taxonomy_domain
disease	O
,	O
particularly	O
in	O
young	O
children	O
and	O
adolescents	O
,	O
as	O
highlighted	O
by	O
recent	O
MenB	B-species
outbreaks	O
in	O
universities	O
of	O
the	O
United	O
States	O
and	O
Canada	O
.	O

The	O
Bexsero	O
vaccine	O
protects	O
against	O
MenB	B-species
and	O
has	O
recently	O
been	O
approved	O
in	O
>	O
35	O
countries	O
worldwide	O
.	O

Neisseria	B-protein
adhesin	I-protein
A	I-protein
(	O
NadA	B-protein
)	O
present	O
on	O
the	O
meningococcal	B-taxonomy_domain
surface	O
can	O
mediate	O
binding	O
to	O
human	B-species
cells	O
and	O
is	O
one	O
of	O
the	O
three	O
MenB	B-species
vaccine	O
protein	O
antigens	O
.	O

The	O
amount	O
of	O
NadA	B-protein
exposed	O
on	O
the	O
meningococcal	B-taxonomy_domain
surface	O
also	O
influences	O
the	O
antibody	O
-	O
mediated	O
serum	O
bactericidal	O
response	O
measured	O
in	O
vitro	O
.	O

A	O
deep	O
understanding	O
of	O
nadA	B-gene
expression	O
is	O
therefore	O
important	O
,	O
otherwise	O
the	O
contribution	O
of	O
NadA	B-protein
to	O
vaccine	O
-	O
induced	O
protection	O
against	O
meningococcal	B-taxonomy_domain
meningitis	O
may	O
be	O
underestimated	O
.	O

The	O
abundance	O
of	O
surface	O
-	O
exposed	O
NadA	B-protein
is	O
regulated	O
by	O
the	O
ligand	B-protein_type
-	I-protein_type
responsive	I-protein_type
transcriptional	I-protein_type
repressor	I-protein_type
NadR	B-protein
.	O
Here	O
,	O
we	O
present	O
functional	B-evidence
,	I-evidence
biochemical	I-evidence
and	I-evidence
high	I-evidence
-	I-evidence
resolution	I-evidence
structural	I-evidence
data	I-evidence
on	O
NadR	B-protein
.	O
Our	O
studies	O
provide	O
detailed	O
insights	O
into	O
how	O
small	O
molecule	O
ligands	O
,	O
such	O
as	O
hydroxyphenylacetate	B-chemical
derivatives	O
,	O
found	O
in	O
relevant	O
host	O
niches	O
,	O
modulate	O
the	O
structure	O
and	O
activity	O
of	O
NadR	B-protein
,	O
by	O
‘	O
conformational	O
selection	O
’	O
of	O
inactive	B-protein_state
forms	O
.	O

These	O
findings	O
shed	O
light	O
on	O
the	O
regulation	O
of	O
NadR	B-protein
,	O
a	O
key	O
MarR	B-protein_type
-	O
family	O
virulence	O
factor	O
of	O
this	O
important	O
human	B-species
pathogen	O
.	O

The	O
‘	O
Reverse	B-experimental_method
Vaccinology	I-experimental_method
’	O
approach	O
was	O
pioneered	O
to	O
identify	O
antigens	O
for	O
a	O
protein	O
-	O
based	O
vaccine	O
against	O
serogroup	B-species
B	I-species
Neisseria	I-species
meningitidis	I-species
(	O
MenB	B-species
),	O
a	O
human	B-species
pathogen	O
causing	O
potentially	O
-	O
fatal	O
sepsis	O
and	O
invasive	O
meningococcal	B-taxonomy_domain
disease	O
.	O

Indeed	O
,	O
Reverse	B-experimental_method
Vaccinology	I-experimental_method
identified	O
Neisseria	B-protein
adhesin	I-protein
A	I-protein
(	O
NadA	B-protein
),	O
a	O
surface	O
-	O
exposed	O
protein	O
involved	O
in	O
epithelial	O
cell	O
invasion	O
and	O
found	O
in	O
~	O
30	O
%	O
of	O
clinical	O
isolates	O
.	O

Recently	O
,	O
we	O
reported	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
NadA	B-protein
,	O
providing	O
insights	O
into	O
its	O
biological	O
and	O
immunological	O
functions	O
.	O

Recombinant	O
NadA	B-protein
elicits	O
a	O
strong	O
bactericidal	O
immune	O
response	O
and	O
is	O
therefore	O
included	O
in	O
the	O
Bexsero	O
vaccine	O
that	O
protects	O
against	O
MenB	B-species
and	O
which	O
was	O
recently	O
approved	O
in	O
over	O
35	O
countries	O
worldwide	O
.	O

Previous	O
studies	O
revealed	O
that	O
nadA	B-gene
expression	O
levels	O
are	O
mainly	O
regulated	O
by	O
the	O
Neisseria	B-protein
adhesin	I-protein
A	I-protein
Regulator	I-protein
(	O
NadR	B-protein
).	O

Although	O
additional	O
factors	O
influence	O
nadA	B-gene
expression	O
,	O
we	O
focused	O
on	O
its	O
regulation	O
by	O
NadR	B-protein
,	O
the	O
major	O
mediator	O
of	O
NadA	B-protein
phase	O
variable	O
expression	O
.	O

Studies	O
of	O
NadR	B-protein
also	O
have	O
broader	O
implications	O
,	O
since	O
a	O
genome	O
-	O
wide	O
analysis	O
of	O
MenB	B-species
wild	B-protein_state
-	I-protein_state
type	I-protein_state
and	O
nadR	B-gene
knock	B-protein_state
-	I-protein_state
out	I-protein_state
strains	O
revealed	O
that	O
NadR	B-protein
influences	O
the	O
regulation	O
of	O
>	O
30	O
genes	O
,	O
including	O
maf	O
genes	O
,	O
from	O
the	O
multiple	O
adhesin	B-protein_type
family	O
.	O

These	O
genes	O
encode	O
a	O
wide	O
variety	O
of	O
proteins	O
connected	O
to	O
many	O
biological	O
processes	O
contributing	O
to	O
bacterial	B-taxonomy_domain
survival	O
,	O
adaptation	O
in	O
the	O
host	O
niche	O
,	O
colonization	O
and	O
invasion	O
.	O

NadR	B-protein
belongs	O
to	O
the	O
MarR	B-protein_type
(	O
Multiple	B-protein_type
Antibiotic	I-protein_type
Resistance	I-protein_type
Regulator	I-protein_type
)	O
family	O
,	O
a	O
group	O
of	O
ligand	B-protein_type
-	I-protein_type
responsive	I-protein_type
transcriptional	I-protein_type
regulators	I-protein_type
ubiquitous	O
in	O
bacteria	B-taxonomy_domain
and	O
archaea	B-taxonomy_domain
.	O

MarR	B-protein_type
family	O
proteins	O
can	O
promote	O
bacterial	B-taxonomy_domain
survival	O
in	O
the	O
presence	O
of	O
antibiotics	O
,	O
toxic	O
chemicals	O
,	O
organic	O
solvents	O
or	O
reactive	O
oxygen	O
species	O
and	O
can	O
regulate	O
virulence	O
factor	O
expression	O
.	O

MarR	B-protein_type
homologues	O
can	O
act	O
either	O
as	O
transcriptional	O
repressors	O
or	O
as	O
activators	O
.	O

Although	O
>	O
50	O
MarR	B-protein_type
family	O
structures	B-evidence
are	O
known	O
,	O
a	O
molecular	O
understanding	O
of	O
their	O
ligand	O
-	O
dependent	O
regulatory	O
mechanisms	O
is	O
still	O
limited	O
,	O
often	O
hampered	O
by	O
lack	O
of	O
identification	O
of	O
their	O
ligands	O
and	O
/	O
or	O
DNA	O
targets	O
.	O

A	O
potentially	O
interesting	O
exception	O
comes	O
from	O
the	O
ligand	B-protein_state
-	I-protein_state
free	I-protein_state
and	O
salicylate	B-protein_state
-	I-protein_state
bound	I-protein_state
forms	O
of	O
the	O
Methanobacterium	B-species
thermoautotrophicum	I-species
protein	O
MTH313	B-protein
which	O
revealed	O
that	O
two	O
salicylate	B-chemical
molecules	O
bind	O
to	O
one	O
MTH313	B-protein
dimer	B-oligomeric_state
and	O
induce	O
large	O
conformational	O
changes	O
,	O
apparently	O
sufficient	O
to	O
prevent	O
DNA	O
binding	O
.	O

However	O
,	O
the	O
homologous	O
archeal	B-taxonomy_domain
Sulfolobus	B-species
tokodaii	I-species
protein	O
ST1710	B-protein
presented	O
essentially	O
the	O
same	O
structure	B-evidence
in	O
ligand	B-protein_state
-	I-protein_state
free	I-protein_state
and	O
salicylate	B-protein_state
-	I-protein_state
bound	I-protein_state
forms	O
,	O
apparently	O
contrasting	O
the	O
mechanism	O
proposed	O
for	O
MTH313	B-protein
.	O

Despite	O
these	O
apparent	O
differences	O
,	O
MTH313	B-protein
and	O
ST1710	B-protein
bind	O
salicylate	B-chemical
in	O
approximately	O
the	O
same	O
site	O
,	O
between	O
their	O
dimerization	B-structure_element
and	I-structure_element
DNA	I-structure_element
-	I-structure_element
binding	I-structure_element
domains	I-structure_element
.	O

However	O
,	O
it	O
is	O
unknown	O
whether	O
salicylate	B-chemical
is	O
a	O
relevant	O
in	O
vivo	O
ligand	O
of	O
either	O
of	O
these	O
two	O
proteins	O
,	O
which	O
share	O
~	O
20	O
%	O
sequence	O
identity	O
with	O
NadR	B-protein
,	O
rendering	O
unclear	O
the	O
interpretation	O
of	O
these	O
findings	O
in	O
relation	O
to	O
the	O
regulatory	O
mechanisms	O
of	O
NadR	B-protein
or	O
other	O
MarR	B-protein_type
family	O
proteins	O
.	O

NadR	B-protein
binds	O
nadA	B-gene
on	O
three	O
different	O
operators	O
(	O
OpI	O
,	O
OpII	O
and	O
OpIII	O
).	O

The	O
DNA	O
-	O
binding	O
activity	O
of	O
NadR	B-protein
is	O
attenuated	O
in	O
vitro	O
upon	O
addition	O
of	O
various	O
hydroxyphenylacetate	B-chemical
(	O
HPA	B-chemical
)	O
derivatives	O
,	O
including	O
4	B-chemical
-	I-chemical
HPA	I-chemical
.	O

4	B-chemical
-	I-chemical
HPA	I-chemical
is	O
a	O
small	O
molecule	O
derived	O
from	O
mammalian	B-taxonomy_domain
aromatic	O
amino	O
acid	O
catabolism	O
and	O
is	O
released	O
in	O
human	B-species
saliva	O
,	O
where	O
it	O
has	O
been	O
detected	O
at	O
micromolar	O
concentration	O
.	O

In	O
the	O
presence	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
,	O
NadR	B-protein
is	O
unable	O
to	O
bind	O
the	O
nadA	B-gene
promoter	O
and	O
nadA	B-gene
gene	O
expression	O
is	O
induced	O
.	O

In	O
vivo	O
,	O
the	O
presence	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
in	O
the	O
host	O
niche	O
of	O
N	B-species
.	I-species
meningitidis	I-species
serves	O
as	O
an	O
inducer	O
of	O
NadA	B-protein
production	O
,	O
thereby	O
promoting	O
bacterial	B-taxonomy_domain
adhesion	O
to	O
host	O
cells	O
.	O

Further	O
,	O
we	O
recently	O
reported	O
that	O
3Cl	B-chemical
,	I-chemical
4	I-chemical
-	I-chemical
HPA	I-chemical
,	O
produced	O
during	O
inflammation	O
,	O
is	O
another	O
inducer	O
of	O
nadA	B-gene
expression	O
.	O

Extending	O
our	O
previous	O
studies	O
based	O
on	O
hydrogen	B-experimental_method
-	I-experimental_method
deuterium	I-experimental_method
exchange	I-experimental_method
mass	I-experimental_method
spectrometry	I-experimental_method
(	O
HDX	B-experimental_method
-	I-experimental_method
MS	I-experimental_method
),	O
here	O
we	O
sought	O
to	O
reveal	O
the	O
molecular	O
mechanisms	O
and	O
effects	O
of	O
NadR	B-protein
/	O
HPA	B-chemical
interactions	O
via	O
X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
,	O
NMR	B-experimental_method
spectroscopy	I-experimental_method
and	O
complementary	O
biochemical	B-experimental_method
and	I-experimental_method
in	I-experimental_method
vivo	I-experimental_method
mutagenesis	I-experimental_method
studies	I-experimental_method
.	O

We	O
obtained	O
detailed	O
new	O
insights	O
into	O
ligand	O
specificity	O
,	O
how	O
the	O
ligand	O
allosterically	O
influences	O
the	O
DNA	O
-	O
binding	O
ability	O
of	O
NadR	B-protein
,	O
and	O
the	O
regulation	O
of	O
nadA	B-gene
expression	O
,	O
thus	O
also	O
providing	O
a	O
deeper	O
structural	O
understanding	O
of	O
the	O
ligand	O
-	O
responsive	O
MarR	B-protein_type
super	O
-	O
family	O
.	O

Moreover	O
,	O
these	O
findings	O
are	O
important	O
because	O
the	O
activity	O
of	O
NadR	B-protein
impacts	O
the	O
potential	O
coverage	O
provided	O
by	O
anti	O
-	O
NadA	B-protein
antibodies	O
elicited	O
by	O
the	O
Bexsero	O
vaccine	O
and	O
influences	O
host	O
-	O
bacteria	B-taxonomy_domain
interactions	O
that	O
contribute	O
to	O
meningococcal	B-taxonomy_domain
pathogenesis	O
.	O

NadR	B-protein
is	O
dimeric	B-oligomeric_state
and	O
is	O
stabilized	O
by	O
specific	O
hydroxyphenylacetate	B-chemical
ligands	O

Recombinant	O
NadR	B-protein
was	O
produced	O
in	O
E	B-species
.	I-species
coli	I-species
using	O
an	O
expression	B-experimental_method
construct	I-experimental_method
prepared	O
from	O
N	B-species
.	I-species
meningitidis	I-species
serogroup	I-species
B	I-species
strain	I-species
MC58	I-species
.	O

Standard	O
chromatographic	O
techniques	O
were	O
used	O
to	O
obtain	O
a	O
highly	O
purified	O
sample	O
of	O
NadR	B-protein
(	O
see	O
Materials	O
and	O
Methods	O
).	O

In	O
analytical	B-experimental_method
size	I-experimental_method
-	I-experimental_method
exclusion	I-experimental_method
high	I-experimental_method
-	I-experimental_method
performance	I-experimental_method
liquid	I-experimental_method
chromatography	I-experimental_method
(	O
SE	B-experimental_method
-	I-experimental_method
HPLC	I-experimental_method
)	O
experiments	O
coupled	O
with	O
multi	B-experimental_method
-	I-experimental_method
angle	I-experimental_method
laser	I-experimental_method
light	I-experimental_method
scattering	I-experimental_method
(	O
MALLS	B-experimental_method
),	O
NadR	B-protein
presented	O
a	O
single	O
species	O
with	O
an	O
absolute	O
molecular	O
mass	O
of	O
35	O
kDa	O
(	O
S1	O
Fig	O
).	O

These	O
data	O
showed	O
that	O
NadR	B-protein
was	O
dimeric	B-oligomeric_state
in	O
solution	O
,	O
since	O
the	O
theoretical	O
molecular	O
mass	O
of	O
the	O
NadR	B-protein
dimer	B-oligomeric_state
is	O
33	O
.	O
73	O
kDa	O
;	O
and	O
,	O
there	O
was	O
no	O
change	O
in	O
oligomeric	O
state	O
on	O
addition	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
.	O

The	O
thermal	O
stability	O
of	O
NadR	B-protein
was	O
examined	O
using	O
differential	B-experimental_method
scanning	I-experimental_method
calorimetry	I-experimental_method
(	O
DSC	B-experimental_method
).	O

Since	O
ligand	O
-	O
binding	O
often	O
increases	O
protein	O
stability	O
,	O
we	O
also	O
investigated	O
the	O
effect	O
of	O
various	O
HPAs	B-chemical
(	O
Fig	O
1A	O
)	O
on	O
the	O
melting	B-evidence
temperature	I-evidence
(	O
Tm	B-evidence
)	O
of	O
NadR	B-protein
.	O
As	O
a	O
control	O
of	O
specificity	O
,	O
we	O
also	O
tested	O
salicylate	B-chemical
,	O
a	O
known	O
ligand	O
of	O
some	O
MarR	B-protein_type
proteins	O
previously	O
reported	O
to	O
increase	O
the	O
Tm	B-evidence
of	O
ST1710	B-protein
and	O
MTH313	B-protein
.	O

The	O
Tm	B-evidence
of	O
NadR	B-protein
was	O
67	O
.	O
4	O
±	O
0	O
.	O
1	O
°	O
C	O
in	O
the	O
absence	B-protein_state
of	I-protein_state
ligand	I-protein_state
,	O
and	O
was	O
unaffected	O
by	O
salicylate	B-chemical
.	O

However	O
,	O
an	O
increased	O
thermal	O
stability	O
was	O
induced	O
by	O
4	B-chemical
-	I-chemical
HPA	I-chemical
and	O
,	O
to	O
a	O
lesser	O
extent	O
,	O
by	O
3	B-chemical
-	I-chemical
HPA	I-chemical
.	O

Interestingly	O
,	O
NadR	B-protein
displayed	O
the	O
greatest	O
Tm	B-evidence
increase	O
upon	O
addition	O
of	O
3Cl	B-chemical
,	I-chemical
4	I-chemical
-	I-chemical
HPA	I-chemical
(	O
Table	O
1	O
and	O
Fig	O
1B	O
).	O

Stability	O
of	O
NadR	B-protein
is	O
increased	O
by	O
small	O
molecule	O
ligands	O
.	O

(	O
A	O
)	O
Molecular	O
structures	O
of	O
3	B-chemical
-	I-chemical
HPA	I-chemical
(	O
MW	O
152	O
.	O
2	O
),	O
4	B-chemical
-	I-chemical
HPA	I-chemical
(	O
MW	O
152	O
.	O
2	O
),	O
3Cl	B-chemical
,	I-chemical
4	I-chemical
-	I-chemical
HPA	I-chemical
(	O
MW	O
186	O
.	O
6	O
)	O
and	O
salicylic	B-chemical
acid	I-chemical
(	O
MW	O
160	O
.	O
1	O
).	O
(	O
B	O
)	O
DSC	B-experimental_method
profiles	B-evidence
,	O
colored	O
as	O
follows	O
:	O
apo	B-protein_state
-	O
NadR	B-protein
(	O
violet	O
),	O
NadR	B-complex_assembly
+	I-complex_assembly
salicylate	I-complex_assembly
(	O
red	O
),	O
NadR	B-complex_assembly
+	I-complex_assembly
3	I-complex_assembly
-	I-complex_assembly
HPA	I-complex_assembly
(	O
green	O
),	O
NadR	B-complex_assembly
+	I-complex_assembly
4	I-complex_assembly
-	I-complex_assembly
HPA	I-complex_assembly
(	O
blue	O
),	O
NadR	B-complex_assembly
+	I-complex_assembly
3Cl	I-complex_assembly
,	I-complex_assembly
4	I-complex_assembly
-	I-complex_assembly
HPA	I-complex_assembly
(	O
pink	O
).	O

All	O
DSC	B-experimental_method
profiles	B-evidence
are	O
representative	O
of	O
triplicate	O
experiments	O
.	O

Melting	B-evidence
-	I-evidence
point	I-evidence
(	O
Tm	B-evidence
)	O
and	O
its	O
ligand	O
-	O
induced	O
increase	O
(	O
ΔTm	B-evidence
)	O
derived	O
from	O
DSC	B-experimental_method
thermostability	B-experimental_method
experiments	I-experimental_method
.	O

Dissociation	B-evidence
constants	I-evidence
(	O
KD	B-evidence
)	O
of	O
the	O
NadR	B-protein
/	O
ligand	O
interactions	O
from	O
SPR	B-experimental_method
steady	I-experimental_method
-	I-experimental_method
state	I-experimental_method
binding	I-experimental_method
experiments	I-experimental_method
.	O

Ligand	O
Tm	B-evidence
(°	O
C	O
)	O
ΔTm	B-evidence
(°	O
C	O
)	O
KD	B-evidence
(	O
mM	O
)	O
No	O
ligand	O
67	O
.	O
4	O
±	O
0	O
.	O
1	O
n	O
.	O
a	O
.	O
n	O
.	O
a	O
.	O

3	B-chemical
-	I-chemical
HPA	I-chemical
70	O
.	O
0	O
±	O
0	O
.	O
1	O
2	O
.	O
7	O
2	O
.	O
7	O
±	O
0	O
.	O
1	O
4	B-chemical
-	I-chemical
HPA	I-chemical
70	O
.	O
7	O
±	O
0	O
.	O
1	O
3	O
.	O
3	O
1	O
.	O
5	O
±	O
0	O
.	O
1	O
3Cl	B-chemical
,	I-chemical
4	I-chemical
-	I-chemical
HPA	I-chemical
71	O
.	O
3	O
±	O
0	O
.	O
2	O
3	O
.	O
9	O
1	O
.	O
1	O
±	O
0	O
.	O
1	O

NadR	B-protein
displays	O
distinct	O
binding	B-evidence
affinities	I-evidence
for	O
hydroxyphenylacetate	B-chemical
ligands	O

To	O
further	O
investigate	O
the	O
binding	O
of	O
HPAs	B-chemical
to	O
NadR	B-protein
,	O
we	O
used	O
surface	B-experimental_method
plasmon	I-experimental_method
resonance	I-experimental_method
(	O
SPR	B-experimental_method
).	O

The	O
SPR	B-experimental_method
sensorgrams	B-evidence
revealed	O
very	O
fast	O
association	O
and	O
dissociation	O
events	O
,	O
typical	O
of	O
small	O
molecule	O
ligands	O
,	O
thus	O
prohibiting	O
a	O
detailed	O
study	O
of	O
binding	O
kinetics	O
.	O

However	O
,	O
steady	B-experimental_method
-	I-experimental_method
state	I-experimental_method
SPR	I-experimental_method
analyses	O
of	O
the	O
NadR	B-complex_assembly
-	I-complex_assembly
HPA	I-complex_assembly
interactions	O
allowed	O
determination	O
of	O
the	O
equilibrium	B-evidence
dissociation	I-evidence
constants	I-evidence
(	O
KD	B-evidence
)	O
(	O
Table	O
1	O
and	O
S2	O
Fig	O
).	O

The	O
interactions	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
and	O
3Cl	B-chemical
,	I-chemical
4	I-chemical
-	I-chemical
HPA	I-chemical
with	O
NadR	B-protein
exhibited	O
KD	B-evidence
values	O
of	O
1	O
.	O
5	O
mM	O
and	O
1	O
.	O
1	O
mM	O
,	O
respectively	O
.	O

3	B-chemical
-	I-chemical
HPA	I-chemical
showed	O
a	O
weaker	O
interaction	O
,	O
with	O
a	O
KD	B-evidence
of	O
2	O
.	O
7	O
mM	O
,	O
while	O
salicylate	B-chemical
showed	O
only	O
a	O
very	O
weak	O
response	O
that	O
did	O
not	O
reach	O
saturation	O
,	O
indicating	O
a	O
non	O
-	O
specific	O
interaction	O
with	O
NadR	B-protein
.	O
A	O
ranking	O
of	O
these	O
KD	B-evidence
values	O
showed	O
that	O
3Cl	B-chemical
,	I-chemical
4	I-chemical
-	I-chemical
HPA	I-chemical
was	O
the	O
tightest	O
binder	O
,	O
and	O
thus	O
matched	O
the	O
ranking	O
of	O
ligand	O
-	O
induced	O
Tm	B-evidence
increases	O
observed	O
in	O
the	O
DSC	B-experimental_method
experiments	O
.	O

Although	O
these	O
KD	B-evidence
values	O
indicate	O
rather	O
weak	O
interactions	O
,	O
they	O
are	O
similar	O
to	O
the	O
values	O
reported	O
previously	O
for	O
the	O
MarR	B-protein_type
/	O
salicylate	B-chemical
interaction	O
(	O
KD	O
~	O
1	O
mM	O
)	O
and	O
the	O
MTH313	B-protein
/	O
salicylate	B-chemical
interaction	O
(	O
KD	O
2	O
–	O
3	O
mM	O
),	O
and	O
approximately	O
20	O
-	O
fold	O
tighter	O
than	O
the	O
ST1710	B-protein
/	O
salicylate	B-chemical
interaction	O
(	O
KD	O
~	O
20	O
mM	O
).	O

Crystal	B-evidence
structures	I-evidence
of	O
holo	B-protein_state
-	O
NadR	B-protein
and	O
apo	B-protein_state
-	O
NadR	B-protein

To	O
fully	O
characterize	O
the	O
NadR	B-protein
/	O
HPA	B-chemical
interactions	O
,	O
we	O
sought	O
to	O
determine	O
crystal	B-evidence
structures	I-evidence
of	O
NadR	B-protein
in	O
ligand	B-protein_state
-	I-protein_state
bound	I-protein_state
(	O
holo	B-protein_state
)	O
and	O
ligand	B-protein_state
-	I-protein_state
free	I-protein_state
(	O
apo	B-protein_state
)	O
forms	O
.	O

First	O
,	O
we	O
crystallized	B-experimental_method
NadR	B-protein
(	O
a	O
selenomethionine	B-experimental_method
-	I-experimental_method
labelled	I-experimental_method
derivative	I-experimental_method
)	O
in	O
the	O
presence	O
of	O
a	O
200	O
-	O
fold	O
molar	O
excess	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
.	O

The	O
structure	B-evidence
of	O
the	O
NadR	B-complex_assembly
/	I-complex_assembly
4	I-complex_assembly
-	I-complex_assembly
HPA	I-complex_assembly
complex	O
was	O
determined	O
at	O
2	O
.	O
3	O
Å	O
resolution	O
using	O
a	O
combination	O
of	O
the	O
single	B-experimental_method
-	I-experimental_method
wavelength	I-experimental_method
anomalous	I-experimental_method
dispersion	I-experimental_method
(	O
SAD	B-experimental_method
)	O
and	O
molecular	B-experimental_method
replacement	I-experimental_method
(	O
MR	B-experimental_method
)	O
methods	O
,	O
and	O
was	O
refined	O
to	O
R	B-evidence
work	I-evidence
/	I-evidence
R	I-evidence
free	I-evidence
values	O
of	O
20	O
.	O
9	O
/	O
26	O
.	O
0	O
%	O
(	O
Table	O
2	O
).	O

Despite	O
numerous	O
attempts	O
,	O
we	O
were	O
unable	O
to	O
obtain	O
high	O
-	O
quality	O
crystals	B-evidence
of	O
NadR	B-protein
complexed	B-protein_state
with	I-protein_state
3Cl	B-chemical
,	I-chemical
4	I-chemical
-	I-chemical
HPA	I-chemical
,	O
3	B-chemical
,	I-chemical
4	I-chemical
-	I-chemical
HPA	I-chemical
,	O
3	B-chemical
-	I-chemical
HPA	I-chemical
or	O
DNA	O
targets	O
.	O

However	O
,	O
it	O
was	O
eventually	O
possible	O
to	O
crystallize	B-experimental_method
apo	B-protein_state
-	O
NadR	B-protein
,	O
and	O
the	O
structure	B-evidence
was	O
determined	O
at	O
2	O
.	O
7	O
Å	O
resolution	O
by	O
MR	B-experimental_method
methods	O
using	O
the	O
NadR	B-complex_assembly
/	I-complex_assembly
4	I-complex_assembly
-	I-complex_assembly
HPA	I-complex_assembly
complex	O
as	O
the	O
search	O
model	O
.	O

The	O
apo	B-protein_state
-	O
NadR	B-protein
structure	B-evidence
was	O
refined	O
to	O
R	B-evidence
work	I-evidence
/	I-evidence
R	I-evidence
free	I-evidence
values	O
of	O
19	O
.	O
1	O
/	O
26	O
.	O
8	O
%	O
(	O
Table	O
2	O
).	O

Data	O
collection	O
and	O
refinement	O
statistics	O
for	O
NadR	B-protein
structures	B-evidence
.	O

The	O
asymmetric	O
unit	O
of	O
the	O
NadR	B-complex_assembly
/	I-complex_assembly
4	I-complex_assembly
-	I-complex_assembly
HPA	I-complex_assembly
crystals	B-evidence
(	O
holo	B-protein_state
-	O
NadR	B-protein
)	O
contained	O
one	O
NadR	B-protein
homodimer	B-oligomeric_state
,	O
while	O
the	O
apo	B-protein_state
-	O
NadR	B-protein
crystals	B-evidence
contained	O
two	O
homodimers	B-oligomeric_state
.	O

In	O
the	O
apo	B-protein_state
-	O
NadR	B-protein
crystals	B-evidence
,	O
the	O
two	O
homodimers	B-oligomeric_state
were	O
related	O
by	O
a	O
rotation	O
of	O
~	O
90	O
°;	O
the	O
observed	O
association	O
of	O
the	O
two	O
dimers	B-oligomeric_state
was	O
presumably	O
merely	O
an	O
effect	O
of	O
crystal	O
packing	O
,	O
since	O
the	O
interface	B-site
between	O
the	O
two	O
homodimers	B-oligomeric_state
is	O
small	O
(<	O
550	O
Å2	O
of	O
buried	O
surface	O
area	O
),	O
and	O
is	O
not	O
predicted	O
to	O
be	O
physiologically	O
relevant	O
by	O
the	O
PISA	O
software	O
.	O

Moreover	O
,	O
our	O
SE	B-experimental_method
-	I-experimental_method
HPLC	I-experimental_method
/	I-experimental_method
MALLS	I-experimental_method
analyses	O
(	O
see	O
above	O
)	O
revealed	O
that	O
in	O
solution	O
NadR	B-protein
is	O
dimeric	B-oligomeric_state
,	O
and	O
previous	O
studies	O
using	O
native	B-experimental_method
mass	I-experimental_method
spectrometry	I-experimental_method
(	O
MS	B-experimental_method
)	O
revealed	O
dimers	B-oligomeric_state
,	O
not	O
tetramers	B-oligomeric_state
.	O

The	O
NadR	B-protein
homodimer	B-oligomeric_state
bound	B-protein_state
to	I-protein_state
4	B-chemical
-	I-chemical
HPA	I-chemical
has	O
a	O
dimerization	B-site
interface	I-site
mostly	O
involving	O
the	O
top	O
of	O
its	O
‘	O
triangular	B-protein_state
’	O
form	O
,	O
while	O
the	O
two	O
DNA	B-structure_element
-	I-structure_element
binding	I-structure_element
domains	I-structure_element
are	O
located	O
at	O
the	O
base	O
(	O
Fig	O
2A	O
).	O

High	O
-	O
quality	O
electron	B-evidence
density	I-evidence
maps	I-evidence
allowed	O
clear	O
identification	O
of	O
the	O
bound	B-protein_state
ligand	O
,	O
4	B-chemical
-	I-chemical
HPA	I-chemical
(	O
Fig	O
2B	O
).	O

The	O
overall	O
structure	B-evidence
of	O
NadR	B-protein
shows	O
dimensions	O
of	O
~	O
50	O
×	O
65	O
×	O
50	O
Å	O
and	O
a	O
large	O
homodimer	B-site
interface	I-site
that	O
buries	O
a	O
total	O
surface	O
area	O
of	O
~	O
4800	O
Å2	O
.	O

Each	O
NadR	B-protein
monomer	B-oligomeric_state
consists	O
of	O
six	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
and	O
two	O
short	B-structure_element
β	I-structure_element
-	I-structure_element
strands	I-structure_element
,	O
with	O
helices	B-structure_element
α1	B-structure_element
,	O
α5	B-structure_element
,	O
and	O
α6	B-structure_element
forming	O
the	O
dimer	B-site
interface	I-site
.	O

Helices	B-structure_element
α3	B-structure_element
and	O
α4	B-structure_element
form	O
a	O
helix	B-structure_element
-	I-structure_element
turn	I-structure_element
-	I-structure_element
helix	I-structure_element
motif	I-structure_element
,	O
followed	O
by	O
the	O
“	O
wing	B-structure_element
motif	I-structure_element
”	O
comprised	O
of	O
two	O
short	B-structure_element
antiparallel	I-structure_element
β	I-structure_element
-	I-structure_element
strands	I-structure_element
(	O
β1	B-structure_element
-	I-structure_element
β2	I-structure_element
)	O
linked	O
by	O
a	O
relatively	O
long	O
and	O
flexible	O
loop	B-structure_element
.	O

Interestingly	O
,	O
in	O
the	O
α4	B-structure_element
-	I-structure_element
β2	I-structure_element
region	I-structure_element
,	O
the	O
stretch	O
of	O
residues	O
from	O
R64	B-residue_range
-	I-residue_range
R91	I-residue_range
presents	O
seven	O
positively	O
-	O
charged	O
side	O
chains	O
,	O
all	O
available	O
for	O
potential	O
interactions	O
with	O
DNA	B-chemical
.	O

Together	O
,	O
these	O
structural	O
elements	O
constitute	O
the	O
winged	B-structure_element
helix	I-structure_element
-	I-structure_element
turn	I-structure_element
-	I-structure_element
helix	I-structure_element
(	O
wHTH	B-structure_element
)	O
DNA	B-structure_element
-	I-structure_element
binding	I-structure_element
domain	I-structure_element
and	O
,	O
together	O
with	O
the	O
dimeric	B-oligomeric_state
organization	O
,	O
are	O
the	O
hallmarks	O
of	O
MarR	B-protein_type
family	O
structures	B-evidence
.	O

The	O
crystal	B-evidence
structure	I-evidence
of	O
NadR	B-protein
in	B-protein_state
complex	I-protein_state
with	I-protein_state
4	B-chemical
-	I-chemical
HPA	I-chemical
.	O

(	O
A	O
)	O
The	O
holo	B-protein_state
-	O
NadR	B-protein
homodimer	B-oligomeric_state
is	O
depicted	O
in	O
green	O
and	O
blue	O
for	O
chains	B-structure_element
A	I-structure_element
and	I-structure_element
B	I-structure_element
respectively	O
,	O
while	O
yellow	O
sticks	O
depict	O
the	O
4	B-chemical
-	I-chemical
HPA	I-chemical
ligand	O
(	O
labelled	O
).	O

For	O
simplicity	O
,	O
secondary	O
structure	O
elements	O
are	O
labelled	O
for	O
chain	B-structure_element
B	I-structure_element
only	O
.	O

Red	O
dashes	O
show	O
hypothetical	O
positions	O
of	O
chain	B-structure_element
B	I-structure_element
residues	O
88	B-residue_range
–	I-residue_range
90	I-residue_range
that	O
were	O
not	O
modeled	O
due	O
to	O
lack	O
of	O
electron	B-evidence
density	I-evidence
.	O

(	O
B	O
)	O
A	O
zoom	O
into	O
the	O
pocket	B-site
occupied	O
by	O
4	B-chemical
-	I-chemical
HPA	I-chemical
shows	O
that	O
the	O
ligand	O
contacts	O
both	O
chains	B-structure_element
A	I-structure_element
and	I-structure_element
B	I-structure_element
;	O
blue	O
mesh	O
shows	O
electron	B-evidence
density	I-evidence
around	O
4	B-chemical
-	I-chemical
HPA	I-chemical
calculated	O
from	O
a	O
composite	B-evidence
omit	I-evidence
map	I-evidence
(	O
omitting	O
4	B-chemical
-	I-chemical
HPA	I-chemical
),	O
using	O
phenix	B-experimental_method
.	O

The	O
map	B-evidence
is	O
contoured	O
at	O
1σ	O
and	O
the	O
figure	O
was	O
prepared	O
with	O
a	O
density	B-evidence
mesh	I-evidence
carve	O
factor	O
of	O
1	O
.	O
7	O
,	O
using	O
Pymol	O
(	O
www	O
.	O
pymol	O
.	O
org	O
).	O

A	O
single	O
conserved	B-protein_state
leucine	B-residue_name
residue	O
(	O
L130	B-residue_name_number
)	O
is	O
crucial	O
for	O
dimerization	O

The	O
NadR	B-protein
dimer	B-site
interface	I-site
is	O
formed	O
by	O
at	O
least	O
32	O
residues	O
,	O
which	O
establish	O
numerous	O
inter	O
-	O
chain	O
salt	O
bridges	O
or	O
hydrogen	O
bonds	O
,	O
and	O
many	O
hydrophobic	O
packing	O
interactions	O
(	O
Fig	O
3A	O
and	O
3B	O
).	O

To	O
determine	O
which	O
residues	O
were	O
most	O
important	O
for	O
dimerization	O
,	O
we	O
studied	O
the	O
interface	B-site
in	O
silico	O
and	O
identified	O
several	O
residues	O
as	O
potential	O
mediators	O
of	O
key	O
stabilizing	O
interactions	O
.	O

Using	O
site	B-experimental_method
-	I-experimental_method
directed	I-experimental_method
mutagenesis	I-experimental_method
,	O
a	O
panel	O
of	O
eight	O
mutant	B-protein_state
NadR	B-protein
proteins	O
was	O
prepared	O
(	O
including	O
mutations	O
H7A	B-mutant
,	O
S9A	B-mutant
,	O
N11A	B-mutant
,	O
D112A	B-mutant
,	O
R114A	B-mutant
,	O
Y115A	B-mutant
,	O
K126A	B-mutant
,	O
L130K	B-mutant
and	O
L133K	B-mutant
),	O
sufficient	O
to	O
explore	O
the	O
entire	O
dimer	B-site
interface	I-site
.	O

Each	O
mutant	B-protein_state
NadR	B-protein
protein	O
was	O
purified	O
,	O
and	O
then	O
its	O
oligomeric	O
state	O
was	O
examined	O
by	O
analytical	B-experimental_method
SE	I-experimental_method
-	I-experimental_method
HPLC	I-experimental_method
.	O

Almost	O
all	O
the	O
mutants	O
showed	O
the	O
same	O
elution	O
profile	O
as	O
the	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
(	O
WT	B-protein_state
)	O
NadR	B-protein
protein	O
.	O

Only	O
the	O
L130K	B-mutant
mutation	O
induced	O
a	O
notable	O
change	O
in	O
the	O
oligomeric	O
state	O
of	O
NadR	B-protein
(	O
Fig	O
3C	O
).	O

Further	O
,	O
in	O
SE	B-experimental_method
-	I-experimental_method
MALLS	I-experimental_method
analyses	O
,	O
the	O
L130K	B-mutant
mutant	B-protein_state
displayed	O
two	O
distinct	O
species	O
in	O
solution	O
,	O
approximately	O
80	O
%	O
being	O
monomeric	B-oligomeric_state
(	O
a	O
19	O
kDa	O
species	O
),	O
and	O
only	O
20	O
%	O
retaining	O
the	O
typical	O
native	O
dimeric	B-oligomeric_state
state	O
(	O
a	O
35	O
kDa	O
species	O
)	O
(	O
Fig	O
3D	O
),	O
demonstrating	O
that	O
Leu130	B-residue_name_number
is	O
crucial	O
for	O
stable	O
dimerization	O
.	O

It	O
is	O
notable	O
that	O
L130	B-residue_name_number
is	O
usually	O
present	O
as	O
Leu	B-residue_name
,	O
or	O
an	O
alternative	O
bulky	O
hydrophobic	O
amino	O
acid	O
(	O
e	O
.	O
g	O
.	O
Phe	B-residue_name
,	O
Val	B-residue_name
),	O
in	O
many	O
MarR	B-protein_type
family	O
proteins	O
,	O
suggesting	O
a	O
conserved	B-protein_state
role	O
in	O
stabilizing	O
the	O
dimer	B-site
interface	I-site
.	O

In	O
contrast	O
,	O
most	O
of	O
the	O
other	O
residues	O
identified	O
in	O
the	O
NadR	B-protein
dimer	B-site
interface	I-site
were	O
poorly	B-protein_state
conserved	I-protein_state
in	O
the	O
MarR	B-protein_type
family	O
.	O

Analysis	O
of	O
the	O
NadR	B-protein
dimer	B-site
interface	I-site
.	O

(	O
A	O
)	O
Both	O
orientations	O
show	O
chain	B-structure_element
A	I-structure_element
,	O
green	O
backbone	O
ribbon	O
,	O
colored	O
red	O
to	O
highlight	O
all	O
locations	O
involved	O
in	O
dimerization	O
;	O
namely	O
,	O
inter	O
-	O
chain	O
salt	O
bridges	O
or	O
hydrogen	O
bonds	O
involving	O
Q4	B-residue_name_number
,	O
S5	B-residue_name_number
,	O
K6	B-residue_name_number
,	O
H7	B-residue_name_number
,	O
S9	B-residue_name_number
,	O
I10	B-residue_name_number
,	O
N11	B-residue_name_number
,	O
I15	B-residue_name_number
,	O
Q16	B-residue_name_number
,	O
R18	B-residue_name_number
,	O
D36	B-residue_name_number
,	O
R43	B-residue_name_number
,	O
A46	B-residue_name_number
,	O
Q59	B-residue_name_number
,	O
C61	B-residue_name_number
,	O
Y104	B-residue_name_number
,	O
D112	B-residue_name_number
,	O
R114	B-residue_name_number
,	O
Y115	B-residue_name_number
,	O
D116	B-residue_name_number
,	O
E119	B-residue_name_number
,	O
K126	B-residue_name_number
,	O
E136	B-residue_name_number
,	O
E141	B-residue_name_number
,	O
N145	B-residue_name_number
,	O
and	O
the	O
hydrophobic	O
packing	O
interactions	O
involving	O
I10	B-residue_name_number
,	O
I12	B-residue_name_number
,	O
L14	B-residue_name_number
,	O
I15	B-residue_name_number
,	O
R18	B-residue_name_number
,	O
Y115	B-residue_name_number
,	O
I118	B-residue_name_number
,	O
L130	B-residue_name_number
,	O
L133	B-residue_name_number
,	O
L134	B-residue_name_number
and	O
L137	B-residue_name_number
.	O

Chain	B-structure_element
B	I-structure_element
,	O
grey	O
surface	O
,	O
is	O
marked	O
blue	O
to	O
highlight	O
residues	O
probed	O
by	O
site	B-experimental_method
-	I-experimental_method
directed	I-experimental_method
mutagenesis	I-experimental_method
(	O
E136	B-residue_name_number
only	O
makes	O
a	O
salt	O
bridge	O
with	O
K126	B-residue_name_number
,	O
therefore	O
it	O
was	O
sufficient	O
to	O
make	O
the	O
K126A	B-mutant
mutation	O
to	O
assess	O
the	O
importance	O
of	O
this	O
ionic	O
interaction	O
;	O
the	O
H7	B-residue_name_number
position	O
is	O
labelled	O
for	O
monomer	B-oligomeric_state
A	B-structure_element
,	O
since	O
electron	B-evidence
density	I-evidence
was	O
lacking	O
for	O
monomer	B-oligomeric_state
B	B-structure_element
).	O
(	O
B	O
)	O
A	O
zoom	O
into	O
the	O
environment	O
of	O
helix	B-structure_element
α6	B-structure_element
to	O
show	O
how	O
residue	O
L130	B-residue_name_number
chain	B-structure_element
B	I-structure_element
(	O
blue	O
side	O
chain	O
)	O
is	O
a	O
focus	O
of	O
hydrophobic	O
packing	O
interactions	O
with	O
L130	B-residue_name_number
,	O
L133	B-residue_name_number
,	O
L134	B-residue_name_number
and	O
L137	B-residue_name_number
of	O
chain	B-structure_element
A	I-structure_element
(	O
red	O
side	O
chains	O
).	O

(	O
C	O
)	O
SE	B-experimental_method
-	I-experimental_method
HPLC	I-experimental_method
analyses	O
of	O
all	O
mutant	B-protein_state
forms	O
of	O
NadR	B-protein
are	O
compared	O
with	O
the	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
(	O
WT	B-protein_state
)	O
protein	O
.	O

The	O
WT	B-protein_state
and	O
most	O
of	O
the	O
mutants	O
show	O
a	O
single	O
elution	O
peak	O
with	O
an	O
absorbance	O
maximum	O
at	O
17	O
.	O
5	O
min	O
.	O

Only	O
the	O
mutation	O
L130K	B-mutant
has	O
a	O
noteworthy	O
effect	O
on	O
the	O
oligomeric	O
state	O
,	O
inducing	O
a	O
second	O
peak	O
with	O
a	O
longer	O
retention	O
time	O
and	O
a	O
second	O
peak	O
maximum	O
at	O
18	O
.	O
6	O
min	O
.	O

To	O
a	O
much	O
lesser	O
extent	O
,	O
the	O
L133K	B-mutant
mutation	O
also	O
appears	O
to	O
induce	O
a	O
‘	O
shoulder	O
’	O
to	O
the	O
main	O
peak	O
,	O
suggesting	O
very	O
weak	O
ability	O
to	O
disrupt	O
the	O
dimer	B-oligomeric_state
.	O
(	O
D	O
)	O
SE	B-experimental_method
-	I-experimental_method
HPLC	I-experimental_method
/	I-experimental_method
MALLS	I-experimental_method
analyses	O
of	O
the	O
L130K	B-mutant
mutant	B-protein_state
,	O
shows	O
20	O
%	O
dimer	B-oligomeric_state
and	O
80	O
%	O
monomer	B-oligomeric_state
.	O

The	O
holo	B-protein_state
-	O
NadR	B-protein
structure	B-evidence
presents	O
only	O
one	O
occupied	O
ligand	B-site
-	I-site
binding	I-site
pocket	I-site

The	O
NadR	B-complex_assembly
/	I-complex_assembly
4	I-complex_assembly
-	I-complex_assembly
HPA	I-complex_assembly
structure	B-evidence
revealed	O
the	O
ligand	B-site
-	I-site
binding	I-site
site	I-site
nestled	O
between	O
the	O
dimerization	B-structure_element
and	I-structure_element
DNA	I-structure_element
-	I-structure_element
binding	I-structure_element
domains	I-structure_element
(	O
Fig	O
2	O
).	O

The	O
ligand	O
showed	O
a	O
different	O
position	O
and	O
orientation	O
compared	O
to	O
salicylate	B-chemical
complexed	B-protein_state
with	I-protein_state
MTH313	B-protein
and	O
ST1710	B-protein
(	O
see	O
Discussion	O
).	O

The	O
binding	B-site
pocket	I-site
was	O
almost	O
entirely	O
filled	O
by	O
4	B-chemical
-	I-chemical
HPA	I-chemical
and	O
one	O
water	B-chemical
molecule	O
,	O
although	O
there	O
also	O
remained	O
a	O
small	O
tunnel	B-site
2	O
-	O
4Å	O
in	O
diameter	O
and	O
5	O
-	O
6Å	O
long	O
leading	O
from	O
the	O
pocket	B-site
(	O
proximal	O
to	O
the	O
4	O
-	O
hydroxyl	O
position	O
)	O
to	O
the	O
protein	O
surface	O
.	O

The	O
tunnel	B-site
was	O
lined	O
with	O
rather	O
hydrophobic	O
amino	O
acids	O
,	O
and	O
did	O
not	O
contain	O
water	B-chemical
molecules	O
.	O

Unexpectedly	O
,	O
only	O
one	O
monomer	B-oligomeric_state
of	O
the	O
holo	B-protein_state
-	O
NadR	B-protein
homodimer	B-oligomeric_state
contained	O
4	B-chemical
-	I-chemical
HPA	I-chemical
in	O
the	O
binding	B-site
pocket	I-site
,	O
whereas	O
the	O
corresponding	O
pocket	B-site
of	O
the	O
other	O
monomer	B-oligomeric_state
was	O
unoccupied	O
by	O
ligand	O
,	O
despite	O
the	O
large	O
excess	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
used	O
in	O
the	O
crystallization	O
conditions	O
.	O

Inspection	O
of	O
the	O
protein	B-site
-	I-site
ligand	I-site
interaction	I-site
network	I-site
revealed	O
no	O
bonds	O
from	O
NadR	B-protein
backbone	O
groups	O
to	O
the	O
ligand	O
,	O
but	O
several	O
key	O
side	O
chain	O
mediated	O
hydrogen	O
(	O
H	O
)-	O
bonds	O
and	O
ionic	O
interactions	O
,	O
most	O
notably	O
between	O
the	O
carboxylate	O
group	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
and	O
Ser9	B-residue_name_number
of	O
chain	B-structure_element
A	I-structure_element
(	O
SerA9	B-residue_name_number
),	O
and	O
chain	B-structure_element
B	I-structure_element
residues	O
TrpB39	B-residue_name_number
,	O
ArgB43	B-residue_name_number
and	O
TyrB115	B-residue_name_number
(	O
Fig	O
4A	O
).	O

At	O
the	O
other	O
‘	O
end	O
’	O
of	O
the	O
ligand	O
,	O
the	O
4	O
-	O
hydroxyl	O
group	O
was	O
proximal	O
to	O
AspB36	B-residue_name_number
,	O
with	O
which	O
it	O
may	O
establish	O
an	O
H	O
-	O
bond	O
(	O
see	O
bond	O
distances	O
in	O
Table	O
3	O
).	O

The	O
water	B-chemical
molecule	O
observed	O
in	O
the	O
pocket	O
was	O
bound	O
by	O
the	O
carboxylate	O
group	O
and	O
the	O
side	O
chains	O
of	O
SerA9	B-residue_name_number
and	O
AsnA11	B-residue_name_number
.	O

Atomic	O
details	O
of	O
NadR	B-protein
/	O
HPA	B-chemical
interactions	O
.	O

A	O
)	O
A	O
stereo	O
-	O
view	O
zoom	O
into	O
the	O
binding	B-site
pocket	I-site
showing	O
side	O
chain	O
sticks	O
for	O
all	O
interactions	O
between	O
NadR	B-protein
and	O
4	B-chemical
-	I-chemical
HPA	I-chemical
.	O

Green	O
and	O
blue	O
ribbons	O
depict	O
NadR	B-protein
chains	B-structure_element
A	I-structure_element
and	I-structure_element
B	I-structure_element
,	O
respectively	O
.	O

4	B-chemical
-	I-chemical
HPA	I-chemical
is	O
shown	O
in	O
yellow	O
sticks	O
,	O
with	O
oxygen	O
atoms	O
in	O
red	O
.	O

A	O
water	B-chemical
molecule	O
is	O
shown	O
by	O
the	O
red	O
sphere	O
.	O

The	O
entire	O
set	O
of	O
residues	O
making	O
H	O
-	O
bonds	O
or	O
non	O
-	O
bonded	O
contacts	O
with	O
4	B-chemical
-	I-chemical
HPA	I-chemical
is	O
as	O
follows	O
:	O
SerA9	B-residue_name_number
,	O
AsnA11	B-residue_name_number
,	O
LeuB21	B-residue_name_number
,	O
MetB22	B-residue_name_number
,	O
PheB25	B-residue_name_number
,	O
LeuB29	B-residue_name_number
,	O
AspB36	B-residue_name_number
,	O
TrpB39	B-residue_name_number
,	O
ArgB43	B-residue_name_number
,	O
ValB111	B-residue_name_number
and	O
TyrB115	B-residue_name_number
(	O
automated	O
analysis	O
performed	O
using	O
PDBsum	B-experimental_method
and	O
verified	O
manually	O
).	O

Residues	O
AsnA11	B-residue_name_number
and	O
ArgB18	B-residue_name_number
likely	O
make	O
indirect	O
yet	O
local	O
contributions	O
to	O
ligand	O
binding	O
,	O
mainly	O
by	O
stabilizing	O
the	O
position	O
of	O
AspB36	B-residue_name_number
.	O

Side	O
chains	O
mediating	O
hydrophobic	O
interactions	O
are	O
shown	O
in	O
orange	O
.	O
(	O
B	O
)	O
A	O
model	O
was	O
prepared	O
to	O
visualize	O
putative	O
interactions	O
of	O
3Cl	B-chemical
,	I-chemical
4	I-chemical
-	I-chemical
HPA	I-chemical
(	O
pink	O
)	O
with	O
NadR	B-protein
,	O
revealing	O
the	O
potential	O
for	O
additional	O
contacts	O
(	O
dashed	O
lines	O
)	O
of	O
the	O
chloro	O
moiety	O
(	O
green	O
stick	O
)	O
with	O
LeuB29	B-residue_name_number
and	O
AspB36	B-residue_name_number
.	O

List	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
atoms	O
bound	O
to	O
NadR	B-protein
via	O
ionic	O
interactions	O
and	O
/	O
or	O
H	O
-	O
bonds	O
.	O

4	B-chemical
-	I-chemical
HPA	I-chemical
atom	O
NadR	B-protein
residue	O
/	O
atom	O
Distance	O
(	O
Å	O
)	O
O2	O
TrpB39	B-residue_name_number
/	O
NE1	O
2	O
.	O
83	O
O2	O
ArgB43	B-residue_name_number
/	O
NH1	O
2	O
.	O
76	O
O1	O
ArgB43	B-residue_name_number
/	O
NH1	O
3	O
.	O
84	O
O1	O
SerA9	B-residue_name_number
/	O
OG	O
2	O
.	O
75	O
O1	O
TyrB115	B-residue_name_number
/	O
OH	O
2	O
.	O
50	O
O2	O
Water	B-chemical
(*	O
Ser9	B-residue_name_number
/	O
Asn11	B-residue_name_number
)	O
2	O
.	O
88	O
OH	O
AspB36	B-residue_name_number
/	O
OD1	O
/	O
OD2	O
3	O
.	O
6	O
/	O
3	O
.	O
7	O

*	O
Bond	O
distance	O
between	O
the	O
ligand	O
carboxylate	O
group	O
and	O
the	O
water	B-chemical
molecule	O
,	O
which	O
in	O
turn	O
makes	O
H	O
-	O
bond	O
to	O
the	O
SerA9	B-residue_name_number
and	O
AsnA11	B-residue_name_number
side	O
chains	O
.	O

In	O
addition	O
to	O
the	O
H	O
-	O
bonds	O
involving	O
the	O
carboxylate	O
and	O
hydroxyl	O
groups	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
,	O
binding	O
of	O
the	O
phenyl	O
moiety	O
appeared	O
to	O
be	O
stabilized	O
by	O
several	O
van	O
der	O
Waals	O
’	O
contacts	O
,	O
particularly	O
those	O
involving	O
the	O
hydrophobic	O
side	O
chain	O
atoms	O
of	O
LeuB21	B-residue_name_number
,	O
MetB22	B-residue_name_number
,	O
PheB25	B-residue_name_number
,	O
LeuB29	B-residue_name_number
and	O
ValB111	B-residue_name_number
(	O
Fig	O
4A	O
).	O

Notably	O
,	O
the	O
phenyl	O
ring	O
of	O
PheB25	B-residue_name_number
was	O
positioned	O
parallel	O
to	O
the	O
phenyl	O
ring	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
,	O
potentially	O
forming	O
π	O
-	O
π	O
parallel	O
-	O
displaced	O
stacking	O
interactions	O
.	O

Consequently	O
,	O
residues	O
in	O
the	O
4	B-site
-	I-site
HPA	I-site
binding	I-site
pocket	I-site
are	O
mostly	O
contributed	O
by	O
NadR	B-protein
chain	B-structure_element
B	I-structure_element
,	O
and	O
effectively	O
created	O
a	O
polar	O
‘	O
floor	O
’	O
and	O
a	O
hydrophobic	O
‘	O
ceiling	O
’,	O
which	O
house	O
the	O
ligand	O
.	O

Collectively	O
,	O
this	O
mixed	O
network	O
of	O
polar	O
and	O
hydrophobic	O
interactions	O
endows	O
NadR	B-protein
with	O
a	O
strong	O
recognition	O
pattern	O
for	O
HPAs	B-chemical
,	O
with	O
additional	O
medium	O
-	O
range	O
interactions	O
potentially	O
established	O
with	O
the	O
hydroxyl	O
group	O
at	O
the	O
4	O
-	O
position	O
.	O

Structure	O
-	O
activity	O
relationships	O
:	O
molecular	O
basis	O
of	O
enhanced	O
stabilization	O
by	O
3Cl	B-chemical
,	I-chemical
4	I-chemical
-	I-chemical
HPA	I-chemical

We	O
modelled	B-experimental_method
the	O
binding	O
of	O
other	O
HPAs	B-chemical
by	O
in	B-experimental_method
silico	I-experimental_method
superposition	I-experimental_method
onto	O
4	B-chemical
-	I-chemical
HPA	I-chemical
in	O
the	O
holo	B-protein_state
-	O
NadR	B-protein
structure	B-evidence
,	O
and	O
thereby	O
obtained	O
molecular	O
explanations	O
for	O
the	O
binding	O
specificities	O
of	O
diverse	O
ligands	O
.	O

For	O
example	O
,	O
similar	O
to	O
4	B-chemical
-	I-chemical
HPA	I-chemical
,	O
the	O
binding	O
of	O
3Cl	B-chemical
,	I-chemical
4	I-chemical
-	I-chemical
HPA	I-chemical
could	O
involve	O
multiple	O
bonds	O
towards	O
the	O
carboxylate	O
group	O
of	O
the	O
ligand	O
and	O
some	O
to	O
the	O
4	O
-	O
hydroxyl	O
group	O
.	O

Additionally	O
,	O
the	O
side	O
chains	O
of	O
LeuB29	B-residue_name_number
and	O
AspB36	B-residue_name_number
would	O
be	O
only	O
2	O
.	O
6	O
–	O
3	O
.	O
5	O
Å	O
from	O
the	O
chlorine	O
atom	O
,	O
thus	O
providing	O
van	O
der	O
Waals	O
’	O
interactions	O
or	O
H	O
-	O
bonds	O
to	O
generate	O
the	O
additional	O
binding	B-evidence
affinity	I-evidence
observed	O
for	O
3Cl	B-chemical
,	I-chemical
4	I-chemical
-	I-chemical
HPA	I-chemical
(	O
Fig	O
4B	O
).	O

The	O
presence	O
of	O
a	O
single	O
hydroxyl	O
group	O
at	O
position	O
2	O
,	O
as	O
in	O
2	B-chemical
-	I-chemical
HPA	I-chemical
,	O
rather	O
than	O
at	O
position	O
4	O
,	O
would	O
eliminate	O
the	O
possibility	O
of	O
favorable	O
interactions	O
with	O
AspB36	B-residue_name_number
,	O
resulting	O
in	O
the	O
lack	O
of	O
NadR	B-protein
regulation	O
by	O
2	B-chemical
-	I-chemical
HPA	I-chemical
described	O
previously	O
.	O

Finally	O
,	O
salicylate	B-chemical
is	O
presumably	O
unable	O
to	O
specifically	O
bind	O
NadR	B-protein
due	O
to	O
the	O
2	O
-	O
hydroxyl	O
substitution	O
and	O
the	O
shorter	O
aliphatic	O
chain	O
connecting	O
its	O
carboxylate	O
group	O
(	O
Fig	O
1A	O
):	O
the	O
compound	O
simply	O
seems	O
too	O
small	O
to	O
simultaneously	O
establish	O
the	O
network	O
of	O
beneficial	O
bonds	O
observed	O
in	O
the	O
NadR	B-protein
/	O
HPA	B-chemical
interactions	O
.	O

Analysis	O
of	O
the	O
pockets	B-site
reveals	O
the	O
molecular	O
basis	O
for	O
asymmetric	O
binding	O
and	O
stoichiometry	O

However	O
,	O
studies	O
based	O
on	O
tryptophan	B-experimental_method
fluorescence	I-experimental_method
were	O
confounded	O
by	O
the	O
fluorescence	O
of	O
the	O
HPA	B-chemical
ligands	O
,	O
and	O
isothermal	B-experimental_method
titration	I-experimental_method
calorimetry	I-experimental_method
(	O
ITC	B-experimental_method
)	O
was	O
unfeasible	O
due	O
to	O
the	O
need	O
for	O
very	O
high	O
concentrations	O
of	O
NadR	B-protein
in	O
the	O
ITC	B-experimental_method
chamber	O
(	O
due	O
to	O
the	O
relatively	O
low	O
affinity	O
),	O
which	O
exceeded	O
the	O
solubility	O
limits	O
of	O
the	O
protein	O
.	O

However	O
,	O
it	O
was	O
possible	O
to	O
calculate	O
the	O
binding	B-evidence
stoichiometry	I-evidence
of	O
the	O
NadR	B-complex_assembly
-	I-complex_assembly
HPA	I-complex_assembly
interactions	O
using	O
an	O
SPR	B-experimental_method
-	O
based	O
approach	O
.	O

In	O
SPR	B-experimental_method
,	O
the	O
signal	O
measured	O
is	O
proportional	O
to	O
the	O
total	O
molecular	O
mass	O
proximal	O
to	O
the	O
sensor	O
surface	O
;	O
consequently	O
,	O
if	O
the	O
molecular	O
weights	O
of	O
the	O
interactors	O
are	O
known	O
,	O
then	O
the	O
stoichiometry	O
of	O
the	O
resulting	O
complex	O
can	O
be	O
determined	O
.	O

This	O
approach	O
relies	O
on	O
the	O
assumption	O
that	O
the	O
captured	O
protein	O
(‘	O
the	O
ligand	O
’,	O
according	O
to	O
SPR	B-experimental_method
conventions	O
)	O
is	O
100	O
%	O
active	O
and	O
freely	O
-	O
accessible	O
to	O
potential	O
interactors	O
(‘	O
the	O
analytes	O
’).	O

Firstly	O
,	O
NadR	B-protein
is	O
expected	O
to	O
be	O
covalently	O
immobilized	O
on	O
the	O
sensor	O
chip	O
as	O
a	O
dimer	B-oligomeric_state
in	O
random	O
orientations	O
,	O
since	O
it	O
is	O
a	O
stable	B-protein_state
dimer	B-oligomeric_state
in	O
solution	O
and	O
has	O
sixteen	O
lysines	B-residue_name
well	O
-	O
distributed	O
around	O
its	O
surface	O
,	O
all	O
able	O
to	O
act	O
as	O
potential	O
sites	O
for	O
amine	O
coupling	O
to	O
the	O
chip	O
,	O
and	O
none	O
of	O
which	O
are	O
close	O
to	O
the	O
ligand	B-site
-	I-site
binding	I-site
pocket	I-site
.	O

Secondly	O
,	O
the	O
HPA	B-chemical
analytes	O
are	O
all	O
very	O
small	O
(	O
MW	O
150	O
–	O
170	O
,	O
Fig	O
1A	O
)	O
and	O
therefore	O
are	O
expected	O
to	O
be	O
able	O
to	O
diffuse	O
readily	O
into	O
all	O
potential	O
binding	B-site
sites	I-site
,	O
irrespective	O
of	O
the	O
random	O
orientations	O
of	O
the	O
immobilized	O
NadR	B-protein
dimers	B-oligomeric_state
on	O
the	O
chip	O
.	O

The	O
stoichiometry	O
of	O
the	O
NadR	B-complex_assembly
-	I-complex_assembly
HPA	I-complex_assembly
interactions	O
was	O
determined	O
using	O
Eq	O
1	O
(	O
see	O
Materials	O
and	O
Methods	O
),	O
and	O
revealed	O
stoichiometries	B-evidence
of	O
1	O
.	O
13	O
for	O
4	B-chemical
-	I-chemical
HPA	I-chemical
,	O
1	O
.	O
02	O
for	O
3	B-chemical
-	I-chemical
HPA	I-chemical
,	O
and	O
1	O
.	O
21	O
for	O
3Cl	B-chemical
,	I-chemical
4	I-chemical
-	I-chemical
HPA	I-chemical
,	O
strongly	O
suggesting	O
that	O
one	O
NadR	B-protein
dimer	B-oligomeric_state
bound	B-protein_state
to	I-protein_state
1	O
HPA	B-chemical
analyte	O
molecule	O
.	O

The	O
crystallographic	B-evidence
data	I-evidence
,	O
supported	O
by	O
the	O
SPR	B-experimental_method
studies	O
of	O
binding	B-evidence
stoichiometry	I-evidence
,	O
revealed	O
the	O
lack	O
of	O
a	O
second	O
4	B-chemical
-	I-chemical
HPA	I-chemical
molecule	O
in	O
the	O
homodimer	B-oligomeric_state
,	O
suggesting	O
negative	O
co	O
-	O
operativity	O
,	O
a	O
phenomenon	O
previously	O
described	O
for	O
the	O
MTH313	B-protein
/	O
salicylate	B-chemical
interaction	O
and	O
for	O
other	O
MarR	B-protein_type
family	O
proteins	O
.	O

To	O
explore	O
the	O
molecular	O
basis	O
of	O
asymmetry	O
in	O
holo	B-protein_state
-	O
NadR	B-protein
,	O
we	O
superposed	B-experimental_method
its	O
ligand	B-protein_state
-	I-protein_state
free	I-protein_state
monomer	B-oligomeric_state
(	O
chain	B-structure_element
A	I-structure_element
)	O
onto	O
the	O
ligand	B-protein_state
-	I-protein_state
occupied	I-protein_state
monomer	B-oligomeric_state
(	O
chain	B-structure_element
B	I-structure_element
).	O

Overall	O
,	O
the	O
superposition	B-experimental_method
revealed	O
a	O
high	O
degree	O
of	O
structural	O
similarity	O
(	O
Cα	O
root	B-evidence
mean	I-evidence
square	I-evidence
deviation	I-evidence
(	O
rmsd	B-evidence
)	O
of	O
1	O
.	O
5Å	O
),	O
though	O
on	O
closer	O
inspection	O
a	O
rotational	O
difference	O
of	O
~	O
9	O
degrees	O
along	O
the	O
long	O
axis	O
of	O
helix	B-structure_element
α6	B-structure_element
was	O
observed	O
,	O
suggesting	O
that	O
4	B-chemical
-	I-chemical
HPA	I-chemical
induced	O
a	O
slight	O
conformational	O
change	O
(	O
Fig	O
5A	O
).	O

However	O
,	O
since	O
residues	O
of	O
helix	B-structure_element
α6	B-structure_element
were	O
not	O
directly	O
involved	O
in	O
ligand	O
binding	O
,	O
an	O
explanation	O
for	O
the	O
lack	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
in	O
monomer	B-oligomeric_state
A	B-structure_element
did	O
not	O
emerge	O
by	O
analyzing	O
only	O
these	O
backbone	O
atom	O
positions	O
,	O
suggesting	O
that	O
a	O
more	O
complex	O
series	O
of	O
allosteric	O
events	O
may	O
occur	O
.	O

Indeed	O
,	O
we	O
noted	O
interesting	O
differences	O
in	O
the	O
side	O
chains	O
of	O
Met22	B-residue_name_number
,	O
Phe25	B-residue_name_number
and	O
Arg43	B-residue_name_number
,	O
which	O
in	O
monomer	B-oligomeric_state
B	B-structure_element
are	O
used	O
to	O
contact	O
the	O
ligand	O
while	O
in	O
monomer	B-oligomeric_state
A	B-structure_element
they	O
partially	O
occupied	O
the	O
pocket	B-site
and	O
collectively	O
reduced	O
its	O
volume	O
significantly	O
.	O

Specifically	O
,	O
upon	O
analysis	O
with	O
the	O
CASTp	B-experimental_method
software	O
,	O
the	O
pocket	B-site
in	O
chain	B-structure_element
B	I-structure_element
containing	O
the	O
4	B-chemical
-	I-chemical
HPA	I-chemical
exhibited	O
a	O
total	O
volume	O
of	O
approximately	O
370	O
Å3	O
,	O
while	O
the	O
pocket	B-site
in	O
chain	B-structure_element
A	I-structure_element
was	O
occupied	O
by	O
these	O
three	O
side	O
chains	O
that	O
adopted	O
‘	O
inward	B-protein_state
’	O
positions	O
and	O
thereby	O
divided	O
the	O
space	O
into	O
a	O
few	O
much	O
smaller	O
pockets	O
,	O
each	O
with	O
volume	O
<	O
50	O
Å3	O
,	O
evidently	O
rendering	O
chain	B-structure_element
A	I-structure_element
unfavorable	O
for	O
ligand	O
binding	O
.	O

Most	O
notably	O
,	O
atomic	O
clashes	O
between	O
the	O
ligand	O
and	O
the	O
side	O
chains	O
of	O
MetA22	B-residue_name_number
,	O
PheA25	B-residue_name_number
and	O
ArgA43	B-residue_name_number
would	O
occur	O
if	O
4	B-chemical
-	I-chemical
HPA	I-chemical
were	O
present	O
in	O
the	O
monomer	B-oligomeric_state
A	B-structure_element
pocket	B-site
(	O
Fig	O
5B	O
).	O

Subsequently	O
,	O
analyses	O
of	O
the	O
pockets	B-site
in	O
apo	B-protein_state
-	O
NadR	B-protein
revealed	O
that	O
in	O
the	O
absence	B-protein_state
of	I-protein_state
ligand	I-protein_state
the	O
long	O
Arg43	B-residue_name_number
side	O
chain	O
was	O
always	O
in	O
the	O
open	O
‘	O
outward	B-protein_state
’	O
position	O
compatible	O
with	O
binding	O
to	O
the	O
4	B-chemical
-	I-chemical
HPA	I-chemical
carboxylate	O
group	O
.	O

In	O
contrast	O
,	O
the	O
apo	B-protein_state
-	O
form	O
Met22	B-residue_name_number
and	O
Phe25	B-residue_name_number
residues	O
were	O
still	O
encroaching	O
the	O
spaces	O
of	O
the	O
4	O
-	O
hydroxyl	O
group	O
and	O
the	O
phenyl	O
ring	O
of	O
the	O
ligand	O
,	O
respectively	O
(	O
Fig	O
5C	O
).	O

The	O
‘	O
outward	B-protein_state
’	O
position	O
of	O
Arg43	B-residue_name_number
generated	O
an	O
open	B-protein_state
apo	B-protein_state
-	O
form	O
pocket	B-site
with	O
volume	O
approximately	O
380Å3	O
.	O

Taken	O
together	O
,	O
these	O
observations	O
suggest	O
that	O
Arg43	B-residue_name_number
is	O
a	O
major	O
determinant	O
of	O
ligand	O
binding	O
,	O
and	O
that	O
its	O
‘	O
inward	B-protein_state
’	O
position	O
inhibits	O
the	O
binding	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
to	O
the	O
empty	O
pocket	B-site
of	O
holo	B-protein_state
-	O
NadR	B-protein
.	O

Structural	O
differences	O
of	O
NadR	B-protein
in	O
ligand	B-protein_state
-	I-protein_state
bound	I-protein_state
or	O
free	B-protein_state
forms	O
.	O

(	O
A	O
)	O
Aligned	B-experimental_method
monomers	B-oligomeric_state
of	O
holo	B-protein_state
-	O
NadR	B-protein
(	O
chain	B-structure_element
A	I-structure_element
:	O
green	O
;	O
chain	B-structure_element
B	I-structure_element
:	O
blue	O
),	O
reveal	O
major	O
overall	O
differences	O
by	O
the	O
shift	O
of	O
helix	B-structure_element
α6	B-structure_element
.	O
(	O
B	O
)	O
Comparison	B-experimental_method
of	O
the	O
two	O
binding	B-site
pockets	I-site
in	O
holo	B-protein_state
-	O
NadR	B-protein
shows	O
that	O
in	O
the	O
ligand	B-protein_state
-	I-protein_state
free	I-protein_state
monomer	B-oligomeric_state
A	B-structure_element
(	O
green	O
)	O
residues	O
Met22	B-residue_name_number
,	O
Phe25	B-residue_name_number
and	O
Arg43	B-residue_name_number
adopt	O
‘	O
inward	B-protein_state
’	O
positions	O
(	O
highlighted	O
by	O
arrows	O
)	O
compared	O
to	O
the	O
ligand	B-protein_state
-	I-protein_state
occupied	I-protein_state
pocket	B-site
(	O
blue	O
residues	O
);	O
these	O
‘	O
inward	B-protein_state
’	O
conformations	O
appear	O
unfavorable	O
for	O
binding	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
due	O
to	O
clashes	O
with	O
the	O
4	O
-	O
hydroxyl	O
group	O
,	O
the	O
phenyl	O
ring	O
and	O
the	O
carboxylate	O
group	O
,	O
respectively	O
.	O

In	O
these	O
crystals	B-evidence
,	O
the	O
ArgA43	B-residue_name_number
side	O
chain	O
showed	O
two	O
alternate	O
conformations	O
,	O
modelled	O
with	O
50	O
%	O
occupancy	O
in	O
each	O
state	O
,	O
as	O
indicated	O
by	O
the	O
two	O
‘	O
mirrored	O
’	O
arrows	O
.	O

The	O
inner	O
conformer	O
is	O
the	O
one	O
that	O
would	O
display	O
major	O
clashes	O
if	O
4	B-chemical
-	I-chemical
HPA	I-chemical
were	O
present	O
.	O
(	O
C	O
)	O
Comparison	O
of	O
the	O
empty	O
pocket	B-site
from	O
holo	B-protein_state
-	O
NadR	B-protein
(	O
green	O
residues	O
)	O
with	O
the	O
four	O
empty	O
pockets	B-site
of	O
apo	B-protein_state
-	O
NadR	B-protein
(	O
grey	O
residues	O
),	O
shows	O
that	O
in	O
the	O
absence	B-protein_state
of	I-protein_state
4	B-chemical
-	I-chemical
HPA	I-chemical
the	O
Arg43	B-residue_name_number
side	O
chain	O
is	O
always	O
observed	O
in	O
the	O
‘	O
outward	B-protein_state
’	O
conformation	O
.	O

Finally	O
,	O
we	O
applied	O
15N	B-experimental_method
heteronuclear	I-experimental_method
solution	I-experimental_method
NMR	I-experimental_method
spectroscopy	I-experimental_method
to	O
examine	O
the	O
interaction	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
with	O
apo	B-protein_state
NadR	B-protein
.	O
We	O
collected	O
NMR	B-experimental_method
spectra	B-evidence
on	O
NadR	B-protein
in	B-protein_state
the	I-protein_state
presence	I-protein_state
and	O
absence	B-protein_state
of	I-protein_state
4	B-chemical
-	I-chemical
HPA	I-chemical
(	O
see	O
Materials	O
and	O
Methods	O
).	O

The	O
1H	B-experimental_method
-	I-experimental_method
15N	I-experimental_method
TROSY	I-experimental_method
-	I-experimental_method
HSQC	I-experimental_method
spectrum	B-evidence
of	O
apo	B-protein_state
-	O
NadR	B-protein
,	O
acquired	O
at	O
25	O
°	O
C	O
,	O
displayed	O
approximately	O
140	O
distinct	O
peaks	O
(	O
Fig	O
6A	O
),	O
most	O
of	O
which	O
correspond	O
to	O
backbone	O
amide	O
N	O
-	O
H	O
groups	O
.	O

The	O
broad	O
spectral	O
dispersion	O
and	O
the	O
number	O
of	O
peaks	O
observed	O
,	O
which	O
is	O
close	O
to	O
the	O
number	O
of	O
expected	O
backbone	O
amide	O
N	O
-	O
H	O
groups	O
for	O
this	O
polypeptide	O
,	O
confirmed	O
that	O
apo	B-protein_state
-	O
NadR	B-protein
is	O
well	B-protein_state
-	I-protein_state
folded	I-protein_state
under	O
these	O
conditions	O
and	O
exhibits	O
one	O
conformation	O
appreciable	O
on	O
the	O
NMR	B-experimental_method
timescale	O
,	O
i	O
.	O
e	O
.	O
in	O
the	O
NMR	B-experimental_method
experiments	O
at	O
25	O
°	O
C	O
,	O
two	O
or	O
more	O
distinct	O
conformations	O
of	O
apo	B-protein_state
-	O
NadR	B-protein
monomers	B-oligomeric_state
were	O
not	O
readily	O
apparent	O
.	O

Upon	O
the	O
addition	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
,	O
over	O
45	O
peaks	O
showed	O
chemical	O
shift	O
perturbations	O
,	O
i	O
.	O
e	O
.	O
changed	O
position	O
in	O
the	O
spectrum	O
or	O
disappeared	O
,	O
while	O
the	O
remaining	O
peaks	O
remained	O
unchanged	O
.	O

This	O
observation	O
showed	O
that	O
4	B-chemical
-	I-chemical
HPA	I-chemical
was	O
able	O
to	O
bind	O
NadR	B-protein
and	O
induce	O
notable	O
changes	O
in	O
specific	O
regions	O
of	O
the	O
protein	O
.	O

NMR	B-experimental_method
spectra	B-evidence
of	O
NadR	B-protein
in	B-protein_state
the	I-protein_state
presence	I-protein_state
and	O
absence	B-protein_state
of	I-protein_state
4	B-chemical
-	I-chemical
HPA	I-chemical
.	O

(	O
A	O
)	O
Superposition	B-experimental_method
of	O
two	O
1H	B-experimental_method
-	I-experimental_method
15N	I-experimental_method
TROSY	I-experimental_method
-	I-experimental_method
HSQC	I-experimental_method
spectra	B-evidence
recorded	O
at	O
25	O
°	O
C	O
on	O
apo	B-protein_state
-	O
NadR	B-protein
(	O
cyan	O
)	O
and	O
on	O
NadR	B-protein
in	O
the	O
presence	B-protein_state
of	I-protein_state
4	B-chemical
-	I-chemical
HPA	I-chemical
(	O
red	O
).	O

(	O
B	O
,	O
C	O
)	O
Overlay	B-experimental_method
of	O
selected	O
regions	O
of	O
the	O
1H	B-experimental_method
-	I-experimental_method
15N	I-experimental_method
TROSY	I-experimental_method
-	I-experimental_method
HSQC	I-experimental_method
spectra	B-evidence
acquired	O
at	O
25	O
°	O
C	O
of	O
apo	B-protein_state
-	O
NadR	B-protein
(	O
cyan	O
)	O
and	O
NadR	B-complex_assembly
/	I-complex_assembly
4	I-complex_assembly
-	I-complex_assembly
HPA	I-complex_assembly
(	O
red	O
)	O
superimposed	B-experimental_method
with	O
the	O
spectra	B-evidence
acquired	O
at	O
10	O
°	O
C	O
of	O
apo	B-protein_state
-	O
NadR	B-protein
(	O
blue	O
)	O
and	O
NadR	B-complex_assembly
/	I-complex_assembly
4	I-complex_assembly
-	I-complex_assembly
HPA	I-complex_assembly
(	O
green	O
).	O

The	O
spectra	B-evidence
acquired	O
at	O
10	O
°	O
C	O
are	O
excluded	O
from	O
panel	O
A	O
for	O
simplicity	O
.	O

However	O
,	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
4	B-chemical
-	I-chemical
HPA	I-chemical
,	O
the	O
1H	B-experimental_method
-	I-experimental_method
15N	I-experimental_method
TROSY	I-experimental_method
-	I-experimental_method
HSQC	I-experimental_method
spectrum	B-evidence
of	O
NadR	B-protein
displayed	O
approximately	O
140	O
peaks	O
,	O
as	O
for	O
apo	B-protein_state
-	O
NadR	B-protein
,	O
i	O
.	O
e	O
.	O
two	O
distinct	O
stable	O
conformations	O
(	O
that	O
might	O
have	O
potentially	O
revealed	O
the	O
molecular	O
asymmetry	O
observed	O
crystallographically	B-experimental_method
)	O
were	O
not	O
notable	O
.	O

Considering	O
the	O
small	O
size	O
,	O
fast	O
diffusion	O
and	O
relatively	O
low	O
binding	B-evidence
affinity	I-evidence
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
,	O
it	O
would	O
not	O
be	O
surprising	O
if	O
the	O
ligand	O
associates	O
and	O
dissociates	O
rapidly	O
on	O
the	O
NMR	B-experimental_method
time	O
scale	O
,	O
resulting	O
in	O
only	O
one	O
set	O
of	O
peaks	O
whose	O
chemical	O
shifts	O
represent	O
the	O
average	O
environment	O
of	O
the	O
bound	B-protein_state
and	O
unbound	B-protein_state
states	O
.	O

Interestingly	O
,	O
by	O
cooling	O
the	O
samples	O
to	O
10	O
°	O
C	O
,	O
we	O
observed	O
that	O
a	O
number	O
of	O
those	O
peaks	O
strongly	O
affected	O
by	O
4	B-chemical
-	I-chemical
HPA	I-chemical
(	O
and	O
therefore	O
likely	O
to	O
be	O
in	O
the	O
ligand	B-site
-	I-site
binding	I-site
site	I-site
)	O
demonstrated	O
evidence	O
of	O
peak	O
splitting	O
,	O
i	O
.	O
e	O
.	O
a	O
tendency	O
to	O
become	O
two	O
distinct	O
peaks	O
rather	O
than	O
one	O
single	O
peak	O
(	O
Fig	O
6B	O
and	O
6C	O
).	O

These	O
doubled	O
peaks	O
may	O
therefore	O
reveal	O
that	O
the	O
cooler	O
temperature	O
partially	O
trapped	O
the	O
existence	O
in	O
solution	O
of	O
two	O
distinct	O
states	O
,	O
in	O
presence	B-protein_state
or	O
absence	B-protein_state
of	I-protein_state
4	B-chemical
-	I-chemical
HPA	I-chemical
,	O
with	O
minor	O
conformational	O
differences	O
occurring	O
at	O
least	O
in	O
proximity	O
to	O
the	O
binding	B-site
pocket	I-site
.	O

Although	O
more	O
comprehensive	O
NMR	B-experimental_method
experiments	O
and	O
full	O
chemical	O
shift	O
assignment	O
of	O
the	O
spectra	B-evidence
would	O
be	O
required	O
to	O
precisely	O
define	O
this	O
multi	O
-	O
state	O
behavior	O
,	O
the	O
NMR	B-experimental_method
data	O
clearly	O
demonstrate	O
that	O
NadR	B-protein
exhibits	O
conformational	O
flexibility	O
which	O
is	O
modulated	O
by	O
4	B-chemical
-	I-chemical
HPA	I-chemical
in	O
solution	O
.	O

Apo	B-protein_state
-	O
NadR	B-protein
structures	B-evidence
reveal	O
intrinsic	O
conformational	O
flexibility	O

The	O
apo	B-protein_state
-	O
NadR	B-protein
crystal	B-evidence
structure	I-evidence
contained	O
two	O
homodimers	B-oligomeric_state
in	O
the	O
asymmetric	O
unit	O
(	O
chains	B-structure_element
A	I-structure_element
+	I-structure_element
B	I-structure_element
and	O
chains	B-structure_element
C	I-structure_element
+	I-structure_element
D	I-structure_element
).	O

Upon	O
overall	O
structural	B-experimental_method
superposition	I-experimental_method
,	O
these	O
dimers	B-oligomeric_state
revealed	O
a	O
few	O
minor	O
differences	O
in	O
the	O
α6	B-structure_element
helix	I-structure_element
(	O
a	O
major	O
component	O
of	O
the	O
dimer	B-site
interface	I-site
)	O
and	O
the	O
helices	B-structure_element
α4	B-structure_element
-	I-structure_element
α5	I-structure_element
(	O
the	O
DNA	B-site
binding	I-site
region	I-site
),	O
and	O
an	O
rmsd	B-evidence
of	O
1	O
.	O
55Å	O
(	O
Fig	O
7A	O
).	O

Similarly	O
,	O
the	O
entire	O
holo	B-protein_state
-	O
homodimer	B-oligomeric_state
could	O
be	O
closely	B-experimental_method
superposed	I-experimental_method
onto	O
each	O
of	O
the	O
apo	B-protein_state
-	O
homodimers	B-oligomeric_state
,	O
showing	O
rmsd	B-evidence
values	O
of	O
1	O
.	O
29Å	O
and	O
1	O
.	O
31Å	O
,	O
and	O
with	O
more	O
notable	O
differences	O
in	O
the	O
α6	B-structure_element
helix	I-structure_element
positions	O
(	O
Fig	O
7B	O
).	O

The	O
slightly	O
larger	O
rmsd	B-evidence
between	O
the	O
two	O
apo	B-protein_state
-	O
homodimers	B-oligomeric_state
,	O
rather	O
than	O
between	O
apo	B-protein_state
-	O
and	O
holo	B-protein_state
-	O
homodimers	B-oligomeric_state
,	O
further	O
indicate	O
that	O
apo	B-protein_state
-	O
NadR	B-protein
possesses	O
a	O
notable	O
degree	O
of	O
intrinsic	O
conformational	O
flexibility	O
.	O

Overall	O
apo	B-protein_state
-	O
and	O
holo	B-protein_state
-	O
NadR	B-protein
structures	B-evidence
are	O
similar	O
.	O

(	O
A	O
)	O
Pairwise	B-experimental_method
alignment	I-experimental_method
of	O
the	O
two	O
distinct	O
apo	B-protein_state
-	O
NadR	B-protein
homodimers	B-oligomeric_state
(	O
AB	B-structure_element
and	O
CD	B-structure_element
)	O
present	O
in	O
the	O
apo	B-protein_state
-	O
NadR	B-protein
crystals	B-evidence
.	O
(	O
B	O
)	O
Alignment	B-experimental_method
of	O
the	O
holo	B-protein_state
-	O
NadR	B-protein
homodimer	B-oligomeric_state
(	O
green	O
and	O
blue	O
chains	O
)	O
onto	O
the	O
apo	B-protein_state
-	O
NadR	B-protein
homodimers	B-oligomeric_state
.	O

Here	O
,	O
larger	O
differences	O
are	O
observed	O
in	O
the	O
α6	B-structure_element
helices	I-structure_element
(	O
top	O
).	O

4	B-chemical
-	I-chemical
HPA	I-chemical
stabilizes	O
concerted	O
conformational	O
changes	O
in	O
NadR	B-protein
that	O
prevent	O
DNA	O
-	O
binding	O

To	O
further	O
investigate	O
the	O
conformational	O
rearrangements	O
of	O
NadR	B-protein
,	O
we	O
performed	O
local	B-experimental_method
structural	I-experimental_method
alignments	I-experimental_method
using	O
only	O
a	O
subset	O
of	O
residues	O
in	O
the	O
DNA	B-structure_element
-	I-structure_element
binding	I-structure_element
helix	I-structure_element
(	O
α4	B-structure_element
).	O

By	O
selecting	B-experimental_method
and	O
aligning	B-experimental_method
residues	O
Arg64	B-residue_range
-	I-residue_range
Ala77	I-residue_range
of	O
one	O
α4	B-structure_element
helix	I-structure_element
per	O
dimer	B-oligomeric_state
,	O
superposition	B-experimental_method
of	O
the	O
holo	B-protein_state
-	O
homodimer	B-oligomeric_state
onto	O
the	O
two	O
apo	B-protein_state
-	O
homodimers	B-oligomeric_state
revealed	O
differences	O
in	O
the	O
monomer	B-oligomeric_state
conformations	O
of	O
each	O
structure	B-evidence
.	O

While	O
one	O
monomer	B-oligomeric_state
from	O
each	O
structure	B-evidence
was	O
closely	O
superimposable	O
(	O
Fig	O
8A	O
,	O
left	O
side	O
),	O
the	O
second	O
monomer	B-oligomeric_state
displayed	O
quite	O
large	O
differences	O
(	O
Fig	O
8A	O
,	O
right	O
side	O
).	O

Most	O
notably	O
,	O
the	O
position	O
of	O
the	O
DNA	B-chemical
-	O
binding	O
helix	B-structure_element
α4	B-structure_element
shifted	O
by	O
as	O
much	O
as	O
6	O
Å	O
(	O
Fig	O
8B	O
).	O

Accordingly	O
,	O
helix	B-structure_element
α4	B-structure_element
was	O
also	O
found	O
to	O
be	O
one	O
of	O
the	O
most	O
dynamic	O
regions	O
in	O
previous	O
HDX	B-experimental_method
-	I-experimental_method
MS	I-experimental_method
analyses	O
of	O
apo	B-protein_state
-	O
NadR	B-protein
in	O
solution	O
.	O

Structural	B-experimental_method
comparisons	I-experimental_method
of	O
NadR	B-protein
and	O
modelling	O
of	O
interactions	O
with	O
DNA	B-chemical
.	O

(	O
A	O
)	O
The	O
holo	B-protein_state
-	O
homodimer	B-oligomeric_state
structure	B-evidence
is	O
shown	O
as	O
green	O
and	O
blue	O
cartoons	O
,	O
for	O
chain	B-structure_element
A	I-structure_element
and	I-structure_element
B	I-structure_element
,	O
respectively	O
,	O
while	O
the	O
two	O
homodimers	B-oligomeric_state
of	O
apo	B-protein_state
-	O
NadR	B-protein
are	O
both	O
cyan	O
and	O
pale	O
blue	O
for	O
chains	O
A	B-structure_element
/	I-structure_element
C	I-structure_element
and	O
B	B-structure_element
/	I-structure_element
D	I-structure_element
,	O
respectively	O
.	O

The	O
three	O
homodimers	B-oligomeric_state
(	O
chains	O
AB	B-structure_element
holo	B-protein_state
,	O
AB	B-structure_element
apo	B-protein_state
,	O
and	O
CD	B-structure_element
apo	B-protein_state
)	O
were	O
overlaid	B-experimental_method
by	O
structural	B-experimental_method
alignment	I-experimental_method
exclusively	O
of	O
all	O
heavy	O
atoms	O
in	O
residues	O
R64	B-residue_range
-	I-residue_range
A77	I-residue_range
(	O
shown	O
in	O
red	O
,	O
with	O
side	O
chain	O
sticks	O
)	O
of	O
chains	O
A	B-structure_element
holo	B-protein_state
,	O
A	B-structure_element
apo	B-protein_state
,	O
and	O
C	B-structure_element
apo	B-protein_state
,	O
belonging	O
to	O
helix	B-structure_element
α4	B-structure_element
(	O
left	O
).	O

The	O
α4	B-structure_element
helices	I-structure_element
aligned	O
closely	O
,	O
Cα	O
rmsd	B-evidence
0	O
.	O
2Å	O
for	O
14	O
residues	O
.	O

(	O
B	O
)	O
The	O
relative	O
positions	O
of	O
the	O
α4	B-structure_element
helices	I-structure_element
of	O
the	O
4	B-protein_state
-	I-protein_state
HPA	I-protein_state
-	I-protein_state
bound	I-protein_state
holo	B-protein_state
homodimer	B-oligomeric_state
chain	B-structure_element
B	I-structure_element
(	O
blue	O
),	O
and	O
of	O
apo	B-protein_state
homodimers	B-oligomeric_state
AB	B-structure_element
and	O
CD	B-structure_element
(	O
showing	O
chains	B-structure_element
B	I-structure_element
and	I-structure_element
D	I-structure_element
)	O
in	O
pale	O
blue	O
.	O

Dashes	O
indicate	O
the	O
Ala77	B-residue_name_number
Cα	O
atoms	O
,	O
in	O
the	O
most	O
highly	O
shifted	O
region	O
of	O
the	O
‘	O
non	O
-	O
fixed	O
’	O
α4	B-structure_element
helix	I-structure_element
.	O

(	O
C	O
)	O
The	O
double	O
-	O
stranded	O
DNA	B-chemical
molecule	O
(	O
grey	O
cartoon	O
)	O
from	O
the	O
OhrR	B-complex_assembly
-	I-complex_assembly
ohrA	I-complex_assembly
complex	O
is	O
shown	O
after	O
superposition	B-experimental_method
with	O
NadR	B-protein
,	O
to	O
highlight	O
the	O
expected	O
positions	O
of	O
the	O
NadR	B-protein
α4	B-structure_element
helices	I-structure_element
in	O
the	O
DNA	B-chemical
major	O
grooves	O
.	O

For	O
clarity	O
,	O
only	O
the	O
α4	B-structure_element
helices	I-structure_element
are	O
shown	O
in	O
panels	O
(	O
B	O
)	O
and	O
(	O
C	O
).	O
(	O
D	O
)	O
Upon	O
comparison	O
with	O
the	O
experimentally	O
-	O
determined	O
OhrR	B-complex_assembly
:	I-complex_assembly
ohrA	I-complex_assembly
structure	B-evidence
(	O
grey	O
),	O
the	O
α4	B-structure_element
helix	I-structure_element
of	O
holo	B-protein_state
-	O
NadR	B-protein
(	O
blue	O
)	O
is	O
shifted	O
~	O
8Å	O
out	O
of	O
the	O
major	O
groove	O
.	O

However	O
,	O
structural	B-experimental_method
comparisons	I-experimental_method
revealed	O
that	O
the	O
shift	O
of	O
holo	B-protein_state
-	O
NadR	B-protein
helix	B-structure_element
α4	B-structure_element
induced	O
by	O
the	O
presence	B-protein_state
of	I-protein_state
4	B-chemical
-	I-chemical
HPA	I-chemical
was	O
also	O
accompanied	O
by	O
several	O
changes	O
at	O
the	O
holo	B-protein_state
dimer	B-site
interface	I-site
,	O
while	O
such	O
extensive	O
structural	O
differences	O
were	O
not	O
observed	O
in	O
the	O
apo	B-protein_state
dimer	B-site
interfaces	I-site
,	O
particularly	O
notable	O
when	O
comparing	O
the	O
α6	B-structure_element
helices	I-structure_element
(	O
S3	O
Fig	O
).	O

In	O
summary	O
,	O
compared	O
to	O
ligand	B-protein_state
-	I-protein_state
stabilized	I-protein_state
holo	B-protein_state
-	O
NadR	B-protein
,	O
apo	B-protein_state
-	O
NadR	B-protein
displayed	O
an	O
intrinsic	O
flexibility	O
focused	O
in	O
the	O
DNA	B-site
-	I-site
binding	I-site
region	I-site
.	O

This	O
was	O
also	O
evident	O
in	O
the	O
greater	O
disorder	O
(	O
i	O
.	O
e	O
.	O
less	O
well	O
-	O
defined	O
electron	B-evidence
density	I-evidence
)	O
in	O
the	O
β1	B-structure_element
-	I-structure_element
β2	I-structure_element
loops	I-structure_element
of	O
the	O
apo	B-protein_state
dimers	B-oligomeric_state
(	O
density	B-evidence
for	O
16	O
residues	O
per	O
dimer	B-oligomeric_state
was	O
missing	O
)	O
compared	O
to	O
the	O
holo	B-protein_state
dimer	B-oligomeric_state
(	O
density	B-evidence
for	O
only	O
3	O
residues	O
was	O
missing	O
).	O

In	O
holo	B-protein_state
-	O
NadR	B-protein
,	O
the	O
distance	O
separating	O
the	O
two	O
DNA	O
-	O
binding	O
α4	B-structure_element
helices	I-structure_element
was	O
32	O
Å	O
,	O
while	O
in	O
apo	B-protein_state
-	O
NadR	B-protein
it	O
was	O
29	O
Å	O
for	O
homodimer	B-oligomeric_state
AB	B-structure_element
,	O
and	O
34	O
Å	O
for	O
homodimer	B-oligomeric_state
CD	B-structure_element
(	O
Fig	O
8C	O
).	O

Thus	O
,	O
the	O
apo	B-protein_state
-	O
homodimer	B-oligomeric_state
AB	B-structure_element
presented	O
the	O
DNA	B-structure_element
-	I-structure_element
binding	I-structure_element
helices	I-structure_element
in	O
a	O
conformation	O
similar	O
to	O
that	O
observed	O
in	O
the	O
protein	O
:	O
DNA	O
complex	O
of	O
OhrR	B-complex_assembly
:	I-complex_assembly
ohrA	I-complex_assembly
from	O
Bacillus	B-species
subtilis	I-species
(	O
Fig	O
8C	O
).	O

Interestingly	O
,	O
OhrR	B-protein
contacts	O
ohrA	B-gene
across	O
22	O
base	O
pairs	O
(	O
bp	O
),	O
and	O
similarly	O
the	O
main	O
NadR	B-protein
target	B-site
sites	I-site
identified	O
in	O
the	O
nadA	B-gene
promoter	O
(	O
the	O
operators	O
Op	O
I	O
and	O
Op	O
II	O
)	O
both	O
span	O
22	O
bp	O
.	O

Pairwise	B-experimental_method
superpositions	I-experimental_method
showed	O
that	O
the	O
NadR	B-protein
apo	B-protein_state
-	O
homodimer	B-oligomeric_state
AB	B-structure_element
was	O
the	O
most	O
similar	O
to	O
OhrR	B-protein
(	O
rmsd	B-evidence
2	O
.	O
6	O
Å	O
),	O
while	O
the	O
holo	B-protein_state
-	O
homodimer	B-oligomeric_state
was	O
the	O
most	O
divergent	O
(	O
rmsd	B-evidence
3	O
.	O
3	O
Å	O
)	O
(	O
Fig	O
8C	O
).	O

Assuming	O
the	O
same	O
DNA	B-chemical
-	O
binding	O
mechanism	O
is	O
used	O
by	O
OhrR	B-protein
and	O
NadR	B-protein
,	O
the	O
apo	B-protein_state
-	O
homodimer	B-oligomeric_state
AB	B-structure_element
seems	O
ideally	O
pre	O
-	O
configured	O
for	O
DNA	B-chemical
binding	O
,	O
while	O
4	B-chemical
-	I-chemical
HPA	I-chemical
appeared	O
to	O
stabilize	O
holo	B-protein_state
-	O
NadR	B-protein
in	O
a	O
conformation	O
poorly	O
suited	O
for	O
DNA	B-chemical
binding	O
.	O

Specifically	O
,	O
in	O
addition	O
to	O
the	O
different	O
inter	B-evidence
-	I-evidence
helical	I-evidence
translational	I-evidence
distances	I-evidence
,	O
the	O
α4	B-structure_element
helices	I-structure_element
in	O
the	O
holo	B-protein_state
-	O
NadR	B-protein
homodimer	B-oligomeric_state
were	O
also	O
reoriented	O
,	O
resulting	O
in	O
movement	O
of	O
α4	B-structure_element
out	O
of	O
the	O
major	O
groove	O
,	O
by	O
up	O
to	O
8Å	O
,	O
and	O
presumably	O
preventing	O
efficient	O
DNA	B-chemical
binding	O
in	O
the	O
presence	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
(	O
Fig	O
8D	O
).	O

When	O
aligned	B-experimental_method
with	O
OhrR	B-protein
,	O
the	O
apo	B-protein_state
-	O
homodimer	B-oligomeric_state
CD	B-structure_element
presented	O
yet	O
another	O
different	O
intermediate	O
conformation	O
(	O
rmsd	B-evidence
2	O
.	O
9Å	O
),	O
apparently	O
not	O
ideally	O
pre	O
-	O
configured	O
for	O
DNA	B-chemical
binding	O
,	O
but	O
which	O
in	O
solution	O
can	O
presumably	O
readily	O
adopt	O
the	O
AB	B-structure_element
conformation	O
due	O
to	O
the	O
intrinsic	O
flexibility	O
described	O
above	O
.	O

NadR	B-protein
residues	O
His7	B-residue_name_number
,	O
Ser9	B-residue_name_number
,	O
Asn11	B-residue_name_number
and	O
Phe25	B-residue_name_number
are	O
essential	O
for	O
regulation	O
of	O
NadA	B-protein
expression	O
in	O
vivo	O

While	O
previous	O
studies	O
had	O
correctly	O
suggested	O
the	O
involvement	O
of	O
several	O
NadR	B-protein
residues	O
in	O
ligand	O
binding	O
,	O
the	O
crystal	B-evidence
structures	I-evidence
presented	O
here	O
revealed	O
additional	O
residues	O
with	O
previously	O
unknown	O
roles	O
in	O
dimerization	O
and	O
/	O
or	O
binding	O
to	O
4	B-chemical
-	I-chemical
HPA	I-chemical
.	O

To	O
explore	O
the	O
functional	O
involvement	O
of	O
these	O
residues	O
,	O
we	O
characterized	O
the	O
behavior	O
of	O
four	O
new	O
NadR	B-protein
mutants	O
(	O
H7A	B-mutant
,	O
S9A	B-mutant
,	O
N11A	B-mutant
and	O
F25A	B-mutant
)	O
in	O
an	O
in	O
vivo	O
assay	O
using	O
the	O
previously	O
described	O
MC58	B-mutant
-	I-mutant
Δ1843	I-mutant
nadR	B-gene
-	O
null	O
mutant	B-protein_state
strain	O
,	O
which	O
was	O
complemented	O
either	O
by	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
nadR	B-gene
or	O
by	O
the	O
nadR	B-gene
mutants	B-protein_state
.	O

NadA	B-protein
protein	O
abundance	O
levels	O
were	O
assessed	O
by	O
Western	B-experimental_method
blotting	I-experimental_method
to	O
evaluate	O
the	O
ability	O
of	O
the	O
NadR	B-protein
mutants	B-protein_state
to	O
repress	O
the	O
nadA	B-gene
promoter	O
,	O
in	O
the	O
presence	O
or	O
absence	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
.	O

The	O
nadR	B-gene
H7A	B-mutant
,	O
S9A	B-mutant
and	O
F25A	B-mutant
complemented	O
strains	O
showed	O
hyper	O
-	O
repression	O
of	O
nadA	B-gene
expression	O
in	O
vivo	O
,	O
i	O
.	O
e	O
.	O
these	O
mutants	O
repressed	O
nadA	B-gene
more	O
efficiently	O
than	O
the	O
NadR	B-protein
WT	B-protein_state
protein	O
,	O
either	O
in	O
the	O
presence	O
or	O
absence	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
,	O
while	O
complementation	O
with	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
nadR	B-gene
resulted	O
in	O
high	O
production	O
of	O
NadA	B-protein
only	O
in	O
the	O
presence	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
(	O
Fig	O
9	O
).	O

Interestingly	O
,	O
and	O
on	O
the	O
contrary	O
,	O
the	O
nadR	B-gene
N11A	B-mutant
complemented	O
strain	O
showed	O
hypo	O
-	O
repression	O
(	O
i	O
.	O
e	O
.	O
exhibited	O
high	O
expression	O
of	O
nadA	B-gene
both	O
in	O
absence	O
and	O
presence	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
).	O

This	O
mutagenesis	B-experimental_method
data	O
revealed	O
that	O
NadR	B-protein
residues	O
His7	B-residue_name_number
,	O
Ser9	B-residue_name_number
,	O
Asn11	B-residue_name_number
and	O
Phe25	B-residue_name_number
play	O
key	O
roles	O
in	O
the	O
ligand	O
-	O
mediated	O
regulation	O
of	O
NadR	B-protein
;	O
they	O
are	O
each	O
involved	O
in	O
the	O
controlled	O
de	O
-	O
repression	O
of	O
the	O
nadA	B-gene
promoter	O
and	O
synthesis	O
of	O
NadA	B-protein
in	O
response	O
to	O
4	B-chemical
-	I-chemical
HPA	I-chemical
in	O
vivo	O
.	O

Structure	B-experimental_method
-	I-experimental_method
based	I-experimental_method
point	I-experimental_method
mutations	I-experimental_method
shed	O
light	O
on	O
ligand	O
-	O
induced	O
regulation	O
of	O
NadR	B-protein
.	O

Western	B-experimental_method
blot	I-experimental_method
analyses	O
of	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
(	O
WT	B-protein_state
)	O
strain	O
(	O
lanes	O
1	O
–	O
2	O
)	O
or	O
isogenic	O
nadR	B-gene
knockout	O
strains	O
(	O
ΔNadR	B-mutant
)	O
complemented	O
to	O
express	O
the	O
indicated	O
NadR	B-protein
WT	B-protein_state
or	O
mutant	B-protein_state
proteins	O
(	O
lanes	O
3	O
–	O
12	O
)	O
or	O
not	O
complemented	O
(	O
lanes	O
13	O
–	O
14	O
),	O
grown	O
in	O
the	O
presence	O
(	O
even	O
lanes	O
)	O
or	O
absence	O
(	O
odd	O
lanes	O
)	O
of	O
5mM	O
4	B-chemical
-	I-chemical
HPA	I-chemical
,	O
showing	O
NadA	B-protein
and	O
NadR	B-protein
expression	O
.	O

Complementation	O
of	O
ΔNadR	B-mutant
with	O
WT	B-protein_state
NadR	B-protein
enables	O
induction	O
of	O
nadA	B-gene
expression	O
by	O
4	B-chemical
-	I-chemical
HPA	I-chemical
.	O

The	O
H7A	B-mutant
,	O
S9A	B-mutant
and	O
F25A	B-mutant
mutants	O
efficiently	O
repress	O
nadA	B-gene
expression	O
but	O
are	O
less	O
ligand	O
-	O
responsive	O
than	O
WT	B-protein_state
NadR	B-protein
.	O
The	O
N11A	B-mutant
mutant	B-protein_state
does	O
not	O
efficiently	O
repress	O
nadA	B-gene
expression	O
either	O
in	O
presence	O
or	O
absence	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
.	O
(	O
The	O
protein	O
abundance	O
levels	O
of	O
the	O
meningococcal	B-taxonomy_domain
factor	B-protein
H	I-protein
binding	I-protein
protein	I-protein
(	O
fHbp	B-protein
)	O
were	O
used	O
as	O
a	O
gel	O
loading	O
control	O
).	O

NadA	B-protein
is	O
a	O
surface	O
-	O
exposed	O
meningococcal	B-taxonomy_domain
protein	O
contributing	O
to	O
pathogenesis	O
,	O
and	O
is	O
one	O
of	O
three	O
main	O
antigens	O
present	O
in	O
the	O
vaccine	O
Bexsero	O
.	O

A	O
detailed	O
understanding	O
of	O
the	O
in	O
vitro	O
repression	O
of	O
nadA	B-gene
expression	O
by	O
the	O
transcriptional	B-protein_type
regulator	I-protein_type
NadR	B-protein
is	O
important	O
,	O
both	O
because	O
it	O
is	O
a	O
relevant	O
disease	O
-	O
related	O
model	O
of	O
how	O
small	O
-	O
molecule	O
ligands	O
can	O
regulate	O
MarR	B-protein_type
family	O
proteins	O
and	O
thereby	O
impact	O
bacterial	B-taxonomy_domain
virulence	O
,	O
and	O
because	O
nadA	B-gene
expression	O
levels	O
are	O
linked	O
to	O
the	O
prediction	O
of	O
vaccine	O
coverage	O
.	O

The	O
repressive	O
activity	O
of	O
NadR	B-protein
can	O
be	O
relieved	O
by	O
hydroxyphenylacetate	B-chemical
(	O
HPA	B-chemical
)	O
ligands	O
,	O
and	O
HDX	B-experimental_method
-	I-experimental_method
MS	I-experimental_method
studies	O
previously	O
indicated	O
that	O
4	B-chemical
-	I-chemical
HPA	I-chemical
stabilizes	O
dimeric	B-oligomeric_state
NadR	B-protein
in	O
a	O
configuration	O
incompatible	O
with	O
DNA	O
binding	O
.	O

Despite	O
these	O
and	O
other	O
studies	O
,	O
the	O
molecular	O
mechanisms	O
by	O
which	O
ligands	O
regulate	O
MarR	B-protein_type
family	O
proteins	O
are	O
relatively	O
poorly	O
understood	O
and	O
likely	O
differ	O
depending	O
on	O
the	O
specific	O
ligand	O
.	O

Given	O
the	O
importance	O
of	O
NadR	B-protein
-	O
mediated	O
regulation	O
of	O
NadA	B-protein
levels	O
in	O
the	O
contexts	O
of	O
meningococcal	B-taxonomy_domain
pathogenesis	O
,	O
we	O
sought	O
to	O
characterize	O
NadR	B-protein
,	O
and	O
its	O
interaction	O
with	O
ligands	O
,	O
at	O
atomic	O
resolution	O
.	O

Firstly	O
,	O
we	O
confirmed	O
that	O
NadR	B-protein
is	O
dimeric	B-oligomeric_state
in	O
solution	O
and	O
demonstrated	O
that	O
it	O
retains	O
its	O
dimeric	B-oligomeric_state
state	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
4	B-chemical
-	I-chemical
HPA	I-chemical
,	O
indicating	O
that	O
induction	O
of	O
a	O
monomeric	B-oligomeric_state
status	O
is	O
not	O
the	O
manner	O
by	O
which	O
4	B-chemical
-	I-chemical
HPA	I-chemical
regulates	O
NadR	B-protein
.	O
These	O
observations	O
were	O
in	O
agreement	O
with	O
(	O
i	O
)	O
a	O
previous	O
study	O
of	O
NadR	B-protein
performed	O
using	O
SEC	B-experimental_method
and	O
mass	B-experimental_method
spectrometry	I-experimental_method
,	O
and	O
(	O
ii	O
)	O
crystallographic	B-experimental_method
studies	I-experimental_method
showing	O
that	O
several	O
MarR	B-protein_type
homologues	O
are	O
dimeric	B-oligomeric_state
.	O

We	O
also	O
used	O
structure	B-experimental_method
-	I-experimental_method
guided	I-experimental_method
site	I-experimental_method
-	I-experimental_method
directed	I-experimental_method
mutagenesis	I-experimental_method
to	O
identify	O
an	O
important	O
conserved	B-protein_state
residue	O
,	O
Leu130	B-residue_name_number
,	O
which	O
stabilizes	O
the	O
NadR	B-protein
dimer	B-site
interface	I-site
,	O
knowledge	O
of	O
which	O
may	O
also	O
inform	O
future	O
studies	O
to	O
explore	O
the	O
regulatory	O
mechanisms	O
of	O
other	O
MarR	B-protein_type
family	O
proteins	O
.	O

Secondly	O
,	O
we	O
assessed	B-experimental_method
the	I-experimental_method
thermal	I-experimental_method
stability	I-experimental_method
and	O
unfolding	O
of	O
NadR	B-protein
in	B-protein_state
the	I-protein_state
presence	I-protein_state
or	O
absence	B-protein_state
of	I-protein_state
ligands	O
.	O

All	O
DSC	B-experimental_method
profiles	B-evidence
showed	O
a	O
single	O
peak	O
,	O
suggesting	O
that	O
a	O
single	O
unfolding	O
event	O
simultaneously	O
disrupted	O
the	O
dimer	B-oligomeric_state
and	O
the	O
monomer	B-oligomeric_state
.	O

HPA	O
ligands	O
specifically	O
increased	O
the	O
stability	O
of	O
NadR	B-protein
.	O
The	O
largest	O
effects	O
were	O
induced	O
by	O
the	O
naturally	O
-	O
occurring	O
compounds	O
4	B-chemical
-	I-chemical
HPA	I-chemical
and	O
3Cl	B-chemical
,	I-chemical
4	I-chemical
-	I-chemical
HPA	I-chemical
,	O
which	O
,	O
in	O
SPR	B-experimental_method
assays	I-experimental_method
,	O
were	O
found	O
to	O
bind	O
NadR	B-protein
with	O
KD	B-evidence
values	O
of	O
1	O
.	O
5	O
mM	O
and	O
1	O
.	O
1	O
mM	O
,	O
respectively	O
.	O

Although	O
these	O
NadR	B-protein
/	O
HPA	O
interactions	O
appeared	O
rather	O
weak	O
,	O
their	O
distinct	O
affinities	O
and	O
specificities	O
matched	O
their	O
in	O
vitro	O
effects	O
and	O
their	O
biological	O
relevance	O
appears	O
similar	O
to	O
previous	O
proposals	O
that	O
certain	O
small	O
molecules	O
,	O
including	O
some	O
antibiotics	O
,	O
in	O
the	O
millimolar	O
concentration	O
range	O
may	O
be	O
broad	O
inhibitors	O
of	O
MarR	B-protein_type
family	O
proteins	O
.	O

Indeed	O
,	O
4	B-chemical
-	I-chemical
HPA	I-chemical
is	O
found	O
in	O
human	B-species
saliva	O
and	O
3Cl	B-chemical
,	I-chemical
4	I-chemical
-	I-chemical
HPA	I-chemical
is	O
produced	O
during	O
inflammatory	O
processes	O
,	O
suggesting	O
that	O
these	O
natural	O
ligands	O
are	O
encountered	O
by	O
N	B-species
.	I-species
meningitidis	I-species
in	O
the	O
mucosa	O
of	O
the	O
oropharynx	O
during	O
infections	O
.	O

It	O
is	O
also	O
possible	O
that	O
NadR	B-protein
responds	O
to	O
currently	O
unidentified	O
HPA	B-chemical
analogues	O
.	O

Indeed	O
,	O
in	O
the	O
NadR	B-complex_assembly
/	I-complex_assembly
4	I-complex_assembly
-	I-complex_assembly
HPA	I-complex_assembly
complex	O
there	O
was	O
a	O
water	B-chemical
molecule	O
close	O
to	O
the	O
carboxylate	O
group	O
and	O
also	O
a	O
small	O
unfilled	O
tunnel	B-site
~	O
5Å	O
long	O
,	O
both	O
factors	O
suggesting	O
that	O
alternative	O
larger	O
ligands	O
could	O
occupy	O
the	O
pocket	O
.	O

The	O
ability	O
to	O
respond	O
to	O
various	O
ligands	O
might	O
enable	O
NadR	B-protein
in	O
vivo	O
to	O
orchestrate	O
multiple	O
response	O
mechanisms	O
and	O
modulate	O
expression	O
of	O
genes	O
other	O
than	O
nadA	B-gene
.	O
Ultimately	O
,	O
confirmation	O
of	O
the	O
relevance	O
of	O
each	O
ligand	O
will	O
require	O
a	O
deeper	O
understanding	O
of	O
the	O
available	O
concentration	O
in	O
vivo	O
in	O
the	O
host	O
niche	O
during	O
bacterial	B-taxonomy_domain
colonization	O
and	O
inflammation	O
.	O

Here	O
,	O
we	O
determined	O
the	O
first	O
crystal	B-evidence
structures	I-evidence
of	O
apo	B-protein_state
-	O
NadR	B-protein
and	O
holo	B-protein_state
-	O
NadR	B-protein
.	O
These	O
experimentally	O
-	O
determined	O
structures	B-evidence
enabled	O
a	O
new	O
detailed	O
characterization	O
of	O
the	O
ligand	B-site
-	I-site
binding	I-site
pocket	I-site
.	O

In	O
holo	B-protein_state
-	O
NadR	B-protein
,	O
4	B-chemical
-	I-chemical
HPA	I-chemical
interacted	O
directly	O
with	O
at	O
least	O
11	O
polar	O
and	O
hydrophobic	O
residues	O
.	O

Several	O
,	O
but	O
not	O
all	O
,	O
of	O
these	O
interactions	O
were	O
predicted	O
previously	O
by	O
homology	B-experimental_method
modelling	I-experimental_method
combined	O
with	O
ligand	B-experimental_method
docking	I-experimental_method
in	O
silico	O
.	O

Subsequently	O
,	O
we	O
established	O
the	O
functional	O
importance	O
of	O
His7	B-residue_name_number
,	O
Ser9	B-residue_name_number
,	O
Asn11	B-residue_name_number
and	O
Phe25	B-residue_name_number
in	O
the	O
in	O
vitro	O
response	O
of	O
meningococcus	B-taxonomy_domain
to	O
4	B-chemical
-	I-chemical
HPA	I-chemical
,	O
via	O
site	B-experimental_method
-	I-experimental_method
directed	I-experimental_method
mutagenesis	I-experimental_method
.	O

More	O
unexpectedly	O
,	O
the	O
crystal	B-evidence
structure	I-evidence
revealed	O
that	O
only	O
one	O
molecule	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
was	O
bound	B-protein_state
per	O
NadR	B-protein
dimer	B-oligomeric_state
.	O

We	O
confirmed	O
this	O
stoichiometry	O
in	O
solution	O
using	O
SPR	B-experimental_method
methods	O
.	O

We	O
also	O
used	O
heteronuclear	B-experimental_method
NMR	I-experimental_method
spectroscopy	I-experimental_method
to	O
detect	O
substantial	O
conformational	O
changes	O
of	O
NadR	B-protein
occurring	O
in	O
solution	O
upon	O
addition	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
.	O

Moreover	O
,	O
NMR	B-experimental_method
spectra	B-evidence
at	O
10	O
°	O
C	O
suggested	O
the	O
existence	O
of	O
two	O
distinct	O
conformations	O
of	O
NadR	B-protein
in	O
the	O
vicinity	O
of	O
the	O
ligand	B-site
-	I-site
binding	I-site
pocket	I-site
.	O

More	O
powerfully	O
,	O
our	O
unique	O
crystallographic	B-evidence
observation	I-evidence
of	O
this	O
‘	O
occupied	B-protein_state
vs	O
unoccupied	B-protein_state
site	O
’	O
asymmetry	O
in	O
the	O
NadR	B-complex_assembly
/	I-complex_assembly
4	I-complex_assembly
-	I-complex_assembly
HPA	I-complex_assembly
interaction	O
is	O
,	O
to	O
our	O
knowledge	O
,	O
the	O
first	O
example	O
reported	O
for	O
a	O
MarR	B-protein_type
family	O
protein	O
.	O

Structural	B-experimental_method
analyses	I-experimental_method
suggested	O
that	O
‘	O
inward	B-protein_state
’	O
side	O
chain	O
positions	O
of	O
Met22	B-residue_name_number
,	O
Phe25	B-residue_name_number
and	O
especially	O
Arg43	B-residue_name_number
precluded	O
binding	O
of	O
a	O
second	O
ligand	O
molecule	O
.	O

Such	O
a	O
mechanism	O
indicates	O
negative	O
cooperativity	O
,	O
which	O
may	O
enhance	O
the	O
ligand	O
-	O
responsiveness	O
of	O
NadR	B-protein
.	O

Comparisons	O
of	O
the	O
NadR	B-complex_assembly
/	I-complex_assembly
4	I-complex_assembly
-	I-complex_assembly
HPA	I-complex_assembly
complex	O
with	O
available	O
MarR	B-protein_type
family	O
/	O
salicylate	B-chemical
complexes	O
revealed	O
that	O
4	B-chemical
-	I-chemical
HPA	I-chemical
has	O
a	O
previously	O
unobserved	O
binding	O
mode	O
.	O

Briefly	O
,	O
in	O
the	O
M	B-species
.	I-species
thermoautotrophicum	I-species
MTH313	B-protein
dimer	B-oligomeric_state
,	O
one	O
molecule	O
of	O
salicylate	B-chemical
binds	O
in	O
the	O
pocket	B-site
of	O
each	O
monomer	B-oligomeric_state
,	O
though	O
with	O
two	O
rather	O
different	O
positions	O
and	O
orientations	O
,	O
only	O
one	O
of	O
which	O
(	O
site	B-site
-	I-site
1	I-site
)	O
is	O
thought	O
to	O
be	O
biologically	O
relevant	O
(	O
Fig	O
10A	O
).	O

In	O
the	O
S	B-species
.	I-species
tokodaii	I-species
protein	O
ST1710	B-protein
,	O
salicylate	B-chemical
binds	O
to	O
the	O
same	O
position	O
in	O
each	O
monomer	B-oligomeric_state
of	O
the	O
dimer	B-oligomeric_state
,	O
in	O
a	O
site	O
equivalent	O
to	O
the	O
putative	O
biologically	O
relevant	O
site	O
of	O
MTH313	B-protein
(	O
Fig	O
10B	O
).	O

Unlike	O
other	O
MarR	B-protein_type
family	O
proteins	O
which	O
revealed	O
multiple	O
ligand	O
binding	O
interactions	O
,	O
we	O
observed	O
only	O
1	O
molecule	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
bound	B-protein_state
to	I-protein_state
NadR	B-protein
,	O
suggesting	O
a	O
more	O
specific	O
and	O
less	O
promiscuous	O
interaction	O
.	O

In	O
NadR	B-protein
,	O
the	O
single	O
molecule	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
binds	O
in	O
a	O
position	O
distinctly	O
different	O
from	O
the	O
salicylate	B-site
binding	I-site
site	I-site
:	O
translated	O
by	O
>	O
10	O
Å	O
and	O
with	O
a	O
180	O
°	O
inverted	O
orientation	O
(	O
Fig	O
10C	O
).	O

NadR	B-protein
shows	O
a	O
ligand	B-site
binding	I-site
site	I-site
distinct	O
from	O
other	O
MarR	B-protein_type
homologues	O
.	O

(	O
A	O
)	O
A	O
structural	B-experimental_method
alignment	I-experimental_method
of	O
MTH313	B-protein
chains	B-structure_element
A	I-structure_element
and	I-structure_element
B	I-structure_element
shows	O
that	O
salicylate	B-chemical
is	O
bound	B-protein_state
in	O
distinct	O
locations	O
in	O
each	O
monomer	B-oligomeric_state
;	O
site	B-site
-	I-site
1	I-site
(	O
thought	O
to	O
be	O
the	O
biologically	O
relevant	O
site	O
)	O
and	O
site	B-site
-	I-site
2	I-site
differ	O
by	O
~	O
7Å	O
(	O
indicated	O
by	O
black	O
dotted	O
line	O
)	O
and	O
also	O
by	O
ligand	O
orientation	O
.	O

(	O
B	O
)	O
A	O
structural	B-experimental_method
alignment	I-experimental_method
of	O
MTH313	B-protein
chain	B-structure_element
A	I-structure_element
and	O
ST1710	B-protein
(	O
pink	O
)	O
(	O
Cα	O
rmsd	B-evidence
2	O
.	O
3Å	O
),	O
shows	O
that	O
they	O
bind	O
salicylate	B-chemical
in	O
equivalent	O
sites	O
(	O
differing	O
by	O
only	O
~	O
3Å	O
)	O
and	O
with	O
the	O
same	O
orientation	O
.	O

(	O
C	O
)	O
Addition	O
of	O
holo	B-protein_state
-	O
NadR	B-protein
(	O
chain	B-structure_element
B	I-structure_element
,	O
blue	O
)	O
to	O
the	O
alignment	B-experimental_method
reveals	O
that	O
bound	B-protein_state
4	B-chemical
-	I-chemical
HPA	I-chemical
differs	O
in	O
position	O
by	O
>	O
10	O
Å	O
compared	O
to	O
salicylate	B-chemical
,	O
and	O
adopts	O
a	O
novel	O
orientation	O
.	O

Interestingly	O
,	O
a	O
crystal	B-evidence
structure	I-evidence
was	O
previously	O
reported	O
for	O
a	O
functionally	O
-	O
uncharacterized	O
meningococcal	B-taxonomy_domain
homologue	O
of	O
NadR	B-protein
,	O
termed	O
NMB1585	B-protein
,	O
which	O
shares	O
16	O
%	O
sequence	O
identity	O
with	O
NadR	B-protein
.	O
The	O
two	O
structures	B-evidence
can	O
be	O
closely	O
aligned	O
(	O
rmsd	B-evidence
2	O
.	O
3	O
Å	O
),	O
but	O
NMB1585	B-protein
appears	O
unsuited	O
for	O
binding	O
HPAs	B-chemical
,	O
since	O
its	O
corresponding	O
‘	B-site
pocket	I-site
’	O
region	O
is	O
occupied	O
by	O
several	O
bulky	O
hydrophobic	O
side	O
chains	O
.	O

It	O
can	O
be	O
speculated	O
that	O
MarR	B-protein_type
family	O
members	O
have	O
evolved	O
separately	O
to	O
engage	O
distinct	O
signaling	O
molecules	O
,	O
thus	O
enabling	O
bacteria	B-taxonomy_domain
to	O
use	O
the	O
overall	O
conserved	O
MarR	B-protein_type
scaffold	O
to	O
adapt	O
and	O
respond	O
to	O
diverse	O
changing	O
environmental	O
stimuli	O
experienced	O
in	O
their	O
natural	O
niches	O
.	O

Alternatively	O
,	O
it	O
is	O
possible	O
that	O
other	O
MarR	B-protein_type
homologues	O
(	O
e	O
.	O
g	O
.	O
NMB1585	B-protein
)	O
may	O
have	O
no	O
extant	O
functional	O
binding	B-site
pocket	I-site
and	O
thus	O
may	O
have	O
lost	O
the	O
ability	O
to	O
respond	O
to	O
a	O
ligand	O
,	O
acting	O
instead	O
as	O
constitutive	O
DNA	B-chemical
-	O
binding	O
regulatory	O
proteins	O
.	O

The	O
apo	B-protein_state
-	O
NadR	B-protein
crystal	B-evidence
structures	I-evidence
revealed	O
two	O
dimers	B-oligomeric_state
with	O
slightly	O
different	O
conformations	O
,	O
most	O
divergent	O
in	O
the	O
DNA	B-structure_element
-	I-structure_element
binding	I-structure_element
domain	I-structure_element
.	O

It	O
is	O
not	O
unusual	O
for	O
a	O
crystal	B-evidence
structure	I-evidence
to	O
reveal	O
multiple	O
copies	O
of	O
the	O
same	O
protein	O
in	O
very	O
slightly	O
different	O
conformations	O
,	O
which	O
are	O
likely	O
representative	O
of	O
the	O
lowest	O
-	O
energy	O
conformations	O
sampled	O
by	O
the	O
dynamic	O
ensemble	O
of	O
molecular	O
states	O
occurring	O
in	O
solution	O
,	O
and	O
which	O
likely	O
have	O
only	O
small	O
energetic	O
differences	O
,	O
as	O
described	O
previously	O
for	O
MexR	B-protein
(	O
a	O
MarR	B-protein_type
protein	O
)	O
or	O
more	O
recently	O
for	O
the	O
solute	B-protein_type
-	I-protein_type
binding	I-protein_type
protein	I-protein_type
FhuD2	B-protein
.	O

Further	O
,	O
the	O
holo	B-protein_state
-	O
NadR	B-protein
structure	B-evidence
was	O
overall	O
more	O
different	O
from	O
the	O
two	O
apo	B-protein_state
-	O
NadR	B-protein
structures	B-evidence
(	O
rmsd	B-evidence
values	O
~	O
1	O
.	O
3Å	O
),	O
suggesting	O
that	O
the	O
ligand	O
selected	O
and	O
stabilized	O
yet	O
another	O
conformation	O
of	O
NadR	B-protein
.	O
These	O
observations	O
suggest	O
that	O
4	B-chemical
-	I-chemical
HPA	I-chemical
,	O
and	O
potentially	O
other	O
similar	O
ligands	O
,	O
can	O
shift	O
the	O
molecular	O
equilibrium	O
,	O
changing	O
the	O
energy	O
barriers	O
that	O
separate	O
active	B-protein_state
and	O
inactive	B-protein_state
states	O
,	O
and	O
stabilizing	O
the	O
specific	O
conformation	O
of	O
NadR	B-protein
poorly	O
suited	O
to	O
bind	O
DNA	B-chemical
.	O

Comparisons	O
of	O
the	O
apo	B-protein_state
-	O
and	O
holo	B-protein_state
-	O
NadR	B-protein
structures	B-evidence
revealed	O
that	O
the	O
largest	O
differences	O
occurred	O
in	O
the	O
DNA	B-chemical
-	O
binding	O
helix	B-structure_element
α4	B-structure_element
.	O

The	O
shift	O
of	O
helix	B-structure_element
α4	B-structure_element
in	O
holo	B-protein_state
-	O
NadR	B-protein
was	O
also	O
accompanied	O
by	O
rearrangements	O
at	O
the	O
dimer	B-site
interface	I-site
,	O
involving	O
helices	B-structure_element
α1	B-structure_element
,	O
α5	B-structure_element
,	O
and	O
α6	B-structure_element
,	O
and	O
this	O
holo	B-protein_state
-	O
form	O
appeared	O
poorly	O
suited	O
for	O
DNA	B-chemical
-	O
binding	O
when	O
compared	O
with	O
the	O
known	O
OhrR	B-complex_assembly
:	I-complex_assembly
ohrA	I-complex_assembly
complex	O
.	O

While	O
some	O
flexibility	O
of	O
helix	B-structure_element
α4	B-structure_element
was	O
also	O
observed	O
in	O
the	O
two	O
apo	B-protein_state
-	O
structures	B-evidence
,	O
concomitant	O
changes	O
in	O
the	O
dimer	B-site
interfaces	I-site
were	O
not	O
observed	O
,	O
possibly	O
due	O
to	O
the	O
absence	B-protein_state
of	I-protein_state
ligand	I-protein_state
.	O

One	O
of	O
the	O
two	O
conformations	O
of	O
apo	B-protein_state
-	O
NadR	B-protein
appeared	O
ideally	O
suited	O
for	O
DNA	B-chemical
-	O
binding	O
.	O

Overall	O
,	O
these	O
analyses	O
suggest	O
that	O
the	O
apo	B-protein_state
-	O
NadR	B-protein
dimer	B-oligomeric_state
has	O
a	O
pre	O
-	O
existing	O
equilibrium	O
that	O
samples	O
a	O
variety	O
of	O
conformations	O
,	O
some	O
of	O
which	O
are	O
compatible	O
with	O
DNA	B-chemical
binding	O
.	O

The	O
noted	O
flexibility	O
may	O
also	O
explain	O
how	O
NadR	B-protein
can	O
adapt	O
to	O
bind	O
various	O
DNA	B-chemical
target	O
sequences	O
with	O
slightly	O
different	O
structural	O
features	O
.	O

Subsequently	O
,	O
upon	O
ligand	O
binding	O
,	O
holo	B-protein_state
-	O
NadR	B-protein
adopts	O
a	O
structure	O
less	O
suited	O
for	O
DNA	B-chemical
-	O
binding	O
and	O
this	O
conformation	O
is	O
selected	O
and	O
stabilized	O
by	O
a	O
network	O
of	O
protein	O
-	O
ligand	O
interactions	O
and	O
concomitant	O
rearrangements	O
at	O
the	O
NadR	B-protein
holo	B-protein_state
dimer	B-site
interface	I-site
.	O

In	O
an	O
alternative	O
and	O
less	O
extensive	O
manner	O
,	O
the	O
binding	O
of	O
two	O
salicylate	B-chemical
molecules	O
to	O
the	O
M	B-species
.	I-species
thermoautotrophicum	I-species
protein	O
MTH313	B-protein
appeared	O
to	O
induce	O
large	O
changes	O
in	O
the	O
wHTH	B-structure_element
domain	I-structure_element
,	O
which	O
was	O
associated	O
with	O
reduced	O
DNA	O
-	O
binding	O
activity	O
.	O

Here	O
we	O
have	O
presented	O
two	O
new	O
crystal	B-evidence
structures	I-evidence
of	O
the	O
transcription	B-protein_type
factor	I-protein_type
,	O
NadR	B-protein
,	O
which	O
regulates	O
expression	O
of	O
the	O
meningococcal	B-taxonomy_domain
surface	O
protein	O
,	O
virulence	O
factor	O
and	O
vaccine	O
antigen	O
NadA	B-protein
.	O
Detailed	O
structural	B-experimental_method
analyses	I-experimental_method
provided	O
a	O
molecular	O
explanation	O
for	O
the	O
ligand	O
-	O
responsive	O
regulation	O
by	O
NadR	B-protein
on	O
the	O
majority	O
of	O
the	O
promoters	O
of	O
meningococcal	B-taxonomy_domain
genes	O
regulated	O
by	O
NadR	B-protein
,	O
including	O
nadA	B-gene
.	O
Intriguingly	O
,	O
NadR	B-protein
exhibits	O
a	O
reversed	O
regulatory	O
mechanism	O
on	O
a	O
second	O
class	O
of	O
promoters	O
,	O
including	O
mafA	B-gene
of	O
the	O
multiple	O
adhesin	O
family	O
–	O
i	O
.	O
e	O
.	O
NadR	B-protein
represses	O
these	O
genes	O
in	O
the	O
presence	O
but	O
not	O
absence	O
of	O
4	B-chemical
-	I-chemical
HPA	I-chemical
.	O

The	O
latter	O
may	O
influence	O
the	O
surface	O
abundance	O
or	O
secretion	O
of	O
maf	O
proteins	O
,	O
an	O
emerging	O
class	O
of	O
highly	B-protein_state
conserved	I-protein_state
meningococcal	B-taxonomy_domain
putative	O
adhesins	O
and	O
toxins	O
with	O
many	O
important	O
roles	O
.	O

Further	O
work	O
is	O
required	O
to	O
investigate	O
how	O
the	O
two	O
different	O
promoter	O
types	O
influence	O
the	O
ligand	O
-	O
responsiveness	O
of	O
NadR	B-protein
during	O
bacterial	B-taxonomy_domain
infection	O
and	O
may	O
provide	O
insights	O
into	O
the	O
regulatory	O
mechanisms	O
occurring	O
during	O
these	O
host	O
-	O
pathogen	O
interactions	O
.	O

Ultimately	O
,	O
knowledge	O
of	O
the	O
ligand	O
-	O
dependent	O
activity	O
of	O
NadR	B-protein
will	O
continue	O
to	O
deepen	O
our	O
understanding	O
of	O
nadA	B-gene
expression	O
levels	O
,	O
which	O
influence	O
meningococcal	B-taxonomy_domain
pathogenesis	O
.	O

Structure	O
of	O
an	O
OhrR	O
-	O
ohrA	B-gene
operator	O
complex	O
reveals	O
the	O
DNA	O
binding	O
mechanism	O
of	O
the	O
MarR	O
family	O

The	O
structure	O
of	O
NMB1585	B-protein
,	O
a	O
MarR	O
-	O
family	O
regulator	O
from	O
Neisseria	O
meningitidis	O

The	O
Structural	O
Basis	O
of	O
Coenzyme	B-chemical
A	I-chemical
Recycling	O
in	O
a	O
Bacterial	B-taxonomy_domain
Organelle	O

Bacterial	B-taxonomy_domain
Microcompartments	B-complex_assembly
(	O
BMCs	B-complex_assembly
)	O
are	O
proteinaceous	O
organelles	O
that	O
encapsulate	O
critical	O
segments	O
of	O
autotrophic	O
and	O
heterotrophic	O
metabolic	O
pathways	O
;	O
they	O
are	O
functionally	O
diverse	O
and	O
are	O
found	O
across	O
23	O
different	O
phyla	O
.	O

The	O
majority	O
of	O
catabolic	B-protein_state
BMCs	B-complex_assembly
(	O
metabolosomes	B-complex_assembly
)	O
compartmentalize	O
a	O
common	O
core	O
of	O
enzymes	O
to	O
metabolize	O
compounds	O
via	O
a	O
toxic	O
and	O
/	O
or	O
volatile	O
aldehyde	B-chemical
intermediate	O
.	O

The	O
core	O
enzyme	O
phosphotransacylase	B-protein_type
(	O
PTAC	B-protein_type
)	O
recycles	O
Coenzyme	B-chemical
A	I-chemical
and	O
generates	O
an	O
acyl	B-chemical
phosphate	I-chemical
that	O
can	O
serve	O
as	O
an	O
energy	O
source	O
.	O

The	O
PTAC	B-protein_type
predominantly	O
associated	O
with	O
metabolosomes	B-complex_assembly
(	O
PduL	B-protein_type
)	O
has	O
no	O
sequence	O
homology	O
to	O
the	O
PTAC	B-protein_type
ubiquitous	O
among	O
fermentative	B-taxonomy_domain
bacteria	I-taxonomy_domain
(	O
Pta	B-protein_type
).	O

Here	O
,	O
we	O
report	O
two	O
high	O
-	O
resolution	O
PduL	B-protein_type
crystal	B-evidence
structures	I-evidence
with	B-protein_state
bound	I-protein_state
substrates	I-protein_state
.	O

The	O
PduL	B-protein_type
fold	B-structure_element
is	O
unrelated	O
to	O
that	B-structure_element
of	O
Pta	B-protein_type
;	O
it	O
contains	O
a	O
dimetal	B-site
active	I-site
site	I-site
involved	O
in	O
a	O
catalytic	O
mechanism	O
distinct	O
from	O
that	O
of	O
the	O
housekeeping	B-protein_state
PTAC	B-protein_type
.	O

Accordingly	O
,	O
PduL	B-protein_type
and	O
Pta	B-protein_type
exemplify	O
functional	O
,	O
but	O
not	O
structural	O
,	O
convergent	O
evolution	O
.	O

The	O
PduL	B-protein_type
structure	B-evidence
,	O
in	O
the	O
context	O
of	O
the	O
catalytic	O
core	O
,	O
completes	O
our	O
understanding	O
of	O
the	O
structural	O
basis	O
of	O
cofactor	O
recycling	O
in	O
the	O
metabolosome	B-complex_assembly
lumen	O
.	O

This	O
study	O
describes	O
the	O
structure	B-evidence
of	O
a	O
novel	O
phosphotransacylase	B-protein_type
enzyme	O
that	O
facilitates	O
the	O
recycling	O
of	O
the	O
essential	O
cofactor	O
acetyl	B-chemical
-	I-chemical
CoA	I-chemical
within	O
a	O
bacterial	B-taxonomy_domain
organelle	O
and	O
discusses	O
the	O
properties	O
of	O
the	O
enzyme	O
'	O
s	O
active	B-site
site	I-site
and	O
how	O
it	O
is	O
packaged	O
into	O
the	O
organelle	O
.	O

In	O
metabolism	O
,	O
molecules	O
with	O
“	O
high	O
-	O
energy	O
”	O
bonds	O
(	O
e	O
.	O
g	O
.,	O
ATP	B-chemical
and	O
Acetyl	B-chemical
~	I-chemical
CoA	I-chemical
)	O
are	O
critical	O
for	O
both	O
catabolic	O
and	O
anabolic	O
processes	O
.	O

The	O
phosphotransacylase	B-protein_type
(	O
Pta	B-protein_type
)	O
enzyme	O
catalyzes	O
the	O
conversion	O
between	O
acyl	B-chemical
-	I-chemical
CoA	I-chemical
and	O
acyl	B-chemical
-	I-chemical
phosphate	I-chemical
.	O

This	O
reaction	O
directly	O
links	O
an	O
acyl	B-chemical
-	I-chemical
CoA	I-chemical
with	O
ATP	B-chemical
generation	O
via	O
substrate	O
-	O
level	O
phosphorylation	O
,	O
producing	O
short	B-chemical
-	I-chemical
chain	I-chemical
fatty	I-chemical
acids	I-chemical
(	O
e	O
.	O
g	O
.,	O
acetate	B-chemical
),	O
and	O
also	O
provides	O
a	O
path	O
for	O
short	B-chemical
-	I-chemical
chain	I-chemical
fatty	I-chemical
acids	I-chemical
to	O
enter	O
central	O
metabolism	O
.	O

Due	O
to	O
this	O
key	O
function	O
,	O
Pta	O
is	O
conserved	B-protein_state
across	O
the	O
bacterial	B-taxonomy_domain
kingdom	I-taxonomy_domain
.	O

Recently	O
,	O
a	O
new	O
type	O
of	O
phosphotransacylase	B-protein_type
was	O
described	O
that	O
shares	O
no	O
evolutionary	O
relation	O
to	O
Pta	B-protein_type
.	O

This	O
enzyme	O
,	O
PduL	B-protein_type
,	O
is	O
exclusively	B-protein_state
associated	O
with	O
organelles	O
called	O
bacterial	B-taxonomy_domain
microcompartments	B-complex_assembly
,	O
which	O
are	O
used	O
to	O
catabolize	O
various	O
compounds	O
.	O

Not	O
only	O
does	O
PduL	B-protein_type
facilitate	O
substrate	O
level	O
phosphorylation	O
,	O
but	O
it	O
also	O
is	O
critical	O
for	O
cofactor	O
recycling	O
within	O
,	O
and	O
product	O
efflux	O
from	O
,	O
the	O
organelle	O
.	O

We	O
solved	B-experimental_method
the	O
structure	B-evidence
of	O
this	O
convergent	B-protein_state
phosphotransacylase	B-protein_type
and	O
show	O
that	O
it	O
is	O
completely	O
structurally	O
different	O
from	O
Pta	B-protein_type
,	O
including	O
its	O
active	B-site
site	I-site
architecture	O
.	O

Bacterial	B-taxonomy_domain
Microcompartments	B-complex_assembly
(	O
BMCs	B-complex_assembly
)	O
are	O
organelles	O
that	O
encapsulate	O
enzymes	O
for	O
sequential	O
biochemical	O
reactions	O
within	O
a	O
protein	O
shell	B-structure_element
.	O

The	O
shell	B-structure_element
is	O
typically	O
composed	O
of	O
three	O
types	O
of	O
protein	O
subunits	O
,	O
which	O
form	O
either	O
hexagonal	B-protein_state
(	O
BMC	B-complex_assembly
-	I-complex_assembly
H	I-complex_assembly
and	O
BMC	B-complex_assembly
-	I-complex_assembly
T	I-complex_assembly
)	O
or	O
pentagonal	B-protein_state
(	O
BMC	B-complex_assembly
-	I-complex_assembly
P	I-complex_assembly
)	O
tiles	O
that	O
assemble	O
into	O
a	O
polyhedral	B-protein_state
shell	B-structure_element
.	O

The	O
facets	O
of	O
the	O
shell	B-structure_element
are	O
composed	O
primarily	O
of	O
hexamers	B-oligomeric_state
that	O
are	O
typically	O
perforated	O
by	O
pores	B-site
lined	O
with	O
highly	B-protein_state
conserved	I-protein_state
,	O
polar	B-protein_state
residues	B-structure_element
that	O
presumably	O
function	O
as	O
the	O
conduits	O
for	O
metabolites	O
into	O
and	O
out	O
of	O
the	O
shell	B-structure_element
.	O

The	O
vitamin	B-complex_assembly
B12	I-complex_assembly
-	I-complex_assembly
dependent	I-complex_assembly
propanediol	I-complex_assembly
-	I-complex_assembly
utilizing	I-complex_assembly
(	I-complex_assembly
PDU	I-complex_assembly
)	I-complex_assembly
BMC	I-complex_assembly
was	O
one	O
of	O
the	O
first	O
functionally	O
characterized	O
catabolic	B-protein_state
BMCs	B-complex_assembly
;	O
subsequently	O
,	O
other	O
types	O
have	O
been	O
implicated	O
in	O
the	O
degradation	O
of	O
ethanolamine	B-chemical
,	O
choline	B-chemical
,	O
fucose	B-chemical
,	O
rhamnose	B-chemical
,	O
and	O
ethanol	B-chemical
,	O
all	O
of	O
which	O
produce	O
different	O
aldehyde	B-chemical
intermediates	O
(	O
Table	O
1	O
).	O

More	O
recently	O
,	O
bioinformatic	B-experimental_method
studies	I-experimental_method
have	O
demonstrated	O
the	O
widespread	O
distribution	O
of	O
BMCs	B-complex_assembly
among	O
diverse	O
bacterial	B-taxonomy_domain
phyla	I-taxonomy_domain
and	O
grouped	O
them	O
into	O
23	O
different	O
functional	O
types	O
.	O

The	O
reactions	O
carried	O
out	O
in	O
the	O
majority	O
of	O
catabolic	B-protein_state
BMCs	B-complex_assembly
(	O
also	O
known	O
as	O
metabolosomes	B-complex_assembly
)	O
fit	O
a	O
generalized	O
biochemical	O
paradigm	O
for	O
the	O
oxidation	O
of	O
aldehydes	B-chemical
(	O
Fig	O
1	O
).	O

This	O
involves	O
a	O
BMC	B-complex_assembly
-	O
encapsulated	O
signature	O
enzyme	O
that	O
generates	O
a	O
toxic	O
and	O
/	O
or	O
volatile	O
aldehyde	B-chemical
that	O
the	O
BMC	B-complex_assembly
shell	B-structure_element
sequesters	O
from	O
the	O
cytosol	O
.	O

The	O
aldehyde	B-chemical
is	O
subsequently	O
converted	O
into	O
an	O
acyl	B-chemical
-	I-chemical
CoA	I-chemical
by	O
aldehyde	B-protein_type
dehydrogenase	I-protein_type
,	O
which	O
uses	O
NAD	B-chemical
+	I-chemical
and	O
CoA	B-chemical
as	O
cofactors	O
.	O

These	O
two	O
cofactors	O
are	O
relatively	O
large	O
,	O
and	O
their	O
diffusion	O
across	O
the	O
protein	B-structure_element
shell	I-structure_element
is	O
thought	O
to	O
be	O
restricted	O
,	O
necessitating	O
their	O
regeneration	O
within	O
the	O
BMC	B-complex_assembly
lumen	O
.	O

NAD	B-chemical
+	I-chemical
is	O
recycled	O
via	O
alcohol	B-protein_type
dehydrogenase	I-protein_type
,	O
and	O
CoA	B-chemical
is	O
recycled	O
via	O
phosphotransacetylase	B-protein_type
(	O
PTAC	B-protein_type
)	O
(	O
Fig	O
1	O
).	O

The	O
final	O
product	O
of	O
the	O
BMC	B-complex_assembly
,	O
an	O
acyl	B-chemical
-	I-chemical
phosphate	I-chemical
,	O
can	O
then	O
be	O
used	O
to	O
generate	O
ATP	B-chemical
via	O
acyl	B-protein_type
kinase	I-protein_type
,	O
or	O
revert	O
back	O
to	O
acyl	B-chemical
-	I-chemical
CoA	I-chemical
by	O
Pta	B-protein_type
for	O
biosynthesis	O
.	O

Collectively	O
,	O
the	O
aldehyde	B-protein_type
and	I-protein_type
alcohol	I-protein_type
dehydrogenases	I-protein_type
,	O
as	O
well	O
as	O
the	O
PTAC	B-protein_type
,	O
constitute	O
the	O
common	O
metabolosome	B-complex_assembly
core	O
.	O

General	O
biochemical	O
model	O
of	O
aldehyde	B-protein_state
-	I-protein_state
degrading	I-protein_state
BMCs	B-complex_assembly
(	O
metabolosomes	B-complex_assembly
)	O
illustrating	O
the	O
common	O
metabolosome	B-complex_assembly
core	O
enzymes	O
and	O
reactions	O
.	O

Substrates	O
and	O
cofactors	O
involving	O
the	O
PTAC	B-protein_type
reaction	O
are	O
shown	O
in	O
red	O
;	O
other	O
substrates	O
and	O
enzymes	O
are	O
shown	O
in	O
black	O
,	O
and	O
other	O
cofactors	O
are	O
shown	O
in	O
gray	O
.	O

Characterized	O
and	O
predicted	O
catabolic	B-protein_state
BMC	B-complex_assembly
(	O
metabolosome	B-complex_assembly
)	O
types	O
that	O
represent	O
the	O
aldehyde	B-chemical
-	O
degrading	O
paradigm	O
(	O
for	O
definition	O
of	O
types	O
see	O
Kerfeld	O
and	O
Erbilgin	O
).	O

Name	O
PTAC	B-protein_type
Type	O
Sequestered	O
Aldehyde	B-chemical
PDU	B-complex_assembly
*	O
PduL	B-protein_type
propionaldehyde	B-chemical
EUT1	B-complex_assembly
PTA_PTB	B-protein_type
acetaldehyde	B-chemical
EUT2	B-complex_assembly
PduL	B-protein_type
acetaldehyde	B-chemical
ETU	B-complex_assembly
None	O
acetaldehyde	B-chemical
GRM1	B-complex_assembly
/	I-complex_assembly
CUT	I-complex_assembly
PduL	B-protein_type
acetaldehyde	B-chemical
GRM2	B-complex_assembly
PduL	B-protein_type
acetaldehyde	B-chemical
GRM3	B-complex_assembly
*,	I-complex_assembly
4	I-complex_assembly
PduL	B-protein_type
propionaldehyde	B-chemical
GRM5	B-complex_assembly
/	I-complex_assembly
GRP	I-complex_assembly
PduL	B-protein_type
propionaldehyde	B-chemical
PVM	B-complex_assembly
*	O
PduL	B-protein_type
lactaldehyde	B-chemical
RMM1	B-complex_assembly
,	I-complex_assembly
2	I-complex_assembly
None	O
unknown	O
SPU	B-complex_assembly
PduL	B-protein_type
unknown	O

*	O
PduL	B-protein_type
from	O
these	O
functional	O
types	O
of	O
metabolosomes	B-complex_assembly
were	O
purified	O
in	O
this	O
study	O
.	O

The	O
activities	O
of	O
core	O
enzymes	O
are	O
not	O
confined	O
to	O
BMC	B-complex_assembly
-	O
associated	O
functions	O
:	O
aldehyde	B-protein_type
and	I-protein_type
alcohol	I-protein_type
dehydrogenases	I-protein_type
are	O
utilized	O
in	O
diverse	O
metabolic	O
reactions	O
,	O
and	O
PTAC	B-protein_type
catalyzes	O
a	O
key	O
biochemical	O
reaction	O
in	O
the	O
process	O
of	O
obtaining	O
energy	O
during	O
fermentation	O
.	O

The	O
concerted	O
functioning	O
of	O
a	O
PTAC	B-protein_type
and	O
an	O
acetate	B-protein_type
kinase	I-protein_type
(	O
Ack	B-protein_type
)	O
is	O
crucial	O
for	O
ATP	B-chemical
generation	O
in	O
the	O
fermentation	O
of	O
pyruvate	B-chemical
to	O
acetate	B-chemical
(	O
see	O
Reactions	O
1	O
and	O
2	O
).	O

Both	O
enzymes	O
are	O
,	O
however	O
,	O
not	O
restricted	O
to	O
fermentative	B-taxonomy_domain
organisms	I-taxonomy_domain
.	O

They	O
can	O
also	O
work	O
in	O
the	O
reverse	O
direction	O
to	O
activate	O
acetate	B-chemical
to	O
the	O
CoA	B-chemical
-	I-chemical
thioester	I-chemical
.	O

This	O
occurs	O
,	O
for	O
example	O
,	O
during	O
acetoclastic	O
methanogenesis	O
in	O
the	O
archaeal	B-taxonomy_domain
Methanosarcina	B-taxonomy_domain
species	I-taxonomy_domain
.	O

Reaction	O
1	O
:	O
acetyl	B-chemical
-	I-chemical
S	I-chemical
-	I-chemical
CoA	I-chemical
+	O
Pi	B-chemical
←→	O
acetyl	B-chemical
phosphate	I-chemical
+	O
CoA	B-chemical
-	I-chemical
SH	I-chemical
(	O
PTAC	B-protein_type
)	O

Reaction	O
2	O
:	O
acetyl	B-chemical
phosphate	I-chemical
+	O
ADP	B-chemical
←→	O
acetate	B-chemical
+	O
ATP	B-chemical
(	O
Ack	B-protein_type
)	O

The	O
canonical	O
PTAC	B-protein_type
,	O
Pta	B-protein_type
,	O
is	O
an	O
ancient	O
enzyme	O
found	O
in	O
some	O
eukaryotes	B-taxonomy_domain
and	O
archaea	B-taxonomy_domain
,	O
and	O
widespread	O
among	O
the	O
bacteria	B-taxonomy_domain
;	O
90	O
%	O
of	O
the	O
bacterial	B-taxonomy_domain
genomes	O
in	O
the	O
Integrated	O
Microbial	O
Genomes	O
database	O
contain	O
a	O
gene	O
encoding	O
the	O
PTA_PTB	B-protein_type
phosphotransacylase	I-protein_type
(	O
Pfam	O
domain	O
PF01515	B-structure_element
).	O

Pta	B-protein_type
has	O
been	O
extensively	O
characterized	O
due	O
to	O
its	O
key	O
role	O
in	O
fermentation	O
.	O

More	O
recently	O
,	O
a	O
second	O
type	O
of	O
PTAC	B-protein_type
without	O
any	O
sequence	O
homology	O
to	O
Pta	B-protein_type
was	O
identified	O
.	O

This	O
protein	O
,	O
PduL	B-protein_type
(	O
Pfam	O
domain	O
PF06130	B-structure_element
),	O
was	O
shown	O
to	O
catalyze	O
the	O
conversion	O
of	O
propionyl	B-chemical
-	I-chemical
CoA	I-chemical
to	O
propionyl	B-chemical
-	I-chemical
phosphate	I-chemical
and	O
is	O
associated	O
with	O
a	O
BMC	B-complex_assembly
involved	O
in	O
propanediol	O
utilization	O
,	O
the	O
PDU	B-complex_assembly
BMC	I-complex_assembly
.	O

Both	O
pduL	B-gene
and	O
pta	B-gene
genes	O
can	O
be	O
found	O
in	O
genetic	O
loci	O
of	O
functionally	O
distinct	O
BMCs	B-complex_assembly
,	O
although	O
the	O
PduL	B-protein_type
type	O
is	O
much	O
more	O
prevalent	O
,	O
being	O
found	O
in	O
all	O
but	O
one	O
type	O
of	O
metabolosome	B-gene
locus	I-gene
:	O
EUT1	B-gene
(	O
Table	O
1	O
).	O

Furthermore	O
,	O
in	O
the	O
Integrated	O
Microbial	O
Genomes	O
Database	O
,	O
91	O
%	O
of	O
genomes	O
that	O
encode	O
PF06130	B-structure_element
also	O
encode	O
genes	O
for	O
shell	O
proteins	O
.	O

As	O
a	O
member	O
of	O
the	O
core	O
biochemical	O
machinery	O
of	O
functionally	O
diverse	O
aldehyde	B-protein_state
-	I-protein_state
oxidizing	I-protein_state
metabolosomes	B-complex_assembly
,	O
PduL	B-protein_type
must	O
have	O
a	O
certain	O
level	O
of	O
substrate	O
plasticity	O
(	O
see	O
Table	O
1	O
)	O
that	O
is	O
not	O
required	O
of	O
Pta	B-protein_type
,	O
which	O
has	O
generally	O
been	O
observed	O
to	O
prefer	O
acetyl	B-chemical
-	I-chemical
CoA	I-chemical
.	O
PduL	B-protein_type
from	O
the	O
PDU	B-complex_assembly
BMC	I-complex_assembly
of	O
Salmonella	B-species
enterica	I-species
favors	O
propionyl	B-chemical
-	I-chemical
CoA	I-chemical
over	O
acetyl	B-chemical
-	I-chemical
CoA	I-chemical
,	O
and	O
it	O
is	O
likely	O
that	O
PduL	B-protein_type
orthologs	O
in	O
functionally	O
diverse	O
BMCs	B-complex_assembly
would	O
have	O
substrate	O
preferences	O
for	O
other	O
CoA	B-chemical
derivatives	O
.	O

Another	O
distinctive	O
feature	O
of	O
BMC	B-protein_state
-	I-protein_state
associated	I-protein_state
PduL	B-protein_type
homologs	O
is	O
an	O
N	O
-	O
terminal	O
encapsulation	B-structure_element
peptide	I-structure_element
(	O
EP	B-structure_element
)	O
that	O
is	O
thought	O
to	O
“	O
target	O
”	O
proteins	O
for	O
encapsulation	O
by	O
the	O
BMC	B-complex_assembly
shell	B-structure_element
.	O

EPs	B-structure_element
are	O
frequently	O
found	O
on	O
BMC	B-protein_type
-	I-protein_type
associated	I-protein_type
proteins	I-protein_type
and	O
have	O
been	O
shown	O
to	O
interact	O
with	O
shell	O
proteins	O
.	O

EPs	B-structure_element
have	O
also	O
been	O
observed	O
to	O
cause	O
proteins	O
to	O
aggregate	O
,	O
and	O
this	O
has	O
recently	O
been	O
suggested	O
to	O
be	O
functionally	O
relevant	O
as	O
an	O
initial	O
step	O
in	O
metabolosome	B-complex_assembly
assembly	O
,	O
in	O
which	O
a	O
multifunctional	O
protein	O
core	O
is	O
formed	O
,	O
around	O
which	O
the	O
shell	B-structure_element
assembles	O
.	O

Of	O
the	O
three	O
common	O
metabolosome	B-complex_assembly
core	O
enzymes	O
,	O
crystal	B-evidence
structures	I-evidence
are	O
available	O
for	O
both	O
the	O
alcohol	B-protein_type
and	I-protein_type
aldehyde	I-protein_type
dehydrogenases	I-protein_type
.	O

In	O
contrast	O
,	O
the	O
structure	B-evidence
of	O
PduL	B-protein_type
,	O
the	O
PTAC	B-protein_type
found	O
in	O
the	O
vast	O
majority	O
of	O
catabolic	B-protein_state
BMCs	B-complex_assembly
,	O
has	O
not	O
been	O
determined	O
.	O

This	O
is	O
a	O
major	O
gap	O
in	O
our	O
understanding	O
of	O
metabolosome	B-complex_assembly
-	O
encapsulated	O
biochemistry	O
and	O
cofactor	O
recycling	O
.	O

Moreover	O
,	O
it	O
will	O
be	O
useful	O
for	O
guiding	O
efforts	O
to	O
engineer	O
novel	O
BMC	B-complex_assembly
cores	O
for	O
biotechnological	O
applications	O
.	O

The	O
primary	O
structure	O
of	O
PduL	B-protein_type
homologs	O
is	O
subdivided	O
into	O
two	O
PF06130	B-structure_element
domains	O
,	O
each	O
roughly	O
80	B-residue_range
residues	I-residue_range
in	I-residue_range
length	I-residue_range
.	O

No	O
available	O
protein	O
structures	O
contain	O
the	O
PF06130	B-structure_element
domain	O
,	O
and	O
homology	B-experimental_method
searches	I-experimental_method
using	O
the	O
primary	O
structure	O
of	O
PduL	B-protein_type
do	O
not	O
return	O
any	O
significant	O
results	O
that	O
would	O
allow	O
prediction	O
of	O
the	O
structure	B-evidence
.	O

Moreover	O
,	O
the	O
evident	O
novelty	O
of	O
PduL	B-protein_type
makes	O
its	O
structure	B-evidence
interesting	O
in	O
the	O
context	O
of	O
convergent	O
evolution	O
of	O
PTAC	B-protein_type
function	O
;	O
to	O
-	O
date	O
,	O
only	O
the	O
Pta	B-protein_type
active	B-site
site	I-site
and	O
catalytic	O
mechanism	O
is	O
known	O
.	O

Here	O
we	O
report	O
high	O
-	O
resolution	O
crystal	B-evidence
structures	I-evidence
of	O
a	O
PduL	B-protein_type
-	I-protein_type
type	I-protein_type
PTAC	I-protein_type
in	O
both	O
CoA	B-protein_state
-	I-protein_state
and	O
phosphate	B-protein_state
-	I-protein_state
bound	I-protein_state
forms	O
,	O
completing	O
our	O
understanding	O
of	O
the	O
structural	O
basis	O
of	O
catalysis	O
by	O
the	O
metabolosome	B-complex_assembly
common	O
core	O
enzymes	O
.	O

We	O
propose	O
a	O
catalytic	O
mechanism	O
analogous	O
but	O
yet	O
distinct	O
from	O
the	O
ubiquitous	O
Pta	B-protein_type
enzyme	O
,	O
highlighting	O
the	O
functional	O
convergence	O
of	O
two	O
enzymes	O
with	O
completely	O
different	O
structures	O
and	O
metal	O
requirements	O
.	O

We	O
also	O
investigate	O
the	O
quaternary	O
structures	O
of	O
three	O
different	O
PduL	B-protein_type
homologs	O
and	O
situate	O
our	O
findings	O
in	O
the	O
context	O
of	O
organelle	O
biogenesis	O
in	O
functionally	O
diverse	O
BMCs	B-complex_assembly
.	O

Structure	B-experimental_method
Determination	I-experimental_method
of	O
PduL	B-protein_type

We	O
cloned	B-experimental_method
,	I-experimental_method
expressed	I-experimental_method
,	I-experimental_method
and	I-experimental_method
purified	I-experimental_method
three	O
different	O
PduL	B-protein_type
homologs	O
from	O
functionally	O
distinct	O
BMCs	B-complex_assembly
(	O
Table	O
1	O
):	O
from	O
the	O
well	O
-	O
studied	O
pdu	B-gene
locus	I-gene
in	O
S	B-species
.	I-species
enterica	I-species
Typhimurium	I-species
LT2	I-species
(	O
sPduL	B-protein
),	O
from	O
the	O
recently	O
characterized	O
pvm	B-gene
locus	I-gene
in	O
Planctomyces	B-species
limnophilus	I-species
(	O
pPduL	B-protein
),	O
and	O
from	O
the	O
grm3	B-gene
locus	I-gene
in	O
Rhodopseudomonas	B-species
palustris	I-species
BisB18	I-species
(	O
rPduL	B-protein
).	O

While	O
purifying	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
sPduL	B-protein
,	O
we	O
observed	O
a	O
tendency	O
to	O
aggregation	O
as	O
described	O
previously	O
,	O
with	O
a	O
large	O
fraction	O
of	O
the	O
expressed	O
protein	O
found	O
in	O
the	O
insoluble	O
fraction	O
in	O
a	O
white	O
,	O
cake	O
-	O
like	O
pellet	O
.	O

Remarkably	O
,	O
after	O
removing	B-experimental_method
the	O
N	O
-	O
terminal	O
putative	O
EP	B-structure_element
(	O
27	B-residue_range
amino	I-residue_range
acids	I-residue_range
),	O
most	O
of	O
the	O
sPduLΔEP	B-mutant
protein	O
was	O
in	O
the	O
soluble	O
fraction	O
upon	O
cell	O
lysis	O
.	O

Similar	O
differences	O
in	O
solubility	O
were	O
observed	O
for	O
pPduL	B-protein
and	O
rPduL	B-protein
when	O
comparing	O
EP	B-protein_state
-	I-protein_state
truncated	I-protein_state
forms	O
to	O
the	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
protein	O
,	O
but	O
none	O
were	O
quite	O
as	O
dramatic	O
as	O
for	O
sPduL	B-protein
.	O
We	O
confirmed	O
that	O
all	O
homologs	O
were	O
active	B-protein_state
(	O
S1a	O
and	O
S1b	O
Fig	O
).	O

Among	O
these	O
,	O
we	O
were	O
only	O
able	O
to	O
obtain	O
diffraction	B-evidence
-	I-evidence
quality	I-evidence
crystals	I-evidence
of	O
rPduL	B-protein
after	O
removing	B-experimental_method
the	O
N	O
-	O
terminal	O
putative	O
EP	B-structure_element
(	O
33	B-residue_range
amino	I-residue_range
acids	I-residue_range
,	O
also	O
see	O
Fig	O
2a	O
)	O
(	O
rPduLΔEP	B-mutant
).	O

Truncated	B-protein_state
rPduLΔEP	B-mutant
had	O
comparable	O
enzymatic	O
activity	O
to	O
the	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
enzyme	O
(	O
S1a	O
Fig	O
).	O

Structural	O
overview	O
of	O
R	B-species
.	I-species
palustris	I-species
PduL	B-protein_type
from	O
the	O
grm3	B-gene
locus	I-gene
.	O

(	O
a	O
)	O
Primary	O
and	O
secondary	O
structure	O
of	O
rPduL	B-protein
(	O
tubes	O
represent	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
,	O
arrows	O
β	B-structure_element
-	I-structure_element
sheets	I-structure_element
and	O
dashed	O
line	O
residues	O
disordered	O
in	O
the	O
structure	B-evidence
.	O

The	O
first	B-residue_range
33	I-residue_range
amino	I-residue_range
acids	I-residue_range
are	O
present	O
only	O
in	O
the	O
wildtype	O
construct	O
and	O
contains	O
the	O
predicted	O
EP	B-structure_element
alpha	B-structure_element
helix	I-structure_element
,	O
α0	B-structure_element
);	O
the	O
truncated	B-protein_state
rPduLΔEP	B-mutant
that	O
was	O
crystallized	B-experimental_method
begins	O
with	O
M	B-residue_name
-	O
G	B-residue_name
-	O
V	B-residue_name
.	O
Coloring	O
is	O
according	O
to	O
structural	O
domains	O
(	O
domain	B-structure_element
1	I-structure_element
D36	B-residue_range
-	I-residue_range
N46	I-residue_range
/	O
Q155	B-residue_range
-	I-residue_range
C224	I-residue_range
,	O
blue	O
;	O
loop	B-structure_element
insertion	I-structure_element
G61	B-residue_range
-	I-residue_range
E81	I-residue_range
,	O
grey	O
;	O
domain	B-structure_element
2	I-structure_element
R47	B-residue_range
-	I-residue_range
F60	I-residue_range
/	O
E82	B-residue_range
-	I-residue_range
A154	I-residue_range
,	O
red	O
).	O

Metal	B-site
coordination	I-site
residues	I-site
are	O
highlighted	O
in	O
light	O
blue	O
and	O
CoA	B-site
contacting	I-site
residues	I-site
in	O
magenta	O
,	O
residues	O
contacting	O
the	O
CoA	B-chemical
of	O
the	O
other	O
chain	O
are	O
also	O
outlined	O
.	O

(	O
b	O
)	O
Cartoon	O
representation	O
of	O
the	O
structure	B-evidence
colored	O
by	O
domains	O
and	O
including	O
secondary	O
structure	B-evidence
numbering	O
.	O

Coenzyme	B-chemical
A	I-chemical
is	O
shown	O
in	O
magenta	O
sticks	O
and	O
Zinc	B-chemical
(	O
grey	O
)	O
as	O
spheres	O
.	O

We	O
collected	B-experimental_method
a	I-experimental_method
native	I-experimental_method
dataset	I-experimental_method
from	O
rPduLΔEP	B-mutant
crystals	B-evidence
diffracting	O
to	O
a	O
resolution	O
of	O
1	O
.	O
54	O
Å	O
(	O
Table	O
2	O
).	O

Using	O
a	O
mercury	B-experimental_method
-	I-experimental_method
derivative	I-experimental_method
crystal	I-experimental_method
form	O
diffracting	O
to	O
1	O
.	O
99	O
Å	O
(	O
Table	O
2	O
),	O
we	O
obtained	O
high	O
quality	O
electron	B-evidence
density	I-evidence
for	O
model	O
building	O
and	O
used	O
the	O
initial	O
model	O
to	O
refine	O
against	O
the	O
native	O
data	O
to	O
Rwork	B-evidence
/	O
Rfree	B-evidence
values	O
of	O
18	O
.	O
9	O
/	O
22	O
.	O
1	O
%.	O

There	O
are	O
two	O
PduL	B-protein_type
molecules	O
in	O
the	O
asymmetric	O
unit	O
of	O
the	O
P212121	O
unit	O
cell	O
.	O

We	O
were	O
able	O
to	O
fit	O
all	O
of	O
the	O
primary	O
structure	O
of	O
PduLΔEP	B-mutant
into	O
the	O
electron	B-evidence
density	I-evidence
with	O
the	O
exception	O
of	O
three	O
amino	O
acids	O
at	O
the	O
N	O
-	O
terminus	O
and	O
two	O
amino	O
acids	O
at	O
the	O
C	O
-	O
terminus	O
(	O
Fig	O
2a	O
);	O
the	O
model	O
is	O
of	O
excellent	O
quality	O
(	O
Table	O
2	O
).	O

A	O
CoA	B-chemical
cofactor	O
as	O
well	O
as	O
two	O
metal	O
ions	O
are	O
clearly	O
resolved	O
in	O
the	O
density	B-evidence
(	O
for	O
omit	B-evidence
maps	I-evidence
of	O
CoA	B-chemical
see	O
S2	O
Fig	O
).	O

Structurally	O
,	O
PduL	B-protein_type
consists	O
of	O
two	O
domains	B-structure_element
(	O
Fig	O
2	O
,	O
blue	O
/	O
red	O
),	O
each	O
a	O
beta	B-structure_element
-	I-structure_element
barrel	I-structure_element
that	O
is	O
capped	O
on	O
both	O
ends	O
by	O
short	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
.	O

β	B-structure_element
-	I-structure_element
Barrel	I-structure_element
1	I-structure_element
consists	O
of	O
the	O
N	O
-	O
terminal	O
β	B-structure_element
strand	I-structure_element
and	O
β	B-structure_element
strands	I-structure_element
from	O
the	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
half	I-structure_element
of	O
the	O
polypeptide	O
chain	O
(	O
β1	B-structure_element
,	O
β10	B-structure_element
-	I-structure_element
β14	I-structure_element
;	O
residues	O
37	B-residue_range
–	I-residue_range
46	I-residue_range
and	O
155	B-residue_range
–	I-residue_range
224	I-residue_range
).	O

β	B-structure_element
-	I-structure_element
Barrel	I-structure_element
2	I-structure_element
consists	O
mainly	O
of	O
the	O
central	O
segment	O
of	O
primary	O
structure	O
(	O
β2	B-structure_element
,	O
β5	B-structure_element
–	I-structure_element
β9	I-structure_element
;	O
residues	O
47	B-residue_range
–	I-residue_range
60	I-residue_range
and	O
82	B-residue_range
–	I-residue_range
154	I-residue_range
)	O
(	O
Fig	O
2	O
,	O
red	O
),	O
but	O
is	O
interrupted	O
by	O
a	O
short	B-structure_element
two	I-structure_element
-	I-structure_element
strand	I-structure_element
beta	I-structure_element
sheet	I-structure_element
(	O
β3	B-structure_element
-	I-structure_element
β4	I-structure_element
,	O
residues	O
61	B-residue_range
–	I-residue_range
81	I-residue_range
).	O

This	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
is	O
involved	O
in	O
contacts	O
between	O
the	O
two	O
domains	O
and	O
forms	O
a	O
lid	O
over	O
the	O
active	B-site
site	I-site
.	O

Residues	O
in	O
this	O
region	O
(	O
Gln42	B-residue_name_number
,	O
Pro43	B-residue_name_number
,	O
Gly44	B-residue_name_number
),	O
covering	O
the	O
active	B-site
site	I-site
,	O
are	O
strongly	B-protein_state
conserved	I-protein_state
(	O
Fig	O
3	O
).	O

This	O
structural	O
arrangement	O
is	O
completely	O
different	O
from	O
the	O
functionally	O
related	O
Pta	B-protein_type
,	O
which	O
is	O
composed	O
of	O
two	O
domains	B-structure_element
,	O
each	O
consisting	O
of	O
a	O
central	O
flat	O
beta	B-structure_element
sheet	I-structure_element
with	O
alpha	B-structure_element
-	I-structure_element
helices	I-structure_element
on	O
the	O
top	O
and	O
bottom	O
.	O

Primary	O
structure	O
conservation	O
of	O
the	O
PduL	B-protein_type
protein	O
family	O
.	O

Sequence	O
logo	O
calculated	O
from	O
the	O
multiple	B-experimental_method
sequence	I-experimental_method
alignment	I-experimental_method
of	O
PduL	B-protein_type
homologs	O
(	O
see	O
Materials	O
and	O
Methods	O
),	O
but	O
not	B-protein_state
including	I-protein_state
putative	O
EP	B-structure_element
sequences	O
.	O

Residues	O
100	O
%	O
conserved	O
across	O
all	O
PduL	B-protein_type
homologs	O
in	O
our	O
dataset	O
are	O
noted	O
with	O
an	O
asterisk	O
,	O
and	O
residues	O
conserved	O
in	O
over	O
90	O
%	O
of	O
sequences	O
are	O
noted	O
with	O
a	O
colon	O
.	O

The	O
sequences	O
aligning	O
to	O
the	O
PF06130	B-structure_element
domain	O
(	O
determined	O
by	O
BLAST	O
)	O
are	O
highlighted	O
in	O
red	O
and	O
blue	O
.	O

The	O
position	O
numbers	O
shown	O
correspond	O
to	O
the	O
residue	O
numbering	O
of	O
rPduL	B-protein
;	O
note	O
that	O
some	O
positions	O
in	O
the	O
logo	O
represent	O
gaps	O
in	O
the	O
rPduL	B-protein
sequence	O
.	O

There	O
are	O
two	O
PduL	B-protein_type
molecules	O
in	O
the	O
asymmetric	O
unit	O
forming	O
a	O
butterfly	B-protein_state
-	I-protein_state
shaped	I-protein_state
dimer	B-oligomeric_state
(	O
Fig	O
4c	O
).	O

Consistent	O
with	O
this	O
,	O
results	O
from	O
size	B-experimental_method
exclusion	I-experimental_method
chromatography	I-experimental_method
of	O
rPduLΔEP	B-mutant
suggest	O
that	O
it	O
is	O
a	O
dimer	B-oligomeric_state
in	O
solution	O
(	O
Fig	O
5e	O
).	O

The	O
interface	B-site
between	O
the	O
two	O
chains	O
buries	O
882	O
Å2	O
per	O
monomer	B-oligomeric_state
and	O
is	O
mainly	O
formed	O
by	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
2	I-structure_element
and	I-structure_element
4	I-structure_element
and	O
parts	O
of	O
β	B-structure_element
-	I-structure_element
sheets	I-structure_element
12	I-structure_element
and	I-structure_element
14	I-structure_element
,	O
as	O
well	O
as	O
a	O
π	O
–	O
π	O
stacking	O
of	O
the	O
adenine	B-chemical
moiety	O
of	O
CoA	B-chemical
with	O
Phe116	B-residue_name_number
of	O
the	O
adjacent	O
chain	O
(	O
Fig	O
4c	O
).	O

The	O
folds	O
of	O
the	O
two	O
chains	O
in	O
the	O
asymmetric	O
unit	O
are	O
very	O
similar	O
,	O
superimposing	B-experimental_method
with	O
a	O
rmsd	B-evidence
of	O
0	O
.	O
16	O
Å	O
over	O
2	O
,	O
306	O
aligned	O
atom	O
pairs	O
.	O

The	O
peripheral	O
helices	B-structure_element
and	O
the	O
short	B-structure_element
antiparallel	I-structure_element
β3	I-structure_element
–	I-structure_element
4	I-structure_element
sheet	I-structure_element
mediate	O
most	O
of	O
the	O
crystal	O
contacts	O
.	O

Details	O
of	O
active	B-site
site	I-site
,	O
dimeric	B-oligomeric_state
assembly	O
,	O
and	O
sequence	O
conservation	O
of	O
PduL	B-protein_type
.	O

(	O
a	O
,	O
b	O
)	O
Proposed	O
active	B-site
site	I-site
of	O
PduL	B-protein_type
with	O
relevant	O
residues	O
shown	O
as	O
sticks	O
in	O
atom	O
coloring	O
(	O
nitrogen	B-chemical
blue	O
,	O
oxygen	B-chemical
red	O
,	O
sulfur	B-chemical
yellow	O
),	O
zinc	B-chemical
as	O
grey	O
colored	O
spheres	O
and	O
coordinating	O
ordered	O
water	B-chemical
molecules	O
in	O
red	O
.	O

Distances	O
between	O
atom	O
centers	O
are	O
indicated	O
in	O
Å	O
.	O
(	O
a	O
)	O
Coenzyme	B-chemical
A	I-chemical
containing	O
,	O
(	O
b	O
)	O
phosphate	B-protein_state
-	I-protein_state
bound	I-protein_state
structure	B-evidence
.	O

(	O
c	O
)	O
View	O
of	O
the	O
dimer	B-oligomeric_state
in	O
the	O
asymmetric	O
unit	O
from	O
the	O
side	O
,	O
domains	B-structure_element
1	I-structure_element
and	I-structure_element
2	I-structure_element
colored	O
as	O
in	O
Fig	O
2	O
and	O
the	O
two	O
chains	O
differentiated	O
by	O
blue	O
/	O
red	O
versus	O
slate	O
/	O
firebrick	O
.	O

The	O
asterisk	O
and	O
double	O
arrow	O
marks	O
the	O
location	O
of	O
the	O
π	O
–	O
π	O
interaction	O
between	O
F116	B-residue_name_number
and	O
the	O
CoA	B-chemical
base	O
of	O
the	O
other	O
dimer	B-oligomeric_state
chain	O
.	O

(	O
d	O
)	O
Surface	O
representation	O
of	O
the	O
structure	B-evidence
with	O
indicated	O
conservation	O
(	O
red	O
:	O
high	O
,	O
white	O
:	O
intermediate	O
,	O
yellow	O
:	O
low	O
).	O

Size	B-experimental_method
exclusion	I-experimental_method
chromatography	I-experimental_method
of	O
PduL	B-protein_type
homologs	O
.	O

(	O
a	O
)–(	O
c	O
):	O
Chromatograms	B-evidence
of	O
sPduL	B-protein
(	O
a	O
),	O
rPduL	B-protein
(	O
b	O
),	O
and	O
pPduL	B-protein
(	O
c	O
)	O
with	O
(	O
orange	O
)	O
or	O
without	O
(	O
blue	O
)	O
the	O
predicted	O
EP	B-structure_element
,	O
post	O
-	O
nickel	B-experimental_method
affinity	I-experimental_method
purification	I-experimental_method
,	O
applied	O
over	O
a	O
preparative	O
size	O
exclusion	O
column	O
(	O
see	O
Materials	O
and	O
Methods	O
).	O

(	O
d	O
)–(	O
f	O
):	O
Chromatograms	B-evidence
of	O
sPduL	B-protein
(	O
d	O
),	O
rPduL	B-protein
(	O
e	O
),	O
and	O
pPduL	B-protein
(	O
f	O
)	O
post	O
-	O
preparative	O
size	B-experimental_method
exclusion	I-experimental_method
chromatography	I-experimental_method
with	O
different	O
size	O
fractions	O
separated	O
,	O
applied	O
over	O
an	O
analytical	O
size	O
exclusion	O
column	O
(	O
see	O
Materials	O
and	O
Methods	O
).	O

All	O
chromatograms	B-evidence
are	O
cropped	O
to	O
show	O
only	O
the	O
linear	O
range	O
of	O
separation	O
based	O
on	O
standard	O
runs	O
,	O
shown	O
in	O
black	O
squares	O
with	O
a	O
dashed	O
linear	O
trend	O
line	O
.	O

Active	B-site
Site	I-site
Properties	O

CoA	B-chemical
and	O
the	O
metal	O
ions	O
bind	O
between	O
the	O
two	O
domains	O
,	O
presumably	O
in	O
the	O
active	B-site
site	I-site
(	O
Figs	O
2b	O
and	O
4a	O
).	O

To	O
identify	O
the	O
bound	O
metals	O
,	O
we	O
performed	O
an	O
X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
fluorescence	I-experimental_method
scan	I-experimental_method
on	O
the	O
crystals	B-evidence
at	O
various	O
wavelengths	O
(	O
corresponding	O
to	O
the	O
K	O
-	O
edges	O
of	O
Mn	B-chemical
,	O
Fe	B-chemical
,	O
Co	B-chemical
,	O
Ni	B-chemical
,	O
Cu	B-chemical
,	O
and	O
Zn	B-chemical
).	O

There	O
was	O
a	O
large	O
signal	O
at	O
the	O
zinc	O
edge	O
,	O
and	O
we	O
tested	O
for	O
the	O
presence	O
of	O
zinc	B-chemical
by	O
collecting	B-experimental_method
full	I-experimental_method
data	I-experimental_method
sets	I-experimental_method
before	I-experimental_method
and	I-experimental_method
after	I-experimental_method
the	I-experimental_method
Zn	I-experimental_method
K	I-experimental_method
-	I-experimental_method
edge	I-experimental_method
(	I-experimental_method
1	I-experimental_method
.	I-experimental_method
2861	I-experimental_method
and	I-experimental_method
1	I-experimental_method
.	I-experimental_method
2822	I-experimental_method
Å	I-experimental_method
,	O
respectively	O
).	O

The	O
large	O
differences	O
between	O
the	O
anomalous	O
signals	O
confirm	O
the	O
presence	O
of	O
zinc	B-chemical
at	O
both	O
metal	O
sites	O
(	O
S3	O
Fig	O
).	O

The	O
first	O
zinc	B-chemical
ion	O
(	O
Zn1	B-chemical
)	O
is	O
in	O
a	O
tetrahedral	O
coordination	O
state	O
with	O
His48	B-residue_name_number
,	O
His50	B-residue_name_number
,	O
Glu109	B-residue_name_number
,	O
and	O
the	O
CoA	B-chemical
sulfur	B-chemical
(	O
Fig	O
4a	O
).	O

The	O
second	O
(	O
Zn2	B-chemical
)	O
is	O
in	O
octahedral	O
coordination	O
by	O
three	O
conserved	B-protein_state
histidine	B-residue_name
residues	O
(	O
His157	B-residue_name_number
,	O
His159	B-residue_name_number
and	O
His204	B-residue_name_number
)	O
as	O
well	O
as	O
three	O
water	B-chemical
molecules	O
(	O
Fig	O
4a	O
).	O

The	O
nitrogen	O
atom	O
coordinating	O
the	O
zinc	B-chemical
is	O
the	O
Nε	O
in	O
each	O
histidine	B-residue_name
residue	O
,	O
as	O
is	O
typical	O
for	O
this	O
interaction	O
.	O

When	O
the	O
crystals	B-experimental_method
were	I-experimental_method
soaked	I-experimental_method
in	O
a	O
sodium	B-chemical
phosphate	I-chemical
solution	O
for	O
2	O
d	O
prior	O
to	O
data	O
collection	O
,	O
the	O
CoA	B-chemical
dissociates	O
,	O
and	O
density	B-evidence
for	O
a	O
phosphate	B-chemical
molecule	O
is	O
visible	O
at	O
the	O
active	B-site
site	I-site
(	O
Table	O
2	O
,	O
Fig	O
4b	O
).	O

The	O
phosphate	B-protein_state
-	I-protein_state
bound	I-protein_state
structure	B-evidence
aligns	B-experimental_method
well	O
with	O
the	O
CoA	B-protein_state
-	I-protein_state
bound	I-protein_state
structure	B-evidence
(	O
0	O
.	O
43	O
Å	O
rmsd	B-evidence
over	O
2	O
,	O
361	O
atoms	O
for	O
the	O
monomer	B-oligomeric_state
,	O
0	O
.	O
83	O
Å	O
over	O
5	O
,	O
259	O
aligned	O
atoms	O
for	O
the	O
dimer	B-oligomeric_state
).	O

The	O
phosphate	B-chemical
contacts	O
both	O
zinc	B-chemical
atoms	O
(	O
Fig	O
4b	O
)	O
and	O
replaces	O
the	O
coordination	O
by	O
CoA	B-chemical
at	O
Zn1	B-chemical
;	O
the	O
coordination	O
for	O
Zn2	B-chemical
changes	O
from	O
octahedral	O
with	O
three	O
bound	O
waters	B-chemical
to	O
tetrahedral	O
with	O
a	O
phosphate	B-chemical
ion	O
as	O
one	O
of	O
the	O
ligands	O
(	O
Fig	O
4b	O
).	O

Conserved	B-protein_state
Arg103	B-residue_name_number
seems	O
to	O
be	O
involved	O
in	O
maintaining	O
the	O
phosphate	B-chemical
in	O
that	O
position	O
.	O

The	O
two	O
zinc	B-chemical
atoms	O
are	O
slightly	O
closer	O
together	O
in	O
the	O
phosphate	B-protein_state
-	I-protein_state
bound	I-protein_state
form	O
(	O
5	O
.	O
8	O
Å	O
vs	O
6	O
.	O
3	O
Å	O
),	O
possibly	O
due	O
to	O
the	O
bridging	O
effect	O
of	O
the	O
phosphate	B-chemical
.	O

An	O
additional	O
phosphate	B-chemical
molecule	O
is	O
bound	O
at	O
a	O
crystal	O
contact	O
interface	O
,	O
perhaps	O
accounting	O
for	O
the	O
14	O
Å	O
shorter	O
c	O
-	O
axis	O
in	O
the	O
phosphate	B-protein_state
-	I-protein_state
bound	I-protein_state
crystal	O
form	O
(	O
Table	O
2	O
).	O

Oligomeric	O
States	O
of	O
PduL	B-protein_type
Orthologs	O
Are	O
Influenced	O
by	O
the	O
EP	B-structure_element

Interestingly	O
,	O
some	O
of	O
the	O
residues	O
important	O
for	O
dimerization	O
of	O
rPduL	B-protein
,	O
particularly	O
Phe116	B-residue_name_number
,	O
are	O
poorly	B-protein_state
conserved	I-protein_state
across	O
PduL	B-protein_type
homologs	O
associated	O
with	O
functionally	O
diverse	O
BMCs	B-complex_assembly
(	O
Figs	O
4c	O
and	O
3	O
),	O
suggesting	O
that	O
they	O
may	O
have	O
alternative	O
oligomeric	O
states	O
.	O

We	O
tested	O
this	O
hypothesis	O
by	O
performing	O
size	B-experimental_method
exclusion	I-experimental_method
chromatography	I-experimental_method
on	O
both	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
and	O
truncated	O
variants	O
(	O
lacking	B-protein_state
the	O
EP	B-structure_element
,	O
ΔEP	B-mutant
)	O
of	O
sPduL	B-protein
,	O
rPduL	B-protein
,	O
and	O
pPduL	B-protein
.	O
These	O
three	O
homologs	O
are	O
found	O
in	O
functionally	O
distinct	O
BMCs	B-complex_assembly
(	O
Table	O
1	O
).	O

It	O
has	O
been	O
proposed	O
that	O
the	O
catabolic	B-protein_state
BMCs	B-complex_assembly
may	O
assemble	O
in	O
a	O
core	O
-	O
first	O
manner	O
,	O
with	O
the	O
luminal	O
enzymes	O
(	O
signature	O
enzyme	O
,	O
aldehyde	B-protein_type
,	I-protein_type
and	I-protein_type
alcohol	I-protein_type
dehydrogenases	I-protein_type
and	O
the	O
BMC	B-complex_assembly
PTAC	B-protein_type
)	O
forming	O
an	O
initial	O
bolus	O
,	O
or	O
prometabolosome	O
,	O
around	O
which	O
a	O
shell	B-structure_element
assembles	O
.	O

Given	O
the	O
diversity	O
of	O
signature	O
enzymes	O
(	O
Table	O
1	O
),	O
it	O
is	O
plausible	O
that	O
PduL	B-protein_type
orthologs	O
may	O
adopt	O
different	O
oligomeric	O
states	O
that	O
reflect	O
the	O
differences	O
in	O
the	O
proteins	O
being	O
packaged	O
with	O
them	O
in	O
the	O
organelle	O
lumen	O
.	O

We	O
found	O
that	O
not	O
only	O
did	O
the	O
different	O
orthologs	O
appear	O
to	O
assemble	O
into	O
different	O
oligomeric	O
states	O
,	O
but	O
that	O
quaternary	O
structure	O
was	O
dependent	O
on	O
whether	O
or	O
not	O
the	O
EP	B-structure_element
was	O
present	O
.	O

Full	B-protein_state
-	I-protein_state
length	I-protein_state
sPduL	B-protein
was	O
unstable	O
in	O
solution	O
—	O
precipitating	O
over	O
time	O
—	O
and	O
eluted	O
throughout	O
the	O
entire	O
volume	O
of	O
a	O
size	O
exclusion	O
column	O
,	O
indicating	O
it	O
was	O
nonspecifically	O
aggregating	O
.	O

However	O
,	O
when	O
the	O
putative	O
EP	B-structure_element
(	O
residues	O
1	B-residue_range
–	I-residue_range
27	I-residue_range
)	O
was	O
removed	B-experimental_method
(	O
sPduL	B-mutant
ΔEP	I-mutant
),	O
the	O
truncated	B-protein_state
protein	O
was	O
stable	O
and	O
eluted	O
as	O
a	O
single	O
peak	O
(	O
Fig	O
5a	O
)	O
consistent	O
with	O
the	O
size	O
of	O
a	O
monomer	B-oligomeric_state
(	O
Fig	O
5d	O
,	O
blue	O
curve	O
).	O

In	O
contrast	O
,	O
both	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
rPduL	B-protein
and	O
pPduL	B-protein
appeared	O
to	O
exist	O
in	O
two	O
distinct	O
oligomeric	O
states	O
(	O
Fig	O
5b	O
and	O
5c	O
respectively	O
,	O
orange	O
curves	O
),	O
one	O
form	O
of	O
the	O
approximate	O
size	O
of	O
a	O
dimer	B-oligomeric_state
and	O
the	O
second	O
,	O
a	O
higher	O
molecular	O
weight	O
oligomer	B-oligomeric_state
(~	O
150	O
kDa	O
).	O

Upon	O
deletion	B-experimental_method
of	O
the	O
putative	O
EP	B-structure_element
(	O
residues	O
1	B-residue_range
–	I-residue_range
47	I-residue_range
for	O
rPduL	B-protein
,	O
and	O
1	B-residue_range
–	I-residue_range
20	I-residue_range
for	O
pPduL	B-protein
),	O
there	O
was	O
a	O
distinct	O
change	O
in	O
the	O
elution	O
profiles	O
(	O
Fig	O
5b	O
and	O
5c	O
respectively	O
,	O
blue	O
curves	O
).	O

pPduLΔEP	B-mutant
eluted	O
as	O
two	O
smaller	O
forms	O
,	O
possibly	O
corresponding	O
to	O
a	O
trimer	B-oligomeric_state
and	O
a	O
monomer	B-oligomeric_state
.	O

In	O
contrast	O
,	O
rPduLΔEP	B-mutant
eluted	O
as	O
one	O
smaller	O
oligomer	O
,	O
possibly	O
a	O
dimer	B-oligomeric_state
.	O

We	O
also	O
analyzed	O
purified	O
rPduL	B-protein
and	O
rPduLΔEP	B-mutant
by	O
size	B-experimental_method
exclusion	I-experimental_method
chromatography	I-experimental_method
coupled	O
with	O
multiangle	B-experimental_method
light	I-experimental_method
scattering	I-experimental_method
(	O
SEC	B-experimental_method
-	I-experimental_method
MALS	I-experimental_method
)	O
for	O
a	O
complementary	O
approach	O
to	O
assessing	O
oligomeric	O
state	O
.	O

SEC	B-experimental_method
-	I-experimental_method
MALS	I-experimental_method
analysis	O
of	O
rPdulΔEP	B-mutant
is	O
consistent	O
with	O
a	O
dimer	B-oligomeric_state
(	O
as	O
observed	O
in	O
the	O
crystal	B-evidence
structure	I-evidence
)	O
with	O
a	O
weighted	B-evidence
average	I-evidence
(	I-evidence
Mw	I-evidence
)	I-evidence
and	I-evidence
number	I-evidence
average	I-evidence
(	I-evidence
Mn	I-evidence
)	I-evidence
of	I-evidence
the	I-evidence
molar	I-evidence
mass	I-evidence
of	O
58	O
.	O
4	O
kDa	O
+/−	O
11	O
.	O
2	O
%	O
and	O
58	O
.	O
8	O
kDa	O
+/−	O
10	O
.	O
9	O
%,	O
respectively	O
(	O
S4a	O
Fig	O
).	O

rPduL	B-protein
full	B-protein_state
length	I-protein_state
runs	O
as	O
Mw	B-evidence
=	O
140	O
.	O
3	O
kDa	O
+/−	O
1	O
.	O
2	O
%	O
and	O
Mn	B-evidence
=	O
140	O
.	O
5	O
kDa	O
+/−	O
1	O
.	O
2	O
%.	O

This	O
corresponds	O
to	O
an	O
oligomeric	O
state	O
of	O
six	B-oligomeric_state
subunits	I-oligomeric_state
(	O
calculated	O
molecular	B-evidence
weight	I-evidence
of	O
144	O
kDa	O
).	O

Collectively	O
,	O
these	O
data	O
strongly	O
suggest	O
that	O
the	O
N	O
-	O
terminal	O
EP	B-structure_element
of	O
PduL	B-protein_type
plays	O
a	O
role	O
in	O
defining	O
the	O
quaternary	O
structure	O
of	O
the	O
protein	O
.	O

The	O
BMC	B-complex_assembly
shell	B-structure_element
not	O
only	O
sequesters	O
specific	O
enzymes	O
but	O
also	O
their	O
cofactors	O
,	O
thereby	O
establishing	O
a	O
private	O
cofactor	O
pool	O
dedicated	O
to	O
the	O
encapsulated	O
reactions	O
.	O

In	O
catabolic	B-protein_state
BMCs	B-complex_assembly
,	O
CoA	B-chemical
and	O
NAD	B-chemical
+	I-chemical
must	O
be	O
continually	O
recycled	O
within	O
the	O
organelle	O
(	O
Fig	O
1	O
).	O

Homologs	O
of	O
the	O
predominant	O
cofactor	O
utilizer	O
(	O
aldehyde	B-protein_type
dehydrogenase	I-protein_type
)	O
and	O
NAD	B-chemical
+	I-chemical
regenerator	O
(	O
alcohol	B-protein_type
dehydrogenase	I-protein_type
)	O
have	O
been	O
structurally	O
characterized	O
,	O
but	O
until	O
now	O
structural	O
information	O
was	O
lacking	O
for	O
PduL	B-protein_type
,	O
which	O
recycles	O
CoA	B-chemical
in	O
the	O
organelle	O
lumen	O
.	O

Curiously	O
,	O
while	O
the	O
housekeeping	B-protein_state
Pta	B-protein_type
could	O
provide	O
this	O
function	O
,	O
and	O
indeed	O
does	O
so	O
in	O
the	O
case	O
of	O
one	O
type	O
of	O
ethanolamine	B-complex_assembly
-	I-complex_assembly
utilizing	I-complex_assembly
(	I-complex_assembly
EUT	I-complex_assembly
)	I-complex_assembly
BMC	I-complex_assembly
,	O
the	O
evolutionarily	O
unrelated	O
PduL	B-protein_type
fulfills	O
this	O
function	O
for	O
the	O
majority	O
of	O
metabolosomes	B-complex_assembly
using	O
a	O
novel	O
structure	B-evidence
and	O
active	B-site
site	I-site
for	O
convergent	O
evolution	O
of	O
function	O
.	O

The	O
Tertiary	O
Structure	O
of	O
PduL	B-protein_type
Is	O
Formed	O
by	O
Discontinuous	O
Segments	O
of	O
Primary	O
Structure	O

The	O
structure	B-evidence
of	O
PduL	B-protein_type
consists	O
of	O
two	B-structure_element
β	I-structure_element
-	I-structure_element
barrel	I-structure_element
domains	I-structure_element
capped	O
by	O
short	B-structure_element
alpha	I-structure_element
helical	I-structure_element
segments	I-structure_element
(	O
Fig	O
2b	O
).	O

The	O
two	O
domains	O
are	O
structurally	O
very	O
similar	O
(	O
superimposing	B-experimental_method
with	O
a	O
rmsd	B-evidence
of	O
1	O
.	O
34	O
Å	O
(	O
over	O
123	O
out	O
of	O
320	O
/	O
348	O
aligned	O
backbone	O
atoms	O
,	O
S5a	O
Fig	O
).	O

However	O
,	O
the	O
amino	O
acid	O
sequences	O
of	O
the	O
two	O
domains	O
are	O
only	O
16	O
%	O
identical	O
(	O
mainly	O
the	O
RHxH	B-structure_element
motif	I-structure_element
,	O
β2	B-structure_element
and	O
β10	B-structure_element
),	O
and	O
34	O
%	O
similar	O
.	O

Our	O
structure	B-evidence
reveals	O
that	O
the	O
two	O
assigned	O
PF06130	B-structure_element
domains	O
(	O
Fig	O
3	O
)	O
do	O
not	O
form	O
structurally	O
discrete	O
units	O
;	O
this	O
reduces	O
the	O
apparent	O
sequence	O
conservation	O
at	O
the	O
level	O
of	O
primary	O
structure	O
.	O

One	O
strand	B-structure_element
of	O
the	O
domain	B-structure_element
1	I-structure_element
beta	B-structure_element
barrel	I-structure_element
(	O
shown	O
in	O
blue	O
in	O
Fig	O
2	O
)	O
is	O
contributed	O
by	O
the	O
N	O
-	O
terminus	O
,	O
while	O
the	O
rest	O
of	O
the	O
domain	O
is	O
formed	O
by	O
the	O
residues	O
from	O
the	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
half	I-structure_element
of	O
the	O
protein	B-protein_type
.	O

When	O
aligned	B-experimental_method
by	O
structure	B-evidence
,	O
the	O
β1	B-structure_element
strand	I-structure_element
of	O
the	O
first	B-structure_element
domain	I-structure_element
(	O
Fig	O
2a	O
and	O
2b	O
,	O
blue	O
)	O
corresponds	O
to	O
the	O
final	B-structure_element
strand	I-structure_element
of	O
the	O
second	B-structure_element
domain	I-structure_element
(	O
β9	B-structure_element
),	O
effectively	O
making	O
the	O
domains	O
continuous	O
if	O
the	O
first	O
strand	O
was	O
transplanted	O
to	O
the	O
C	O
-	O
terminus	O
.	O

Refined	O
domain	O
assignment	O
based	O
on	O
our	O
structure	B-evidence
should	O
be	O
able	O
to	O
predict	O
domains	O
of	O
PF06130	B-structure_element
homologs	O
much	O
more	O
accurately	O
.	O

The	O
closest	O
structural	O
homolog	O
of	O
the	O
PduL	B-protein_type
barrel	B-structure_element
domain	I-structure_element
is	O
a	O
subdomain	O
of	O
a	O
multienzyme	O
complex	O
,	O
the	O
alpha	B-structure_element
subunit	I-structure_element
of	O
ethylbenzene	B-protein_type
dehydrogenase	I-protein_type
(	O
S5b	O
Fig	O
,	O
rmsd	B-evidence
of	O
2	O
.	O
26	O
Å	O
over	O
226	O
aligned	O
atoms	O
consisting	O
of	O
one	O
beta	B-structure_element
barrel	I-structure_element
and	O
one	O
capping	B-structure_element
helix	I-structure_element
).	O

In	O
contrast	O
to	O
PduL	B-protein_type
,	O
there	O
is	O
only	O
one	O
barrel	B-structure_element
present	O
in	O
ethylbenzene	B-protein_type
dehydrogenase	I-protein_type
,	O
and	O
there	O
is	O
no	O
comparable	O
active	B-site
site	I-site
arrangement	O
.	O

The	O
PduL	B-protein_type
signature	O
primary	O
structure	O
,	O
two	O
PF06130	B-structure_element
domains	O
,	O
occurs	O
in	O
some	O
multidomain	O
proteins	O
,	O
most	O
of	O
them	O
annotated	O
as	O
Acks	B-protein_type
,	O
suggesting	O
that	O
PduL	B-protein_type
may	O
also	O
replace	O
Pta	B-protein_type
in	O
variants	O
of	O
the	O
phosphotransacetylase	B-protein_type
-	O
Ack	B-protein_type
pathway	O
.	O

These	O
PduL	B-protein_type
homologs	O
lack	B-protein_state
EPs	B-structure_element
,	O
and	O
their	B-protein_type
fusion	O
to	O
Ack	B-protein_type
may	O
have	O
evolved	O
as	O
a	O
way	O
to	O
facilitate	O
substrate	O
channeling	O
between	O
the	O
two	O
enzymes	O
.	O

Implications	O
for	O
Metabolosome	B-complex_assembly
Core	O
Assembly	O

For	O
BMC	B-complex_assembly
-	O
encapsulated	O
proteins	O
to	O
properly	O
function	O
together	O
,	O
they	O
must	O
be	O
targeted	O
to	O
the	O
lumen	O
and	O
assemble	O
into	O
an	O
organization	O
that	O
facilitates	O
substrate	O
/	O
product	O
channeling	O
among	O
the	O
different	O
catalytic	B-site
sites	I-site
of	O
the	O
signature	O
and	O
core	O
enzymes	O
.	O

The	O
N	B-structure_element
-	I-structure_element
terminal	I-structure_element
extension	I-structure_element
on	O
PduL	B-protein_type
homologs	O
may	O
serve	O
both	O
of	O
these	O
functions	O
.	O

The	B-structure_element
extension	I-structure_element
shares	O
many	O
features	O
with	O
previously	O
characterized	O
EPs	B-structure_element
:	O
it	O
is	O
present	O
only	O
in	O
homologs	O
associated	O
with	O
BMC	B-gene
loci	I-gene
,	O
and	O
it	O
is	O
predicted	O
to	O
form	O
an	O
amphipathic	B-protein_state
α	B-structure_element
-	I-structure_element
helix	I-structure_element
.	O

Moreover	O
,	O
its	O
removal	B-experimental_method
affects	O
the	O
oligomeric	O
state	O
of	O
the	O
protein	O
.	O

EP	B-structure_element
-	O
mediated	O
oligomerization	O
has	O
been	O
observed	O
for	O
the	O
signature	O
and	O
core	O
BMC	B-complex_assembly
enzymes	O
;	O
for	O
example	O
,	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
propanediol	B-protein_type
dehydratase	I-protein_type
and	O
ethanolamine	B-protein_type
ammonia	I-protein_type
-	I-protein_type
lyase	I-protein_type
(	O
signature	O
enzymes	O
for	O
PDU	B-complex_assembly
and	O
EUT	B-complex_assembly
BMCs	I-complex_assembly
)	O
subunits	O
are	O
also	O
insoluble	O
,	O
but	O
become	O
soluble	O
upon	O
removal	O
of	O
the	O
predicted	O
EP	B-structure_element
.	O

sPduL	B-protein
has	O
also	O
previously	O
been	O
reported	O
to	O
localize	O
to	O
inclusion	O
bodies	O
when	O
overexpressed	B-experimental_method
;	O
we	O
show	O
here	O
that	O
this	O
is	O
dependent	O
on	O
the	O
presence	O
of	O
the	O
EP	B-structure_element
.	O

This	O
propensity	O
of	O
the	O
EP	B-structure_element
to	O
cause	O
proteins	O
to	O
form	O
complexes	O
(	O
Fig	O
5	O
)	O
might	O
not	O
be	O
a	O
coincidence	O
,	O
but	O
could	O
be	O
a	O
necessary	O
step	O
in	O
the	O
assembly	O
of	O
BMCs	B-complex_assembly
.	O

Structured	O
aggregation	O
of	O
the	O
core	O
enzymes	O
has	O
been	O
proposed	O
to	O
be	O
the	O
initial	O
step	O
in	O
metabolosome	B-complex_assembly
assembly	O
and	O
is	O
known	O
to	O
be	O
the	O
first	O
step	O
of	O
β	O
-	O
carboxysome	O
biogenesis	O
,	O
where	O
the	O
core	O
enzyme	O
Ribulose	B-protein_type
Bisphosphate	I-protein_type
Carboxylase	I-protein_type
/	I-protein_type
Oxygenase	I-protein_type
(	O
RuBisCO	B-protein_type
)	O
is	O
aggregated	O
by	O
the	O
CcmM	B-protein_type
protein	O
.	O

Likewise	O
,	O
CsoS2	B-protein_type
,	O
a	O
protein	O
in	O
the	O
α	B-complex_assembly
-	I-complex_assembly
carboxysome	I-complex_assembly
core	O
,	O
also	O
aggregates	O
when	O
purified	O
and	O
is	O
proposed	O
to	O
facilitate	O
the	O
nucleation	O
and	O
encapsulation	O
of	O
RuBisCO	B-protein_type
molecules	O
in	O
the	O
lumen	O
of	O
the	O
organelle	O
.	O

This	O
role	O
for	O
EPs	B-structure_element
in	O
BMC	B-complex_assembly
assembly	O
is	O
in	O
addition	O
to	O
their	O
interaction	O
with	O
shell	O
proteins	O
.	O

Moreover	O
,	O
the	O
PduL	B-protein_type
crystal	B-evidence
structures	I-evidence
offer	O
a	O
clue	O
as	O
to	O
how	O
required	O
cofactors	O
enter	O
the	O
BMC	B-complex_assembly
lumen	O
during	O
assembly	O
.	O

Free	O
CoA	B-chemical
and	O
NAD	B-chemical
+/	I-chemical
H	B-chemical
could	O
potentially	O
be	O
bound	O
to	O
the	O
enzymes	O
as	O
the	O
core	O
assembles	O
and	O
is	O
encapsulated	O
.	O

Our	O
PduL	B-protein_type
crystals	B-evidence
contained	O
CoA	B-chemical
that	O
was	O
captured	O
from	O
the	O
Escherichia	B-species
coli	I-species
cytosol	O
,	O
indicating	O
that	O
the	O
“	O
ground	O
state	O
”	O
of	O
PduL	B-protein_type
is	O
in	O
the	O
CoA	B-protein_state
-	I-protein_state
bound	I-protein_state
form	O
;	O
this	O
could	O
provide	O
an	O
elegantly	O
simple	O
means	O
of	O
guaranteeing	O
a	O
1	O
:	O
1	O
ratio	O
of	O
CoA	B-complex_assembly
:	I-complex_assembly
PduL	I-complex_assembly
within	O
the	O
metabolosome	B-complex_assembly
lumen	O
.	O

Active	B-site
Site	I-site
Identification	O
and	O
Structural	O
Insights	O
into	O
Catalysis	O

The	O
active	B-site
site	I-site
of	O
PduL	B-protein_type
is	O
formed	O
at	O
the	O
interface	B-site
of	O
the	O
two	O
structural	O
domains	B-structure_element
(	O
Fig	O
2b	O
).	O

As	O
expected	O
,	O
the	O
amino	O
acid	O
sequence	O
conservation	O
is	O
highest	O
in	O
the	O
region	O
around	O
the	O
proposed	O
active	B-site
site	I-site
(	O
Fig	O
4d	O
);	O
highly	B-protein_state
conserved	I-protein_state
residues	O
are	O
also	O
involved	O
in	O
CoA	B-chemical
binding	O
(	O
Figs	O
2a	O
and	O
3	O
,	O
residues	O
Ser45	B-residue_name_number
,	O
Lys70	B-residue_name_number
,	O
Arg97	B-residue_name_number
,	O
Leu99	B-residue_name_number
,	O
His204	B-residue_name_number
,	O
Asn211	B-residue_name_number
).	O

All	O
of	O
the	O
metal	B-site
-	I-site
coordinating	I-site
residues	I-site
(	O
Fig	O
2a	O
)	O
are	O
absolutely	B-protein_state
conserved	I-protein_state
,	O
implicating	O
them	O
in	O
catalysis	O
or	O
the	O
correct	O
spatial	O
orientation	O
of	O
the	O
substrates	O
.	O

Arg103	B-residue_name_number
,	O
which	O
contacts	O
the	O
phosphate	B-chemical
(	O
Fig	O
4b	O
),	O
is	O
present	O
in	O
all	O
PduL	B-protein_type
homologs	O
.	O

The	O
close	O
resemblance	O
between	O
the	O
structures	O
binding	O
CoA	B-chemical
and	O
phosphate	B-chemical
likely	O
indicates	O
that	O
no	O
large	O
changes	O
in	O
protein	O
conformation	O
are	O
involved	O
in	O
catalysis	O
,	O
and	O
that	O
our	O
crystal	B-evidence
structures	I-evidence
are	O
representative	O
of	O
the	O
active	B-protein_state
form	O
.	O

The	O
native	O
substrate	O
for	O
the	O
forward	O
reaction	O
of	O
rPduL	B-protein
and	O
pPduL	B-protein
,	O
propionyl	B-chemical
-	I-chemical
CoA	I-chemical
,	O
most	O
likely	O
binds	O
to	O
the	O
enzyme	O
in	O
the	O
same	O
way	O
at	O
the	O
observed	O
nucleotide	B-chemical
and	O
pantothenic	B-chemical
acid	I-chemical
moiety	O
,	O
but	O
the	O
propionyl	O
group	O
in	O
the	O
CoA	B-chemical
-	I-chemical
thioester	I-chemical
might	O
point	O
in	O
a	O
different	O
direction	O
.	O

There	O
is	O
a	O
pocket	B-site
nearby	O
the	O
active	B-site
site	I-site
between	O
the	O
well	B-protein_state
-	I-protein_state
conserved	I-protein_state
residues	O
Ser45	B-residue_name_number
and	O
Ala154	B-residue_name_number
,	O
which	O
could	O
accommodate	O
the	O
propionyl	O
group	O
(	O
S6	O
Fig	O
).	O

A	O
homology	B-experimental_method
model	I-experimental_method
of	O
sPduL	B-protein
indicates	O
that	O
the	O
residues	O
making	O
up	O
this	O
pocket	B-site
and	O
the	O
surrounding	O
active	B-site
site	I-site
region	O
are	O
identical	O
to	O
that	O
of	O
rPduL	B-protein
,	O
which	O
is	O
not	O
surprising	O
,	O
because	O
these	O
two	O
homologs	O
presumably	O
have	O
the	O
same	O
propionyl	B-chemical
-	I-chemical
CoA	I-chemical
substrate	O
.	O

The	O
homology	B-experimental_method
model	I-experimental_method
of	O
pPduL	B-protein
also	O
has	O
identical	O
residues	O
making	O
up	O
the	O
pocket	B-site
,	O
but	O
with	O
a	O
key	O
difference	O
in	O
the	O
vicinity	O
of	O
the	O
active	B-site
site	I-site
:	O
Gln77	B-residue_name_number
of	O
rPduL	B-protein
is	O
replaced	O
by	O
a	O
tyrosine	B-residue_name
(	O
Tyr77	B-residue_name_number
)	O
in	O
pPduL	B-protein
.	O
The	O
physiological	O
substrate	O
of	O
pPduL	B-protein
(	O
Table	O
1	O
)	O
is	O
thought	O
to	O
be	O
lactyl	B-chemical
-	I-chemical
CoA	I-chemical
,	O
which	O
contains	O
an	O
additional	O
hydroxyl	O
group	O
relative	O
to	O
propionyl	B-chemical
-	I-chemical
CoA	I-chemical
.	O
The	O
presence	O
of	O
an	O
aromatic	B-protein_state
residue	B-structure_element
at	O
this	O
position	O
may	O
underlie	O
the	O
substrate	O
preference	O
of	O
the	O
PduL	B-protein_type
enzyme	O
from	O
the	O
pvm	B-gene
locus	I-gene
.	O

Indeed	O
,	O
in	O
the	O
majority	O
of	O
PduLs	B-protein_type
encoded	O
in	O
pvm	B-gene
loci	I-gene
,	O
Gln77	B-residue_name_number
is	O
substituted	O
by	O
either	O
a	O
Tyr	B-residue_name
or	O
Phe	B-residue_name
,	O
whereas	O
it	O
is	O
typically	O
a	O
Gln	B-residue_name
or	O
Glu	B-residue_name
in	O
PduLs	B-protein_type
in	O
all	O
other	O
BMC	B-complex_assembly
types	O
that	O
degrade	O
acetyl	B-chemical
-	I-chemical
or	O
propionyl	B-chemical
-	I-chemical
CoA	I-chemical
.	O
A	O
comparison	B-experimental_method
of	O
the	O
PduL	B-protein_type
active	B-site
site	I-site
to	O
that	O
of	O
the	O
functionally	O
identical	O
Pta	B-protein_type
suggests	O
that	O
the	O
two	O
enzymes	O
have	O
distinctly	O
different	O
mechanisms	O
.	O

The	O
catalytic	O
mechanism	O
of	O
Pta	B-protein_type
involves	O
the	O
abstraction	O
of	O
a	O
thiol	O
hydrogen	O
by	O
an	O
aspartate	B-residue_name
residue	O
,	O
resulting	O
in	O
the	O
nucleophilic	O
attack	O
of	O
thiolate	O
upon	O
the	O
carbonyl	O
carbon	O
of	O
acetyl	B-chemical
-	I-chemical
phosphate	I-chemical
,	O
oriented	O
by	O
an	O
arginine	B-residue_name
and	O
stabilized	O
by	O
a	O
serine	B-residue_name
—	O
there	O
are	O
no	O
metals	O
involved	O
.	O

In	O
contrast	O
,	O
in	O
the	O
rPduL	B-protein
structure	B-evidence
,	O
there	O
are	O
no	O
conserved	O
aspartate	B-residue_name
residues	O
in	O
or	O
around	O
the	O
active	B-site
site	I-site
,	O
and	O
the	O
only	O
well	B-protein_state
-	I-protein_state
conserved	I-protein_state
glutamate	B-residue_name
residue	O
in	O
the	O
active	B-site
site	I-site
is	O
involved	O
in	O
coordinating	O
one	O
of	O
the	O
metal	O
ions	O
.	O

These	O
observations	O
strongly	O
suggest	O
that	O
an	O
acidic	B-protein_state
residue	B-structure_element
is	O
not	O
directly	O
involved	O
in	O
catalysis	O
by	O
PduL	B-protein_type
.	O
Instead	O
,	O
the	O
dimetal	B-site
active	I-site
site	I-site
of	O
PduL	B-protein_type
may	O
create	O
a	O
nucleophile	O
from	O
one	O
of	O
the	O
hydroxyl	O
groups	O
on	O
free	O
phosphate	B-chemical
to	O
attack	O
the	O
carbonyl	O
carbon	O
of	O
the	O
thioester	O
bond	O
of	O
an	O
acyl	B-chemical
-	I-chemical
CoA	I-chemical
.	O
In	O
the	O
reverse	O
direction	O
,	O
the	O
metal	O
ion	O
(	O
s	O
)	O
could	O
stabilize	O
the	O
thiolate	O
anion	O
that	O
would	O
attack	O
the	O
carbonyl	O
carbon	O
of	O
an	O
acyl	B-chemical
-	I-chemical
phosphate	I-chemical
;	O
a	O
similar	O
mechanism	O
has	O
been	O
described	O
for	O
phosphatases	B-protein_type
where	O
hydroxyl	O
groups	O
or	O
hydroxide	O
ions	O
can	O
act	O
as	O
a	O
base	O
when	O
coordinated	O
by	O
a	O
dimetal	B-site
active	I-site
site	I-site
.	O

Our	O
structures	B-evidence
provide	O
the	O
foundation	O
for	O
studies	O
to	O
elucidate	O
the	O
details	O
of	O
the	O
catalytic	O
mechanism	O
of	O
PduL	B-protein_type
.	O
Conserved	B-protein_state
residues	O
in	O
the	O
active	B-site
site	I-site
that	O
may	O
contribute	O
to	O
substrate	O
binding	O
and	O
/	O
or	O
transition	O
state	O
stabilization	O
include	O
Ser127	B-residue_name_number
,	O
Arg103	B-residue_name_number
,	O
Arg194	B-residue_name_number
,	O
Gln107	B-residue_name_number
,	O
Gln74	B-residue_name_number
,	O
and	O
Gln	B-residue_name_number
/	O
Glu77	B-residue_name_number
.	O

In	O
the	O
phosphate	B-protein_state
-	I-protein_state
bound	I-protein_state
crystal	B-evidence
structure	I-evidence
,	O
Ser127	B-residue_name_number
and	O
Arg103	B-residue_name_number
appear	O
to	O
position	O
the	O
phosphate	B-chemical
(	O
Fig	O
4b	O
).	O

Alternatively	O
,	O
Arg103	B-residue_name_number
might	O
act	O
as	O
a	O
base	O
to	O
render	O
the	O
phosphate	B-chemical
more	O
nucleophilic	O
.	O

The	O
functional	O
groups	O
of	O
Gln74	B-residue_name_number
,	O
Gln	B-residue_name_number
/	O
Glu77	B-residue_name_number
,	O
and	O
Arg194	B-residue_name_number
are	O
directed	O
away	O
from	O
the	O
active	B-site
site	I-site
in	O
both	O
CoA	B-protein_state
and	O
phosphate	B-protein_state
-	I-protein_state
bound	I-protein_state
crystal	B-evidence
structures	I-evidence
and	O
do	O
not	O
appear	O
to	O
be	O
involved	O
in	O
hydrogen	O
bonding	O
with	O
these	O
substrates	O
,	O
although	O
they	O
could	O
be	O
important	O
for	O
positioning	O
an	O
acyl	B-chemical
-	I-chemical
phosphate	I-chemical
.	O

The	O
free	O
CoA	B-protein_state
-	I-protein_state
bound	I-protein_state
form	O
is	O
presumably	O
poised	O
for	O
attack	O
upon	O
an	O
acyl	B-chemical
-	I-chemical
phosphate	I-chemical
,	O
indicating	O
that	O
the	O
enzyme	O
initially	O
binds	O
CoA	B-chemical
as	O
opposed	O
to	O
acyl	B-chemical
-	I-chemical
phosphate	I-chemical
.	O

This	O
hypothesis	O
is	O
strengthened	O
by	O
the	O
fact	O
that	O
the	O
CoA	B-protein_state
-	I-protein_state
bound	I-protein_state
crystals	B-evidence
were	O
obtained	O
without	O
added	O
CoA	B-chemical
,	O
indicating	O
that	O
the	O
protein	O
bound	B-protein_state
CoA	B-chemical
from	O
the	O
E	B-species
.	I-species
coli	I-species
expression	O
strain	O
and	O
retained	O
it	O
throughout	O
purification	O
and	O
crystallization	O
.	O

The	O
phosphate	B-protein_state
-	I-protein_state
bound	I-protein_state
structure	B-evidence
indicates	O
that	O
in	O
the	O
opposite	O
reaction	O
direction	O
phosphate	B-chemical
is	O
bound	O
first	O
,	O
and	O
then	O
an	O
acyl	B-chemical
-	I-chemical
CoA	I-chemical
enters	O
.	O

The	O
two	O
high	O
-	O
resolution	O
crystal	B-evidence
structures	I-evidence
presented	O
here	O
will	O
serve	O
as	O
the	O
foundation	O
for	O
mechanistic	O
studies	O
on	O
this	O
noncanonical	O
PTAC	B-protein_type
enzyme	O
to	O
determine	O
how	O
the	O
dimetal	B-site
active	I-site
site	I-site
functions	O
to	O
catalyze	O
both	O
forward	O
and	O
reverse	O
reactions	O
.	O

Functional	O
,	O
but	O
Not	O
Structural	O
,	O
Convergence	O
of	O
PduL	B-protein_type
and	O
Pta	B-protein_type

PduL	B-protein_type
and	O
Pta	B-protein_type
are	O
mechanistically	O
and	O
structurally	O
distinct	O
enzymes	O
that	O
catalyze	O
the	O
same	O
reaction	O
,	O
a	O
prime	O
example	O
of	O
evolutionary	O
convergence	O
upon	O
a	O
function	O
.	O

There	O
are	O
several	O
examples	O
of	O
such	O
functional	O
convergence	O
of	O
enzymes	O
,	O
although	O
typically	O
the	O
enzymes	O
have	O
independently	O
evolved	O
similar	O
,	O
or	O
even	O
identical	O
active	B-site
sites	I-site
;	O
for	O
example	O
,	O
the	O
carbonic	B-protein_type
anhydrase	I-protein_type
family	O
.	O

However	O
,	O
apparently	O
less	O
frequent	O
is	O
functional	O
convergence	O
that	O
is	O
supported	O
by	O
distinctly	O
different	O
active	B-site
sites	I-site
and	O
accordingly	O
catalytic	O
mechanism	O
,	O
as	O
revealed	O
by	O
comparison	O
of	O
the	O
structures	O
of	O
Pta	B-protein_type
and	O
PduL	B-protein_type
.	O
One	O
well	O
-	O
studied	O
example	O
of	O
this	O
is	O
the	O
β	B-protein_type
-	I-protein_type
lactamase	I-protein_type
family	O
of	O
enzymes	O
,	O
in	O
which	O
the	O
active	B-site
site	I-site
of	O
Class	O
A	O
and	O
Class	O
C	O
enzymes	O
involve	O
serine	O
-	O
based	O
catalysis	O
,	O
but	O
Class	O
B	O
enzymes	O
are	O
metalloproteins	B-protein_type
.	O

This	O
is	O
not	O
surprising	O
,	O
as	O
β	B-protein_type
-	I-protein_type
lactamases	I-protein_type
are	O
not	O
so	O
widespread	O
among	O
bacteria	B-taxonomy_domain
and	O
therefore	O
would	O
be	O
expected	O
to	O
have	O
evolved	O
independently	O
several	O
times	O
as	O
a	O
defense	O
mechanism	O
against	O
β	O
-	O
lactam	O
antibiotics	O
.	O

However	O
,	O
nearly	O
all	O
bacteria	B-taxonomy_domain
encode	O
Pta	B-protein_type
,	O
and	O
it	O
is	O
not	O
immediately	O
clear	O
why	O
the	O
Pta	B-protein_type
/	O
PduL	B-protein_type
functional	O
convergence	O
should	O
have	O
evolved	O
:	O
it	O
would	O
seem	O
to	O
be	O
evolutionarily	O
more	O
resourceful	O
for	O
the	O
Pta	B-gene
-	I-gene
encoding	I-gene
gene	I-gene
to	O
be	O
duplicated	O
and	O
repurposed	O
for	O
BMCs	B-complex_assembly
,	O
as	O
is	O
apparently	O
the	O
case	O
in	O
one	O
type	O
of	O
BMC	B-complex_assembly
—	I-complex_assembly
EUT1	I-complex_assembly
(	O
Table	O
1	O
).	O

There	O
could	O
be	O
some	O
intrinsic	O
biochemical	O
difference	O
between	O
the	O
two	O
enzymes	O
that	O
renders	O
PduL	B-protein_type
a	O
more	O
attractive	O
candidate	O
for	O
encapsulation	O
in	O
a	O
BMC	B-complex_assembly
—	O
for	O
example	O
,	O
PduL	B-protein_type
might	O
be	O
more	O
amenable	O
to	O
tight	O
packaging	O
,	O
or	O
is	O
better	O
suited	O
for	O
the	O
chemical	O
microenvironment	O
formed	O
within	O
the	O
lumen	O
of	O
the	O
BMC	B-complex_assembly
,	O
which	O
can	O
be	O
quite	O
different	O
from	O
the	O
cytosol	O
.	O

Further	O
biochemical	O
comparison	O
between	O
the	O
two	O
PTACs	B-protein_type
will	O
likely	O
yield	O
exciting	O
results	O
that	O
could	O
answer	O
this	O
evolutionary	O
question	O
.	O

BMCs	B-complex_assembly
are	O
now	O
known	O
to	O
be	O
widespread	O
among	O
the	O
bacteria	B-taxonomy_domain
and	O
are	O
involved	O
in	O
critical	O
segments	O
of	O
both	O
autotrophic	O
and	O
heterotrophic	O
biochemical	O
pathways	O
that	O
confer	O
to	O
the	O
host	O
organism	O
a	O
competitive	O
(	O
metabolic	O
)	O
advantage	O
in	O
select	O
niches	O
.	O

As	O
one	O
of	O
the	O
three	O
common	O
metabolosome	B-complex_assembly
core	O
enzymes	O
,	O
the	O
structure	B-evidence
of	O
PduL	B-protein_type
provides	O
a	O
key	O
missing	O
piece	O
to	O
our	O
structural	O
picture	O
of	O
the	O
shared	O
core	O
biochemistry	O
(	O
Fig	O
1	O
)	O
of	O
functionally	O
diverse	O
catabolic	B-protein_state
BMCs	B-complex_assembly
.	O

We	O
have	O
observed	O
the	O
oligomeric	O
state	O
differences	O
of	O
PduL	B-protein_type
to	O
correlate	O
with	O
the	O
presence	O
of	O
an	O
EP	B-structure_element
,	O
providing	O
new	O
insight	O
into	O
the	O
function	O
of	O
this	O
sequence	O
extension	O
in	O
BMC	B-complex_assembly
assembly	O
.	O

Moreover	O
,	O
our	O
results	O
suggest	O
a	O
means	O
for	O
Coenzyme	B-chemical
A	I-chemical
incorporation	O
during	O
metabolosome	B-complex_assembly
biogenesis	O
.	O

A	O
detailed	O
understanding	O
of	O
the	O
underlying	O
principles	O
governing	O
the	O
assembly	O
and	O
internal	O
structural	O
organization	O
of	O
BMCs	B-complex_assembly
is	O
a	O
requisite	O
for	O
synthetic	O
biologists	O
to	O
design	O
custom	O
nanoreactors	O
that	O
use	O
BMC	B-complex_assembly
architectures	O
as	O
a	O
template	O
.	O

Furthermore	O
,	O
given	O
the	O
growing	O
number	O
of	O
metabolosomes	B-complex_assembly
implicated	O
in	O
pathogenesis	O
,	O
the	O
PduL	B-protein_type
structure	B-evidence
will	O
be	O
useful	O
in	O
the	O
development	O
of	O
therapeutics	O
.	O

The	O
fact	O
that	O
PduL	B-protein_type
is	O
confined	O
almost	O
exclusively	O
to	O
metabolosomes	B-complex_assembly
can	O
be	O
used	O
to	O
develop	O
an	O
inhibitor	O
that	O
blocks	O
only	O
PduL	B-protein_type
and	O
not	O
Pta	B-protein_type
as	O
a	O
way	O
to	O
selectively	O
disrupt	O
BMC	B-complex_assembly
-	O
based	O
metabolism	O
,	O
while	O
not	O
affecting	O
most	O
commensal	O
organisms	O
that	O
require	O
PTAC	B-protein_type
activity	O
.	O

Structural	O
basis	O
for	O
the	O
regulation	O
of	O
enzymatic	O
activity	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
by	O
domain	O
-	O
domain	O
interactions	O

Regnase	B-protein
-	I-protein
1	I-protein
is	O
an	O
RNase	B-protein_type
that	O
directly	O
cleaves	O
mRNAs	B-chemical
of	O
inflammatory	O
genes	O
such	O
as	O
IL	B-protein_type
-	I-protein_type
6	I-protein_type
and	O
IL	B-protein_type
-	I-protein_type
12p40	I-protein_type
,	O
and	O
negatively	O
regulates	O
cellular	O
inflammatory	O
responses	O
.	O

Here	O
,	O
we	O
report	O
the	O
structures	B-evidence
of	O
four	O
domains	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
from	O
Mus	B-species
musculus	I-species
—	O
the	O
N	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
(	O
NTD	B-structure_element
),	O
PilT	B-structure_element
N	I-structure_element
-	I-structure_element
terminus	I-structure_element
like	I-structure_element
(	O
PIN	B-structure_element
)	O
domain	O
,	O
zinc	B-structure_element
finger	I-structure_element
(	O
ZF	B-structure_element
)	O
domain	O
and	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
(	O
CTD	B-structure_element
).	O

The	O
PIN	B-structure_element
domain	O
harbors	O
the	O
RNase	B-protein_type
catalytic	B-site
center	I-site
;	O
however	O
,	O
it	O
is	O
insufficient	O
for	O
enzymatic	O
activity	O
.	O

We	O
found	O
that	O
the	O
NTD	B-structure_element
associates	O
with	O
the	O
PIN	B-structure_element
domain	O
and	O
significantly	O
enhances	O
its	O
RNase	B-protein_type
activity	O
.	O

The	O
PIN	B-structure_element
domain	O
forms	O
a	O
head	B-protein_state
-	I-protein_state
to	I-protein_state
-	I-protein_state
tail	I-protein_state
oligomer	B-oligomeric_state
and	O
the	O
dimer	B-site
interface	I-site
overlaps	O
with	O
the	O
NTD	B-site
binding	I-site
site	I-site
.	O

Interestingly	O
,	O
mutations	B-experimental_method
blocking	O
PIN	B-structure_element
oligomerization	O
had	O
no	O
RNase	B-protein_type
activity	O
,	O
indicating	O
that	O
both	O
oligomerization	O
and	O
NTD	B-structure_element
binding	O
are	O
crucial	O
for	O
RNase	B-protein_type
activity	O
in	O
vitro	O
.	O

These	O
results	O
suggest	O
that	O
Regnase	B-protein
-	I-protein
1	I-protein
RNase	B-protein_type
activity	O
is	O
tightly	O
controlled	O
by	O
both	O
intramolecular	O
(	O
NTD	B-structure_element
-	O
PIN	B-structure_element
)	O
and	O
intermolecular	O
(	O
PIN	B-structure_element
-	O
PIN	B-structure_element
)	O
interactions	O
.	O

The	O
initial	O
sensing	O
of	O
infection	O
is	O
mediated	O
by	O
a	O
set	O
of	O
pattern	B-protein_type
-	I-protein_type
recognition	I-protein_type
receptors	I-protein_type
(	O
PRRs	B-protein_type
)	O
such	O
Toll	B-protein_type
-	I-protein_type
like	I-protein_type
receptors	I-protein_type
(	O
TLRs	B-protein_type
)	O
and	O
the	O
intracellular	O
signaling	O
cascades	O
triggered	O
by	O
TLRs	B-protein_type
evoke	O
transcriptional	O
expression	O
of	O
inflammatory	O
mediators	O
that	O
coordinate	O
the	O
elimination	O
of	O
pathogens	O
and	O
infected	O
cells	O
.	O

Regnase	B-protein
-	I-protein
1	I-protein
(	O
also	O
known	O
as	O
Zc3h12a	B-protein
and	O
MCPIP1	B-protein
)	O
is	O
an	O
RNase	B-protein_type
whose	O
expression	O
level	O
is	O
stimulated	O
by	O
lipopolysaccharides	B-chemical
and	O
prevents	O
autoimmune	O
diseases	O
by	O
directly	O
controlling	O
the	O
stability	O
of	O
mRNAs	B-chemical
of	O
inflammatory	O
genes	O
such	O
as	O
interleukin	O
(	B-protein_type
IL	I-protein_type
)-	I-protein_type
6	I-protein_type
,	O
IL	B-protein_type
-	I-protein_type
1β	I-protein_type
,	O
IL	B-protein_type
-	I-protein_type
2	I-protein_type
,	O
and	O
IL	B-protein_type
-	I-protein_type
12p40	I-protein_type
.	O

Regnase	B-protein
-	I-protein
1	I-protein
accelerates	O
target	O
mRNA	B-chemical
degradation	O
via	O
their	O
3	B-structure_element
′-	I-structure_element
terminal	I-structure_element
untranslated	I-structure_element
region	I-structure_element
(	O
3	B-structure_element
′	I-structure_element
UTR	I-structure_element
),	O
and	O
also	O
degrades	O
its	O
own	O
mRNA	B-chemical
.	O

Regnase	B-protein
-	I-protein
1	I-protein
is	O
a	O
member	O
of	O
Regnase	B-protein_type
family	I-protein_type
and	O
is	O
composed	O
of	O
a	O
PilT	B-structure_element
N	I-structure_element
-	I-structure_element
terminus	I-structure_element
like	I-structure_element
(	O
PIN	B-structure_element
)	O
domain	O
followed	O
by	O
a	O
CCCH	B-structure_element
-	I-structure_element
type	I-structure_element
zinc	I-structure_element
–	I-structure_element
finger	I-structure_element
(	O
ZF	B-structure_element
)	O
domain	O
,	O
which	O
are	O
conserved	B-protein_state
among	O
Regnase	B-protein_type
family	I-protein_type
members	I-protein_type
.	O

Recently	O
,	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
Regnase	B-protein
-	I-protein
1	I-protein
PIN	B-structure_element
domain	O
derived	O
from	O
Homo	B-species
sapiens	I-species
was	O
reported	O
.	O

The	O
structure	B-evidence
combined	O
with	O
functional	O
analyses	O
revealed	O
that	O
four	O
catalytically	O
important	O
Asp	B-residue_name
residues	O
form	O
the	O
catalytic	B-site
center	I-site
and	O
stabilize	O
Mg2	B-chemical
+	I-chemical
binding	O
that	O
is	O
crucial	O
for	O
RNase	B-protein_type
activity	O
.	O

Several	O
CCCH	B-structure_element
-	I-structure_element
type	I-structure_element
ZF	I-structure_element
motifs	I-structure_element
in	O
RNA	B-protein_type
-	I-protein_type
binding	I-protein_type
proteins	I-protein_type
have	O
been	O
reported	O
to	O
directly	O
bind	O
RNA	B-chemical
.	O

In	O
addition	O
,	O
Regnase	B-protein
-	I-protein
1	I-protein
has	O
been	O
predicted	O
to	O
possess	O
other	O
domains	O
in	O
the	O
N	B-structure_element
-	I-structure_element
and	I-structure_element
C	I-structure_element
-	I-structure_element
terminal	I-structure_element
regions	I-structure_element
.	O

However	O
,	O
the	O
structure	B-evidence
and	O
function	O
of	O
the	O
ZF	B-structure_element
domain	O
,	O
N	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
(	O
NTD	B-structure_element
)	O
and	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
(	O
CTD	B-structure_element
)	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
have	O
not	O
been	O
solved	O
.	O

Here	O
,	O
we	O
performed	O
structural	B-experimental_method
and	I-experimental_method
functional	I-experimental_method
analyses	I-experimental_method
of	O
individual	O
domains	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
derived	O
from	O
Mus	B-species
musculus	I-species
in	O
order	O
to	O
understand	O
the	O
catalytic	O
activity	O
in	O
vitro	O
.	O

Our	O
data	O
revealed	O
that	O
the	O
catalytic	O
activity	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
is	O
regulated	O
through	O
both	O
intra	O
and	O
intermolecular	O
domain	O
interactions	O
in	O
vitro	O
.	O

The	O
NTD	B-structure_element
plays	O
a	O
crucial	O
role	O
in	O
efficient	O
cleavage	O
of	O
target	O
mRNA	B-chemical
,	O
through	O
intramolecular	O
NTD	B-structure_element
-	O
PIN	B-structure_element
interactions	O
.	O

Moreover	O
,	O
Regnase	B-protein
-	I-protein
1	I-protein
functions	O
as	O
a	O
dimer	B-oligomeric_state
through	O
intermolecular	O
PIN	B-structure_element
-	O
PIN	B-structure_element
interactions	O
during	O
cleavage	O
of	O
target	O
mRNA	B-chemical
.	O

Our	O
findings	O
suggest	O
that	O
Regnase	B-protein
-	I-protein
1	I-protein
cleaves	O
its	O
target	O
mRNA	B-chemical
by	O
an	O
NTD	B-protein_state
-	I-protein_state
activated	I-protein_state
functional	B-protein_state
PIN	B-structure_element
dimer	B-oligomeric_state
,	O
while	O
the	O
ZF	B-structure_element
increases	O
RNA	B-chemical
affinity	O
in	O
the	O
vicinity	O
of	O
the	O
PIN	B-structure_element
dimer	B-oligomeric_state
.	O

Domain	O
structures	B-evidence
of	O
Regnase	B-protein
-	I-protein
1	I-protein

We	O
analyzed	O
Rengase	B-protein
-	I-protein
1	I-protein
derived	O
from	O
Mus	B-species
musculus	I-species
and	O
solved	B-experimental_method
the	O
structures	B-evidence
of	O
the	O
four	O
domains	O
;	O
NTD	B-structure_element
,	O
PIN	B-structure_element
,	O
ZF	B-structure_element
,	O
and	O
CTD	B-structure_element
individually	O
by	O
X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
or	O
NMR	B-experimental_method
(	O
Fig	O
.	O
1a	O
–	O
e	O
).	O

X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
was	O
attempted	O
for	O
the	O
fragment	O
containing	O
both	O
the	O
PIN	B-structure_element
and	O
ZF	B-structure_element
domains	O
,	O
however	O
,	O
electron	B-evidence
density	I-evidence
was	O
observed	O
only	O
for	O
the	O
PIN	B-structure_element
domain	O
(	O
Fig	O
.	O
1c	O
),	O
consistent	O
with	O
a	O
previous	O
report	O
on	O
Regnase	B-protein
-	I-protein
1	I-protein
derived	O
from	O
Homo	B-species
sapiens	I-species
.	O

This	O
suggests	O
that	O
the	O
PIN	B-structure_element
and	O
ZF	B-structure_element
domains	O
exist	O
independently	O
without	O
interacting	O
with	O
each	O
other	O
.	O

The	O
domain	O
structures	B-evidence
of	O
NTD	B-structure_element
,	O
ZF	B-structure_element
,	O
and	O
CTD	B-structure_element
were	O
determined	O
by	O
NMR	B-experimental_method
(	O
Fig	O
.	O
1b	O
,	O
d	O
,	O
e	O
).	O

The	O
NTD	B-structure_element
and	O
CTD	B-structure_element
are	O
both	O
composed	O
of	O
three	O
α	B-structure_element
helices	I-structure_element
,	O
and	O
structurally	O
resemble	O
ubiquitin	B-protein
conjugating	I-protein
enzyme	I-protein
E2	I-protein
K	I-protein
(	O
PDB	O
ID	O
:	O
3K9O	O
)	O
and	O
ubiquitin	B-protein
associated	I-protein
protein	I-protein
1	I-protein
(	O
PDB	O
ID	O
:	O
4AE4	O
),	O
respectively	O
,	O
according	O
to	O
the	O
Dali	B-experimental_method
server	I-experimental_method
.	O

Contribution	O
of	O
each	O
domain	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
to	O
the	O
mRNA	B-chemical
binding	O
activity	O

Although	O
the	O
PIN	B-structure_element
domain	O
is	O
responsible	O
for	O
the	O
catalytic	O
activity	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
,	O
the	O
roles	O
of	O
the	O
other	O
domains	O
are	O
largely	O
unknown	O
.	O

First	O
,	O
we	O
evaluated	O
a	O
role	O
of	O
the	O
NTD	B-structure_element
and	O
ZF	B-structure_element
domains	O
for	O
mRNA	B-chemical
binding	O
by	O
an	O
in	B-experimental_method
vitro	I-experimental_method
gel	I-experimental_method
shift	I-experimental_method
assay	I-experimental_method
(	O
Fig	O
.	O
1f	O
).	O

Fluorescently	B-protein_state
5	I-protein_state
′-	I-protein_state
labeled	I-protein_state
RNA	B-chemical
corresponding	O
to	O
nucleotides	O
82	O
–	O
106	O
of	O
the	O
IL	B-protein_type
-	I-protein_type
6	I-protein_type
mRNA	B-chemical
3	B-structure_element
′	I-structure_element
UTR	I-structure_element
and	O
the	O
catalytically	O
inactive	B-protein_state
mutant	B-protein_state
(	O
D226N	B-mutant
and	O
D244N	B-mutant
)	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
—	O
hereafter	O
referred	O
to	O
as	O
the	O
DDNN	B-mutant
mutant	B-protein_state
—	O
were	O
utilized	O
.	O

Upon	O
addition	O
of	O
a	O
larger	O
amount	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
,	O
the	O
fluorescence	B-evidence
of	O
free	B-protein_state
RNA	B-chemical
decreased	O
,	O
indicating	O
that	O
Regnase	B-protein
-	I-protein
1	I-protein
bound	B-protein_state
to	I-protein_state
the	O
RNA	B-chemical
.	O

Based	O
on	O
the	O
decrease	O
in	O
the	O
free	O
RNA	B-chemical
fluorescence	O
band	O
,	O
we	O
evaluated	O
the	O
contribution	O
of	O
each	O
domain	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
to	O
RNA	B-chemical
binding	O
.	O

While	O
the	O
RNA	B-chemical
binding	O
ability	O
was	O
not	O
significantly	O
changed	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
NTD	B-structure_element
,	O
it	O
increased	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
the	O
ZF	B-structure_element
domain	O
(	O
Fig	O
.	O
1f	O
,	O
g	O
and	O
Supplementary	O
Fig	O
.	O
1	O
).	O

Direct	O
binding	O
of	O
the	O
ZF	B-structure_element
domain	O
and	O
RNA	B-chemical
were	O
confirmed	O
by	O
NMR	B-experimental_method
spectral	B-evidence
changes	I-evidence
.	O

The	O
fitting	O
of	O
the	O
titration	B-evidence
curve	I-evidence
of	O
Y314	B-residue_name_number
resulted	O
in	O
an	O
apparent	O
dissociation	B-evidence
constant	I-evidence
(	O
Kd	B-evidence
)	O
of	O
10	O
±	O
1	O
.	O
1	O
μM	O
(	O
Supplementary	O
Fig	O
.	O
2	O
).	O

These	O
results	O
indicate	O
that	O
not	O
only	O
the	O
PIN	B-structure_element
but	O
also	O
the	O
ZF	B-structure_element
domain	O
contribute	O
to	O
RNA	B-chemical
binding	O
,	O
while	O
the	O
NTD	B-structure_element
is	O
not	O
likely	O
to	O
be	O
involved	O
in	O
direct	O
interaction	O
with	O
RNA	B-chemical
.	O

Contribution	O
of	O
each	O
domain	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
to	O
RNase	B-protein_type
activity	O

In	O
order	O
to	O
characterize	O
the	O
role	O
of	O
each	O
domain	O
in	O
the	O
RNase	B-protein_type
activity	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
,	O
we	O
performed	O
an	O
in	B-experimental_method
vitro	I-experimental_method
cleavage	I-experimental_method
assay	I-experimental_method
using	O
fluorescently	B-protein_state
5	I-protein_state
′-	I-protein_state
labeled	I-protein_state
RNA	B-chemical
corresponding	O
to	O
nucleotides	O
82	O
–	O
106	O
of	O
the	O
IL	B-protein_type
-	I-protein_type
6	I-protein_type
mRNA	B-chemical
3	B-structure_element
′	I-structure_element
UTR	I-structure_element
(	O
Fig	O
.	O
1g	O
).	O

Regnase	B-protein
-	I-protein
1	I-protein
constructs	O
consisting	O
of	O
NTD	B-mutant
-	I-mutant
PIN	I-mutant
-	I-mutant
ZF	I-mutant
completely	O
cleaved	O
the	O
target	O
mRNA	B-chemical
and	O
generated	O
the	O
cleaved	O
products	O
.	O

The	O
apparent	O
half	O
-	O
life	O
(	O
T1	O
/	O
2	O
)	O
of	O
the	O
RNase	B-protein_type
activity	O
was	O
about	O
20	O
minutes	O
.	O

Regnase	B-protein
-	I-protein
1	I-protein
lacking	B-protein_state
the	O
ZF	B-structure_element
domain	O
generated	O
a	O
smaller	O
but	O
appreciable	O
amount	O
of	O
cleaved	O
product	O
(	O
T1	O
/	O
2	O
~	O
70	O
minutes	O
),	O
while	O
those	O
lacking	B-protein_state
the	O
NTD	B-structure_element
did	O
not	O
generate	O
cleaved	O
products	O
(	O
T1	O
/	O
2	O
>	O
90	O
minutes	O
).	O

It	O
should	O
be	O
noted	O
that	O
NTD	B-mutant
-	I-mutant
PIN	I-mutant
(	I-mutant
DDNN	I-mutant
)-	I-mutant
ZF	I-mutant
,	O
which	O
possesses	O
the	O
NTD	B-structure_element
but	O
lacks	B-protein_state
the	O
catalytic	B-site
residues	I-site
in	O
PIN	B-structure_element
,	O
completely	O
lost	O
all	O
RNase	B-protein_type
activity	O
(	O
Fig	O
.	O
1g	O
,	O
right	O
panel	O
),	O
as	O
expected	O
,	O
confirming	O
that	O
the	O
RNase	B-protein_type
catalytic	B-site
center	I-site
is	O
located	O
in	O
the	O
PIN	B-structure_element
domain	O
.	O

Taken	O
together	O
with	O
the	O
results	O
in	O
the	O
previous	O
section	O
,	O
we	O
conclude	O
that	O
the	O
NTD	B-structure_element
is	O
crucial	O
for	O
the	O
RNase	B-protein_type
activity	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
in	O
vitro	O
,	O
although	O
it	O
does	O
not	O
contribute	O
to	O
the	O
direct	O
mRNA	B-chemical
binding	O
.	O

Dimer	B-oligomeric_state
formation	O
of	O
the	O
PIN	B-structure_element
domains	O

During	O
purification	B-experimental_method
by	O
gel	B-experimental_method
filtration	I-experimental_method
,	O
the	O
PIN	B-structure_element
domain	O
exhibited	O
extremely	O
asymmetric	O
elution	O
peaks	O
in	O
a	O
concentration	O
dependent	O
manner	O
(	O
Fig	O
.	O
2a	O
).	O

By	O
comparison	B-experimental_method
with	I-experimental_method
the	I-experimental_method
elution	I-experimental_method
volume	I-experimental_method
of	I-experimental_method
standard	I-experimental_method
marker	I-experimental_method
proteins	I-experimental_method
,	O
the	O
PIN	B-structure_element
domain	O
was	O
assumed	O
to	O
be	O
in	O
equilibrium	O
between	O
a	O
monomer	B-oligomeric_state
and	O
a	O
dimer	B-oligomeric_state
in	O
solution	O
at	O
concentrations	O
in	O
the	O
20	O
–	O
200	O
μM	O
range	O
.	O

The	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
PIN	B-structure_element
domain	O
has	O
been	O
determined	O
in	O
three	O
distinct	O
crystal	B-evidence
forms	I-evidence
with	O
a	O
space	O
group	O
of	O
P3121	O
(	O
form	O
I	O
in	O
this	O
study	O
and	O
PDB	O
ID	O
3V33	O
),	O
P3221	O
(	O
form	O
II	O
in	O
this	O
study	O
),	O
and	O
P41	O
(	O
PDB	O
ID	O
3V32	O
and	O
3V34	O
),	O
respectively	O
.	O

We	O
found	O
that	O
the	O
PIN	B-structure_element
domain	O
formed	O
a	O
head	B-protein_state
-	I-protein_state
to	I-protein_state
-	I-protein_state
tail	I-protein_state
oligomer	B-oligomeric_state
that	O
was	O
commonly	O
observed	O
in	O
all	O
three	O
crystal	B-evidence
forms	I-evidence
in	O
spite	O
of	O
the	O
different	O
crystallization	O
conditions	O
(	O
Supplementary	O
Fig	O
.	O
3	O
).	O

Mutation	B-experimental_method
of	O
Arg215	B-residue_name_number
,	O
whose	O
side	O
chain	O
faces	O
to	O
the	O
opposite	O
side	O
of	O
the	O
oligomeric	B-site
surface	I-site
,	O
to	O
Glu	B-residue_name
preserved	O
the	O
monomer	B-oligomeric_state
/	O
dimer	B-oligomeric_state
equilibrium	O
,	O
similar	O
to	O
the	O
wild	B-protein_state
type	I-protein_state
.	O

On	O
the	O
other	O
hand	O
,	O
single	B-experimental_method
mutations	I-experimental_method
of	O
side	O
chains	O
involved	O
in	O
the	O
PIN	B-structure_element
–	O
PIN	B-structure_element
oligomeric	O
interaction	O
resulted	O
in	O
monomer	B-oligomeric_state
formation	O
,	O
judging	O
from	O
gel	B-experimental_method
filtration	I-experimental_method
(	O
Fig	O
.	O
2a	O
,	O
b	O
).	O

Wild	B-protein_state
type	I-protein_state
and	O
monomeric	B-oligomeric_state
PIN	B-structure_element
mutants	B-protein_state
(	O
P212A	B-mutant
and	O
D278R	B-mutant
)	O
were	O
also	O
analyzed	O
by	O
NMR	B-experimental_method
.	O

The	O
spectra	B-evidence
indicate	O
that	O
the	O
dimer	B-site
interface	I-site
of	O
the	O
wild	B-protein_state
type	I-protein_state
PIN	B-structure_element
domain	O
were	O
significantly	O
broadened	O
compared	O
to	O
the	O
monomeric	B-oligomeric_state
mutants	B-protein_state
(	O
Supplementary	O
Fig	O
.	O
4	O
).	O

These	O
results	O
indicate	O
that	O
the	O
PIN	B-structure_element
domain	O
forms	O
a	O
head	B-protein_state
-	I-protein_state
to	I-protein_state
-	I-protein_state
tail	I-protein_state
oligomer	B-oligomeric_state
in	O
solution	O
similar	O
to	O
the	O
crystal	B-evidence
structure	I-evidence
.	O

Interestingly	O
,	O
the	O
monomeric	B-oligomeric_state
PIN	B-structure_element
mutants	B-protein_state
P212A	B-mutant
,	O
R214A	B-mutant
,	O
and	O
D278R	B-mutant
had	O
no	O
significant	O
RNase	B-protein_type
activity	O
for	O
IL	B-protein_type
-	I-protein_type
6	I-protein_type
mRNA	B-chemical
in	O
vitro	O
(	O
Fig	O
.	O
2c	O
).	O

The	O
side	O
chains	O
of	O
these	O
residues	O
point	O
away	O
from	O
the	O
catalytic	B-site
center	I-site
on	O
the	O
same	O
molecule	O
(	O
Fig	O
.	O
2b	O
).	O

Therefore	O
,	O
we	O
concluded	O
that	O
head	B-protein_state
-	I-protein_state
to	I-protein_state
-	I-protein_state
tail	I-protein_state
PIN	B-structure_element
dimerization	O
,	O
together	O
with	O
the	O
NTD	B-structure_element
,	O
are	O
required	O
for	O
Regnase	B-protein
-	I-protein
1	I-protein
RNase	B-protein_type
activity	O
in	O
vitro	O
.	O

Domain	O
-	O
domain	O
interaction	O
between	O
the	O
NTD	B-structure_element
and	O
the	O
PIN	B-structure_element
domain	O

While	O
the	O
NTD	B-structure_element
does	O
not	O
contribute	O
to	O
RNA	B-chemical
binding	O
(	O
Fig	O
.	O
1f	O
,	O
g	O
,	O
and	O
Supplementary	O
Fig	O
.	O
1	O
),	O
it	O
increases	O
the	O
RNase	B-protein_type
activity	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
(	O
Fig	O
.	O
1h	O
).	O

In	O
order	O
to	O
gain	O
insight	O
into	O
the	O
molecular	O
mechanism	O
of	O
the	O
NTD	B-structure_element
-	O
mediated	O
enhancement	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
RNase	B-protein_type
activity	O
,	O
we	O
further	O
investigated	O
the	O
domain	O
-	O
domain	O
interaction	O
between	O
the	O
NTD	B-structure_element
and	O
the	O
PIN	B-structure_element
domain	O
using	O
NMR	B-experimental_method
.	O

We	O
used	O
the	O
catalytically	B-protein_state
inactive	I-protein_state
monomeric	B-oligomeric_state
PIN	B-structure_element
mutant	B-protein_state
possessing	O
both	O
the	O
DDNN	B-mutant
and	O
D278R	B-mutant
mutations	O
to	O
avoid	O
dimer	B-oligomeric_state
formation	O
of	O
the	O
PIN	B-structure_element
domain	O
.	O

The	O
NMR	B-experimental_method
signals	O
from	O
the	O
PIN	B-structure_element
domain	O
(	O
residues	O
V177	B-residue_name_number
,	O
F210	B-residue_range
-	I-residue_range
T211	I-residue_range
,	O
R214	B-residue_name_number
,	O
F228	B-residue_range
-	I-residue_range
L232	I-residue_range
,	O
and	O
F234	B-residue_range
-	I-residue_range
S236	I-residue_range
)	O
exhibited	O
significant	O
chemical	O
shift	O
changes	O
upon	O
addition	B-experimental_method
of	I-experimental_method
the	O
NTD	B-structure_element
(	O
Fig	O
.	O
3a	O
).	O

Likewise	O
,	O
upon	O
addition	B-experimental_method
of	I-experimental_method
the	O
PIN	B-structure_element
domain	O
,	O
NMR	B-experimental_method
signals	O
derived	O
from	O
R56	B-residue_name_number
,	O
L58	B-residue_range
-	I-residue_range
G59	I-residue_range
,	O
and	O
V86	B-residue_range
-	I-residue_range
H88	I-residue_range
in	O
the	O
NTD	B-structure_element
exhibited	O
large	O
chemical	O
shift	O
changes	O
and	O
residues	O
D53	B-residue_name_number
,	O
F55	B-residue_name_number
,	O
K57	B-residue_name_number
,	O
Y60	B-residue_range
-	I-residue_range
S61	I-residue_range
,	O
V68	B-residue_name_number
,	O
T80	B-residue_range
-	I-residue_range
G83	I-residue_range
,	O
L85	B-residue_name_number
,	O
and	O
G89	B-residue_name_number
of	O
the	O
NTD	B-structure_element
as	O
well	O
as	O
side	O
chain	O
amide	O
signals	O
of	O
N79	B-residue_name_number
exhibited	O
small	O
but	O
appreciable	O
chemical	O
shift	O
changes	O
(	O
Fig	O
.	O
3b	O
and	O
Supplementary	O
Fig	O
.	O
5	O
).	O

These	O
results	O
clearly	O
indicate	O
a	O
direct	O
interaction	O
between	O
the	O
PIN	B-structure_element
domain	O
and	O
the	O
NTD	B-structure_element
.	O

Based	O
on	O
the	O
titration	B-evidence
curve	I-evidence
for	O
the	O
chemical	B-evidence
shift	I-evidence
changes	I-evidence
of	O
L58	B-residue_name_number
,	O
the	O
apparent	O
Kd	B-evidence
between	O
the	O
isolated	O
NTD	B-structure_element
and	O
PIN	B-structure_element
was	O
estimated	O
to	O
be	O
110	O
±	O
5	O
.	O
8	O
μM	O
.	O
Considering	O
the	O
fact	O
that	O
the	O
NTD	B-structure_element
and	O
PIN	B-structure_element
domains	O
are	O
attached	O
by	O
a	O
linker	B-structure_element
,	O
the	O
actual	O
binding	B-evidence
affinity	I-evidence
is	O
expected	O
much	O
higher	O
in	O
the	O
native	B-protein_state
protein	O
.	O

Mapping	O
the	O
residues	O
with	O
chemical	O
shift	O
changes	O
reveals	O
the	O
putative	O
PIN	B-site
/	I-site
NTD	I-site
interface	I-site
,	O
which	O
includes	O
a	O
helix	B-structure_element
that	O
harbors	O
catalytic	O
residues	O
D225	B-residue_name_number
and	O
D226	B-residue_name_number
on	O
the	O
PIN	B-structure_element
domain	O
(	O
Fig	O
.	O
3a	O
).	O

Interestingly	O
,	O
the	O
putative	O
binding	B-site
site	I-site
for	O
the	O
NTD	B-structure_element
overlaps	O
with	O
the	O
PIN	B-site
-	I-site
PIN	I-site
dimer	I-site
interface	I-site
,	O
implying	O
that	O
NTD	B-structure_element
binding	O
can	O
“	O
terminate	O
”	O
PIN	B-structure_element
-	O
PIN	B-structure_element
oligomerization	O
(	O
Fig	O
.	O
2b	O
).	O

An	O
in	B-experimental_method
silico	I-experimental_method
docking	I-experimental_method
of	O
the	O
NTD	B-structure_element
and	O
PIN	B-structure_element
domains	O
using	O
chemical	B-evidence
shift	I-evidence
restraints	I-evidence
provided	O
a	O
model	O
consistent	O
with	O
the	O
NMR	B-experimental_method
experiments	O
(	O
Fig	O
.	O
3c	O
).	O

Residues	O
critical	O
for	O
Regnase	B-protein
-	I-protein
1	I-protein
RNase	B-protein_type
activity	O

To	O
gain	O
insight	O
into	O
the	O
residues	O
critical	O
for	O
Regnase	B-protein
-	I-protein
1	I-protein
RNase	B-protein_type
activity	O
,	O
each	O
basic	O
or	O
aromatic	O
residue	O
located	O
around	O
the	O
catalytic	B-site
site	I-site
of	O
the	O
PIN	B-structure_element
oligomer	B-oligomeric_state
was	O
mutated	B-experimental_method
to	I-experimental_method
alanine	B-residue_name
,	O
and	O
the	O
oligomerization	O
and	O
RNase	B-protein_type
activity	O
were	O
investigated	O
(	O
Fig	O
.	O
4	O
).	O

From	O
the	O
gel	B-experimental_method
filtration	I-experimental_method
assays	I-experimental_method
,	O
all	O
mutants	B-protein_state
except	O
R214A	B-mutant
formed	O
dimers	B-oligomeric_state
,	O
suggesting	O
that	O
any	O
lack	O
of	O
RNase	B-protein_type
activity	O
in	O
the	O
mutants	B-protein_state
,	O
except	O
R214A	B-mutant
,	O
was	O
directly	O
due	O
to	O
mutational	O
effects	O
of	O
the	O
specific	O
residues	O
and	O
not	O
to	O
abrogation	O
of	O
dimer	B-oligomeric_state
formation	O
.	O

The	O
W182A	B-mutant
,	O
R183A	B-mutant
,	O
and	O
R214A	B-mutant
mutants	B-protein_state
markedly	O
lost	O
cleavage	O
activity	O
for	O
IL	B-protein_type
-	I-protein_type
6	I-protein_type
mRNA	B-chemical
as	O
well	O
as	O
for	O
Regnase	B-protein
-	I-protein
1	I-protein
mRNA	B-chemical
.	O

The	O
K184A	B-mutant
,	O
R215A	B-mutant
,	O
and	O
R220A	B-mutant
mutants	B-protein_state
moderately	O
but	O
significantly	O
decreased	O
the	O
cleavage	O
activity	O
for	O
both	O
target	O
mRNAs	B-chemical
.	O

The	O
importance	O
of	O
K219	B-residue_name_number
and	O
R247	B-residue_name_number
was	O
slightly	O
different	O
for	O
IL	B-protein_type
-	I-protein_type
6	I-protein_type
and	O
Regnase	B-protein
-	I-protein
1	I-protein
mRNA	B-chemical
;	O
both	O
K219	B-residue_name_number
and	O
R247	B-residue_name_number
were	O
more	O
important	O
in	O
the	O
cleavage	O
of	O
IL	B-protein_type
-	I-protein_type
6	I-protein_type
mRNA	B-chemical
than	O
for	O
Regnase	B-protein
-	I-protein
1	I-protein
mRNA	B-chemical
.	O

The	O
other	O
mutated	O
residues	O
—	O
K152	B-residue_name_number
,	O
R158	B-residue_name_number
,	O
R188	B-residue_name_number
,	O
R200	B-residue_name_number
,	O
K204	B-residue_name_number
,	O
K206	B-residue_name_number
,	O
K257	B-residue_name_number
,	O
and	O
R258	B-residue_name_number
—	O
were	O
not	O
critical	O
for	O
RNase	B-protein_type
activity	O
.	O

The	O
importance	O
of	O
residues	O
W182	B-residue_name_number
and	O
R183	B-residue_name_number
can	O
readily	O
be	O
understood	O
in	O
terms	O
of	O
the	O
monomeric	B-oligomeric_state
PIN	B-structure_element
structure	B-evidence
as	O
they	O
are	O
located	O
near	O
to	O
the	O
RNase	B-protein_type
catalytic	B-site
site	I-site
;	O
however	O
,	O
the	O
importance	O
of	O
residue	O
K184	B-residue_name_number
,	O
which	O
points	O
away	O
from	O
the	O
active	B-site
site	I-site
is	O
more	O
easily	O
rationalized	O
in	O
terms	O
of	O
the	O
oligomeric	O
structure	B-evidence
,	O
in	O
which	O
the	O
“	O
secondary	O
”	O
chain	O
’	O
s	O
residue	O
K184	B-residue_name_number
is	O
positioned	O
near	O
the	O
“	O
primary	B-protein_state
”	I-protein_state
chain	O
’	O
s	O
catalytic	B-site
site	I-site
(	O
Fig	O
.	O
4	O
).	O

In	O
contrast	O
,	O
R214	B-residue_name_number
is	O
important	O
for	O
oligomerization	O
of	O
the	O
PIN	B-structure_element
domain	O
and	O
the	O
“	O
secondary	O
”	O
chain	O
’	O
s	O
residue	O
R214	B-residue_name_number
is	O
also	O
positioned	O
near	O
the	O
“	O
primary	B-protein_state
”	O
chain	O
’	O
s	O
active	B-site
site	I-site
within	O
the	O
dimer	B-site
interface	I-site
.	O

It	O
should	O
be	O
noted	O
that	O
the	O
putative	B-site
-	I-site
RNA	I-site
binding	I-site
residues	I-site
K184	B-residue_name_number
and	O
R214	B-residue_name_number
are	O
unique	O
to	O
Regnase	B-protein
-	I-protein
1	I-protein
among	O
PIN	B-structure_element
domains	O
.	O

Molecular	O
mechanism	O
of	O
target	O
mRNA	B-chemical
cleavage	O
by	O
the	O
PIN	B-structure_element
dimer	B-oligomeric_state

Our	O
mutational	B-experimental_method
experiments	I-experimental_method
indicated	O
that	O
the	O
observed	O
dimer	B-oligomeric_state
is	O
functional	O
and	O
that	O
the	O
role	O
of	O
the	O
secondary	B-protein_state
PIN	B-structure_element
domain	O
is	O
to	O
position	O
Regnase	B-protein
-	I-protein
1	I-protein
-	O
unique	O
RNA	B-site
binding	I-site
residues	I-site
near	O
the	O
active	B-site
site	I-site
of	O
the	O
primary	B-protein_state
PIN	B-structure_element
domain	O
.	O

If	O
this	O
model	O
is	O
correct	O
,	O
then	O
we	O
reasoned	O
that	O
a	O
catalytically	B-protein_state
inactive	I-protein_state
PIN	B-structure_element
and	O
a	O
PIN	B-structure_element
lacking	B-protein_state
the	O
putative	O
RNA	B-site
-	I-site
binding	I-site
residues	I-site
ought	O
to	O
be	O
inactive	B-protein_state
in	O
isolation	O
but	O
become	O
active	B-protein_state
when	O
mixed	O
together	O
.	O

In	O
order	O
to	O
test	O
this	O
hypothesis	O
,	O
we	O
performed	O
in	B-experimental_method
vitro	I-experimental_method
cleavage	I-experimental_method
assays	I-experimental_method
using	O
combinations	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
mutants	B-protein_state
that	O
had	O
no	O
or	O
decreased	O
RNase	B-protein_type
activities	O
by	O
themselves	O
(	O
Fig	O
.	O
5	O
).	O

One	O
group	O
consisted	O
of	O
catalytically	B-protein_state
active	I-protein_state
PIN	B-structure_element
domains	O
with	O
mutation	B-experimental_method
of	I-experimental_method
basic	O
residues	O
found	O
in	O
the	O
previous	O
section	O
to	O
confer	O
decreased	O
RNase	B-protein_type
activity	O
(	O
Fig	O
.	O
4	O
).	O

These	O
were	O
paired	O
with	O
a	O
DDNN	B-mutant
mutant	B-protein_state
that	O
had	O
no	O
RNase	B-protein_type
activity	O
by	O
itself	O
.	O

When	O
any	O
members	O
of	O
the	O
two	O
groups	O
are	O
mixed	O
,	O
two	O
kinds	O
of	O
heterodimers	B-oligomeric_state
can	O
be	O
formed	O
:	O
one	O
is	O
composed	O
of	O
a	O
DDNN	B-mutant
primary	B-protein_state
PIN	B-structure_element
and	O
a	O
basic	O
residue	O
mutant	B-protein_state
secondary	B-protein_state
PIN	B-structure_element
and	O
is	O
expected	O
to	O
exhibit	O
no	O
RNase	B-protein_type
activity	O
;	O
the	O
other	O
is	O
composed	O
of	O
a	O
basic	O
residue	O
mutant	B-protein_state
primary	B-protein_state
PIN	B-structure_element
and	O
a	O
DDNN	B-mutant
secondary	B-protein_state
PIN	B-structure_element
and	O
is	O
predicted	O
to	O
rescue	O
RNase	B-protein_type
activity	O
(	O
Fig	O
.	O
5a	O
).	O

When	O
we	O
compared	O
the	O
fluorescence	B-evidence
intensity	I-evidence
of	O
uncleaved	B-protein_state
IL	B-protein_type
-	I-protein_type
6	I-protein_type
mRNA	B-chemical
,	O
basic	O
residue	O
mutants	B-protein_state
W182A	B-mutant
,	O
K184A	B-mutant
,	O
R214A	B-mutant
,	O
and	O
R220A	B-mutant
were	O
rescued	O
upon	O
addition	O
of	O
the	O
DDNN	B-mutant
mutant	B-protein_state
(	O
Fig	O
.	O
5b	O
).	O

Consistently	O
,	O
when	O
we	O
compared	O
the	O
fluorescence	B-evidence
intensity	I-evidence
of	O
the	O
uncleaved	B-protein_state
Regnase	B-protein
-	I-protein
1	I-protein
mRNA	B-chemical
,	O
basic	O
residue	O
mutants	B-protein_state
K184A	B-mutant
and	O
R214A	B-mutant
were	O
rescued	O
upon	O
addition	O
of	O
the	O
DDNN	B-mutant
mutant	B-protein_state
(	O
Fig	O
.	O
5c	O
).	O

Rescue	O
of	O
K184A	B-mutant
and	O
R214A	B-mutant
by	O
the	O
DDNN	B-mutant
mutant	B-protein_state
was	O
also	O
confirmed	O
by	O
a	O
significant	O
increase	O
in	O
the	O
cleaved	O
products	O
.	O

This	O
is	O
particularly	O
significant	O
because	O
the	O
side	O
chains	O
of	O
K184	B-residue_name_number
and	O
R214	B-residue_name_number
in	O
the	O
primary	B-protein_state
PIN	B-structure_element
are	O
oriented	O
away	O
from	O
their	O
own	O
catalytic	B-site
center	I-site
,	O
while	O
those	O
in	O
the	O
secondary	B-protein_state
PIN	B-structure_element
face	O
toward	O
the	O
catalytic	B-site
center	I-site
of	O
the	O
primary	B-protein_state
PIN	B-structure_element
.	O

R214	B-residue_name_number
is	O
an	O
important	O
residue	O
for	O
dimer	B-oligomeric_state
formation	O
as	O
shown	O
in	O
Fig	O
.	O
2	O
,	O
therefore	O
,	O
R214A	B-mutant
in	O
the	O
secondary	B-protein_state
PIN	B-structure_element
cannot	O
dimerize	O
.	O

According	O
to	O
the	O
proposed	O
model	O
,	O
an	O
R214A	B-mutant
PIN	B-structure_element
domain	O
can	O
only	O
form	O
a	O
dimer	B-oligomeric_state
when	O
the	O
DDNN	B-mutant
PIN	B-structure_element
acts	O
as	O
the	O
secondary	B-protein_state
PIN	B-structure_element
.	O

Taken	O
together	O
,	O
the	O
rescue	O
experiments	O
above	O
support	O
the	O
proposed	O
model	O
in	O
which	O
the	O
head	B-protein_state
-	I-protein_state
to	I-protein_state
-	I-protein_state
tail	I-protein_state
dimer	B-oligomeric_state
is	O
functional	O
in	O
vitro	O
.	O

We	O
determined	O
the	O
individual	O
domain	O
structures	B-evidence
of	O
Regnase	B-protein
-	I-protein
1	I-protein
by	O
NMR	B-experimental_method
and	O
X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
.	O

Although	O
the	O
function	O
of	O
the	O
CTD	B-structure_element
remains	O
elusive	O
,	O
we	O
revealed	O
the	O
functions	O
of	O
the	O
NTD	B-structure_element
,	O
PIN	B-structure_element
,	O
and	O
ZF	B-structure_element
domains	O
.	O

A	O
Regnase	B-protein
-	I-protein
1	I-protein
construct	O
consisting	O
of	O
PIN	B-structure_element
and	O
ZF	B-structure_element
domains	O
derived	O
from	O
Mus	B-species
musculus	I-species
was	O
crystallized	B-experimental_method
;	O
however	O
,	O
the	O
electron	B-evidence
density	I-evidence
of	O
the	O
ZF	B-structure_element
domain	O
was	O
low	O
,	O
indicating	O
that	O
the	O
ZF	B-structure_element
domain	O
is	O
highly	B-protein_state
mobile	I-protein_state
in	O
the	O
absence	B-protein_state
of	I-protein_state
target	O
mRNA	B-chemical
or	O
possibly	O
other	O
protein	O
-	O
protein	O
interactions	O
.	O

Our	O
NMR	B-experimental_method
experiments	O
confirmed	O
direct	O
binding	O
of	O
the	O
ZF	B-structure_element
domain	O
to	O
IL	B-protein_type
-	I-protein_type
6	I-protein_type
mRNA	B-chemical
with	O
a	O
Kd	B-evidence
of	O
10	O
±	O
1	O
.	O
1	O
μM	O
.	O
Furthermore	O
,	O
an	O
in	B-experimental_method
vitro	I-experimental_method
gel	I-experimental_method
shift	I-experimental_method
assay	I-experimental_method
indicated	O
that	O
Regnase	B-protein
-	I-protein
1	I-protein
containing	O
the	O
ZF	B-structure_element
domain	O
enhanced	O
target	O
mRNA	B-chemical
-	O
binding	O
,	O
but	O
the	O
protein	O
-	O
RNA	B-chemical
complex	O
remained	O
in	O
the	O
bottom	O
of	O
the	O
well	O
without	O
entering	O
into	O
the	O
polyacrylamide	O
gel	O
.	O

These	O
results	O
indicate	O
that	O
Regnase	B-protein
-	I-protein
1	I-protein
directly	O
binds	O
to	O
RNA	B-chemical
and	O
precipitates	O
under	O
such	O
experimental	O
conditions	O
.	O

Due	O
to	O
this	O
limitation	O
,	O
it	O
is	O
difficult	O
to	O
perform	O
further	O
structural	B-experimental_method
analyses	I-experimental_method
of	O
mRNA	B-complex_assembly
-	I-complex_assembly
Regnase	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
complexes	O
by	O
X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
or	O
NMR	B-experimental_method
.	O

The	O
previously	O
reported	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
Regnase	B-protein
-	I-protein
1	I-protein
PIN	B-structure_element
domain	O
derived	O
from	O
Homo	B-species
sapiens	I-species
is	O
nearly	O
identical	O
to	O
the	O
one	O
derived	O
from	O
Mus	B-species
musculus	I-species
in	O
this	O
study	O
,	O
with	O
a	O
backbone	O
RMSD	B-evidence
of	O
0	O
.	O
2	O
Å	O
.	O
The	O
amino	O
acid	O
sequences	O
corresponding	O
to	O
PIN	B-structure_element
(	O
residues	O
134	B-residue_range
–	I-residue_range
295	I-residue_range
)	O
are	O
the	O
two	O
non	O
-	O
identical	O
residues	O
are	O
substituted	O
with	O
similar	O
amino	O
acids	O
.	O

Both	O
the	O
mouse	B-taxonomy_domain
and	O
human	B-species
PIN	B-structure_element
domains	O
form	O
head	B-protein_state
-	I-protein_state
to	I-protein_state
-	I-protein_state
tail	I-protein_state
oligomers	B-oligomeric_state
in	O
three	O
distinct	O
crystal	B-evidence
forms	I-evidence
.	O

Rao	O
and	O
co	O
-	O
workers	O
previously	O
argued	O
that	O
PIN	B-structure_element
dimerization	O
is	O
likely	O
to	O
be	O
a	O
crystallographic	O
artifact	O
with	O
no	O
physiological	O
significance	O
,	O
since	O
monomers	B-oligomeric_state
were	O
dominant	O
in	O
their	O
analytical	B-experimental_method
ultra	I-experimental_method
-	I-experimental_method
centrifugation	I-experimental_method
experiments	O
.	O

In	O
contrast	O
,	O
our	O
gel	B-experimental_method
filtration	I-experimental_method
data	O
,	O
mutational	B-experimental_method
analyses	I-experimental_method
,	O
and	O
NMR	B-experimental_method
spectra	B-evidence
all	O
indicate	O
that	O
the	O
PIN	B-structure_element
domain	O
forms	O
a	O
head	B-protein_state
-	I-protein_state
to	I-protein_state
-	I-protein_state
tail	I-protein_state
dimer	B-oligomeric_state
in	O
solution	O
in	O
a	O
manner	O
similar	O
to	O
the	O
crystal	B-evidence
structure	I-evidence
.	O

This	O
inconsistency	O
might	O
be	O
due	O
to	O
difference	O
in	O
the	O
analytical	O
methods	O
and	O
/	O
or	O
protein	O
concentrations	O
used	O
in	O
each	O
experiment	O
,	O
since	O
the	O
oligomer	B-oligomeric_state
formation	O
of	O
PIN	B-structure_element
was	O
dependent	O
on	O
the	O
protein	O
concentration	O
in	O
our	O
study	O
.	O

Single	B-experimental_method
mutations	I-experimental_method
to	O
residues	O
involved	O
in	O
the	O
putative	O
oligomeric	O
interaction	O
of	O
PIN	B-structure_element
monomerized	B-oligomeric_state
as	O
expected	O
and	O
these	O
mutants	B-protein_state
lost	O
their	O
RNase	B-protein_type
activity	O
as	O
well	O
.	O

Since	O
the	O
NMR	B-experimental_method
spectra	B-evidence
of	O
monomeric	B-oligomeric_state
mutants	B-protein_state
overlaps	O
with	O
those	O
of	O
the	O
oligomeric	O
forms	O
,	O
it	O
is	O
unlikely	O
that	O
the	O
tertiary	O
structure	O
of	O
the	O
monomeric	B-oligomeric_state
mutants	B-protein_state
were	O
affected	O
by	O
the	O
mutations	O
.	O
(	O
Supplementary	O
Fig	O
.	O
4b	O
,	O
c	O
).	O

Based	O
on	O
these	O
observations	O
,	O
we	O
concluded	O
that	O
PIN	B-structure_element
-	O
PIN	B-structure_element
dimer	B-oligomeric_state
formation	O
is	O
critical	O
for	O
Regnase	B-protein
-	I-protein
1	I-protein
RNase	B-protein_type
activity	O
in	O
vitro	O
.	O

Within	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
PIN	B-structure_element
dimer	B-oligomeric_state
,	O
the	O
Regnase	B-protein
-	I-protein
1	I-protein
specific	O
basic	O
regions	O
in	O
both	O
the	O
“	O
primary	B-protein_state
”	O
and	O
“	O
secondary	B-protein_state
”	O
PINs	B-structure_element
are	O
located	O
around	O
the	O
catalytic	B-site
site	I-site
of	O
the	O
primary	O
PIN	B-structure_element
(	O
Supplementary	O
Fig	O
.	O
6	O
).	O

Moreover	O
,	O
our	O
structure	B-experimental_method
-	I-experimental_method
based	I-experimental_method
mutational	I-experimental_method
analyses	I-experimental_method
showed	O
these	O
two	O
Regnase	B-protein
-	I-protein
1	I-protein
specific	O
basic	O
regions	O
were	O
essential	O
for	O
target	O
mRNA	B-chemical
cleavage	O
in	O
vitro	O
.	O

The	O
cleavage	B-experimental_method
assay	I-experimental_method
also	O
showed	O
that	O
the	O
NTD	B-structure_element
is	O
crucial	O
for	O
efficient	O
mRNA	B-chemical
cleavage	O
.	O

Moreover	O
,	O
we	O
found	O
that	O
the	O
NTD	B-structure_element
associates	O
with	O
the	O
oligomeric	B-site
surface	I-site
of	O
the	O
primary	B-protein_state
PIN	B-structure_element
,	O
docking	O
to	O
a	O
helix	B-structure_element
that	O
harbors	O
its	O
catalytic	B-site
residues	I-site
(	O
Figs	O
2b	O
and	O
3a	O
).	O

Taken	O
together	O
,	O
this	O
suggests	O
that	O
the	O
NTD	B-structure_element
and	O
the	O
PIN	B-structure_element
domain	O
compete	O
for	O
a	O
common	B-site
binding	I-site
site	I-site
.	O

The	O
affinity	B-evidence
of	O
the	O
domain	O
-	O
domain	O
interaction	O
between	O
two	O
PIN	B-structure_element
domains	O
(	O
Kd	B-evidence
=	O
~	O
10	O
−	O
4	O
M	O
)	O
is	O
similar	O
to	O
that	O
of	O
the	O
NTD	B-structure_element
-	O
PIN	B-structure_element
(	O
Kd	B-evidence
=	O
110	O
±	O
5	O
.	O
8	O
μM	O
)	O
interactions	O
;	O
however	O
,	O
the	O
covalent	O
connection	O
corresponding	O
to	O
residues	O
90	B-residue_range
–	I-residue_range
133	I-residue_range
between	O
the	O
NTD	B-structure_element
and	O
the	O
primary	B-protein_state
PIN	B-structure_element
will	O
greatly	O
enhance	O
the	O
intramolecular	O
domain	O
interaction	O
in	O
the	O
case	O
of	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
Regnase	B-protein
-	I-protein
1	I-protein
.	O

While	O
further	O
analyses	O
are	O
necessary	O
to	O
prove	O
this	O
point	O
,	O
our	O
preliminary	O
docking	B-experimental_method
and	I-experimental_method
molecular	I-experimental_method
dynamics	I-experimental_method
simulations	I-experimental_method
indicate	O
that	O
NTD	B-structure_element
-	O
binding	O
rearranges	O
the	O
catalytic	B-site
residues	I-site
of	O
the	O
PIN	B-structure_element
domain	O
toward	O
an	O
active	B-protein_state
conformation	O
suitable	O
for	O
binding	O
Mg2	B-chemical
+.	I-chemical

In	O
this	O
context	O
,	O
it	O
is	O
interesting	O
that	O
,	O
in	O
response	O
to	O
TCR	O
stimulation	O
,	O
Malt1	B-protein
cleaves	O
Regnase	B-protein
-	I-protein
1	I-protein
at	O
R111	B-residue_name_number
to	O
control	O
immune	O
responses	O
in	O
vivo	O
.	O

This	O
result	O
is	O
consistent	O
with	O
a	O
model	O
in	O
which	O
the	O
NTD	B-structure_element
acts	O
as	O
an	O
enhancer	O
,	O
and	O
cleavage	O
of	O
the	O
linker	B-structure_element
lowers	O
enzymatic	O
activity	O
dramatically	O
.	O

Based	O
on	O
these	O
structural	B-experimental_method
and	I-experimental_method
functional	I-experimental_method
analyses	I-experimental_method
of	O
Regnase	B-protein
-	I-protein
1	I-protein
domain	O
-	O
domain	O
interactions	O
,	O
we	O
performed	O
docking	B-experimental_method
simulations	I-experimental_method
of	O
the	O
NTD	B-structure_element
,	O
PIN	B-structure_element
dimer	B-oligomeric_state
,	O
and	O
IL	B-protein_type
-	I-protein_type
6	I-protein_type
mRNA	B-chemical
.	O

We	O
incorporated	O
information	O
from	O
the	O
cleavage	B-site
site	I-site
of	O
IL	B-protein_type
-	I-protein_type
6	I-protein_type
mRNA	B-chemical
in	O
vitro	O
is	O
indicated	O
by	O
denaturing	O
polyacrylamide	B-experimental_method
gel	I-experimental_method
electrophoresis	I-experimental_method
(	O
Supplementary	O
Fig	O
.	O
7a	O
,	O
b	O
).	O

The	O
docking	B-experimental_method
result	O
revealed	O
multiple	O
RNA	B-chemical
binding	O
modes	O
that	O
satisfied	O
the	O
experimental	O
results	O
in	O
vitro	O
(	O
Supplementary	O
Fig	O
.	O
7c	O
,	O
d	O
),	O
however	O
,	O
it	O
should	O
be	O
noted	O
that	O
,	O
in	O
vivo	O
,	O
there	O
would	O
likely	O
be	O
many	O
other	O
RNA	B-protein_type
-	I-protein_type
binding	I-protein_type
proteins	I-protein_type
that	O
would	O
protect	O
loop	B-structure_element
regions	O
from	O
cleavage	O
by	O
Regnase	B-protein
-	I-protein
1	I-protein
.	O

The	O
overall	O
model	O
of	O
regulation	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
RNase	B-protein_type
activity	O
through	O
domain	O
-	O
domain	O
interactions	O
in	O
vitro	O
is	O
summarized	O
in	O
Fig	O
.	O
6	O
.	O

In	O
the	O
absence	B-protein_state
of	I-protein_state
target	O
mRNA	B-chemical
,	O
the	O
PIN	B-structure_element
domain	O
forms	O
head	B-protein_state
-	I-protein_state
to	I-protein_state
-	I-protein_state
tail	I-protein_state
oligomers	B-oligomeric_state
at	O
high	O
concentration	O
.	O

A	O
fully	B-protein_state
active	I-protein_state
catalytic	B-site
center	I-site
can	O
be	O
formed	O
only	O
when	O
the	O
NTD	B-structure_element
associates	O
with	O
the	O
oligomer	B-oligomeric_state
surface	O
of	O
the	O
PIN	B-structure_element
domain	O
,	O
which	O
terminates	O
the	O
head	B-protein_state
-	I-protein_state
to	I-protein_state
-	I-protein_state
tail	I-protein_state
oligomer	B-oligomeric_state
formation	O
in	O
one	O
direction	O
(	O
primary	B-protein_state
PIN	B-structure_element
),	O
and	O
forms	O
a	O
functional	B-protein_state
dimer	B-oligomeric_state
together	O
with	O
the	O
neighboring	O
PIN	B-structure_element
(	O
secondary	B-protein_state
PIN	B-structure_element
).	O

While	O
further	O
investigations	O
on	O
the	O
domain	O
-	O
domain	O
interactions	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
in	O
vivo	O
are	O
necessary	O
,	O
these	O
intramolecular	O
and	O
intermolecular	O
domain	O
interactions	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
appear	O
to	O
structurally	O
constrain	O
Regnase	B-protein
-	I-protein
1activity	I-protein
,	O
which	O
,	O
in	O
turn	O
,	O
enables	O
tight	O
regulation	O
of	O
immune	O
responses	O
.	O

For	O
the	O
domain	O
-	O
domain	O
interaction	O
analyses	O
between	O
the	O
NTD	O
and	O
the	O
PIN	O
domain	O
,	O
1H	O
-	O
15N	O
HSQC	O
spectra	O
of	O
uniformly	O
15N	O
-	O
labeled	O
proteins	O
in	O
the	O
concentration	O
of	O
100	O
μM	O
were	O
obtained	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
3	O
or	O
6	O
molar	O
equivalents	O
of	O
unlabeled	O
proteins	O
.	O

Structural	B-experimental_method
and	I-experimental_method
functional	I-experimental_method
analyses	I-experimental_method
of	O
Regnase	B-protein
-	I-protein
1	I-protein
.	O

(	O
a	O
)	O
Domain	O
architecture	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
.	O
(	O
b	O
)	O
Solution	B-evidence
structure	I-evidence
of	O
the	O
NTD	B-structure_element
.	O
(	O
c	O
)	O
Crystal	B-evidence
structure	I-evidence
of	O
the	O
PIN	B-structure_element
domain	O
.	O

Catalytic	B-protein_state
Asp	B-residue_name
residues	O
were	O
shown	O
in	O
sticks	O
.	O

(	O
d	O
)	O
Solution	B-evidence
structure	I-evidence
of	O
the	O
ZF	B-structure_element
domain	O
.	O

Three	O
Cys	B-residue_name
residues	O
and	O
one	O
His	B-residue_name
residue	O
responsible	O
for	O
Zn2	O
+-	O
binding	O
were	O
shown	O
in	O
sticks	O
.	O

(	O
e	O
)	O
Solution	B-evidence
structure	I-evidence
of	O
the	O
CTD	B-structure_element
.	O

All	O
the	O
structures	B-evidence
were	O
colored	O
in	O
rainbow	O
from	O
N	O
-	O
terminus	O
(	O
blue	O
)	O
to	O
C	O
-	O
terminus	O
(	O
red	O
).	O

(	O
f	O
)	O
In	B-experimental_method
vitro	I-experimental_method
gel	I-experimental_method
shift	I-experimental_method
binding	I-experimental_method
assay	I-experimental_method
between	O
Regnase	B-protein
-	I-protein
1	I-protein
and	O
IL	B-protein_type
-	I-protein_type
6	I-protein_type
mRNA	B-chemical
.	O

Fluorescence	B-evidence
intensity	I-evidence
of	O
the	O
free	B-protein_state
IL	B-protein_type
-	I-protein_type
6	I-protein_type
in	O
each	O
sample	O
was	O
indicated	O
as	O
the	O
percentage	O
against	O
that	O
in	O
the	O
absence	B-protein_state
of	I-protein_state
Regnase	B-protein
-	I-protein
1	I-protein
.	O

(	O
g	O
)	O
Binding	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
and	O
IL	B-protein_type
-	I-protein_type
6	I-protein_type
mRNA	B-chemical
was	O
plotted	O
.	O

The	O
percentage	O
of	O
the	O
bound	O
IL	B-protein_type
-	I-protein_type
6	I-protein_type
was	O
calculated	O
based	O
on	O
the	O
fluorescence	B-evidence
intensities	I-evidence
of	O
the	O
free	O
IL	B-protein_type
-	I-protein_type
6	I-protein_type
quantified	O
in	O
(	O
f	O
).	O

(	O
h	O
)	O
In	B-experimental_method
vitro	I-experimental_method
cleavage	I-experimental_method
assay	I-experimental_method
of	O
Regnase	B-protein
-	I-protein
1	I-protein
to	O
IL	B-protein_type
-	I-protein_type
6	I-protein_type
mRNA	B-chemical
.	O

Fluorescence	B-evidence
intensity	I-evidence
of	O
the	O
uncleaved	B-protein_state
IL	B-protein_type
-	I-protein_type
6	I-protein_type
mRNA	B-chemical
was	O
indicated	O
as	O
the	O
percentage	O
against	O
that	O
in	O
the	O
absence	B-protein_state
of	I-protein_state
Regnase	B-protein
-	I-protein
1	I-protein
.	O

Head	B-protein_state
-	I-protein_state
to	I-protein_state
-	I-protein_state
tail	I-protein_state
oligomer	B-oligomeric_state
formation	O
of	O
the	O
PIN	B-structure_element
domain	O
is	O
crucial	O
for	O
the	O
RNase	B-protein_type
activity	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
.	O

(	O
a	O
)	O
Gel	B-experimental_method
filtration	I-experimental_method
analyses	I-experimental_method
of	O
the	O
PIN	B-structure_element
domain	O
.	O

(	O
b	O
)	O
Dimer	B-oligomeric_state
structure	B-evidence
of	O
the	O
PIN	B-structure_element
domain	O
.	O

Two	O
PIN	B-structure_element
molecules	O
in	O
the	O
crystal	B-evidence
were	O
colored	O
white	O
and	O
green	O
,	O
respectively	O
.	O

Catalytic	B-site
residues	I-site
and	O
mutated	O
residues	O
were	O
shown	O
in	O
sticks	O
.	O

Residues	O
important	O
for	O
the	O
oligomeric	O
interaction	O
were	O
colored	O
red	O
,	O
while	O
R215	B-residue_name_number
that	O
was	O
dispensable	O
for	O
the	O
oligomeric	O
interaction	O
was	O
colored	O
blue	O
.	O
(	O
c	O
)	O
RNase	B-protein_type
activity	O
of	O
monomeric	B-oligomeric_state
mutants	B-protein_state
for	O
IL	B-protein_type
-	I-protein_type
6	I-protein_type
mRNA	B-chemical
was	O
analyzed	O
.	O

Domain	O
-	O
domain	O
interaction	O
between	O
the	O
NTD	B-structure_element
and	O
the	O
PIN	B-structure_element
domain	O
.	O

(	O
a	O
)	O
NMR	B-experimental_method
analyses	I-experimental_method
of	O
the	O
NTD	B-structure_element
-	O
binding	O
to	O
the	O
PIN	B-structure_element
domain	O
.	O

The	O
residues	O
with	O
significant	O
chemical	O
shift	O
changes	O
were	O
labeled	O
in	O
the	O
overlaid	B-experimental_method
spectra	B-evidence
(	O
left	O
)	O
and	O
colored	O
red	O
on	O
the	O
surface	O
and	O
ribbon	O
structure	O
of	O
the	O
PIN	B-structure_element
domain	O
(	O
right	O
).	O

Pro	B-residue_name
and	O
the	O
residues	O
without	O
analysis	O
were	O
colored	O
black	O
and	O
gray	O
,	O
respectively	O
.	O

(	O
b	O
)	O
NMR	B-experimental_method
analyses	I-experimental_method
of	O
the	O
PIN	B-structure_element
-	O
binding	O
to	O
the	O
NTD	B-structure_element
.	O

The	O
residues	O
with	O
significant	B-evidence
chemical	I-evidence
shift	I-evidence
changes	I-evidence
were	O
labeled	O
in	O
the	O
overlaid	B-experimental_method
spectra	B-evidence
(	O
left	O
)	O
and	O
colored	O
red	O
,	O
yellow	O
,	O
or	O
green	O
on	O
the	O
surface	O
and	O
ribbon	O
structure	O
of	O
the	O
NTD	B-structure_element
.	O

S62	B-residue_name_number
was	O
colored	O
gray	O
and	O
excluded	O
from	O
the	O
analysis	O
,	O
due	O
to	O
low	O
signal	O
intensity	O
.	O

(	O
c	O
)	O
Docking	O
model	O
of	O
the	O
NTD	B-structure_element
and	O
the	O
PIN	B-structure_element
domain	O
.	O

The	O
NTD	B-structure_element
and	O
the	O
PIN	B-structure_element
domain	O
are	O
shown	O
in	O
cyan	O
and	O
white	O
,	O
respectively	O
.	O

Residues	O
in	O
close	O
proximity	O
(<	O
5	O
Å	O
)	O
to	O
each	O
other	O
in	O
the	O
docking	B-evidence
structure	I-evidence
were	O
colored	O
yellow	O
.	O

Catalytic	B-site
residues	I-site
of	O
the	O
PIN	B-structure_element
domain	O
are	O
shown	O
in	O
sticks	O
,	O
and	O
the	O
residues	O
that	O
exhibited	O
significant	B-evidence
chemical	I-evidence
shift	I-evidence
changes	I-evidence
in	O
(	O
a	O
,	O
b	O
)	O
were	O
labeled	O
.	O

Critical	O
residues	O
in	O
the	O
PIN	B-structure_element
domain	O
for	O
the	O
RNase	B-protein_type
activity	O
of	O
Regnase	B-protein
-	I-protein
1	I-protein
.	O

(	O
a	O
)	O
In	B-experimental_method
vitro	I-experimental_method
cleavage	I-experimental_method
assay	I-experimental_method
of	O
basic	O
residue	O
mutants	B-protein_state
for	O
IL	B-protein_type
-	I-protein_type
6	I-protein_type
mRNA	B-chemical
.	O

(	O
b	O
)	O
In	B-experimental_method
vitro	I-experimental_method
cleavage	I-experimental_method
assay	I-experimental_method
of	O
basic	O
residue	O
mutants	B-protein_state
for	O
Regnase	B-protein
-	I-protein
1	I-protein
mRNA	B-chemical
.	O

The	O
fluorescence	B-evidence
intensity	I-evidence
of	O
the	O
uncleaved	B-protein_state
mRNA	B-chemical
was	O
quantified	O
and	O
the	O
results	O
were	O
mapped	O
on	O
the	O
PIN	B-structure_element
dimer	B-oligomeric_state
structure	B-evidence
.	O

Mutated	O
basic	O
residues	O
were	O
shown	O
in	O
sticks	O
and	O
those	O
with	O
significantly	O
reduced	O
RNase	B-protein_type
activities	O
were	O
colored	O
red	O
or	O
yellow	O
.	O

Heterodimer	O
formation	O
by	O
combination	O
of	O
the	O
Regnase	B-protein
-	I-protein
1	I-protein
basic	O
residue	O
mutants	B-protein_state
and	O
the	O
DDNN	B-mutant
mutant	B-protein_state
restored	O
the	O
RNase	B-protein_type
activity	O
.	O

(	O
a	O
)	O
Cartoon	O
representation	O
of	O
the	O
concept	O
of	O
the	O
experiment	O
.	O
(	O
b	O
)	O
In	B-experimental_method
vitro	I-experimental_method
cleavage	I-experimental_method
assay	I-experimental_method
of	O
Regnase	B-protein
-	I-protein
1	I-protein
for	O
IL	B-protein_type
-	I-protein_type
6	I-protein_type
mRNA	B-chemical
.	O

(	O
c	O
)	O
In	B-experimental_method
vitro	I-experimental_method
cleavage	I-experimental_method
assay	I-experimental_method
of	O
Regnase	B-protein
-	I-protein
1	I-protein
for	O
Regnase	B-protein
-	I-protein
1	I-protein
mRNA	B-chemical
.	O

The	O
fluorescence	B-evidence
intensity	I-evidence
of	O
the	O
uncleaved	B-protein_state
mRNA	B-chemical
was	O
quantified	O
and	O
the	O
results	O
were	O
mapped	O
on	O
the	O
PIN	B-structure_element
dimer	B-oligomeric_state
.	O

The	O
mutations	O
whose	O
RNase	B-protein_type
activities	O
were	O
not	O
increased	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
DDNN	B-mutant
mutant	B-protein_state
were	O
colored	O
in	O
blue	O
on	O
the	O
primary	O
PIN	B-structure_element
.	O

The	O
mutations	O
whose	O
RNase	B-protein_type
activities	O
were	O
restored	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
DDNN	B-mutant
mutant	B-protein_state
were	O
colored	O
in	O
red	O
or	O
yellow	O
on	O
the	O
primary	O
PIN	B-structure_element
.	O

Schematic	O
representation	O
of	O
regulation	O
of	O
the	O
Regnase	B-protein
-	I-protein
1	I-protein
catalytic	O
activity	O
through	O
the	O
domain	O
-	O
domain	O
interactions	O
.	O

Ribosome	B-protein_type
biogenesis	I-protein_type
factor	I-protein_type
Tsr3	B-protein
is	O
the	O
aminocarboxypropyl	B-protein_type
transferase	I-protein_type
responsible	O
for	O
18S	B-chemical
rRNA	I-chemical
hypermodification	O
in	O
yeast	B-taxonomy_domain
and	O
humans	B-species

The	O
chemically	O
most	O
complex	O
modification	O
in	O
eukaryotic	B-taxonomy_domain
rRNA	B-chemical
is	O
the	O
conserved	B-protein_state
hypermodified	B-protein_state
nucleotide	B-chemical
N1	B-chemical
-	I-chemical
methyl	I-chemical
-	I-chemical
N3	I-chemical
-	I-chemical
aminocarboxypropyl	I-chemical
-	I-chemical
pseudouridine	I-chemical
(	O
m1acp3Ψ	B-chemical
)	O
located	O
next	O
to	O
the	O
P	B-site
-	I-site
site	I-site
tRNA	B-chemical
on	O
the	O
small	O
subunit	O
18S	B-chemical
rRNA	I-chemical
.	O

While	O
S	B-chemical
-	I-chemical
adenosylmethionine	I-chemical
was	O
identified	O
as	O
the	O
source	O
of	O
the	O
aminocarboxypropyl	B-chemical
(	O
acp	B-chemical
)	O
group	O
more	O
than	O
40	O
years	O
ago	O
the	O
enzyme	O
catalyzing	O
the	O
acp	B-chemical
transfer	O
remained	O
elusive	O
.	O

Here	O
we	O
identify	O
the	O
cytoplasmic	O
ribosome	O
biogenesis	O
protein	O
Tsr3	B-protein
as	O
the	O
responsible	O
enzyme	O
in	O
yeast	B-taxonomy_domain
and	O
human	B-species
cells	O
.	O

In	O
functionally	O
impaired	O
Tsr3	B-protein
-	O
mutants	B-protein_state
,	O
a	O
reduced	O
level	O
of	O
acp	B-chemical
modification	O
directly	O
correlates	O
with	O
increased	O
20S	B-chemical
pre	I-chemical
-	I-chemical
rRNA	I-chemical
accumulation	O
.	O

The	O
crystal	B-evidence
structure	I-evidence
of	O
archaeal	B-taxonomy_domain
Tsr3	B-protein
homologs	O
revealed	O
the	O
same	O
fold	O
as	O
in	O
SPOUT	B-protein_type
-	I-protein_type
class	I-protein_type
RNA	I-protein_type
-	I-protein_type
methyltransferases	I-protein_type
but	O
a	O
distinct	O
SAM	B-site
binding	I-site
mode	I-site
.	O

This	O
unique	O
SAM	B-site
binding	I-site
mode	I-site
explains	O
why	O
Tsr3	B-protein
transfers	O
the	O
acp	B-chemical
and	O
not	O
the	O
methyl	O
group	O
of	O
SAM	B-chemical
to	O
its	O
substrate	O
.	O

Structurally	O
,	O
Tsr3	B-protein
therefore	O
represents	O
a	O
novel	O
class	O
of	O
acp	B-protein_type
transferase	I-protein_type
enzymes	O
.	O

Eukaryotic	B-taxonomy_domain
ribosome	O
biogenesis	O
is	O
highly	O
complex	O
and	O
requires	O
a	O
large	O
number	O
of	O
non	O
-	O
ribosomal	O
proteins	O
and	O
small	B-chemical
non	I-chemical
-	I-chemical
coding	I-chemical
RNAs	I-chemical
in	O
addition	O
to	O
ribosomal	B-chemical
RNAs	I-chemical
(	O
rRNAs	B-chemical
)	O
and	O
proteins	O
.	O

During	O
eukaryotic	B-taxonomy_domain
ribosome	O
biogenesis	O
several	O
dozens	O
of	O
rRNA	B-chemical
nucleotides	B-chemical
become	O
chemically	O
modified	O
.	O

The	O
most	O
abundant	O
rRNA	B-chemical
modifications	O
are	O
methylations	B-ptm
at	O
the	O
2	O
′-	O
OH	O
ribose	B-chemical
moieties	O
and	O
isomerizations	O
of	O
uridine	B-chemical
residues	O
to	O
pseudouridine	B-chemical
,	O
catalyzed	O
by	O
small	B-complex_assembly
nucleolar	I-complex_assembly
ribonucleoprotein	I-complex_assembly
particles	I-complex_assembly
(	O
snoRNPs	B-complex_assembly
).	O

In	O
addition	O
,	O
18S	B-chemical
and	O
25S	B-chemical
(	O
yeast	B-taxonomy_domain
)/	O
28S	B-chemical
(	O
humans	B-species
)	O
rRNAs	B-chemical
contain	O
several	O
base	O
modifications	O
catalyzed	O
by	O
site	O
-	O
specific	O
and	O
snoRNA	B-chemical
-	O
independent	O
enzymes	O
.	O

In	O
Saccharomyces	B-species
cerevisiae	I-species
18S	B-chemical
rRNA	I-chemical
contains	O
four	O
base	O
methylations	B-ptm
,	O
two	O
acetylations	B-ptm
and	O
a	O
single	O
3	B-chemical
-	I-chemical
amino	I-chemical
-	I-chemical
3	I-chemical
-	I-chemical
carboxypropyl	I-chemical
(	O
acp	B-chemical
)	O
modification	O
,	O
whereas	O
six	O
base	O
methylations	B-ptm
are	O
present	O
in	O
the	O
25S	B-chemical
rRNA	I-chemical
.	O

While	O
in	O
humans	B-species
the	O
18S	B-chemical
rRNA	I-chemical
base	O
modifications	O
are	O
highly	B-protein_state
conserved	I-protein_state
,	O
only	O
three	O
of	O
the	O
yeast	B-taxonomy_domain
base	O
modifications	O
catalyzed	O
by	O
ScRrp8	B-protein
/	O
HsNML	B-protein
,	O
ScRcm1	B-protein
/	O
HsNSUN5	B-protein
and	O
ScNop2	B-protein
/	O
HsNSUN1	B-protein
are	O
preserved	O
in	O
the	O
corresponding	O
human	B-species
28S	B-chemical
rRNA	I-chemical
.	O

Ribosomal	B-chemical
RNA	I-chemical
modifications	O
have	O
been	O
suggested	O
to	O
optimize	O
ribosome	O
function	O
,	O
although	O
in	O
most	O
cases	O
this	O
remains	O
to	O
be	O
clearly	O
established	O
.	O

They	O
might	O
contribute	O
to	O
increased	O
RNA	B-chemical
stability	O
by	O
providing	O
additional	O
hydrogen	O
bonds	O
(	O
pseudouridines	B-chemical
),	O
improved	O
base	O
stacking	O
(	O
pseudouridines	B-chemical
and	O
base	B-ptm
methylations	I-ptm
)	O
or	O
an	O
increased	O
resistance	O
against	O
hydrolysis	O
(	O
ribose	B-ptm
methylations	I-ptm
).	O

Most	O
modified	O
rRNA	B-chemical
nucleotides	B-chemical
cluster	O
in	O
the	O
vicinity	O
of	O
the	O
decoding	B-site
or	O
the	O
peptidyl	B-site
transferase	I-site
center	I-site
,	O
suggesting	O
an	O
influence	O
on	O
ribosome	O
functionality	O
and	O
stability	O
.	O

Defects	O
of	O
rRNA	B-chemical
modification	O
enzymes	O
often	O
lead	O
to	O
disturbed	O
ribosome	O
biogenesis	O
or	O
functionally	O
impaired	O
ribosomes	O
,	O
although	O
the	O
lack	O
of	O
individual	O
rRNA	B-chemical
modifications	O
often	O
has	O
no	O
or	O
only	O
a	O
slight	O
influence	O
on	O
the	O
cell	O
.	O

The	O
chemically	O
most	O
complex	O
modification	O
is	O
located	O
in	O
the	O
loop	B-structure_element
capping	I-structure_element
helix	I-structure_element
31	I-structure_element
of	O
18S	B-chemical
rRNA	I-chemical
(	O
Supplementary	O
Figure	O
S1B	O
).	O

There	O
a	O
uridine	B-residue_name
(	O
U1191	B-residue_name_number
in	O
yeast	B-taxonomy_domain
)	O
is	O
modified	O
to	O
1	B-chemical
-	I-chemical
methyl	I-chemical
-	I-chemical
3	I-chemical
-(	I-chemical
3	I-chemical
-	I-chemical
amino	I-chemical
-	I-chemical
3	I-chemical
-	I-chemical
carboxypropyl	I-chemical
)-	I-chemical
pseudouridine	I-chemical
(	O
m1acp3Ψ	B-chemical
,	O
Figure	O
1A	O
).	O

This	O
base	O
modification	O
was	O
first	O
described	O
in	O
1968	O
for	O
hamster	B-taxonomy_domain
cells	O
and	O
is	O
conserved	B-protein_state
in	I-protein_state
eukaryotes	B-taxonomy_domain
.	O

This	O
hypermodified	B-protein_state
nucleotide	B-chemical
,	O
which	O
is	O
located	O
at	O
the	O
P	B-site
-	I-site
site	I-site
tRNA	B-chemical
,	O
is	O
synthesized	O
in	O
three	O
steps	O
beginning	O
with	O
the	O
snR35	B-chemical
H	B-structure_element
/	I-structure_element
ACA	I-structure_element
snoRNP	B-complex_assembly
guided	O
conversion	O
of	O
uridine	B-chemical
into	O
pseudouridine	B-chemical
.	O

In	O
a	O
second	O
step	O
,	O
the	O
essential	O
SPOUT	B-protein_type
-	I-protein_type
class	I-protein_type
methyltransferase	I-protein_type
Nep1	B-protein
/	O
Emg1	B-protein
modifies	O
the	O
pseudouridine	B-chemical
to	O
N1	B-chemical
-	I-chemical
methylpseudouridine	I-chemical
.	O

Methylation	B-ptm
can	O
only	O
occur	O
once	O
pseudouridylation	B-ptm
has	O
taken	O
place	O
,	O
as	O
the	O
latter	O
reaction	O
generates	O
the	O
substrate	O
for	O
the	O
former	O
.	O

The	O
final	O
acp	B-chemical
modification	O
leading	O
to	O
N1	B-chemical
-	I-chemical
methyl	I-chemical
-	I-chemical
N3	I-chemical
-	I-chemical
aminocarboxypropyl	I-chemical
-	I-chemical
pseudouridine	I-chemical
occurs	O
late	O
during	O
40S	B-complex_assembly
biogenesis	O
in	O
the	O
cytoplasm	O
,	O
while	O
the	O
two	O
former	O
reactions	O
are	O
taking	O
place	O
in	O
the	O
nucleolus	O
and	O
nucleus	O
,	O
and	O
is	O
independent	O
from	O
pseudouridylation	B-ptm
or	O
methylation	O
.	O

Both	O
the	O
methyl	O
and	O
the	O
acp	O
group	O
are	O
derived	O
from	O
S	B-chemical
-	I-chemical
adenosylmethionine	I-chemical
(	O
SAM	B-chemical
),	O
but	O
the	O
enzyme	O
responsible	O
for	O
acp	B-chemical
modification	O
remained	O
elusive	O
for	O
more	O
than	O
40	O
years	O
.	O

Tsr3	B-protein
is	O
necessary	O
for	O
acp	B-chemical
modification	O
of	O
18S	B-chemical
rRNA	I-chemical
in	O
yeast	B-taxonomy_domain
and	O
human	B-species
.	O
(	O
A	O
)	O
Hypermodified	B-protein_state
nucleotide	B-chemical
m1acp3Ψ	B-chemical
is	O
synthesized	O
in	O
three	O
steps	O
:	O
pseudouridylation	B-ptm
catalyzed	O
by	O
snoRNP35	B-complex_assembly
,	O
N1	B-ptm
-	I-ptm
methylation	I-ptm
catalyzed	O
by	O
methyltransferase	B-protein_type
Nep1	B-protein
and	O
N3	O
-	O
acp	B-chemical
modification	O
catalyzed	O
by	O
Tsr3	B-protein
.	O

The	O
asterisk	O
indicates	O
the	O
C1	O
-	O
atom	O
labeled	O
in	O
the	O
14C	B-experimental_method
-	I-experimental_method
incorporation	I-experimental_method
assay	I-experimental_method
.	O

(	O
B	O
)	O
RP	B-experimental_method
-	I-experimental_method
HPLC	I-experimental_method
elution	B-evidence
profile	I-evidence
of	O
yeast	B-taxonomy_domain
18S	B-chemical
rRNA	I-chemical
nucleosides	B-chemical
.	O

Hypermodified	B-protein_state
m1acp3Ψ	B-chemical
elutes	O
at	O
7	O
.	O
4	O
min	O
(	O
wild	B-protein_state
type	I-protein_state
,	O
left	O
profile	O
)	O
and	O
is	O
missing	O
in	O
Δtsr3	B-mutant
(	O
middle	O
profile	O
)	O
and	O
Δnep1	B-mutant
Δnop6	I-mutant
mutants	O
(	O
right	O
profile	O
).	O

(	O
C	O
)	O
14C	B-chemical
-	I-chemical
acp	I-chemical
labeling	O
of	O
18S	B-chemical
rRNAs	I-chemical
.	O

Wild	B-protein_state
type	I-protein_state
(	O
WT	B-protein_state
)	O
and	O
plasmid	O
encoded	O
18S	B-chemical
rRNA	I-chemical
(	O
U1191U	B-mutant
)	O
show	O
the	O
14C	B-chemical
-	I-chemical
acp	I-chemical
signal	O
,	O
whereas	O
the	O
14C	B-chemical
-	I-chemical
acp	I-chemical
signal	O
is	O
missing	O
in	O
the	O
U1191A	B-mutant
mutant	B-protein_state
plasmid	O
encoded	O
18S	B-chemical
rRNA	I-chemical
(	O
U1191A	B-mutant
)	O
and	O
Δtsr3	B-mutant
mutants	O
(	O
Δtsr3	B-mutant
).	O

Upper	O
lanes	O
show	O
the	O
ethidium	B-chemical
bromide	I-chemical
staining	O
of	O
the	O
18S	B-chemical
rRNAs	I-chemical
for	O
quantification	O
.	O

All	O
samples	O
were	O
loaded	O
on	O
the	O
gel	O
with	O
two	O
different	O
amounts	O
of	O
5	O
and	O
10	O
μl	O
.	O
(	O
D	O
)	O
Primer	B-experimental_method
extension	I-experimental_method
analysis	I-experimental_method
of	O
acp	B-chemical
modification	O
in	O
yeast	B-taxonomy_domain
18S	B-chemical
rRNA	I-chemical
(	O
right	O
gel	O
)	O
including	O
a	O
sequencing	O
ladder	O
(	O
left	O
gel	O
).	O

The	O
primer	O
extension	O
stop	O
at	O
nucleotide	O
1191	B-residue_number
is	O
missing	O
exclusively	O
in	O
Δtsr3	B-mutant
mutants	O
and	O
Δtsr3	B-mutant
Δsnr35	I-mutant
recombinants	O
.	O

(	O
E	O
)	O
Primer	B-experimental_method
extension	I-experimental_method
analysis	I-experimental_method
of	O
human	B-species
18S	B-chemical
rRNA	I-chemical
after	O
siRNA	B-experimental_method
knockdown	I-experimental_method
of	O
HsNEP1	B-protein
/	O
EMG1	B-protein
(	O
541	O
,	O
542	O
and	O
543	O
)	O
and	O
HsTSR3	B-protein
(	O
544	O
and	O
545	O
)	O
(	O
right	O
gel	O
),	O
including	O
a	O
sequencing	O
ladder	O
(	O
left	O
gel	O
).	O

The	O
primer	O
extension	O
arrest	O
is	O
reduced	O
in	O
HTC116	O
cells	O
transfected	O
with	O
siRNAs	B-chemical
544	O
and	O
545	O
.	O

The	O
efficiency	O
of	O
siRNA	B-chemical
mediated	O
HsTSR3	B-protein
repression	O
correlates	O
with	O
the	O
primer	B-evidence
extension	I-evidence
signals	I-evidence
(	O
see	O
Supplementary	O
Figure	O
S2A	O
).	O

Only	O
a	O
few	O
acp	B-chemical
transferring	O
enzymes	O
have	O
been	O
characterized	O
until	O
now	O
.	O

During	O
the	O
biosynthesis	O
of	O
wybutosine	B-chemical
,	O
a	O
tricyclic	O
nucleoside	B-chemical
present	O
in	O
eukaryotic	B-taxonomy_domain
and	O
archaeal	B-taxonomy_domain
phenylalanine	B-chemical
tRNA	B-chemical
,	O
Tyw2	B-protein
(	O
Trm12	B-protein
in	O
yeast	B-taxonomy_domain
)	O
transfers	O
an	O
acp	B-chemical
group	O
from	O
SAM	B-chemical
to	O
an	O
acidic	O
carbon	O
atom	O
.	O

Archaeal	B-taxonomy_domain
Tyw2	B-protein
has	O
a	O
structure	B-evidence
very	O
similar	O
to	O
Rossmann	B-protein_type
-	I-protein_type
fold	I-protein_type
(	I-protein_type
class	I-protein_type
I	I-protein_type
)	I-protein_type
RNA	I-protein_type
-	I-protein_type
methyltransferases	I-protein_type
,	O
but	O
its	O
distinctive	O
SAM	B-site
-	I-site
binding	I-site
mode	I-site
enables	O
the	O
transfer	O
of	O
the	O
acp	B-chemical
group	O
instead	O
of	O
the	O
methyl	O
group	O
of	O
the	O
cofactor	O
.	O

Another	O
acp	B-chemical
modification	O
has	O
been	O
described	O
in	O
the	O
diphtamide	B-chemical
biosynthesis	O
pathway	O
,	O
where	O
an	O
acp	B-chemical
group	O
is	O
transferred	O
from	O
SAM	B-chemical
to	O
the	O
carbon	O
atom	O
of	O
a	O
histidine	B-residue_name
residue	O
of	O
eukaryotic	B-taxonomy_domain
translation	B-protein_type
elongation	I-protein_type
factor	I-protein_type
2	I-protein_type
by	O
use	O
of	O
a	O
radical	O
mechanism	O
.	O

In	O
a	O
recent	O
bioinformatic	O
study	O
,	O
the	O
uncharacterized	O
yeast	B-taxonomy_domain
gene	O
YOR006c	B-gene
was	O
predicted	O
to	O
be	O
involved	O
in	O
ribosome	O
biogenesis	O
.	O

It	O
is	O
highly	B-protein_state
conserved	I-protein_state
among	O
eukaryotes	B-taxonomy_domain
and	O
archaea	B-taxonomy_domain
(	O
Supplementary	O
Figure	O
S1A	O
)	O
and	O
its	O
deletion	O
leads	O
to	O
an	O
accumulation	O
of	O
the	O
20S	B-chemical
pre	I-chemical
-	I-chemical
rRNA	I-chemical
precursor	O
of	O
18S	B-chemical
rRNA	I-chemical
,	O
suggesting	O
an	O
influence	O
on	O
D	B-site
-	I-site
site	I-site
cleavage	O
during	O
the	O
maturation	O
of	O
the	O
small	O
ribosomal	O
subunit	O
.	O

On	O
this	O
basis	O
,	O
YOR006C	B-gene
was	O
renamed	O
‘	O
Twenty	B-protein
S	I-protein
rRNA	I-protein
accumulation	I-protein
3	I-protein
′	O
(	O
TSR3	B-protein
).	O

However	O
,	O
its	O
function	O
remained	O
unclear	O
although	O
recently	O
a	O
putative	O
nuclease	O
function	O
during	O
18S	B-chemical
rRNA	I-chemical
maturation	O
was	O
predicted	O
.	O

Here	O
,	O
we	O
identify	O
Tsr3	B-protein
as	O
the	O
long	O
-	O
sought	O
acp	B-protein_type
transferase	I-protein_type
that	O
catalyzes	O
the	O
last	O
step	O
in	O
the	O
biosynthesis	O
of	O
the	O
hypermodified	B-protein_state
nucleotide	B-chemical
m1acp3Ψ	B-chemical
in	O
yeast	B-taxonomy_domain
and	O
human	B-species
cells	O
.	O

Furthermore	O
using	O
catalytically	B-protein_state
defective	I-protein_state
mutants	O
of	O
yeast	B-taxonomy_domain
Tsr3	B-protein
we	O
demonstrated	O
that	O
the	O
acp	B-chemical
modification	O
is	O
required	O
for	O
18S	B-chemical
rRNA	I-chemical
maturation	O
.	O

Surprisingly	O
,	O
the	O
crystal	B-evidence
structures	I-evidence
of	O
archaeal	B-taxonomy_domain
homologs	O
revealed	O
that	O
Tsr3	B-protein
is	O
structurally	O
similar	O
to	O
the	O
SPOUT	B-protein_type
-	I-protein_type
class	I-protein_type
RNA	I-protein_type
methyltransferases	I-protein_type
.	O

In	O
contrast	O
,	O
the	O
only	O
other	O
structurally	O
characterized	O
acp	B-protein_type
transferase	I-protein_type
enzyme	O
Tyw2	B-protein
belongs	O
to	O
the	O
Rossmann	B-protein_type
-	I-protein_type
fold	I-protein_type
class	I-protein_type
of	I-protein_type
methyltransferase	I-protein_type
proteins	I-protein_type
.	O

Interestingly	O
,	O
the	O
two	O
structurally	O
very	O
different	O
enzymes	O
use	O
similar	O
strategies	O
in	O
binding	O
the	O
SAM	B-chemical
-	O
cofactor	O
in	O
order	O
to	O
ensure	O
that	O
in	O
contrast	O
to	O
methyltransferases	B-protein_type
the	O
acp	B-chemical
and	O
not	O
the	O
methyl	O
group	O
of	O
SAM	B-chemical
is	O
transferred	O
to	O
the	O
substrate	O
.	O

Tsr3	B-protein
is	O
the	O
enzyme	O
responsible	O
for	O
18S	B-chemical
rRNA	I-chemical
acp	B-chemical
modification	O
in	O
yeast	B-taxonomy_domain
and	O
humans	B-species

The	O
S	B-species
.	I-species
cerevisiae	I-species
18S	B-protein_type
rRNA	I-protein_type
acp	I-protein_type
transferase	I-protein_type
was	O
identified	O
in	O
a	O
systematic	O
genetic	O
screen	O
where	O
numerous	O
deletion	O
mutants	O
from	O
the	O
EUROSCARF	O
strain	O
collection	O
(	O
www	O
.	O
euroscarf	O
.	O
de	O
)	O
were	O
analyzed	O
by	O
HPLC	B-experimental_method
for	O
alterations	O
in	O
18S	B-chemical
rRNA	I-chemical
base	O
modifications	O
.	O

For	O
the	O
Δtsr3	B-mutant
deletion	O
strain	O
the	O
HPLC	B-evidence
elution	I-evidence
profile	I-evidence
of	O
18S	B-chemical
rRNA	I-chemical
nucleosides	B-chemical
(	O
Figure	O
1B	O
)	O
was	O
very	O
similar	O
to	O
that	O
of	O
the	O
pseudouridine	B-protein_type
-	I-protein_type
N1	I-protein_type
methyltransferase	I-protein_type
mutant	B-protein_state
Δnep1	B-mutant
,	O
where	O
a	O
shoulder	O
at	O
∼	O
7	O
.	O
4	O
min	O
elution	O
time	O
was	O
missing	O
in	O
the	O
elution	O
profile	O
.	O

As	O
previously	O
reported	O
this	O
shoulder	O
was	O
identified	O
by	O
ESI	B-experimental_method
-	I-experimental_method
MS	I-experimental_method
as	O
corresponding	O
to	O
m1acp3Ψ	B-chemical
.	O

In	O
order	O
to	O
directly	O
analyze	O
the	O
presence	O
of	O
the	O
acp	B-chemical
modification	O
of	O
nucleotide	B-chemical
1191	B-residue_number
we	O
used	O
an	O
in	B-experimental_method
vivo14C	I-experimental_method
incorporation	I-experimental_method
assay	I-experimental_method
with	O
1	B-chemical
-	I-chemical
14C	I-chemical
-	I-chemical
methionine	I-chemical
.	O

Whereas	O
the	O
acp	B-chemical
labeling	O
of	O
18S	B-chemical
rRNA	I-chemical
was	O
clearly	O
present	O
in	O
the	O
wild	B-protein_state
type	I-protein_state
strain	O
no	O
radioactive	O
labeling	O
could	O
be	O
observed	O
in	O
a	O
Δtsr3	B-mutant
strain	O
(	O
Figure	O
1C	O
).	O

No	O
radioactive	O
labeling	O
was	O
detected	O
in	O
the	O
18S	B-mutant
U1191A	I-mutant
mutant	B-protein_state
which	O
served	O
as	O
a	O
control	O
for	O
the	O
specificity	O
of	O
the	O
14C	B-chemical
-	I-chemical
aminocarboxypropyl	I-chemical
incorporation	O
.	O

As	O
previously	O
shown	O
,	O
only	O
the	O
acp	B-chemical
but	O
none	O
of	O
the	O
other	O
modifications	O
at	O
U1191	B-residue_name_number
of	O
yeast	B-taxonomy_domain
18S	B-chemical
rRNA	I-chemical
blocks	O
reverse	O
transcriptase	O
activity	O
.	O

Therefore	O
the	O
presence	O
of	O
the	O
acp	B-chemical
modification	O
can	O
be	O
directly	O
assessed	O
by	O
primer	B-experimental_method
extension	I-experimental_method
.	O

Indeed	O
,	O
in	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
yeast	B-taxonomy_domain
a	O
strong	O
primer	B-evidence
extension	I-evidence
stop	I-evidence
signal	I-evidence
occurred	O
at	O
position	O
1192	B-residue_number
.	O

In	O
contrast	O
,	O
in	O
a	O
Δtsr3	B-mutant
mutant	B-protein_state
no	O
primer	O
extension	O
stop	O
signal	O
was	O
present	O
at	O
this	O
position	O
.	O

As	O
expected	O
,	O
in	O
a	O
Δsnr35	B-mutant
deletion	B-experimental_method
preventing	O
pseudouridylation	B-ptm
and	O
N1	B-ptm
-	I-ptm
methylation	I-ptm
(	O
resulting	O
in	O
acp3U	B-chemical
)	O
as	O
well	O
as	O
in	O
a	O
Δnep1	B-mutant
deletion	O
strain	O
where	O
pseudouridine	B-chemical
is	O
not	B-protein_state
methylated	I-protein_state
(	O
resulting	O
in	O
acp3Ψ	B-chemical
)	O
a	O
primer	B-evidence
extension	I-evidence
stop	I-evidence
signal	I-evidence
of	O
similar	O
intensity	O
as	O
in	O
the	O
wild	B-protein_state
type	I-protein_state
was	O
observed	O
.	O

In	O
a	O
Δtsr3	B-mutant
Δsnr35	I-mutant
double	O
deletion	O
strain	O
the	O
18S	B-chemical
rRNA	I-chemical
contains	O
an	O
unmodified	B-protein_state
U	B-chemical
and	O
the	O
primer	O
extension	O
stop	O
signal	O
was	O
missing	O
(	O
Figure	O
1D	O
).	O

The	O
Tsr3	B-protein
protein	O
is	O
highly	B-protein_state
conserved	I-protein_state
in	O
yeast	B-taxonomy_domain
and	O
humans	B-species
(	O
50	O
%	O
identity	O
).	O

Human	B-species
18S	B-chemical
rRNA	I-chemical
has	O
also	O
been	O
shown	O
to	O
contain	O
m1acp3Ψ	B-ptm
in	O
the	O
18S	B-chemical
rRNA	I-chemical
at	O
position	O
1248	B-residue_number
.	O

After	O
siRNA	B-experimental_method
-	I-experimental_method
mediated	I-experimental_method
depletion	I-experimental_method
of	O
Tsr3	B-protein
in	O
human	B-species
colon	O
carcinoma	O
HCT116	O
(+/+)	O
cells	O
the	O
acp	B-evidence
primer	I-evidence
extension	I-evidence
arrest	I-evidence
was	O
reduced	O
in	O
comparison	O
to	O
cells	O
transfected	O
with	O
a	O
non	O
-	O
targeting	O
scramble	O
siRNA	B-chemical
control	O
(	O
Figure	O
1E	O
,	O
compare	O
lanes	O
544	O
and	O
scramble	O
).	O

The	O
efficiency	O
of	O
siRNA	B-chemical
-	O
mediated	O
depletion	O
was	O
established	O
by	O
RT	B-experimental_method
-	I-experimental_method
qPCR	I-experimental_method
and	O
found	O
to	O
be	O
very	O
high	O
with	O
siRNA	B-chemical
544	O
(	O
Supplementary	O
Figure	O
S2A	O
,	O
remaining	O
TSR3	B-protein
mRNA	O
level	O
of	O
2	O
%).	O

By	O
comparison	O
,	O
treating	O
cells	O
with	O
siRNA	B-chemical
545	O
,	O
which	O
only	O
reduced	O
the	O
TSR3	B-protein
mRNA	O
to	O
20	O
%,	O
did	O
not	O
markedly	O
reduced	O
the	O
acp	B-chemical
signal	O
.	O

This	O
suggests	O
that	O
low	O
residual	O
levels	O
of	O
HsTsr3	B-protein
are	O
sufficient	O
to	O
modify	O
the	O
RNA	B-chemical
.	O

Thus	O
,	O
HsTsr3	B-protein
is	O
also	O
responsible	O
for	O
the	O
acp	B-chemical
modification	O
of	O
18S	B-chemical
rRNA	I-chemical
nucleotide	B-chemical
Ψ1248	B-ptm
in	O
helix	B-structure_element
31	I-structure_element
.	O

Similar	O
to	O
yeast	B-taxonomy_domain
,	O
siRNA	B-experimental_method
-	I-experimental_method
mediated	I-experimental_method
depletion	I-experimental_method
of	O
the	O
Ψ1248	B-protein_type
N1	I-protein_type
-	I-protein_type
methyltransferase	I-protein_type
Nep1	B-protein
/	O
Emg1	B-protein
had	O
no	O
influence	O
on	O
the	O
primer	B-evidence
extension	I-evidence
arrest	I-evidence
(	O
Figure	O
1E	O
).	O

Phenotypic	O
characterization	O
of	O
Δtsr3	B-mutant
mutants	O

Although	O
the	O
acp	B-chemical
modification	O
of	O
18S	B-chemical
rRNA	I-chemical
is	O
highly	B-protein_state
conserved	I-protein_state
in	O
eukaryotes	B-taxonomy_domain
,	O
yeast	B-taxonomy_domain
Δtsr3	B-mutant
mutants	O
showed	O
only	O
a	O
minor	O
growth	O
defect	O
.	O

However	O
,	O
the	O
Δtsr3	B-mutant
deletion	O
was	O
synthetic	O
sick	O
with	O
a	O
Δsnr35	B-mutant
deletion	O
preventing	O
pseudouridylation	B-ptm
and	O
Nep1	B-protein
-	O
catalyzed	O
methylation	O
of	O
nucleotide	O
1191	B-residue_number
(	O
Figure	O
2A	O
).	O

Interestingly	O
,	O
no	O
increased	O
growth	O
defect	O
could	O
be	O
observed	O
for	O
Δtsr3	B-mutant
Δnep1	I-mutant
recombinants	O
containing	O
the	O
nep1	B-gene
suppressor	O
mutation	O
Δnop6	B-mutant
as	O
well	O
as	O
for	O
Δtsr3	B-mutant
Δsnr35	I-mutant
Δnep1	I-mutant
recombinants	O
with	O
unmodified	B-protein_state
U1191	B-residue_name_number
(	O
Supplementary	O
Figure	O
S2D	O
and	O
E	O
).	O

Phenotypic	O
characterization	O
of	O
yeast	B-taxonomy_domain
TSR3	B-protein
deletion	O
(	O
Δtrs3	B-mutant
)	O
and	O
human	B-species
TSR3	B-protein
depletion	O
(	O
siRNAs	B-chemical
544	O
and	O
545	O
)	O
and	O
cellular	O
localization	O
of	O
yeast	B-taxonomy_domain
Tsr3	B-protein
.	O
(	O
A	O
)	O
Growth	O
of	O
yeast	B-taxonomy_domain
wild	B-protein_state
type	I-protein_state
,	O
Δtsr3	B-mutant
,	O
Δsnr35	B-mutant
and	O
Δtsr3	B-mutant
Δsnr35	I-mutant
segregants	O
after	O
meiosis	O
and	O
tetrad	O
dissection	O
of	O
Δtsr3	B-mutant
/	O
TSR3	B-protein
Δsnr35	B-mutant
/	O
SNR35	B-protein
heterozygous	O
diploids	O
.	O

The	O
Δtsr3	B-mutant
deletion	O
is	O
synthetic	O
sick	O
with	O
a	O
Δsnr35	B-mutant
deletion	O
preventing	O
U1191	B-residue_name_number
pseudouridylation	O
.	O

(	O
B	O
)	O
In	O
agar	B-experimental_method
diffusion	I-experimental_method
assays	I-experimental_method
the	O
yeast	B-taxonomy_domain
Δtsr3	B-mutant
deletion	B-protein_state
mutant	I-protein_state
shows	O
a	O
hypersensitivity	O
against	O
paromomycin	B-chemical
and	O
hygromycin	B-chemical
B	I-chemical
which	O
is	O
further	O
increased	O
by	O
recombination	O
with	O
Δsnr35	B-mutant
.	O
(	O
C	O
)	O
Northern	B-experimental_method
blot	I-experimental_method
analysis	I-experimental_method
with	O
an	O
ITS1	O
hybridization	O
probe	O
after	O
siRNA	B-experimental_method
depletion	I-experimental_method
of	O
HsTSR3	B-protein
(	O
siRNAs	B-chemical
544	O
and	O
545	O
)	O
and	O
a	O
scrambled	O
siRNA	B-chemical
as	O
control	O
.	O

The	O
accumulation	O
of	O
18SE	B-chemical
and	O
47S	B-chemical
and	O
/	O
or	O
45S	B-chemical
pre	I-chemical
-	I-chemical
RNAs	I-chemical
is	O
enforced	O
upon	O
HsTSR3	B-protein
depletion	O
.	O

Right	O
gel	O
:	O
Ethidium	O
bromide	O
staining	O
showing	O
18S	B-chemical
and	O
28S	B-chemical
rRNAs	I-chemical
.	O

(	O
D	O
)	O
Cytoplasmic	O
localization	O
of	O
yeast	B-taxonomy_domain
Tsr3	B-protein
shown	O
by	O
fluorescence	B-experimental_method
microscopy	I-experimental_method
of	O
GFP	B-mutant
-	I-mutant
fused	I-mutant
Tsr3	I-mutant
.	O

From	O
left	O
to	O
right	O
:	O
differential	B-experimental_method
interference	I-experimental_method
contrast	I-experimental_method
(	O
DIC	B-experimental_method
),	O
green	O
fluorescence	O
of	O
GFP	B-mutant
-	I-mutant
Tsr3	I-mutant
,	O
red	O
fluorescence	O
of	O
Nop56	B-mutant
-	I-mutant
mRFP	I-mutant
as	O
nucleolar	O
marker	O
,	O
and	O
merge	O
of	O
GFP	B-mutant
-	I-mutant
Tsr3	I-mutant
/	O
Nop56	B-mutant
-	I-mutant
mRFP	I-mutant
with	O
DIC	B-experimental_method
.	O
(	O
E	O
)	O
Elution	B-evidence
profile	I-evidence
(	O
A254	O
)	O
after	O
sucrose	B-experimental_method
gradient	I-experimental_method
separation	I-experimental_method
of	O
yeast	B-taxonomy_domain
ribosomal	B-complex_assembly
subunits	I-complex_assembly
and	O
polysomes	B-complex_assembly
(	O
upper	O
part	O
)	O
and	O
western	B-experimental_method
blot	I-experimental_method
analysis	O
of	O
3xHA	B-chemical
tagged	O
Tsr3	B-protein
(	O
Tsr3	B-mutant
-	I-mutant
3xHA	I-mutant
)	O
after	O
SDS	B-experimental_method
-	I-experimental_method
PAGE	I-experimental_method
separation	O
of	O
polysome	O
profile	O
fractions	O
taken	O
every	O
20	O
s	O
(	O
lower	O
part	O
).	O

The	O
TSR3	B-protein
gene	O
was	O
genetically	O
modified	O
at	O
its	O
native	O
locus	O
,	O
resulting	O
in	O
a	O
C	O
-	O
terminal	O
fusion	B-protein_state
of	O
Tsr3	B-protein
with	O
a	O
3xHA	B-chemical
epitope	O
expressed	O
by	O
the	O
native	O
promotor	O
in	O
yeast	B-taxonomy_domain
strain	O
CEN	O
.	O
BM258	O
-	O
5B	O
.	O

The	O
influence	O
of	O
the	O
acp	B-chemical
modification	O
of	O
nucleotide	B-chemical
1191	B-residue_number
on	O
ribosome	O
function	O
was	O
analyzed	O
by	O
treating	O
Δtsr3	B-mutant
mutants	O
with	O
protein	O
synthesis	O
inhibitors	O
.	O

Similar	O
to	O
a	O
temperature	O
-	O
sensitive	O
nep1	B-gene
mutant	B-protein_state
,	O
the	O
Δtsr3	B-mutant
deletion	O
caused	O
hypersensitivity	O
to	O
paromomycin	B-chemical
and	O
,	O
to	O
a	O
lesser	O
extent	O
,	O
to	O
hygromycin	B-chemical
B	I-chemical
(	O
Figure	O
2B	O
),	O
but	O
not	O
to	O
G418	B-chemical
or	O
cycloheximide	B-chemical
(	O
data	O
not	O
shown	O
).	O

In	O
accordance	O
with	O
the	O
synthetic	O
sick	O
growth	O
phenotype	O
the	O
paromomycin	B-chemical
and	O
hygromycin	B-chemical
B	I-chemical
hypersensitivity	O
further	O
increased	O
in	O
a	O
Δtsr3	B-mutant
Δsnr35	I-mutant
recombination	O
strain	O
(	O
Figure	O
2B	O
).	O

In	O
a	O
yeast	B-taxonomy_domain
Δtsr3	B-mutant
strain	O
as	O
well	O
as	O
in	O
the	O
Δtsr3	B-mutant
Δsnr35	I-mutant
recombinant	O
20S	B-chemical
pre	I-chemical
-	I-chemical
rRNA	I-chemical
accumulated	O
significantly	O
and	O
the	O
level	O
of	O
mature	O
18S	B-chemical
rRNA	I-chemical
was	O
reduced	O
(	O
Supplementary	O
Figures	O
S2C	O
and	O
S3D	O
),	O
as	O
reported	O
previously	O
.	O

A	O
minor	O
effect	O
on	O
20S	B-chemical
rRNA	I-chemical
accumulation	O
was	O
also	O
observed	O
for	O
Δsnr35	B-mutant
,	O
but	O
-	O
probably	O
due	O
to	O
different	O
strain	O
backgrounds	O
–	O
to	O
a	O
weaker	O
extent	O
than	O
described	O
earlier	O
.	O

In	O
human	B-species
cells	O
,	O
the	O
depletion	B-experimental_method
of	I-experimental_method
HsTsr3	B-protein
in	O
HCT116	O
(+/+)	O
cells	O
caused	O
an	O
accumulation	O
of	O
the	O
human	B-species
20S	B-chemical
pre	I-chemical
-	I-chemical
rRNA	I-chemical
equivalent	O
18S	B-chemical
-	I-chemical
E	I-chemical
suggesting	O
an	O
evolutionary	O
conserved	O
role	O
of	O
Tsr3	B-protein
in	O
the	O
late	O
steps	O
of	O
18S	B-chemical
rRNA	I-chemical
processing	O
(	O
Figure	O
2C	O
and	O
Supplementary	O
Figure	O
S2B	O
).	O

Surprisingly	O
,	O
early	O
nucleolar	O
processing	O
reactions	O
were	O
also	O
inhibited	O
,	O
and	O
this	O
was	O
observed	O
in	O
both	O
yeast	B-taxonomy_domain
Δtsr3	B-mutant
cells	O
(	O
see	O
accumulation	O
of	O
35S	B-complex_assembly
in	O
Supplementary	O
Figure	O
S2C	O
)	O
and	O
Tsr3	B-protein
depleted	O
human	B-species
cells	O
(	O
see	O
47S	B-complex_assembly
/	O
45S	B-complex_assembly
accumulation	O
in	O
Figure	O
2C	O
and	O
Northern	B-experimental_method
blot	I-experimental_method
quantification	O
in	O
Supplementary	O
Figure	O
S2B	O
).	O

Consistent	O
with	O
its	O
role	O
in	O
late	O
18S	B-chemical
rRNA	I-chemical
processing	O
,	O
TSR3	B-protein
deletion	O
leads	O
to	O
a	O
ribosomal	O
subunit	O
imbalance	O
with	O
a	O
reduced	O
40S	B-complex_assembly
to	O
60S	B-complex_assembly
ratio	O
of	O
0	O
.	O
81	O
(	O
σ	O
=	O
0	O
.	O
024	O
)	O
which	O
was	O
further	O
increased	O
in	O
a	O
Δtsr3	B-mutant
Δsnr35	I-mutant
recombinant	O
to	O
0	O
.	O
73	O
(	O
σ	O
=	O
0	O
.	O
023	O
)	O
(	O
Supplementary	O
Figure	O
S2F	O
).	O

In	O
polysome	B-evidence
profiles	I-evidence
,	O
a	O
reduced	O
level	O
of	O
80S	B-complex_assembly
ribosomes	I-complex_assembly
and	O
a	O
strong	O
signal	O
for	O
free	O
60S	B-complex_assembly
subunits	O
was	O
observed	O
in	O
line	O
with	O
the	O
40S	B-complex_assembly
subunit	O
deficiency	O
(	O
Supplementary	O
Figure	O
S2G	O
).	O

Cellular	O
localization	O
of	O
Tsr3	B-protein
in	O
S	B-species
.	I-species
cerevisiae	I-species

Fluorescence	B-experimental_method
microscopy	I-experimental_method
of	O
GFP	B-protein_state
-	I-protein_state
tagged	I-protein_state
Tsr3	B-protein
localized	O
the	O
fusion	O
protein	O
in	O
the	O
cytoplasm	O
of	O
yeast	B-taxonomy_domain
cells	O
and	O
no	O
co	O
-	O
localization	O
with	O
the	O
nucleolar	O
marker	O
protein	O
Nop56	B-protein
could	O
be	O
observed	O
(	O
Figure	O
2D	O
).	O

This	O
agrees	O
with	O
previous	O
biochemical	O
data	O
suggesting	O
that	O
the	O
acp	B-chemical
modification	O
of	O
18S	B-chemical
rRNA	I-chemical
occurs	O
late	O
during	O
40S	B-complex_assembly
subunit	O
biogenesis	O
in	O
the	O
cytoplasm	O
,	O
and	O
makes	O
an	O
additional	O
nuclear	O
localization	O
as	O
reported	O
in	O
a	O
previous	O
large	O
-	O
scale	O
analysis	O
unlikely	O
.	O

After	O
polysome	B-experimental_method
gradient	I-experimental_method
separation	I-experimental_method
C	O
-	O
terminally	O
epitope	O
-	O
labeled	O
Tsr3	B-mutant
-	I-mutant
3xHA	I-mutant
was	O
exclusively	O
detectable	O
in	O
the	O
low	O
-	O
density	O
fraction	O
(	O
Figure	O
2E	O
).	O

Such	O
distribution	B-evidence
on	I-evidence
a	I-evidence
density	I-evidence
gradient	I-evidence
suggests	O
that	O
Tsr3	B-protein
only	O
interacts	O
transiently	O
with	O
pre	B-complex_assembly
-	I-complex_assembly
40S	I-complex_assembly
subunits	I-complex_assembly
,	O
which	O
presumably	O
explains	O
why	O
it	O
was	O
not	O
characterized	O
in	O
pre	B-experimental_method
-	I-experimental_method
ribosome	I-experimental_method
affinity	I-experimental_method
purifications	I-experimental_method
.	O

Structure	B-evidence
of	O
Tsr3	B-protein

Searches	O
for	O
sequence	O
homologs	O
of	O
S	B-species
.	I-species
cerevisiae	I-species
Tsr3	B-protein
(	O
ScTsr3	B-protein
)	O
by	O
us	O
and	O
others	O
revealed	O
that	O
the	O
genomes	O
of	O
many	O
archaea	B-taxonomy_domain
contain	O
genes	O
encoding	O
Tsr3	B-protein_type
-	I-protein_type
like	I-protein_type
proteins	I-protein_type
.	O

However	O
,	O
these	O
archaeal	B-taxonomy_domain
homologs	O
are	O
significantly	O
smaller	O
than	O
ScTsr3	B-protein
(∼	O
190	O
aa	O
in	O
archaea	B-taxonomy_domain
vs	O
.	O
313	O
aa	O
in	O
yeast	B-taxonomy_domain
)	O
due	O
to	O
shortened	O
N	O
-	O
and	O
C	O
-	O
termini	O
(	O
Supplementary	O
Figure	O
S1A	O
).	O

To	O
locate	O
the	O
domains	O
most	O
important	O
for	O
Tsr3	B-protein
activity	O
,	O
ScTsr3	B-protein
fragments	O
of	O
different	O
lengths	O
containing	O
the	O
highly	B-protein_state
conserved	I-protein_state
central	O
part	O
were	O
expressed	B-experimental_method
in	O
a	O
Δtsr3	B-mutant
mutant	B-protein_state
(	O
Figure	O
3A	O
)	O
and	O
analyzed	O
by	O
primer	B-experimental_method
extension	I-experimental_method
(	O
Figure	O
3B	O
)	O
and	O
Northern	B-experimental_method
blotting	I-experimental_method
(	O
Figure	O
3C	O
).	O

N	O
-	O
terminal	O
truncations	B-experimental_method
of	O
up	O
to	O
45	B-residue_range
aa	I-residue_range
and	O
C	O
-	O
terminal	O
truncations	B-experimental_method
of	O
up	O
to	O
76	B-residue_range
aa	I-residue_range
mediated	O
acp	B-chemical
modification	O
as	O
efficiently	O
as	O
the	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
protein	O
and	O
no	O
significant	O
increased	O
levels	O
of	O
20S	B-chemical
pre	I-chemical
-	I-chemical
RNA	I-chemical
were	O
detected	O
.	O

Even	O
a	O
Tsr3	B-protein
fragment	O
with	O
a	O
90	B-residue_range
aa	I-residue_range
C	O
-	O
terminal	O
truncation	O
showed	O
a	O
residual	O
primer	O
extension	O
stop	O
,	O
whereas	O
N	O
-	O
terminal	O
truncations	O
exceeding	O
46	B-residue_range
aa	I-residue_range
almost	O
completely	O
abolished	O
the	O
primer	O
extension	O
arrest	O
(	O
Figure	O
3B	O
).	O

Domain	O
characterization	O
of	O
yeast	B-taxonomy_domain
Tsr3	B-protein
and	O
correlation	O
of	O
acp	B-chemical
modification	O
with	O
late	O
18S	B-chemical
rRNA	I-chemical
processing	O
steps	O
.	O
(	O
A	O
)	O
Scheme	O
of	O
the	O
TSR3	B-protein
gene	O
with	O
truncation	O
positions	O
in	O
the	O
open	O
reading	O
frame	O
.	O

TSR3	B-protein
fragments	O
of	O
different	O
length	O
were	O
expressed	O
under	O
the	O
native	O
promotor	O
from	O
multicopy	O
plasmids	O
in	O
a	O
Δtsr3	B-mutant
deletion	O
strain	O
.	O

(	O
B	O
)	O
Primer	B-experimental_method
extension	I-experimental_method
analysis	I-experimental_method
of	O
18S	B-chemical
rRNA	I-chemical
acp	B-chemical
modification	O
in	O
yeast	B-taxonomy_domain
cells	O
expressing	O
the	O
indicated	O
TSR3	B-protein
fragments	O
.	O

N	O
-	O
terminal	O
deletions	B-experimental_method
of	O
36	B-residue_range
or	O
45	B-residue_range
amino	O
acids	O
and	O
C	O
-	O
terminal	O
deletions	B-experimental_method
of	O
43	B-residue_range
or	O
76	B-residue_range
residues	O
show	O
a	O
primer	B-evidence
extension	I-evidence
stop	I-evidence
comparable	O
to	O
the	O
wild	B-protein_state
type	I-protein_state
.	O

Tsr3	B-protein
fragments	O
37	B-residue_range
–	I-residue_range
223	I-residue_range
or	O
46	B-residue_range
–	I-residue_range
223	I-residue_range
cause	O
a	O
nearly	O
complete	O
loss	O
of	O
the	O
arrest	O
signal	O
.	O

The	O
box	O
highlights	O
the	O
shortest	O
Tsr3	B-protein
fragment	O
(	O
aa	O
46	B-residue_range
–	I-residue_range
270	I-residue_range
)	O
with	O
wild	B-protein_state
type	I-protein_state
activity	O
(	O
strong	O
primer	B-evidence
extension	I-evidence
block	I-evidence
).	O
(	O
C	O
)	O
Northern	B-experimental_method
blot	I-experimental_method
analysis	O
of	O
20S	B-chemical
pre	I-chemical
-	I-chemical
rRNA	I-chemical
accumulation	O
.	O

A	O
weak	O
20S	B-chemical
rRNA	I-chemical
signal	O
,	O
indicating	O
normal	O
processing	O
,	O
is	O
observed	O
for	O
Tsr3	B-protein
fragment	O
46	B-residue_range
–	I-residue_range
270	I-residue_range
(	O
highlighted	O
in	O
a	O
box	O
)	O
showing	O
its	O
functionality	O
.	O

Strong	O
20S	O
rRNA	O
accumulation	O
similar	O
to	O
that	O
of	O
the	O
Δtsr3	B-mutant
deletion	B-experimental_method
is	O
observed	O
for	O
Tsr3	B-protein
fragments	O
37	B-residue_range
–	I-residue_range
223	I-residue_range
or	O
46	B-residue_range
–	I-residue_range
223	I-residue_range
.	O

Thus	O
,	O
the	O
archaeal	B-taxonomy_domain
homologs	O
correspond	O
to	O
the	O
functional	O
core	O
of	O
Tsr3	B-protein
.	O

In	O
order	O
to	O
define	O
the	O
structural	O
basis	O
for	O
Tsr3	B-protein
function	O
,	O
homologs	O
from	O
thermophilic	B-taxonomy_domain
archaea	I-taxonomy_domain
were	O
screened	O
for	O
crystallization	B-experimental_method
.	O

We	O
focused	O
on	O
archaeal	B-taxonomy_domain
species	O
containing	O
a	O
putative	O
Nep1	B-protein
homolog	O
suggesting	O
that	O
these	O
species	O
are	O
in	O
principle	O
capable	O
of	O
synthesizing	O
N1	B-chemical
-	I-chemical
methyl	I-chemical
-	I-chemical
N3	I-chemical
-	I-chemical
acp	I-chemical
-	I-chemical
pseudouridine	I-chemical
.	O

Well	O
diffracting	O
crystals	B-evidence
were	O
obtained	O
for	O
Tsr3	B-protein
homologs	O
from	O
the	O
two	O
crenarchaeal	B-taxonomy_domain
species	O
Vulcanisaeta	B-species
distributa	I-species
(	O
VdTsr3	B-protein
)	O
and	O
Sulfolobus	B-species
solfataricus	I-species
(	O
SsTsr3	B-protein
)	O
which	O
share	O
36	O
%	O
(	O
VdTsr3	B-protein
)	O
and	O
38	O
%	O
(	O
SsTsr3	B-protein
)	O
identity	O
with	O
the	O
ScTsr3	B-protein
core	B-structure_element
region	I-structure_element
(	O
ScTsr3	B-protein
aa	O
46	B-residue_range
–	I-residue_range
223	I-residue_range
).	O

While	O
for	O
S	B-species
.	I-species
solfataricus	I-species
the	O
existence	O
of	O
a	O
modified	O
nucleotide	B-chemical
of	O
unknown	O
chemical	O
composition	O
in	O
the	O
loop	B-structure_element
capping	I-structure_element
helix	I-structure_element
31	I-structure_element
of	O
its	O
16S	B-chemical
rRNA	I-chemical
has	O
been	O
demonstrated	O
,	O
no	O
information	O
regarding	O
rRNA	O
modifications	O
is	O
yet	O
available	O
for	O
V	B-species
.	I-species
distributa	I-species
.	O

Crystals	B-evidence
of	O
VdTsr3	B-protein
diffracted	O
to	O
a	O
resolution	O
of	O
1	O
.	O
6	O
Å	O
whereas	O
crystals	B-evidence
of	O
SsTsr3	B-protein
diffracted	O
to	O
2	O
.	O
25	O
Å	O
.	O
Serendipitously	O
,	O
VdTsr3	B-protein
was	O
purified	O
and	O
crystallized	B-experimental_method
in	B-protein_state
complex	I-protein_state
with	I-protein_state
endogenous	B-protein_state
(	O
E	B-species
.	I-species
coli	I-species
)	O
SAM	B-chemical
(	O
Supplementary	O
Figure	O
S4	O
)	O
while	O
SsTsr3	B-protein
crystals	B-evidence
contained	O
the	O
protein	O
in	O
the	O
apo	B-protein_state
state	O
.	O

The	O
structure	B-evidence
of	O
VdTsr3	B-protein
was	O
solved	O
ab	O
initio	O
,	O
by	O
single	B-experimental_method
-	I-experimental_method
wavelength	I-experimental_method
anomalous	I-experimental_method
diffraction	I-experimental_method
phasing	I-experimental_method
(	O
Se	B-experimental_method
-	I-experimental_method
SAD	I-experimental_method
)	O
with	O
Se	B-chemical
containing	O
derivatives	O
(	O
selenomethionine	B-chemical
and	O
seleno	B-chemical
-	I-chemical
substituted	I-chemical
SAM	I-chemical
).	O

The	O
structure	B-evidence
of	O
SsTsr3	B-protein
was	O
solved	O
by	O
molecular	B-experimental_method
replacement	I-experimental_method
using	O
VdTsr3	B-protein
as	O
a	O
search	O
model	O
(	O
see	O
Supplementary	O
Table	O
S1	O
for	O
data	O
collection	O
and	O
refinement	O
statistics	O
).	O

The	O
structure	B-evidence
of	O
VdTsr3	B-protein
can	O
be	O
divided	O
into	O
two	O
domains	O
(	O
Figure	O
4A	O
).	O

The	O
N	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
(	O
aa	O
1	B-residue_range
–	I-residue_range
92	I-residue_range
)	O
has	O
a	O
mixed	O
α	B-structure_element
/	I-structure_element
β	I-structure_element
-	I-structure_element
structure	I-structure_element
centered	O
around	O
a	O
five	B-structure_element
-	I-structure_element
stranded	I-structure_element
all	I-structure_element
-	I-structure_element
parallel	I-structure_element
β	I-structure_element
-	I-structure_element
sheet	I-structure_element
(	O
Figure	O
4B	O
)	O
with	O
the	O
strand	O
order	O
β5	B-structure_element
↑-	I-structure_element
β3	B-structure_element
↑-	I-structure_element
β4	B-structure_element
↑-	I-structure_element
β1	B-structure_element
↑-	I-structure_element
β2	B-structure_element
↑.	I-structure_element
The	O
loops	B-structure_element
connecting	O
β1	B-structure_element
and	O
β2	B-structure_element
,	O
β3	B-structure_element
and	O
β4	B-structure_element
and	O
β4	B-structure_element
and	O
β5	B-structure_element
include	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
α1	B-structure_element
,	O
α2	B-structure_element
and	O
α3	B-structure_element
,	O
respectively	O
.	O

The	O
loop	B-structure_element
connecting	O
β2	B-structure_element
and	O
β3	B-structure_element
contains	O
a	O
single	O
turn	O
of	O
a	O
310	B-structure_element
-	I-structure_element
helix	I-structure_element
.	O
Helices	B-structure_element
α1	B-structure_element
and	O
α2	B-structure_element
are	O
located	O
on	O
one	O
side	O
of	O
the	O
five	B-structure_element
-	I-structure_element
stranded	I-structure_element
β	I-structure_element
-	I-structure_element
sheet	I-structure_element
while	O
α3	B-structure_element
packs	O
against	O
the	O
opposite	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
surface	O
.	O

The	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
(	O
aa	O
93	B-residue_range
–	I-residue_range
184	I-residue_range
)	O
has	O
a	O
globular	B-structure_element
all	I-structure_element
α	I-structure_element
-	I-structure_element
helical	I-structure_element
structure	I-structure_element
comprising	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
α4	B-structure_element
to	I-structure_element
α9	I-structure_element
.	O

Remarkably	O
,	O
the	O
entire	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
(	O
92	B-residue_range
aa	I-residue_range
)	O
of	O
the	O
protein	O
is	O
threaded	O
through	O
the	O
loop	B-structure_element
which	O
connects	O
β	B-structure_element
-	I-structure_element
strand	I-structure_element
β3	B-structure_element
and	O
α	B-structure_element
-	I-structure_element
helix	I-structure_element
α2	B-structure_element
of	O
the	O
N	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
.	O

Thus	O
,	O
the	O
VdTsr3	B-protein
structure	B-evidence
contains	O
a	O
deep	B-structure_element
trefoil	I-structure_element
knot	I-structure_element
.	O

The	O
structure	B-evidence
of	O
SsTsr3	B-protein
in	O
the	O
apo	B-protein_state
state	O
is	O
very	O
similar	O
to	O
that	O
of	O
VdTsr3	B-protein
(	O
Figure	O
4C	O
)	O
with	O
an	O
RMSD	B-evidence
for	O
equivalent	O
Cα	O
atoms	O
of	O
1	O
.	O
1	O
Å	O
.	O
The	O
only	O
significant	O
difference	O
in	O
the	O
global	O
structure	B-evidence
of	O
the	O
two	O
proteins	O
is	O
the	O
presence	O
of	O
an	O
extended	O
α	B-structure_element
-	I-structure_element
helix	I-structure_element
α8	B-structure_element
and	O
the	O
absence	B-protein_state
of	I-protein_state
α	B-structure_element
-	I-structure_element
helix	I-structure_element
α9	B-structure_element
in	O
SsTsr3	B-protein
.	O

Tsr3	B-protein
has	O
a	O
fold	O
similar	O
to	O
SPOUT	B-protein_type
-	I-protein_type
class	I-protein_type
RNA	I-protein_type
methyltransferases	I-protein_type
.	O
(	O
A	O
)	O
Cartoon	O
representation	O
of	O
the	O
X	B-evidence
-	I-evidence
ray	I-evidence
structure	I-evidence
of	O
VdTsr3	B-protein
in	O
two	O
orientations	O
.	O

β	B-structure_element
-	I-structure_element
strands	I-structure_element
are	O
colored	O
in	O
crimson	O
whereas	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
in	O
the	O
N	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
are	O
colored	O
light	O
blue	O
and	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
in	O
the	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
are	O
colored	O
dark	O
blue	O
.	O

The	O
bound	O
S	B-chemical
-	I-chemical
adenosylmethionine	I-chemical
is	O
shown	O
in	O
a	O
stick	O
representation	O
and	O
colored	O
by	O
atom	O
type	O
.	O

A	O
red	O
arrow	O
marks	O
the	O
location	O
of	O
the	O
topological	B-structure_element
knot	I-structure_element
in	O
the	O
structure	B-evidence
.	O
(	O
B	O
)	O
Secondary	O
structure	O
representation	O
of	O
the	O
VdTsr3	B-protein
structure	B-evidence
.	O

The	O
color	O
coding	O
is	O
the	O
same	O
as	O
in	O
(	O
A	O
).	O
(	O
C	O
)	O
Structural	B-experimental_method
superposition	I-experimental_method
of	O
the	O
X	B-evidence
-	I-evidence
ray	I-evidence
structures	I-evidence
of	O
VdTsr3	B-protein
in	O
the	O
SAM	B-protein_state
-	I-protein_state
bound	I-protein_state
state	O
(	O
red	O
)	O
and	O
SsTsr3	B-protein
(	O
blue	O
)	O
in	O
the	O
apo	B-protein_state
state	O
.	O

The	O
locations	O
of	O
the	O
α	B-structure_element
-	I-structure_element
helix	I-structure_element
α8	B-structure_element
which	O
is	O
longer	O
in	O
SsTsr3	B-protein
and	O
of	O
α	B-structure_element
-	I-structure_element
helix	I-structure_element
α9	B-structure_element
which	O
is	O
only	O
present	O
in	O
VdTsr3	B-protein
are	O
indicated	O
.	O
(	O
D	O
)	O
Secondary	O
structure	O
cartoon	O
(	O
left	O
)	O
of	O
S	B-species
.	I-species
pombe	I-species
Trm10	B-protein
(	O
pdb4jwf	O
)—	O
the	O
SPOUT	B-protein_type
-	I-protein_type
class	I-protein_type
RNA	I-protein_type
methyltransferase	I-protein_type
structurally	O
most	O
similar	O
to	O
Tsr3	B-protein
and	O
superposition	B-experimental_method
of	O
the	O
VdTsr3	B-protein
and	O
Trm10	B-protein
X	B-evidence
-	I-evidence
ray	I-evidence
structures	I-evidence
(	O
right	O
).	O
(	O
E	O
)	O
Analytical	B-experimental_method
gel	I-experimental_method
filtration	I-experimental_method
profiles	B-evidence
for	O
VdTsr3	B-protein
(	O
red	O
)	O
and	O
SsTsr3	B-protein
(	O
blue	O
)	O
show	O
that	O
both	O
proteins	O
are	O
monomeric	B-oligomeric_state
in	O
solution	O
.	O

Vd	B-species
,	O
Vulcanisaeta	B-species
distributa	I-species
;	O
Ss	B-species
,	O
Sulfolobus	B-species
solfataricus	I-species
.	O

Structure	B-experimental_method
predictions	I-experimental_method
suggested	O
that	O
Tsr3	B-protein
might	O
contain	O
a	O
so	O
-	O
called	O
RLI	B-structure_element
domain	I-structure_element
which	O
contains	O
a	O
‘	O
bacterial	B-structure_element
like	I-structure_element
’	I-structure_element
ferredoxin	I-structure_element
fold	I-structure_element
and	O
binds	O
two	O
iron	O
-	O
sulfur	O
clusters	O
through	O
eight	O
conserved	B-protein_state
cysteine	B-residue_name
residues	O
.	O

However	O
,	O
no	O
structural	O
similarity	O
to	O
an	O
RLI	B-structure_element
-	I-structure_element
domain	I-structure_element
was	O
detectable	O
.	O

This	O
is	O
in	O
accordance	O
with	O
the	O
functional	O
analysis	O
of	O
alanine	B-experimental_method
replacement	I-experimental_method
mutations	I-experimental_method
of	O
cysteine	B-residue_name
residues	O
in	O
ScTsr3	B-protein
(	O
Supplementary	O
Figure	O
S3	O
).	O

The	O
β	B-structure_element
-	I-structure_element
strand	I-structure_element
topology	I-structure_element
and	O
the	O
deep	O
C	O
-	O
terminal	O
trefoil	B-structure_element
knot	I-structure_element
of	O
archaeal	B-taxonomy_domain
Tsr3	B-protein
are	O
the	O
structural	O
hallmarks	O
of	O
the	O
SPOUT	B-protein_type
-	I-protein_type
class	I-protein_type
RNA	I-protein_type
-	I-protein_type
methyltransferase	I-protein_type
fold	O
.	O

The	O
closest	O
structural	O
homolog	O
identified	O
in	O
a	O
DALI	B-experimental_method
search	I-experimental_method
is	O
the	O
tRNA	B-protein_type
methyltransferase	I-protein_type
Trm10	B-protein
(	O
DALI	B-evidence
Z	I-evidence
-	I-evidence
score	I-evidence
6	O
.	O
8	O
)	O
which	O
methylates	O
the	O
N1	O
nitrogen	O
of	O
G9	B-residue_name_number
/	O
A9	B-residue_name_number
in	O
many	O
archaeal	B-taxonomy_domain
and	O
eukaryotic	B-taxonomy_domain
tRNAs	B-chemical
by	O
using	O
SAM	B-chemical
as	O
the	O
methyl	O
group	O
donor	O
.	O

In	O
comparison	O
to	O
Tsr3	B-protein
the	O
central	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
element	I-structure_element
of	O
Trm10	B-protein
is	O
extended	O
by	O
one	O
additional	O
β	B-structure_element
-	I-structure_element
strand	I-structure_element
pairing	O
to	O
β2	B-structure_element
.	O

Furthermore	O
,	O
the	O
trefoil	B-structure_element
knot	I-structure_element
of	O
Trm10	B-protein
is	O
not	O
as	O
deep	O
as	O
that	O
of	O
Tsr3	B-protein
(	O
Figure	O
4D	O
).	O

Interestingly	O
,	O
Nep1	B-protein
—	O
the	O
enzyme	O
preceding	O
Tsr3	B-protein
in	O
the	O
biosynthetic	O
pathway	O
for	O
the	O
synthesis	O
of	O
m1acp3Ψ	B-chemical
—	O
also	O
belongs	O
to	O
the	O
SPOUT	B-protein_type
-	I-protein_type
class	I-protein_type
of	I-protein_type
RNA	I-protein_type
methyltransferases	I-protein_type
.	O

However	O
,	O
the	O
structural	O
similarities	O
between	O
Nep1	B-protein
and	O
Tsr3	B-protein
(	O
DALI	B-evidence
Z	I-evidence
-	I-evidence
score	I-evidence
4	O
.	O
4	O
)	O
are	O
less	O
pronounced	O
than	O
between	O
Tsr3	B-protein
and	O
Trm10	B-protein
.	O

Most	O
SPOUT	B-protein_type
-	I-protein_type
class	I-protein_type
RNA	I-protein_type
-	I-protein_type
methyltransferases	I-protein_type
are	O
homodimers	B-oligomeric_state
.	O

A	O
notable	O
exception	O
is	O
Trm10	B-protein
.	O

Gel	B-experimental_method
filtration	I-experimental_method
experiments	O
with	O
both	O
VdTsr3	B-protein
and	O
SsTsr3	B-protein
(	O
Figure	O
4E	O
)	O
showed	O
that	O
both	O
proteins	O
are	O
monomeric	B-oligomeric_state
in	O
solution	O
thereby	O
extending	O
the	O
structural	O
similarities	O
to	O
Trm10	B-protein
.	O

So	O
far	O
,	O
structural	O
information	O
is	O
only	O
available	O
for	O
one	O
other	O
enzyme	O
that	O
transfers	O
the	O
acp	B-chemical
group	O
from	O
SAM	B-chemical
to	O
an	O
RNA	B-chemical
nucleotide	B-chemical
.	O

This	O
enzyme	O
,	O
Tyw2	B-protein
,	O
is	O
part	O
of	O
the	O
biosynthesis	O
pathway	O
of	O
wybutosine	B-chemical
nucleotides	I-chemical
in	O
tRNAs	B-chemical
.	O

However	O
,	O
there	O
are	O
no	O
structural	O
similarities	O
between	O
Tsr3	B-protein
and	O
Tyw2	B-protein
,	O
which	O
contains	O
an	O
all	B-structure_element
-	I-structure_element
parallel	I-structure_element
β	I-structure_element
-	I-structure_element
sheet	I-structure_element
of	O
a	O
different	O
topology	O
and	O
no	O
knot	B-structure_element
structure	I-structure_element
.	O

Instead	O
,	O
Tyw2	B-protein
has	O
a	O
fold	O
typical	O
for	O
the	O
class	B-protein_type
-	I-protein_type
I	I-protein_type
-	I-protein_type
or	I-protein_type
Rossmann	I-protein_type
-	I-protein_type
fold	I-protein_type
class	I-protein_type
of	I-protein_type
methyltransferases	I-protein_type
(	O
Supplementary	O
Figure	O
S5B	O
).	O

Cofactor	O
binding	O
of	O
Tsr3	B-protein

The	O
SAM	B-site
-	I-site
binding	I-site
site	I-site
of	O
Tsr3	B-protein
is	O
located	O
in	O
a	O
deep	O
crevice	O
between	O
the	O
N	B-structure_element
-	I-structure_element
and	I-structure_element
C	I-structure_element
-	I-structure_element
terminal	I-structure_element
domains	I-structure_element
in	O
the	O
vicinity	O
of	O
the	O
trefoil	B-structure_element
knot	I-structure_element
as	O
typical	O
for	O
SPOUT	B-protein_type
-	I-protein_type
class	I-protein_type
RNA	I-protein_type
-	I-protein_type
methyltransferases	I-protein_type
(	O
Figure	O
4A	O
).	O

The	O
adenine	B-chemical
base	O
of	O
the	O
cofactor	O
is	O
recognized	O
by	O
hydrogen	O
bonds	O
between	O
its	O
N1	O
nitrogen	O
and	O
the	O
backbone	O
amide	O
of	O
L93	B-residue_name_number
directly	O
preceding	O
β5	B-structure_element
as	O
well	O
as	O
between	O
its	O
N6	O
-	O
amino	O
group	O
and	O
the	O
backbone	O
carbonyl	O
group	O
of	O
Y108	B-residue_name_number
located	O
in	O
the	O
loop	B-structure_element
connecting	O
β5	B-structure_element
in	O
the	O
N	B-structure_element
-	I-structure_element
terminal	I-structure_element
and	O
α4	B-structure_element
in	O
the	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
(	O
Figure	O
5A	O
).	O

Furthermore	O
,	O
the	O
adenine	B-chemical
base	O
of	O
SAM	B-chemical
is	O
involved	O
in	O
hydrophobic	O
packing	O
interactions	O
with	O
the	O
side	O
chains	O
of	O
L45	B-residue_name_number
(	O
β3	B-structure_element
),	O
P47	B-residue_name_number
and	O
W73	B-residue_name_number
(	O
α3	B-structure_element
)	O
in	O
the	O
N	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
as	O
well	O
as	O
with	O
L93	B-residue_name_number
,	O
L110	B-residue_name_number
(	O
both	O
in	O
the	O
loop	B-structure_element
connecting	O
β5	B-structure_element
and	O
α4	B-structure_element
)	O
and	O
A115	B-residue_name_number
(	O
α5	B-structure_element
)	O
in	O
the	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
.	O

The	O
ribose	B-chemical
2	O
′	O
and	O
3	O
′	O
hydroxyl	O
groups	O
of	O
SAM	B-chemical
are	O
hydrogen	O
bonded	O
to	O
the	O
backbone	O
carbonyl	O
group	O
of	O
I69	B-residue_name_number
.	O

The	O
acp	B-chemical
side	O
chain	O
of	O
SAM	B-chemical
is	O
fixed	O
in	O
position	O
by	O
hydrogen	O
bonding	O
of	O
its	O
carboxylate	O
group	O
to	O
the	O
backbone	O
amide	O
and	O
the	O
side	O
chain	O
hydroxyl	O
group	O
of	O
T19	B-residue_name_number
in	O
α1	B-structure_element
as	O
well	O
as	O
the	O
backbone	O
amide	O
group	O
of	O
T112	B-residue_name_number
in	O
α4	B-structure_element
(	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
).	O

Most	O
importantly	O
,	O
the	O
methyl	O
group	O
of	O
SAM	B-chemical
is	O
buried	O
in	O
a	O
hydrophobic	B-site
pocket	I-site
formed	O
by	O
the	O
sidechains	O
of	O
W73	B-residue_name_number
and	O
A76	B-residue_name_number
both	O
located	O
in	O
α3	B-structure_element
(	O
Figure	O
5A	O
and	O
B	O
).	O

W73	B-residue_name_number
is	O
highly	B-protein_state
conserved	I-protein_state
in	O
all	O
known	O
Tsr3	B-protein_type
proteins	I-protein_type
,	O
whereas	O
A76	B-residue_name_number
can	O
be	O
replaced	O
by	O
other	O
hydrophobic	O
amino	B-chemical
acids	I-chemical
.	O

Consequently	O
,	O
the	O
accessibility	O
of	O
this	O
methyl	O
group	O
for	O
a	O
nucleophilic	O
attack	O
is	O
strongly	O
reduced	O
in	O
comparison	O
with	O
RNA	B-protein_type
-	I-protein_type
methyltransferases	I-protein_type
such	O
as	O
Trm10	B-protein
(	O
Figure	O
5B	O
,	O
C	O
).	O

In	O
contrast	O
,	O
the	O
acp	B-chemical
side	O
chain	O
of	O
SAM	B-chemical
is	O
accessible	O
for	O
reactions	O
in	O
the	O
Tsr3	B-protein_state
-	I-protein_state
bound	I-protein_state
state	O
(	O
Figure	O
5B	O
).	O

SAM	B-chemical
-	O
binding	O
by	O
Tsr3	B-protein
.	O

(	O
A	O
)	O
Close	O
-	O
up	O
view	O
of	O
the	O
SAM	B-site
-	I-site
binding	I-site
pocket	I-site
of	O
VdTsr3	B-protein
.	O

Nitrogen	O
atoms	O
are	O
dark	O
blue	O
,	O
oxygen	O
atoms	O
red	O
,	O
sulfur	B-chemical
atoms	O
orange	O
,	O
carbon	O
atoms	O
of	O
the	O
protein	O
light	O
blue	O
and	O
carbon	O
atoms	O
of	O
SAM	B-chemical
yellow	O
.	O

(	O
B	O
)	O
Solvent	O
accessibility	O
of	O
the	O
acp	B-chemical
group	O
of	O
SAM	B-chemical
bound	B-protein_state
to	I-protein_state
VdTsr3	B-protein
.	O

The	O
solvent	O
accessible	O
surface	O
of	O
the	O
protein	O
is	O
shown	O
in	O
semitransparent	O
gray	O
whereas	O
SAM	B-chemical
is	O
show	O
in	O
a	O
stick	O
representation	O
.	O

A	O
red	O
arrow	O
indicates	O
the	O
reactive	O
CH2	O
-	O
moiety	O
of	O
the	O
acp	B-chemical
group	O
.	O
(	O
C	O
)	O
Solvent	O
accessibility	O
of	O
the	O
SAM	B-chemical
methyl	O
group	O
for	O
SAM	B-chemical
bound	B-protein_state
to	I-protein_state
the	O
RNA	B-protein_type
methyltransferase	I-protein_type
Trm10	B-protein
.	O

Bound	B-protein_state
SAM	B-chemical
was	O
modelled	O
based	O
on	O
the	O
X	B-evidence
-	I-evidence
ray	I-evidence
structure	I-evidence
of	O
the	O
Trm10	B-complex_assembly
/	I-complex_assembly
SAH	I-complex_assembly
-	O
complex	O
(	O
pdb4jwf	O
).	O

A	O
red	O
arrow	O
indicates	O
the	O
SAM	B-chemical
methyl	O
group	O
.	O
(	O
D	O
)	O
Binding	O
of	O
SAM	B-chemical
analogs	O
to	O
SsTsr3	B-protein
.	O

Tryptophan	B-evidence
fluorescence	I-evidence
quenching	I-evidence
curves	I-evidence
upon	O
addition	O
of	O
SAM	B-chemical
(	O
blue	O
),	O
5	B-chemical
′-	I-chemical
methyl	I-chemical
-	I-chemical
thioadenosine	I-chemical
(	O
red	O
)	O
and	O
SAH	B-chemical
(	O
black	O
).	O

(	O
E	O
)	O
Binding	O
of	O
14C	B-chemical
-	I-chemical
labeled	I-chemical
SAM	I-chemical
to	O
SsTsr3	B-protein
.	O

Radioactively	O
labeled	O
SAM	B-chemical
is	O
retained	O
on	O
a	O
filter	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
SsTsr3	B-protein
.	O

Addition	O
of	O
unlabeled	O
SAM	B-chemical
competes	O
with	O
the	O
binding	O
of	O
labeled	O
SAM	B-chemical
.	O

A	O
W66A	B-mutant
-	O
mutant	B-protein_state
of	O
SsTsr3	B-protein
(	O
W73	B-residue_name_number
in	O
VdTsr3	B-protein
)	O
does	O
not	O
bind	O
SAM	B-chemical
.	O

(	O
F	O
)	O
Primer	B-experimental_method
extension	I-experimental_method
(	O
upper	O
left	O
)	O
shows	O
a	O
strongly	O
reduced	O
acp	B-chemical
modification	O
of	O
yeast	B-taxonomy_domain
18S	B-chemical
rRNA	I-chemical
in	O
Δtsr3	B-mutant
cells	O
expressing	O
Tsr3	B-mutant
-	I-mutant
S62D	I-mutant
,	O
-	B-mutant
E111A	I-mutant
or	O
–	B-mutant
W114A	I-mutant
.	O

This	O
correlates	O
with	O
a	O
20S	B-chemical
pre	I-chemical
-	I-chemical
rRNA	I-chemical
accumulation	O
comparable	O
to	O
the	O
Δtsr3	B-mutant
deletion	O
(	O
right	O
:	O
northern	B-experimental_method
blot	I-experimental_method
).	O

3xHA	B-protein_state
tagged	I-protein_state
Tsr3	B-protein
mutants	B-protein_state
are	O
expressed	O
comparable	O
to	O
the	O
wild	B-protein_state
type	I-protein_state
as	O
shown	O
by	O
western	B-experimental_method
blot	I-experimental_method
(	O
lower	O
left	O
).	O

Binding	B-evidence
affinities	I-evidence
for	O
SAM	B-chemical
and	O
its	O
analogs	O
5	B-chemical
′-	I-chemical
methylthioadenosin	I-chemical
and	O
SAH	B-chemical
to	O
SsTsr3	B-protein
were	O
measured	O
using	O
tryptophan	B-experimental_method
fluorescence	I-experimental_method
quenching	I-experimental_method
.	O

VdTsr3	B-protein
could	O
not	O
be	O
used	O
in	O
these	O
experiments	O
since	O
we	O
could	O
not	O
purify	O
it	O
in	O
a	O
stable	B-protein_state
SAM	B-protein_state
-	I-protein_state
free	I-protein_state
form	O
.	O

SsTsr3	B-protein
bound	B-protein_state
SAM	B-chemical
with	O
a	O
KD	B-evidence
of	O
6	O
.	O
5	O
μM	O
,	O
which	O
is	O
similar	O
to	O
SAM	B-evidence
-	I-evidence
KD	I-evidence
'	I-evidence
s	I-evidence
reported	O
for	O
several	O
SPOUT	B-protein_type
-	I-protein_type
class	I-protein_type
methyltransferases	I-protein_type
.	O

5	B-chemical
′-	I-chemical
methylthioadenosin	I-chemical
—	O
the	O
reaction	O
product	O
after	O
the	O
acp	B-chemical
-	O
transfer	O
—	O
binds	O
only	O
∼	O
2	O
.	O
5	O
-	O
fold	O
weaker	O
(	O
KD	O
=	O
16	O
.	O
7	O
μM	O
)	O
compared	O
to	O
SAM	B-chemical
.	O

S	B-chemical
-	I-chemical
adenosylhomocysteine	I-chemical
which	O
lacks	O
the	O
methyl	O
group	O
of	O
SAM	B-chemical
binds	O
with	O
significantly	O
lower	O
affinity	B-evidence
(	O
KD	B-evidence
=	O
55	O
.	O
5	O
μM	O
)	O
(	O
Figure	O
5D	O
).	O

This	O
suggests	O
that	O
the	O
hydrophobic	O
interaction	O
between	O
SAM	B-chemical
'	O
s	O
methyl	O
group	O
and	O
the	O
hydrophobic	B-site
pocket	I-site
of	O
Tsr3	B-protein
is	O
thermodynamically	O
important	O
for	O
the	O
interaction	O
.	O

On	O
the	O
other	O
hand	O
,	O
the	O
loss	O
of	O
hydrogen	O
bonds	O
between	O
the	O
acp	B-chemical
sidechain	O
carboxylate	O
group	O
and	O
the	O
protein	O
appears	O
to	O
be	O
thermodynamically	O
less	O
important	O
but	O
these	O
hydrogen	O
bonds	O
might	O
play	O
a	O
crucial	O
role	O
for	O
the	O
proper	O
orientation	O
of	O
the	O
cofactor	O
side	O
chain	O
in	O
the	O
substrate	B-site
binding	I-site
pocket	I-site
.	O

Accordingly	O
,	O
a	O
W66A	B-mutant
-	O
mutation	B-experimental_method
(	O
W73	B-residue_name_number
in	O
VdTsr3	B-protein
)	O
of	O
SsTsr3	B-protein
significantly	O
diminished	O
SAM	B-evidence
-	I-evidence
binding	I-evidence
in	O
a	O
filter	B-experimental_method
binding	I-experimental_method
assay	I-experimental_method
compared	O
to	O
the	O
wild	B-protein_state
type	I-protein_state
(	O
Figure	O
5E	O
).	O

Furthermore	O
,	O
a	O
W	B-experimental_method
to	I-experimental_method
A	I-experimental_method
mutation	I-experimental_method
at	O
the	O
equivalent	O
position	O
W114	B-residue_name_number
in	O
ScTsr3	B-protein
strongly	O
reduced	O
the	O
in	O
vivo	O
acp	B-protein_type
transferase	I-protein_type
activity	O
(	O
Figure	O
5F	O
).	O

The	O
side	O
chain	O
hydroxyl	O
group	O
of	O
T19	B-residue_name_number
seems	O
of	O
minor	O
importance	O
for	O
SAM	B-chemical
binding	O
since	O
mutations	B-experimental_method
of	O
T17	B-residue_name_number
(	O
T19	B-residue_name_number
in	O
VdTsr3	B-protein
)	O
to	O
either	O
A	B-residue_name
or	O
D	B-residue_name
did	O
not	O
significantly	O
influence	O
the	O
SAM	B-evidence
-	I-evidence
binding	I-evidence
affinity	I-evidence
of	O
SsTsr3	B-protein
(	O
KD	B-evidence
'	O
s	O
=	O
3	O
.	O
9	O
or	O
11	O
.	O
2	O
mM	O
,	O
respectively	O
).	O

Nevertheless	O
,	O
a	O
mutation	B-experimental_method
of	O
the	O
equivalent	O
position	O
S62	B-residue_name_number
of	O
ScTsr3	B-protein
to	O
D	B-residue_name
,	O
but	O
not	O
to	O
A	B-residue_name
,	O
resulted	O
in	O
reduced	O
acp	B-chemical
modification	O
in	O
vivo	O
,	O
as	O
shown	O
by	O
primer	B-experimental_method
extension	I-experimental_method
analysis	I-experimental_method
(	O
Figure	O
5F	O
).	O

The	O
acp	B-chemical
-	O
transfer	O
reaction	O
catalyzed	O
by	O
Tsr3	B-protein
most	O
likely	O
requires	O
the	O
presence	O
of	O
a	O
catalytic	O
base	O
in	O
order	O
to	O
abstract	O
a	O
proton	O
from	O
the	O
N3	O
imino	O
group	O
of	O
the	O
modified	O
pseudouridine	B-chemical
.	O

The	O
side	O
chain	O
of	O
D70	B-residue_name_number
(	O
VdTsr3	B-protein
)	O
located	O
in	O
β4	B-structure_element
is	O
∼	O
5	O
Å	O
away	O
from	O
the	O
SAM	B-chemical
sulfur	O
atom	O
.	O

This	O
residue	O
is	O
conserved	B-protein_state
as	I-protein_state
D	B-residue_name
or	O
E	B-residue_name
both	O
in	O
archaeal	B-taxonomy_domain
and	O
eukaryotic	B-taxonomy_domain
Tsr3	B-protein
homologs	O
.	O

Mutations	B-experimental_method
of	O
the	O
corresponding	O
residue	O
in	O
SsTsr3	B-protein
to	O
A	B-residue_name
(	O
D63	B-residue_name_number
)	O
does	O
not	O
significantly	O
alter	O
the	O
SAM	B-evidence
-	I-evidence
binding	I-evidence
affinity	I-evidence
of	O
the	O
protein	O
(	O
KD	B-evidence
=	O
11	O
.	O
0	O
μM	O
).	O

However	O
,	O
the	O
mutation	B-experimental_method
of	O
the	O
corresponding	O
residue	O
of	O
ScTsr3	B-protein
(	O
E111A	B-mutant
)	O
leads	O
to	O
a	O
significant	O
decrease	O
of	O
the	O
acp	B-protein_type
transferase	I-protein_type
activity	O
in	O
vivo	O
(	O
Figure	O
5F	O
).	O

RNA	O
-	O
binding	O
of	O
Tsr3	B-protein

Analysis	B-experimental_method
of	I-experimental_method
the	I-experimental_method
electrostatic	I-experimental_method
surface	I-experimental_method
properties	I-experimental_method
of	O
VdTsr3	B-protein
clearly	O
identified	O
positively	B-site
charged	I-site
surface	I-site
patches	I-site
in	O
the	O
vicinity	O
of	O
the	O
SAM	B-site
-	I-site
binding	I-site
site	I-site
suggesting	O
a	O
putative	O
RNA	B-site
-	I-site
binding	I-site
site	I-site
(	O
Figure	O
6A	O
).	O

Furthermore	O
,	O
a	O
negatively	O
charged	O
MES	B-chemical
-	O
ion	O
is	O
found	O
in	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
VdTsr3	B-protein
complexed	B-protein_state
to	I-protein_state
the	O
side	O
chain	O
of	O
K22	B-residue_name_number
in	O
helix	B-structure_element
α1	B-structure_element
.	O

Its	O
negatively	O
charged	O
sulfate	B-chemical
group	O
might	O
mimic	O
an	O
RNA	B-chemical
backbone	O
phosphate	O
.	O

Helix	B-structure_element
α1	B-structure_element
contains	O
two	O
more	O
positively	O
charged	O
amino	O
acids	O
K17	B-residue_name_number
and	O
R25	B-residue_name_number
as	O
does	O
the	O
loop	B-structure_element
preceding	O
it	O
(	O
R9	B-residue_name_number
).	O

A	O
second	O
cluster	O
of	O
positively	O
charged	O
residues	O
is	O
found	O
in	O
or	O
near	O
helix	B-structure_element
α3	B-structure_element
(	O
K74	B-residue_name_number
,	O
R75	B-residue_name_number
,	O
K82	B-residue_name_number
,	O
R85	B-residue_name_number
and	O
K87	B-residue_name_number
).	O

Some	O
of	O
these	O
amino	O
acids	O
are	O
conserved	B-protein_state
between	O
archaeal	B-taxonomy_domain
and	O
eukaryotic	B-taxonomy_domain
Tsr3	B-protein
(	O
Supplementary	O
Figure	O
S1A	O
).	O

In	O
the	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
,	O
the	O
surface	O
exposed	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
α5	B-structure_element
and	O
α7	B-structure_element
carry	O
a	O
significant	O
amount	O
of	O
positively	O
charged	O
amino	O
acids	O
.	O

A	O
triple	B-experimental_method
mutation	I-experimental_method
of	O
the	O
conserved	B-protein_state
positively	O
charged	O
residues	O
R60	B-residue_name_number
,	O
K65	B-residue_name_number
and	O
R131	B-residue_name_number
to	O
A	B-residue_name
in	O
ScTsr3	B-protein
resulted	O
in	O
a	O
protein	O
with	O
a	O
significantly	O
impaired	O
acp	B-protein_type
transferase	I-protein_type
activity	O
in	O
vivo	O
(	O
Figure	O
6D	O
)	O
in	O
line	O
with	O
an	O
important	O
functional	O
role	O
for	O
these	O
positively	O
charged	O
residues	O
.	O

RNA	O
-	O
binding	O
of	O
Tsr3	B-protein
.	O

(	O
A	O
)	O
Electrostatic	O
charge	O
distribution	O
on	O
the	O
surface	O
of	O
VdTsr3	B-protein
.	O

SAM	B-chemical
is	O
shown	O
in	O
a	O
stick	O
representation	O
.	O

Also	O
shown	O
in	O
stick	O
representation	O
is	O
a	O
negatively	O
charged	O
MES	B-chemical
ion	O
.	O

Conserved	B-protein_state
basic	O
amino	B-chemical
acids	I-chemical
are	O
labeled	O
.	O
(	O
B	O
)	O
Comparison	O
of	O
the	O
secondary	O
structures	O
of	O
helix	B-structure_element
31	I-structure_element
from	O
the	O
small	O
ribosomal	O
subunit	O
rRNAs	B-chemical
in	O
S	B-species
.	I-species
cerevisiae	I-species
and	O
S	B-species
.	I-species
solfataricus	I-species
with	O
the	O
location	O
of	O
the	O
hypermodified	B-protein_state
nucleotide	B-chemical
indicated	O
in	O
red	O
.	O

For	O
S	B-species
.	I-species
solfataricus	I-species
the	O
chemical	O
identity	O
of	O
the	O
hypermodified	B-protein_state
nucleotide	B-chemical
is	O
not	O
known	O
but	O
the	O
existence	O
of	O
NEP1	B-protein
and	O
TSR3	B-protein
homologs	O
suggest	O
that	O
it	O
is	O
indeed	O
N1	B-chemical
-	I-chemical
methyl	I-chemical
-	I-chemical
N3	I-chemical
-	I-chemical
acp	I-chemical
-	I-chemical
pseudouridine	I-chemical
.	O

(	O
C	O
)	O
Binding	O
of	O
SsTsr3	B-protein
to	O
RNA	B-chemical
.	O

5	O
′-	O
fluoresceine	B-chemical
labeled	O
RNA	B-chemical
oligonucleotides	O
corresponding	O
either	O
to	O
the	O
native	B-protein_state
(	O
20mer	B-oligomeric_state
–	O
see	O
inset	O
)	O
or	O
a	O
stabilized	B-protein_state
(	O
20mer_GC	B-oligomeric_state
-	O
inset	O
)	O
helix	B-structure_element
31	I-structure_element
of	O
the	O
small	O
ribosomal	O
subunit	O
rRNA	B-chemical
from	O
S	B-species
.	I-species
solfataricus	I-species
were	O
titrated	B-experimental_method
with	I-experimental_method
increasing	I-experimental_method
amounts	I-experimental_method
of	O
SsTsr3	B-protein
and	O
the	O
changes	O
in	O
the	O
fluoresceine	B-chemical
fluorescence	B-evidence
anisotropy	I-evidence
were	O
measured	O
and	O
fitted	O
to	O
a	O
binding	B-evidence
curve	I-evidence
(	O
20mer	B-oligomeric_state
–	O
red	O
,	O
20mer_GC	B-oligomeric_state
–	O
blue	O
).	O

Oligo	B-chemical
-	I-chemical
U9	I-chemical
-	I-chemical
RNA	I-chemical
was	O
used	O
for	O
comparison	O
(	O
black	O
).	O

The	O
20mer_GC	B-oligomeric_state
RNA	B-chemical
was	O
also	O
titrated	B-experimental_method
with	O
SsTsr3	B-protein
in	O
the	O
presence	O
of	O
2	O
mM	O
SAM	B-chemical
(	O
purple	O
).	O
(	O
D	O
)	O
Mutants	B-protein_state
of	O
ScTsr3	B-protein
R60	B-residue_name_number
,	O
K65	B-residue_name_number
or	O
R131	B-residue_name_number
(	O
equivalent	O
to	O
K17	B-residue_name_number
,	O
K22	B-residue_name_number
and	O
R91	B-residue_name_number
in	O
VdTsr3	B-protein
)	O
expressed	B-experimental_method
in	O
Δtsr3	B-mutant
yeast	B-taxonomy_domain
cells	O
show	O
a	O
primer	B-evidence
extension	I-evidence
stop	I-evidence
comparable	O
to	O
the	O
wild	B-protein_state
type	I-protein_state
.	O

Combination	B-experimental_method
of	I-experimental_method
the	I-experimental_method
three	I-experimental_method
point	I-experimental_method
mutations	I-experimental_method
(	O
R60A	B-mutant
/	O
K65A	B-mutant
/	O
R131A	B-mutant
)	O
leads	O
to	O
a	O
strongly	O
reduced	O
acp	B-chemical
modification	O
of	O
18S	B-chemical
rRNA	I-chemical
.	O

In	O
order	O
to	O
explore	O
the	O
RNA	O
-	O
ligand	O
specificity	O
of	O
Tsr3	B-protein
we	O
titrated	B-experimental_method
SsTsr3	B-protein
prepared	O
in	O
RNase	B-protein_state
-	I-protein_state
free	I-protein_state
form	O
with	O
5	O
′-	O
fluoresceine	B-chemical
-	O
labeled	O
RNA	B-chemical
and	O
determined	O
the	O
affinity	B-evidence
by	O
fluorescence	B-experimental_method
anisotropy	I-experimental_method
measurements	I-experimental_method
.	O

SsTsr3	B-protein
in	O
the	O
apo	B-protein_state
state	O
bound	B-protein_state
a	O
20mer	B-oligomeric_state
RNA	B-chemical
corresponding	O
to	O
helix	B-structure_element
31	I-structure_element
of	O
S	B-species
.	I-species
solfataricus	I-species
16S	B-chemical
rRNA	I-chemical
(	O
Figure	O
6B	O
)	O
with	O
a	O
KD	B-evidence
of	O
1	O
.	O
9	O
μM	O
and	O
to	O
a	O
version	O
of	O
this	O
hairpin	B-structure_element
stabilized	O
by	O
additional	O
GC	O
base	O
pairs	O
(	O
20mer	B-oligomeric_state
-	I-oligomeric_state
GC	I-oligomeric_state
)	O
with	O
a	O
KD	B-evidence
of	O
0	O
.	O
6	O
μM	O
(	O
Figure	O
6C	O
).	O

A	O
single	O
stranded	O
oligoU	B-chemical
-	I-chemical
RNA	I-chemical
bound	B-protein_state
with	O
a	O
10	O
-	O
fold	O
-	O
reduced	O
affinity	B-evidence
(	O
6	O
.	O
0	O
μM	O
).	O

The	O
presence	O
of	O
saturating	O
amounts	O
of	O
SAM	B-chemical
(	O
2	O
mM	O
)	O
did	O
not	O
have	O
a	O
significant	O
influence	O
on	O
the	O
RNA	B-evidence
-	I-evidence
affinity	I-evidence
of	O
SsTsr3	B-protein
(	O
KD	B-evidence
of	O
1	O
.	O
7	O
μM	O
for	O
the	O
20mer	B-oligomeric_state
-	I-oligomeric_state
GC	I-oligomeric_state
-	O
RNA	B-chemical
)	O
suggesting	O
no	O
cooperativity	O
in	O
substrate	O
binding	O
.	O

U1191	B-residue_name_number
is	O
the	O
only	O
hypermodified	B-protein_state
base	O
in	O
the	O
yeast	B-taxonomy_domain
18S	B-chemical
rRNA	I-chemical
and	O
is	O
strongly	B-protein_state
conserved	I-protein_state
in	O
eukaryotes	B-taxonomy_domain
.	O

The	O
formation	O
of	O
1	B-chemical
-	I-chemical
methyl	I-chemical
-	I-chemical
3	I-chemical
-(	I-chemical
3	I-chemical
-	I-chemical
amino	I-chemical
-	I-chemical
3	I-chemical
-	I-chemical
carboxypropyl	I-chemical
)-	I-chemical
pseudouridine	I-chemical
(	O
m1acp3Ψ	B-chemical
)	O
is	O
very	O
complex	O
requiring	O
three	O
successive	O
modification	O
reactions	O
involving	O
one	O
H	B-structure_element
/	I-structure_element
ACA	I-structure_element
snoRNP	B-complex_assembly
(	O
snR35	B-protein
)	O
and	O
two	O
protein	O
enzymes	O
(	O
Nep1	B-protein
/	O
Emg1	B-protein
and	O
Tsr3	B-protein
).	O

This	O
makes	O
it	O
unique	O
in	O
eukaryotic	B-taxonomy_domain
rRNA	B-chemical
modification	O
.	O

The	O
m1acp3Ψ	B-chemical
base	O
is	O
located	O
at	O
the	O
tip	O
of	O
helix	B-structure_element
31	I-structure_element
on	O
the	O
18S	B-chemical
rRNA	I-chemical
(	O
Supplementary	O
Figure	O
S1B	O
)	O
which	O
,	O
together	O
with	O
helices	B-structure_element
18	I-structure_element
,	I-structure_element
24	I-structure_element
,	I-structure_element
34	I-structure_element
and	I-structure_element
44	I-structure_element
,	O
contribute	O
to	O
building	O
the	O
decoding	O
center	O
of	O
the	O
small	O
ribosomal	O
subunit	O
.	O

A	O
similar	O
modification	O
(	O
acp3U	B-chemical
)	O
was	O
identified	O
in	O
Haloferax	B-species
volcanii	I-species
and	O
corresponding	O
modified	O
nucleotides	B-chemical
were	O
also	O
shown	O
to	O
occur	O
in	O
other	O
archaea	B-taxonomy_domain
.	O

As	O
shown	O
here	O
TSR3	B-protein
encodes	O
the	O
transferase	O
catalyzing	O
the	O
acp	B-chemical
modification	O
as	O
the	O
last	O
step	O
in	O
the	O
biosynthesis	O
of	O
m1acp3Ψ	B-chemical
in	O
yeast	B-taxonomy_domain
and	O
human	B-species
cells	O
.	O

Unexpectedly	O
,	O
archaeal	B-taxonomy_domain
Tsr3	B-protein
has	O
a	O
structure	B-evidence
similar	O
to	O
SPOUT	B-protein_type
-	I-protein_type
class	I-protein_type
RNA	I-protein_type
methyltransferases	I-protein_type
,	O
and	O
it	O
is	O
the	O
first	O
example	O
for	O
an	O
enzyme	O
of	O
this	O
class	O
transferring	O
an	O
acp	B-chemical
group	O
,	O
due	O
to	O
a	O
modified	O
SAM	B-site
-	I-site
binding	I-site
pocket	I-site
that	O
exposes	O
the	O
acp	B-chemical
instead	O
of	O
the	O
methyl	O
group	O
of	O
SAM	B-chemical
to	O
its	O
RNA	B-chemical
substrate	O
.	O

Similar	O
to	O
the	O
structurally	O
unrelated	O
Rossmann	B-protein_type
-	I-protein_type
fold	I-protein_type
Tyw2	I-protein_type
acp	I-protein_type
transferase	I-protein_type
,	O
the	O
SAM	B-chemical
methyl	O
group	O
of	O
Tsr3	B-protein
is	O
bound	O
in	O
an	O
inaccessible	O
hydrophobic	B-site
pocket	I-site
whereas	O
the	O
acp	B-chemical
side	O
chain	O
becomes	O
accessible	O
for	O
a	O
nucleophilic	O
attack	O
by	O
the	O
N3	O
of	O
pseudouridine	B-chemical
.	O

In	O
contrast	O
,	O
in	O
the	O
structurally	O
closely	O
related	O
RNA	B-protein_type
methyltransferase	I-protein_type
Trm10	B-protein
the	O
methyl	O
group	O
of	O
the	O
cofactor	O
SAM	B-chemical
is	O
accessible	O
whereas	O
its	O
acp	B-chemical
side	O
chain	O
is	O
buried	O
inside	O
the	O
protein	O
.	O

This	O
suggests	O
that	O
enzymes	O
with	O
a	O
SAM	B-protein_type
-	I-protein_type
dependent	I-protein_type
acp	I-protein_type
transferase	I-protein_type
activity	O
might	O
have	O
evolved	O
from	O
SAM	B-protein_type
-	I-protein_type
dependent	I-protein_type
methyltransferases	I-protein_type
by	O
slight	O
modifications	O
of	O
the	O
SAM	B-site
-	I-site
binding	I-site
pocket	I-site
.	O

Thus	O
,	O
additional	O
examples	O
for	O
acp	B-protein_type
transferase	I-protein_type
enzymes	O
might	O
be	O
found	O
with	O
similarities	O
to	O
other	O
structural	O
classes	O
of	O
methyltransferases	B-protein_type
.	O

In	O
contrast	O
to	O
Nep1	B-protein
,	O
the	O
enzyme	O
preceding	O
Tsr3	B-protein
in	O
the	O
m1acp3Ψ	B-chemical
biosynthesis	O
pathway	O
,	O
Tsr3	B-protein
binds	O
rather	O
weakly	O
and	O
with	O
little	O
specificity	O
to	O
its	O
isolated	O
substrate	O
RNA	B-chemical
.	O

This	O
suggests	O
that	O
Tsr3	B-protein
is	O
not	O
stably	O
incorporated	O
into	O
pre	B-complex_assembly
-	I-complex_assembly
ribosomal	I-complex_assembly
particles	I-complex_assembly
and	O
that	O
its	O
binding	O
to	O
the	O
nascent	O
ribosomal	B-complex_assembly
subunit	I-complex_assembly
possibly	O
requires	O
additional	O
interactions	O
with	O
other	O
pre	O
-	O
ribosomal	O
components	O
.	O

Consistently	O
,	O
in	O
sucrose	B-experimental_method
gradient	I-experimental_method
analysis	I-experimental_method
,	O
Tsr3	B-protein
was	O
found	O
in	O
low	O
-	O
molecular	O
weight	O
fractions	O
rather	O
than	O
with	O
pre	B-complex_assembly
-	I-complex_assembly
ribosome	I-complex_assembly
containing	O
high	O
-	O
molecular	O
weight	O
fractions	O
.	O

In	O
contrast	O
to	O
several	O
enzymes	O
that	O
catalyze	O
base	O
specific	O
modifications	O
in	O
rRNAs	B-chemical
Tsr3	B-protein
is	O
not	O
an	O
essential	O
protein	O
.	O

Typically	O
,	O
other	O
small	B-protein_type
subunit	I-protein_type
rRNA	I-protein_type
methyltransferases	I-protein_type
as	O
Dim1	B-protein
,	O
Bud23	B-protein
and	O
Nep1	B-protein
/	O
Emg1	B-protein
carry	O
dual	O
functions	O
,	O
in	O
ribosome	O
biogenesis	O
and	O
rRNA	B-chemical
modification	O
,	O
and	O
it	O
is	O
their	O
involvement	O
in	O
pre	B-chemical
-	I-chemical
RNA	I-chemical
processing	O
that	O
is	O
essential	O
rather	O
than	O
their	O
RNA	O
-	O
methylating	O
activity	O
(,	O
discussed	O
in	O
7	O
).	O

In	O
contrast	O
,	O
for	O
several	O
Tsr3	B-protein
mutants	O
(	O
SAM	B-protein_state
-	I-protein_state
binding	I-protein_state
and	O
cysteine	B-protein_state
mutations	I-protein_state
)	O
we	O
found	O
a	O
systematic	O
correlation	O
between	O
the	O
loss	O
of	O
acp	B-chemical
modification	O
and	O
the	O
efficiency	O
of	O
18S	B-chemical
rRNA	I-chemical
maturation	O
.	O

This	O
demonstrates	O
that	O
,	O
unlike	O
the	O
other	O
small	O
subunit	O
rRNA	B-chemical
base	O
modifications	O
,	O
the	O
acp	B-chemical
modification	O
is	O
required	O
for	O
efficient	O
pre	B-chemical
-	I-chemical
rRNA	I-chemical
processing	O
.	O

Recently	O
,	O
structural	B-experimental_method
,	I-experimental_method
functional	I-experimental_method
,	I-experimental_method
and	I-experimental_method
CRAC	I-experimental_method
(	I-experimental_method
cross	I-experimental_method
-	I-experimental_method
linking	I-experimental_method
and	I-experimental_method
cDNA	I-experimental_method
analysis	I-experimental_method
)	I-experimental_method
experiments	I-experimental_method
of	O
late	O
assembly	O
factors	O
involved	O
in	O
cytoplasmic	O
processing	O
of	O
40S	B-complex_assembly
subunits	I-complex_assembly
,	O
along	O
with	O
cryo	B-experimental_method
-	I-experimental_method
EM	I-experimental_method
studies	O
of	O
the	O
late	B-protein_state
pre	B-complex_assembly
-	I-complex_assembly
40S	I-complex_assembly
subunits	I-complex_assembly
have	O
provided	O
important	O
insights	O
into	O
late	O
pre	B-complex_assembly
-	I-complex_assembly
40S	I-complex_assembly
processing	O
.	O

Apart	O
from	O
most	O
of	O
the	O
ribosomal	O
proteins	O
,	O
cytoplasmic	O
pre	B-complex_assembly
-	I-complex_assembly
40S	I-complex_assembly
particles	I-complex_assembly
contain	O
20S	B-chemical
rRNA	I-chemical
and	O
at	O
least	O
seven	O
non	B-protein_type
-	I-protein_type
ribosomal	I-protein_type
proteins	I-protein_type
including	O
the	O
D	B-protein_type
-	I-protein_type
site	I-protein_type
endonuclease	I-protein_type
Nob1	B-protein
as	O
well	O
as	O
Tsr1	B-protein
,	O
a	O
putative	O
GTPase	B-protein_type
and	O
Rio2	B-protein
which	O
block	O
the	O
mRNA	B-site
channel	I-site
and	O
the	O
initiator	B-site
tRNA	I-site
binding	I-site
site	I-site
,	O
respectively	O
,	O
thus	O
preventing	O
translation	O
initiation	O
.	O

After	O
structural	O
changes	O
,	O
possibly	O
driven	O
by	O
GTP	B-chemical
hydrolysis	O
,	O
which	O
go	O
together	O
with	O
the	O
formation	O
of	O
the	O
decoding	B-site
site	I-site
,	O
the	O
20S	B-chemical
pre	I-chemical
-	I-chemical
rRNA	I-chemical
becomes	O
accessible	O
for	O
Nob1	B-protein
cleavage	O
at	O
site	B-site
D	I-site
.	O
This	O
also	O
involves	O
joining	O
of	O
pre	B-complex_assembly
-	I-complex_assembly
40S	I-complex_assembly
and	O
60S	B-complex_assembly
subunits	I-complex_assembly
to	O
80S	B-complex_assembly
-	I-complex_assembly
like	I-complex_assembly
particles	I-complex_assembly
in	O
a	O
translation	O
-	O
like	O
cycle	O
promoted	O
by	O
eIF5B	B-protein
.	O

The	O
cleavage	O
step	O
most	O
likely	O
acts	O
as	O
a	O
quality	O
control	O
check	O
that	O
ensures	O
the	O
proper	O
40S	B-complex_assembly
subunit	I-complex_assembly
assembly	O
with	O
only	O
completely	O
processed	O
precursors	O
.	O

Finally	O
,	O
termination	B-protein_type
factor	I-protein_type
Rli1	B-protein
,	O
an	O
ATPase	B-protein_type
,	O
promotes	O
the	O
dissociation	O
of	O
assembly	O
factors	O
and	O
the	O
80S	B-complex_assembly
-	I-complex_assembly
like	I-complex_assembly
complex	I-complex_assembly
dissociates	O
and	O
releases	O
the	O
mature	B-protein_state
40S	B-complex_assembly
subunit	I-complex_assembly
.	O

Interestingly	O
,	O
differences	O
in	O
the	O
level	O
of	O
acp	B-chemical
modification	O
were	O
demonstrated	O
for	O
different	O
steps	O
of	O
the	O
cytoplasmic	O
pre	B-complex_assembly
-	I-complex_assembly
40S	I-complex_assembly
subunit	I-complex_assembly
maturation	O
after	O
analyzing	O
purified	O
20S	B-chemical
pre	I-chemical
-	I-chemical
rRNAs	I-chemical
using	O
different	O
purification	O
bait	O
proteins	O
.	O

Early	O
cytoplasmic	O
pre	B-complex_assembly
-	I-complex_assembly
40S	I-complex_assembly
subunits	I-complex_assembly
still	O
containing	O
the	O
ribosome	B-protein_type
assembly	I-protein_type
factors	I-protein_type
Tsr1	B-protein
,	O
Ltv1	B-protein
,	O
Enp1	B-protein
and	O
Rio2	B-protein
were	O
not	O
or	O
only	O
partially	O
acp	B-protein_state
modified	I-protein_state
.	O

In	O
contrast	O
,	O
late	O
pre	B-complex_assembly
-	I-complex_assembly
40S	I-complex_assembly
subunits	I-complex_assembly
containing	O
Nob1	B-protein
and	O
Rio1	B-protein
or	O
already	O
associated	O
with	O
60S	B-complex_assembly
subunits	I-complex_assembly
in	O
80S	B-complex_assembly
-	I-complex_assembly
like	I-complex_assembly
particles	I-complex_assembly
showed	O
acp	B-chemical
modification	O
levels	O
comparable	O
to	O
mature	B-protein_state
40S	B-complex_assembly
subunits	I-complex_assembly
.	O

Thus	O
,	O
the	O
acp	B-chemical
transfer	O
to	O
m1Ψ1191	B-residue_name_number
occurs	O
during	O
the	O
step	O
at	O
which	O
Rio2	B-protein
leaves	O
the	O
pre	B-complex_assembly
-	I-complex_assembly
40S	I-complex_assembly
particle	I-complex_assembly
.	O

These	O
data	O
and	O
the	O
finding	O
that	O
a	O
missing	O
acp	B-chemical
modification	O
hinders	O
pre	B-chemical
-	I-chemical
20S	I-chemical
rRNA	I-chemical
processing	O
,	O
suggest	O
that	O
the	O
acp	B-chemical
modification	O
together	O
with	O
the	O
release	O
of	O
Rio2	B-protein
promotes	O
the	O
formation	O
of	O
the	O
decoding	B-site
site	I-site
and	O
thus	O
D	B-site
-	I-site
site	I-site
cleavage	O
by	O
Nob1	B-protein
.	O

The	O
interrelation	O
between	O
acp	B-chemical
modification	O
and	O
Rio2	B-protein
release	O
is	O
also	O
supported	O
by	O
CRAC	B-experimental_method
analysis	I-experimental_method
showing	O
that	O
Rio2	B-protein
binds	O
to	O
helix	B-structure_element
31	I-structure_element
next	O
to	O
the	O
Ψ1191	B-residue_name_number
residue	O
that	O
receives	O
the	O
acp	B-chemical
modification	O
.	O

Therefore	O
,	O
Rio2	B-protein
either	O
blocks	O
the	O
access	O
of	O
Tsr3	B-protein
to	O
helix	B-structure_element
31	I-structure_element
,	O
and	O
acp	B-chemical
modification	O
can	O
only	O
occur	O
after	O
Rio2	B-protein
is	O
released	O
,	O
or	O
the	O
acp	B-chemical
modification	O
of	O
m1Ψ1191	B-residue_name_number
and	O
putative	O
subsequent	O
conformational	O
changes	O
of	O
20S	B-chemical
rRNA	I-chemical
weaken	O
the	O
binding	O
of	O
Rio2	B-protein
to	O
helix	B-structure_element
31	I-structure_element
and	O
support	O
its	O
release	O
from	O
the	O
pre	B-chemical
-	I-chemical
rRNA	I-chemical
.	O

In	O
summary	O
,	O
by	O
identifying	O
Tsr3	B-protein
as	O
the	O
enzyme	O
responsible	O
for	O
introducing	O
the	O
acp	B-chemical
group	O
to	O
the	O
hypermodified	B-protein_state
m1acp3Ψ	B-chemical
nucleotide	B-chemical
at	O
position	O
1191	B-residue_number
(	O
yeast	B-taxonomy_domain
)/	O
1248	B-residue_number
(	O
humans	B-species
)	O
of	O
18S	B-chemical
rRNA	I-chemical
we	O
added	O
one	O
of	O
the	O
last	O
remaining	O
pieces	O
to	O
the	O
puzzle	O
of	O
eukaryotic	B-taxonomy_domain
small	B-chemical
ribosomal	I-chemical
subunit	I-chemical
rRNA	I-chemical
modifications	O
.	O

The	O
current	O
data	O
together	O
with	O
the	O
finding	O
that	O
acp	B-chemical
modification	O
takes	O
place	O
at	O
the	O
very	O
last	O
step	O
in	O
pre	B-complex_assembly
-	I-complex_assembly
40S	I-complex_assembly
subunit	I-complex_assembly
maturation	O
indicate	O
that	O
the	O
acp	B-chemical
modification	O
probably	O
supports	O
the	O
formation	O
of	O
the	O
decoding	B-site
site	I-site
and	O
efficient	O
20S	B-chemical
pre	I-chemical
-	I-chemical
rRNA	I-chemical
D	B-site
-	I-site
site	I-site
cleavage	O
.	O

Furthermore	O
,	O
our	O
structural	B-evidence
data	I-evidence
unravelled	O
how	O
the	O
regioselectivity	O
of	O
SAM	B-chemical
-	O
dependent	O
group	O
transfer	O
reactions	O
can	O
be	O
tuned	O
by	O
distinct	O
small	O
evolutionary	O
adaptions	O
of	O
the	O
ligand	B-site
binding	I-site
pocket	I-site
of	O
SAM	B-protein_type
-	I-protein_type
binding	I-protein_type
enzymes	I-protein_type
.	O

Biosynthesis	O
of	O
a	O
hypermodified	B-protein_state
nucleotide	O
in	O
Saccharomyces	O
carlsbergensis	O
17S	O
and	O
HeLa	O
-	O
cell	O
18S	O
ribosomal	O
ribonucleic	O
acid	O

Presence	O
of	O
a	O
hypermodified	B-protein_state
nucleotide	O
in	O
HeLa	O
cell	O
18	O
S	O
and	O
Saccharomyces	O
carlsbergensis	O
17	O
S	O
ribosomal	O
RNAs	O

Mutations	O
in	O
the	O
nucleolar	O
proteins	O
Tma23	O
and	O
Nop6	O
suppress	O
the	O
malfunction	O
of	O
the	O
Nep1	B-protein_type
protein	O

The	O
yeast	O
ribosome	O
synthesis	O
factor	O
Emg1	B-protein_type
is	O
a	O
novel	O
member	O
of	O
the	O
superfamily	O
of	O
alpha	O
/	O
beta	O
knot	O
fold	O
methyltransferases	O

Crystal	B-evidence
Structure	I-evidence
and	O
Activity	B-experimental_method
Studies	I-experimental_method
of	O
the	O
C11	B-protein_type
Cysteine	B-protein_type
Peptidase	I-protein_type
from	O
Parabacteroides	B-species
merdae	I-species
in	O
the	O
Human	B-species
Gut	O
Microbiome	O
*	O

Clan	B-protein_type
CD	I-protein_type
cysteine	I-protein_type
peptidases	I-protein_type
,	O
a	O
structurally	O
related	O
group	O
of	O
peptidases	B-protein_type
that	O
include	O
mammalian	B-taxonomy_domain
caspases	B-protein_type
,	O
exhibit	O
a	O
wide	O
range	O
of	O
important	O
functions	O
,	O
along	O
with	O
a	O
variety	O
of	O
specificities	O
and	O
activation	O
mechanisms	O
.	O

However	O
,	O
for	O
the	O
clostripain	B-protein_type
family	I-protein_type
(	O
denoted	O
C11	B-protein_type
),	O
little	O
is	O
currently	O
known	O
.	O

Here	O
,	O
we	O
describe	O
the	O
first	O
crystal	B-evidence
structure	I-evidence
of	O
a	O
C11	B-protein_type
protein	O
from	O
the	O
human	B-species
gut	O
bacterium	B-taxonomy_domain
,	O
Parabacteroides	B-species
merdae	I-species
(	O
PmC11	B-protein
),	O
determined	O
to	O
1	O
.	O
7	O
-	O
Å	O
resolution	O
.	O

PmC11	B-protein
is	O
a	O
monomeric	B-oligomeric_state
cysteine	B-protein_type
peptidase	I-protein_type
that	O
comprises	O
an	O
extended	B-structure_element
caspase	I-structure_element
-	I-structure_element
like	I-structure_element
α	I-structure_element
/	I-structure_element
β	I-structure_element
/	I-structure_element
α	I-structure_element
sandwich	I-structure_element
and	O
an	O
unusual	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
.	O

It	O
shares	O
core	O
structural	O
elements	O
with	O
clan	B-protein_type
CD	I-protein_type
cysteine	I-protein_type
peptidases	I-protein_type
but	O
otherwise	O
structurally	O
differs	O
from	O
the	O
other	O
families	O
in	O
the	O
clan	O
.	O

These	O
studies	O
also	O
revealed	O
a	O
well	O
ordered	O
break	O
in	O
the	O
polypeptide	O
chain	O
at	O
Lys147	B-residue_name_number
,	O
resulting	O
in	O
a	O
large	O
conformational	O
rearrangement	O
close	O
to	O
the	O
active	B-site
site	I-site
.	O

Biochemical	B-experimental_method
and	I-experimental_method
kinetic	I-experimental_method
analysis	I-experimental_method
revealed	O
Lys147	B-residue_name_number
to	O
be	O
an	O
intramolecular	B-site
processing	I-site
site	I-site
at	O
which	O
cleavage	B-ptm
is	O
required	O
for	O
full	B-protein_state
activation	I-protein_state
of	O
the	O
enzyme	B-protein
,	O
suggesting	O
an	O
autoinhibitory	O
mechanism	O
for	O
self	O
-	O
preservation	O
.	O

PmC11	B-protein
has	O
an	O
acidic	B-site
binding	I-site
pocket	I-site
and	O
a	O
preference	O
for	O
basic	O
substrates	O
,	O
and	O
accepts	O
substrates	O
with	O
Arg	B-residue_name
and	O
Lys	B-residue_name
in	O
P1	B-residue_number
and	O
does	O
not	O
require	O
Ca2	B-chemical
+	I-chemical
for	O
activity	O
.	O

Collectively	O
,	O
these	O
data	O
provide	O
insights	O
into	O
the	O
mechanism	O
and	O
activity	O
of	O
PmC11	B-protein
and	O
a	O
detailed	O
framework	O
for	O
studies	O
on	O
C11	B-protein_type
peptidases	I-protein_type
from	O
other	O
phylogenetic	O
kingdoms	O
.	O

Cysteine	B-protein_type
peptidases	I-protein_type
play	O
crucial	O
roles	O
in	O
the	O
virulence	O
of	O
bacterial	B-taxonomy_domain
and	O
other	O
eukaryotic	B-taxonomy_domain
pathogens	O
.	O

In	O
the	O
MEROPS	O
peptidase	O
database	O
,	O
clan	B-protein_type
CD	I-protein_type
contains	O
groups	O
(	O
or	O
families	O
)	O
of	O
cysteine	B-protein_type
peptidases	I-protein_type
that	O
share	O
some	O
highly	B-protein_state
conserved	I-protein_state
structural	O
elements	O
.	O

Clan	B-protein_type
CD	I-protein_type
families	I-protein_type
are	O
typically	O
described	O
using	O
the	O
name	O
of	O
their	O
archetypal	O
,	O
or	O
founding	O
,	O
member	O
and	O
also	O
given	O
an	O
identification	O
number	O
preceded	O
by	O
a	O
“	O
C	O
,”	O
to	O
denote	O
cysteine	B-protein_type
peptidase	I-protein_type
.	O

Although	O
seven	O
families	O
(	O
C14	O
is	O
additionally	O
split	O
into	O
three	O
subfamilies	O
)	O
have	O
been	O
described	O
for	O
this	O
clan	O
,	O
crystal	B-evidence
structures	I-evidence
have	O
only	O
been	O
determined	O
from	O
four	O
:	O
legumain	B-protein
(	O
C13	B-protein_type
),	O
caspase	B-protein
(	O
C14a	B-protein_type
),	O
paracaspase	B-protein
(	O
C14b	B-protein_type
(	I-protein_type
P	I-protein_type
),	O
metacaspase	B-protein
(	O
C14b	B-protein_type
(	I-protein_type
M	I-protein_type
),	O
gingipain	B-protein
(	O
C25	B-protein_type
),	O
and	O
the	O
cysteine	B-structure_element
peptidase	I-structure_element
domain	I-structure_element
(	O
CPD	B-structure_element
)	O
of	O
various	O
toxins	O
(	O
C80	B-protein_type
).	O

No	O
structural	O
information	O
is	O
available	O
for	O
clostripain	B-protein
(	O
C11	B-protein_type
),	O
separase	B-protein
(	O
C50	B-protein_type
),	O
or	O
PrtH	B-protein
-	I-protein
peptidase	I-protein
(	O
C85	B-protein_type
).	O

Clan	B-protein_type
CD	I-protein_type
enzymes	I-protein_type
have	O
a	O
highly	B-protein_state
conserved	I-protein_state
His	B-site
/	I-site
Cys	I-site
catalytic	I-site
dyad	I-site
and	O
exhibit	O
strict	O
specificity	O
for	O
the	O
P1	B-residue_number
residue	O
of	O
their	O
substrates	O
.	O

However	O
,	O
despite	O
these	O
similarities	O
,	O
clan	B-protein_type
CD	I-protein_type
forms	O
a	O
functionally	O
diverse	O
group	O
of	O
enzymes	O
:	O
the	O
overall	O
structural	O
diversity	O
between	O
(	O
and	O
at	O
times	O
within	O
)	O
the	O
various	O
families	O
provides	O
these	O
peptidases	B-protein_type
with	O
a	O
wide	O
variety	O
of	O
substrate	O
specificities	O
and	O
activation	O
mechanisms	O
.	O

The	O
archetypal	O
and	O
arguably	O
most	O
notable	O
family	O
in	O
the	O
clan	O
is	O
that	O
of	O
the	O
mammalian	B-taxonomy_domain
caspases	B-protein_type
(	O
C14a	B-protein_type
),	O
although	O
clan	B-protein_type
CD	I-protein_type
members	O
are	O
distributed	O
throughout	O
the	O
entire	O
phylogenetic	O
kingdom	O
and	O
are	O
often	O
required	O
in	O
fundamental	O
biological	O
processes	O
.	O

Interestingly	O
,	O
little	O
is	O
known	O
about	O
the	O
structure	O
or	O
function	O
of	O
the	O
C11	B-protein_type
proteins	O
,	O
despite	O
their	O
widespread	O
distribution	O
and	O
its	O
archetypal	O
member	O
,	O
clostripain	B-protein
from	O
Clostridium	B-species
histolyticum	I-species
,	O
first	O
reported	O
in	O
the	O
literature	O
in	O
1938	O
.	O

Clostripain	B-protein
has	O
been	O
described	O
as	O
an	O
arginine	B-protein_type
-	I-protein_type
specific	I-protein_type
peptidase	I-protein_type
with	O
a	O
requirement	O
for	O
Ca2	B-chemical
+	I-chemical
and	O
loss	O
of	O
an	O
internal	B-structure_element
nonapeptide	I-structure_element
for	O
full	B-protein_state
activation	I-protein_state
;	O
lack	O
of	O
structural	O
information	O
on	O
the	O
family	O
appears	O
to	O
have	O
prohibited	O
further	O
investigation	O
.	O

As	O
part	O
of	O
an	O
ongoing	O
project	O
to	O
characterize	O
commensal	O
bacteria	B-taxonomy_domain
in	O
the	O
microbiome	O
that	O
inhabit	O
the	O
human	B-species
gut	O
,	O
the	O
structure	B-evidence
of	O
C11	B-protein_type
peptidase	I-protein_type
,	O
PmC11	B-protein
,	O
from	O
Parabacteroides	B-species
merdae	I-species
was	O
determined	O
using	O
the	O
Joint	O
Center	O
for	O
Structural	O
Genomics	O
(	O
JCSG	O
)	O
4	O
HTP	O
structural	O
biology	O
pipeline	O
.	O

The	O
structure	B-experimental_method
was	I-experimental_method
analyzed	I-experimental_method
,	O
and	O
the	O
enzyme	O
was	O
biochemically	B-experimental_method
characterized	I-experimental_method
to	O
provide	O
the	O
first	O
structure	O
/	O
function	O
correlation	O
for	O
a	O
C11	B-protein_type
peptidase	I-protein_type
.	O

Structure	B-evidence
of	O
PmC11	B-protein

The	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
catalytically	B-protein_state
active	I-protein_state
form	O
of	O
PmC11	B-protein
revealed	O
an	O
extended	B-structure_element
caspase	I-structure_element
-	I-structure_element
like	I-structure_element
α	I-structure_element
/	I-structure_element
β	I-structure_element
/	I-structure_element
α	I-structure_element
sandwich	I-structure_element
architecture	O
comprised	O
of	O
a	O
central	O
nine	B-structure_element
-	I-structure_element
stranded	I-structure_element
β	I-structure_element
-	I-structure_element
sheet	I-structure_element
,	O
with	O
an	O
unusual	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
(	O
CTD	B-structure_element
),	O
starting	O
at	O
Lys250	B-residue_name_number
.	O

A	O
single	B-ptm
cleavage	I-ptm
was	O
observed	O
in	O
the	O
polypeptide	O
chain	O
at	O
Lys147	B-residue_name_number
(	O
Fig	O
.	O
1	O
,	O
A	O
and	O
B	O
),	O
where	O
both	O
ends	O
of	O
the	O
cleavage	B-site
site	I-site
are	O
fully	O
visible	O
and	O
well	O
ordered	O
in	O
the	O
electron	B-evidence
density	I-evidence
.	O

The	O
central	O
nine	B-structure_element
-	I-structure_element
stranded	I-structure_element
β	I-structure_element
-	I-structure_element
sheet	I-structure_element
(	O
β1	B-structure_element
–	I-structure_element
β9	I-structure_element
)	O
of	O
PmC11	B-protein
consists	O
of	O
six	O
parallel	B-structure_element
and	O
three	O
anti	B-structure_element
-	I-structure_element
parallel	I-structure_element
β	I-structure_element
-	I-structure_element
strands	I-structure_element
with	O
4	O
↑	O
3	O
↓	O
2	O
↑	O
1	O
↑	O
5	O
↑	O
6	O
↑	O
7	O
↓	O
8	O
↓	O
9	O
↑	O
topology	O
(	O
Fig	O
.	O
1A	O
)	O
and	O
the	O
overall	O
structure	B-evidence
includes	O
14	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
with	O
six	O
(	O
α1	B-structure_element
–	I-structure_element
α2	I-structure_element
and	O
α4	B-structure_element
–	I-structure_element
α7	I-structure_element
)	O
closely	O
surrounding	O
the	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
in	O
an	O
approximately	O
parallel	O
orientation	O
.	O

Helices	B-structure_element
α1	B-structure_element
,	O
α7	B-structure_element
,	O
and	O
α6	B-structure_element
are	O
located	O
on	O
one	O
side	O
of	O
the	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
with	O
α2	B-structure_element
,	O
α4	B-structure_element
,	O
and	O
α5	B-structure_element
on	O
the	O
opposite	O
side	O
(	O
Fig	O
.	O
1A	O
).	O

Helix	B-structure_element
α3	B-structure_element
sits	O
at	O
the	O
end	O
of	O
the	O
loop	B-structure_element
following	O
β5	B-structure_element
(	O
L5	B-structure_element
),	O
just	O
preceding	O
the	O
Lys147	B-residue_name_number
cleavage	B-site
site	I-site
,	O
with	O
both	O
L5	B-structure_element
and	O
α3	B-structure_element
pointing	O
away	O
from	O
the	O
central	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
and	O
toward	O
the	O
CTD	B-structure_element
,	O
which	O
starts	O
with	O
α8	B-structure_element
.	O

The	O
structure	B-evidence
also	O
includes	O
two	O
short	O
β	B-structure_element
-	I-structure_element
hairpins	I-structure_element
(	O
βA	B-structure_element
–	I-structure_element
βB	I-structure_element
and	O
βD	B-structure_element
–	I-structure_element
βE	I-structure_element
)	O
and	O
a	O
small	B-structure_element
β	I-structure_element
-	I-structure_element
sheet	I-structure_element
(	O
βC	B-structure_element
–	I-structure_element
βF	I-structure_element
),	O
which	O
is	O
formed	O
from	O
two	O
distinct	O
regions	O
of	O
the	O
sequence	O
(	O
βC	B-structure_element
precedes	O
α11	B-structure_element
,	O
α12	B-structure_element
and	O
β9	B-structure_element
,	O
whereas	O
βF	B-structure_element
follows	O
the	O
βD	B-structure_element
-	I-structure_element
βE	I-structure_element
hairpin	B-structure_element
)	O
in	O
the	O
middle	O
of	O
the	O
CTD	B-structure_element
(	O
Fig	O
.	O
1B	O
).	O

Crystal	B-evidence
structure	I-evidence
of	O
a	O
C11	B-protein_type
peptidase	I-protein_type
from	O
P	B-species
.	I-species
merdae	I-species
.	O

A	O
,	O
primary	B-experimental_method
sequence	I-experimental_method
alignment	I-experimental_method
of	O
PmC11	B-protein
(	O
Uniprot	O
ID	O
A7A9N3	O
)	O
and	O
clostripain	B-protein
(	O
Uniprot	O
ID	O
P09870	O
)	O
from	O
C	B-species
.	I-species
histolyticum	I-species
with	O
identical	O
residues	O
highlighted	O
in	O
gray	O
shading	O
.	O

The	O
secondary	O
structure	O
of	O
PmC11	B-protein
from	O
the	O
crystal	B-evidence
structure	I-evidence
is	O
mapped	O
onto	O
its	O
sequence	O
with	O
the	O
position	O
of	O
the	O
PmC11	B-protein
catalytic	B-site
dyad	I-site
,	O
autocatalytic	B-site
cleavage	I-site
site	I-site
(	O
Lys147	B-residue_name_number
),	O
and	O
S1	B-site
binding	I-site
pocket	I-site
Asp	B-residue_name
(	O
Asp177	B-residue_name_number
)	O
highlighted	O
by	O
a	O
red	O
star	O
,	O
a	O
red	O
downturned	O
triangle	O
,	O
and	O
a	O
red	O
upturned	O
triangle	O
,	O
respectively	O
.	O

Connecting	O
loops	B-structure_element
are	O
colored	O
gray	O
,	O
the	O
main	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
is	O
in	O
orange	O
,	O
with	O
other	O
strands	O
in	O
olive	O
,	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
are	O
in	O
blue	O
,	O
and	O
the	O
nonapeptide	B-structure_element
linker	I-structure_element
of	O
clostripain	B-protein
that	O
is	O
excised	O
upon	O
autocleavage	B-ptm
is	O
underlined	O
in	O
red	O
.	O

Sequences	O
around	O
the	O
catalytic	B-site
site	I-site
of	O
clostripain	B-protein
and	O
PmC11	B-protein
align	O
well	O
.	O

B	O
,	O
topology	O
diagram	O
of	O
PmC11	B-protein
colored	O
as	O
in	O
A	O
except	O
that	O
additional	O
(	O
non	O
-	O
core	O
)	O
β	B-structure_element
-	I-structure_element
strands	I-structure_element
are	O
in	O
yellow	O
.	O

Helices	O
found	O
on	O
either	O
side	O
of	O
the	O
central	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
are	O
shown	O
above	O
and	O
below	O
the	O
sheet	B-structure_element
,	O
respectively	O
.	O

The	O
position	O
of	O
the	O
catalytic	B-site
dyad	I-site
(	O
H	B-residue_name
,	O
C	B-residue_name
)	O
and	O
the	O
processing	B-site
site	I-site
(	O
Lys147	B-residue_name_number
)	O
are	O
highlighted	O
.	O

Helices	O
(	O
1	O
–	O
14	O
)	O
and	O
β	B-structure_element
-	I-structure_element
strands	I-structure_element
(	O
1	O
–	O
9	O
and	O
A	O
-	O
F	O
)	O
are	O
numbered	O
from	O
the	O
N	O
terminus	O
.	O

The	O
core	B-structure_element
caspase	I-structure_element
-	I-structure_element
fold	I-structure_element
is	O
highlighted	O
in	O
a	O
box	O
.	O

C	O
,	O
tertiary	O
structure	O
of	O
PmC11	B-protein
.	O

The	O
N	O
and	O
C	O
termini	O
(	O
N	O
and	O
C	O
)	O
of	O
PmC11	B-protein
along	O
with	O
the	O
central	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
(	O
1	O
–	O
9	O
),	O
helix	B-structure_element
α5	B-structure_element
,	O
and	O
helices	B-structure_element
α8	B-structure_element
,	O
α11	B-structure_element
,	O
and	O
α13	B-structure_element
from	O
the	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
,	O
are	O
all	O
labeled	O
.	O

Loops	O
are	O
colored	O
gray	O
,	O
the	O
main	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
is	O
in	O
orange	O
,	O
with	O
other	O
β	B-structure_element
-	I-structure_element
strands	I-structure_element
in	O
yellow	O
,	O
and	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
are	O
in	O
blue	O
.	O

The	O
CTD	B-structure_element
of	O
PmC11	B-protein
is	O
composed	O
of	O
a	O
tight	B-structure_element
helical	I-structure_element
bundle	I-structure_element
formed	O
from	O
helices	B-structure_element
α8	B-structure_element
–	I-structure_element
α14	I-structure_element
and	O
includes	O
strands	B-structure_element
βC	B-structure_element
and	O
βF	B-structure_element
,	O
and	O
β	B-structure_element
-	I-structure_element
hairpin	I-structure_element
βD	B-structure_element
–	I-structure_element
βE	I-structure_element
.	O
The	O
CTD	B-structure_element
sits	O
entirely	O
on	O
one	O
side	O
of	O
the	O
enzyme	O
interacting	O
only	O
with	O
α3	B-structure_element
,	O
α5	B-structure_element
,	O
β9	B-structure_element
,	O
and	O
the	O
loops	B-structure_element
surrounding	O
β8	B-structure_element
.	O

Of	O
the	O
interacting	O
secondary	O
structure	O
elements	O
,	O
α5	B-structure_element
is	O
perhaps	O
the	O
most	O
interesting	O
.	O

This	B-structure_element
helix	I-structure_element
makes	O
a	O
total	O
of	O
eight	O
hydrogen	O
bonds	O
with	O
the	O
CTD	B-structure_element
,	O
including	O
one	O
salt	O
bridge	O
(	O
Arg191	B-residue_name_number
-	O
Asp255	B-residue_name_number
)	O
and	O
is	O
surrounded	O
by	O
the	O
CTD	B-structure_element
on	O
one	O
side	O
and	O
the	O
main	B-structure_element
core	I-structure_element
of	O
the	O
enzyme	O
on	O
the	O
other	O
,	O
acting	O
like	O
a	O
linchpin	O
holding	O
both	O
components	O
together	O
(	O
Fig	O
.	O
1C	O
).	O

PmC11	B-protein
is	O
,	O
as	O
expected	O
,	O
most	O
structurally	O
similar	O
to	O
other	O
members	O
of	O
clan	B-protein_type
CD	I-protein_type
with	O
the	O
top	O
hits	O
in	O
a	O
search	O
of	O
known	O
structures	B-evidence
being	O
caspase	B-protein
-	I-protein
7	I-protein
,	O
gingipain	B-protein
-	I-protein
K	I-protein
,	O
and	O
legumain	B-protein
(	O
PBD	O
codes	O
4hq0	O
,	O
4tkx	O
,	O
and	O
4aw9	O
,	O
respectively	O
)	O
(	O
Table	O
2	O
).	O

The	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
is	O
unique	O
to	O
PmC11	B-protein
within	O
clan	B-protein_type
CD	I-protein_type
and	O
structure	B-experimental_method
comparisons	I-experimental_method
for	O
this	B-structure_element
domain	I-structure_element
alone	I-structure_element
does	O
not	O
produce	O
any	O
hits	O
in	O
the	O
PDB	O
(	O
DaliLite	B-experimental_method
,	O
PDBeFold	B-experimental_method
),	O
suggesting	O
a	O
completely	O
novel	O
fold	O
.	O

As	O
the	O
archetypal	O
and	O
arguably	O
most	O
well	O
studied	O
member	O
of	O
clan	B-protein_type
CD	I-protein_type
,	O
the	O
caspases	B-protein_type
were	O
used	O
as	O
the	O
basis	O
to	O
investigate	O
the	O
structure	O
/	O
function	O
relationships	O
in	O
PmC11	B-protein
,	O
with	O
caspase	B-protein
-	I-protein
7	I-protein
as	O
the	O
representative	O
member	O
.	O

Six	O
of	O
the	O
central	O
β	B-structure_element
-	I-structure_element
strands	I-structure_element
in	O
PmC11	B-protein
(	O
β1	B-structure_element
–	I-structure_element
β2	I-structure_element
and	O
β5	B-structure_element
–	I-structure_element
β8	I-structure_element
)	O
share	O
the	O
same	O
topology	O
as	O
the	O
six	B-structure_element
-	I-structure_element
stranded	I-structure_element
β	I-structure_element
-	I-structure_element
sheet	I-structure_element
found	O
in	O
caspases	B-protein_type
,	O
with	O
strands	B-structure_element
β3	B-structure_element
,	O
β4	B-structure_element
,	O
and	O
β9	B-structure_element
located	O
on	O
the	O
outside	O
of	O
this	O
core	B-structure_element
structure	I-structure_element
(	O
Fig	O
.	O
1B	O
,	O
box	O
).	O

His133	B-residue_name_number
and	O
Cys179	B-residue_name_number
were	O
found	O
at	O
locations	O
structurally	O
homologous	O
to	O
the	O
caspase	B-protein_type
catalytic	B-site
dyad	I-site
,	O
and	O
other	O
clan	B-protein_type
CD	I-protein_type
structures	B-evidence
,	O
at	O
the	O
C	O
termini	O
of	O
strands	B-structure_element
β5	B-structure_element
and	O
β6	B-structure_element
,	O
respectively	O
(	O
Figs	O
.	O
1	O
,	O
A	O
and	O
B	O
,	O
and	O
2A	O
).	O

A	O
multiple	B-experimental_method
sequence	I-experimental_method
alignment	I-experimental_method
of	O
C11	B-protein_type
proteins	O
revealed	O
that	O
these	O
residues	O
are	O
highly	B-protein_state
conserved	I-protein_state
(	O
data	O
not	O
shown	O
).	O

Summary	O
of	O
PDBeFOLD	B-experimental_method
superposition	I-experimental_method
of	O
structures	O
found	O
to	O
be	O
most	O
similar	O
to	O
PmC11	B-protein
in	O
the	O
PBD	O
based	O
on	O
DaliLite	B-experimental_method

Biochemical	B-experimental_method
and	I-experimental_method
structural	I-experimental_method
characterization	I-experimental_method
of	O
PmC11	B-protein
.	O

A	O
,	O
ribbon	O
representation	O
of	O
the	O
overall	O
structure	O
of	O
PmC11	B-protein
illustrating	O
the	O
catalytic	B-site
site	I-site
,	O
cleavage	O
site	O
displacement	O
,	O
and	O
potential	O
S1	B-site
binding	I-site
site	I-site
.	O

The	O
overall	O
structure	B-evidence
of	O
PmC11	B-protein
is	O
shown	O
in	O
gray	O
,	O
looking	O
down	O
into	O
the	O
catalytic	B-site
site	I-site
with	O
the	O
catalytic	B-site
dyad	I-site
in	O
red	O
.	O

The	O
two	O
ends	O
of	O
the	O
autolytic	B-site
cleavage	I-site
site	I-site
(	O
Lys147	B-residue_name_number
and	O
Ala148	B-residue_name_number
,	O
green	O
)	O
are	O
displaced	O
by	O
19	O
.	O
5	O
Å	O
(	O
thin	O
black	O
line	O
)	O
from	O
one	O
another	O
and	O
residues	O
in	O
the	O
potential	O
substrate	B-site
binding	I-site
pocket	I-site
are	O
highlighted	O
in	O
blue	O
.	O

B	O
,	O
size	B-experimental_method
exclusion	I-experimental_method
chromatography	I-experimental_method
of	O
PmC11	B-protein
.	O

PmC11	O
migrates	O
as	O
a	O
monomer	B-oligomeric_state
with	O
a	O
molecular	O
mass	O
around	O
41	O
kDa	O
calculated	O
from	O
protein	O
standards	O
of	O
known	O
molecular	O
weights	O
.	O

Elution	O
fractions	O
across	O
the	O
major	O
peak	O
(	O
1	O
–	O
6	O
)	O
were	O
analyzed	O
by	O
SDS	B-experimental_method
-	I-experimental_method
PAGE	I-experimental_method
on	O
a	O
4	O
–	O
12	O
%	O
gel	O
in	O
MES	O
buffer	O
.	O

C	O
,	O
the	O
active	B-protein_state
form	O
of	O
PmC11	B-protein
and	O
two	O
mutants	O
,	O
PmC11C179A	B-mutant
(	O
C	O
)	O
and	O
PmC11K147A	B-mutant
(	O
K	O
),	O
were	O
examined	O
by	O
SDS	B-experimental_method
-	I-experimental_method
PAGE	I-experimental_method
(	O
lane	O
1	O
)	O
and	O
Western	B-experimental_method
blot	I-experimental_method
analysis	O
using	O
an	O
anti	O
-	O
His	O
antibody	O
(	O
lane	O
2	O
)	O
show	O
that	O
PmC11	B-protein
autoprocesses	B-ptm
,	O
whereas	O
mutants	O
,	O
PmC11C179A	B-mutant
and	O
PmC11K147A	B-mutant
,	O
do	O
not	O
show	O
autoprocessing	B-ptm
in	O
vitro	O
.	O

D	O
,	O
cysteine	O
peptidase	O
activity	O
of	O
PmC11	B-protein
.	O

Km	O
and	O
Vmax	B-evidence
of	O
PmC11	B-protein
and	O
K147A	B-mutant
mutant	O
were	O
determined	O
by	O
monitoring	O
change	O
in	O
the	O
fluorescence	O
corresponding	O
to	O
AMC	O
release	O
from	O
Bz	B-chemical
-	I-chemical
R	I-chemical
-	I-chemical
AMC	I-chemical
.	O

E	O
,	O
intermolecular	B-ptm
processing	I-ptm
of	O
PmC11C179A	B-mutant
by	O
PmC11	B-protein
.	O

PmC11C179A	O
(	O
20	O
μg	O
)	O
was	O
incubated	O
overnight	O
at	O
37	O
°	O
C	O
with	O
increasing	O
amounts	O
of	O
processed	O
PmC11	B-protein
and	O
analyzed	O
on	O
a	O
10	O
%	O
SDS	B-experimental_method
-	I-experimental_method
PAGE	I-experimental_method
gel	O
.	O

Inactive	O
PmC11C179A	B-mutant
was	O
not	O
processed	O
to	O
a	O
major	O
extent	O
by	O
active	B-protein_state
PmC11	B-protein
until	O
around	O
a	O
ratio	O
of	O
1	O
:	O
4	O
(	O
5	O
μg	O
of	O
active	B-protein_state
PmC11	B-protein
).	O

A	O
single	O
lane	O
of	O
20	O
μg	O
of	O
active	B-protein_state
PmC11	B-protein
(	O
labeled	O
20	O
)	O
is	O
shown	O
for	O
comparison	O
.	O

F	O
,	O
activity	B-evidence
of	O
PmC11	B-protein
against	O
basic	O
substrates	O
.	O

G	O
,	O
electrostatic	O
surface	O
potential	O
of	O
PmC11	B-protein
shown	O
in	O
a	O
similar	O
orientation	O
,	O
where	O
blue	O
and	O
red	O
denote	O
positively	O
and	O
negatively	O
charged	O
surface	O
potential	O
,	O
respectively	O
,	O
contoured	O
at	O
±	O
5	O
kT	O
/	O
e	O
.	O

The	O
position	O
of	O
the	O
catalytic	B-site
dyad	I-site
,	O
one	O
potential	O
key	B-site
substrate	I-site
binding	I-site
residue	I-site
Asp177	B-residue_name_number
,	O
and	O
the	O
ends	O
of	O
the	O
cleavage	B-site
site	I-site
Lys147	B-residue_name_number
and	O
Ala148	B-residue_name_number
are	O
indicated	O
.	O

Five	O
of	O
the	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
surrounding	O
the	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
of	O
PmC11	B-protein
(	O
α1	B-structure_element
,	O
α2	B-structure_element
,	O
α4	B-structure_element
,	O
α6	B-structure_element
,	O
and	O
α7	B-structure_element
)	O
are	O
found	O
in	O
similar	O
positions	O
to	O
the	O
five	O
structurally	B-protein_state
conserved	I-protein_state
helices	B-structure_element
in	O
caspases	B-protein_type
and	O
other	O
members	O
of	O
clan	B-protein_type
CD	I-protein_type
,	O
apart	O
from	O
family	O
C80	B-protein_type
.	O

Other	O
than	O
its	O
more	O
extended	B-structure_element
β	I-structure_element
-	I-structure_element
sheet	I-structure_element
,	O
PmC11	B-protein
differs	O
most	O
significantly	O
from	O
other	O
clan	B-protein_type
CD	I-protein_type
members	O
at	O
its	O
C	O
terminus	O
,	O
where	O
the	O
CTD	B-structure_element
contains	O
a	O
further	O
seven	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
and	O
four	O
β	B-structure_element
-	I-structure_element
strands	I-structure_element
after	O
β8	B-structure_element
.	O

Autoprocessing	B-ptm
of	O
PmC11	B-protein

Purification	B-experimental_method
of	O
recombinant	O
PmC11	B-protein
(	O
molecular	O
mass	O
=	O
42	O
.	O
6	O
kDa	O
)	O
revealed	O
partial	O
processing	O
into	O
two	O
cleavage	O
products	O
of	O
26	O
.	O
4	O
and	O
16	O
.	O
2	O
kDa	O
,	O
related	O
to	O
the	O
observed	O
cleavage	B-ptm
at	O
Lys147	B-residue_name_number
in	O
the	O
crystal	B-evidence
structure	I-evidence
(	O
Fig	O
.	O
2A	O
).	O

Incubation	B-experimental_method
of	O
PmC11	B-protein
at	O
37	O
°	O
C	O
for	O
16	O
h	O
,	O
resulted	O
in	O
a	O
fully	B-protein_state
processed	I-protein_state
enzyme	O
that	O
remained	O
as	O
an	O
intact	B-protein_state
monomer	B-oligomeric_state
when	O
applied	O
to	O
a	O
size	O
-	O
exclusion	O
column	O
(	O
Fig	O
.	O
2B	O
).	O

The	O
single	O
cleavage	B-site
site	I-site
of	O
PmC11	B-protein
at	O
Lys147	B-residue_name_number
is	O
found	O
immediately	O
after	O
α3	B-structure_element
,	O
in	O
loop	B-structure_element
L5	B-structure_element
within	O
the	O
central	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
(	O
Figs	O
.	O
1	O
,	O
A	O
and	O
B	O
,	O
and	O
2A	O
).	O

The	O
two	O
ends	O
of	O
the	O
cleavage	B-site
site	I-site
are	O
remarkably	O
well	O
ordered	O
in	O
the	O
crystal	B-evidence
structure	I-evidence
and	O
displaced	O
from	O
one	O
another	O
by	O
19	O
.	O
5	O
Å	O
(	O
Fig	O
.	O
2A	O
).	O

Moreover	O
,	O
the	O
C	O
-	O
terminal	O
side	O
of	O
the	O
cleavage	B-site
site	I-site
resides	O
near	O
the	O
catalytic	B-site
dyad	I-site
with	O
Ala148	B-residue_name_number
being	O
4	O
.	O
5	O
and	O
5	O
.	O
7	O
Å	O
from	O
His133	B-residue_name_number
and	O
Cys179	B-residue_name_number
,	O
respectively	O
.	O

Consequently	O
,	O
it	O
appears	O
feasible	O
that	O
the	O
helix	B-structure_element
attached	O
to	O
Lys147	B-residue_name_number
(	O
α3	B-structure_element
)	O
could	O
be	O
responsible	O
for	O
steric	O
autoinhibition	O
of	O
PmC11	B-protein
when	O
Lys147	B-residue_name_number
is	O
covalently	O
bonded	O
to	O
Ala148	B-residue_name_number
.	O

Thus	O
,	O
the	O
cleavage	B-ptm
would	O
be	O
required	O
for	O
full	B-protein_state
activation	I-protein_state
of	O
PmC11	B-protein
.	O

To	O
investigate	O
this	O
possibility	O
,	O
two	O
mutant	O
forms	O
of	O
the	O
enzyme	O
were	O
created	O
:	O
PmC11C179A	B-mutant
(	O
a	O
catalytically	B-protein_state
inactive	I-protein_state
mutant	I-protein_state
)	O
and	O
PmC11K147A	B-mutant
(	O
a	O
cleavage	B-protein_state
-	I-protein_state
site	I-protein_state
mutant	I-protein_state
).	O

Initial	O
SDS	B-experimental_method
-	I-experimental_method
PAGE	I-experimental_method
and	O
Western	B-experimental_method
blot	I-experimental_method
analysis	O
of	O
both	O
mutants	O
revealed	O
no	O
discernible	O
processing	O
occurred	O
as	O
compared	O
with	O
active	B-protein_state
PmC11	B-protein
(	O
Fig	O
.	O
2C	O
).	O

The	O
PmC11K147A	B-mutant
mutant	B-protein_state
enzyme	O
had	O
a	O
markedly	O
different	O
reaction	B-evidence
rate	I-evidence
(	O
Vmax	B-evidence
)	O
compared	O
with	O
WT	B-protein_state
,	O
where	O
the	O
reaction	B-evidence
velocity	I-evidence
of	O
PmC11	B-protein
was	O
10	O
times	O
greater	O
than	O
that	O
of	O
PmC11K147A	B-mutant
(	O
Fig	O
.	O
2D	O
).	O

Taken	O
together	O
,	O
these	O
data	O
reveal	O
that	O
PmC11	B-protein
requires	O
processing	O
at	O
Lys147	B-residue_name_number
for	O
optimum	O
activity	O
.	O

To	O
investigate	O
whether	O
processing	O
is	O
a	O
result	O
of	O
intra	O
-	O
or	O
intermolecular	O
cleavage	O
,	O
the	O
PmC11C179A	B-mutant
mutant	B-protein_state
was	O
incubated	B-experimental_method
with	I-experimental_method
increasing	I-experimental_method
concentrations	I-experimental_method
of	O
processed	B-protein_state
and	O
activated	B-protein_state
PmC11	B-protein
.	O

These	O
studies	O
revealed	O
that	O
there	O
was	O
no	O
apparent	O
cleavage	O
of	O
PmC11C179A	B-mutant
by	O
the	O
active	B-protein_state
enzyme	O
at	B-experimental_method
low	I-experimental_method
concentrations	I-experimental_method
of	O
PmC11	B-protein
and	O
that	O
only	O
limited	O
cleavage	O
was	O
observed	O
when	O
the	O
ratio	O
of	O
active	B-protein_state
enzyme	O
(	O
PmC11	B-protein
:	O
PmC11C179A	B-mutant
)	O
was	O
increased	B-experimental_method
to	I-experimental_method
∼	I-experimental_method
1	I-experimental_method
:	I-experimental_method
10	I-experimental_method
and	I-experimental_method
1	I-experimental_method
:	I-experimental_method
4	I-experimental_method
,	O
with	O
complete	O
cleavage	O
observed	O
at	O
a	O
ratio	B-experimental_method
of	I-experimental_method
1	I-experimental_method
:	I-experimental_method
1	I-experimental_method
(	O
Fig	O
.	O
2E	O
).	O

This	O
suggests	O
that	O
cleavage	B-ptm
of	O
PmC11C179A	B-mutant
was	O
most	O
likely	O
an	O
effect	O
of	O
the	O
increasing	O
concentration	O
of	O
PmC11	B-protein
and	O
intermolecular	O
cleavage	O
.	O

Collectively	O
,	O
these	O
data	O
suggest	O
that	O
the	O
pro	B-protein_state
-	I-protein_state
form	I-protein_state
of	O
PmC11	B-protein
is	O
autoinhibited	B-protein_state
by	O
a	O
section	O
of	O
L5	B-structure_element
blocking	O
access	O
to	O
the	O
active	B-site
site	I-site
,	O
prior	O
to	O
intramolecular	B-ptm
cleavage	I-ptm
at	O
Lys147	B-residue_name_number
.	O

This	O
cleavage	B-ptm
subsequently	O
allows	O
movement	O
of	O
the	O
region	O
containing	O
Lys147	B-residue_name_number
and	O
the	O
active	B-site
site	I-site
to	O
open	B-protein_state
up	O
for	O
substrate	O
access	O
.	O

Substrate	O
Specificity	O
of	O
PmC11	B-protein

The	O
autocatalytic	B-ptm
cleavage	I-ptm
of	O
PmC11	B-protein
at	O
Lys147	B-residue_name_number
(	O
sequence	O
KLK	O
∧	O
A	O
)	O
demonstrates	O
that	O
the	O
enzyme	O
accepts	O
substrates	O
with	O
Lys	B-residue_name
in	O
the	O
P1	B-residue_number
position	O
.	O

As	O
expected	O
,	O
PmC11	B-protein
showed	O
no	O
activity	O
against	O
substrates	O
with	O
Pro	B-residue_name
or	O
Asp	B-residue_name
in	O
P1	B-residue_number
but	O
was	O
active	B-protein_state
toward	O
substrates	O
with	O
a	O
basic	O
residue	O
in	O
P1	B-residue_number
such	O
as	O
Bz	B-chemical
-	I-chemical
R	I-chemical
-	I-chemical
AMC	I-chemical
,	O
Z	B-chemical
-	I-chemical
GGR	I-chemical
-	I-chemical
AMC	I-chemical
,	O
and	O
BOC	B-chemical
-	I-chemical
VLK	I-chemical
-	I-chemical
AMC	I-chemical
.	O

The	O
rate	O
of	O
cleavage	O
was	O
∼	O
3	O
-	O
fold	O
greater	O
toward	O
the	O
single	O
Arg	B-residue_name
substrate	O
Bz	B-chemical
-	I-chemical
R	I-chemical
-	I-chemical
AMC	I-chemical
than	O
for	O
the	O
other	O
two	O
(	O
Fig	O
.	O
2F	O
)	O
and	O
,	O
unexpectedly	O
,	O
PmC11	B-protein
showed	O
no	O
activity	O
toward	O
BOC	B-chemical
-	I-chemical
K	I-chemical
-	I-chemical
AMC	I-chemical
.	O

These	O
results	O
confirm	O
that	O
PmC11	B-protein
accepts	O
substrates	O
containing	O
Arg	B-residue_name
or	O
Lys	B-residue_name
in	O
P1	B-residue_number
with	O
a	O
possible	O
preference	O
for	O
Arg	B-residue_name
.	O

The	O
catalytic	B-site
dyad	I-site
of	O
PmC11	B-protein
sits	O
near	O
the	O
bottom	O
of	O
an	O
open	B-protein_state
pocket	B-site
on	O
the	O
surface	O
of	O
the	O
enzyme	O
at	O
a	O
conserved	B-protein_state
location	I-protein_state
in	O
the	O
clan	O
CD	B-protein_type
family	I-protein_type
.	O

The	O
PmC11	B-protein
structure	B-evidence
reveals	O
that	O
the	O
catalytic	B-site
dyad	I-site
forms	O
part	O
of	O
a	O
large	O
acidic	B-site
pocket	I-site
(	O
Fig	O
.	O
2G	O
),	O
consistent	O
with	O
a	O
binding	B-site
site	I-site
for	O
a	O
basic	O
substrate	O
.	O

This	O
pocket	B-site
is	O
lined	O
with	O
the	O
potential	O
functional	O
side	O
chains	O
of	O
Asn50	B-residue_name_number
,	O
Asp177	B-residue_name_number
,	O
and	O
Thr204	B-residue_name_number
with	O
Gly134	B-residue_name_number
,	O
Asp207	B-residue_name_number
,	O
and	O
Met205	B-residue_name_number
also	O
contributing	O
to	O
the	O
pocket	B-site
(	O
Fig	O
.	O
2A	O
).	O

Interestingly	O
,	O
these	O
residues	O
are	O
in	O
regions	O
that	O
are	O
structurally	B-protein_state
similar	I-protein_state
to	O
those	O
involved	O
in	O
the	O
S1	B-site
binding	I-site
pockets	I-site
of	O
other	O
clan	B-protein_type
CD	I-protein_type
members	I-protein_type
(	O
shown	O
in	O
Ref	O
.).	O

Because	O
PmC11	B-protein
recognizes	O
basic	O
substrates	O
,	O
the	O
tetrapeptide	O
inhibitor	O
Z	B-chemical
-	I-chemical
VRPR	I-chemical
-	I-chemical
FMK	I-chemical
was	O
tested	O
as	O
an	O
enzyme	O
inhibitor	O
and	O
was	O
found	O
to	O
inhibit	B-protein_state
both	O
the	O
autoprocessing	B-ptm
and	O
activity	O
of	O
PmC11	B-protein
(	O
Fig	O
.	O
3A	O
).	O

Z	B-chemical
-	I-chemical
VRPR	I-chemical
-	I-chemical
FMK	I-chemical
was	O
also	O
shown	O
to	O
bind	O
to	O
the	O
enzyme	O
:	O
a	O
size	B-evidence
-	I-evidence
shift	I-evidence
was	O
observed	O
,	O
by	O
SDS	B-experimental_method
-	I-experimental_method
PAGE	I-experimental_method
analysis	O
,	O
in	O
the	O
larger	O
processed	O
product	O
of	O
PmC11	B-protein
suggesting	O
that	O
the	O
inhibitor	B-protein_state
bound	I-protein_state
to	O
the	O
active	B-site
site	I-site
(	O
Fig	O
.	O
3B	O
).	O

A	O
structure	B-experimental_method
overlay	I-experimental_method
of	O
PmC11	B-protein
with	O
the	O
MALT1	B-protein
-	I-protein
paracacaspase	I-protein
(	O
MALT1	B-protein
-	I-protein
P	I-protein
),	O
in	O
complex	B-protein_state
with	O
Z	B-chemical
-	I-chemical
VRPR	I-chemical
-	I-chemical
FMK	I-chemical
,	O
revealed	O
that	O
the	O
PmC11	B-protein
dyad	B-site
sits	O
in	O
a	O
very	O
similar	O
position	O
to	O
that	O
of	O
active	B-protein_state
MALT1	B-protein
-	I-protein
P	I-protein
and	O
that	O
Asn50	B-residue_name_number
,	O
Asp177	B-residue_name_number
,	O
and	O
Asp207	B-residue_name_number
superimpose	O
well	O
with	O
the	O
principal	O
MALT1	B-protein
-	I-protein
P	I-protein
inhibitor	B-site
binding	I-site
residues	I-site
(	O
Asp365	B-residue_name_number
,	O
Asp462	B-residue_name_number
,	O
and	O
Glu500	B-residue_name_number
,	O
respectively	O
(	O
VRPR	B-chemical
-	I-chemical
FMK	I-chemical
from	O
MALT1	B-protein
-	I-protein
P	I-protein
with	O
the	O
corresponding	O
PmC11	B-protein
residues	O
from	O
the	O
structural	B-experimental_method
overlay	I-experimental_method
is	O
shown	O
in	O
Fig	O
.	O
1D	O
),	O
as	O
described	O
in	O
Ref	O
.).	O

Asp177	B-residue_name_number
is	O
located	O
near	O
the	O
catalytic	B-protein_state
cysteine	B-residue_name
and	O
is	O
conserved	B-protein_state
throughout	I-protein_state
the	O
C11	B-protein_type
family	I-protein_type
,	O
suggesting	O
it	O
is	O
the	O
primary	O
S1	B-site
binding	I-site
site	I-site
residue	I-site
.	O

In	O
the	O
structure	B-evidence
of	O
PmC11	B-protein
,	O
Asp207	B-residue_name_number
resides	O
on	O
a	O
flexible	O
loop	B-structure_element
pointing	O
away	O
from	O
the	O
S1	B-site
binding	I-site
pocket	I-site
(	O
Fig	O
.	O
3C	O
).	O

However	O
,	O
this	O
loop	B-structure_element
has	O
been	O
shown	O
to	O
be	O
important	O
for	O
substrate	O
binding	O
in	O
clan	B-protein_type
CD	I-protein_type
and	O
this	O
residue	O
could	O
easily	O
rotate	O
and	O
be	O
involved	O
in	O
substrate	O
binding	O
in	O
PmC11	B-protein
.	O

Thus	O
,	O
Asn50	B-residue_name_number
,	O
Asp177	B-residue_name_number
,	O
and	O
Asp207	B-residue_name_number
are	O
most	O
likely	O
responsible	O
for	O
the	O
substrate	O
specificity	O
of	O
PmC11	B-protein
.	O

Asp177	B-residue_name_number
is	O
highly	B-protein_state
conserved	I-protein_state
throughout	O
the	O
clan	B-protein_type
CD	I-protein_type
C11	I-protein_type
peptidases	I-protein_type
and	O
is	O
thought	O
to	O
be	O
primarily	O
responsible	O
for	O
substrate	O
specificity	O
of	O
the	O
clan	B-protein_type
CD	I-protein_type
enzymes	I-protein_type
,	O
as	O
also	O
illustrated	O
from	O
the	O
proximity	O
of	O
these	O
residues	O
relative	O
to	O
the	O
inhibitor	O
Z	B-chemical
-	I-chemical
VRPR	I-chemical
-	I-chemical
FMK	I-chemical
when	O
PmC11	B-protein
is	O
overlaid	B-experimental_method
on	O
the	O
MALT1	B-protein
-	I-protein
P	I-protein
structure	B-evidence
(	O
Fig	O
.	O
3C	O
).	O

PmC11	B-protein
binds	O
and	O
is	O
inhibited	O
by	O
Z	B-chemical
-	I-chemical
VRPR	I-chemical
-	I-chemical
FMK	I-chemical
and	O
does	O
not	O
require	O
Ca2	B-chemical
+	I-chemical
for	O
activity	O
.	O

A	O
,	O
PmC11	O
activity	O
is	O
inhibited	O
by	O
Z	B-chemical
-	I-chemical
VRPR	I-chemical
-	I-chemical
FMK	I-chemical
.	O

Cleavage	O
of	O
Bz	B-chemical
-	I-chemical
R	I-chemical
-	I-chemical
AMC	I-chemical
by	O
PmC11	B-protein
was	O
measured	O
in	O
a	O
fluorometric	B-experimental_method
activity	I-experimental_method
assay	I-experimental_method
with	O
(+,	O
purple	O
)	O
and	O
without	O
(−,	O
red	O
)	O
Z	B-chemical
-	I-chemical
VRPR	I-chemical
-	I-chemical
FMK	I-chemical
.	O

B	O
,	O
gel	B-experimental_method
-	I-experimental_method
shift	I-experimental_method
assay	I-experimental_method
reveals	O
that	O
Z	B-chemical
-	I-chemical
VRPR	I-chemical
-	I-chemical
FMK	I-chemical
binds	O
to	O
PmC11	B-protein
.	O

PmC11	O
was	O
incubated	B-experimental_method
with	O
(+)	O
or	O
without	O
(−)	O
Z	B-chemical
-	I-chemical
VRPR	I-chemical
-	I-chemical
FMK	I-chemical
and	O
the	O
samples	O
analyzed	O
on	O
a	O
10	O
%	O
SDS	B-experimental_method
-	I-experimental_method
PAGE	I-experimental_method
gel	O
.	O

A	O
size	B-evidence
shift	I-evidence
can	O
be	O
observed	O
in	O
the	O
larger	O
processed	O
product	O
of	O
PmC11	B-protein
(	O
26	O
.	O
1	O
kDa	O
).	O

C	O
,	O
PmC11	B-protein
with	O
the	O
Z	B-chemical
-	I-chemical
VRPR	I-chemical
-	I-chemical
FMK	I-chemical
from	O
the	O
MALT1	B-protein
-	I-protein
paracacaspase	I-protein
(	O
MALT1	B-protein
-	I-protein
P	I-protein
)	O
superimposed	B-experimental_method
.	O

A	O
three	B-experimental_method
-	I-experimental_method
dimensional	I-experimental_method
structural	I-experimental_method
overlay	I-experimental_method
of	O
Z	B-chemical
-	I-chemical
VRPR	I-chemical
-	I-chemical
FMK	I-chemical
from	O
the	O
MALT1	B-protein
-	I-protein
P	I-protein
complex	O
onto	O
PmC11	B-protein
.	O

The	O
position	O
and	O
orientation	O
of	O
Z	B-chemical
-	I-chemical
VRPR	I-chemical
-	I-chemical
FMK	I-chemical
was	O
taken	O
from	O
superposition	B-experimental_method
of	O
the	O
PmC11	B-protein
and	O
MALTI_P	B-protein
structures	B-evidence
and	O
indicates	O
the	O
presumed	O
active	B-site
site	I-site
of	O
PmC11	B-protein
.	O

Residues	O
surrounding	O
the	O
inhibitor	O
are	O
labeled	O
and	O
represent	O
potentially	O
important	O
binding	B-site
site	I-site
residues	I-site
,	O
labeled	O
in	O
black	O
and	O
shown	O
in	O
an	O
atomic	O
representation	O
.	O

C	O
,	O
divalent	O
cations	O
do	O
not	O
increase	O
the	O
activity	O
of	O
PmC11	B-protein
.	O

The	O
cleavage	O
of	O
Bz	B-chemical
-	I-chemical
R	I-chemical
-	I-chemical
AMC	I-chemical
by	O
PmC11	B-protein
was	O
measured	O
in	O
the	O
presence	O
of	O
the	O
cations	O
Ca2	B-chemical
+,	I-chemical
Mn2	B-chemical
+,	I-chemical
Zn2	B-chemical
+,	I-chemical
Co2	B-chemical
+,	I-chemical
Cu2	B-chemical
+,	I-chemical
Mg2	B-chemical
+,	I-chemical
and	O
Fe3	B-chemical
+	I-chemical
with	O
EGTA	B-chemical
as	O
a	O
negative	O
control	O
,	O
and	O
relative	B-experimental_method
fluorescence	I-experimental_method
measured	I-experimental_method
against	I-experimental_method
time	I-experimental_method
(	O
min	O
).	O

The	O
addition	B-experimental_method
of	I-experimental_method
cations	I-experimental_method
produced	O
no	O
improvement	O
in	O
activity	O
of	O
PmC11	B-protein
when	O
compared	O
in	O
the	O
presence	O
of	O
EGTA	B-chemical
,	O
suggesting	O
that	O
PmC11	B-protein
does	O
not	O
require	O
metal	O
ions	O
for	O
proteolytic	O
activity	O
.	O

Furthermore	O
,	O
Cu2	B-chemical
+,	I-chemical
Fe2	B-chemical
+,	I-chemical
and	O
Zn2	B-chemical
+	I-chemical
appear	O
to	O
inhibit	B-protein_state
PmC11	B-protein
.	O

Comparison	O
with	O
Clostripain	B-protein

Clostripain	B-protein
from	O
C	B-species
.	I-species
histolyticum	I-species
is	O
the	O
founding	O
member	O
of	O
the	O
C11	B-protein_type
family	I-protein_type
of	O
peptidases	B-protein_type
and	O
contains	O
an	O
additional	O
149	B-residue_range
residues	I-residue_range
compared	O
with	O
PmC11	B-protein
.	O

A	O
multiple	B-experimental_method
sequence	I-experimental_method
alignment	I-experimental_method
revealed	O
that	O
most	O
of	O
the	O
secondary	B-structure_element
structural	I-structure_element
elements	I-structure_element
are	O
conserved	B-protein_state
between	O
the	O
two	O
enzymes	O
,	O
although	O
they	O
are	O
only	O
∼	O
23	O
%	O
identical	O
(	O
Fig	O
.	O
1A	O
).	O

Nevertheless	O
,	O
PmC11	B-protein
may	O
be	O
a	O
good	O
model	O
for	O
the	O
core	O
structure	O
of	O
clostripain	B-protein
.	O

The	O
primary	B-experimental_method
structural	I-experimental_method
alignment	I-experimental_method
also	O
shows	O
that	O
the	O
catalytic	B-site
dyad	I-site
in	O
PmC11	B-protein
is	O
structurally	B-protein_state
conserved	I-protein_state
in	O
clostripain	B-protein
(	O
Fig	O
.	O
1A	O
).	O

Unlike	O
PmC11	B-protein
,	O
clostripain	B-protein
has	O
two	O
cleavage	B-site
sites	I-site
(	O
Arg181	B-residue_name_number
and	O
Arg190	B-residue_name_number
),	O
which	O
results	O
in	O
the	O
removal	O
of	O
a	O
nonapeptide	B-structure_element
,	O
and	O
is	O
required	O
for	O
full	B-protein_state
activation	I-protein_state
of	O
the	O
enzyme	O
(	O
highlighted	O
in	O
Fig	O
.	O
1A	O
).	O

Interestingly	O
,	O
Arg190	B-residue_name_number
was	O
found	O
to	O
align	O
with	O
Lys147	B-residue_name_number
in	O
PmC11	B-protein
.	O

In	O
addition	O
,	O
the	O
predicted	O
primary	O
S1	B-site
-	I-site
binding	I-site
residue	I-site
in	O
PmC11	B-protein
Asp177	B-residue_name_number
also	O
overlays	B-experimental_method
with	O
the	O
residue	O
predicted	O
to	O
be	O
the	O
P1	B-site
specificity	I-site
determining	I-site
residue	I-site
in	O
clostripain	B-protein
(	O
Asp229	B-residue_name_number
,	O
Fig	O
.	O
1A	O
).	O

As	O
studies	O
on	O
clostripain	B-protein
revealed	O
addition	O
of	O
Ca2	B-chemical
+	I-chemical
ions	O
are	O
required	O
for	O
full	B-protein_state
activation	I-protein_state
,	O
the	O
Ca2	B-chemical
+	I-chemical
dependence	O
of	O
PmC11	B-protein
was	O
examined	O
.	O

Surprisingly	O
,	O
Ca2	B-chemical
+	I-chemical
did	O
not	O
enhance	O
PmC11	B-protein
activity	O
and	O
,	O
furthermore	O
,	O
other	O
divalent	O
cations	O
,	O
Mg2	B-chemical
+,	I-chemical
Mn2	B-chemical
+,	I-chemical
Co2	B-chemical
+,	I-chemical
Fe2	B-chemical
+,	I-chemical
Zn2	B-chemical
+,	I-chemical
and	O
Cu2	B-chemical
+,	I-chemical
were	O
not	O
necessary	O
for	O
PmC11	B-protein
activity	O
(	O
Fig	O
.	O
3D	O
).	O

In	O
support	O
of	O
these	O
findings	O
,	O
EGTA	B-chemical
did	O
not	O
inhibit	O
PmC11	B-protein
suggesting	O
that	O
,	O
unlike	O
clostripain	B-protein
,	O
PmC11	B-protein
does	O
not	O
require	O
Ca2	B-chemical
+	I-chemical
or	O
other	O
divalent	O
cations	O
,	O
for	O
activity	O
.	O

The	O
crystal	B-evidence
structure	I-evidence
of	O
PmC11	B-protein
now	O
provides	O
three	O
-	O
dimensional	O
information	O
for	O
a	O
member	O
of	O
the	O
clostripain	B-protein
C11	B-protein_type
family	I-protein_type
of	O
cysteine	B-protein_type
peptidases	I-protein_type
.	O

The	O
enzyme	O
exhibits	O
all	O
of	O
the	O
key	O
structural	O
elements	O
of	O
clan	B-protein_type
CD	I-protein_type
members	I-protein_type
,	O
but	O
is	O
unusual	O
in	O
that	O
it	O
has	O
a	O
nine	O
-	O
stranded	O
central	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
with	O
a	O
novel	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
.	O

The	O
structural	O
similarity	O
of	O
PmC11	B-protein
with	O
its	O
nearest	O
structural	O
neighbors	O
in	O
the	O
PDB	O
is	O
decidedly	O
low	O
,	O
overlaying	O
better	O
with	O
six	O
-	O
stranded	O
caspase	B-protein
-	I-protein
7	I-protein
than	O
any	O
of	O
the	O
other	O
larger	O
members	O
of	O
the	O
clan	O
(	O
Table	O
2	O
).	O

The	O
substrate	O
specificity	O
of	O
PmC11	B-protein
is	O
Arg	B-residue_name
/	O
Lys	B-residue_name
and	O
the	O
crystal	B-evidence
structure	I-evidence
revealed	O
an	O
acidic	B-site
pocket	I-site
for	O
specific	O
binding	O
of	O
such	O
basic	O
substrates	O
.	O

In	O
addition	O
,	O
the	O
structure	B-evidence
suggested	O
a	O
mechanism	O
of	O
self	O
-	O
inhibition	O
in	O
both	O
PmC11	B-protein
and	O
clostripain	B-protein
and	O
an	O
activation	O
mechanism	O
that	O
requires	O
autoprocessing	B-ptm
.	O

PmC11	B-protein
differs	O
from	O
clostripain	B-protein
in	O
that	O
is	O
does	O
not	O
appear	O
to	O
require	O
divalent	O
cations	O
for	O
activation	O
.	O

Several	O
other	O
members	O
of	O
clan	B-protein_type
CD	I-protein_type
require	O
processing	B-ptm
for	O
full	B-protein_state
activation	I-protein_state
including	O
legumain	B-protein
,	O
gingipain	B-protein
-	I-protein
R	I-protein
,	O
MARTX	B-protein
-	I-protein
CPD	I-protein
,	O
and	O
the	O
effector	B-protein_type
caspases	I-protein_type
,	O
e	O
.	O
g	O
.	O
caspase	B-protein
-	I-protein
7	I-protein
.	O

To	O
date	O
,	O
the	O
effector	B-protein_type
caspases	I-protein_type
are	O
the	O
only	O
group	O
of	O
enzymes	O
that	O
require	O
cleavage	B-ptm
of	O
a	O
loop	B-structure_element
within	O
the	O
central	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
.	O

This	O
is	O
also	O
the	O
case	O
in	O
PmC11	B-protein
,	O
although	O
the	O
cleavage	B-ptm
loop	B-structure_element
is	O
structurally	O
different	O
to	O
that	O
found	O
in	O
the	O
caspases	B-protein_type
and	O
follows	O
the	O
catalytic	B-protein_state
His	B-residue_name
(	O
Fig	O
.	O
1A	O
),	O
as	O
opposed	O
to	O
the	O
Cys	B-residue_name
in	O
the	O
caspases	B-protein_type
.	O

All	O
other	O
clan	B-protein_type
CD	I-protein_type
members	I-protein_type
requiring	O
cleavage	B-ptm
for	O
full	B-protein_state
activation	I-protein_state
do	O
so	O
at	O
sites	B-site
external	O
to	O
their	O
central	O
sheets	B-structure_element
.	O

The	O
caspases	B-protein_type
and	O
gingipain	B-protein
-	I-protein
R	I-protein
both	O
undergo	O
intermolecular	B-ptm
(	I-ptm
trans	I-ptm
)	I-ptm
cleavage	I-ptm
and	O
legumain	B-protein
and	O
MARTX	B-protein
-	I-protein
CPD	I-protein
are	O
reported	O
to	O
perform	O
intramolecular	B-ptm
(	I-ptm
cis	I-ptm
)	I-ptm
cleavage	I-ptm
.	O

In	O
addition	O
,	O
several	O
members	O
of	O
clan	B-protein_type
CD	I-protein_type
exhibit	O
self	O
-	O
inhibition	O
,	O
whereby	O
regions	B-structure_element
of	O
the	O
enzyme	O
block	O
access	O
to	O
the	O
active	B-site
site	I-site
.	O

Like	O
PmC11	B-protein
,	O
these	O
structures	O
show	O
preformed	O
catalytic	O
machinery	O
and	O
,	O
for	O
a	O
substrate	O
to	O
gain	O
access	O
,	O
movement	O
and	O
/	O
or	O
cleavage	B-ptm
of	O
the	O
blocking	B-structure_element
region	I-structure_element
is	O
required	O
.	O

The	O
structure	B-evidence
of	O
PmC11	B-protein
gives	O
the	O
first	O
insight	O
into	O
this	O
class	O
of	O
relatively	O
unexplored	O
family	O
of	O
proteins	O
and	O
should	O
allow	O
important	O
catalytic	O
and	O
substrate	O
binding	O
residues	O
to	O
be	O
identified	O
in	O
a	O
variety	O
of	O
orthologues	O
.	O

Indeed	O
,	O
insights	O
gained	O
from	O
an	O
analysis	O
of	O
the	O
PmC11	B-protein
structure	B-evidence
revealed	O
the	O
identity	O
of	O
the	O
Trypanosoma	B-species
brucei	I-species
PNT1	B-protein
protein	O
as	O
a	O
C11	B-protein_type
cysteine	I-protein_type
peptidase	I-protein_type
with	O
an	O
essential	O
role	O
in	O
organelle	O
replication	O
.	O

The	O
PmC11	B-protein
structure	B-evidence
should	O
provide	O
a	O
good	O
basis	O
for	O
structural	B-experimental_method
modeling	I-experimental_method
and	O
,	O
given	O
the	O
importance	O
of	O
other	O
clan	B-protein_type
CD	I-protein_type
enzymes	I-protein_type
,	O
this	O
work	O
should	O
also	O
advance	O
the	O
exploration	O
of	O
these	O
peptidases	B-protein_type
and	O
potentially	O
identify	O
new	O
biologically	O
important	O
substrates	O
.	O

Structural	O
insights	O
into	O
the	O
regulatory	O
mechanism	O
of	O
the	O
Pseudomonas	B-species
aeruginosa	I-species
YfiBNR	B-complex_assembly
system	O

YfiBNR	B-complex_assembly
is	O
a	O
recently	O
identified	O
bis	B-chemical
-(	I-chemical
3	I-chemical
’-	I-chemical
5	I-chemical
’)-	I-chemical
cyclic	I-chemical
dimeric	I-chemical
GMP	I-chemical
(	O
c	B-chemical
-	I-chemical
di	I-chemical
-	I-chemical
GMP	I-chemical
)	O
signaling	O
system	O
in	O
opportunistic	O
pathogens	O
.	O

In	O
response	O
to	O
cell	O
stress	O
,	O
YfiB	B-protein
in	O
the	O
outer	O
membrane	O
can	O
sequester	O
the	O
periplasmic	O
protein	O
YfiR	B-protein
,	O
releasing	O
its	O
inhibition	O
of	O
YfiN	B-protein
on	O
the	O
inner	O
membrane	O
and	O
thus	O
provoking	O
the	O
diguanylate	O
cyclase	O
activity	O
of	O
YfiN	B-protein
to	O
induce	O
c	B-chemical
-	I-chemical
di	I-chemical
-	I-chemical
GMP	I-chemical
production	O
.	O

Here	O
,	O
we	O
report	O
the	O
crystal	B-evidence
structures	I-evidence
of	O
YfiB	B-protein
alone	B-protein_state
and	O
of	O
an	O
active	B-protein_state
mutant	B-protein_state
YfiBL43P	B-mutant
complexed	B-protein_state
with	I-protein_state
YfiR	B-protein
with	O
2	O
:	O
2	O
stoichiometry	O
.	O

Structural	B-experimental_method
analyses	I-experimental_method
revealed	O
that	O
in	O
contrast	O
to	O
the	O
compact	B-protein_state
conformation	I-protein_state
of	O
the	O
dimeric	B-oligomeric_state
YfiB	B-protein
alone	B-protein_state
,	O
YfiBL43P	B-mutant
adopts	O
a	O
stretched	B-protein_state
conformation	I-protein_state
allowing	O
activated	B-protein_state
YfiB	B-protein
to	O
penetrate	O
the	O
peptidoglycan	B-chemical
(	O
PG	B-chemical
)	O
layer	O
and	O
access	O
YfiR	B-protein
.	O
YfiBL43P	B-mutant
shows	O
a	O
more	O
compact	O
PG	B-site
-	I-site
binding	I-site
pocket	I-site
and	O
much	O
higher	O
PG	B-evidence
binding	I-evidence
affinity	I-evidence
than	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
YfiB	B-protein
,	O
suggesting	O
a	O
tight	O
correlation	O
between	O
PG	O
binding	O
and	O
YfiB	B-protein
activation	O
.	O

In	O
addition	O
,	O
our	O
crystallographic	B-experimental_method
analyses	I-experimental_method
revealed	O
that	O
YfiR	B-protein
binds	O
Vitamin	B-chemical
B6	I-chemical
(	O
VB6	B-chemical
)	O
or	O
L	B-chemical
-	I-chemical
Trp	I-chemical
at	O
a	O
YfiB	B-site
-	I-site
binding	I-site
site	I-site
and	O
that	O
both	O
VB6	B-chemical
and	O
L	B-chemical
-	I-chemical
Trp	I-chemical
are	O
able	O
to	O
reduce	O
YfiBL43P	B-mutant
-	O
induced	O
biofilm	O
formation	O
.	O

Based	O
on	O
the	O
structural	B-evidence
and	I-evidence
biochemical	I-evidence
data	I-evidence
,	O
we	O
propose	O
an	O
updated	O
regulatory	O
model	O
of	O
the	O
YfiBNR	B-complex_assembly
system	O
.	O

Bis	B-chemical
-(	I-chemical
3	I-chemical
’-	I-chemical
5	I-chemical
’)-	I-chemical
cyclic	I-chemical
dimeric	I-chemical
GMP	I-chemical
(	O
c	B-chemical
-	I-chemical
di	I-chemical
-	I-chemical
GMP	I-chemical
)	O
is	O
a	O
ubiquitous	O
second	O
messenger	O
that	O
bacteria	B-taxonomy_domain
use	O
to	O
facilitate	O
behavioral	O
adaptations	O
to	O
their	O
ever	O
-	O
changing	O
environment	O
.	O

An	O
increase	O
in	O
c	B-chemical
-	I-chemical
di	I-chemical
-	I-chemical
GMP	I-chemical
promotes	O
biofilm	O
formation	O
,	O
and	O
a	O
decrease	O
results	O
in	O
biofilm	O
degradation	O
(	O
Boehm	O
et	O
al	O
.,;	O
Duerig	O
et	O
al	O
.,;	O
Hickman	O
et	O
al	O
.,;	O
Jenal	O
,;	O
Romling	O
et	O
al	O
.,).	O

The	O
c	B-chemical
-	I-chemical
di	I-chemical
-	I-chemical
GMP	I-chemical
level	O
is	O
regulated	O
by	O
two	O
reciprocal	O
enzyme	O
systems	O
,	O
namely	O
,	O
diguanylate	B-protein_type
cyclases	I-protein_type
(	O
DGCs	B-protein_type
)	O
that	O
synthesize	O
c	B-chemical
-	I-chemical
di	I-chemical
-	I-chemical
GMP	I-chemical
and	O
phosphodiesterases	B-protein_type
(	O
PDEs	B-protein_type
)	O
that	O
hydrolyze	O
c	B-chemical
-	I-chemical
di	I-chemical
-	I-chemical
GMP	I-chemical
(	O
Kulasakara	O
et	O
al	O
.,;	O
Ross	O
et	O
al	O
.,;	O
Ross	O
et	O
al	O
.,).	O
Many	O
of	O
these	O
enzymes	O
are	O
multiple	O
-	O
domain	O
proteins	O
containing	O
a	O
variable	O
N	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
that	O
commonly	O
acts	O
as	O
a	O
signal	O
sensor	O
or	O
transduction	O
module	O
,	O
followed	O
by	O
the	O
relatively	B-protein_state
conserved	I-protein_state
GGDEF	B-structure_element
motif	I-structure_element
in	O
DGCs	B-protein_type
or	O
EAL	B-structure_element
/	I-structure_element
HD	I-structure_element
-	I-structure_element
GYP	I-structure_element
domains	I-structure_element
in	O
PDEs	B-protein_type
(	O
Hengge	O
,;	O
Navarro	O
et	O
al	O
.,;	O
Schirmer	O
and	O
Jenal	O
,).	O

Intriguingly	O
,	O
studies	O
in	O
diverse	O
species	O
have	O
revealed	O
that	O
a	O
single	O
bacterium	B-taxonomy_domain
can	O
have	O
dozens	O
of	O
DGCs	B-protein_type
and	O
PDEs	B-protein_type
(	O
Hickman	O
et	O
al	O
.,;	O
Kirillina	O
et	O
al	O
.,;	O
Kulasakara	O
et	O
al	O
.,;	O
Tamayo	O
et	O
al	O
.,).	O

In	O
Pseudomonas	B-species
aeruginosa	I-species
in	O
particular	O
,	O
42	O
genes	O
containing	O
putative	O
DGCs	B-protein_type
and	O
/	O
or	O
PDEs	B-protein_type
were	O
identified	O
(	O
Kulasakara	O
et	O
al	O
.,).	O

The	O
functional	O
role	O
of	O
a	O
number	O
of	O
downstream	O
effectors	O
of	O
c	B-chemical
-	I-chemical
di	I-chemical
-	I-chemical
GMP	I-chemical
has	O
been	O
characterized	O
as	O
affecting	O
exopolysaccharide	B-chemical
(	O
EPS	B-chemical
)	O
production	O
,	O
transcription	O
,	O
motility	O
,	O
and	O
surface	O
attachment	O
(	O
Caly	O
et	O
al	O
.,;	O
Camilli	O
and	O
Bassler	O
,;	O
Ha	O
and	O
O	O
’	O
Toole	O
,;	O
Pesavento	O
and	O
Hengge	O
,).	O

However	O
,	O
due	O
to	O
the	O
intricacy	O
of	O
c	B-chemical
-	I-chemical
di	I-chemical
-	I-chemical
GMP	I-chemical
signaling	O
networks	O
and	O
the	O
diversity	O
of	O
experimental	O
cues	O
,	O
the	O
detailed	O
mechanisms	O
by	O
which	O
these	O
signaling	O
pathways	O
specifically	O
sense	O
and	O
integrate	O
different	O
inputs	O
remain	O
largely	O
elusive	O
.	O

Biofilm	O
formation	O
protects	O
pathogenic	O
bacteria	B-taxonomy_domain
from	O
antibiotic	O
treatment	O
,	O
and	O
c	O
-	O
di	O
-	O
GMP	O
-	O
regulated	O
biofilm	O
formation	O
has	O
been	O
extensively	O
studied	O
in	O
P	B-species
.	I-species
aeruginosa	I-species
(	O
Evans	O
,;	O
Kirisits	O
et	O
al	O
.,;	O
Malone	O
,;	O
Reinhardt	O
et	O
al	O
.,).	O

In	O
the	O
lungs	O
of	O
cystic	O
fibrosis	O
(	O
CF	O
)	O
patients	O
,	O
adherent	O
biofilm	O
formation	O
and	O
the	O
appearance	O
of	O
small	O
colony	O
variant	O
(	O
SCV	O
)	O
morphologies	O
of	O
P	B-species
.	I-species
aeruginosa	I-species
correlate	O
with	O
prolonged	O
persistence	O
of	O
infection	O
and	O
poor	O
lung	O
function	O
(	O
Govan	O
and	O
Deretic	O
,;	O
Haussler	O
et	O
al	O
.,;	O
Haussler	O
et	O
al	O
.,;	O
Parsek	O
and	O
Singh	O
,;	O
Smith	O
et	O
al	O
.,).	O

Recently	O
,	O
Malone	O
and	O
coworkers	O
identified	O
the	O
tripartite	B-protein_state
c	B-chemical
-	I-chemical
di	I-chemical
-	I-chemical
GMP	I-chemical
signaling	O
module	O
system	O
YfiBNR	B-complex_assembly
(	O
also	O
known	O
as	O
AwsXRO	B-complex_assembly
(	O
Beaumont	O
et	O
al	O
.,;	O
Giddens	O
et	O
al	O
.,)	O
or	O
Tbp	B-complex_assembly
(	O
Ueda	O
and	O
Wood	O
,))	O
by	O
genetic	B-experimental_method
screening	I-experimental_method
for	O
mutants	O
that	O
displayed	O
SCV	O
phenotypes	O
in	O
P	B-species
.	I-species
aeruginosa	I-species
PAO1	I-species
(	O
Malone	O
et	O
al	O
.,;	O
Malone	O
et	O
al	O
.,).	O

The	O
YfiBNR	B-complex_assembly
system	O
contains	O
three	O
protein	O
members	O
and	O
modulates	O
intracellular	O
c	B-chemical
-	I-chemical
di	I-chemical
-	I-chemical
GMP	I-chemical
levels	O
in	O
response	O
to	O
signals	O
received	O
in	O
the	O
periplasm	O
(	O
Malone	O
et	O
al	O
.,).	O

More	O
recently	O
,	O
this	O
system	O
was	O
also	O
reported	O
in	O
other	O
Gram	B-taxonomy_domain
-	I-taxonomy_domain
negative	I-taxonomy_domain
bacteria	I-taxonomy_domain
,	O
such	O
as	O
Escherichia	B-species
coli	I-species
(	O
Hufnagel	O
et	O
al	O
.,;	O
Raterman	O
et	O
al	O
.,;	O
Sanchez	O
-	O
Torres	O
et	O
al	O
.,),	O
Klebsiella	B-species
pneumonia	I-species
(	O
Huertas	O
et	O
al	O
.,)	O
and	O
Yersinia	B-species
pestis	I-species
(	O
Ren	O
et	O
al	O
.,).	O

YfiN	B-protein
is	O
an	O
integral	O
inner	O
-	O
membrane	O
protein	O
with	O
two	O
potential	O
transmembrane	B-structure_element
helices	I-structure_element
,	O
a	O
periplasmic	O
Per	B-structure_element
-	I-structure_element
Arnt	I-structure_element
-	I-structure_element
Sim	I-structure_element
(	O
PAS	B-structure_element
)	O
domain	O
,	O
and	O
cytosolic	O
domains	O
containing	O
a	O
HAMP	B-structure_element
domain	I-structure_element
(	O
mediate	O
input	O
-	O
output	O
signaling	O
in	O
histidine	B-protein_type
kinases	I-protein_type
,	O
adenylyl	B-protein_type
cyclases	I-protein_type
,	O
methyl	B-protein_type
-	I-protein_type
accepting	I-protein_type
chemotaxis	I-protein_type
proteins	I-protein_type
,	O
and	O
phosphatases	B-protein_type
)	O
and	O
a	O
C	O
-	O
terminal	O
GGDEF	B-structure_element
domain	I-structure_element
indicating	O
a	O
DGC	B-protein_type
’	O
s	O
function	O
(	O
Giardina	O
et	O
al	O
.,;	O
Malone	O
et	O
al	O
.,).	O

YfiN	B-protein
is	O
repressed	B-protein_state
by	I-protein_state
specific	O
interaction	O
between	O
its	O
periplasmic	O
PAS	B-structure_element
domain	I-structure_element
and	O
the	O
periplasmic	O
protein	O
YfiR	B-protein
(	O
Malone	O
et	O
al	O
.,).	O

YfiB	B-protein
is	O
an	O
OmpA	B-protein_type
/	I-protein_type
Pal	I-protein_type
-	I-protein_type
like	I-protein_type
outer	O
-	O
membrane	O
lipoprotein	B-protein_type
(	O
Parsons	O
et	O
al	O
.,)	O
that	O
can	O
activate	O
YfiN	B-protein
by	O
sequestering	O
YfiR	B-protein
(	O
Malone	O
et	O
al	O
.,)	O
in	O
an	O
unknown	O
manner	O
.	O

Whether	O
YfiB	B-protein
directly	O
recruits	O
YfiR	B-protein
or	O
recruits	O
YfiR	B-protein
via	O
a	O
third	O
partner	O
is	O
an	O
open	O
question	O
.	O

After	O
the	O
sequestration	O
of	O
YfiR	B-protein
by	O
YfiB	B-protein
,	O
the	O
c	B-chemical
-	I-chemical
di	I-chemical
-	I-chemical
GMP	I-chemical
produced	O
by	O
activated	B-protein_state
YfiN	B-protein
increases	O
the	O
biosynthesis	O
of	O
the	O
Pel	B-chemical
and	O
Psl	B-chemical
EPSs	B-chemical
,	O
resulting	O
in	O
the	O
appearance	O
of	O
the	O
SCV	O
phenotype	O
,	O
which	O
indicates	O
enhanced	O
biofilm	O
formation	O
(	O
Malone	O
et	O
al	O
.,).	O

It	O
has	O
been	O
reported	O
that	O
the	O
activation	O
of	O
YfiN	B-protein
may	O
be	O
induced	O
by	O
redox	O
-	O
driven	O
misfolding	O
of	O
YfiR	B-protein
(	O
Giardina	O
et	O
al	O
.,;	O
Malone	O
et	O
al	O
.,;	O
Malone	O
et	O
al	O
.,).	O

It	O
is	O
also	O
proposed	O
that	O
the	O
sequestration	O
of	O
YfiR	B-protein
by	O
YfiB	B-protein
can	O
be	O
induced	O
by	O
certain	O
YfiB	B-protein
-	O
mediated	O
cell	O
wall	O
stress	O
,	O
and	O
mutagenesis	B-experimental_method
studies	I-experimental_method
revealed	O
a	O
number	O
of	O
activation	B-structure_element
residues	I-structure_element
of	O
YfiB	B-protein
that	O
were	O
located	O
in	O
close	O
proximity	O
to	O
the	O
predicted	B-protein_state
first	B-structure_element
helix	I-structure_element
of	O
the	O
periplasmic	B-structure_element
domain	I-structure_element
(	O
Malone	O
et	O
al	O
.,).	O

In	O
addition	O
,	O
quorum	O
sensing	O
-	O
related	O
dephosphorylation	O
of	O
the	O
PAS	B-structure_element
domain	I-structure_element
of	O
YfiN	B-protein
may	O
also	O
be	O
involved	O
in	O
the	O
regulation	O
(	O
Ueda	O
and	O
Wood	O
,;	O
Xu	O
et	O
al	O
.,).	O

Recently	O
,	O
we	O
solved	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
YfiR	B-protein
in	O
both	O
the	O
non	B-protein_state
-	I-protein_state
oxidized	I-protein_state
and	O
the	O
oxidized	B-protein_state
states	O
,	O
revealing	O
breakage	O
/	O
formation	O
of	O
one	O
disulfide	B-ptm
bond	I-ptm
(	O
Cys71	B-residue_name_number
-	O
Cys110	B-residue_name_number
)	O
and	O
local	O
conformational	O
change	O
around	O
the	O
other	O
one	O
(	O
Cys145	B-residue_name_number
-	O
Cys152	B-residue_name_number
),	O
indicating	O
that	O
Cys145	B-residue_name_number
-	O
Cys152	B-residue_name_number
plays	O
an	O
important	O
role	O
in	O
maintaining	O
the	O
correct	O
folding	O
of	O
YfiR	B-protein
(	O
Yang	O
et	O
al	O
.,).	O

In	O
the	O
present	O
study	O
,	O
we	O
solved	O
the	O
crystal	B-evidence
structures	I-evidence
of	O
an	O
N	O
-	O
terminal	O
truncated	B-protein_state
form	O
of	O
YfiB	B-protein
(	O
34	B-residue_range
–	I-residue_range
168	I-residue_range
)	O
and	O
YfiR	B-protein
in	B-protein_state
complex	I-protein_state
with	I-protein_state
an	O
active	B-protein_state
mutant	B-protein_state
YfiBL43P	B-mutant
.	O

Most	O
recently	O
,	O
Li	O
and	O
coworkers	O
reported	O
the	O
crystal	B-evidence
structures	I-evidence
of	O
YfiB	B-protein
(	O
27	B-residue_range
–	I-residue_range
168	I-residue_range
)	O
alone	B-protein_state
and	O
YfiRC71S	B-mutant
in	B-protein_state
complex	I-protein_state
with	I-protein_state
YfiB	B-protein
(	O
59	B-residue_range
–	I-residue_range
168	I-residue_range
)	O
(	O
Li	O
et	O
al	O
.,).	O

Compared	O
with	O
the	O
reported	O
complex	O
structure	O
,	O
YfiBL43P	B-mutant
in	O
our	O
YfiB	B-complex_assembly
-	I-complex_assembly
YfiR	I-complex_assembly
complex	O
structure	B-evidence
has	O
additional	O
visible	O
N	O
-	O
terminal	O
residues	O
44	B-residue_range
–	I-residue_range
58	I-residue_range
that	O
are	O
shown	O
to	O
play	O
essential	O
roles	O
in	O
YfiB	B-protein
activation	O
and	O
biofilm	O
formation	O
.	O

Therefore	O
,	O
we	O
are	O
able	O
to	O
visualize	O
the	O
detailed	O
allosteric	O
arrangement	O
of	O
the	O
N	O
-	O
terminal	O
structure	O
of	O
YfiB	B-protein
and	O
its	O
important	O
role	O
in	O
YfiB	B-complex_assembly
-	I-complex_assembly
YfiR	I-complex_assembly
interaction	O
.	O

In	O
addition	O
,	O
we	O
found	O
that	O
the	O
YfiBL43P	B-mutant
shows	O
a	O
much	O
higher	O
PG	B-evidence
-	I-evidence
binding	I-evidence
affinity	I-evidence
than	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
YfiB	B-protein
,	O
most	O
likely	O
due	O
to	O
its	O
more	O
compact	O
PG	B-site
-	I-site
binding	I-site
pocket	I-site
.	O

Moreover	O
,	O
we	O
found	O
that	O
Vitamin	B-chemical
B6	I-chemical
(	O
VB6	B-chemical
)	O
or	O
L	B-chemical
-	I-chemical
Trp	I-chemical
can	O
bind	O
YfiR	B-protein
with	O
an	O
affinity	B-evidence
in	O
the	O
ten	O
millimolar	O
range	O
.	O

Together	O
with	O
functional	O
data	O
,	O
these	O
results	O
provide	O
new	O
mechanistic	O
insights	O
into	O
how	O
activated	B-protein_state
YfiB	B-protein
sequesters	O
YfiR	B-protein
and	O
releases	O
the	O
suppression	O
of	O
YfiN	B-protein
.	O
These	O
findings	O
may	O
facilitate	O
the	O
development	O
and	O
optimization	O
of	O
anti	O
-	O
biofilm	O
drugs	O
for	O
the	O
treatment	O
of	O
chronic	O
infections	O
.	O

Overall	O
structure	B-evidence
of	O
YfiB	B-protein

We	O
obtained	O
two	O
crystal	B-evidence
forms	I-evidence
of	O
YfiB	B-protein
(	O
residues	O
34	B-residue_range
–	I-residue_range
168	I-residue_range
,	O
lacking	B-protein_state
the	O
signal	B-structure_element
peptide	I-structure_element
from	O
residues	O
1	B-residue_range
–	I-residue_range
26	I-residue_range
and	O
periplasmic	O
residues	O
27	B-residue_range
–	I-residue_range
33	I-residue_range
),	O
crystal	O
forms	O
I	O
and	O
II	O
,	O
belonging	O
to	O
space	O
groups	O
P21	O
and	O
P41	O
,	O
respectively	O
.	O

Overall	O
structure	B-evidence
of	O
YfiB	B-protein
.	O
(	O
A	O
)	O
The	O
overall	O
structure	B-evidence
of	O
the	O
YfiB	B-protein
monomer	B-oligomeric_state
.	O
(	O
B	O
)	O
A	O
topology	O
diagram	O
of	O
the	O
YfiB	B-protein
monomer	B-oligomeric_state
.	O
(	O
C	O
and	O
D	O
)	O
The	O
analytical	B-experimental_method
ultracentrifugation	I-experimental_method
experiment	O
results	O
for	O
the	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
YfiB	B-protein
and	O
YfiBL43P	B-mutant

Two	O
dimeric	B-oligomeric_state
types	O
of	O
YfiB	B-protein
dimer	B-oligomeric_state
.	O
(	O
A	O
–	O
C	O
)	O
The	O
“	O
head	B-protein_state
to	I-protein_state
head	I-protein_state
”	O
dimer	B-oligomeric_state
.	O

The	O
“	O
back	B-protein_state
to	I-protein_state
back	I-protein_state
”	O
dimer	B-oligomeric_state
.	O

(	O
A	O
)	O
and	O
(	O
E	O
)	O
indicate	O
the	O
front	O
views	O
of	O
the	O
two	O
dimers	B-oligomeric_state
,	O
(	O
B	O
)	O
and	O
(	O
F	O
)	O
indicate	O
the	O
top	O
views	O
of	O
the	O
two	O
dimers	B-oligomeric_state
,	O
and	O
(	O
C	O
)	O
and	O
(	O
D	O
)	O
indicate	O
the	O
details	O
of	O
the	O
two	O
dimeric	B-site
interfaces	I-site

The	O
crystal	B-evidence
structure	I-evidence
of	O
YfiB	B-protein
monomer	B-oligomeric_state
consists	O
of	O
a	O
five	B-structure_element
-	I-structure_element
stranded	I-structure_element
β	I-structure_element
-	I-structure_element
sheet	I-structure_element
(	O
β1	B-structure_element
-	I-structure_element
2	I-structure_element
-	I-structure_element
5	I-structure_element
-	I-structure_element
3	I-structure_element
-	I-structure_element
4	I-structure_element
)	O
flanked	O
by	O
five	B-structure_element
α	I-structure_element
-	I-structure_element
helices	I-structure_element
(	O
α1	B-structure_element
–	I-structure_element
5	I-structure_element
)	O
on	O
one	O
side	O
.	O

In	O
addition	O
,	O
there	O
is	O
a	O
short	O
helix	B-structure_element
turn	I-structure_element
connecting	O
the	O
β4	B-structure_element
strand	I-structure_element
and	O
α4	B-structure_element
helix	I-structure_element
(	O
Fig	O
.	O
1A	O
and	O
1B	O
).	O

Each	O
crystal	O
form	O
contains	O
three	O
different	O
dimeric	B-oligomeric_state
types	O
of	O
YfiB	B-protein
,	O
two	O
of	O
which	O
are	O
present	O
in	O
both	O
,	O
suggesting	O
that	O
the	O
rest	O
of	O
the	O
dimeric	B-oligomeric_state
types	O
may	O
result	O
from	O
crystal	O
packing	O
.	O

Here	O
,	O
we	O
refer	O
to	O
the	O
two	O
dimeric	B-oligomeric_state
types	O
as	O
“	O
head	B-protein_state
to	I-protein_state
head	I-protein_state
”	O
and	O
“	O
back	B-protein_state
to	I-protein_state
back	I-protein_state
”	O
according	O
to	O
the	O
interacting	O
mode	O
(	O
Fig	O
.	O
2A	O
and	O
2E	O
),	O
with	O
the	O
total	O
buried	O
surface	O
areas	O
being	O
316	O
.	O
8	O
Å2	O
and	O
554	O
.	O
3	O
Å2	O
,	O
respectively	O
.	O

The	O
“	O
head	B-protein_state
to	I-protein_state
head	I-protein_state
”	O
dimer	B-oligomeric_state
exhibits	O
a	O
clamp	B-protein_state
shape	I-protein_state
.	O

The	O
dimerization	O
occurs	O
mainly	O
via	O
hydrophobic	O
interactions	O
formed	O
by	O
A37	B-residue_name_number
and	O
I40	B-residue_name_number
on	O
the	O
α1	B-structure_element
helices	I-structure_element
,	O
L50	B-residue_name_number
on	O
the	O
β1	B-structure_element
strands	I-structure_element
,	O
and	O
W55	B-residue_name_number
on	O
the	O
β2	B-structure_element
strands	I-structure_element
of	O
both	O
molecules	O
,	O
making	O
a	O
hydrophobic	B-site
interacting	I-site
core	I-site
(	O
Fig	O
.	O
2A	O
–	O
C	O
).	O

The	O
“	O
back	B-protein_state
to	I-protein_state
back	I-protein_state
”	O
dimer	B-oligomeric_state
presents	O
a	O
Y	B-protein_state
shape	I-protein_state
.	O

The	O
dimeric	O
interaction	O
is	O
mainly	O
hydrophilic	O
,	O
occurring	O
among	O
the	O
main	O
-	O
chain	O
and	O
side	O
-	O
chain	O
atoms	O
of	O
N68	B-residue_name_number
,	O
L69	B-residue_name_number
,	O
D70	B-residue_name_number
and	O
R71	B-residue_name_number
on	O
the	O
α2	B-structure_element
-	I-structure_element
α3	I-structure_element
loops	I-structure_element
and	O
R116	B-residue_name_number
and	O
S120	B-residue_name_number
on	O
the	O
α4	B-structure_element
helices	I-structure_element
of	O
both	O
molecules	O
,	O
resulting	O
in	O
a	O
complex	O
hydrogen	B-site
bond	I-site
network	I-site
(	O
Fig	O
.	O
2D	O
–	O
F	O
).	O

The	O
YfiB	B-complex_assembly
-	I-complex_assembly
YfiR	I-complex_assembly
interaction	O

Overall	O
structure	B-evidence
of	O
the	O
YfiB	B-complex_assembly
-	I-complex_assembly
YfiR	I-complex_assembly
complex	O
and	O
the	O
conserved	B-site
surface	I-site
in	O
YfiR	B-protein
.	O
(	O
A	O
)	O
The	O
overall	O
structure	B-evidence
of	O
the	O
YfiB	B-complex_assembly
-	I-complex_assembly
YfiR	I-complex_assembly
complex	O
.	O

The	O
YfiBL43P	B-mutant
molecules	O
are	O
shown	O
in	O
cyan	O
and	O
yellow	O
.	O

The	O
YfiR	B-protein
molecules	O
are	O
shown	O
in	O
green	O
and	O
magenta	O
.	O

Two	O
interacting	O
regions	O
are	O
highlighted	O
by	O
red	O
rectangles	O
.	O
(	O
B	O
)	O
Structural	B-experimental_method
superposition	I-experimental_method
of	O
apo	B-protein_state
YfiB	B-protein
and	O
YfiR	B-protein_state
-	I-protein_state
bound	I-protein_state
YfiBL43P	B-mutant
.	O

To	O
illustrate	O
the	O
differences	O
between	O
apo	B-protein_state
YfiB	B-protein
and	O
YfiR	B-protein_state
-	I-protein_state
bound	I-protein_state
YfiBL43P	B-mutant
,	O
the	O
apo	B-protein_state
YfiB	B-protein
is	O
shown	O
in	O
pink	O
,	O
except	O
residues	O
34	B-residue_range
–	I-residue_range
70	I-residue_range
are	O
shown	O
in	O
red	O
,	O
whereas	O
the	O
YfiR	B-protein_state
-	I-protein_state
bound	I-protein_state
YfiBL43P	B-mutant
is	O
shown	O
in	O
cyan	O
,	O
except	O
residues	O
44	B-residue_range
–	I-residue_range
70	I-residue_range
are	O
shown	O
in	O
blue	O
.	O
(	O
C	O
)	O
Close	O
-	O
up	O
view	O
of	O
the	O
differences	O
between	O
apo	B-protein_state
YfiB	B-protein
and	O
YfiR	B-protein_state
-	I-protein_state
bound	I-protein_state
YfiBL43P	B-mutant
.	O

The	O
residues	O
proposed	O
to	O
contribute	O
to	O
YfiB	B-protein
activation	O
are	O
illustrated	O
in	O
sticks	O
.	O

The	O
key	O
residues	O
in	O
apo	B-protein_state
YfiB	B-protein
are	O
shown	O
in	O
red	O
and	O
those	O
in	O
YfiBL43P	B-mutant
are	O
shown	O
in	O
blue	O
.	O
(	O
D	O
)	O
Close	O
-	O
up	O
views	O
showing	O
interactions	O
in	O
regions	B-structure_element
I	I-structure_element
and	I-structure_element
II	I-structure_element
.	O

YfiBL43P	B-mutant
and	O
YfiR	B-protein
are	O
shown	O
in	O
cyan	O
and	O
green	O
,	O
respectively	O
.	O
(	O
E	O
and	O
F	O
)	O
The	O
conserved	B-site
surface	I-site
in	O
YfiR	B-protein
contributes	O
to	O
the	O
interaction	O
with	O
YfiB	B-protein
.	O
(	O
G	O
)	O
The	O
residues	B-structure_element
of	O
YfiR	B-protein
responsible	O
for	O
interacting	O
with	O
YfiB	B-protein
are	O
shown	O
in	O
green	O
sticks	O
,	O
and	O
the	O
proposed	O
YfiN	B-site
-	I-site
interacting	I-site
residues	I-site
are	O
shown	O
in	O
yellow	O
sticks	O
.	O

The	O
red	O
sticks	O
,	O
which	O
represent	O
the	O
YfiB	B-site
-	I-site
interacting	I-site
residues	I-site
,	O
are	O
also	O
responsible	O
for	O
the	O
proposed	O
interactions	O
with	O
YfiN	B-protein

To	O
gain	O
structural	O
insights	O
into	O
the	O
YfiB	B-complex_assembly
-	I-complex_assembly
YfiR	I-complex_assembly
interaction	O
,	O
we	O
co	B-experimental_method
-	I-experimental_method
expressed	I-experimental_method
YfiB	B-protein
(	O
residues	O
34	B-residue_range
–	I-residue_range
168	I-residue_range
)	O
and	O
YfiR	B-protein
(	O
residues	O
35	B-residue_range
–	I-residue_range
190	I-residue_range
,	O
lacking	B-protein_state
the	O
signal	B-structure_element
peptide	I-structure_element
),	O
but	O
failed	O
to	O
obtain	O
the	O
complex	O
,	O
in	O
accordance	O
with	O
a	O
previous	O
report	O
in	O
which	O
no	B-protein_state
stable	I-protein_state
complex	O
of	O
YfiB	B-complex_assembly
-	I-complex_assembly
YfiR	I-complex_assembly
was	O
observed	O
(	O
Malone	O
et	O
al	O
.,).	O

It	O
has	O
been	O
reported	O
that	O
single	B-experimental_method
mutants	I-experimental_method
of	I-experimental_method
Q39	B-residue_name_number
,	O
L43	B-residue_name_number
,	O
F48	B-residue_name_number
and	O
W55	B-residue_name_number
contribute	O
to	O
YfiB	B-protein
activation	O
leading	O
to	O
the	O
induction	O
of	O
the	O
SCV	O
phenotype	O
in	O
P	B-species
.	I-species
aeruginosa	I-species
PAO1	I-species
(	O
Malone	O
et	O
al	O
.,).	O

It	O
is	O
likely	O
that	O
these	O
residues	O
may	O
be	O
involved	O
in	O
the	O
conformational	O
changes	O
of	O
YfiB	B-protein
that	O
are	O
related	O
to	O
YfiR	B-protein
sequestration	O
(	O
Fig	O
.	O
3C	O
).	O

Therefore	O
,	O
we	O
constructed	B-experimental_method
two	I-experimental_method
such	I-experimental_method
single	I-experimental_method
mutants	I-experimental_method
of	O
YfiB	B-protein
(	O
YfiBL43P	B-mutant
and	O
YfiBF48S	B-mutant
).	O

As	O
expected	O
,	O
both	O
mutants	O
form	O
a	O
stable	B-protein_state
complex	B-protein_state
with	I-protein_state
YfiR	B-protein
.	O
Finally	O
,	O
we	O
crystalized	B-experimental_method
YfiR	B-protein
in	B-protein_state
complex	I-protein_state
with	I-protein_state
the	O
YfiBL43P	B-mutant
mutant	B-protein_state
and	O
solved	O
the	O
structure	B-evidence
at	O
1	O
.	O
78	O
Å	O
resolution	O
by	O
molecular	B-experimental_method
replacement	I-experimental_method
using	O
YfiR	B-protein
and	O
YfiB	B-protein
as	O
models	O
.	O

The	O
YfiB	B-complex_assembly
-	I-complex_assembly
YfiR	I-complex_assembly
complex	O
is	O
a	O
2	O
:	O
2	O
heterotetramer	B-oligomeric_state
(	O
Fig	O
.	O
3A	O
)	O
in	O
which	O
the	O
YfiR	B-protein
dimer	B-oligomeric_state
is	O
clamped	O
by	O
two	O
separated	O
YfiBL43P	B-mutant
molecules	O
with	O
a	O
total	O
buried	O
surface	O
area	O
of	O
3161	O
.	O
2	O
Å2	O
.	O

The	O
YfiR	B-protein
dimer	B-oligomeric_state
in	O
the	O
complex	O
is	O
identical	O
to	O
the	O
non	B-protein_state
-	I-protein_state
oxidized	I-protein_state
YfiR	B-protein
dimer	B-oligomeric_state
alone	B-protein_state
(	O
Yang	O
et	O
al	O
.,),	O
with	O
only	O
Cys145	B-residue_name_number
-	O
Cys152	B-residue_name_number
of	O
the	O
two	O
disulfide	B-ptm
bonds	I-ptm
well	O
formed	O
,	O
suggesting	O
Cys71	B-residue_name_number
-	O
Cys110	B-residue_name_number
disulfide	B-ptm
bond	I-ptm
formation	O
is	O
not	O
essential	O
for	O
forming	O
YfiB	B-complex_assembly
-	I-complex_assembly
YfiR	I-complex_assembly
complex	O
.	O

The	O
N	O
-	O
terminal	O
structural	O
conformation	O
of	O
YfiBL43P	B-mutant
,	O
from	O
the	O
foremost	O
N	O
-	O
terminus	O
to	O
residue	O
D70	B-residue_name_number
,	O
is	O
significantly	O
altered	O
compared	O
with	O
that	O
of	O
the	O
apo	B-protein_state
YfiB	B-protein
.	O
The	O
majority	O
of	O
the	O
α1	B-structure_element
helix	I-structure_element
(	O
residues	O
34	B-residue_range
–	I-residue_range
43	I-residue_range
)	O
is	O
invisible	O
on	O
the	O
electron	B-evidence
density	I-evidence
map	I-evidence
,	O
and	O
the	O
α2	B-structure_element
helix	I-structure_element
and	O
β1	B-structure_element
and	O
β2	B-structure_element
strands	I-structure_element
are	O
rearranged	O
to	O
form	O
a	O
long	O
loop	B-structure_element
containing	O
two	O
short	O
α	B-structure_element
-	I-structure_element
helix	I-structure_element
turns	I-structure_element
(	O
Fig	O
.	O
3B	O
and	O
3C	O
),	O
thus	O
embracing	O
the	O
YfiR	B-protein
dimer	B-oligomeric_state
.	O

The	O
observed	O
changes	O
in	O
conformation	O
of	O
YfiB	B-protein
and	O
the	O
results	O
of	O
mutagenesis	B-experimental_method
suggest	O
a	O
mechanism	O
by	O
which	O
YfiB	B-protein
sequesters	O
YfiR	B-protein
.	O

The	O
YfiB	B-site
-	I-site
YfiR	I-site
interface	I-site
can	O
be	O
divided	O
into	O
two	O
regions	O
(	O
Fig	O
.	O
3A	O
and	O
3D	O
).	O

Region	B-structure_element
I	I-structure_element
is	O
formed	O
by	O
numerous	O
main	O
-	O
chain	O
and	O
side	O
-	O
chain	O
hydrophilic	O
interactions	O
between	O
residues	O
E45	B-residue_name_number
,	O
G47	B-residue_name_number
and	O
E53	B-residue_name_number
from	O
the	O
N	O
-	O
terminal	O
extended	O
loop	B-structure_element
of	O
YfiB	B-protein
and	O
residues	O
S57	B-residue_name_number
,	O
R60	B-residue_name_number
,	O
A89	B-residue_name_number
and	O
H177	B-residue_name_number
from	O
YfiR	B-protein
(	O
Fig	O
.	O
3D	O
-	O
I	O
(	O
i	O
)).	O

Additionally	O
,	O
three	O
hydrophobic	B-site
anchoring	I-site
sites	I-site
exist	O
in	O
region	B-structure_element
I	I-structure_element
.	O
The	O
residues	O
F48	B-residue_name_number
and	O
W55	B-residue_name_number
of	O
YfiB	B-protein
are	O
inserted	O
into	O
the	O
hydrophobic	B-site
cores	I-site
mainly	O
formed	O
by	O
the	O
main	O
chain	O
and	O
side	O
chain	O
carbon	O
atoms	O
of	O
residues	O
S57	B-residue_name_number
/	O
Q88	B-residue_name_number
/	O
A89	B-residue_name_number
/	O
N90	B-residue_name_number
and	O
R60	B-residue_name_number
/	O
R175	B-residue_name_number
/	O
H177	B-residue_name_number
of	O
YfiR	B-protein
,	O
respectively	O
;	O
and	O
F57	B-residue_name_number
of	O
YfiB	B-protein
is	O
inserted	O
into	O
the	O
hydrophobic	B-site
pocket	I-site
formed	O
by	O
L166	B-residue_name_number
/	O
I169	B-residue_name_number
/	O
V176	B-residue_name_number
/	O
P178	B-residue_name_number
/	O
L181	B-residue_name_number
of	O
YfiR	B-protein
(	O
Fig	O
.	O
3D	O
-	O
I	O
(	O
ii	O
)).	O

In	O
region	B-structure_element
II	I-structure_element
,	O
the	O
side	O
chains	O
of	O
R96	B-residue_name_number
,	O
E98	B-residue_name_number
and	O
E157	B-residue_name_number
from	O
YfiB	B-protein
interact	O
with	O
the	O
side	O
chains	O
of	O
E163	B-residue_name_number
,	O
S146	B-residue_name_number
and	O
R171	B-residue_name_number
from	O
YfiR	B-protein
,	O
respectively	O
.	O

Additionally	O
,	O
the	O
main	O
chains	O
of	O
I163	B-residue_name_number
and	O
V165	B-residue_name_number
from	O
YfiB	B-protein
form	O
hydrogen	O
bonds	O
with	O
the	O
main	O
chains	O
of	O
L166	B-residue_name_number
and	O
A164	B-residue_name_number
from	O
YfiR	B-protein
,	O
respectively	O
,	O
and	O
the	O
main	O
chain	O
of	O
P166	B-residue_name_number
from	O
YfiB	B-protein
interacts	O
with	O
the	O
side	O
chain	O
of	O
R185	B-residue_name_number
from	O
YfiR	B-protein
(	O
Fig	O
.	O
3D	O
-	O
II	O
).	O

These	O
two	O
regions	O
contribute	O
a	O
robust	O
hydrogen	B-site
-	I-site
bonding	I-site
network	I-site
to	O
the	O
YfiB	B-site
-	I-site
YfiR	I-site
interface	I-site
,	O
resulting	O
in	O
a	O
tightly	O
bound	O
complex	O
.	O

Based	O
on	O
the	O
observations	O
that	O
two	O
separated	O
YfiBL43P	B-mutant
molecules	O
form	O
a	O
2	O
:	O
2	O
complex	O
structure	B-evidence
with	O
YfiR	B-protein
dimer	B-oligomeric_state
,	O
we	O
performed	O
an	O
analytical	B-experimental_method
ultracentrifugation	I-experimental_method
experiment	O
to	O
check	O
the	O
oligomeric	O
states	O
of	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
YfiB	B-protein
and	O
YfiBL43P	B-mutant
.	O

The	O
results	O
showed	O
that	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
YfiB	B-protein
exists	O
in	O
both	O
monomeric	B-oligomeric_state
and	O
dimeric	B-oligomeric_state
states	O
in	O
solution	O
,	O
while	O
YfiBL43P	B-mutant
primarily	O
adopts	O
the	O
monomer	B-oligomeric_state
state	O
in	O
solution	O
(	O
Fig	O
.	O
1C	O
–	O
D	O
).	O

This	O
suggests	O
that	O
the	O
N	O
-	O
terminus	O
of	O
YfiB	B-protein
plays	O
an	O
important	O
role	O
in	O
forming	O
the	O
dimeric	B-oligomeric_state
YfiB	B-protein
in	O
solution	O
and	O
that	O
the	O
conformational	O
change	O
of	O
residue	O
L43	B-residue_name_number
is	O
associated	O
with	O
the	O
stretch	O
of	O
the	O
N	O
-	O
terminus	O
and	O
opening	O
of	O
the	O
dimer	B-oligomeric_state
.	O

Therefore	O
,	O
it	O
is	O
possible	O
that	O
both	O
dimeric	B-oligomeric_state
types	O
might	O
exist	O
in	O
solution	O
.	O

For	O
simplicity	O
,	O
we	O
only	O
discuss	O
the	O
“	O
head	B-protein_state
to	I-protein_state
head	I-protein_state
”	O
dimer	B-oligomeric_state
in	O
the	O
following	O
text	O
.	O

The	O
PG	B-site
-	I-site
binding	I-site
site	I-site
of	O
YfiB	B-protein

The	O
PG	B-site
-	I-site
binding	I-site
site	I-site
in	O
YfiB	B-protein
.	O
(	O
A	O
)	O
Structural	B-experimental_method
superposition	I-experimental_method
of	O
the	O
PG	B-site
-	I-site
binding	I-site
sites	I-site
of	O
the	O
H	B-species
.	I-species
influenzae	I-species
Pal	B-complex_assembly
/	I-complex_assembly
PG	I-complex_assembly
-	I-complex_assembly
P	I-complex_assembly
complex	O
and	O
YfiR	B-protein_state
-	I-protein_state
bound	I-protein_state
YfiBL43P	B-mutant
complexed	B-protein_state
with	I-protein_state
sulfate	B-chemical
ions	O
.	O

(	O
B	O
)	O
Close	O
-	O
up	O
view	O
showing	O
the	O
key	O
residues	O
of	O
Pal	B-protein_type
interacting	O
with	O
the	O
m	B-chemical
-	I-chemical
Dap5	I-chemical
ε	I-chemical
-	I-chemical
carboxylate	I-chemical
group	O
of	O
PG	B-chemical
-	I-chemical
P	I-chemical
.	O
Pal	B-protein_type
is	O
shown	O
in	O
wheat	O
and	O
PG	B-chemical
-	I-chemical
P	I-chemical
is	O
in	O
magenta	O
.	O

(	O
C	O
)	O
Close	O
-	O
up	O
view	O
showing	O
the	O
key	O
residues	O
of	O
YfiR	B-protein_state
-	I-protein_state
bound	I-protein_state
YfiBL43P	B-mutant
interacting	O
with	O
a	O
sulfate	B-chemical
ion	O
.	O

YfiR	B-protein_state
-	I-protein_state
bound	I-protein_state
YfiBL43P	B-mutant
is	O
shown	O
in	O
cyan	O
;	O
the	O
sulfate	B-chemical
ion	O
,	O
in	O
green	O
;	O
and	O
the	O
water	B-chemical
molecule	O
,	O
in	O
yellow	O
.	O
(	O
D	O
)	O
Structural	B-experimental_method
superposition	I-experimental_method
of	O
the	O
PG	B-site
-	I-site
binding	I-site
sites	I-site
of	O
apo	B-protein_state
YfiB	B-protein
and	O
YfiR	B-protein_state
-	I-protein_state
bound	I-protein_state
YfiBL43P	B-mutant
,	O
the	O
key	O
residues	O
are	O
shown	O
in	O
stick	O
.	O

Apo	B-protein_state
YfiB	B-protein
is	O
shown	O
in	O
yellow	O
and	O
YfiR	B-protein_state
-	I-protein_state
bound	I-protein_state
YfiBL43P	B-mutant
in	O
cyan	O
.	O
(	O
E	O
and	O
F	O
)	O
MST	B-experimental_method
data	O
and	O
analysis	O
for	O
binding	B-evidence
affinities	I-evidence
of	O
(	O
E	O
)	O
YfiB	B-protein
wild	B-protein_state
-	I-protein_state
type	I-protein_state
and	O
(	O
F	O
)	O
YfiBL43P	B-mutant
with	O
PG	B-chemical
.	O
(	O
G	O
)	O
The	O
sequence	B-experimental_method
alignment	I-experimental_method
of	O
P	B-species
.	I-species
aeruginosa	I-species
and	O
E	B-species
.	I-species
coli	I-species
sources	O
of	O
YfiB	B-protein
,	O
Pal	B-protein_type
and	O
the	O
periplasmic	B-structure_element
domain	I-structure_element
of	O
OmpA	B-protein_type

PG	B-protein_type
-	I-protein_type
associated	I-protein_type
lipoprotein	I-protein_type
(	O
Pal	B-protein_type
)	O
is	O
highly	B-protein_state
conserved	I-protein_state
in	O
Gram	B-taxonomy_domain
-	I-taxonomy_domain
negative	I-taxonomy_domain
bacteria	I-taxonomy_domain
and	O
anchors	O
to	O
the	O
outer	O
membrane	O
through	O
an	O
N	O
-	O
terminal	O
lipid	O
attachment	O
and	O
to	O
PG	O
layer	O
through	O
its	O
periplasmic	B-structure_element
domain	I-structure_element
,	O
which	O
is	O
implicated	O
in	O
maintaining	O
outer	O
membrane	O
integrity	O
.	O

Previous	O
homology	B-experimental_method
modeling	I-experimental_method
studies	O
suggested	O
that	O
YfiB	B-protein
contains	O
a	O
Pal	B-site
-	I-site
like	I-site
PG	I-site
-	I-site
binding	I-site
site	I-site
(	O
Parsons	O
et	O
al	O
.,),	O
and	O
the	O
mutation	B-experimental_method
of	I-experimental_method
two	I-experimental_method
residues	I-experimental_method
at	O
this	O
site	O
,	O
D102	B-residue_name_number
and	O
G105	B-residue_name_number
,	O
reduces	O
the	O
ability	O
for	O
biofilm	O
formation	O
and	O
surface	O
attachment	O
(	O
Malone	O
et	O
al	O
.,).	O

In	O
the	O
YfiB	B-complex_assembly
-	I-complex_assembly
YfiR	I-complex_assembly
complex	O
,	O
one	O
sulfate	B-chemical
ion	O
is	O
found	O
at	O
the	O
bottom	O
of	O
each	O
YfiBL43P	B-mutant
molecule	O
(	O
Fig	O
.	O
3A	O
)	O
and	O
forms	O
a	O
strong	O
hydrogen	O
bond	O
with	O
D102	B-residue_name_number
of	O
YfiBL43P	B-mutant
(	O
Fig	O
.	O
4A	O
and	O
4C	O
).	O

Structural	B-experimental_method
superposition	I-experimental_method
between	O
YfiBL43P	B-mutant
and	O
Haemophilus	B-species
influenzae	I-species
Pal	B-protein_type
complexed	B-protein_state
with	I-protein_state
biosynthetic	O
peptidoglycan	B-chemical
precursor	I-chemical
(	O
PG	B-chemical
-	I-chemical
P	I-chemical
),	O
UDP	B-chemical
-	I-chemical
N	I-chemical
-	I-chemical
acetylmuramyl	I-chemical
-	I-chemical
L	I-chemical
-	I-chemical
Ala	I-chemical
-	I-chemical
α	I-chemical
-	I-chemical
D	I-chemical
-	I-chemical
Glu	I-chemical
-	I-chemical
m	I-chemical
-	I-chemical
Dap	I-chemical
-	I-chemical
D	I-chemical
-	I-chemical
Ala	I-chemical
-	I-chemical
D	I-chemical
-	I-chemical
Ala	I-chemical
(	O
m	B-chemical
-	I-chemical
Dap	I-chemical
is	O
meso	B-chemical
-	I-chemical
diaminopimelate	I-chemical
)	O
(	O
PDB	O
code	O
:	O
2aiz	O
)	O
(	O
Parsons	O
et	O
al	O
.,),	O
revealed	O
that	O
the	O
sulfate	B-chemical
ion	O
is	O
located	O
at	O
the	O
position	O
of	O
the	O
m	B-chemical
-	I-chemical
Dap5	I-chemical
ϵ	I-chemical
-	I-chemical
carboxylate	I-chemical
group	O
in	O
the	O
Pal	B-complex_assembly
/	I-complex_assembly
PG	I-complex_assembly
-	I-complex_assembly
P	I-complex_assembly
complex	O
(	O
Fig	O
.	O
4A	O
).	O

In	O
the	O
Pal	B-complex_assembly
/	I-complex_assembly
PG	I-complex_assembly
-	I-complex_assembly
P	I-complex_assembly
complex	O
structure	B-evidence
,	O
the	O
m	B-chemical
-	I-chemical
Dap5	I-chemical
ϵ	I-chemical
-	I-chemical
carboxylate	I-chemical
group	O
interacts	O
with	O
the	O
side	O
-	O
chain	O
atoms	O
of	O
D71	B-residue_name_number
and	O
the	O
main	O
-	O
chain	O
amide	O
of	O
D37	B-residue_name_number
(	O
Fig	O
.	O
4B	O
).	O

Similarly	O
,	O
in	O
the	O
YfiR	B-protein_state
-	I-protein_state
bound	I-protein_state
YfiBL43P	B-mutant
structure	B-evidence
,	O
the	O
sulfate	B-chemical
ion	O
interacts	O
with	O
the	O
side	O
-	O
chain	O
atoms	O
of	O
D102	B-residue_name_number
(	O
corresponding	O
to	O
D71	B-residue_name_number
in	O
Pal	B-protein_type
)	O
and	O
R117	B-residue_name_number
(	O
corresponding	O
to	O
R86	B-residue_name_number
in	O
Pal	B-protein_type
)	O
and	O
the	O
main	O
-	O
chain	O
amide	O
of	O
N68	B-residue_name_number
(	O
corresponding	O
to	O
D37	B-residue_name_number
in	O
Pal	B-protein_type
).	O

Moreover	O
,	O
a	O
water	B-chemical
molecule	O
was	O
found	O
to	O
bridge	O
the	O
sulfate	B-chemical
ion	O
and	O
the	O
side	O
chains	O
of	O
N67	B-residue_name_number
and	O
D102	B-residue_name_number
,	O
strengthening	O
the	O
hydrogen	B-site
bond	I-site
network	I-site
(	O
Fig	O
.	O
4C	O
).	O

In	O
addition	O
,	O
sequence	B-experimental_method
alignment	I-experimental_method
of	O
YfiB	B-protein
with	O
Pal	B-protein_type
and	O
the	O
periplasmic	B-structure_element
domain	I-structure_element
of	O
OmpA	B-protein_type
(	O
proteins	O
containing	O
PG	B-site
-	I-site
binding	I-site
site	I-site
)	O
showed	O
that	O
N68	B-residue_name_number
and	O
D102	B-residue_name_number
are	O
highly	B-protein_state
conserved	I-protein_state
(	O
Fig	O
.	O
4G	O
,	O
blue	O
stars	O
),	O
suggesting	O
that	O
these	O
residues	O
contribute	O
to	O
the	O
PG	O
-	O
binding	O
ability	O
of	O
YfiB	B-protein
.	O

Interestingly	O
,	O
superposition	B-experimental_method
of	O
apo	B-protein_state
YfiB	B-protein
with	O
YfiR	B-protein_state
-	I-protein_state
bound	I-protein_state
YfiBL43P	B-mutant
revealed	O
that	O
the	O
PG	B-site
-	I-site
binding	I-site
region	I-site
is	O
largely	O
altered	O
mainly	O
due	O
to	O
different	B-protein_state
conformation	I-protein_state
of	O
the	O
N68	B-residue_name_number
containing	O
loop	B-structure_element
.	O

Compared	O
to	O
YfiBL43P	B-mutant
,	O
the	O
N68	B-residue_name_number
-	O
containing	O
loop	B-structure_element
of	O
the	O
apo	B-protein_state
YfiB	B-protein
flips	O
away	O
about	O
7	O
Å	O
,	O
and	O
D102	B-residue_name_number
and	O
R117	B-residue_name_number
swing	O
slightly	O
outward	O
;	O
thus	O
,	O
the	O
PG	B-site
-	I-site
binding	I-site
pocket	I-site
is	O
enlarged	O
with	O
no	O
sulfate	B-chemical
ion	O
or	O
water	B-chemical
bound	O
(	O
Fig	O
.	O
4D	O
).	O

Therefore	O
,	O
we	O
proposed	O
that	O
the	O
PG	B-chemical
-	O
binding	O
ability	O
of	O
inactive	B-protein_state
YfiB	B-protein
might	O
be	O
weaker	O
than	O
that	O
of	O
active	B-protein_state
YfiB	B-protein
.	O
To	O
validate	O
this	O
,	O
we	O
performed	O
a	O
microscale	B-experimental_method
thermophoresis	I-experimental_method
(	O
MST	B-experimental_method
)	O
assay	O
to	O
measure	O
the	O
binding	B-evidence
affinities	I-evidence
of	O
PG	B-chemical
to	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
YfiB	B-protein
and	O
YfiBL43P	B-mutant
,	O
respectively	O
.	O

The	O
results	O
indicated	O
that	O
the	O
PG	B-evidence
-	I-evidence
binding	I-evidence
affinity	I-evidence
of	O
YfiBL43P	B-mutant
is	O
65	O
.	O
5	O
μmol	O
/	O
L	O
,	O
which	O
is	O
about	O
16	O
-	O
fold	O
stronger	O
than	O
that	O
of	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
YfiB	B-protein
(	O
Kd	O
=	O
1	O
.	O
1	O
mmol	O
/	O
L	O
)	O
(	O
Fig	O
.	O
4E	O
–	O
F	O
).	O

As	O
the	O
experiment	O
is	O
performed	O
in	B-protein_state
the	I-protein_state
absence	I-protein_state
of	I-protein_state
YfiR	B-protein
,	O
it	O
suggests	O
that	O
an	O
increase	O
in	O
the	O
PG	B-evidence
-	I-evidence
binding	I-evidence
affinity	I-evidence
of	O
YfiB	B-protein
is	O
not	O
a	O
result	O
of	O
YfiB	B-complex_assembly
-	I-complex_assembly
YfiR	I-complex_assembly
interaction	O
and	O
is	O
highly	O
coupled	O
to	O
the	O
activation	O
of	O
YfiB	B-protein
characterized	O
by	O
a	O
stretched	B-protein_state
N	I-protein_state
-	I-protein_state
terminal	I-protein_state
conformation	I-protein_state
.	O

The	O
conserved	B-site
surface	I-site
in	O
YfiR	B-protein
is	O
functional	O
for	O
binding	O
YfiB	B-protein
and	O
YfiN	B-protein

Calculation	O
using	O
the	O
ConSurf	B-experimental_method
Server	I-experimental_method
(	O
http	O
://	O
consurf	O
.	O
tau	O
.	O
ac	O
.	O
il	O
/),	O
which	O
estimates	O
the	O
evolutionary	B-evidence
conservation	I-evidence
of	O
amino	O
acid	O
positions	O
and	O
visualizes	O
information	O
on	O
the	O
structure	B-site
surface	I-site
,	O
revealed	O
a	O
conserved	B-site
surface	I-site
on	O
YfiR	B-protein
that	O
contributes	O
to	O
the	O
interaction	O
with	O
YfiB	B-protein
(	O
Fig	O
.	O
3E	O
and	O
3F	O
).	O

Interestingly	O
,	O
the	O
majority	O
of	O
this	O
conserved	B-site
surface	I-site
contributes	O
to	O
the	O
interaction	O
with	O
YfiB	B-protein
(	O
Fig	O
.	O
3E	O
and	O
3F	O
).	O

Malone	O
JG	O
et	O
al	O
.	O
have	O
reported	O
that	O
F151	B-residue_name_number
,	O
E163	B-residue_name_number
,	O
I169	B-residue_name_number
and	O
Q187	B-residue_name_number
,	O
located	O
near	O
the	O
C	O
-	O
terminus	O
of	O
YfiR	B-protein
,	O
comprise	O
a	O
putative	O
YfiN	B-site
binding	I-site
site	I-site
(	O
Malone	O
et	O
al	O
.,).	O

Interestingly	O
,	O
these	O
residues	O
are	O
part	O
of	O
the	O
conserved	B-site
surface	I-site
of	O
YfiR	B-protein
(	O
Fig	O
.	O
3G	O
).	O

F151	B-residue_name_number
,	O
E163	B-residue_name_number
and	O
I169	B-residue_name_number
form	O
a	O
hydrophobic	B-site
core	I-site
while	O
,	O
Q187	B-residue_name_number
is	O
located	O
at	O
the	O
end	O
of	O
the	O
α6	B-structure_element
helix	I-structure_element
.	O

E163	B-residue_name_number
and	O
I169	B-residue_name_number
are	O
YfiB	B-site
-	I-site
interacting	I-site
residues	I-site
of	O
YfiR	B-protein
,	O
in	O
which	O
E163	B-residue_name_number
forms	O
a	O
hydrogen	O
bond	O
with	O
R96	B-residue_name_number
of	O
YfiB	B-protein
(	O
Fig	O
.	O
3D	O
-	O
II	O
)	O
and	O
I169	B-residue_name_number
is	O
involved	O
in	O
forming	O
the	O
L166	B-residue_name_number
/	O
I169	B-residue_name_number
/	O
V176	B-residue_name_number
/	O
P178	B-residue_name_number
/	O
L181	B-residue_name_number
hydrophobic	B-site
core	I-site
for	O
anchoring	O
F57	B-residue_name_number
of	O
YfiB	B-protein
(	O
Fig	O
.	O
3D	O
-	O
I	O
(	O
ii	O
)).	O

Collectively	O
,	O
a	O
part	O
of	O
the	O
YfiB	B-site
-	I-site
YfiR	I-site
interface	I-site
overlaps	O
with	O
the	O
proposed	O
YfiR	B-site
-	I-site
YfiN	I-site
interface	I-site
,	O
suggesting	O
alteration	O
in	O
the	O
association	O
-	O
disassociation	O
equilibrium	O
of	O
YfiR	B-protein
-	O
YfiN	B-protein
and	O
hence	O
the	O
ability	O
of	O
YfiB	B-protein
to	O
sequester	O
YfiR	B-protein
.	O

YfiR	B-protein
binds	O
small	O
molecules	O

Previous	O
studies	O
indicated	O
that	O
YfiR	B-protein
constitutes	O
a	O
YfiB	B-protein
-	O
independent	O
sensing	O
device	O
that	O
can	O
activate	O
YfiN	B-protein
in	O
response	O
to	O
the	O
redox	O
status	O
of	O
the	O
periplasm	O
,	O
and	O
we	O
have	O
reported	O
YfiR	B-protein
structures	B-evidence
in	O
both	O
the	O
non	B-protein_state
-	I-protein_state
oxidized	I-protein_state
and	O
the	O
oxidized	B-protein_state
states	O
earlier	O
,	O
revealing	O
that	O
the	O
Cys145	B-residue_name_number
-	O
Cys152	B-residue_name_number
disulfide	B-ptm
bond	I-ptm
plays	O
an	O
essential	O
role	O
in	O
maintaining	O
the	O
correct	O
folding	O
of	O
YfiR	B-protein
(	O
Yang	O
et	O
al	O
.,).	O

However	O
,	O
whether	O
YfiR	B-protein
is	O
involved	O
in	O
other	O
regulatory	O
mechanisms	O
is	O
still	O
an	O
open	O
question	O
.	O

Overall	O
Structures	B-evidence
of	O
VB6	B-protein_state
-	I-protein_state
bound	I-protein_state
and	O
Trp	B-protein_state
-	I-protein_state
bound	I-protein_state
YfiR	B-protein
.	O
(	O
A	O
)	O
Superposition	B-experimental_method
of	O
the	O
overall	O
structures	B-evidence
of	O
VB6	B-protein_state
-	I-protein_state
bound	I-protein_state
and	O
Trp	B-protein_state
-	I-protein_state
bound	I-protein_state
YfiR	B-protein
.	O
(	O
B	O
)	O
Close	O
-	O
up	O
views	O
showing	O
the	O
key	O
residues	O
of	O
YfiR	B-protein
that	O
bind	O
VB6	B-chemical
and	O
L	B-chemical
-	I-chemical
Trp	I-chemical
.	O

The	O
electron	B-evidence
densities	I-evidence
of	O
VB6	B-chemical
and	O
Trp	B-chemical
are	O
countered	O
at	O
3	O
.	O
0σ	O
and	O
2	O
.	O
3σ	O
,	O
respectively	O
,	O
in	O
|	B-evidence
Fo	I-evidence
|-|	I-evidence
Fc	I-evidence
|	I-evidence
maps	I-evidence
.	O
(	O
C	O
)	O
Superposition	B-experimental_method
of	O
the	O
hydrophobic	B-site
pocket	I-site
of	O
YfiR	B-protein
with	O
VB6	B-chemical
,	O
L	B-chemical
-	I-chemical
Trp	I-chemical
and	O
F57	B-residue_name_number
of	O
YfiB	B-protein

Intriguingly	O
,	O
a	O
Dali	B-experimental_method
search	I-experimental_method
(	O
Holm	O
and	O
Rosenstrom	O
,)	O
indicated	O
that	O
the	O
closest	O
homologs	O
of	O
YfiR	B-protein
shared	O
the	O
characteristic	O
of	O
being	O
able	O
to	O
bind	O
several	O
structurally	O
similar	O
small	O
molecules	O
,	O
such	O
as	O
L	B-chemical
-	I-chemical
Trp	I-chemical
,	O
L	B-chemical
-	I-chemical
Phe	I-chemical
,	O
B	O
-	O
group	O
vitamins	O
and	O
their	O
analogs	O
,	O
encouraging	O
us	O
to	O
test	O
whether	O
YfiR	B-protein
can	O
recognize	O
these	O
molecules	O
.	O

For	O
this	O
purpose	O
,	O
we	O
co	B-experimental_method
-	I-experimental_method
crystallized	I-experimental_method
YfiR	B-protein
or	O
soaked	B-experimental_method
YfiR	B-protein
crystals	B-evidence
with	O
different	O
small	O
molecules	O
,	O
including	O
L	B-chemical
-	I-chemical
Trp	I-chemical
and	O
B	O
-	O
group	O
vitamins	O
.	O

Fortunately	O
,	O
we	O
found	O
obvious	O
small	B-evidence
-	I-evidence
molecule	I-evidence
density	I-evidence
in	O
the	O
VB6	B-protein_state
-	I-protein_state
bound	I-protein_state
and	O
Trp	B-protein_state
-	I-protein_state
bound	I-protein_state
YfiR	B-protein
crystal	B-evidence
structures	I-evidence
(	O
Fig	O
.	O
5A	O
and	O
5B	O
),	O
and	O
in	O
both	O
structures	B-evidence
,	O
the	O
YfiR	B-protein
dimers	B-oligomeric_state
resemble	O
the	O
oxidized	B-protein_state
YfiR	B-protein
structure	B-evidence
in	O
which	O
both	O
two	O
disulfide	B-ptm
bonds	I-ptm
are	O
well	O
formed	O
(	O
Yang	O
et	O
al	O
.,).	O

Functional	O
analysis	O
of	O
VB6	B-chemical
and	O
L	B-chemical
-	I-chemical
Trp	I-chemical
.	O
(	O
A	O
and	O
B	O
)	O
The	O
effect	B-experimental_method
of	I-experimental_method
increasing	I-experimental_method
concentrations	I-experimental_method
of	O
VB6	B-chemical
or	O
L	B-chemical
-	I-chemical
Trp	I-chemical
on	O
YfiBL43P	B-mutant
-	O
induced	O
attachment	O
(	O
bars	O
).	O

The	O
relative	B-evidence
optical	I-evidence
density	I-evidence
is	O
represented	O
as	O
curves	O
.	O

Wild	B-protein_state
-	I-protein_state
type	I-protein_state
YfiB	B-protein
is	O
used	O
as	O
negative	O
control	O
.	O

(	O
C	O
and	O
D	O
)	O
BIAcore	B-experimental_method
data	O
and	O
analysis	O
for	O
binding	B-evidence
affinities	I-evidence
of	O
(	O
C	O
)	O
VB6	B-chemical
and	O
(	O
D	O
)	O
L	B-chemical
-	I-chemical
Trp	I-chemical
with	O
YfiR	B-protein
.	O
(	O
E	O
–	O
G	O
)	O
ITC	B-experimental_method
data	O
and	O
analysis	O
for	O
titration	B-experimental_method
of	O
(	O
E	O
)	O
YfiB	B-protein
wild	B-protein_state
-	I-protein_state
type	I-protein_state
,	O
(	O
F	O
)	O
YfiBL43P	O
,	O
and	O
(	O
G	O
)	O
YfiBL43P	B-mutant
/	O
F57A	B-mutant
into	O
YfiR	B-protein

Structural	B-experimental_method
analyses	I-experimental_method
revealed	O
that	O
the	O
VB6	B-chemical
and	O
L	B-chemical
-	I-chemical
Trp	I-chemical
molecules	O
are	O
bound	B-protein_state
at	I-protein_state
the	O
periphery	O
of	O
the	O
YfiR	B-protein
dimer	B-oligomeric_state
,	O
but	O
not	O
at	O
the	O
dimer	B-site
interface	I-site
.	O

Interestingly	O
,	O
VB6	B-chemical
and	O
L	B-chemical
-	I-chemical
Trp	I-chemical
were	O
found	O
to	O
occupy	O
the	O
same	O
hydrophobic	B-site
pocket	I-site
,	O
formed	O
by	O
L166	B-residue_name_number
/	O
I169	B-residue_name_number
/	O
V176	B-residue_name_number
/	O
P178	B-residue_name_number
/	O
L181	B-residue_name_number
of	O
YfiR	B-protein
,	O
which	O
is	O
also	O
a	O
binding	B-site
pocket	I-site
for	O
F57	B-residue_name_number
of	O
YfiB	B-protein
,	O
as	O
observed	O
in	O
the	O
YfiB	B-complex_assembly
-	I-complex_assembly
YfiR	I-complex_assembly
complex	O
(	O
Fig	O
.	O
5C	O
).	O

To	O
evaluate	O
the	O
importance	O
of	O
F57	B-residue_name_number
in	O
YfiBL43P	B-complex_assembly
-	I-complex_assembly
YfiR	I-complex_assembly
interaction	O
,	O
the	O
binding	B-evidence
affinities	I-evidence
of	O
YfiBL43P	B-mutant
and	O
YfiBL43P	B-mutant
/	O
F57A	B-mutant
for	O
YfiR	B-protein
were	O
measured	O
by	O
isothermal	B-experimental_method
titration	I-experimental_method
calorimetry	I-experimental_method
(	O
ITC	B-experimental_method
).	O

The	O
results	O
showed	O
Kd	B-evidence
values	O
of	O
1	O
.	O
4	O
×	O
10	O
−	O
7	O
mol	O
/	O
L	O
and	O
5	O
.	O
3	O
×	O
10	O
−	O
7	O
mol	O
/	O
L	O
for	O
YfiBL43P	B-mutant
and	O
YfiBL43P	B-mutant
/	O
F57A	B-mutant
,	O
respectively	O
,	O
revealing	O
that	O
the	O
YfiBL43P	B-mutant
/	O
F57A	B-mutant
mutant	B-protein_state
caused	O
a	O
3	O
.	O
8	O
-	O
fold	O
reduction	O
in	O
the	O
binding	B-evidence
affinity	I-evidence
compared	O
with	O
the	O
YfiBL43P	B-mutant
mutant	B-protein_state
(	O
Fig	O
.	O
6F	O
and	O
6G	O
).	O

In	O
parallel	O
,	O
to	O
better	O
understand	O
the	O
putative	O
functional	O
role	O
of	O
VB6	B-chemical
and	O
L	B-chemical
-	I-chemical
Trp	I-chemical
,	O
yfiB	B-gene
was	O
deleted	B-experimental_method
in	O
a	O
PAO1	B-species
wild	B-protein_state
-	I-protein_state
type	I-protein_state
strain	O
,	O
and	O
a	O
construct	B-experimental_method
expressing	I-experimental_method
the	O
YfiBL43P	B-mutant
mutant	B-protein_state
was	O
transformed	B-experimental_method
into	I-experimental_method
the	O
PAO1	B-species
ΔyfiB	B-mutant
strain	O
to	O
trigger	O
YfiBL43P	B-mutant
-	O
induced	O
biofilm	O
formation	O
.	O

Growth	B-experimental_method
and	I-experimental_method
surface	I-experimental_method
attachment	I-experimental_method
assays	I-experimental_method
were	O
carried	O
out	O
for	O
the	O
yfiB	B-mutant
-	I-mutant
L43P	I-mutant
strain	O
in	O
the	O
presence	O
of	O
increasing	B-experimental_method
concentrations	I-experimental_method
of	O
VB6	B-chemical
or	O
L	B-chemical
-	I-chemical
Trp	I-chemical
.	O

As	O
shown	O
in	O
Fig	O
.	O
6A	O
and	O
6B	O
,	O
the	O
over	B-experimental_method
-	I-experimental_method
expression	I-experimental_method
of	O
YfiBL43P	B-mutant
induced	O
strong	O
surface	O
attachment	O
and	O
much	O
slower	O
growth	O
of	O
the	O
yfiB	B-mutant
-	I-mutant
L43P	I-mutant
strain	O
,	O
and	O
as	O
expected	O
,	O
a	O
certain	O
amount	O
of	O
VB6	B-chemical
or	O
L	B-chemical
-	I-chemical
Trp	I-chemical
(	O
4	O
–	O
6	O
mmol	O
/	O
L	O
for	O
VB6	B-chemical
and	O
6	O
–	O
10	O
mmol	O
/	O
L	O
for	O
L	B-chemical
-	I-chemical
Trp	I-chemical
)	O
could	O
reduce	O
the	O
surface	O
attachment	O
.	O

Interestingly	O
,	O
at	O
a	O
concentration	O
higher	O
than	O
8	O
mmol	O
/	O
L	O
,	O
VB6	B-chemical
lost	O
its	O
ability	O
to	O
inhibit	O
biofilm	O
formation	O
,	O
implying	O
that	O
the	O
VB6	B-chemical
-	O
involving	O
regulatory	O
mechanism	O
is	O
highly	O
complicated	O
and	O
remains	O
to	O
be	O
further	O
investigated	O
.	O

Of	O
note	O
,	O
both	O
VB6	B-chemical
and	O
L	B-chemical
-	I-chemical
Trp	I-chemical
have	O
been	O
reported	O
to	O
correlate	O
with	O
biofilm	O
formation	O
in	O
certain	O
Gram	B-taxonomy_domain
-	I-taxonomy_domain
negative	I-taxonomy_domain
bacteria	I-taxonomy_domain
(	O
Grubman	O
et	O
al	O
.,;	O
Shimazaki	O
et	O
al	O
.,).	O

In	O
Helicobacter	B-species
pylori	I-species
in	O
particular	O
,	O
VB6	B-chemical
biosynthetic	O
enzymes	O
act	O
as	O
novel	O
virulence	O
factors	O
,	O
and	O
VB6	B-chemical
is	O
required	O
for	O
full	O
motility	O
and	O
virulence	O
(	O
Grubman	O
et	O
al	O
.,).	O

In	O
E	B-species
.	I-species
coli	I-species
,	O
mutants	O
with	O
decreased	O
tryptophan	B-chemical
synthesis	O
show	O
greater	O
biofilm	O
formation	O
,	O
and	O
matured	O
biofilm	O
is	O
degraded	O
by	O
L	B-chemical
-	I-chemical
tryptophan	I-chemical
addition	O
(	O
Shimazaki	O
et	O
al	O
.,).	O

To	O
answer	O
the	O
question	O
whether	O
competition	O
of	O
VB6	B-chemical
or	O
L	B-chemical
-	I-chemical
Trp	I-chemical
for	O
the	O
YfiB	B-protein
F57	B-site
-	I-site
binding	I-site
pocket	I-site
of	O
YfiR	B-protein
plays	O
an	O
essential	O
role	O
in	O
inhibiting	O
biofilm	O
formation	O
,	O
we	O
measured	O
the	O
binding	B-evidence
affinities	I-evidence
of	O
VB6	B-chemical
and	O
L	B-chemical
-	I-chemical
Trp	I-chemical
for	O
YfiR	B-protein
via	O
BIAcore	B-experimental_method
experiments	O
.	O

The	O
results	O
showed	O
relatively	O
weak	O
Kd	B-evidence
values	O
of	O
35	O
.	O
2	O
mmol	O
/	O
L	O
and	O
76	O
.	O
9	O
mmol	O
/	O
L	O
for	O
VB6	B-chemical
and	O
L	B-chemical
-	I-chemical
Trp	I-chemical
,	O
respectively	O
(	O
Fig	O
.	O
6C	O
and	O
6D	O
).	O

Based	O
on	O
our	O
results	O
,	O
we	O
concluded	O
that	O
VB6	B-chemical
or	O
L	B-chemical
-	I-chemical
Trp	I-chemical
can	O
bind	O
to	O
YfiR	B-protein
,	O
however	O
,	O
VB6	B-chemical
or	O
L	B-chemical
-	I-chemical
Trp	I-chemical
alone	B-protein_state
may	O
have	O
little	O
effects	O
in	O
interrupting	O
the	O
YfiB	B-complex_assembly
-	I-complex_assembly
YfiR	I-complex_assembly
interaction	O
,	O
the	O
mechanism	O
by	O
which	O
VB6	B-chemical
or	O
L	B-chemical
-	I-chemical
Trp	I-chemical
inhibits	O
biofilm	O
formation	O
remains	O
unclear	O
and	O
requires	O
further	O
investigation	O
.	O

Previous	O
studies	O
suggested	O
that	O
in	O
response	O
to	O
cell	O
stress	O
,	O
YfiB	B-protein
in	O
the	O
outer	O
membrane	O
sequesters	O
the	O
periplasmic	O
protein	O
YfiR	B-protein
,	O
releasing	O
its	O
inhibition	O
of	O
YfiN	B-protein
on	O
the	O
inner	O
membrane	O
and	O
thus	O
inducing	O
the	O
diguanylate	O
cyclase	O
activity	O
of	O
YfiN	B-protein
to	O
allow	O
c	B-chemical
-	I-chemical
di	I-chemical
-	I-chemical
GMP	I-chemical
production	O
(	O
Giardina	O
et	O
al	O
.,;	O
Malone	O
et	O
al	O
.,;	O
Malone	O
et	O
al	O
.,).	O

Here	O
,	O
we	O
report	O
the	O
crystal	B-evidence
structures	I-evidence
of	O
YfiB	B-protein
alone	B-protein_state
and	O
an	O
active	B-protein_state
mutant	B-protein_state
YfiBL43P	B-mutant
in	B-protein_state
complex	I-protein_state
with	I-protein_state
YfiR	B-protein
,	O
indicating	O
that	O
YfiR	B-protein
forms	O
a	O
2	O
:	O
2	O
complex	B-protein_state
with	I-protein_state
YfiB	B-protein
via	O
a	O
region	O
composed	O
of	O
conserved	O
residues	O
.	O

Our	O
structural	B-experimental_method
data	I-experimental_method
analysis	I-experimental_method
shows	O
that	O
the	O
activated	B-protein_state
YfiB	B-protein
has	O
an	O
N	B-structure_element
-	I-structure_element
terminal	I-structure_element
portion	I-structure_element
that	O
is	O
largely	O
altered	O
,	O
adopting	O
a	O
stretched	B-protein_state
conformation	I-protein_state
compared	O
with	O
the	O
compact	B-protein_state
conformation	I-protein_state
of	O
the	O
apo	B-protein_state
YfiB	B-protein
.	O
The	O
apo	B-protein_state
YfiB	B-protein
structure	B-evidence
constructed	O
beginning	O
at	O
residue	O
34	B-residue_number
has	O
a	O
compact	B-protein_state
conformation	I-protein_state
of	O
approximately	O
45	O
Å	O
in	O
length	O
.	O

In	O
addition	O
to	O
the	O
preceding	B-residue_range
8	I-residue_range
aa	I-residue_range
loop	B-structure_element
(	O
from	O
the	O
lipid	O
acceptor	O
Cys26	B-residue_range
to	I-residue_range
Gly34	I-residue_range
),	O
the	O
full	B-protein_state
length	I-protein_state
of	O
the	O
periplasmic	O
portion	O
of	O
apo	B-protein_state
YfiB	B-protein
can	O
reach	O
approximately	O
60	O
Å	O
.	O
It	O
was	O
reported	O
that	O
the	O
distance	O
between	O
the	O
outer	O
membrane	O
and	O
the	O
cell	O
wall	O
is	O
approximately	O
50	O
Å	O
and	O
that	O
the	O
thickness	O
of	O
the	O
PG	O
layer	O
is	O
approximately	O
70	O
Å	O
(	O
Matias	O
et	O
al	O
.,).	O

Thus	O
,	O
YfiB	B-protein
alone	B-protein_state
represents	O
an	O
inactive	B-protein_state
form	O
that	O
may	O
only	O
partially	O
insert	O
into	O
the	O
PG	O
matrix	O
.	O

By	O
contrast	O
,	O
YfiR	B-protein_state
-	I-protein_state
bound	I-protein_state
YfiBL43P	B-mutant
(	O
residues	O
44	B-residue_range
–	I-residue_range
168	I-residue_range
)	O
has	O
a	O
stretched	B-protein_state
conformation	I-protein_state
of	O
approximately	O
55	O
Å	O
in	O
length	O
.	O

In	O
addition	O
to	O
the	O
17	B-residue_range
preceding	I-residue_range
intracellular	I-residue_range
residues	I-residue_range
(	O
from	O
the	O
lipid	O
acceptor	O
Cys26	B-residue_range
to	I-residue_range
Leu43	I-residue_range
),	O
the	O
length	O
of	O
the	O
intracellular	O
portion	O
of	O
active	B-protein_state
YfiB	B-protein
may	O
extend	O
over	O
100	O
Å	O
,	O
assuming	O
a	O
fully	B-protein_state
stretched	I-protein_state
conformation	I-protein_state
.	O

Provided	O
that	O
the	O
diameter	O
of	O
the	O
widest	O
part	O
of	O
the	O
YfiB	B-protein
dimer	B-oligomeric_state
is	O
approximately	O
64	O
Å	O
,	O
which	O
is	O
slightly	O
smaller	O
than	O
the	O
smallest	O
diameter	O
of	O
the	O
PG	O
pore	O
(	O
70	O
Å	O
)	O
(	O
Meroueh	O
et	O
al	O
.,),	O
the	O
YfiB	B-protein
dimer	B-oligomeric_state
should	O
be	O
able	O
to	O
penetrate	O
the	O
PG	O
layer	O
.	O

Regulatory	O
model	O
of	O
the	O
YfiBNR	B-complex_assembly
tripartite	B-protein_state
system	O
.	O

The	O
periplasmic	B-structure_element
domain	I-structure_element
of	O
YfiB	B-protein
and	O
the	O
YfiB	B-complex_assembly
-	I-complex_assembly
YfiR	I-complex_assembly
complex	O
are	O
depicted	O
according	O
to	O
the	O
crystal	B-evidence
structures	I-evidence
.	O

The	O
lipid	O
acceptor	O
Cys26	B-residue_name_number
is	O
indicated	O
as	O
blue	O
ball	O
.	O

The	O
loop	B-structure_element
connecting	O
Cys26	B-residue_name_number
and	O
Gly34	B-residue_name_number
of	O
YfiB	B-protein
is	O
modeled	O
.	O

The	O
PAS	B-structure_element
domain	I-structure_element
of	O
YfiN	B-protein
is	O
shown	O
as	O
pink	O
oval	O
.	O

Once	O
activated	B-protein_state
by	O
certain	O
cell	O
stress	O
,	O
the	O
dimeric	B-oligomeric_state
YfiB	B-protein
transforms	O
from	O
a	O
compact	B-protein_state
conformation	I-protein_state
to	O
a	O
stretched	B-protein_state
conformation	I-protein_state
,	O
allowing	O
the	O
periplasmic	B-structure_element
domain	I-structure_element
of	O
the	O
membrane	B-protein_state
-	I-protein_state
anchored	I-protein_state
YfiB	B-protein
to	O
penetrate	O
the	O
cell	O
wall	O
and	O
sequester	O
the	O
YfiR	B-protein
dimer	B-oligomeric_state
,	O
thus	O
relieving	O
the	O
repression	O
of	O
YfiN	B-protein

These	O
results	O
,	O
together	O
with	O
our	O
observation	O
that	O
activated	B-protein_state
YfiB	B-protein
has	O
a	O
much	O
higher	O
cell	B-evidence
wall	I-evidence
binding	I-evidence
affinity	I-evidence
,	O
and	O
previous	O
mutagenesis	O
data	O
showing	O
that	O
(	O
1	O
)	O
both	O
PG	B-chemical
binding	O
and	O
membrane	O
anchoring	O
are	O
required	O
for	O
YfiB	B-protein
activity	O
and	O
(	O
2	O
)	O
activating	O
mutations	O
possessing	O
an	O
altered	O
N	O
-	O
terminal	O
loop	B-structure_element
length	O
are	O
dominant	O
over	O
the	O
loss	O
of	O
PG	B-chemical
binding	O
(	O
Malone	O
et	O
al	O
.,),	O
suggest	O
an	O
updated	O
regulatory	O
model	O
of	O
the	O
YfiBNR	B-complex_assembly
system	O
(	O
Fig	O
.	O
7	O
).	O

In	O
this	O
model	O
,	O
in	O
response	O
to	O
a	O
particular	O
cell	O
stress	O
that	O
is	O
yet	O
to	O
be	O
identified	O
,	O
the	O
dimeric	B-oligomeric_state
YfiB	B-protein
is	O
activated	B-protein_state
from	O
a	O
compact	B-protein_state
,	O
inactive	B-protein_state
conformation	B-protein_state
to	O
a	O
stretched	B-protein_state
conformation	I-protein_state
,	O
which	O
possesses	O
increased	O
PG	B-chemical
binding	O
affinity	O
.	O

This	O
allows	O
the	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
portion	I-structure_element
of	O
the	O
membrane	B-protein_state
-	I-protein_state
anchored	I-protein_state
YfiB	B-protein
to	O
reach	O
,	O
bind	O
and	O
penetrate	O
the	O
cell	O
wall	O
and	O
sequester	O
the	O
YfiR	B-protein
dimer	B-oligomeric_state
.	O

The	O
YfiBNR	B-complex_assembly
system	O
provides	O
a	O
good	O
example	O
of	O
a	O
delicate	O
homeostatic	O
system	O
that	O
integrates	O
multiple	O
signals	O
to	O
regulate	O
the	O
c	B-chemical
-	I-chemical
di	I-chemical
-	I-chemical
GMP	I-chemical
level	O
.	O

Homologs	O
of	O
the	O
YfiBNR	B-complex_assembly
system	O
are	O
functionally	B-protein_state
conserved	I-protein_state
in	O
P	B-species
.	I-species
aeruginosa	I-species
(	O
Malone	O
et	O
al	O
.,;	O
Malone	O
et	O
al	O
.,),	O
E	B-species
.	I-species
coli	I-species
(	O
Hufnagel	O
et	O
al	O
.,;	O
Raterman	O
et	O
al	O
.,;	O
Sanchez	O
-	O
Torres	O
et	O
al	O
.,),	O
K	B-species
.	I-species
pneumonia	I-species
(	O
Huertas	O
et	O
al	O
.,)	O
and	O
Y	B-species
.	I-species
pestis	I-species
(	O
Ren	O
et	O
al	O
.,),	O
where	O
they	O
affect	O
c	B-chemical
-	I-chemical
di	I-chemical
-	I-chemical
GMP	I-chemical
production	O
and	O
biofilm	O
formation	O
.	O

The	O
mechanism	O
by	O
which	O
activated	B-protein_state
YfiB	B-protein
relieves	O
the	O
repression	O
of	O
YfiN	B-protein
may	O
be	O
applicable	O
to	O
the	O
YfiBNR	B-complex_assembly
system	O
in	O
other	O
bacteria	B-taxonomy_domain
and	O
to	O
analogous	O
outside	O
-	O
in	O
signaling	O
for	O
c	B-chemical
-	I-chemical
di	I-chemical
-	I-chemical
GMP	I-chemical
production	O
,	O
which	O
in	O
turn	O
may	O
be	O
relevant	O
to	O
the	O
development	O
of	O
drugs	O
that	O
can	O
circumvent	O
complicated	O
antibiotic	O
resistance	O
.	O

Predictive	O
features	O
of	O
ligand	O
‐	O
specific	O
signaling	O
through	O
the	O
estrogen	B-protein_type
receptor	I-protein_type

Some	O
estrogen	B-protein
receptor	I-protein
‐	I-protein
α	I-protein
(	O
ERα	B-protein
)‐	O
targeted	O
breast	O
cancer	O
therapies	O
such	O
as	O
tamoxifen	B-chemical
have	O
tissue	O
‐	O
selective	O
or	O
cell	O
‐	O
specific	O
activities	O
,	O
while	O
others	O
have	O
similar	O
activities	O
in	O
different	O
cell	O
types	O
.	O

To	O
identify	O
biophysical	O
determinants	O
of	O
cell	O
‐	O
specific	O
signaling	O
and	O
breast	O
cancer	O
cell	O
proliferation	O
,	O
we	O
synthesized	B-experimental_method
241	O
ERα	B-protein
ligands	O
based	O
on	O
19	O
chemical	O
scaffolds	O
,	O
and	O
compared	O
ligand	O
response	O
using	O
quantitative	B-experimental_method
bioassays	I-experimental_method
for	O
canonical	O
ERα	B-protein
activities	O
and	O
X	B-experimental_method
‐	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
.	O

Ligands	O
that	O
regulate	O
the	O
dynamics	O
and	O
stability	O
of	O
the	O
coactivator	B-site
‐	I-site
binding	I-site
site	I-site
in	O
the	O
C	O
‐	O
terminal	O
ligand	B-structure_element
‐	I-structure_element
binding	I-structure_element
domain	I-structure_element
,	O
called	O
activation	B-structure_element
function	I-structure_element
‐	I-structure_element
2	I-structure_element
(	O
AF	B-structure_element
‐	I-structure_element
2	I-structure_element
),	O
showed	O
similar	O
activity	O
profiles	O
in	O
different	O
cell	O
types	O
.	O

Such	O
ligands	O
induced	O
breast	O
cancer	O
cell	O
proliferation	O
in	O
a	O
manner	O
that	O
was	O
predicted	O
by	O
the	O
canonical	O
recruitment	O
of	O
the	O
coactivators	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
and	O
induction	O
of	O
the	O
GREB1	B-protein
proliferative	O
gene	O
.	O

For	O
some	O
ligand	O
series	O
,	O
a	O
single	O
inter	B-evidence
‐	I-evidence
atomic	I-evidence
distance	I-evidence
in	O
the	O
ligand	B-structure_element
‐	I-structure_element
binding	I-structure_element
domain	I-structure_element
predicted	O
their	O
proliferative	O
effects	O
.	O

In	O
contrast	O
,	O
the	O
N	O
‐	O
terminal	O
coactivator	B-site
‐	I-site
binding	I-site
site	I-site
,	O
activation	B-structure_element
function	I-structure_element
‐	I-structure_element
1	I-structure_element
(	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
),	O
determined	O
cell	O
‐	O
specific	O
signaling	O
induced	O
by	O
ligands	O
that	O
used	O
alternate	O
mechanisms	O
to	O
control	O
cell	O
proliferation	O
.	O

Thus	O
,	O
incorporating	O
systems	B-experimental_method
structural	I-experimental_method
analyses	I-experimental_method
with	O
quantitative	B-experimental_method
chemical	I-experimental_method
biology	I-experimental_method
reveals	O
how	O
ligands	O
can	O
achieve	O
distinct	O
allosteric	O
signaling	O
outcomes	O
through	O
ERα	B-protein
.	O

Many	O
drugs	O
are	O
small	O
‐	O
molecule	O
ligands	O
of	O
allosteric	O
signaling	O
proteins	O
,	O
including	O
G	B-protein_type
protein	I-protein_type
‐	I-protein_type
coupled	I-protein_type
receptors	I-protein_type
(	O
GPCRs	B-protein_type
)	O
and	O
nuclear	B-protein_type
receptors	I-protein_type
such	O
as	O
ERα	B-protein
.	O

Small	O
‐	O
molecule	O
ligands	O
control	O
receptor	O
activity	O
by	O
modulating	O
recruitment	O
of	O
effector	O
enzymes	O
to	O
distal	O
regions	O
of	O
the	O
receptor	O
,	O
relative	O
to	O
the	O
ligand	B-site
‐	I-site
binding	I-site
site	I-site
.	O

For	O
example	O
,	O
selective	O
estrogen	B-protein_type
receptor	I-protein_type
modulators	I-protein_type
(	O
SERMs	B-protein_type
)	O
such	O
as	O
tamoxifen	B-chemical
(	O
Nolvadex	B-chemical
®;	I-chemical
AstraZeneca	O
)	O
or	O
raloxifene	B-chemical
(	O
Evista	B-chemical
®;	I-chemical
Eli	O
Lilly	O
)	O
(	O
Fig	O
1A	O
)	O
block	O
the	O
ERα	B-protein
‐	O
mediated	O
proliferative	O
effects	O
of	O
the	O
native	O
estrogen	B-chemical
,	O
17β	B-chemical
‐	I-chemical
estradiol	I-chemical
(	O
E2	B-chemical
),	O
on	O
breast	O
cancer	O
cells	O
,	O
but	O
promote	O
beneficial	O
estrogenic	O
effects	O
on	O
bone	O
mineral	O
density	O
and	O
adverse	O
estrogenic	O
effects	O
such	O
as	O
uterine	O
proliferation	O
,	O
fatty	O
liver	O
,	O
or	O
stroke	O
(	O
Frolik	O
et	O
al	O
,	O
1996	O
;	O
Fisher	O
et	O
al	O
,	O
1998	O
;	O
McDonnell	O
et	O
al	O
,	O
2002	O
;	O
Jordan	O
,	O
2003	O
).	O

Allosteric	O
control	O
of	O
ERα	B-protein
activity	O

Chemical	O
structures	O
of	O
some	O
common	O
ERα	B-protein
ligands	O
.	O

E2	B-chemical
‐	O
rings	O
are	O
numbered	O
A	O
‐	O
D	O
.	O
The	O
E	O
‐	O
ring	O
is	O
the	O
common	O
site	O
of	O
attachment	O
for	O
BSC	O
found	O
in	O
many	O
SERMS	B-protein_type
.	O

ERα	B-protein
domain	O
organization	O
lettered	O
,	O
A	O
‐	O
F	O
.	O
DBD	B-structure_element
,	O
DNA	B-structure_element
‐	I-structure_element
binding	I-structure_element
domain	I-structure_element
;	O
LBD	B-structure_element
,	O
ligand	B-structure_element
‐	I-structure_element
binding	I-structure_element
domain	I-structure_element
;	O
AF	B-structure_element
,	O
activation	B-structure_element
function	I-structure_element

Schematic	O
illustration	O
of	O
the	O
canonical	O
ERα	B-protein
signaling	O
pathway	O
.	O

Linear	O
causality	O
model	O
for	O
ERα	B-protein
‐	O
mediated	O
cell	O
proliferation	O
.	O

Branched	O
causality	O
model	O
for	O
ERα	B-protein
‐	O
mediated	O
cell	O
proliferation	O
.	O

ERα	B-protein
contains	O
structurally	B-protein_state
conserved	I-protein_state
globular	B-structure_element
domains	I-structure_element
of	O
the	O
nuclear	B-protein_type
receptor	I-protein_type
superfamily	I-protein_type
,	O
including	O
a	O
DNA	B-structure_element
‐	I-structure_element
binding	I-structure_element
domain	I-structure_element
(	O
DBD	B-structure_element
)	O
that	O
is	O
connected	O
by	O
a	O
flexible	B-protein_state
hinge	B-structure_element
region	I-structure_element
to	O
the	O
ligand	B-structure_element
‐	I-structure_element
binding	I-structure_element
domain	I-structure_element
(	O
LBD	B-structure_element
),	O
as	O
well	O
as	O
unstructured	B-protein_state
AB	B-structure_element
and	O
F	B-structure_element
domains	O
at	O
its	O
amino	O
and	O
carboxyl	O
termini	O
,	O
respectively	O
(	O
Fig	O
1B	O
).	O

The	O
LBD	B-structure_element
contains	O
a	O
ligand	O
‐	O
dependent	O
coactivator	B-site
‐	I-site
binding	I-site
site	I-site
called	O
activation	B-structure_element
function	I-structure_element
‐	I-structure_element
2	I-structure_element
(	O
AF	B-structure_element
‐	I-structure_element
2	I-structure_element
).	O

However	O
,	O
the	O
agonist	O
activity	O
of	O
SERMs	B-protein_type
derives	O
from	O
activation	B-structure_element
function	I-structure_element
‐	I-structure_element
1	I-structure_element
(	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
)—	O
a	O
coactivator	B-site
recruitment	I-site
site	I-site
located	O
in	O
the	O
AB	B-structure_element
domain	O
(	O
Berry	O
et	O
al	O
,	O
1990	O
;	O
Shang	O
&	O
Brown	O
,	O
2002	O
;	O
Abot	O
et	O
al	O
,	O
2013	O
).	O

AF	B-structure_element
‐	I-structure_element
1	I-structure_element
and	O
AF	B-structure_element
‐	I-structure_element
2	I-structure_element
bind	O
distinct	O
but	O
overlapping	O
sets	O
of	O
coregulators	O
(	O
Webb	O
et	O
al	O
,	O
1998	O
;	O
Endoh	O
et	O
al	O
,	O
1999	O
;	O
Delage	O
‐	O
Mourroux	O
et	O
al	O
,	O
2000	O
;	O
Yi	O
et	O
al	O
,	O
2015	O
).	O

AF	B-structure_element
‐	I-structure_element
2	I-structure_element
binds	O
the	O
signature	O
LxxLL	B-structure_element
motif	I-structure_element
peptides	O
of	O
coactivators	O
such	O
as	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
(	O
also	O
known	O
as	O
SRC	B-protein
‐	I-protein
1	I-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
).	O

AF	B-structure_element
‐	I-structure_element
1	I-structure_element
binds	O
a	O
separate	O
surface	O
on	O
these	O
coactivators	O
(	O
Webb	O
et	O
al	O
,	O
1998	O
;	O
Yi	O
et	O
al	O
,	O
2015	O
).	O

Yet	O
,	O
it	O
is	O
unknown	O
how	O
different	O
ERα	B-protein
ligands	O
control	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
through	O
the	O
LBD	B-structure_element
,	O
and	O
whether	O
this	O
inter	O
‐	O
domain	O
communication	O
is	O
required	O
for	O
cell	O
‐	O
specific	O
signaling	O
or	O
anti	O
‐	O
proliferative	O
responses	O
.	O

In	O
the	O
canonical	O
model	O
of	O
the	O
ERα	B-protein
signaling	O
pathway	O
(	O
Fig	O
1C	O
),	O
E2	B-protein_state
‐	I-protein_state
bound	I-protein_state
ERα	B-protein
forms	O
a	O
homodimer	B-oligomeric_state
that	O
binds	O
DNA	O
at	O
estrogen	B-site
‐	I-site
response	I-site
elements	I-site
(	O
EREs	B-site
),	O
recruits	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
(	O
Metivier	O
et	O
al	O
,	O
2003	O
;	O
Johnson	O
&	O
O	O
'	O
Malley	O
,	O
2012	O
),	O
and	O
activates	O
the	O
GREB1	B-protein
gene	O
,	O
which	O
is	O
required	O
for	O
proliferation	O
of	O
ERα	B-protein
‐	O
positive	O
breast	O
cancer	O
cells	O
(	O
Ghosh	O
et	O
al	O
,	O
2000	O
;	O
Rae	O
et	O
al	O
,	O
2005	O
;	O
Deschenes	O
et	O
al	O
,	O
2007	O
;	O
Liu	O
et	O
al	O
,	O
2012	O
;	O
Srinivasan	O
et	O
al	O
,	O
2013	O
).	O

However	O
,	O
ERα	B-protein
‐	O
mediated	O
proliferative	O
responses	O
vary	O
in	O
a	O
ligand	O
‐	O
dependent	O
manner	O
(	O
Srinivasan	O
et	O
al	O
,	O
2013	O
);	O
thus	O
,	O
it	O
is	O
not	O
known	O
whether	O
this	O
canonical	O
model	O
is	O
widely	O
applicable	O
across	O
diverse	O
ERα	B-protein
ligands	O
.	O

Our	O
long	O
‐	O
term	O
goal	O
is	O
to	O
be	O
able	O
to	O
predict	O
proliferative	O
or	O
anti	O
‐	O
proliferative	O
activity	O
of	O
a	O
ligand	O
in	O
different	O
tissues	O
from	O
its	O
crystal	B-evidence
structure	I-evidence
by	O
identifying	O
different	O
structural	O
perturbations	O
that	O
lead	O
to	O
specific	O
signaling	O
outcomes	O
.	O

The	O
simplest	O
response	O
model	O
for	O
ligand	O
‐	O
specific	O
proliferative	O
effects	O
is	O
a	O
linear	O
causality	O
model	O
,	O
where	O
the	O
degree	O
of	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
recruitment	O
determines	O
GREB1	B-protein
expression	O
,	O
which	O
in	O
turn	O
drives	O
ligand	O
‐	O
specific	O
cell	O
proliferation	O
(	O
Fig	O
1D	O
).	O

In	O
this	O
signaling	O
model	O
,	O
multiple	O
coregulator	O
binding	O
events	O
and	O
target	O
genes	O
(	O
Won	O
Jeong	O
et	O
al	O
,	O
2012	O
;	O
Nwachukwu	O
et	O
al	O
,	O
2014	O
),	O
LBD	B-structure_element
conformation	O
,	O
nucleocytoplasmic	O
shuttling	O
,	O
the	O
occupancy	O
and	O
dynamics	O
of	O
DNA	O
binding	O
,	O
and	O
other	O
biophysical	O
features	O
could	O
contribute	O
independently	O
to	O
cell	O
proliferation	O
(	O
Lickwar	O
et	O
al	O
,	O
2012	O
).	O

To	O
test	O
these	O
signaling	O
models	O
,	O
we	O
profiled	O
a	O
diverse	O
library	O
of	O
ERα	B-protein
ligands	O
using	O
systems	O
biology	O
approaches	O
to	O
X	B-experimental_method
‐	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
and	O
chemical	B-experimental_method
biology	I-experimental_method
(	O
Srinivasan	O
et	O
al	O
,	O
2013	O
),	O
including	O
a	O
series	O
of	O
quantitative	O
bioassays	O
for	O
ERα	B-protein
function	O
that	O
were	O
statistically	O
robust	O
and	O
reproducible	O
,	O
based	O
on	O
the	O
Z	B-evidence
’‐	I-evidence
statistic	I-evidence
(	O
Fig	O
EV1A	O
and	O
B	O
;	O
see	O
Materials	O
and	O
Methods	O
).	O

We	O
also	O
determined	B-experimental_method
the	O
structures	B-evidence
of	O
76	O
distinct	O
ERα	B-protein
LBD	B-structure_element
complexes	O
bound	B-protein_state
to	I-protein_state
different	O
ligand	O
types	O
,	O
which	O
allowed	O
us	O
to	O
understand	O
how	O
diverse	O
ligand	O
scaffolds	O
distort	O
the	O
active	B-protein_state
conformation	O
of	O
the	O
ERα	B-protein
LBD	B-structure_element
.	O

Our	O
findings	O
here	O
indicate	O
that	O
specific	O
structural	O
perturbations	O
can	O
be	O
tied	O
to	O
ligand	O
‐	O
selective	O
domain	O
usage	O
and	O
signaling	O
patterns	O
,	O
thus	O
providing	O
a	O
framework	O
for	O
structure	O
‐	O
based	O
design	O
of	O
improved	O
breast	O
cancer	O
therapeutics	O
,	O
and	O
understanding	O
the	O
different	O
phenotypic	O
effects	O
of	O
environmental	O
estrogens	B-chemical
.	O

High	O
‐	O
throughput	O
screens	O
for	O
ERα	B-protein
ligand	O
profiling	O

Summary	O
of	O
ligand	B-experimental_method
screening	I-experimental_method
assays	I-experimental_method
used	O
to	O
measure	O
ER	O
‐	O
mediated	O
activities	O
.	O

ERE	B-structure_element
,	O
estrogen	B-structure_element
‐	I-structure_element
response	I-structure_element
element	I-structure_element
;	O
Luc	B-experimental_method
,	O
luciferase	B-experimental_method
reporter	I-experimental_method
gene	I-experimental_method
;	O
M2H	B-experimental_method
,	O
mammalian	B-experimental_method
2	I-experimental_method
‐	I-experimental_method
hybrid	I-experimental_method
;	O
UAS	B-structure_element
,	O
upstream	B-structure_element
‐	I-structure_element
activating	I-structure_element
sequence	I-structure_element
.	O

Strength	O
of	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
signaling	O
does	O
not	O
determine	O
cell	O
‐	O
specific	O
signaling	O

To	O
compare	O
ERα	B-protein
signaling	O
induced	O
by	O
diverse	O
ligand	O
types	O
,	O
we	O
synthesized	B-experimental_method
and	I-experimental_method
assayed	I-experimental_method
a	O
library	O
of	O
241	O
ERα	B-protein
ligands	O
containing	O
19	O
distinct	O
molecular	O
scaffolds	O
.	O

These	O
include	O
15	O
indirect	O
modulator	O
series	O
,	O
which	O
lack	B-protein_state
a	O
SERM	B-protein_type
‐	I-protein_type
like	I-protein_type
side	O
chain	O
and	O
modulate	O
coactivator	O
binding	O
indirectly	O
from	O
the	O
ligand	B-site
‐	I-site
binding	I-site
pocket	I-site
(	O
Fig	O
2A	O
–	O
E	O
;	O
Dataset	O
EV1	O
)	O
(	O
Zheng	O
et	O
al	O
,	O
2012	O
)	O
(	O
Zhu	O
et	O
al	O
,	O
2012	O
)	O
(	O
Muthyala	O
et	O
al	O
,	O
2003	O
;	O
Seo	O
et	O
al	O
,	O
2006	O
)	O
(	O
Srinivasan	O
et	O
al	O
,	O
2013	O
)	O
(	O
Wang	O
et	O
al	O
,	O
2012	O
)	O
(	O
Liao	O
et	O
al	O
,	O
2014	O
)	O
(	O
Min	O
et	O
al	O
,	O
2013	O
).	O

We	O
also	O
generated	O
four	O
direct	O
modulator	O
series	O
with	O
side	O
chains	O
designed	O
to	O
directly	O
dislocate	O
h12	B-structure_element
and	O
thereby	O
completely	O
occlude	O
the	O
AF	B-site
‐	I-site
2	I-site
surface	I-site
(	O
Fig	O
2C	O
and	O
E	O
;	O
Dataset	O
EV1	O
)	O
(	O
Kieser	O
et	O
al	O
,	O
2010	O
).	O

Ligand	B-experimental_method
profiling	I-experimental_method
using	O
our	O
quantitative	B-experimental_method
bioassays	I-experimental_method
revealed	O
a	O
wide	O
range	O
of	O
ligand	O
‐	O
induced	O
GREB1	B-protein
expression	O
,	O
reporter	O
gene	O
activities	O
,	O
ERα	B-protein
‐	O
coactivator	O
interactions	O
,	O
and	O
proliferative	O
effects	O
on	O
MCF	O
‐	O
7	O
breast	O
cancer	O
cells	O
(	O
Figs	O
EV1	O
and	O
EV2A	O
–	O
J	O
).	O

This	O
wide	O
variance	O
enabled	O
us	O
to	O
probe	O
specific	O
features	O
of	O
ERα	B-protein
signaling	O
using	O
ligand	B-experimental_method
class	I-experimental_method
analyses	I-experimental_method
,	O
and	O
identify	O
signaling	O
patterns	O
shared	O
by	O
specific	O
ligand	O
series	O
or	O
scaffolds	O
.	O

Classes	O
of	O
compounds	O
in	O
the	O
ERα	B-protein
ligand	O
library	O

Structure	B-evidence
of	O
the	O
E2	B-protein_state
‐	I-protein_state
bound	I-protein_state
ERα	B-protein
LBD	B-structure_element
in	B-protein_state
complex	I-protein_state
with	I-protein_state
an	O
NCOA2	B-protein
peptide	O
of	O
(	O
PDB	O
1GWR	O
).	O

Structural	O
details	O
of	O
the	O
ERα	B-protein
LBD	B-structure_element
bound	B-protein_state
to	I-protein_state
the	O
indicated	O
ligands	O
.	O

Unlike	O
E2	B-chemical
(	O
PDB	O
1GWR	O
),	O
TAM	B-chemical
is	O
a	O
direct	O
modulator	O
with	O
a	O
BSC	O
that	O
dislocates	O
h12	B-structure_element
to	O
block	O
the	O
NCOA2	B-site
‐	I-site
binding	I-site
site	I-site
(	O
PDB	O
3ERT	O
).	O

OBHS	B-chemical
is	O
an	O
indirect	O
modulator	O
that	O
dislocates	O
the	O
h11	B-structure_element
C	O
‐	O
terminus	O
to	O
destabilize	O
the	O
h11	B-site
–	I-site
h12	I-site
interface	I-site
(	O
PDB	O
4ZN9	O
).	O

The	O
ERα	B-protein
ligand	O
library	O
contains	O
241	O
ligands	O
representing	O
15	O
indirect	O
modulator	O
scaffolds	O
,	O
plus	O
4	O
direct	O
modulator	O
scaffolds	O
.	O

ERα	B-protein
ligands	O
induced	O
a	O
range	O
of	O
agonist	O
activity	O
profiles	O

To	O
this	O
end	O
,	O
we	O
compared	O
the	O
average	O
ligand	O
‐	O
induced	O
GREB1	B-protein
mRNA	O
levels	O
in	O
MCF	O
‐	O
7	O
cells	O
and	O
3	B-experimental_method
×	I-experimental_method
ERE	I-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
reporter	O
gene	O
activity	O
in	O
Ishikawa	O
endometrial	O
cancer	O
cells	O
(	O
E	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
)	O
or	O
in	O
HepG2	O
cells	O
transfected	O
with	O
wild	B-protein_state
‐	I-protein_state
type	I-protein_state
ERα	B-protein
(	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
ERα	B-protein
‐	O
WT	B-protein_state
)	O
(	O
Figs	O
3A	O
and	O
EV2A	O
–	O
C	O
).	O

Direct	O
modulators	O
showed	O
significant	O
differences	O
in	O
average	O
activity	O
between	O
cell	O
types	O
except	O
OBHS	B-chemical
‐	I-chemical
ASC	I-chemical
analogs	O
,	O
which	O
had	O
similar	O
low	O
agonist	O
activities	O
in	O
the	O
three	O
cell	O
types	O
.	O

While	O
it	O
was	O
known	O
that	O
direct	O
modulators	O
such	O
as	O
tamoxifen	B-chemical
drive	O
cell	O
‐	O
specific	O
signaling	O
,	O
these	O
experiments	O
reveal	O
that	O
indirect	O
modulators	O
also	O
drive	O
cell	O
‐	O
specific	O
signaling	O
,	O
since	O
eight	O
of	O
fourteen	O
classes	O
showed	O
significant	O
differences	O
in	O
average	O
activity	O
(	O
Figs	O
3A	O
and	O
EV2A	O
–	O
C	O
).	O

Ligand	O
‐	O
specific	O
signaling	O
underlies	O
ERα	B-protein
‐	O
mediated	O
cell	O
proliferation	O

(	O
A	O
)	O
Ligand	O
‐	O
specific	O
ERα	B-protein
activities	O
in	O
HepG2	O
,	O
Ishikawa	O
and	O
MCF	O
‐	O
7	O
cells	O
.	O

The	O
ligand	O
‐	O
induced	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
ERα	B-protein
‐	O
WT	B-protein_state
and	O
E	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
activities	O
and	O
GREB1	B-protein
mRNA	O
levels	O
are	O
shown	O
by	O
scaffold	O
(	O
mean	O
+	O
SD	O
).	O

(	O
B	O
)	O
Ligand	O
class	B-experimental_method
analysis	I-experimental_method
of	O
the	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
ERα	B-protein
‐	O
WT	B-protein_state
and	O
ERα	B-mutant
‐	I-mutant
ΔAB	I-mutant
activities	O
in	O
HepG2	O
cells	O
.	O

Significant	O
sensitivity	O
to	O
AB	B-structure_element
domain	O
deletion	O
was	O
determined	O
by	O
Student	B-experimental_method
'	I-experimental_method
s	I-experimental_method
t	I-experimental_method
‐	I-experimental_method
test	I-experimental_method
(	O
n	O
=	O
number	O
of	O
ligands	O
per	O
scaffold	O
in	O
Fig	O
2	O
).	O

Correlation	B-experimental_method
and	I-experimental_method
regression	I-experimental_method
analyses	I-experimental_method
in	O
a	O
large	O
test	O
set	O
.	O

In	O
cluster	O
1	O
,	O
the	O
first	O
three	O
comparisons	O
(	O
rows	O
)	O
showed	O
significant	O
positive	O
correlations	O
(	O
F	B-experimental_method
‐	I-experimental_method
test	I-experimental_method
for	O
nonzero	O
slope	O
,	O
P	B-evidence
≤	O
0	O
.	O
05	O
).	O

In	O
cluster	O
2	O
,	O
only	O
one	O
of	O
these	O
comparisons	O
revealed	O
a	O
significant	O
positive	O
correlation	O
,	O
while	O
none	O
was	O
significant	O
in	O
cluster	O
3	O
.	O
+,	O
statistically	O
significant	O
correlations	O
gained	O
by	O
deletion	B-experimental_method
of	O
the	O
AB	B-structure_element
or	O
F	B-structure_element
domains	O
.	O

−,	O
significant	O
correlations	O
lost	O
upon	O
deletion	O
of	O
AB	B-structure_element
or	O
F	B-structure_element
domains	O
.	O

Tamoxifen	B-chemical
depends	O
on	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
for	O
its	O
cell	O
‐	O
specific	O
activity	O
(	O
Sakamoto	O
et	O
al	O
,	O
2002	O
);	O
therefore	O
,	O
we	O
asked	O
whether	O
cell	O
‐	O
specific	O
signaling	O
observed	O
here	O
is	O
due	O
to	O
a	O
similar	O
dependence	O
on	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
for	O
activity	O
(	O
Fig	O
EV1	O
).	O

To	O
test	O
this	O
idea	O
,	O
we	O
compared	O
the	O
average	B-evidence
L	I-evidence
‐	I-evidence
Luc	I-evidence
activities	I-evidence
of	O
each	O
scaffold	O
in	O
HepG2	O
cells	O
co	B-experimental_method
‐	I-experimental_method
transfected	I-experimental_method
with	O
wild	B-protein_state
‐	I-protein_state
type	I-protein_state
ERα	B-protein
or	O
with	O
ERα	B-protein
lacking	B-protein_state
the	I-protein_state
AB	B-structure_element
domain	O
(	O
Figs	O
1B	O
and	O
EV1	O
).	O

While	O
E2	B-chemical
showed	O
similar	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
ERα	B-protein
‐	O
WT	B-protein_state
and	O
ERα	B-mutant
‐	I-mutant
ΔAB	I-mutant
activities	O
,	O
tamoxifen	B-chemical
showed	O
complete	O
loss	O
of	O
activity	O
without	B-protein_state
the	O
AB	B-structure_element
domain	O
(	O
Fig	O
EV1B	O
).	O

Deletion	B-experimental_method
of	I-experimental_method
the	O
AB	B-structure_element
domain	O
significantly	O
reduced	O
the	O
average	B-evidence
L	I-evidence
‐	I-evidence
Luc	I-evidence
activities	I-evidence
of	O
14	O
scaffolds	O
(	O
Student	B-experimental_method
'	I-experimental_method
s	I-experimental_method
t	I-experimental_method
‐	I-experimental_method
test	I-experimental_method
,	O
P	B-evidence
≤	O
0	O
.	O
05	O
)	O
(	O
Fig	O
3B	O
).	O

These	O
“	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
‐	O
sensitive	O
”	O
activities	O
were	O
exhibited	O
by	O
both	O
direct	O
and	O
indirect	O
modulators	O
,	O
and	O
were	O
not	O
limited	O
to	O
scaffolds	O
that	O
showed	O
cell	O
‐	O
specific	O
signaling	O
(	O
Fig	O
3A	O
and	O
B	O
).	O

Thus	O
,	O
the	O
strength	O
of	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
signaling	O
does	O
not	O
determine	O
cell	O
‐	O
specific	O
signaling	O
.	O

Identifying	O
cell	O
‐	O
specific	O
signaling	O
clusters	O
in	O
ERα	B-protein
ligand	O
classes	O

For	O
each	O
ligand	O
class	O
or	O
scaffold	O
,	O
we	O
calculated	O
the	O
Pearson	B-evidence
'	I-evidence
s	I-evidence
correlation	I-evidence
coefficient	I-evidence
,	O
r	B-evidence
,	O
for	O
pairwise	O
comparison	O
of	O
activity	O
profiles	O
in	O
breast	O
(	O
GREB1	B-protein
),	O
liver	O
(	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
),	O
and	O
endometrial	O
cells	O
(	O
E	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
).	O

The	O
value	O
of	O
r	B-evidence
ranges	O
from	O
−	O
1	O
to	O
1	O
,	O
and	O
it	O
defines	O
the	O
extent	O
to	O
which	O
the	O
data	O
fit	O
a	O
straight	O
line	O
when	O
compounds	O
show	O
similar	O
agonist	O
/	O
antagonist	O
activity	O
profiles	O
between	O
cell	O
types	O
(	O
Fig	O
EV3A	O
).	O

We	O
also	O
calculated	O
the	O
coefficient	B-evidence
of	I-evidence
determination	I-evidence
,	O
r	B-evidence
2	I-evidence
,	O
which	O
describes	O
the	O
percentage	O
of	O
variance	O
in	O
a	O
dependent	O
variable	O
such	O
as	O
proliferation	O
that	O
can	O
be	O
predicted	O
by	O
an	O
independent	O
variable	O
such	O
as	O
GREB1	B-protein
expression	O
.	O

We	O
present	O
both	O
calculations	O
as	O
r	B-evidence
2	I-evidence
to	O
readily	O
compare	O
signaling	O
specificities	O
using	O
a	O
heat	O
map	O
on	O
which	O
the	O
red	O
–	O
yellow	O
palette	O
indicates	O
significant	O
positive	O
correlations	O
(	O
P	B-evidence
≤	O
0	O
.	O
05	O
,	O
F	B-experimental_method
‐	I-experimental_method
test	I-experimental_method
for	O
nonzero	O
slope	O
),	O
while	O
the	O
blue	O
palette	O
denotes	O
negative	O
correlations	O
(	O
Fig	O
3C	O
–	O
F	O
).	O

The	O
side	O
chain	O
of	O
OBHS	B-chemical
‐	I-chemical
BSC	I-chemical
analogs	O
induces	O
cell	O
‐	O
specific	O
signaling	O

Correlation	O
analysis	O
of	O
OBHS	B-chemical
versus	O
OBHS	B-chemical
‐	I-chemical
BSC	I-chemical
activity	O
across	O
cell	O
types	O
.	O

Correlation	O
analysis	O
of	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
ERα	B-mutant
‐	I-mutant
ΔAB	I-mutant
activity	O
versus	O
endogenous	O
ERα	B-protein
activity	O
of	O
OBHS	B-chemical
analogs	O
.	O

In	O
panel	O
(	O
D	O
),	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
ERα	B-protein
‐	O
WT	B-protein_state
activity	O
from	O
panel	O
(	O
B	O
)	O
is	O
shown	O
for	O
comparison	O
.	O

Correlation	O
analysis	O
of	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
ERα	B-mutant
‐	I-mutant
ΔF	I-mutant
activity	O
versus	O
endogenous	O
ERα	B-protein
activities	O
of	O
OBHS	B-chemical
analogs	O
.	O

Correlation	O
analysis	O
of	O
MCF	O
‐	O
7	O
cell	O
proliferation	O
versus	O
NCOA2	B-protein
/	I-protein
3	I-protein
recruitment	O
or	O
GREB1	B-protein
levels	O
observed	O
in	O
response	O
to	O
(	O
G	O
)	O
OBHS	B-chemical
‐	I-chemical
N	I-chemical
and	O
(	O
H	O
)	O
OBHS	B-chemical
‐	I-chemical
BSC	I-chemical
analogs	O
.	O

Scaffolds	O
in	O
cluster	O
1	O
exhibited	O
strongly	O
correlated	O
GREB1	B-protein
levels	O
,	O
E	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
and	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
activity	O
profiles	O
across	O
the	O
three	O
cell	O
types	O
(	O
Fig	O
3C	O
lanes	O
1	O
–	O
4	O
),	O
suggesting	O
these	O
ligands	O
use	O
similar	O
ERα	B-protein
signaling	O
pathways	O
in	O
the	O
breast	O
,	O
endometrial	O
,	O
and	O
liver	O
cell	O
types	O
.	O

This	O
cluster	O
includes	O
WAY	B-chemical
‐	I-chemical
C	I-chemical
,	O
OBHS	B-chemical
,	O
OBHS	B-chemical
‐	I-chemical
N	I-chemical
,	O
and	O
triaryl	B-chemical
‐	I-chemical
ethylene	I-chemical
analogs	O
,	O
all	O
of	O
which	O
are	O
indirect	O
modulators	O
.	O

This	O
cluster	O
includes	O
two	O
classes	O
of	O
direct	O
modulators	O
(	O
cyclofenil	B-chemical
‐	I-chemical
ASC	I-chemical
and	O
WAY	B-chemical
dimer	I-chemical
),	O
and	O
six	O
classes	O
of	O
indirect	O
modulators	O
(	O
2	B-chemical
,	I-chemical
5	I-chemical
‐	I-chemical
DTP	I-chemical
,	O
3	B-chemical
,	I-chemical
4	I-chemical
‐	I-chemical
DTP	I-chemical
,	O
S	B-chemical
‐	I-chemical
OBHS	I-chemical
‐	I-chemical
2	I-chemical
and	O
S	B-chemical
‐	I-chemical
OBHS	I-chemical
‐	I-chemical
3	I-chemical
,	O
furan	B-chemical
,	O
and	O
WAY	B-chemical
‐	I-chemical
D	I-chemical
).	O

For	O
example	O
,	O
3	B-chemical
,	I-chemical
4	I-chemical
‐	I-chemical
DTP	I-chemical
,	O
furan	B-chemical
,	O
and	O
S	B-chemical
‐	I-chemical
OBHS	I-chemical
‐	I-chemical
2	I-chemical
drove	O
positively	O
correlated	O
GREB1	B-protein
levels	O
and	O
E	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
but	O
not	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
ERα	B-protein
‐	O
WT	B-protein_state
activity	O
(	O
Fig	O
3C	O
lanes	O
5	O
–	O
7	O
).	O

In	O
contrast	O
,	O
WAY	B-chemical
dimer	I-chemical
and	O
WAY	B-chemical
‐	I-chemical
D	I-chemical
analogs	O
drove	O
positively	O
correlated	O
GREB1	B-protein
levels	O
and	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
ERα	B-protein
‐	O
WT	B-protein_state
but	O
not	O
E	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
activity	O
(	O
Fig	O
3C	O
lanes	O
8	O
and	O
9	O
).	O

This	O
cluster	O
includes	O
two	O
direct	O
modulator	O
scaffolds	O
(	O
OBHS	B-chemical
‐	I-chemical
ASC	I-chemical
and	O
OBHS	B-chemical
‐	I-chemical
BSC	I-chemical
),	O
and	O
five	O
indirect	O
modulator	O
scaffolds	O
(	O
A	B-chemical
‐	I-chemical
CD	I-chemical
,	O
cyclofenil	B-chemical
,	O
3	B-chemical
,	I-chemical
4	I-chemical
‐	I-chemical
DTPD	I-chemical
,	O
imine	B-chemical
,	O
and	O
imidazopyridine	B-chemical
).	O

These	O
results	O
suggest	O
that	O
addition	O
of	O
an	O
extended	O
side	O
chain	O
to	O
an	O
ERα	B-protein
ligand	O
scaffold	O
is	O
sufficient	O
to	O
induce	O
cell	O
‐	O
specific	O
signaling	O
,	O
where	O
the	O
relative	O
activity	O
profiles	O
of	O
the	O
individual	O
ligands	O
change	O
between	O
cell	O
types	O
.	O

This	O
is	O
demonstrated	O
by	O
directly	O
comparing	O
the	O
signaling	O
specificities	O
of	O
matched	O
OBHS	B-chemical
(	O
indirect	O
modulator	O
,	O
cluster	O
1	O
)	O
and	O
OBHS	B-chemical
‐	I-chemical
BSC	I-chemical
analogs	O
(	O
direct	O
modulator	O
,	O
cluster	O
3	O
),	O
which	O
differ	O
only	O
in	O
the	O
basic	O
side	O
chain	O
(	O
Fig	O
2E	O
).	O

The	O
activities	O
of	O
OBHS	B-chemical
analogs	O
were	O
positively	O
correlated	O
across	O
the	O
three	O
cell	O
types	O
,	O
but	O
the	O
side	O
chain	O
of	O
OBHS	B-chemical
‐	I-chemical
BSC	I-chemical
analogs	O
was	O
sufficient	O
to	O
abolish	O
these	O
correlations	O
(	O
Figs	O
3C	O
lanes	O
1	O
and	O
19	O
,	O
and	O
EV3A	O
–	O
C	O
).	O

Thus	O
,	O
examining	O
the	O
correlated	O
patterns	O
of	O
ERα	B-protein
activity	O
within	O
each	O
scaffold	O
demonstrates	O
that	O
an	O
extended	O
side	O
chain	O
is	O
not	O
required	O
for	O
cell	O
‐	O
specific	O
signaling	O
.	O

Modulation	O
of	O
signaling	O
specificity	O
by	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element

To	O
evaluate	O
the	O
role	O
of	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
and	O
the	O
F	B-structure_element
domain	O
in	O
ERα	B-protein
signaling	O
specificity	O
,	O
we	O
compared	O
activity	O
of	O
truncated	O
ERα	B-protein
constructs	O
in	O
HepG2	O
liver	O
cells	O
with	O
endogenous	O
ERα	B-protein
activity	O
in	O
the	O
other	O
cell	O
types	O
.	O

The	O
positive	O
correlation	O
between	O
the	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
and	O
E	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
activities	O
or	O
GREB1	B-protein
levels	O
induced	O
by	O
scaffolds	O
in	O
cluster	O
1	O
was	O
generally	O
retained	O
without	O
the	O
AB	B-structure_element
domain	O
,	O
or	O
the	O
F	B-structure_element
domain	O
(	O
Fig	O
3D	O
lanes	O
1	O
–	O
4	O
).	O

This	O
demonstrates	O
that	O
the	O
signaling	O
specificities	O
underlying	O
these	O
positive	O
correlations	O
are	O
not	O
modified	O
by	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
.	O

OBHS	B-chemical
analogs	O
showed	O
an	O
average	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
ERα	B-mutant
‐	I-mutant
ΔAB	I-mutant
activity	O
of	O
3	O
.	O
2	O
%	O
±	O
3	O
(	O
mean	O
+	O
SEM	O
)	O
relative	O
to	O
E2	B-chemical
.	O

Despite	O
this	O
nearly	O
complete	O
lack	O
of	O
activity	O
,	O
the	O
pattern	O
of	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
ERα	B-mutant
‐	I-mutant
ΔAB	I-mutant
activity	O
was	O
still	O
highly	O
correlated	O
with	O
the	O
E	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
activity	O
and	O
GREB1	B-protein
expression	O
(	O
Fig	O
EV3D	O
and	O
E	O
),	O
demonstrating	O
that	O
very	O
small	O
AF	B-structure_element
‐	I-structure_element
2	I-structure_element
activities	O
can	O
be	O
amplified	O
by	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
to	O
produce	O
robust	O
signals	O
.	O

Similarly	O
,	O
deletion	B-experimental_method
of	I-experimental_method
the	O
F	B-structure_element
domain	O
did	O
not	O
abolish	O
correlations	O
between	O
the	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
and	O
E	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
or	O
GREB1	B-protein
levels	O
induced	O
by	O
OBHS	B-chemical
analogs	O
(	O
Fig	O
EV3F	O
).	O

These	O
similar	O
patterns	O
of	O
ligand	O
activity	O
in	O
the	O
wild	B-protein_state
‐	I-protein_state
type	I-protein_state
and	O
deletion	O
mutants	B-protein_state
suggest	O
that	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
and	O
the	O
F	B-structure_element
domain	O
purely	O
amplify	O
the	O
AF	B-structure_element
‐	I-structure_element
2	I-structure_element
activities	O
of	O
ligands	O
in	O
cluster	O
1	O
.	O

In	O
contrast	O
,	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
was	O
a	O
determinant	O
of	O
signaling	O
specificity	O
for	O
scaffolds	O
in	O
cluster	O
2	O
.	O

Deletion	B-experimental_method
of	I-experimental_method
the	O
AB	B-structure_element
or	O
F	B-structure_element
domain	O
altered	O
correlations	O
for	O
six	O
of	O
the	O
eight	O
scaffolds	O
in	O
this	O
cluster	O
(	O
2	B-chemical
,	I-chemical
5	I-chemical
‐	I-chemical
DTP	I-chemical
,	O
3	B-chemical
,	I-chemical
4	I-chemical
‐	I-chemical
DTP	I-chemical
,	O
S	B-chemical
‐	I-chemical
OBHS	I-chemical
‐	I-chemical
3	I-chemical
,	O
WAY	B-chemical
‐	I-chemical
D	I-chemical
,	O
WAY	B-chemical
dimer	I-chemical
,	O
and	O
cyclofenil	B-chemical
‐	I-chemical
ASC	I-chemical
)	O
(	O
Fig	O
3D	O
lanes	O
5	O
–	O
12	O
).	O

Comparing	O
Fig	O
3C	O
and	O
D	O
,	O
the	O
+	O
and	O
−	O
signs	O
indicate	O
where	O
the	O
deletion	B-experimental_method
mutant	I-experimental_method
assays	I-experimental_method
led	O
to	O
a	O
gain	O
or	O
loss	O
of	O
statically	O
significant	O
correlation	O
,	O
respectively	O
.	O

Thus	O
,	O
in	O
cluster	O
2	O
,	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
substantially	O
modulated	O
the	O
specificity	O
of	O
ligands	O
with	O
cell	O
‐	O
specific	O
activity	O
(	O
Fig	O
3D	O
lanes	O
5	O
–	O
12	O
).	O

For	O
ligands	O
in	O
cluster	O
3	O
,	O
we	O
could	O
not	O
eliminate	O
a	O
role	O
for	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
in	O
determining	O
signaling	O
specificity	O
,	O
since	O
this	O
cluster	O
lacked	O
positively	O
correlated	O
activity	O
profiles	O
(	O
Fig	O
3C	O
),	O
and	O
deletion	B-experimental_method
of	I-experimental_method
the	O
AB	B-structure_element
or	O
F	B-structure_element
domain	O
rarely	O
induced	O
such	O
correlations	O
(	O
Fig	O
3D	O
),	O
except	O
for	O
A	B-chemical
‐	I-chemical
CD	I-chemical
and	O
OBHS	B-chemical
‐	I-chemical
ASC	I-chemical
analogs	O
,	O
where	O
deletion	B-experimental_method
of	I-experimental_method
the	O
AB	B-structure_element
domain	O
or	O
F	B-structure_element
domain	O
led	O
to	O
positive	O
correlations	O
with	O
E	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
activity	O
and	O
/	O
or	O
GREB1	B-protein
levels	O
(	O
Fig	O
3D	O
lanes	O
13	O
and	O
18	O
).	O

Thus	O
,	O
ligands	O
in	O
cluster	O
2	O
rely	O
on	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
for	O
both	O
activity	O
(	O
Fig	O
3B	O
)	O
and	O
signaling	O
specificity	O
(	O
Fig	O
3D	O
).	O

Ligand	O
‐	O
specific	O
control	O
of	O
GREB1	B-protein
expression	O

To	O
determine	O
whether	O
ligand	O
classes	O
control	O
expression	O
of	O
native	O
ERα	B-protein
target	O
genes	O
through	O
the	O
canonical	O
linear	O
signaling	O
pathway	O
,	O
we	O
performed	O
pairwise	B-experimental_method
linear	I-experimental_method
regression	I-experimental_method
analyses	I-experimental_method
using	O
ERα	B-complex_assembly
–	I-complex_assembly
NCOA1	I-complex_assembly
/	I-complex_assembly
2	I-complex_assembly
/	I-complex_assembly
3	I-complex_assembly
interactions	O
in	O
M2H	B-experimental_method
assay	I-experimental_method
as	O
independent	O
predictors	O
of	O
GREB1	B-protein
expression	O
(	O
the	O
dependent	O
variable	O
)	O
(	O
Figs	O
EV1	O
and	O
EV2A	O
,	O
F	O
–	O
H	O
).	O

In	O
cluster	O
1	O
,	O
the	O
recruitment	O
of	O
NCOA1	B-protein
and	O
NCOA2	B-protein
was	O
highest	O
for	O
WAY	B-chemical
‐	I-chemical
C	I-chemical
,	O
followed	O
by	O
triaryl	B-chemical
‐	I-chemical
ethylene	I-chemical
,	O
OBHS	B-chemical
‐	I-chemical
N	I-chemical
,	O
and	O
OBHS	B-chemical
series	O
,	O
while	O
for	O
NCOA3	B-protein
,	O
OBHS	B-chemical
‐	I-chemical
N	I-chemical
compounds	O
induced	O
the	O
most	O
recruitment	O
and	O
OBHS	B-chemical
ligands	O
were	O
inverse	O
agonists	O
(	O
Fig	O
EV2F	O
–	O
H	O
).	O

The	O
average	O
induction	O
of	O
GREB1	B-protein
by	O
cluster	O
1	O
ligands	O
showed	O
greater	O
variance	O
,	O
with	O
a	O
range	O
between	O
~	O
25	O
and	O
~	O
75	O
%	O
for	O
OBHS	B-chemical
and	O
a	O
range	O
from	O
full	O
agonist	O
to	O
inverse	O
agonist	O
for	O
the	O
others	O
in	O
cluster	O
1	O
(	O
Fig	O
EV2A	O
).	O

GREB1	B-protein
levels	O
induced	O
by	O
OBHS	B-chemical
analogs	O
were	O
determined	O
by	O
recruitment	O
of	O
NCOA1	B-protein
but	O
not	O
NCOA2	B-protein
/	I-protein
3	I-protein
(	O
Fig	O
3E	O
lane	O
1	O
),	O
suggesting	O
that	O
there	O
may	O
be	O
alternate	O
or	O
preferential	O
use	O
of	O
these	O
coactivators	O
by	O
different	O
classes	O
.	O

However	O
,	O
in	O
cluster	O
1	O
,	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
recruitment	O
generally	O
predicted	O
GREB1	B-protein
levels	O
(	O
Fig	O
3E	O
lanes	O
1	O
–	O
4	O
),	O
consistent	O
with	O
the	O
canonical	O
signaling	O
model	O
(	O
Fig	O
1D	O
).	O

For	O
clusters	O
2	O
and	O
3	O
,	O
GREB1	B-protein
activity	O
was	O
generally	O
not	O
predicted	O
by	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
recruitment	O
.	O

Direct	O
modulators	O
showed	O
low	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
recruitment	O
(	O
Fig	O
EV2F	O
–	O
H	O
),	O
but	O
only	O
OBHS	B-chemical
‐	I-chemical
ASC	I-chemical
analogs	O
had	O
NCOA2	B-protein
recruitment	O
profiles	O
that	O
predicted	O
a	O
full	O
range	O
of	O
effects	O
on	O
GREB1	B-protein
levels	O
(	O
Figs	O
3E	O
lanes	O
9	O
,	O
11	O
,	O
18	O
–	O
19	O
,	O
and	O
EV2A	O
).	O

The	O
indirect	O
modulators	O
in	O
clusters	O
2	O
and	O
3	O
stimulated	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
recruitment	O
and	O
GREB1	B-protein
expression	O
with	O
substantial	O
variance	O
(	O
Figs	O
3A	O
and	O
EV2F	O
–	O
H	O
).	O

However	O
,	O
ligand	O
‐	O
induced	O
GREB1	B-protein
levels	O
were	O
generally	O
not	O
determined	O
by	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
recruitment	O
(	O
Fig	O
3E	O
lanes	O
5	O
–	O
19	O
),	O
consistent	O
with	O
an	O
alternate	O
causality	O
model	O
(	O
Fig	O
1E	O
).	O

Out	O
of	O
11	O
indirect	O
modulator	O
series	O
in	O
cluster	O
2	O
or	O
3	O
,	O
only	O
the	O
S	B-chemical
‐	I-chemical
OBHS	I-chemical
‐	I-chemical
3	I-chemical
class	O
had	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
recruitment	O
profiles	O
that	O
predicted	O
GREB1	B-protein
levels	O
(	O
Fig	O
3E	O
lane	O
12	O
).	O

These	O
results	O
suggest	O
that	O
compounds	O
that	O
show	O
cell	O
‐	O
specific	O
signaling	O
do	O
not	O
activate	O
GREB1	B-protein
,	O
or	O
use	O
coactivators	O
other	O
than	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
to	O
control	O
GREB1	B-protein
expression	O
(	O
Fig	O
1E	O
).	O

To	O
determine	O
mechanisms	O
for	O
ligand	O
‐	O
dependent	O
control	O
of	O
breast	O
cancer	O
cell	O
proliferation	O
,	O
we	O
performed	O
linear	B-experimental_method
regression	I-experimental_method
analyses	I-experimental_method
across	O
the	O
19	O
scaffolds	O
using	O
MCF	O
‐	O
7	O
cell	O
proliferation	O
as	O
the	O
dependent	O
variable	O
,	O
and	O
the	O
other	O
activities	O
as	O
independent	O
variables	O
(	O
Fig	O
3F	O
).	O

In	O
cluster	O
1	O
,	O
E	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
and	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
activities	O
,	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
recruitment	O
,	O
and	O
GREB1	B-protein
levels	O
generally	O
predicted	O
the	O
proliferative	O
response	O
(	O
Fig	O
3F	O
lanes	O
2	O
–	O
4	O
).	O

With	O
the	O
OBHS	B-chemical
‐	I-chemical
N	I-chemical
compounds	O
,	O
NCOA3	B-protein
and	O
GREB1	B-protein
showed	O
near	O
perfect	O
prediction	O
of	O
proliferation	O
(	O
Fig	O
EV3G	O
),	O
with	O
unexplained	O
variance	O
similar	O
to	O
the	O
noise	O
in	O
the	O
assays	O
.	O

The	O
lack	O
of	O
significant	O
predictors	O
for	O
OBHS	B-chemical
analogs	O
(	O
Fig	O
3F	O
lane	O
1	O
)	O
reflects	O
their	O
small	O
range	O
of	O
proliferative	O
effects	O
on	O
MCF	O
‐	O
7	O
cells	O
(	O
Fig	O
EV2I	O
).	O

The	O
significant	O
correlations	O
with	O
GREB1	B-protein
expression	O
and	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
recruitment	O
observed	O
in	O
this	O
cluster	O
are	O
consistent	O
with	O
the	O
canonical	O
signaling	O
model	O
(	O
Fig	O
1D	O
),	O
where	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
recruitment	O
determines	O
GREB1	B-protein
expression	O
,	O
which	O
then	O
drives	O
proliferation	O
.	O

Despite	O
this	O
phenotypic	O
variance	O
,	O
proliferation	O
was	O
not	O
generally	O
predicted	O
by	O
correlated	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
recruitment	O
and	O
GREB1	B-protein
induction	O
(	O
Figs	O
3F	O
lanes	O
5	O
–	O
19	O
,	O
and	O
EV3H	O
).	O

Out	O
of	O
15	O
ligand	O
series	O
in	O
these	O
clusters	O
,	O
only	O
2	B-chemical
,	I-chemical
5	I-chemical
‐	I-chemical
DTP	I-chemical
analogs	O
induced	O
a	O
proliferative	O
response	O
that	O
was	O
predicted	O
by	O
GREB1	B-protein
levels	O
,	O
which	O
were	O
not	O
determined	O
by	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
recruitment	O
(	O
Fig	O
3E	O
and	O
F	O
lane	O
10	O
).	O

3	B-chemical
,	I-chemical
4	I-chemical
‐	I-chemical
DTP	I-chemical
,	O
cyclofenil	B-chemical
,	O
3	B-chemical
,	I-chemical
4	I-chemical
‐	I-chemical
DTPD	I-chemical
,	O
and	O
imidazopyridine	B-chemical
analogs	O
had	O
NCOA1	B-protein
/	I-protein
3	I-protein
recruitment	O
profiles	O
that	O
predicted	O
their	O
proliferative	O
effects	O
,	O
without	O
determining	O
GREB1	B-protein
levels	O
(	O
Fig	O
3E	O
and	O
F	O
,	O
lanes	O
5	O
and	O
14	O
–	O
16	O
).	O

Similarly	O
,	O
S	B-chemical
‐	I-chemical
OBHS	I-chemical
‐	I-chemical
3	I-chemical
,	O
cyclofenil	B-chemical
‐	I-chemical
ASC	I-chemical
,	O
and	O
OBHS	B-chemical
‐	I-chemical
ASC	I-chemical
had	O
positively	O
correlated	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
recruitment	O
and	O
GREB1	B-protein
levels	O
,	O
but	O
none	O
of	O
these	O
activities	O
determined	O
their	O
proliferative	O
effects	O
(	O
Fig	O
3E	O
and	O
F	O
lanes	O
11	O
–	O
12	O
and	O
18	O
).	O

For	O
ligands	O
that	O
show	O
cell	O
‐	O
specific	O
signaling	O
,	O
ERα	B-protein
‐	O
mediated	O
recruitment	O
of	O
other	O
coregulators	O
and	O
activation	O
of	O
other	O
target	O
genes	O
likely	O
determine	O
their	O
proliferative	O
effects	O
on	O
MCF	O
‐	O
7	O
cells	O
.	O

NCOA3	B-protein
occupancy	O
at	O
GREB1	B-protein
did	O
not	O
predict	O
the	O
proliferative	O
response	O

We	O
also	O
questioned	O
whether	O
promoter	O
occupancy	O
by	O
coactivators	O
is	O
statistically	O
robust	O
and	O
reproducible	O
for	O
ligand	O
class	O
analysis	O
using	O
a	O
chromatin	B-experimental_method
immunoprecipitation	I-experimental_method
(	I-experimental_method
ChIP	I-experimental_method
)‐	I-experimental_method
based	I-experimental_method
quantitative	I-experimental_method
assay	I-experimental_method
,	I-experimental_method
and	O
whether	O
it	O
has	O
a	O
better	O
predictive	O
power	O
than	O
the	O
M2H	B-experimental_method
assay	I-experimental_method
.	O

ERα	B-protein
and	O
NCOA3	B-protein
cycle	O
on	O
and	O
off	O
the	O
GREB1	B-protein
promoter	O
(	O
Nwachukwu	O
et	O
al	O
,	O
2014	O
).	O

Therefore	O
,	O
we	O
first	O
performed	O
a	O
time	B-experimental_method
‐	I-experimental_method
course	I-experimental_method
study	I-experimental_method
,	O
and	O
found	O
that	O
E2	B-chemical
and	O
the	O
WAY	B-chemical
‐	I-chemical
C	I-chemical
analog	O
,	O
AAPII	B-chemical
‐	I-chemical
151	I-chemical
‐	I-chemical
4	I-chemical
,	O
induced	O
recruitment	O
of	O
NCOA3	B-protein
to	O
the	O
GREB1	B-protein
promoter	O
in	O
a	O
temporal	O
cycle	O
that	O
peaked	O
after	O
45	O
min	O
in	O
MCF	O
‐	O
7	O
cells	O
(	O
Fig	O
4A	O
).	O

At	O
this	O
time	O
point	O
,	O
other	O
WAY	B-chemical
‐	I-chemical
C	I-chemical
analogs	O
also	O
induced	O
recruitment	O
of	O
NCOA3	B-protein
at	O
this	O
site	O
to	O
varying	O
degrees	O
(	O
Fig	O
4B	O
).	O

The	O
Z	B-evidence
’	I-evidence
for	O
this	O
assay	O
was	O
0	O
.	O
6	O
,	O
showing	O
statistical	O
robustness	O
(	O
see	O
Materials	O
and	O
Methods	O
).	O

We	O
prepared	O
biological	O
replicates	O
with	O
different	O
cell	O
passage	O
numbers	O
and	O
separately	O
prepared	O
samples	O
,	O
which	O
showed	O
r	B-evidence
2	I-evidence
of	O
0	O
.	O
81	O
,	O
demonstrating	O
high	O
reproducibility	O
(	O
Fig	O
4C	O
).	O

NCOA3	B-protein
occupancy	O
at	O
GREB1	B-protein
is	O
statistically	O
robust	O
but	O
does	O
not	O
predict	O
transcriptional	O
activity	O

Kinetic	B-experimental_method
ChIP	I-experimental_method
assay	I-experimental_method
examining	O
recruitment	O
of	O
NCOA3	B-protein
to	O
the	O
GREB1	B-protein
gene	O
in	O
MCF	O
‐	O
7	O
cells	O
stimulated	O
with	O
E2	B-chemical
or	O
the	O
indicated	O
WAY	B-chemical
‐	I-chemical
C	I-chemical
analog	O
.	O

NCOA3	B-protein
occupancy	O
at	O
GREB1	B-protein
was	O
compared	O
by	O
ChIP	B-experimental_method
assay	I-experimental_method
45	O
min	O
after	O
stimulation	O
with	O
vehicle	O
,	O
E2	B-chemical
,	O
or	O
the	O
WAY	B-chemical
‐	I-chemical
C	I-chemical
analogs	O
.	O

In	O
panel	O
(	O
B	O
),	O
the	O
average	O
recruitment	O
of	O
two	O
biological	O
replicates	O
are	O
shown	O
as	O
mean	O
+	O
SEM	O
,	O
and	O
the	O
Z	B-evidence
‐	I-evidence
score	I-evidence
is	O
indicated	O
.	O

In	O
panel	O
(	O
C	O
),	O
correlation	B-experimental_method
analysis	I-experimental_method
was	O
performed	O
for	O
two	O
biological	O
replicates	O
.	O

Linear	B-experimental_method
regression	I-experimental_method
analyses	I-experimental_method
comparing	O
the	O
ability	O
of	O
NCOA3	B-protein
recruitment	O
,	O
measured	O
by	O
ChIP	B-experimental_method
or	O
M2H	B-experimental_method
,	O
to	O
predict	O
other	O
agonist	O
activities	O
of	O
WAY	B-chemical
‐	I-chemical
C	I-chemical
analogs	O
.	O
*	O
Significant	O
positive	O
correlation	O
(	O
F	B-experimental_method
‐	I-experimental_method
test	I-experimental_method
for	O
nonzero	O
slope	O
,	O
P	B-evidence
‐	I-evidence
value	I-evidence
).	O

The	O
M2H	B-experimental_method
assay	I-experimental_method
for	O
NCOA3	B-protein
recruitment	O
broadly	O
correlated	O
with	O
the	O
other	O
assays	O
,	O
and	O
was	O
predictive	O
for	O
GREB1	B-protein
expression	O
and	O
cell	O
proliferation	O
(	O
Fig	O
3E	O
).	O

However	O
,	O
the	O
ChIP	B-experimental_method
assays	I-experimental_method
for	O
WAY	B-chemical
‐	I-chemical
C	I-chemical
‐	O
induced	O
recruitment	O
of	O
NCOA3	B-protein
to	O
the	O
GREB1	B-protein
promoter	O
did	O
not	O
correlate	O
with	O
any	O
of	O
the	O
other	O
WAY	B-chemical
‐	I-chemical
C	I-chemical
activity	O
profiles	O
(	O
Fig	O
4D	O
),	O
although	O
the	O
positive	O
correlation	O
between	O
ChIP	B-experimental_method
assays	I-experimental_method
and	O
NCOA3	B-protein
recruitment	O
via	O
M2H	B-experimental_method
assay	I-experimental_method
showed	O
a	O
trend	O
toward	O
significance	O
with	O
r	B-evidence
2	I-evidence
=	O
0	O
.	O
36	O
and	O
P	B-evidence
=	O
0	O
.	O
09	O
(	O
F	B-experimental_method
‐	I-experimental_method
test	I-experimental_method
for	O
nonzero	O
slope	O
).	O

Thus	O
,	O
the	O
simplified	O
coactivator	B-experimental_method
‐	I-experimental_method
binding	I-experimental_method
assay	I-experimental_method
showed	O
much	O
greater	O
predictive	O
power	O
than	O
the	O
ChIP	B-experimental_method
assay	I-experimental_method
for	O
ligand	O
‐	O
specific	O
effects	O
on	O
GREB1	B-protein
expression	O
and	O
cell	O
proliferation	O
.	O

ERβ	B-protein
activity	O
is	O
not	O
an	O
independent	O
predictor	O
of	O
cell	O
‐	O
specific	O
activity	O

One	O
difference	O
between	O
MCF	O
‐	O
7	O
breast	O
cancer	O
cells	O
and	O
Ishikawa	O
endometrial	O
cancer	O
cells	O
is	O
the	O
contribution	O
of	O
ERβ	B-protein
to	O
estrogenic	O
response	O
,	O
as	O
Ishikawa	O
cells	O
may	O
express	O
ERβ	B-protein
(	O
Bhat	O
&	O
Pezzuto	O
,	O
2001	O
).	O

When	O
overexpressed	B-experimental_method
in	O
MCF	O
‐	O
7	O
cells	O
,	O
ERβ	B-protein
alters	O
E2	B-chemical
‐	O
induced	O
expression	O
of	O
only	O
a	O
subset	O
of	O
ERα	B-protein
‐	O
target	O
genes	O
(	O
Wu	O
et	O
al	O
,	O
2011	O
),	O
raising	O
the	O
possibility	O
that	O
ligand	O
‐	O
induced	O
ERβ	B-protein
activity	O
may	O
contribute	O
to	O
E	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
activities	O
,	O
and	O
thus	O
underlie	O
the	O
lack	O
of	O
correlation	O
between	O
the	O
E	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
and	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
ERα	B-protein
‐	O
WT	B-protein_state
activities	O
or	O
GREB1	B-protein
levels	O
induced	O
by	O
cell	O
‐	O
specific	O
modulators	O
in	O
cluster	O
2	O
and	O
cluster	O
3	O
(	O
Fig	O
3C	O
).	O

To	O
test	O
this	O
idea	O
,	O
we	O
determined	O
the	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
ERβ	O
activity	O
profiles	O
of	O
the	O
ligands	O
(	O
Fig	O
EV1	O
).	O

All	O
direct	O
modulator	O
and	O
two	O
indirect	O
modulator	O
scaffolds	O
(	O
OBHS	B-chemical
and	O
S	B-chemical
‐	I-chemical
OBHS	I-chemical
‐	I-chemical
3	I-chemical
)	O
lacked	O
ERβ	O
agonist	O
activity	O
.	O

For	O
most	O
scaffolds	O
,	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
ERβ	O
and	O
E	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
activities	O
were	O
not	O
correlated	O
,	O
except	O
for	O
2	B-chemical
,	I-chemical
5	I-chemical
‐	I-chemical
DTP	I-chemical
and	O
cyclofenil	B-chemical
analogs	O
,	O
which	O
showed	O
moderate	O
but	O
significant	O
correlations	O
(	O
Fig	O
EV4A	O
).	O

Nevertheless	O
,	O
the	O
E	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
activities	O
of	O
both	O
2	B-chemical
,	I-chemical
5	I-chemical
‐	I-chemical
DTP	I-chemical
and	O
cyclofenil	B-chemical
analogs	O
were	O
better	O
predicted	O
by	O
their	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
ERα	B-protein
‐	O
WT	B-protein_state
than	O
L	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
ERβ	B-protein
activities	O
(	O
Fig	O
EV4A	O
and	O
B	O
).	O

ERβ	B-protein
activity	O
is	O
not	O
an	O
independent	O
predictor	O
of	O
E	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
activity	O

ERβ	B-protein
activity	O
in	O
HepG2	O
cells	O
rarely	O
correlates	O
with	O
E	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
activity	O
.	O

ERα	B-protein
activity	O
of	O
2	B-chemical
,	I-chemical
5	I-chemical
‐	I-chemical
DTP	I-chemical
and	O
cyclofenil	B-chemical
analogs	O
correlates	O
with	O
E	B-experimental_method
‐	I-experimental_method
Luc	I-experimental_method
activity	O
.	O

Data	O
information	O
:	O
The	O
r	O
2	O
and	O
P	B-evidence
values	I-evidence
for	O
the	O
indicated	O
correlations	O
are	O
shown	O
in	O
both	O
panels	O
.	O
*	O
Significant	O
positive	O
correlation	O
(	O
F	B-experimental_method
‐	I-experimental_method
test	I-experimental_method
for	O
nonzero	O
slope	O
,	O
P	B-evidence
‐	I-evidence
value	I-evidence
)	O

To	O
overcome	O
barriers	O
to	O
crystallization	B-experimental_method
of	O
ERα	B-protein
LBD	B-structure_element
complexes	O
,	O
we	O
developed	O
a	O
conformation	B-experimental_method
‐	I-experimental_method
trapping	I-experimental_method
X	I-experimental_method
‐	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
approach	O
using	O
the	O
ERα	B-mutant
‐	I-mutant
Y537S	I-mutant
mutation	O
(	O
Nettles	O
et	O
al	O
,	O
2008	O
;	O
Bruning	O
et	O
al	O
,	O
2010	O
;	O
Srinivasan	O
et	O
al	O
,	O
2013	O
).	O

To	O
further	O
validate	O
this	O
approach	O
,	O
we	O
solved	B-experimental_method
the	O
structure	B-evidence
of	O
the	O
ERα	B-mutant
‐	I-mutant
Y537S	I-mutant
LBD	B-structure_element
in	B-protein_state
complex	I-protein_state
with	I-protein_state
diethylstilbestrol	B-chemical
(	O
DES	B-chemical
),	O
which	O
bound	O
identically	O
in	O
the	O
wild	B-protein_state
‐	I-protein_state
type	I-protein_state
and	O
ERα	B-mutant
‐	I-mutant
Y537S	I-mutant
LBDs	B-structure_element
,	O
demonstrating	O
again	O
that	O
this	O
surface	O
mutation	O
stabilizes	O
h12	B-structure_element
dynamics	O
to	O
facilitate	O
crystallization	O
without	O
changing	O
ligand	O
binding	O
(	O
Appendix	O
Fig	O
S1A	O
and	O
B	O
)	O
(	O
Nettles	O
et	O
al	O
,	O
2008	O
;	O
Bruning	O
et	O
al	O
,	O
2010	O
;	O
Delfosse	O
et	O
al	O
,	O
2012	O
).	O

Using	O
this	O
approach	O
,	O
we	O
solved	B-experimental_method
76	O
ERα	B-protein
LBD	B-structure_element
structures	B-evidence
in	O
the	O
active	B-protein_state
conformation	I-protein_state
and	O
bound	B-protein_state
to	I-protein_state
ligands	I-protein_state
studied	O
here	O
(	O
Appendix	O
Fig	O
S1C	O
).	O

Eleven	O
of	O
these	O
structures	B-evidence
have	O
been	O
published	O
,	O
while	O
65	O
are	O
new	O
,	O
including	O
the	O
DES	B-protein_state
‐	I-protein_state
bound	I-protein_state
ERα	B-mutant
‐	I-mutant
Y537S	I-mutant
LBD	B-structure_element
.	O

We	O
present	O
57	O
of	O
these	O
new	O
structures	B-evidence
here	O
(	O
Dataset	O
EV2	O
),	O
while	O
the	O
remaining	O
eight	O
new	O
structures	B-evidence
bound	B-protein_state
to	I-protein_state
OBHS	B-chemical
‐	I-chemical
N	I-chemical
analogs	O
will	O
be	O
published	O
elsewhere	O
(	O
S	O
.	O
Srinivasan	O
et	O
al	O
,	O
in	O
preparation	O
).	O

Examining	O
many	O
closely	O
related	O
structures	B-evidence
allows	O
us	O
to	O
visualize	O
subtle	O
structural	O
differences	O
,	O
in	O
effect	O
using	O
X	B-experimental_method
‐	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
as	O
a	O
systems	O
biology	O
tool	O
.	O

The	O
indirect	O
modulator	O
scaffolds	O
in	O
cluster	O
1	O
did	O
not	O
show	O
cell	O
‐	O
specific	O
signaling	O
(	O
Fig	O
3C	O
),	O
but	O
shared	O
common	O
structural	O
perturbations	O
that	O
we	O
designed	O
to	O
modulate	O
h12	B-structure_element
dynamics	O
.	O

Based	O
on	O
our	O
original	O
OBHS	B-chemical
structure	B-evidence
,	O
the	O
OBHS	B-chemical
,	O
OBHS	B-chemical
‐	I-chemical
N	I-chemical
,	O
and	O
triaryl	B-chemical
‐	I-chemical
ethylene	I-chemical
compounds	O
were	O
modified	O
with	O
h11	B-structure_element
‐	O
directed	O
pendant	O
groups	O
(	O
Zheng	O
et	O
al	O
,	O
2012	O
;	O
Zhu	O
et	O
al	O
,	O
2012	O
;	O
Liao	O
et	O
al	O
,	O
2014	O
).	O

Superposing	B-experimental_method
the	O
LBDs	B-structure_element
based	O
on	O
the	O
class	O
of	O
bound	O
ligands	O
provides	O
an	O
ensemble	O
view	O
of	O
the	O
structural	O
variance	O
and	O
clarifies	O
what	O
part	O
of	O
the	O
ligand	B-site
‐	I-site
binding	I-site
pocket	I-site
is	O
differentially	O
perturbed	O
or	O
targeted	O
.	O

The	O
24	O
structures	B-evidence
containing	O
OBHS	B-chemical
,	O
OBHS	B-chemical
‐	I-chemical
N	I-chemical
,	O
or	O
triaryl	B-chemical
‐	I-chemical
ethylene	I-chemical
analogs	O
showed	O
structural	O
diversity	O
in	O
the	O
same	O
part	O
of	O
the	O
scaffolds	O
(	O
Figs	O
5A	O
and	O
EV5A	O
),	O
and	O
the	O
same	O
region	O
of	O
the	O
LBD	B-structure_element
—	O
the	O
C	O
‐	O
terminal	O
end	O
of	O
h11	B-structure_element
(	O
Figs	O
5B	O
and	O
C	O
,	O
and	O
EV5B	O
),	O
which	O
in	O
turn	O
nudges	O
h12	B-structure_element
(	O
Fig	O
5C	O
and	O
D	O
).	O

We	O
observed	O
that	O
the	O
OBHS	B-chemical
‐	I-chemical
N	I-chemical
analogs	O
displaced	O
h11	B-structure_element
along	O
a	O
vector	O
away	O
from	O
Leu354	B-residue_name_number
in	O
a	O
region	O
of	O
h3	B-structure_element
that	O
is	O
unaffected	O
by	O
the	O
ligands	O
,	O
and	O
toward	O
the	O
dimer	B-site
interface	I-site
.	O

For	O
the	O
triaryl	B-chemical
‐	I-chemical
ethylene	I-chemical
analogs	O
,	O
the	O
displacement	O
of	O
h11	B-structure_element
was	O
in	O
a	O
perpendicular	O
direction	O
,	O
away	O
from	O
Ile424	B-residue_name_number
in	O
h8	B-structure_element
and	O
toward	O
h12	B-structure_element
.	O

Remarkably	O
,	O
these	O
individual	O
inter	B-evidence
‐	I-evidence
atomic	I-evidence
distances	I-evidence
showed	O
a	O
ligand	O
class	O
‐	O
specific	O
ability	O
to	O
significantly	O
predict	O
proliferative	O
effects	O
(	O
Fig	O
5E	O
and	O
F	O
),	O
demonstrating	O
the	O
feasibility	O
of	O
developing	O
a	O
minimal	O
set	O
of	O
activity	O
predictors	O
from	O
crystal	B-evidence
structures	I-evidence
.	O

Structure	B-experimental_method
‐	I-experimental_method
class	I-experimental_method
analysis	I-experimental_method
of	O
triaryl	B-chemical
‐	I-chemical
ethylene	I-chemical
analogs	O
.	O

Triaryl	B-chemical
‐	I-chemical
ethylene	I-chemical
analogs	O
bound	B-protein_state
to	I-protein_state
the	O
superposed	B-experimental_method
crystal	B-evidence
structures	I-evidence
of	O
the	O
ERα	B-protein
LBD	B-structure_element
are	O
shown	O
.	O

Arrows	O
indicate	O
chemical	O
variance	O
in	O
the	O
orientation	O
of	O
the	O
different	O
h11	B-structure_element
‐	O
directed	O
ligand	O
side	O
groups	O
(	O
PDB	O
5DK9	O
,	O
5DKB	O
,	O
5DKE	O
,	O
5DKG	O
,	O
5DKS	O
,	O
5DL4	O
,	O
5DLR	O
,	O
5DMC	O
,	O
5DMF	O
and	O
5DP0	O
).	O

Triaryl	B-chemical
‐	I-chemical
ethylene	I-chemical
analogs	O
induce	O
variance	O
of	O
ERα	B-protein
conformations	O
at	O
the	O
C	O
‐	O
terminal	O
region	O
of	O
h11	B-structure_element
.	O

Panel	O
(	O
B	O
)	O
shows	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
a	O
triaryl	B-chemical
‐	I-chemical
ethylene	I-chemical
analog	O
‐	O
bound	O
ERα	B-protein
LBD	B-structure_element
(	O
PDB	O
5DLR	O
).	O

The	O
h11	B-site
–	I-site
h12	I-site
interface	I-site
(	O
circled	O
)	O
includes	O
the	O
C	O
‐	O
terminal	O
part	O
of	O
h11	B-structure_element
.	O

This	O
region	O
was	O
expanded	O
in	O
panel	O
(	O
C	O
),	O
where	O
the	O
10	O
triaryl	B-chemical
‐	I-chemical
ethylene	I-chemical
analog	O
‐	O
bound	O
ERα	B-protein
LBD	B-structure_element
structures	B-evidence
(	O
see	O
Datasets	O
EV1	O
and	O
EV2	O
)	O
were	O
superposed	B-experimental_method
to	O
show	O
variations	O
in	O
the	O
h11	B-structure_element
C	O
‐	O
terminus	O
(	O
PDB	O
5DK9	O
,	O
5DKB	O
,	O
5DKE	O
,	O
5DKG	O
,	O
5DKS	O
,	O
5DL4	O
,	O
5DLR	O
,	O
5DMC	O
,	O
5DMF	O
,	O
and	O
5DP0	O
).	O

ERα	B-protein
LBDs	B-structure_element
in	B-protein_state
complex	I-protein_state
with	I-protein_state
diethylstilbestrol	B-chemical
(	O
DES	B-chemical
)	O
or	O
a	O
triaryl	B-chemical
‐	I-chemical
ethylene	I-chemical
analog	O
were	O
superposed	B-experimental_method
to	O
show	O
that	O
the	O
ligand	O
‐	O
induced	O
difference	O
in	O
h11	B-structure_element
conformation	O
is	O
transmitted	O
to	O
the	O
C	O
‐	O
terminus	O
of	O
h12	B-structure_element
(	O
PDB	O
4ZN7	O
,	O
5DMC	O
).	O

Inter	B-evidence
‐	I-evidence
atomic	I-evidence
distances	I-evidence
predict	O
the	O
proliferative	O
effects	O
of	O
specific	O
ligand	O
series	O
.	O

Ile424	B-residue_name_number
–	O
His524	B-residue_name_number
distance	B-evidence
measured	O
in	O
the	O
crystal	B-evidence
structures	I-evidence
correlates	O
with	O
the	O
proliferative	O
effect	O
of	O
triaryl	B-chemical
‐	I-chemical
ethylene	I-chemical
analogs	O
in	O
MCF	O
‐	O
7	O
cells	O
.	O

In	O
contrast	O
,	O
the	O
Leu354	B-residue_name_number
–	O
Leu525	B-residue_name_number
distance	B-evidence
correlates	O
with	O
the	O
proliferative	O
effects	O
of	O
OBHS	B-chemical
‐	I-chemical
N	I-chemical
analogs	O
in	O
MCF	O
‐	O
7	O
cells	O
.	O

Structure	B-experimental_method
‐	I-experimental_method
class	I-experimental_method
analysis	I-experimental_method
of	O
WAY	B-chemical
‐	I-chemical
C	I-chemical
analogs	O
.	O

WAY	B-chemical
‐	I-chemical
C	I-chemical
side	O
groups	O
subtly	O
nudge	O
h12	B-structure_element
Leu540	B-residue_name_number
.	O

ERα	B-protein
LBD	B-structure_element
structures	B-evidence
bound	B-protein_state
to	I-protein_state
4	O
distinct	O
WAY	B-chemical
‐	I-chemical
C	I-chemical
analogs	O
were	O
superposed	B-experimental_method
(	O
PDB	O
4	O
IU7	O
,	O
4IV4	O
,	O
4IVW	O
,	O
4IW6	O
)	O
(	O
see	O
Datasets	O
EV1	O
and	O
EV2	O
).	O

Structure	B-experimental_method
‐	I-experimental_method
class	I-experimental_method
analysis	I-experimental_method
of	O
indirect	O
modulators	O

Structure	B-experimental_method
‐	I-experimental_method
class	I-experimental_method
analysis	I-experimental_method
of	O
indirect	O
modulators	O
in	O
cluster	O
1	O
.	O

Crystal	B-evidence
structures	I-evidence
of	O
the	O
ERα	B-protein
LBD	B-structure_element
bound	B-protein_state
to	I-protein_state
OBHS	B-chemical
and	O
OBHS	B-chemical
‐	I-chemical
N	I-chemical
analogs	O
were	O
superposed	B-experimental_method
.	O

Arrows	O
indicate	O
chemical	O
variance	O
in	O
the	O
orientation	O
of	O
the	O
different	O
h11	B-structure_element
‐	O
directed	O
ligand	O
side	O
groups	O
.	O

Panel	O
(	O
B	O
)	O
shows	O
the	O
ligand	O
‐	O
induced	O
conformational	O
variation	O
at	O
the	O
C	O
‐	O
terminal	O
region	O
of	O
h11	B-structure_element
(	O
OBHS	B-chemical
:	O
PDB	O
4ZN9	O
,	O
4ZNH	O
,	O
4ZNS	O
,	O
4ZNT	O
,	O
4ZNU	O
,	O
4ZNV	O
,	O
and	O
4ZNW	O
;	O
OBHS	B-chemical
‐	I-chemical
N	I-chemical
:	O
PDB	O
4ZUB	O
,	O
4ZUC	O
,	O
4ZWH	O
,	O
4ZWK	O
,	O
5BNU	O
,	O
5BP6	O
,	O
5BPR	O
,	O
and	O
5BQ4	O
).	O

Structure	B-experimental_method
‐	I-experimental_method
class	I-experimental_method
analysis	I-experimental_method
of	O
indirect	O
modulators	O
in	O
clusters	O
2	O
and	O
3	O
.	O

Crystal	B-evidence
structures	I-evidence
of	O
the	O
ERα	B-protein
LBD	B-structure_element
bound	B-protein_state
to	I-protein_state
ligands	O
with	O
cell	O
‐	O
specific	O
activities	O
were	O
superposed	B-experimental_method
.	O

The	O
bound	O
ligands	O
are	O
shown	O
,	O
and	O
arrows	O
indicate	O
considerable	O
variation	O
in	O
the	O
orientation	O
of	O
the	O
different	O
h3	B-structure_element
‐,	O
h8	B-structure_element
‐,	O
h11	B-structure_element
‐,	O
or	O
h12	B-structure_element
‐	O
directed	O
ligand	O
side	O
groups	O
.	O

As	O
visualized	O
in	O
four	O
LBD	B-structure_element
structures	B-evidence
(	O
Srinivasan	O
et	O
al	O
,	O
2013	O
),	O
WAY	B-chemical
‐	I-chemical
C	I-chemical
analogs	O
were	O
designed	O
with	O
small	O
substitutions	O
that	O
slightly	O
nudge	O
h12	B-structure_element
Leu540	B-residue_name_number
,	O
without	O
exiting	O
the	O
ligand	B-site
‐	I-site
binding	I-site
pocket	I-site
(	O
Fig	O
5G	O
and	O
H	O
).	O

Therefore	O
,	O
changing	O
h12	B-structure_element
dynamics	O
maintains	O
the	O
canonical	O
signaling	O
pathway	O
defined	O
by	O
E2	B-chemical
(	O
Fig	O
1D	O
)	O
to	O
support	O
AF	B-structure_element
‐	I-structure_element
2	I-structure_element
‐	O
driven	O
signaling	O
and	O
recruit	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
for	O
GREB1	B-protein
‐	O
stimulated	O
proliferation	O
.	O

Ligands	O
with	O
cell	O
‐	O
specific	O
activity	O
alter	O
the	O
shape	O
of	O
the	O
AF	B-site
‐	I-site
2	I-site
surface	I-site

Direct	O
modulators	O
like	O
tamoxifen	B-chemical
drive	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
‐	O
dependent	O
cell	O
‐	O
specific	O
activity	O
by	O
completely	O
occluding	O
AF	B-structure_element
‐	I-structure_element
2	I-structure_element
,	O
but	O
it	O
is	O
not	O
known	O
how	O
indirect	O
modulators	O
produce	O
cell	O
‐	O
specific	O
ERα	B-protein
activity	O
.	O

Therefore	O
,	O
we	O
examined	O
another	O
50	O
LBD	B-structure_element
structures	B-evidence
containing	O
ligands	O
in	O
clusters	O
2	O
and	O
3	O
.	O

These	O
structures	B-evidence
demonstrated	O
that	O
cell	O
‐	O
specific	O
activity	O
derived	O
from	O
altering	O
the	O
shape	O
of	O
the	O
AF	B-site
‐	I-site
2	I-site
surface	I-site
without	O
an	O
extended	O
side	O
chain	O
.	O

Ligands	O
in	O
cluster	O
2	O
and	O
cluster	O
3	O
showed	O
conformational	O
heterogeneity	O
in	O
parts	O
of	O
the	O
scaffold	O
that	O
were	O
directed	O
toward	O
multiple	O
regions	O
of	O
the	O
receptor	O
including	O
h3	B-structure_element
,	O
h8	B-structure_element
,	O
h11	B-structure_element
,	O
h12	B-structure_element
,	O
and	O
/	O
or	O
the	O
β	B-structure_element
‐	I-structure_element
sheets	I-structure_element
(	O
Fig	O
EV5C	O
–	O
G	O
).	O

For	O
instance	O
,	O
S	B-chemical
‐	I-chemical
OBHS	I-chemical
‐	I-chemical
2	I-chemical
and	O
S	B-chemical
‐	I-chemical
OBHS	I-chemical
‐	I-chemical
3	I-chemical
analogs	O
(	O
Fig	O
2	O
)	O
had	O
similar	O
ERα	B-protein
activity	O
profiles	O
in	O
the	O
different	O
cell	O
types	O
(	O
Fig	O
EV2A	O
–	O
C	O
),	O
but	O
the	O
2	O
‐	O
versus	O
3	O
‐	O
methyl	O
substituted	O
phenol	O
rings	O
altered	O
the	O
correlated	O
signaling	O
patterns	O
in	O
different	O
cell	O
types	O
(	O
Fig	O
3B	O
lanes	O
7	O
and	O
12	O
).	O

This	O
difference	O
in	O
ligand	O
positioning	O
altered	O
the	O
AF	B-site
‐	I-site
2	I-site
surface	I-site
via	O
a	O
shift	O
in	O
the	O
N	O
‐	O
terminus	O
of	O
h12	B-structure_element
,	O
which	O
directly	O
contacts	O
the	O
coactivator	O
.	O

This	O
effect	O
is	O
evident	O
in	O
a	O
single	O
structure	B-evidence
due	O
to	O
its	O
1	O
Å	O
magnitude	O
(	O
Fig	O
6A	O
and	O
B	O
).	O

The	O
shifts	O
in	O
h12	B-structure_element
residues	O
Asp538	B-residue_name_number
and	O
Leu539	B-residue_name_number
led	O
to	O
rotation	O
of	O
the	O
coactivator	O
peptide	O
(	O
Fig	O
6C	O
).	O

Thus	O
,	O
cell	O
‐	O
specific	O
activity	O
can	O
stem	O
from	O
perturbation	O
of	O
the	O
AF	B-site
‐	I-site
2	I-site
surface	I-site
without	O
an	O
extended	O
side	O
chain	O
,	O
which	O
presumably	O
alters	O
the	O
receptor	O
–	O
coregulator	O
interaction	O
profile	O
.	O

S	B-chemical
‐	I-chemical
OBHS	I-chemical
‐	I-chemical
2	I-chemical
/	I-chemical
3	I-chemical
analogs	O
subtly	O
distort	O
the	O
AF	B-site
‐	I-site
2	I-site
surface	I-site
.	O

Panel	O
(	O
A	O
)	O
shows	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
an	O
S	B-protein_state
‐	I-protein_state
OBHS	I-protein_state
‐	I-protein_state
3	I-protein_state
‐	I-protein_state
bound	I-protein_state
ERα	B-protein
LBD	B-structure_element
(	O
PDB	O
5DUH	O
).	O

The	O
h3	B-site
–	I-site
h12	I-site
interface	I-site
(	O
circled	O
)	O
at	O
AF	B-structure_element
‐	I-structure_element
2	I-structure_element
(	O
pink	O
)	O
was	O
expanded	O
in	O
panels	O
(	O
B	O
,	O
C	O
).	O

The	O
S	B-protein_state
‐	I-protein_state
OBHS	I-protein_state
‐	I-protein_state
2	I-protein_state
/	I-protein_state
3	I-protein_state
‐	I-protein_state
bound	I-protein_state
ERα	B-protein
LBDs	B-structure_element
were	O
superposed	B-experimental_method
to	O
show	O
shifts	O
in	O
h3	B-structure_element
(	O
panel	O
B	O
)	O
and	O
the	O
NCOA2	B-protein
peptide	O
docked	O
at	O
the	O
AF	B-site
‐	I-site
2	I-site
surface	I-site
(	O
panel	O
C	O
).	O

Crystal	B-evidence
structures	I-evidence
show	O
that	O
2	B-chemical
,	I-chemical
5	I-chemical
‐	I-chemical
DTP	I-chemical
analogs	O
shift	O
h3	B-structure_element
and	O
h11	B-structure_element
further	O
apart	O
compared	O
to	O
an	O
A	O
‐	O
CD	O
‐	O
ring	O
estrogen	B-chemical
(	O
PDB	O
4PPS	O
,	O
5DRM	O
,	O
5DRJ	O
).	O

The	O
2F	O
o	O
‐	O
F	O
c	O
electron	O
density	O
map	O
and	O
F	O
o	O
‐	O
F	O
c	O
difference	O
map	O
of	O
a	O
2	B-protein_state
,	I-protein_state
5	I-protein_state
‐	I-protein_state
DTP	I-protein_state
‐	I-protein_state
bound	I-protein_state
structure	B-evidence
(	O
PDB	O
5DRJ	O
)	O
were	O
contoured	O
at	O
1	O
.	O
0	O
sigma	O
and	O
±	O
3	O
.	O
0	O
sigma	O
,	O
respectively	O
.	O

Average	O
(	O
mean	O
+	O
SEM	O
)	O
α	B-evidence
‐	I-evidence
carbon	I-evidence
distance	I-evidence
measured	O
from	O
h3	B-structure_element
Thr347	B-residue_name_number
to	O
h11	B-structure_element
Leu525	B-residue_name_number
of	O
A	B-protein_state
‐	I-protein_state
CD	I-protein_state
‐,	I-protein_state
2	I-protein_state
,	I-protein_state
5	I-protein_state
‐	I-protein_state
DTP	I-protein_state
‐,	I-protein_state
and	I-protein_state
3	I-protein_state
,	I-protein_state
4	I-protein_state
‐	I-protein_state
DTPD	I-protein_state
‐	I-protein_state
bound	I-protein_state
ERα	B-protein
LBDs	B-structure_element
.	O

*	O
Two	O
‐	O
tailed	O
Student	B-experimental_method
'	I-experimental_method
s	I-experimental_method
t	I-experimental_method
‐	I-experimental_method
test	I-experimental_method
,	O
P	B-evidence
=	O
0	O
.	O
002	O
(	O
PDB	O
A	B-chemical
‐	I-chemical
CD	I-chemical
:	O
5DI7	O
,	O
5DID	O
,	O
5DIE	O
,	O
5DIG	O
,	O
and	O
4PPS	O
;	O
2	B-chemical
,	I-chemical
5	I-chemical
‐	I-chemical
DTP	I-chemical
:	O
4IWC	O
,	O
5DRM	O
,	O
and	O
5DRJ	O
;	O
3	B-chemical
,	I-chemical
4	I-chemical
‐	I-chemical
DTPD	I-chemical
:	O
5DTV	O
and	O
5DU5	O
).	O

Crystal	B-evidence
structures	I-evidence
show	O
that	O
a	O
3	B-chemical
,	I-chemical
4	I-chemical
‐	I-chemical
DTPD	I-chemical
analog	O
shifts	O
h3	B-structure_element
(	O
F	B-structure_element
)	O
and	O
the	O
NCOA2	B-protein
(	O
G	O
)	O
peptide	O
compared	O
to	O
an	O
A	B-chemical
‐	I-chemical
CD	I-chemical
‐	O
ring	O
estrogen	B-chemical
(	O
PDB	O
4PPS	O
,	O
5DTV	O
).	O

Hierarchical	B-experimental_method
clustering	I-experimental_method
of	O
ligand	O
‐	O
specific	O
binding	O
of	O
154	O
interacting	O
peptides	O
to	O
the	O
ERα	B-protein
LBD	B-structure_element
was	O
performed	O
in	O
triplicate	O
by	O
MARCoNI	B-experimental_method
analysis	I-experimental_method
.	O

The	O
2	B-chemical
,	I-chemical
5	I-chemical
‐	I-chemical
DTP	I-chemical
analogs	O
showed	O
perturbation	O
of	O
h11	B-structure_element
,	O
as	O
well	O
as	O
h3	B-structure_element
,	O
which	O
forms	O
part	O
of	O
the	O
AF	B-site
‐	I-site
2	I-site
surface	I-site
.	O

These	O
compounds	O
bind	O
the	O
LBD	B-structure_element
in	O
an	O
unusual	O
fashion	O
because	O
they	O
have	O
a	O
phenol	O
‐	O
to	O
‐	O
phenol	O
length	O
of	O
~	O
12	O
Å	O
,	O
which	O
is	O
longer	O
than	O
steroids	O
and	O
other	O
prototypical	O
ERα	B-protein
agonists	O
that	O
are	O
~	O
10	O
Å	O
in	O
length	O
.	O

One	O
phenol	O
pushed	O
further	O
toward	O
h3	B-structure_element
(	O
Fig	O
6D	O
),	O
while	O
the	O
other	O
phenol	O
pushed	O
toward	O
the	O
C	O
‐	O
terminus	O
of	O
h11	B-structure_element
to	O
a	O
greater	O
extent	O
than	O
A	B-chemical
‐	I-chemical
CD	I-chemical
‐	O
ring	O
estrogens	B-chemical
(	O
Nwachukwu	O
et	O
al	O
,	O
2014	O
),	O
which	O
are	O
close	O
structural	O
analogs	O
of	O
E2	B-chemical
that	O
lack	O
a	O
B	O
‐	O
ring	O
(	O
Fig	O
2	O
).	O

To	O
quantify	O
this	O
difference	O
,	O
we	O
compared	O
the	O
distance	B-evidence
between	O
α	O
‐	O
carbons	O
at	O
h3	B-structure_element
Thr347	B-residue_name_number
and	O
h11	B-structure_element
Leu525	B-residue_name_number
in	O
the	O
set	O
of	O
structures	B-evidence
containing	O
2	B-chemical
,	I-chemical
5	I-chemical
‐	I-chemical
DTP	I-chemical
analogs	O
(	O
n	O
=	O
3	O
)	O
or	O
A	B-chemical
‐	I-chemical
CD	I-chemical
‐	O
ring	O
analogs	O
(	O
n	O
=	O
5	O
)	O
(	O
Fig	O
6E	O
).	O

We	O
observed	O
a	O
difference	O
of	O
0	O
.	O
4	O
Å	O
that	O
was	O
significant	O
(	O
two	O
‐	O
tailed	O
Student	B-experimental_method
'	I-experimental_method
s	I-experimental_method
t	I-experimental_method
‐	I-experimental_method
test	I-experimental_method
,	O
P	B-evidence
=	O
0	O
.	O
002	O
)	O
due	O
to	O
the	O
very	O
tight	O
clustering	O
of	O
the	O
2	B-chemical
,	I-chemical
5	I-chemical
‐	I-chemical
DTP	I-chemical
‐	O
induced	O
LBD	B-structure_element
conformation	O
.	O

The	O
shifts	O
in	O
h3	B-structure_element
suggest	O
these	O
compounds	O
are	O
positioned	O
to	O
alter	O
coregulator	O
preferences	O
.	O

The	O
2	B-chemical
,	I-chemical
5	I-chemical
‐	I-chemical
DTP	I-chemical
and	O
3	B-chemical
,	I-chemical
4	I-chemical
‐	I-chemical
DTP	I-chemical
scaffolds	O
are	O
isomeric	O
,	O
but	O
with	O
aryl	O
groups	O
at	O
obtuse	O
and	O
acute	O
angles	O
,	O
respectively	O
(	O
Fig	O
2	O
).	O

The	O
crystal	B-evidence
structure	I-evidence
of	O
ERα	B-protein
in	B-protein_state
complex	I-protein_state
with	I-protein_state
a	O
3	B-chemical
,	I-chemical
4	I-chemical
‐	I-chemical
DTP	I-chemical
is	O
unknown	O
;	O
however	O
,	O
we	O
solved	B-experimental_method
two	O
crystal	B-evidence
structures	I-evidence
of	O
ERα	B-protein
bound	B-protein_state
to	I-protein_state
3	B-chemical
,	I-chemical
4	I-chemical
‐	I-chemical
DTPD	I-chemical
analogs	O
and	O
one	O
structure	B-evidence
containing	O
a	O
furan	B-chemical
ligand	O
—	O
all	O
of	O
which	O
have	O
a	O
3	O
,	O
4	O
‐	O
diaryl	O
configuration	O
(	O
Fig	O
2	O
;	O
Datasets	O
EV1	O
and	O
EV2	O
).	O

In	O
these	O
structures	B-evidence
,	O
the	O
A	O
‐	O
ring	O
mimetic	O
of	O
the	O
3	B-chemical
,	I-chemical
4	I-chemical
‐	I-chemical
DTPD	I-chemical
scaffold	O
bound	O
h3	B-structure_element
Glu353	B-residue_name_number
as	O
expected	O
,	O
but	O
the	O
other	O
phenol	O
wrapped	O
around	O
h3	B-structure_element
to	O
form	O
a	O
hydrogen	O
bond	O
with	O
Thr347	B-residue_name_number
,	O
indicating	O
a	O
change	O
in	O
binding	O
epitopes	O
in	O
the	O
ERα	B-protein
ligand	B-site
‐	I-site
binding	I-site
pocket	I-site
(	O
Fig	O
6F	O
).	O

The	O
3	B-chemical
,	I-chemical
4	I-chemical
‐	I-chemical
DTPD	I-chemical
analogs	O
also	O
induced	O
a	O
shift	O
in	O
h3	B-structure_element
positioning	O
,	O
which	O
translated	O
again	O
into	O
a	O
shift	O
in	O
the	O
bound	O
coactivator	O
peptide	O
(	O
Fig	O
6F	O
).	O

Therefore	O
,	O
these	O
indirect	O
modulators	O
,	O
including	O
S	B-chemical
‐	I-chemical
OBHS	I-chemical
‐	I-chemical
2	I-chemical
,	O
S	B-chemical
‐	I-chemical
OBHS	I-chemical
‐	I-chemical
3	I-chemical
,	O
2	B-chemical
,	I-chemical
5	I-chemical
‐	I-chemical
DTP	I-chemical
,	O
and	O
3	B-chemical
,	I-chemical
4	I-chemical
‐	I-chemical
DTPD	I-chemical
analogs	O
—	O
all	O
of	O
which	O
show	O
cell	O
‐	O
specific	O
activity	O
profiles	O
—	O
induced	O
shifts	O
in	O
h3	B-structure_element
and	O
h12	B-structure_element
that	O
were	O
transmitted	O
to	O
the	O
coactivator	O
peptide	O
via	O
an	O
altered	O
AF	B-site
‐	I-site
2	I-site
surface	I-site
.	O

To	O
test	O
whether	O
the	O
AF	B-site
‐	I-site
2	I-site
surface	I-site
shows	O
changes	O
in	O
shape	O
in	O
solution	O
,	O
we	O
used	O
the	O
microarray	B-experimental_method
assay	I-experimental_method
for	I-experimental_method
real	I-experimental_method
‐	I-experimental_method
time	I-experimental_method
coregulator	I-experimental_method
–	I-experimental_method
nuclear	I-experimental_method
receptor	I-experimental_method
interaction	I-experimental_method
(	O
MARCoNI	B-experimental_method
)	O
analysis	O
(	O
Aarts	O
et	O
al	O
,	O
2013	O
).	O

Here	O
,	O
the	O
ligand	O
‐	O
dependent	O
interactions	O
of	O
the	O
ERα	B-protein
LBD	B-structure_element
with	O
over	O
150	O
distinct	O
LxxLL	B-structure_element
motif	I-structure_element
peptides	O
were	O
assayed	O
to	O
define	O
structural	O
fingerprints	O
for	O
the	O
AF	B-site
‐	I-site
2	I-site
surface	I-site
,	O
in	O
a	O
manner	O
similar	O
to	O
the	O
use	O
of	O
phage	B-experimental_method
display	I-experimental_method
peptides	I-experimental_method
as	O
structural	O
probes	O
(	O
Connor	O
et	O
al	O
,	O
2001	O
).	O

Despite	O
the	O
similar	O
average	O
activities	O
of	O
these	O
ligand	O
classes	O
(	O
Fig	O
3A	O
and	O
B	O
),	O
2	B-chemical
,	I-chemical
5	I-chemical
‐	I-chemical
DTP	I-chemical
and	O
3	B-chemical
,	I-chemical
4	I-chemical
‐	I-chemical
DTP	I-chemical
analogs	O
displayed	O
remarkably	O
different	O
peptide	O
recruitment	O
patterns	O
(	O
Fig	O
6H	O
),	O
consistent	O
with	O
the	O
structural	B-experimental_method
analyses	I-experimental_method
.	O

Hierarchical	B-experimental_method
clustering	I-experimental_method
revealed	O
that	O
many	O
of	O
the	O
2	B-chemical
,	I-chemical
5	I-chemical
‐	I-chemical
DTP	I-chemical
analogs	O
recapitulated	O
most	O
of	O
the	O
peptide	O
recruitment	O
and	O
dismissal	O
patterns	O
observed	O
with	O
E2	B-chemical
(	O
Fig	O
6H	O
).	O

However	O
,	O
there	O
was	O
a	O
unique	O
cluster	O
of	O
peptides	O
that	O
were	O
recruited	O
by	O
E2	B-chemical
but	O
not	O
the	O
2	B-chemical
,	I-chemical
5	I-chemical
‐	I-chemical
DTP	I-chemical
analogs	O
.	O

In	O
contrast	O
,	O
3	B-chemical
,	I-chemical
4	I-chemical
‐	I-chemical
DTP	I-chemical
analogs	O
dismissed	O
most	O
of	O
the	O
peptides	O
from	O
the	O
AF	B-site
‐	I-site
2	I-site
surface	I-site
(	O
Fig	O
6H	O
).	O

Thus	O
,	O
the	O
isomeric	O
attachment	O
of	O
diaryl	O
groups	O
to	O
the	O
thiophene	B-chemical
core	O
changed	O
the	O
AF	B-site
‐	I-site
2	I-site
surface	I-site
from	O
inside	O
the	O
ligand	B-site
‐	I-site
binding	I-site
pocket	I-site
,	O
as	O
predicted	O
by	O
the	O
crystal	B-evidence
structures	I-evidence
.	O

Together	O
,	O
these	O
findings	O
suggest	O
that	O
without	O
an	O
extended	O
side	O
chain	O
,	O
cell	O
‐	O
specific	O
activity	O
stems	O
from	O
different	O
coregulator	O
recruitment	O
profiles	O
,	O
due	O
to	O
unique	O
ligand	O
‐	O
induced	O
conformations	O
of	O
the	O
AF	B-site
‐	I-site
2	I-site
surface	I-site
,	O
in	O
addition	O
to	O
differential	O
usage	O
of	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
.	O

Indirect	O
modulators	O
in	O
cluster	O
1	O
avoid	O
this	O
by	O
perturbing	O
the	O
h11	B-site
–	I-site
h12	I-site
interface	I-site
,	O
and	O
modulating	O
the	O
dynamics	O
of	O
h12	B-structure_element
without	O
changing	O
the	O
shape	O
of	O
AF	B-structure_element
‐	I-structure_element
2	I-structure_element
when	O
stabilized	O
.	O

Our	O
goal	O
was	O
to	O
identify	O
a	O
minimal	O
set	O
of	O
predictors	O
that	O
would	O
link	O
specific	O
structural	O
perturbations	O
to	O
ERα	B-protein
signaling	O
pathways	O
that	O
control	O
cell	O
‐	O
specific	O
signaling	O
and	O
proliferation	O
.	O

We	O
found	O
a	O
very	O
strong	O
set	O
of	O
predictors	O
,	O
where	O
ligands	O
in	O
cluster	O
1	O
,	O
defined	O
by	O
similar	O
signaling	O
across	O
cell	O
types	O
,	O
showed	O
indirect	O
modulation	O
of	O
h12	B-structure_element
dynamics	O
via	O
the	O
h11	B-site
–	I-site
12	I-site
interface	I-site
or	O
slight	O
contact	O
with	O
h12	B-structure_element
.	O

This	O
perturbation	O
determined	O
proliferation	O
that	O
correlated	O
strongly	O
with	O
AF	B-structure_element
‐	I-structure_element
2	I-structure_element
activity	O
,	O
recruitment	O
of	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
family	O
members	O
,	O
and	O
induction	O
of	O
the	O
GREB1	B-protein
gene	O
,	O
consistent	O
with	O
the	O
canonical	O
ERα	B-protein
signaling	O
pathway	O
(	O
Fig	O
1D	O
).	O

For	O
ligands	O
in	O
cluster	O
1	O
,	O
deletion	B-experimental_method
of	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
reduced	O
activity	O
to	O
varying	O
degrees	O
,	O
but	O
did	O
not	O
change	O
the	O
underlying	O
signaling	O
patterns	O
established	O
through	O
AF	B-structure_element
‐	I-structure_element
2	I-structure_element
.	O

In	O
contrast	O
,	O
an	O
extended	O
side	O
chain	O
designed	O
to	O
directly	O
reposition	O
h12	B-structure_element
and	O
completely	O
disrupt	O
the	O
AF	B-site
‐	I-site
2	I-site
surface	I-site
results	O
in	O
cell	O
‐	O
specific	O
signaling	O
.	O

Compared	O
to	O
cluster	O
1	O
,	O
the	O
structural	O
rules	O
are	O
less	O
clear	O
in	O
clusters	O
2	O
and	O
3	O
,	O
but	O
a	O
number	O
of	O
indirect	O
modulator	O
classes	O
perturbed	O
the	O
LBD	B-structure_element
conformation	O
at	O
the	O
intersection	O
of	O
h3	B-structure_element
,	O
the	O
h12	B-structure_element
N	O
‐	O
terminus	O
,	O
and	O
the	O
AF	B-site
‐	I-site
2	I-site
surface	I-site
.	O

Ligands	O
in	O
these	O
classes	O
altered	O
the	O
shape	O
of	O
AF	B-structure_element
‐	I-structure_element
2	I-structure_element
to	O
affect	O
coregulator	O
preferences	O
.	O

For	O
direct	O
and	O
indirect	O
modulators	O
in	O
cluster	O
2	O
or	O
3	O
,	O
the	O
canonical	O
ERα	B-protein
signaling	O
pathway	O
involving	O
recruitment	O
of	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
and	O
induction	O
of	O
GREB1	B-protein
did	O
not	O
generally	O
predict	O
their	O
proliferative	O
effects	O
,	O
indicating	O
an	O
alternate	O
causal	O
model	O
(	O
Fig	O
1E	O
).	O

These	O
principles	O
outlined	O
above	O
provide	O
a	O
structural	O
basis	O
for	O
how	O
the	O
ligand	B-site
–	I-site
receptor	I-site
interface	I-site
leads	O
to	O
different	O
signaling	O
specificities	O
through	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
and	O
AF	B-structure_element
‐	I-structure_element
2	I-structure_element
.	O

It	O
is	O
noteworthy	O
that	O
regulation	O
of	O
h12	B-structure_element
dynamics	O
indirectly	O
through	O
h11	B-structure_element
can	O
virtually	O
abolish	O
AF	B-structure_element
‐	I-structure_element
2	I-structure_element
activity	O
,	O
and	O
yet	O
still	O
drive	O
robust	O
transcriptional	O
activity	O
through	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
,	O
as	O
demonstrated	O
with	O
the	O
OBHS	B-chemical
series	O
.	O

This	O
finding	O
can	O
be	O
explained	O
by	O
the	O
fact	O
that	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
contain	O
distinct	O
binding	B-site
sites	I-site
for	O
interaction	O
with	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
and	O
AF	B-structure_element
‐	I-structure_element
2	I-structure_element
(	O
McInerney	O
et	O
al	O
,	O
1996	O
;	O
Webb	O
et	O
al	O
,	O
1998	O
),	O
which	O
allows	O
ligands	O
to	O
nucleate	O
ERα	B-complex_assembly
–	I-complex_assembly
NCOA1	I-complex_assembly
/	I-complex_assembly
2	I-complex_assembly
/	I-complex_assembly
3	I-complex_assembly
interaction	O
through	O
AF	B-structure_element
‐	I-structure_element
2	I-structure_element
,	O
and	O
reinforce	O
this	O
interaction	O
with	O
additional	O
binding	O
to	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
.	O

Completely	O
blocking	O
AF	B-structure_element
‐	I-structure_element
2	I-structure_element
with	O
an	O
extended	O
side	O
chain	O
or	O
altering	O
the	O
shape	O
of	O
AF	B-structure_element
‐	I-structure_element
2	I-structure_element
changes	O
the	O
preference	O
away	O
from	O
NCOA1	B-protein
/	I-protein
2	I-protein
/	I-protein
3	I-protein
for	O
determining	O
GREB1	B-protein
levels	O
and	O
proliferation	O
of	O
breast	O
cancer	O
cells	O
.	O

AF	B-structure_element
‐	I-structure_element
2	I-structure_element
blockade	O
also	O
allows	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
to	O
function	O
independently	O
,	O
which	O
is	O
important	O
since	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
drives	O
tissue	O
‐	O
selective	O
effects	O
in	O
vivo	O
.	O

This	O
was	O
demonstrated	O
with	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
knockout	O
mice	O
that	O
show	O
E2	B-chemical
‐	O
dependent	O
vascular	O
protection	O
,	O
but	O
not	O
uterine	O
proliferation	O
,	O
thus	O
highlighting	O
the	O
role	O
of	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
in	O
tissue	O
‐	O
selective	O
or	O
cell	O
‐	O
specific	O
signaling	O
(	O
Billon	O
‐	O
Gales	O
et	O
al	O
,	O
2009	O
;	O
Abot	O
et	O
al	O
,	O
2013	O
).	O

Here	O
,	O
we	O
examined	O
many	O
LBD	B-structure_element
structures	B-evidence
and	O
tested	O
several	O
variables	O
that	O
were	O
not	O
predictive	O
,	O
including	O
ERβ	B-protein
activity	O
,	O
the	O
strength	O
of	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
signaling	O
,	O
and	O
NCOA3	B-protein
occupancy	O
at	O
the	O
GREB1	B-protein
gene	O
.	O

Similarly	O
,	O
we	O
visualized	O
structures	B-evidence
to	O
identify	O
patterns	O
.	O

For	O
example	O
,	O
phage	B-experimental_method
display	I-experimental_method
was	O
used	O
to	O
identify	O
the	O
androgen	O
receptor	O
interactome	O
,	O
which	O
was	O
cloned	O
into	O
an	O
M2H	B-experimental_method
library	O
and	O
used	O
to	O
identify	O
clusters	O
of	O
ligand	O
‐	O
selective	O
interactions	O
(	O
Norris	O
et	O
al	O
,	O
2009	O
).	O

Also	O
,	O
we	O
have	O
used	O
siRNA	B-experimental_method
screening	I-experimental_method
to	O
identify	O
a	O
number	O
of	O
coregulators	O
required	O
for	O
ERα	B-protein
‐	O
mediated	O
repression	O
of	O
the	O
IL	O
‐	O
6	O
gene	O
(	O
Nwachukwu	O
et	O
al	O
,	O
2014	O
).	O

If	O
we	O
calculated	O
inter	B-evidence
‐	I-evidence
atomic	I-evidence
distance	I-evidence
matrices	I-evidence
containing	O
4	O
,	O
000	O
atoms	O
per	O
structure	O
×	O
76	O
ligand	O
–	O
receptor	O
complexes	O
,	O
we	O
would	O
have	O
3	O
×	O
105	O
predictions	O
.	O

We	O
have	O
identified	O
atomic	B-evidence
vectors	I-evidence
for	O
the	O
OBHS	B-chemical
‐	I-chemical
N	I-chemical
and	O
triaryl	B-chemical
‐	I-chemical
ethylene	I-chemical
classes	O
that	O
predict	O
ligand	O
response	O
(	O
Fig	O
5E	O
and	O
F	O
).	O

Indeed	O
,	O
the	O
most	O
anti	O
‐	O
proliferative	O
compound	O
in	O
the	O
OBHS	B-chemical
‐	I-chemical
N	I-chemical
series	O
had	O
a	O
fulvestrant	O
‐	O
like	O
profile	O
across	O
a	O
battery	O
of	O
assays	O
(	O
S	O
.	O
Srinivasan	O
et	O
al	O
,	O
in	O
preparation	O
).	O

Secondly	O
,	O
our	O
finding	O
that	O
WAY	B-chemical
‐	I-chemical
C	I-chemical
compounds	O
do	O
not	O
rely	O
of	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
for	O
signaling	O
efficacy	O
may	O
derive	O
from	O
the	O
slight	O
contacts	O
with	O
h12	B-structure_element
observed	O
in	O
crystal	B-evidence
structures	I-evidence
(	O
Figs	O
3B	O
and	O
5H	O
),	O
unlike	O
other	O
compounds	O
in	O
cluster	O
1	O
that	O
dislocate	O
h11	B-structure_element
and	O
rely	O
on	O
AF	B-structure_element
‐	I-structure_element
1	I-structure_element
for	O
signaling	O
efficacy	O
(	O
Figs	O
3B	O
and	O
5C	O
,	O
and	O
EV5B	O
).	O

Some	O
of	O
these	O
ligands	O
altered	O
the	O
shape	O
of	O
the	O
AF	B-site
‐	I-site
2	I-site
surface	I-site
by	O
perturbing	O
the	O
h3	B-site
–	I-site
h12	I-site
interface	I-site
,	O
thus	O
providing	O
a	O
route	O
to	O
new	O
SERM	O
‐	O
like	O
activity	O
profiles	O
by	O
combining	O
indirect	O
and	O
direct	O
modulation	O
of	O
receptor	O
structure	O
.	O

Incorporation	O
of	O
statistical	O
approaches	O
to	O
understand	O
relationships	O
between	O
structure	O
and	O
signaling	O
variables	O
moves	O
us	O
toward	O
predictive	O
models	O
for	O
complex	O
ERα	B-protein
‐	O
mediated	O
responses	O
such	O
as	O
in	O
vivo	O
uterine	O
proliferation	O
or	O
tumor	O
growth	O
,	O
and	O
more	O
generally	O
toward	O
structure	O
‐	O
based	O
design	O
for	O
other	O
allosteric	O
drug	O
targets	O
including	O
GPCRs	B-protein_type
and	O
other	O
nuclear	B-protein_type
receptors	I-protein_type
.	O

Investigation	O
of	O
the	O
Interaction	O
between	O
Cdc42	B-protein
and	O
Its	O
Effector	O
TOCA1	B-protein

Transducer	B-protein
of	I-protein
Cdc42	I-protein
-	I-protein
dependent	I-protein
actin	I-protein
assembly	I-protein
protein	I-protein
1	I-protein
(	O
TOCA1	B-protein
)	O
is	O
an	O
effector	O
of	O
the	O
Rho	B-protein_type
family	I-protein_type
small	I-protein_type
G	I-protein_type
protein	I-protein_type
Cdc42	B-protein
.	O

It	O
contains	O
a	O
membrane	O
-	O
deforming	O
F	B-structure_element
-	I-structure_element
BAR	I-structure_element
domain	O
as	O
well	O
as	O
a	O
Src	B-structure_element
homology	I-structure_element
3	I-structure_element
(	O
SH3	B-structure_element
)	O
domain	O
and	O
a	O
G	B-structure_element
protein	I-structure_element
-	I-structure_element
binding	I-structure_element
homology	I-structure_element
region	I-structure_element
1	I-structure_element
(	O
HR1	B-structure_element
)	O
domain	O
.	O

TOCA1	B-protein
binding	O
to	O
Cdc42	B-protein
leads	O
to	O
actin	O
rearrangements	O
,	O
which	O
are	O
thought	O
to	O
be	O
involved	O
in	O
processes	O
such	O
as	O
endocytosis	O
,	O
filopodia	O
formation	O
,	O
and	O
cell	O
migration	O
.	O

We	O
have	O
solved	B-experimental_method
the	O
structure	B-evidence
of	O
the	O
HR1	B-structure_element
domain	O
of	O
TOCA1	B-protein
,	O
providing	O
the	O
first	O
structural	B-evidence
data	I-evidence
for	O
this	O
protein	O
.	O

We	O
have	O
found	O
that	O
the	O
TOCA1	B-protein
HR1	B-structure_element
,	O
like	O
the	O
closely	O
related	O
CIP4	B-protein
HR1	B-structure_element
,	O
has	O
interesting	O
structural	O
features	O
that	O
are	O
not	O
observed	O
in	O
other	O
HR1	B-structure_element
domains	O
.	O

We	O
have	O
also	O
investigated	O
the	O
binding	O
of	O
the	O
TOCA	B-protein
HR1	B-structure_element
domain	O
to	O
Cdc42	B-protein
and	O
the	O
potential	O
ternary	O
complex	O
between	O
Cdc42	B-protein
and	O
the	O
G	B-site
protein	I-site
-	I-site
binding	I-site
regions	I-site
of	O
TOCA1	B-protein
and	O
a	O
member	O
of	O
the	O
Wiskott	B-protein_type
-	I-protein_type
Aldrich	I-protein_type
syndrome	I-protein_type
protein	I-protein_type
family	I-protein_type
,	O
N	B-protein
-	I-protein
WASP	I-protein
.	O

TOCA1	B-protein
binds	O
Cdc42	B-protein
with	O
micromolar	O
affinity	O
,	O
in	O
contrast	O
to	O
the	O
nanomolar	O
affinity	O
of	O
the	O
N	B-protein
-	I-protein
WASP	I-protein
G	B-site
protein	I-site
-	I-site
binding	I-site
region	I-site
for	O
Cdc42	B-protein
.	O

NMR	B-experimental_method
experiments	O
show	O
that	O
the	O
Cdc42	B-site
-	I-site
binding	I-site
domain	I-site
from	O
N	B-protein
-	I-protein
WASP	I-protein
is	O
able	O
to	O
displace	O
TOCA1	B-protein
HR1	B-structure_element
from	O
Cdc42	B-protein
,	O
whereas	O
the	O
N	B-protein
-	I-protein
WASP	I-protein
domain	O
but	O
not	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
inhibits	O
actin	O
polymerization	O
.	O

This	O
suggests	O
that	O
TOCA1	B-protein
binding	O
to	O
Cdc42	B-protein
is	O
an	O
early	O
step	O
in	O
the	O
Cdc42	B-protein
-	O
dependent	O
pathways	O
that	O
govern	O
actin	O
dynamics	O
,	O
and	O
the	O
differential	O
binding	B-evidence
affinities	I-evidence
of	O
the	O
effectors	O
facilitate	O
a	O
handover	O
from	O
TOCA1	B-protein
to	O
N	B-protein
-	I-protein
WASP	I-protein
,	O
which	O
can	O
then	O
drive	O
recruitment	O
of	O
the	O
actin	O
-	O
modifying	O
machinery	O
.	O

The	O
Ras	B-protein_type
superfamily	I-protein_type
of	O
small	B-protein_type
GTPases	I-protein_type
comprises	O
over	O
150	O
members	O
that	O
regulate	O
a	O
multitude	O
of	O
cellular	O
processes	O
in	O
eukaryotes	B-taxonomy_domain
.	O

The	O
superfamily	O
can	O
be	O
divided	O
into	O
five	O
families	O
based	O
on	O
structural	O
and	O
functional	O
similarities	O
:	O
Ras	B-protein_type
,	O
Rho	B-protein_type
,	O
Rab	B-protein_type
,	O
Arf	B-protein_type
,	O
and	O
Ran	B-protein_type
.	O

All	O
members	O
share	O
a	O
well	O
defined	O
core	O
structure	O
of	O
∼	O
20	O
kDa	O
known	O
as	O
the	O
G	B-structure_element
domain	I-structure_element
,	O
which	O
is	O
responsible	O
for	O
guanine	B-chemical
nucleotide	I-chemical
binding	O
.	O

These	O
molecular	O
switches	O
cycle	O
between	O
active	B-protein_state
,	O
GTP	B-protein_state
-	I-protein_state
bound	I-protein_state
,	O
and	O
inactive	B-protein_state
,	O
GDP	B-protein_state
-	I-protein_state
bound	I-protein_state
,	O
states	O
with	O
the	O
help	O
of	O
auxiliary	O
proteins	O
.	O

The	O
guanine	B-protein_type
nucleotide	I-protein_type
exchange	I-protein_type
factors	I-protein_type
mediate	O
formation	O
of	O
the	O
active	B-protein_state
state	O
by	O
promoting	O
the	O
dissociation	O
of	O
GDP	B-chemical
,	O
allowing	O
GTP	B-chemical
to	O
bind	O
.	O

The	O
GTPase	B-protein_type
-	I-protein_type
activating	I-protein_type
proteins	I-protein_type
stimulate	O
the	O
rate	O
of	O
intrinsic	O
GTP	B-chemical
hydrolysis	O
,	O
mediating	O
the	O
return	O
to	O
the	O
inactive	B-protein_state
state	O
(	O
reviewed	O
in	O
Ref	O
.).	O

The	O
overall	O
conformation	O
of	O
small	B-protein_type
G	I-protein_type
proteins	I-protein_type
in	O
the	O
active	B-protein_state
and	O
inactive	B-protein_state
states	O
is	O
similar	O
,	O
but	O
they	O
differ	O
significantly	O
in	O
two	O
main	O
regions	O
known	O
as	O
switch	B-site
I	I-site
and	O
switch	B-site
II	I-site
.	O

These	O
regions	O
are	O
responsible	O
for	O
“	O
sensing	O
”	O
the	O
nucleotide	O
state	O
,	O
with	O
the	O
GTP	B-protein_state
-	I-protein_state
bound	I-protein_state
state	O
showing	O
greater	O
rigidity	O
and	O
the	O
GDP	B-protein_state
-	I-protein_state
bound	I-protein_state
state	O
adopting	O
a	O
more	O
relaxed	O
conformation	O
(	O
reviewed	O
in	O
Ref	O
.).	O

In	O
the	O
active	B-protein_state
state	O
,	O
G	B-protein_type
proteins	I-protein_type
bind	O
to	O
an	O
array	O
of	O
downstream	O
effectors	O
,	O
through	O
which	O
they	O
exert	O
their	O
extensive	O
roles	O
within	O
the	O
cell	O
.	O

The	O
structures	B-evidence
of	O
more	O
than	O
60	O
small	O
G	B-protein_type
protein	I-protein_type
·	O
effector	O
complexes	O
have	O
been	O
solved	B-experimental_method
,	O
and	O
,	O
not	O
surprisingly	O
,	O
the	O
switch	B-site
regions	I-site
have	O
been	O
implicated	O
in	O
a	O
large	O
proportion	O
of	O
the	O
G	B-protein_type
protein	I-protein_type
-	O
effector	O
interactions	O
(	O
reviewed	O
in	O
Ref	O
.).	O

However	O
,	O
because	O
each	O
of	O
the	O
150	O
members	O
of	O
the	O
superfamily	O
interacts	O
with	O
multiple	O
effectors	O
,	O
there	O
are	O
still	O
a	O
huge	O
number	O
of	O
known	O
G	B-protein_type
protein	I-protein_type
-	O
effector	O
interactions	O
that	O
have	O
not	O
yet	O
been	O
studied	O
structurally	O
.	O

The	O
Rho	B-protein_type
family	I-protein_type
comprises	O
20	O
members	O
,	O
of	O
which	O
three	O
,	O
RhoA	B-protein
,	O
Rac1	B-protein
,	O
and	O
Cdc42	B-protein
,	O
have	O
been	O
relatively	O
well	O
studied	O
.	O

RhoA	B-protein
acts	O
to	O
rearrange	O
existing	O
actin	O
structures	O
to	O
form	O
stress	O
fibers	O
,	O
whereas	O
Rac1	B-protein
and	O
Cdc42	B-protein
promote	O
de	O
novo	O
actin	O
polymerization	O
to	O
form	O
lamellipodia	O
and	O
filopodia	O
,	O
respectively	O
.	O

A	O
number	O
of	O
RhoA	B-protein
and	O
Rac1	B-protein
effector	O
proteins	O
,	O
including	O
the	O
formins	O
and	O
members	O
of	O
the	O
protein	B-protein_type
kinase	I-protein_type
C	I-protein_type
-	I-protein_type
related	I-protein_type
kinase	I-protein_type
(	O
PRK	B-protein_type
)	O
6	B-protein_type
family	O
,	O
along	O
with	O
Cdc42	B-protein
effectors	O
,	O
including	O
the	O
Wiskott	B-protein_type
-	I-protein_type
Aldrich	I-protein_type
syndrome	I-protein_type
(	O
WASP	B-protein_type
)	O
family	O
and	O
the	O
transducer	O
of	O
Cdc42	B-protein_type
-	I-protein_type
dependent	I-protein_type
actin	I-protein_type
assembly	I-protein_type
(	O
TOCA	B-protein_type
)	O
family	O
,	O
have	O
also	O
been	O
linked	O
to	O
the	O
pathways	O
that	O
govern	O
cytoskeletal	O
dynamics	O
.	O

Cdc42	B-protein
effectors	O
,	O
TOCA1	B-protein
and	O
the	O
ubiquitously	O
expressed	O
member	O
of	O
the	O
WASP	B-protein_type
family	I-protein_type
,	O
N	B-protein
-	I-protein
WASP	I-protein
,	O
have	O
been	O
implicated	O
in	O
the	O
regulation	O
of	O
actin	O
polymerization	O
downstream	O
of	O
Cdc42	B-protein
and	O
phosphatidylinositol	B-chemical
4	I-chemical
,	I-chemical
5	I-chemical
-	I-chemical
bisphosphate	I-chemical
(	O
PI	B-chemical
(	I-chemical
4	I-chemical
,	I-chemical
5	I-chemical
)	I-chemical
P2	I-chemical
).	O

N	B-protein
-	I-protein
WASP	I-protein
exists	O
in	O
an	O
autoinhibited	B-protein_state
conformation	I-protein_state
,	O
which	O
is	O
released	O
upon	O
PI	B-chemical
(	I-chemical
4	I-chemical
,	I-chemical
5	I-chemical
)	I-chemical
P2	I-chemical
and	O
Cdc42	B-protein
binding	O
or	O
by	O
other	O
factors	O
,	O
such	O
as	O
phosphorylation	O
.	O

Following	O
their	O
release	O
,	O
the	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
regions	I-structure_element
of	O
N	B-protein
-	I-protein
WASP	I-protein
are	O
free	O
to	O
interact	O
with	O
G	B-protein_type
-	I-protein_type
actin	I-protein_type
and	O
a	O
known	O
nucleator	O
of	O
actin	O
assembly	O
,	O
the	O
Arp2	B-complex_assembly
/	I-complex_assembly
3	I-complex_assembly
complex	O
.	O

The	O
importance	O
of	O
TOCA1	B-protein
in	O
actin	O
polymerization	O
has	O
been	O
demonstrated	O
in	O
a	O
range	O
of	O
in	O
vitro	O
and	O
in	O
vivo	O
studies	O
,	O
but	O
the	O
exact	O
role	O
of	O
TOCA1	B-protein
in	O
the	O
many	O
pathways	O
involving	O
actin	O
assembly	O
remains	O
unclear	O
.	O

The	O
most	O
widely	O
studied	O
role	O
of	O
TOCA1	B-protein
is	O
in	O
membrane	O
invagination	O
and	O
endocytosis	O
,	O
although	O
it	O
has	O
also	O
been	O
implicated	O
in	O
filopodia	O
formation	O
,	O
neurite	O
elongation	O
,	O
transcriptional	O
reprogramming	O
via	O
nuclear	O
actin	O
,	O
and	O
interaction	O
with	O
ZO	B-protein
-	I-protein
1	I-protein
at	O
tight	O
junctions	O
.	O

TOCA1	B-protein
comprises	O
an	O
N	O
-	O
terminal	O
F	B-structure_element
-	I-structure_element
BAR	I-structure_element
domain	O
,	O
a	O
central	B-structure_element
homology	I-structure_element
region	I-structure_element
1	I-structure_element
(	O
HR1	B-structure_element
)	O
domain	O
,	O
and	O
a	O
C	O
-	O
terminal	O
SH3	B-structure_element
domain	O
.	O

The	O
F	B-structure_element
-	I-structure_element
BAR	I-structure_element
domain	O
is	O
a	O
known	O
dimerization	O
,	O
membrane	O
-	O
binding	O
,	O
and	O
membrane	O
-	O
deforming	O
module	O
found	O
in	O
a	O
number	O
of	O
cell	O
signaling	O
proteins	O
.	O

The	O
TOCA1	B-protein
SH3	B-structure_element
domain	O
has	O
many	O
known	O
binding	O
partners	O
,	O
including	O
N	B-protein
-	I-protein
WASP	I-protein
and	O
dynamin	B-protein
.	O

The	O
HR1	B-structure_element
domain	O
has	O
been	O
directly	O
implicated	O
in	O
the	O
interaction	O
between	O
TOCA1	B-protein
and	O
Cdc42	B-protein
,	O
representing	O
the	O
first	O
Cdc42	B-protein
-	O
HR1	B-structure_element
domain	O
interaction	O
to	O
be	O
identified	O
.	O

Other	O
HR1	B-structure_element
domains	O
studied	O
so	O
far	O
,	O
including	O
those	O
from	O
the	O
PRK	B-protein_type
family	I-protein_type
,	O
have	O
been	O
found	O
to	O
bind	O
their	O
cognate	O
Rho	O
family	O
G	B-protein_type
protein	I-protein_type
-	O
binding	O
partner	O
with	O
high	O
specificity	O
and	O
affinities	B-evidence
in	O
the	O
nanomolar	O
range	O
.	O

The	O
structures	B-evidence
of	O
the	O
PRK1	B-protein
HR1a	B-structure_element
domain	O
in	O
complex	B-protein_state
with	I-protein_state
RhoA	B-protein
and	O
the	O
HR1b	B-structure_element
domain	O
in	O
complex	B-protein_state
with	I-protein_state
Rac1	B-protein
show	O
that	O
the	O
HR1	B-structure_element
domain	O
comprises	O
an	O
anti	B-structure_element
-	I-structure_element
parallel	I-structure_element
coiled	I-structure_element
-	I-structure_element
coil	I-structure_element
that	O
interacts	O
with	O
its	O
G	B-protein_type
protein	I-protein_type
binding	O
partner	O
via	O
both	O
helices	B-structure_element
.	O

Both	O
of	O
the	O
G	B-site
protein	I-site
switch	I-site
regions	I-site
are	O
involved	O
in	O
the	O
interaction	O
.	O

The	O
coiled	B-structure_element
-	I-structure_element
coil	I-structure_element
fold	I-structure_element
is	O
shared	O
by	O
the	O
HR1	B-structure_element
domain	O
of	O
the	O
TOCA	B-protein_type
family	I-protein_type
protein	I-protein_type
,	O
CIP4	B-protein
,	O
and	O
,	O
based	O
on	O
sequence	O
homology	O
,	O
by	O
TOCA1	B-protein
itself	O
.	O

These	O
HR1	B-structure_element
domains	O
,	O
however	O
,	O
show	O
specificity	O
for	O
Cdc42	B-protein
,	O
rather	O
than	O
RhoA	B-protein
or	O
Rac1	B-protein
.	O

How	O
different	O
HR1	B-structure_element
domain	O
proteins	O
distinguish	O
their	O
specific	O
G	B-protein_type
protein	I-protein_type
partners	O
remains	O
only	O
partially	O
understood	O
,	O
and	O
structural	O
characterization	O
of	O
a	O
novel	O
G	B-protein_type
protein	I-protein_type
-	O
HR1	B-structure_element
domain	O
interaction	O
would	O
add	O
to	O
the	O
growing	O
body	O
of	O
information	O
pertaining	O
to	O
these	O
protein	O
complexes	O
.	O

Furthermore	O
,	O
the	O
biological	O
function	O
of	O
the	O
interaction	O
between	O
TOCA1	B-protein
and	O
Cdc42	B-protein
remains	O
poorly	O
understood	O
,	O
and	O
so	O
far	O
there	O
has	O
been	O
no	O
biophysical	O
or	O
structural	O
insight	O
.	O

The	O
interactions	O
of	O
TOCA1	B-protein
and	O
N	B-protein
-	I-protein
WASP	I-protein
with	O
Cdc42	B-protein
as	O
well	O
as	O
with	O
each	O
other	O
have	O
raised	O
questions	O
as	O
to	O
whether	O
the	O
two	O
Cdc42	B-protein
effectors	O
can	O
interact	O
with	O
a	O
single	O
molecule	O
of	O
Cdc42	B-protein
simultaneously	O
.	O

There	O
is	O
some	O
evidence	O
for	O
a	O
ternary	O
complex	O
between	O
Cdc42	B-protein
,	O
N	B-protein
-	I-protein
WASP	I-protein
,	O
and	O
TOCA1	B-protein
,	O
but	O
there	O
was	O
no	O
direct	O
demonstration	O
of	O
simultaneous	O
contacts	O
between	O
the	O
two	O
effectors	O
and	O
a	O
single	O
molecule	O
of	O
Cdc42	B-protein
.	O

Nonetheless	O
,	O
the	O
substantial	O
difference	O
between	O
the	O
structures	B-evidence
of	O
the	O
G	B-site
protein	I-site
-	I-site
binding	I-site
regions	I-site
of	O
the	O
two	O
effectors	O
is	O
intriguing	O
and	O
implies	O
that	O
they	O
bind	O
to	O
Cdc42	B-protein
quite	O
differently	O
,	O
providing	O
motivation	O
for	O
investigating	O
the	O
possibility	O
that	O
Cdc42	B-protein
can	O
bind	O
both	O
effectors	O
concurrently	O
.	O

WASP	B-protein_type
interacts	O
with	O
Cdc42	B-protein
via	O
a	O
conserved	B-protein_state
,	O
unstructured	B-structure_element
binding	I-structure_element
motif	I-structure_element
known	O
as	O
the	O
Cdc42	B-structure_element
-	I-structure_element
and	I-structure_element
Rac	I-structure_element
-	I-structure_element
interactive	I-structure_element
binding	I-structure_element
region	I-structure_element
(	O
CRIB	B-structure_element
),	O
which	O
forms	O
an	O
intermolecular	B-structure_element
β	I-structure_element
-	I-structure_element
sheet	I-structure_element
,	O
expanding	O
the	O
anti	O
-	O
parallel	O
β2	B-structure_element
and	I-structure_element
β3	I-structure_element
strands	I-structure_element
of	O
Cdc42	B-protein
.	O

In	O
contrast	O
,	O
the	O
TOCA	B-protein_type
family	I-protein_type
proteins	I-protein_type
are	O
thought	O
to	O
interact	O
via	O
the	O
HR1	B-structure_element
domain	O
,	O
which	O
may	O
form	O
a	O
triple	B-structure_element
coiled	I-structure_element
-	I-structure_element
coil	I-structure_element
with	O
switch	B-site
II	I-site
of	O
Rac1	B-protein
,	O
like	O
the	O
HR1b	B-structure_element
domain	O
of	O
PRK1	B-protein
.	O

Here	O
,	O
we	O
present	O
the	O
solution	B-experimental_method
NMR	I-experimental_method
structure	B-evidence
of	O
the	O
HR1	B-structure_element
domain	O
of	O
TOCA1	B-protein
,	O
providing	O
the	O
first	O
structural	B-evidence
data	I-evidence
for	O
this	O
protein	O
.	O

We	O
also	O
present	O
data	O
pertaining	O
to	O
binding	O
of	O
the	O
TOCA	B-protein_type
HR1	B-structure_element
domain	O
to	O
Cdc42	B-protein
,	O
which	O
is	O
the	O
first	O
biophysical	O
description	O
of	O
an	O
HR1	B-structure_element
domain	O
binding	O
this	O
particular	O
Rho	B-protein_type
family	I-protein_type
small	I-protein_type
G	I-protein_type
protein	I-protein_type
.	O

Finally	O
,	O
we	O
investigate	O
the	O
potential	O
ternary	O
complex	O
between	O
Cdc42	B-protein
and	O
the	O
G	B-site
protein	I-site
-	I-site
binding	I-site
regions	I-site
of	O
TOCA1	B-protein
and	O
N	B-protein
-	I-protein
WASP	I-protein
,	O
contributing	O
to	O
our	O
understanding	O
of	O
G	B-protein_type
protein	I-protein_type
-	O
effector	O
interactions	O
as	O
well	O
as	O
the	O
roles	O
of	O
Cdc42	B-protein
,	O
N	B-protein
-	I-protein
WASP	I-protein
,	O
and	O
TOCA1	B-protein
in	O
the	O
pathways	O
that	O
govern	O
actin	O
dynamics	O
.	O

Cdc42	B-protein
-	O
TOCA1	B-protein
Binding	O

TOCA1	B-protein
was	O
identified	O
in	O
Xenopus	B-taxonomy_domain
extracts	O
as	O
a	O
protein	O
necessary	O
for	O
Cdc42	B-protein
-	O
dependent	O
actin	O
assembly	O
and	O
was	O
shown	O
to	O
bind	O
to	O
Cdc42	B-complex_assembly
·	I-complex_assembly
GTPγS	I-complex_assembly
but	O
not	O
to	O
Cdc42	B-complex_assembly
·	I-complex_assembly
GDP	I-complex_assembly
or	O
to	O
Rac1	B-protein
and	O
RhoA	B-protein
.	O
Given	O
its	O
homology	O
to	O
other	O
Rho	B-site
family	I-site
binding	I-site
modules	I-site
,	O
it	O
is	O
likely	O
that	O
the	O
HR1	B-structure_element
domain	O
of	O
TOCA1	B-protein
is	O
sufficient	O
to	O
bind	O
Cdc42	B-protein
.	O

The	O
C	B-species
.	I-species
elegans	I-species
TOCA1	B-protein
orthologues	O
also	O
bind	O
to	O
Cdc42	B-protein
via	O
their	O
consensus	O
HR1	B-structure_element
domain	O
.	O

The	O
HR1	B-structure_element
domains	O
from	O
the	O
PRK	B-protein_type
family	I-protein_type
bind	O
their	O
G	B-protein_type
protein	I-protein_type
partners	O
with	O
a	O
high	O
affinity	O
,	O
exhibiting	O
a	O
range	O
of	O
submicromolar	O
dissociation	B-evidence
constants	I-evidence
(	O
Kd	B-evidence
)	O
as	O
low	O
as	O
26	O
nm	O
.	O

A	O
Kd	B-evidence
in	O
the	O
nanomolar	O
range	O
was	O
therefore	O
expected	O
for	O
the	O
interaction	O
of	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
with	O
Cdc42	B-protein
.	O

We	O
generated	O
an	O
X	B-species
.	I-species
tropicalis	I-species
TOCA1	B-protein
HR1	B-structure_element
domain	O
construct	O
encompassing	O
residues	O
330	B-residue_range
–	I-residue_range
426	I-residue_range
.	O

This	O
region	O
comprises	O
the	O
complete	O
HR1	B-structure_element
domain	O
based	O
on	O
secondary	O
structure	O
predictions	O
and	O
sequence	B-experimental_method
alignments	I-experimental_method
with	O
another	O
TOCA	B-protein_type
family	I-protein_type
member	O
,	O
CIP4	B-protein
,	O
whose	O
structure	B-evidence
has	O
been	O
determined	O
.	O

The	O
interaction	O
between	O
[	B-complex_assembly
3H	I-complex_assembly
]	I-complex_assembly
GTP	I-complex_assembly
·	I-complex_assembly
Cdc42	I-complex_assembly
and	O
a	O
C	O
-	O
terminally	O
His	B-protein_state
-	I-protein_state
tagged	I-protein_state
TOCA1	B-protein
HR1	B-structure_element
domain	O
construct	O
was	O
investigated	O
using	O
SPA	B-experimental_method
.	O

The	O
binding	B-evidence
isotherm	I-evidence
for	O
the	O
interaction	O
is	O
shown	O
in	O
Fig	O
.	O
1A	O
,	O
together	O
with	O
the	O
Cdc42	B-protein
-	O
PAK	B-protein
interaction	O
as	O
a	O
positive	O
control	O
.	O

The	O
binding	O
of	O
TOCA1	B-protein
HR1	B-structure_element
to	O
Cdc42	B-protein
was	O
unexpectedly	O
weak	O
,	O
with	O
a	O
Kd	B-evidence
of	O
>	O
1	O
μm	O
.	O

It	O
was	O
not	O
possible	O
to	O
estimate	O
the	O
Kd	B-evidence
more	O
accurately	O
using	O
direct	O
SPA	B-experimental_method
experiments	O
,	O
because	O
saturation	O
could	O
not	O
be	O
reached	O
due	O
to	O
nonspecific	O
signal	O
at	O
higher	O
protein	O
concentrations	O
.	O

The	O
TOCA1	B-protein
HR1	B-structure_element
-	O
Cdc42	B-protein
interaction	O
is	O
low	O
affinity	O
.	O

A	O
,	O
curves	O
derived	O
from	O
direct	B-experimental_method
binding	I-experimental_method
assays	I-experimental_method
in	O
which	O
the	O
indicated	O
concentrations	O
of	O
Cdc42Δ7Q61L	B-complex_assembly
·[	I-complex_assembly
3H	I-complex_assembly
]	I-complex_assembly
GTP	I-complex_assembly
were	O
incubated	B-experimental_method
with	O
30	O
nm	O
GST	B-mutant
-	I-mutant
PAK	I-mutant
or	O
HR1	B-mutant
-	I-mutant
His6	I-mutant
in	O
SPAs	B-experimental_method
.	O

The	O
SPA	B-experimental_method
signal	O
was	O
corrected	O
by	O
subtraction	O
of	O
control	O
data	O
with	O
no	O
GST	B-mutant
-	I-mutant
PAK	I-mutant
or	O
HR1	B-mutant
-	I-mutant
His6	I-mutant
.	O

The	O
data	O
were	O
fitted	O
to	O
a	O
binding	B-evidence
isotherm	I-evidence
to	O
give	O
an	O
apparent	O
Kd	B-evidence
and	O
are	O
expressed	O
as	O
a	O
percentage	O
of	O
the	O
maximum	O
signal	O
;	O
B	O
and	O
C	O
,	O
competition	B-experimental_method
SPA	I-experimental_method
experiments	O
were	O
carried	O
out	O
with	O
the	O
indicated	O
concentrations	O
of	O
ACK	B-protein
GBD	B-structure_element
(	O
B	O
)	O
or	O
HR1	B-structure_element
domain	O
(	O
C	O
)	O
titrated	B-experimental_method
into	O
30	O
nm	O
GST	B-mutant
-	I-mutant
ACK	I-mutant
and	O
either	O
30	O
nm	O
Cdc42Δ7Q61L	B-complex_assembly
·[	I-complex_assembly
3H	I-complex_assembly
]	I-complex_assembly
GTP	I-complex_assembly
or	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
Cdc42Q61L	B-complex_assembly
·[	I-complex_assembly
3H	I-complex_assembly
]	I-complex_assembly
GTP	I-complex_assembly
.	O

The	O
Kd	B-evidence
values	O
derived	O
for	O
the	O
ACK	B-protein
GBD	B-structure_element
with	O
Cdc42Δ7	B-mutant
and	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
Cdc42	B-protein
were	O
0	O
.	O
032	O
±	O
0	O
.	O
01	O
and	O
0	O
.	O
011	O
±	O
0	O
.	O
01	O
μm	O
,	O
respectively	O
.	O

The	O
Kd	B-evidence
values	O
derived	O
for	O
the	O
TOCA1	B-protein
HR1	B-structure_element
with	O
Cdc42Δ7	B-mutant
and	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
Cdc42	B-protein
were	O
6	O
.	O
05	O
±	O
1	O
.	O
96	O
and	O
5	O
.	O
39	O
±	O
1	O
.	O
69	O
μm	O
,	O
respectively	O
.	O

It	O
was	O
possible	O
that	O
the	O
low	O
affinity	O
observed	O
was	O
due	O
to	O
negative	O
effects	O
of	O
immobilization	O
of	O
the	O
HR1	B-structure_element
domain	O
,	O
so	O
other	O
methods	O
were	O
employed	O
,	O
which	O
utilized	O
untagged	B-protein_state
proteins	O
.	O

Isothermal	B-experimental_method
titration	I-experimental_method
calorimetry	I-experimental_method
was	O
carried	O
out	O
,	O
but	O
no	O
heat	O
changes	O
were	O
observed	O
at	O
a	O
range	O
of	O
concentrations	O
and	O
temperatures	O
(	O
data	O
not	O
shown	O
),	O
suggesting	O
that	O
the	O
interaction	O
is	O
predominantly	O
entropically	O
driven	O
.	O

Other	O
G	B-protein_type
protein	I-protein_type
-	O
HR1	B-structure_element
domain	O
interactions	O
have	O
also	O
failed	O
to	O
show	O
heat	O
changes	O
in	O
our	O
hands	O
.	O
7	O
Infrared	B-experimental_method
interferometry	I-experimental_method
with	O
immobilized	B-protein_state
Cdc42	B-protein
was	O
also	O
attempted	O
but	O
was	O
unsuccessful	O
for	O
both	O
TOCA1	B-protein
HR1	B-structure_element
and	O
for	O
the	O
positive	O
control	O
,	O
ACK	B-protein
.	O

The	O
affinity	B-evidence
was	O
therefore	O
determined	O
using	O
competition	B-experimental_method
SPAs	I-experimental_method
.	O

A	O
complex	O
of	O
a	O
GST	B-experimental_method
fusion	I-experimental_method
of	O
the	O
GBD	B-structure_element
of	O
ACK	B-protein
,	O
which	O
binds	O
with	O
a	O
high	O
affinity	O
to	O
Cdc42	B-protein
,	O
with	O
radiolabeled	O
[	B-complex_assembly
3H	I-complex_assembly
]	I-complex_assembly
GTP	I-complex_assembly
·	I-complex_assembly
Cdc42	I-complex_assembly
was	O
preformed	O
,	O
and	O
the	O
effect	O
of	O
increasing	B-experimental_method
concentrations	I-experimental_method
of	O
untagged	B-protein_state
TOCA1	B-protein
HR1	B-structure_element
domain	O
was	O
examined	O
.	O

Competition	O
of	O
GST	B-mutant
-	I-mutant
ACK	I-mutant
GBD	B-structure_element
bound	B-protein_state
to	I-protein_state
[	B-complex_assembly
3H	I-complex_assembly
]	I-complex_assembly
GTP	I-complex_assembly
·	I-complex_assembly
Cdc42	I-complex_assembly
by	O
free	B-protein_state
ACK	B-protein
GBD	B-structure_element
was	O
used	O
as	O
a	O
control	O
and	O
to	O
establish	O
the	O
value	O
of	O
background	O
counts	O
when	O
Cdc42	B-protein
is	O
fully	O
displaced	O
.	O

The	O
data	O
were	O
fitted	O
to	O
a	O
binding	B-evidence
isotherm	I-evidence
describing	O
competition	O
.	O

Free	B-protein_state
ACK	B-protein
competed	O
with	O
itself	O
with	O
an	O
affinity	B-evidence
of	O
32	O
nm	O
,	O
similar	O
to	O
the	O
value	O
obtained	O
by	O
direct	B-experimental_method
binding	I-experimental_method
of	O
23	O
nm	O
.	O

The	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
also	O
fully	O
competed	O
with	O
the	O
GST	B-mutant
-	I-mutant
ACK	I-mutant
but	O
bound	B-protein_state
with	O
an	O
affinity	B-evidence
of	O
6	O
μm	O
(	O
Fig	O
.	O
1	O
,	O
B	O
and	O
C	O
),	O
in	O
agreement	O
with	O
the	O
low	O
affinity	B-evidence
observed	O
in	O
the	O
direct	B-experimental_method
binding	I-experimental_method
experiments	I-experimental_method
.	O

The	O
Cdc42	B-protein
construct	O
used	O
in	O
the	O
binding	B-experimental_method
assays	I-experimental_method
has	O
seven	B-residue_range
residues	I-residue_range
deleted	B-experimental_method
from	O
the	O
C	O
terminus	O
to	O
facilitate	O
purification	O
.	O

These	O
residues	O
are	O
not	O
generally	O
required	O
for	O
G	B-protein_type
protein	I-protein_type
-	O
effector	O
interactions	O
,	O
including	O
the	O
interaction	O
between	O
RhoA	B-protein
and	O
the	O
PRK1	B-protein
HR1a	B-structure_element
domain	O
.	O

In	O
contrast	O
,	O
the	O
C	O
terminus	O
of	O
Rac1	B-protein
contains	O
a	O
polybasic	O
sequence	O
,	O
which	O
is	O
crucial	O
for	O
Rac1	B-protein
binding	O
to	O
the	O
HR1b	B-structure_element
domain	O
from	O
PRK1	B-protein
.	O

As	O
the	O
observed	O
affinity	B-evidence
between	O
TOCA1	B-protein
HR1	B-structure_element
and	O
Cdc42	B-protein
was	O
much	O
lower	O
than	O
expected	O
,	O
we	O
reasoned	O
that	O
the	O
C	O
terminus	O
of	O
Cdc42	B-protein
might	O
be	O
necessary	O
for	O
a	O
high	O
affinity	B-evidence
interaction	O
.	O

The	O
binding	B-experimental_method
experiments	I-experimental_method
were	O
repeated	O
with	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
[	B-complex_assembly
3H	I-complex_assembly
]	I-complex_assembly
GTP	I-complex_assembly
·	I-complex_assembly
Cdc42	I-complex_assembly
,	O
but	O
the	O
affinity	B-evidence
of	O
the	O
HR1	B-structure_element
domain	O
for	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
Cdc42	B-protein
was	O
similar	O
to	O
its	O
affinity	B-evidence
for	O
truncated	B-protein_state
Cdc42	B-protein
(	O
Kd	B-evidence
≈	O
5	O
μm	O
;	O
Fig	O
.	O
1C	O
).	O

Thus	O
,	O
the	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
region	I-structure_element
of	O
Cdc42	B-protein
is	O
not	O
required	O
for	O
maximal	O
binding	O
of	O
TOCA1	B-protein
HR1	B-structure_element
.	O

Another	O
possible	O
explanation	O
for	O
the	O
low	O
affinities	B-evidence
observed	O
was	O
that	O
the	O
HR1	B-structure_element
domain	O
alone	B-protein_state
is	O
not	O
sufficient	O
for	O
maximal	O
binding	O
of	O
the	O
TOCA	B-protein_type
proteins	I-protein_type
to	O
Cdc42	B-protein
and	O
that	O
the	O
other	O
domains	O
are	O
required	O
.	O

Indeed	O
,	O
GST	B-experimental_method
pull	I-experimental_method
-	I-experimental_method
downs	I-experimental_method
performed	O
with	O
in	O
vitro	O
translated	O
human	B-species
TOCA1	B-protein
fragments	O
had	O
suggested	O
that	O
residues	O
N	O
-	O
terminal	O
to	O
the	O
HR1	B-structure_element
domain	O
may	O
be	O
required	O
to	O
stabilize	O
the	O
HR1	B-structure_element
domain	O
structure	O
.	O

Furthermore	O
,	O
both	O
BAR	B-structure_element
and	O
SH3	B-structure_element
domains	O
have	O
been	O
implicated	O
in	O
interactions	O
with	O
small	O
G	B-protein_type
proteins	I-protein_type
(	O
e	O
.	O
g	O
.	O
the	O
BAR	B-structure_element
domain	O
of	O
Arfaptin2	B-protein
binds	O
to	O
Rac1	B-protein
and	O
Arl1	B-protein
),	O
while	O
an	O
SH3	B-structure_element
domain	O
mediates	O
the	O
interaction	O
between	O
Rac1	B-protein
and	O
the	O
guanine	B-protein
nucleotide	I-protein
exchange	I-protein
factor	I-protein
,	O
β	B-protein
-	I-protein
PIX	I-protein
.	O

TOCA1	B-protein
dimerizes	B-oligomeric_state
via	O
its	O
F	B-structure_element
-	I-structure_element
BAR	I-structure_element
domain	O
,	O
which	O
could	O
also	O
affect	O
Cdc42	B-protein
binding	O
,	O
for	O
example	O
by	O
presenting	O
two	O
HR1	B-structure_element
domains	O
for	O
Cdc42	B-protein
interactions	O
.	O

Various	O
TOCA1	B-protein
fragments	O
(	O
Fig	O
.	O
2A	O
)	O
were	O
therefore	O
assessed	O
for	O
binding	O
to	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
Cdc42	B-protein
by	O
direct	O
SPA	B-experimental_method
.	O

The	O
isolated	O
F	B-structure_element
-	I-structure_element
BAR	I-structure_element
domain	O
showed	O
no	O
binding	O
to	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
Cdc42	B-protein
(	O
Fig	O
.	O
2B	O
).	O

Full	B-protein_state
-	I-protein_state
length	I-protein_state
TOCA1	B-protein
and	O
ΔSH3	B-mutant
TOCA1	B-protein
bound	B-protein_state
with	O
micromolar	O
affinity	O
(	O
Fig	O
.	O
2B	O
),	O
in	O
a	O
similar	O
manner	O
to	O
the	O
isolated	O
HR1	B-structure_element
domain	O
(	O
Fig	O
.	O
1A	O
).	O

The	O
HR1	B-mutant
-	I-mutant
SH3	I-mutant
protein	O
could	O
not	O
be	O
purified	O
to	O
homogeneity	O
as	O
a	O
fusion	O
protein	O
,	O
so	O
it	O
was	O
assayed	O
in	O
competition	B-experimental_method
assays	I-experimental_method
after	O
cleavage	O
of	O
the	O
His	O
tag	O
.	O

This	O
construct	O
competed	O
with	O
GST	B-mutant
-	I-mutant
ACK	I-mutant
GBD	B-structure_element
to	O
give	O
a	O
similar	O
affinity	O
to	O
the	O
HR1	B-structure_element
domain	O
alone	B-protein_state
(	O
Kd	B-evidence
=	O
4	O
.	O
6	O
±	O
4	O
μm	O
;	O
Fig	O
.	O
2C	O
).	O

Taken	O
together	O
,	O
these	O
data	O
suggest	O
that	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
is	O
sufficient	O
for	O
maximal	O
binding	O
and	O
that	O
this	O
binding	O
is	O
of	O
a	O
relatively	O
low	O
affinity	O
compared	O
with	O
many	O
other	O
Cdc42	B-protein
·	O
effector	O
complexes	O
.	O

The	O
Cdc42	B-complex_assembly
-	I-complex_assembly
HR1	I-complex_assembly
interaction	O
is	O
of	O
low	O
affinity	O
in	O
the	O
context	O
of	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
protein	O
and	O
in	O
TOCA1	B-protein
paralogues	O
.	O

A	O
,	O
diagram	O
illustrating	O
the	O
TOCA1	B-protein
constructs	O
assayed	O
for	O
Cdc42	B-protein
binding	O
.	O

Domain	O
boundaries	O
are	O
derived	O
from	O
secondary	O
structure	O
predictions	O
;	O
B	O
,	O
binding	B-evidence
curves	I-evidence
derived	O
from	O
direct	B-experimental_method
binding	I-experimental_method
assays	I-experimental_method
,	O
in	O
which	O
the	O
indicated	O
concentrations	O
of	O
Cdc42Δ7Q61L	B-complex_assembly
·[	I-complex_assembly
3H	I-complex_assembly
]	I-complex_assembly
GTP	I-complex_assembly
were	O
incubated	B-experimental_method
with	O
30	O
nm	O
GST	B-mutant
-	I-mutant
ACK	I-mutant
or	O
His	B-protein_state
-	I-protein_state
tagged	I-protein_state
TOCA1	B-protein
constructs	O
,	O
as	O
indicated	O
,	O
in	O
SPAs	B-experimental_method
.	O

The	O
SPA	B-experimental_method
signal	O
was	O
corrected	O
by	O
subtraction	O
of	O
control	O
data	O
with	O
no	O
fusion	O
protein	O
.	O

The	O
data	O
were	O
fitted	O
to	O
a	O
binding	B-evidence
isotherm	I-evidence
to	O
give	O
an	O
apparent	O
Kd	B-evidence
and	O
are	O
expressed	O
as	O
a	O
percentage	O
of	O
the	O
maximum	O
signal	O
.	O

C	O
–	O
E	O
,	O
representative	O
examples	O
of	O
competition	B-experimental_method
SPA	I-experimental_method
experiments	O
carried	O
out	O
with	O
the	O
indicated	O
concentrations	O
of	O
the	O
TOCA1	B-protein
HR1	B-mutant
-	I-mutant
SH3	I-mutant
construct	O
titrated	B-experimental_method
into	O
30	O
nm	O
GST	B-mutant
-	I-mutant
ACK	I-mutant
and	O
30	O
nm	O
Cdc42Δ7Q61L	B-complex_assembly
·[	I-complex_assembly
3H	I-complex_assembly
]	I-complex_assembly
GTP	I-complex_assembly
(	O
C	O
)	O
or	O
HR1CIP4	B-structure_element
(	O
D	O
)	O
or	O
HR1FBP17	B-structure_element
(	O
E	O
)	O
titrated	B-experimental_method
into	O
30	O
nm	O
GST	B-mutant
-	I-mutant
ACK	I-mutant
and	O
30	O
nm	O
Cdc42FLQ61L	B-complex_assembly
·[	I-complex_assembly
3H	I-complex_assembly
]	I-complex_assembly
GTP	I-complex_assembly
.	O

The	O
low	O
affinity	O
of	O
the	O
TOCA1	B-protein
HR1	B-structure_element
-	O
Cdc42	B-protein
interaction	O
raised	O
the	O
question	O
of	O
whether	O
the	O
other	O
known	O
Cdc42	B-protein
-	O
binding	O
TOCA	B-protein_type
family	I-protein_type
proteins	I-protein_type
,	O
FBP17	B-protein
and	O
CIP4	B-protein
,	O
also	O
bind	O
weakly	O
.	O

The	O
HR1	B-structure_element
domains	O
from	O
FBP17	B-protein
and	O
CIP4	B-protein
were	O
purified	B-experimental_method
and	O
assayed	O
for	O
Cdc42	B-protein
binding	O
in	O
competition	B-experimental_method
SPAs	I-experimental_method
,	O
analogous	O
to	O
those	O
carried	O
out	O
with	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
.	O

The	O
affinities	B-evidence
of	O
both	O
the	O
FBP17	B-protein
and	O
CIP4	B-protein
HR1	B-structure_element
domains	O
were	O
also	O
in	O
the	O
low	O
micromolar	O
range	O
(	O
10	O
and	O
5	O
μm	O
,	O
respectively	O
)	O
(	O
Fig	O
.	O
2	O
,	O
D	O
and	O
E	O
),	O
suggesting	O
that	O
low	O
affinity	O
interactions	O
with	O
Cdc42	B-protein
are	O
a	O
common	O
feature	O
within	O
the	O
TOCA	B-protein_type
family	I-protein_type
.	O

Structure	B-evidence
of	O
the	O
TOCA1	B-protein
HR1	B-structure_element
Domain	O

Because	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
was	O
sufficient	O
for	O
maximal	O
Cdc42	B-protein
-	O
binding	O
,	O
we	O
used	O
this	O
construct	O
for	O
structural	O
studies	O
.	O

Initial	O
experiments	O
were	O
performed	O
with	O
TOCA1	B-protein
residues	O
324	B-residue_range
–	I-residue_range
426	I-residue_range
,	O
but	O
we	O
observed	O
that	O
the	O
N	O
terminus	O
was	O
cleaved	O
during	O
purification	O
to	O
yield	O
a	O
new	O
N	O
terminus	O
at	O
residue	O
330	B-residue_number
(	O
data	O
not	O
shown	O
).	O

We	O
therefore	O
engineered	O
a	O
construct	O
comprising	O
residues	O
330	B-residue_range
–	I-residue_range
426	I-residue_range
to	O
produce	O
the	O
minimal	B-protein_state
,	O
stable	B-protein_state
HR1	B-structure_element
domain	O
.	O

2	O
,	O
778	O
non	O
-	O
degenerate	O
NOE	B-evidence
restraints	I-evidence
were	O
used	O
in	O
initial	O
structure	B-experimental_method
calculations	I-experimental_method
(	O
1	O
,	O
791	O
unambiguous	O
and	O
987	O
ambiguous	O
),	O
derived	O
from	O
three	O
-	O
dimensional	O
15N	B-experimental_method
-	I-experimental_method
separated	I-experimental_method
NOESY	I-experimental_method
and	O
13C	B-experimental_method
-	I-experimental_method
separated	I-experimental_method
NOESY	I-experimental_method
experiments	O
.	O

There	O
were	O
1	O
,	O
845	O
unambiguous	O
NOEs	B-evidence
and	O
757	O
ambiguous	O
NOEs	B-evidence
after	O
eight	O
iterations	O
.	O

100	O
structures	B-evidence
were	O
calculated	B-experimental_method
in	O
the	O
final	O
iteration	O
;	O
the	O
50	O
lowest	O
energy	O
structures	B-evidence
were	O
water	O
-	O
refined	O
;	O
and	O
of	O
these	O
,	O
the	O
35	O
lowest	O
energy	O
structures	B-evidence
were	O
analyzed	O
.	O

Table	O
1	O
indicates	O
that	O
the	O
HR1	B-structure_element
domain	O
structure	B-evidence
is	O
well	O
defined	O
by	O
the	O
NMR	B-experimental_method
data	O
.	O

a	O
<	O
SA	O
>,	O
the	O
average	B-evidence
root	I-evidence
mean	I-evidence
square	I-evidence
deviations	I-evidence
for	O
the	O
ensemble	O
±	O
S	O
.	O
D	O
.	O

b	O
<	O
SA	O
>	O
c	O
,	O
values	O
for	O
the	O
structure	B-evidence
that	O
is	O
closest	O
to	O
the	O
mean	O
.	O

The	O
structure	B-evidence
closest	O
to	O
the	O
mean	O
is	O
shown	O
in	O
Fig	O
.	O
3A	O
.	O

The	O
two	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
of	O
the	O
HR1	B-structure_element
domain	O
interact	O
to	O
form	O
an	O
anti	B-structure_element
-	I-structure_element
parallel	I-structure_element
coiled	I-structure_element
-	I-structure_element
coil	I-structure_element
with	O
a	O
slight	O
left	O
-	O
handed	O
twist	O
,	O
reminiscent	O
of	O
the	O
HR1	B-structure_element
domains	O
of	O
CIP4	B-protein
(	O
PDB	O
code	O
2KE4	O
)	O
and	O
PRK1	B-protein
(	O
PDB	O
codes	O
1CXZ	O
and	O
1URF	O
).	O

A	O
sequence	B-experimental_method
alignment	I-experimental_method
illustrating	O
the	O
secondary	O
structure	O
elements	O
of	O
the	O
TOCA1	B-protein
and	O
CIP4	B-protein
HR1	B-structure_element
domains	O
and	O
the	O
HR1a	B-structure_element
and	O
HR1b	B-structure_element
domains	O
from	O
PRK1	B-protein
is	O
shown	O
in	O
Fig	O
.	O
3B	O
.	O

The	O
structure	B-evidence
of	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
.	O

A	O
,	O
the	O
backbone	O
trace	B-evidence
of	O
the	O
35	O
lowest	O
energy	O
structures	B-evidence
of	O
the	O
HR1	B-structure_element
domain	O
overlaid	O
with	O
the	O
structure	B-evidence
closest	O
to	O
the	O
mean	O
is	O
shown	O
alongside	O
a	O
schematic	O
representation	O
of	O
the	O
structure	B-evidence
closest	O
to	O
the	O
mean	O
.	O

Flexible	O
regions	O
at	O
the	O
N	O
and	O
C	O
termini	O
(	O
residues	O
330	B-residue_range
–	I-residue_range
333	I-residue_range
and	O
421	B-residue_range
–	I-residue_range
426	I-residue_range
)	O
are	O
omitted	O
for	O
clarity	O
.	O

B	O
,	O
a	O
sequence	B-experimental_method
alignment	I-experimental_method
of	O
the	O
HR1	B-structure_element
domains	O
from	O
TOCA1	B-protein
,	O
CIP4	B-protein
,	O
and	O
PRK1	B-protein
.	O

The	O
secondary	O
structure	O
was	O
deduced	O
using	O
Stride	B-experimental_method
,	O
based	O
on	O
the	O
Ramachandran	B-evidence
angles	I-evidence
,	O
and	O
is	O
indicated	O
as	O
follows	O
:	O
gray	O
,	O
turn	O
;	O
yellow	O
,	O
α	B-structure_element
-	I-structure_element
helix	I-structure_element
;	O
blue	O
,	O
310	B-structure_element
helix	I-structure_element
;	O
white	O
,	O
coil	O
.	O

C	O
,	O
a	O
close	O
-	O
up	O
of	O
the	O
N	O
-	O
terminal	O
region	O
of	O
TOCA1	B-protein
HR1	B-structure_element
,	O
indicating	O
some	O
of	O
the	O
NOEs	B-evidence
defining	O
its	O
position	O
with	O
respect	O
to	O
the	O
two	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
.	O

Dotted	O
lines	O
,	O
NOE	B-evidence
restraints	I-evidence
.	O

D	O
,	O
a	O
close	O
-	O
up	O
of	O
the	O
interhelix	B-structure_element
loop	I-structure_element
region	O
showing	O
some	O
of	O
the	O
contacts	O
between	O
the	O
loop	B-structure_element
and	O
helix	B-structure_element
1	I-structure_element
.	O

In	O
the	O
HR1a	B-structure_element
domain	O
of	O
PRK1	B-protein
,	O
a	O
region	O
N	O
-	O
terminal	O
to	O
helix	B-structure_element
1	I-structure_element
forms	O
a	O
short	B-structure_element
α	I-structure_element
-	I-structure_element
helix	I-structure_element
,	O
which	O
packs	O
against	O
both	O
helices	O
of	O
the	O
HR1	B-structure_element
domain	O
.	O

This	O
region	O
of	O
TOCA1	B-protein
HR1	B-structure_element
(	O
residues	O
334	B-residue_range
–	I-residue_range
340	I-residue_range
)	O
is	O
well	O
defined	O
in	O
the	O
family	O
of	O
structures	B-evidence
(	O
Fig	O
.	O
3A	O
)	O
but	O
does	O
not	O
form	O
an	O
α	B-structure_element
-	I-structure_element
helix	I-structure_element
.	O

It	O
instead	O
forms	O
a	O
series	O
of	O
turns	O
,	O
defined	O
by	O
NOE	B-evidence
restraints	I-evidence
observed	O
between	O
residues	O
separated	O
by	O
one	O
(	O
residues	O
332	B-residue_range
–	I-residue_range
334	I-residue_range
,	O
333	B-residue_range
–	I-residue_range
335	I-residue_range
,	O
etc	O
.)	O
or	O
two	O
(	O
residues	O
337	B-residue_range
–	I-residue_range
340	I-residue_range
)	O
residues	O
in	O
the	O
sequence	O
and	O
the	O
φ	B-evidence
and	I-evidence
ψ	I-evidence
angles	I-evidence
,	O
assessed	O
using	O
Stride	B-experimental_method
.	O

These	O
turns	O
cause	O
the	O
chain	O
to	O
reverse	O
direction	O
,	O
allowing	O
the	O
N	O
-	O
terminal	O
segment	O
(	O
residues	O
334	B-residue_range
–	I-residue_range
340	I-residue_range
)	O
to	O
contact	O
both	O
helices	O
of	O
the	O
HR1	B-structure_element
domain	O
.	O

Long	O
range	O
NOEs	B-evidence
were	O
observed	O
linking	O
Leu	B-residue_name_number
-	I-residue_name_number
334	I-residue_name_number
,	O
Glu	B-residue_name_number
-	I-residue_name_number
335	I-residue_name_number
,	O
and	O
Asp	B-residue_name_number
-	I-residue_name_number
336	I-residue_name_number
with	O
Trp	B-residue_name_number
-	I-residue_name_number
413	I-residue_name_number
of	O
helix	B-structure_element
2	I-structure_element
,	O
Leu	B-residue_name_number
-	I-residue_name_number
334	I-residue_name_number
with	O
Lys	B-residue_name_number
-	I-residue_name_number
409	I-residue_name_number
of	O
helix	B-structure_element
2	I-structure_element
,	O
and	O
Phe	B-residue_name_number
-	I-residue_name_number
337	I-residue_name_number
and	O
Ser	B-residue_name_number
-	I-residue_name_number
338	I-residue_name_number
with	O
Arg	B-residue_name_number
-	I-residue_name_number
345	I-residue_name_number
,	O
Arg	B-residue_name_number
-	I-residue_name_number
348	I-residue_name_number
,	O
and	O
Leu	B-residue_name_number
-	I-residue_name_number
349	I-residue_name_number
of	O
helix	B-structure_element
1	I-structure_element
.	O

The	O
two	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
of	O
TOCA1	B-protein
HR1	B-structure_element
are	O
separated	O
by	O
a	O
long	O
loop	B-structure_element
of	O
10	O
residues	O
(	O
residues	O
380	B-residue_range
–	I-residue_range
389	I-residue_range
)	O
that	O
contains	O
two	O
short	B-structure_element
310	I-structure_element
helices	I-structure_element
(	O
residues	O
381	B-residue_range
–	I-residue_range
383	I-residue_range
and	O
386	B-residue_range
–	I-residue_range
389	I-residue_range
).	O

Interestingly	O
,	O
side	O
chains	O
of	O
residues	O
within	O
the	O
loop	B-structure_element
region	I-structure_element
point	O
back	O
toward	O
helix	B-structure_element
1	I-structure_element
;	O
for	O
example	O
,	O
there	O
are	O
numerous	O
distinct	O
NOEs	O
between	O
the	O
side	O
chains	O
of	O
Asn	B-residue_name_number
-	I-residue_name_number
380	I-residue_name_number
and	O
Met	B-residue_name_number
-	I-residue_name_number
383	I-residue_name_number
of	O
the	O
loop	B-structure_element
region	I-structure_element
and	O
Tyr	B-residue_name_number
-	I-residue_name_number
377	I-residue_name_number
and	O
Val	B-residue_name_number
-	I-residue_name_number
376	I-residue_name_number
of	O
helix	B-structure_element
1	I-structure_element
(	O
Fig	O
.	O
3D	O
).	O

The	O
backbone	O
NH	O
and	O
CHα	O
groups	O
of	O
Gly	B-residue_name_number
-	I-residue_name_number
384	I-residue_name_number
and	O
Asp	B-residue_name_number
-	I-residue_name_number
385	I-residue_name_number
also	O
show	O
NOEs	O
with	O
the	O
side	O
chain	O
of	O
Tyr	B-residue_name_number
-	I-residue_name_number
377	I-residue_name_number
.	O

Mapping	O
the	O
TOCA1	B-protein
and	O
Cdc42	B-site
Binding	I-site
Interfaces	I-site

The	O
HR1TOCA1	B-site
-	I-site
Cdc42	I-site
interface	I-site
was	O
investigated	O
using	O
NMR	B-experimental_method
spectroscopy	I-experimental_method
.	O

A	O
series	O
of	O
15N	B-experimental_method
HSQC	I-experimental_method
experiments	O
was	O
recorded	O
on	O
15N	B-chemical
-	O
labeled	B-protein_state
TOCA1	B-protein
HR1	B-structure_element
domain	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
increasing	B-experimental_method
concentrations	I-experimental_method
of	O
unlabeled	B-protein_state
Cdc42Δ7Q61L	B-complex_assembly
·	I-complex_assembly
GMPPNP	I-complex_assembly
to	O
map	O
the	O
Cdc42	B-site
-	I-site
binding	I-site
surface	I-site
.	O

A	O
comparison	O
of	O
the	O
15N	B-experimental_method
HSQC	I-experimental_method
spectra	B-evidence
of	O
free	B-protein_state
HR1	B-structure_element
and	O
HR1	B-structure_element
in	O
the	O
presence	B-protein_state
of	I-protein_state
excess	O
Cdc42	B-protein
shows	O
that	O
although	O
some	O
peaks	O
were	O
shifted	O
,	O
several	O
were	O
much	O
broader	O
in	O
the	O
complex	O
,	O
and	O
a	O
considerable	O
subset	O
had	O
disappeared	O
(	O
Fig	O
.	O
4A	O
).	O

This	O
behavior	O
cannot	O
be	O
explained	O
by	O
the	O
increase	O
in	O
molecular	O
mass	O
(	O
from	O
12	O
to	O
33	O
kDa	O
)	O
when	O
Cdc42	B-protein
binds	O
and	O
is	O
more	O
likely	O
to	O
be	O
due	O
to	O
conformational	O
exchange	O
.	O

Overall	O
chemical	B-experimental_method
shift	I-experimental_method
perturbations	I-experimental_method
(	O
CSPs	B-experimental_method
)	O
were	O
calculated	O
for	O
each	O
residue	O
,	O
whereas	O
those	O
that	O
had	O
disappeared	O
were	O
assigned	O
a	O
shift	O
change	O
of	O
0	O
.	O
2	O
(	O
Fig	O
.	O
4B	O
).	O

A	O
peak	O
that	O
disappeared	O
or	O
had	O
a	O
CSP	B-experimental_method
above	O
the	O
mean	O
CSP	B-experimental_method
for	O
the	O
spectrum	O
was	O
considered	O
to	O
be	O
significantly	O
affected	O
.	O

Mapping	O
the	O
binding	B-site
surface	I-site
of	O
Cdc42	B-protein
onto	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
.	O

A	O
,	O
the	O
15N	B-experimental_method
HSQC	I-experimental_method
of	O
200	O
μm	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
is	O
shown	O
in	O
the	O
free	B-protein_state
form	I-protein_state
(	O
black	O
)	O
and	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
a	O
4	O
-	O
fold	O
molar	O
excess	O
of	O
Cdc42Δ7Q61L	B-complex_assembly
·	I-complex_assembly
GMPPNP	I-complex_assembly
(	O
red	O
).	O

B	O
,	O
CSPs	B-experimental_method
were	O
calculated	O
as	O
described	O
under	O
“	O
Experimental	O
Procedures	O
”	O
and	O
are	O
shown	O
for	O
backbone	O
and	O
side	O
chain	O
NH	O
groups	O
.	O

The	O
mean	O
CSP	B-experimental_method
is	O
marked	O
with	O
a	O
red	O
line	O
.	O

Residues	O
that	O
disappeared	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
Cdc42	B-protein
were	O
assigned	O
a	O
CSP	B-experimental_method
of	O
0	O
.	O
2	O
but	O
were	O
excluded	O
when	O
calculating	O
the	O
mean	O
CSP	B-experimental_method
and	O
are	O
indicated	O
with	O
open	O
bars	O
.	O

Those	O
that	O
were	O
not	O
traceable	O
due	O
to	O
spectral	O
overlap	O
were	O
assigned	O
a	O
CSP	B-experimental_method
of	O
zero	O
and	O
are	O
marked	O
with	O
an	O
asterisk	O
below	O
the	O
bar	O
.	O

Residues	O
with	O
affected	O
side	O
chain	O
CSPs	B-experimental_method
derived	O
from	O
13C	B-experimental_method
HSQCs	I-experimental_method
are	O
marked	O
with	O
green	O
asterisks	O
above	O
the	O
bars	O
.	O

C	O
,	O
a	O
schematic	O
representation	O
of	O
the	O
HR1	B-structure_element
domain	O
.	O

Residues	O
with	O
significantly	O
affected	O
backbone	O
or	O
side	O
chain	O
chemical	O
shifts	O
when	O
Cdc42	B-protein_state
bound	I-protein_state
and	O
that	O
are	O
buried	O
are	O
colored	O
dark	O
blue	O
,	O
whereas	O
those	O
that	O
are	O
solvent	B-protein_state
-	I-protein_state
accessible	I-protein_state
are	O
colored	O
yellow	O
.	O

Residues	O
with	O
significantly	O
affected	O
backbone	O
and	O
side	O
chain	O
groups	O
that	O
are	O
solvent	B-protein_state
-	I-protein_state
accessible	I-protein_state
are	O
colored	O
red	O
.	O

A	O
close	O
-	O
up	O
of	O
the	O
binding	B-site
region	I-site
is	O
shown	O
,	O
with	O
affected	O
side	O
chain	O
heavy	O
atoms	O
shown	O
as	O
sticks	O
.	O

D	O
,	O
the	O
G	B-site
protein	I-site
-	I-site
binding	I-site
region	I-site
is	O
marked	O
in	O
red	O
onto	O
structures	B-evidence
of	O
the	O
HR1	B-structure_element
domains	O
as	O
indicated	O
.	O

15N	B-experimental_method
HSQC	I-experimental_method
shift	I-experimental_method
mapping	I-experimental_method
experiments	O
report	O
on	O
changes	O
to	O
amide	O
groups	O
,	O
which	O
are	O
mainly	O
inaccessible	O
because	O
they	O
are	O
buried	O
inside	O
the	O
helices	B-structure_element
and	O
are	O
involved	O
in	O
hydrogen	O
bonds	O
.	O

Therefore	O
,	O
13C	B-experimental_method
HSQC	I-experimental_method
and	O
methyl	B-experimental_method
-	I-experimental_method
selective	I-experimental_method
SOFAST	I-experimental_method
-	I-experimental_method
HMQC	I-experimental_method
experiments	O
were	O
also	O
recorded	O
on	O
15N	B-chemical
,	O
13C	B-chemical
-	O
labeled	B-protein_state
TOCA1	B-protein
HR1	B-structure_element
to	O
yield	O
more	O
information	O
on	O
side	O
chain	O
involvement	O
.	O

Side	O
chains	O
whose	O
CH	O
groups	O
disappeared	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
Cdc42	B-protein
are	O
marked	O
on	O
the	O
graph	O
in	O
Fig	O
.	O
4B	O
with	O
green	O
asterisks	O
.	O

TOCA1	B-protein
residues	O
whose	O
signals	O
were	O
affected	O
by	O
Cdc42	B-protein
binding	O
were	O
mapped	O
onto	O
the	O
structure	B-evidence
of	O
TOCA1	B-protein
HR1	B-structure_element
(	O
Fig	O
.	O
4C	O
).	O

The	O
changes	O
were	O
localized	O
to	O
one	O
end	O
of	O
the	O
coiled	B-structure_element
-	I-structure_element
coil	I-structure_element
,	O
and	O
the	O
binding	B-site
site	I-site
appeared	O
to	O
include	O
residues	O
from	O
both	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
and	O
the	O
loop	B-structure_element
region	I-structure_element
that	O
joins	O
them	O
.	O

The	O
residues	O
in	O
the	O
interhelical	B-structure_element
loop	I-structure_element
and	O
helix	B-structure_element
1	I-structure_element
that	O
contact	O
each	O
other	O
(	O
Fig	O
.	O
3D	O
)	O
show	O
shift	O
changes	O
in	O
their	O
backbone	O
NH	O
and	O
side	O
chains	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
Cdc42	B-protein
.	O

For	O
example	O
,	O
the	O
side	O
chain	O
of	O
Asn	B-residue_name_number
-	I-residue_name_number
380	I-residue_name_number
and	O
the	O
backbones	O
of	O
Val	B-residue_name_number
-	I-residue_name_number
376	I-residue_name_number
and	O
Tyr	B-residue_name_number
-	I-residue_name_number
377	I-residue_name_number
were	O
significantly	O
affected	O
but	O
are	O
all	O
buried	O
in	O
the	O
free	B-protein_state
TOCA1	B-protein
HR1	B-structure_element
structure	B-evidence
,	O
indicating	O
that	O
local	O
conformational	O
changes	O
in	O
the	O
loop	B-structure_element
may	O
facilitate	O
complex	O
formation	O
.	O

The	O
chemical	B-experimental_method
shift	I-experimental_method
mapping	I-experimental_method
data	O
indicate	O
that	O
the	O
G	B-site
protein	I-site
-	I-site
binding	I-site
region	I-site
of	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
is	O
broadly	O
similar	O
to	O
that	O
of	O
the	O
CIP4	B-protein
and	O
PRK1	B-protein
HR1	B-structure_element
domains	O
(	O
Figs	O
.	O
3B	O
and	O
4D	O
).	O

The	O
corresponding	O
15N	B-experimental_method
and	O
13C	B-experimental_method
NMR	I-experimental_method
experiments	O
were	O
also	O
recorded	O
on	O
15N	B-chemical
-	O
Cdc42Δ7Q61L	B-complex_assembly
·	I-complex_assembly
GMPPNP	I-complex_assembly
or	O
15N	B-chemical
/	O
13C	B-chemical
-	O
Cdc42Δ7Q61L	B-complex_assembly
·	I-complex_assembly
GMPPNP	I-complex_assembly
in	O
the	O
presence	B-protein_state
of	I-protein_state
unlabeled	B-protein_state
HR1	B-structure_element
domain	O
.	O

The	O
overall	O
CSP	B-experimental_method
was	O
calculated	O
for	O
each	O
residue	O
.	O

As	O
was	O
the	O
case	O
when	O
labeled	B-protein_state
HR1	B-structure_element
was	O
observed	O
,	O
several	O
peaks	O
were	O
shifted	O
in	O
the	O
complex	O
,	O
but	O
many	O
disappeared	O
,	O
indicating	O
exchange	O
on	O
an	O
unfavorable	O
,	O
millisecond	O
time	O
scale	O
(	O
Fig	O
.	O
5A	O
).	O

Detailed	O
side	O
chain	O
data	O
could	O
not	O
be	O
obtained	O
for	O
all	O
residues	O
due	O
to	O
spectral	O
overlap	O
,	O
but	O
constant	B-experimental_method
time	I-experimental_method
13C	I-experimental_method
HSQC	I-experimental_method
and	O
methyl	B-experimental_method
-	I-experimental_method
selective	I-experimental_method
SOFAST	I-experimental_method
-	I-experimental_method
HMQC	I-experimental_method
experiments	O
provided	O
further	O
information	O
on	O
certain	O
well	O
resolved	O
side	O
chains	O
(	O
marked	O
with	O
green	O
asterisks	O
in	O
Fig	O
.	O
5B	O
).	O

Mapping	O
the	O
binding	B-site
surface	I-site
of	O
the	O
HR1	B-structure_element
domain	O
onto	O
Cdc42	B-protein
.	O

A	O
,	O
the	O
15N	B-experimental_method
HSQC	I-experimental_method
of	O
Cdc42Δ7Q61L	B-complex_assembly
·	I-complex_assembly
GMPPNP	I-complex_assembly
is	O
shown	O
in	O
its	O
free	B-protein_state
form	I-protein_state
(	O
black	O
)	O
and	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
excess	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
(	O
1	O
:	O
2	O
.	O
2	O
,	O
red	O
).	O

B	O
,	O
CSPs	B-experimental_method
are	O
shown	O
for	O
backbone	O
NH	O
groups	O
.	O

The	O
red	O
line	O
indicates	O
the	O
mean	O
CSP	B-experimental_method
,	O
plus	O
one	O
S	O
.	O
D	O
.	O
Residues	O
that	O
disappeared	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
Cdc42	B-protein
were	O
assigned	O
a	O
CSP	B-experimental_method
of	O
0	O
.	O
1	O
and	O
are	O
indicated	O
with	O
open	O
bars	O
.	O

Residues	O
with	O
disappeared	O
peaks	O
in	O
13C	B-experimental_method
HSQC	I-experimental_method
experiments	O
are	O
marked	O
on	O
the	O
chart	O
with	O
green	O
asterisks	O
.	O

C	O
,	O
the	O
residues	O
with	O
significantly	O
affected	O
backbone	O
and	O
side	O
chain	O
groups	O
are	O
highlighted	O
on	O
an	O
NMR	B-experimental_method
structure	B-evidence
of	O
free	B-protein_state
Cdc42Δ7Q61L	B-complex_assembly
·	I-complex_assembly
GMPPNP	I-complex_assembly
;	O
those	O
that	O
are	O
buried	O
are	O
colored	O
dark	O
blue	O
,	O
whereas	O
those	O
that	O
are	O
solvent	B-protein_state
-	I-protein_state
accessible	I-protein_state
are	O
colored	O
red	O
.	O

Residues	O
with	O
either	O
side	O
chain	O
or	O
backbone	O
groups	O
affected	O
are	O
colored	O
blue	O
if	O
buried	O
and	O
yellow	O
if	O
solvent	B-protein_state
-	I-protein_state
accessible	I-protein_state
.	O

Residues	O
without	O
information	O
from	O
shift	B-experimental_method
mapping	I-experimental_method
are	O
colored	O
gray	O
.	O

The	O
flexible	B-protein_state
switch	B-site
regions	I-site
are	O
circled	O
.	O

As	O
many	O
of	O
the	O
peaks	O
disappeared	O
,	O
the	O
mean	B-evidence
chemical	I-evidence
shift	I-evidence
change	I-evidence
was	O
relatively	O
low	O
,	O
so	O
a	O
threshold	O
of	O
the	O
mean	O
plus	O
one	O
S	O
.	O
D	O
.	O
value	O
was	O
used	O
to	O
define	O
a	O
significant	O
CSP	B-experimental_method
.	O

Parts	O
of	O
the	O
switch	B-site
regions	I-site
(	O
Fig	O
.	O
5	O
,	O
B	O
and	O
C	O
)	O
are	O
invisible	O
in	O
NMR	B-experimental_method
spectra	B-evidence
recorded	O
on	O
free	B-protein_state
Cdc42	B-protein
due	O
to	O
conformational	O
exchange	O
.	O

These	O
switch	B-site
regions	I-site
become	O
visible	O
in	O
Cdc42	B-protein
and	O
other	O
small	O
G	B-protein_type
protein	I-protein_type
·	O
effector	O
complexes	O
due	O
to	O
a	O
decrease	O
in	O
conformational	O
freedom	O
upon	O
complex	O
formation	O
.	O

The	O
switch	B-site
regions	I-site
of	O
Cdc42	B-protein
did	O
not	O
,	O
however	O
,	O
become	O
visible	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
.	O

Indeed	O
,	O
Ser	B-residue_name_number
-	I-residue_name_number
30	I-residue_name_number
of	O
switch	B-site
I	I-site
and	O
Arg	B-residue_name_number
-	I-residue_name_number
66	I-residue_name_number
,	O
Arg	B-residue_name_number
-	I-residue_name_number
68	I-residue_name_number
,	O
Leu	B-residue_name_number
-	I-residue_name_number
70	I-residue_name_number
,	O
and	O
Ser	B-residue_name_number
-	I-residue_name_number
71	I-residue_name_number
of	O
switch	B-site
II	I-site
are	O
visible	O
in	O
free	B-protein_state
Cdc42	B-protein
but	O
disappear	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
the	O
HR1	B-structure_element
domain	O
.	O

This	O
suggests	O
that	O
the	O
switch	B-site
regions	I-site
are	O
not	O
rigidified	O
in	O
the	O
HR1	B-structure_element
complex	O
and	O
are	O
still	O
in	O
conformational	O
exchange	O
.	O

Nevertheless	O
,	O
mapping	O
of	O
the	O
affected	O
residues	O
onto	O
the	O
NMR	B-experimental_method
structure	B-evidence
of	O
free	B-protein_state
Cdc42Δ7Q61L	B-complex_assembly
·	I-complex_assembly
GMPPNP	I-complex_assembly
(	O
Fig	O
.	O
5C	O
)	O
8	O
shows	O
that	O
,	O
although	O
they	O
are	O
relatively	O
widespread	O
compared	O
with	O
changes	O
in	O
the	O
HR1	B-structure_element
domain	O
,	O
in	O
general	O
,	O
they	O
are	O
on	O
the	O
face	O
of	O
the	O
protein	O
that	O
includes	O
the	O
switches	B-site
.	O

Although	O
the	O
binding	B-site
interface	I-site
may	O
be	O
overestimated	O
,	O
this	O
suggests	O
that	O
the	O
switch	B-site
regions	I-site
are	O
involved	O
in	O
binding	O
to	O
TOCA1	B-protein
.	O

Modeling	O
the	O
Cdc42	B-complex_assembly
·	I-complex_assembly
TOCA1	I-complex_assembly
HR1	I-complex_assembly
Complex	O

The	O
Cdc42	B-complex_assembly
·	I-complex_assembly
HR1TOCA1	I-complex_assembly
complex	O
was	O
not	O
amenable	O
to	O
full	O
structural	O
analysis	O
due	O
to	O
the	O
weak	O
interaction	O
and	O
the	O
extensive	O
exchange	O
broadening	O
seen	O
in	O
the	O
NMR	B-experimental_method
experiments	O
.	O

HADDOCK	B-experimental_method
was	O
therefore	O
used	O
to	O
perform	O
rigid	O
body	B-experimental_method
docking	I-experimental_method
based	O
on	O
the	O
structures	B-evidence
of	O
free	B-protein_state
HR1	B-structure_element
domain	O
and	O
Cdc42	B-protein
and	O
ambiguous	O
interaction	O
restraints	O
derived	O
from	O
the	O
titration	B-experimental_method
experiments	I-experimental_method
described	O
above	O
.	O

The	O
orientation	O
of	O
the	O
HR1	B-structure_element
domain	O
with	O
respect	O
to	O
Cdc42	B-protein
cannot	O
be	O
definitively	O
concluded	O
in	O
the	O
absence	O
of	O
unambiguous	O
distance	O
restraints	O
;	O
hence	O
,	O
HADDOCK	B-experimental_method
produced	O
a	O
set	O
of	O
models	O
in	O
which	O
the	O
HR1	B-structure_element
domain	O
contacts	O
the	O
same	O
surface	O
on	O
Cdc42	B-protein
but	O
is	O
in	O
various	O
orientations	O
with	O
respect	O
to	O
Cdc42	B-protein
.	O

The	O
cluster	O
with	O
the	O
lowest	O
root	B-evidence
mean	I-evidence
square	I-evidence
deviation	I-evidence
from	O
the	O
lowest	O
energy	O
structure	B-evidence
is	O
assumed	O
to	O
be	O
the	O
best	O
model	O
.	O

By	O
these	O
criteria	O
,	O
in	O
the	O
best	O
model	O
,	O
the	O
HR1	B-structure_element
domain	O
is	O
in	O
a	O
similar	O
orientation	O
to	O
the	O
HR1a	B-structure_element
domain	O
of	O
PRK1	B-protein
bound	B-protein_state
to	I-protein_state
RhoA	B-protein
and	O
the	O
HR1b	B-structure_element
domain	O
bound	B-protein_state
to	I-protein_state
Rac1	B-protein
.	O

A	O
representative	O
model	O
from	O
this	O
cluster	O
is	O
shown	O
in	O
Fig	O
.	O
6A	O
alongside	O
the	O
Rac1	B-complex_assembly
-	I-complex_assembly
HR1b	I-complex_assembly
structure	B-evidence
(	O
PDB	O
code	O
2RMK	O
)	O
in	O
Fig	O
.	O
6B	O
.	O

Model	O
of	O
Cdc42	B-complex_assembly
·	I-complex_assembly
HR1	I-complex_assembly
complex	O
.	O

A	O
,	O
a	O
representative	O
model	O
of	O
the	O
Cdc42	B-complex_assembly
·	I-complex_assembly
HR1	I-complex_assembly
complex	O
from	O
the	O
cluster	O
closest	O
to	O
the	O
lowest	O
energy	O
model	O
produced	O
using	O
HADDOCK	B-experimental_method
.	O

Residues	O
of	O
Cdc42	B-protein
that	O
are	O
affected	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
the	O
HR1	B-structure_element
domain	O
but	O
are	O
not	O
in	O
close	O
proximity	O
to	O
it	O
are	O
colored	O
in	O
red	O
and	O
labeled	O
.	O

B	O
,	O
structure	B-evidence
of	O
Rac1	B-protein
in	B-protein_state
complex	I-protein_state
with	I-protein_state
the	O
HR1b	B-structure_element
domain	O
of	O
PRK1	B-protein
(	O
PDB	O
code	O
2RMK	O
).	O

C	O
,	O
sequence	B-experimental_method
alignment	I-experimental_method
of	O
RhoA	B-protein
,	O
Cdc42	B-protein
and	O
Rac1	B-protein
.	O

Contact	O
residues	O
of	O
RhoA	B-protein
and	O
Rac1	B-protein
to	O
PRK1	B-protein
HR1a	B-structure_element
and	O
HR1b	B-structure_element
,	O
respectively	O
,	O
are	O
colored	O
cyan	O
.	O

Residues	O
of	O
Cdc42	B-protein
that	O
disappear	O
or	O
show	O
chemical	O
shift	O
changes	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
TOCA1	B-protein
are	O
colored	O
cyan	O
if	O
also	O
identified	O
as	O
contacts	O
in	O
RhoA	B-protein
and	O
Rac1	B-protein
and	O
yellow	O
if	O
they	O
are	O
not	O
.	O

Residues	O
equivalent	O
to	O
Rac1	B-protein
and	O
RhoA	B-protein
contact	B-site
sites	I-site
but	O
that	O
are	O
invisible	O
in	O
free	B-protein_state
Cdc42	B-protein
are	O
gray	O
.	O

D	O
,	O
regions	O
of	O
interest	O
of	O
the	O
Cdc42	B-complex_assembly
·	I-complex_assembly
HR1	I-complex_assembly
domain	O
model	O
.	O

The	O
four	O
lowest	O
energy	O
structures	B-evidence
in	O
the	O
chosen	O
HADDOCK	B-experimental_method
cluster	O
are	O
shown	O
overlaid	O
,	O
with	O
the	O
residues	O
of	O
interest	O
shown	O
as	O
sticks	O
and	O
labeled	O
.	O

Cdc42	O
is	O
shown	O
in	O
cyan	O
,	O
and	O
TOCA1	B-protein
is	O
shown	O
in	O
purple	O
.	O

A	O
sequence	B-experimental_method
alignment	I-experimental_method
of	O
RhoA	B-protein
,	O
Cdc42	B-protein
,	O
and	O
Rac1	B-protein
is	O
shown	O
in	O
Fig	O
.	O
6C	O
.	O

The	O
RhoA	B-protein
and	O
Rac1	B-protein
contact	O
residues	O
in	O
the	O
switch	B-site
regions	I-site
are	O
invisible	O
in	O
the	O
spectra	B-evidence
of	O
Cdc42	B-protein
,	O
but	O
they	O
are	O
generally	O
conserved	B-protein_state
between	O
all	O
three	O
G	B-protein_type
proteins	I-protein_type
.	O

Several	O
Cdc42	B-protein
residues	O
identified	O
by	O
chemical	B-experimental_method
shift	I-experimental_method
mapping	I-experimental_method
are	O
not	O
in	O
close	O
contact	O
in	O
the	O
Cdc42	B-complex_assembly
·	I-complex_assembly
TOCA1	I-complex_assembly
model	O
(	O
Fig	O
.	O
6A	O
).	O

Some	O
of	O
these	O
can	O
be	O
rationalized	O
;	O
for	O
example	O
,	O
Thr	B-residue_name_number
-	I-residue_name_number
24Cdc42	I-residue_name_number
,	O
Leu	B-residue_name_number
-	I-residue_name_number
160Cdc42	I-residue_name_number
,	O
and	O
Lys	B-residue_name_number
-	I-residue_name_number
163Cdc42	I-residue_name_number
all	O
pack	O
behind	O
switch	B-site
I	I-site
and	O
are	O
likely	O
to	O
be	O
affected	O
by	O
conformational	O
changes	O
within	O
the	O
switch	B-site
,	O
while	O
Glu	B-residue_name_number
-	I-residue_name_number
95Cdc42	I-residue_name_number
and	O
Lys	B-residue_name_number
-	I-residue_name_number
96Cdc42	I-residue_name_number
are	O
in	O
the	O
helix	B-structure_element
behind	O
switch	B-site
II	I-site
.	O

Other	O
residues	O
that	O
are	O
affected	O
in	O
the	O
Cdc42	B-complex_assembly
·	I-complex_assembly
TOCA1	I-complex_assembly
complex	O
but	O
that	O
do	O
not	O
correspond	O
to	O
contact	O
residues	O
of	O
RhoA	B-protein
or	O
Rac1	B-protein
(	O
Fig	O
.	O
6C	O
)	O
include	O
Gln	B-residue_name_number
-	I-residue_name_number
2Cdc42	I-residue_name_number
,	O
Lys	B-residue_name_number
-	I-residue_name_number
16Cdc42	I-residue_name_number
,	O
Thr	B-residue_name_number
-	I-residue_name_number
52Cdc42	I-residue_name_number
,	O
and	O
Arg	B-residue_name_number
-	I-residue_name_number
68Cdc42	I-residue_name_number
.	O

Lys	B-residue_name_number
-	I-residue_name_number
16Cdc42	I-residue_name_number
is	O
unlikely	O
to	O
be	O
a	O
contact	O
residue	O
because	O
it	O
is	O
involved	O
in	O
nucleotide	O
binding	O
,	O
but	O
the	O
others	O
may	O
represent	O
specific	O
Cdc42	B-complex_assembly
-	I-complex_assembly
TOCA1	I-complex_assembly
contacts	O
.	O

Competition	O
between	O
N	B-protein
-	I-protein
WASP	I-protein
and	O
TOCA1	B-protein

From	O
the	O
known	O
interactions	O
and	O
effects	O
of	O
the	O
proteins	O
in	O
biological	O
systems	O
,	O
it	O
has	O
been	O
suggested	O
that	O
TOCA1	B-protein
and	O
N	B-protein
-	I-protein
WASP	I-protein
could	O
bind	O
Cdc42	B-protein
simultaneously	O
.	O

Studies	O
in	O
CHO	O
cells	O
indicated	O
that	O
a	O
Cdc42	B-complex_assembly
·	I-complex_assembly
N	I-complex_assembly
-	I-complex_assembly
WASP	I-complex_assembly
·	I-complex_assembly
TOCA1	I-complex_assembly
complex	O
existed	O
because	O
FRET	B-evidence
was	O
observed	O
between	O
RFP	B-chemical
-	O
TOCA1	B-protein
and	O
GFP	B-chemical
-	O
N	B-protein
-	I-protein
WASP	I-protein
,	O
and	O
the	O
efficiency	O
was	O
decreased	O
when	O
an	O
N	B-protein
-	I-protein
WASP	I-protein
mutant	B-protein_state
was	O
used	O
that	O
no	O
longer	O
binds	O
Cdc42	B-protein
.	O

An	O
overlay	B-experimental_method
of	O
the	O
HADDOCK	B-experimental_method
model	B-evidence
of	O
the	O
Cdc42	B-complex_assembly
·	I-complex_assembly
HR1TOCA1	I-complex_assembly
complex	O
and	O
the	O
structure	B-evidence
of	O
Cdc42	B-protein
in	B-protein_state
complex	I-protein_state
with	I-protein_state
the	O
GBD	B-structure_element
of	O
the	O
N	B-protein
-	I-protein
WASP	I-protein
homologue	O
,	O
WASP	B-protein
(	O
PDB	O
code	O
1CEE	O
),	O
shows	O
that	O
the	O
HR1	B-structure_element
and	O
GBD	B-site
binding	I-site
sites	I-site
only	O
partly	O
overlap	O
,	O
and	O
,	O
therefore	O
,	O
a	O
ternary	O
complex	O
remained	O
possible	O
(	O
Fig	O
.	O
7A	O
).	O

Interestingly	O
,	O
the	O
presence	B-protein_state
of	I-protein_state
the	O
TOCA1	B-protein
HR1	B-structure_element
would	O
not	O
prevent	O
the	O
core	O
CRIB	B-structure_element
of	O
WASP	B-protein
from	O
binding	O
to	O
Cdc42	B-protein
,	O
although	O
the	O
regions	O
C	O
-	O
terminal	O
to	O
the	O
CRIB	B-structure_element
that	O
are	O
required	O
for	O
high	O
affinity	O
binding	O
of	O
WASP	B-protein
would	O
interfere	O
sterically	O
with	O
the	O
TOCA1	B-protein
HR1	B-structure_element
.	O

A	O
basic	O
region	O
in	O
WASP	B-protein
including	O
three	O
lysines	B-residue_name
(	O
residues	O
230	B-residue_range
–	I-residue_range
232	I-residue_range
),	O
N	O
-	O
terminal	O
to	O
the	O
core	O
CRIB	B-structure_element
,	O
has	O
been	O
implicated	O
in	O
an	O
electrostatic	O
steering	O
mechanism	O
,	O
and	O
these	O
residues	O
would	O
be	O
free	O
to	O
bind	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
TOCA1	B-protein
HR1	B-structure_element
(	O
Fig	O
.	O
7A	O
).	O

The	O
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
displaces	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
.	O

A	O
,	O
the	O
model	O
of	O
the	O
Cdc42	B-complex_assembly
·	I-complex_assembly
TOCA1	I-complex_assembly
HR1	B-structure_element
domain	O
complex	O
overlaid	O
with	O
the	O
Cdc42	B-complex_assembly
-	I-complex_assembly
WASP	I-complex_assembly
structure	B-evidence
.	O

Cdc42	O
is	O
shown	O
in	O
green	O
,	O
and	O
TOCA1	B-protein
is	O
shown	O
in	O
purple	O
.	O

The	O
core	O
CRIB	B-structure_element
region	O
of	O
WASP	B-protein
is	O
shown	O
in	O
red	O
,	O
whereas	O
its	O
basic	O
region	O
is	O
shown	O
in	O
orange	O
and	O
the	O
C	O
-	O
terminal	O
region	O
required	O
for	O
maximal	O
affinity	O
is	O
shown	O
in	O
cyan	O
.	O

A	O
semitransparent	O
surface	O
representation	O
of	O
Cdc42	B-protein
and	O
WASP	B-protein
is	O
shown	O
overlaid	O
with	O
the	O
schematic	O
.	O

B	O
,	O
competition	B-experimental_method
SPA	I-experimental_method
experiments	O
carried	O
out	O
with	O
indicated	O
concentrations	O
of	O
the	O
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
construct	O
titrated	B-experimental_method
into	O
30	O
nm	O
GST	B-mutant
-	I-mutant
ACK	I-mutant
or	O
GST	B-mutant
-	I-mutant
WASP	I-mutant
GBD	B-structure_element
and	O
30	O
nm	O
Cdc42Δ7Q61L	B-complex_assembly
·[	I-complex_assembly
3H	I-complex_assembly
]	I-complex_assembly
GTP	I-complex_assembly
.	O

C	O
,	O
Selected	O
regions	O
of	O
the	O
15N	B-experimental_method
HSQC	I-experimental_method
of	O
145	O
μm	O
Cdc42Δ7Q61L	B-complex_assembly
·	I-complex_assembly
GMPPNP	I-complex_assembly
with	O
the	O
indicated	O
ratios	O
of	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
,	O
the	O
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
,	O
or	O
both	O
,	O
showing	O
that	O
the	O
TOCA	B-protein
HR1	B-structure_element
domain	O
does	O
not	O
displace	O
the	O
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
.	O

D	O
,	O
selected	O
regions	O
of	O
the	O
15N	B-experimental_method
HSQC	I-experimental_method
of	O
600	O
μm	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
in	B-protein_state
complex	I-protein_state
with	I-protein_state
Cdc42	B-protein
in	O
the	O
absence	B-protein_state
and	O
presence	B-protein_state
of	I-protein_state
the	O
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
,	O
showing	O
displacement	O
of	O
Cdc42	B-protein
from	O
the	O
HR1	B-structure_element
domain	O
by	O
N	B-protein
-	I-protein
WASP	I-protein
.	O

An	O
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
construct	O
was	O
produced	O
,	O
and	O
its	O
affinity	B-evidence
for	O
Cdc42	B-protein
was	O
measured	O
by	O
competition	B-experimental_method
SPA	I-experimental_method
(	O
Fig	O
.	O
7B	O
).	O

The	O
Kd	B-evidence
that	O
was	O
determined	O
(	O
37	O
nm	O
)	O
is	O
consistent	O
with	O
the	O
previously	O
reported	O
affinity	B-evidence
.	O

Unlabeled	B-protein_state
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
was	O
titrated	B-experimental_method
into	O
15N	B-chemical
-	O
Cdc42Δ7Q61L	B-complex_assembly
·	I-complex_assembly
GMPPNP	I-complex_assembly
,	O
and	O
the	O
backbone	O
NH	O
groups	O
were	O
monitored	O
using	O
HSQCs	B-experimental_method
(	O
Fig	O
.	O
7C	O
).	O

Unlabeled	B-protein_state
HR1TOCA1	B-structure_element
was	O
then	O
added	O
to	O
the	O
Cdc42	B-complex_assembly
·	I-complex_assembly
N	I-complex_assembly
-	I-complex_assembly
WASP	I-complex_assembly
complex	O
,	O
and	O
no	O
changes	O
were	O
seen	O
,	O
suggesting	O
that	O
the	O
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
was	O
not	O
displaced	O
even	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
a	O
5	O
-	O
fold	O
excess	O
of	O
HR1TOCA1	B-structure_element
.	O

These	O
experiments	O
were	O
recorded	O
at	O
sufficiently	O
high	O
protein	O
concentrations	O
(	O
145	O
μm	O
Cdc42	B-protein
,	O
145	O
μm	O
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
,	O
725	O
μm	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
)	O
to	O
be	O
far	O
in	O
excess	O
of	O
the	O
Kd	B-evidence
values	O
of	O
the	O
individual	O
interactions	O
(	O
TOCA1	B-protein
Kd	B-evidence
≈	O
5	O
μm	O
,	O
N	B-protein
-	I-protein
WASP	I-protein
Kd	B-evidence
=	O
37	O
nm	O
).	O

A	O
comparison	O
of	O
the	O
HSQC	B-experimental_method
experiments	O
recorded	O
on	O
15N	B-chemical
-	O
Cdc42	B-protein
alone	B-protein_state
,	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
TOCA1	B-protein
HR1	B-structure_element
,	O
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
,	O
or	O
both	O
,	O
shows	O
that	O
the	O
spectra	B-evidence
in	O
the	O
presence	B-protein_state
of	I-protein_state
N	B-protein
-	I-protein
WASP	I-protein
and	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
both	O
N	B-protein
-	I-protein
WASP	I-protein
and	O
TOCA1	B-protein
HR1	B-structure_element
are	O
identical	O
(	O
Fig	O
.	O
7C	O
).	O

Furthermore	O
,	O
15N	B-chemical
-	O
TOCA1	B-protein
HR1	B-structure_element
was	O
monitored	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
unlabeled	B-protein_state
Cdc42Δ7Q61L	B-complex_assembly
·	I-complex_assembly
GMPPNP	I-complex_assembly
(	O
1	O
:	O
1	O
)	O
before	O
and	O
after	O
the	O
addition	O
of	O
0	O
.	O
25	O
and	O
1	O
.	O
0	O
eq	O
of	O
unlabeled	B-protein_state
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
.	O

The	O
spectrum	B-evidence
when	O
N	B-protein
-	I-protein
WASP	I-protein
and	O
TOCA1	B-protein
were	O
equimolar	O
was	O
identical	O
to	O
that	O
of	O
the	O
free	B-protein_state
HR1	B-structure_element
domain	O
,	O
whereas	O
the	O
spectrum	B-evidence
in	O
the	O
presence	B-protein_state
of	I-protein_state
0	O
.	O
25	O
eq	O
of	O
N	B-protein
-	I-protein
WASP	I-protein
was	O
intermediate	O
between	O
the	O
TOCA1	B-protein
HR1	B-structure_element
free	B-protein_state
and	O
complex	B-protein_state
spectra	B-evidence
(	O
Fig	O
.	O
7D	O
).	O

When	O
in	O
fast	O
exchange	O
,	O
the	O
NMR	B-experimental_method
signal	O
represents	O
a	O
population	O
-	O
weighted	O
average	O
between	O
free	B-protein_state
and	O
bound	B-protein_state
states	O
,	O
so	O
the	O
intermediate	O
spectrum	B-evidence
indicates	O
that	O
the	O
population	O
comprises	O
a	O
mixture	O
of	O
free	B-protein_state
and	O
bound	B-protein_state
HR1	B-structure_element
domain	O
.	O

Again	O
,	O
the	O
experiments	O
were	O
recorded	O
on	O
protein	O
samples	O
far	O
in	O
excess	O
of	O
the	O
individual	O
Kd	B-evidence
values	O
(	O
600	O
μm	O
each	O
protein	O
).	O

These	O
data	O
indicate	O
that	O
the	O
HR1	B-structure_element
domain	O
is	O
displaced	O
from	O
Cdc42	B-protein
by	O
N	B-protein
-	I-protein
WASP	I-protein
and	O
that	O
a	O
ternary	O
complex	O
comprising	O
TOCA1	B-protein
HR1	B-structure_element
,	O
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
,	O
and	O
Cdc42	B-protein
is	O
not	O
formed	O
.	O

Taken	O
together	O
,	O
the	O
data	O
in	O
Fig	O
.	O
7	O
,	O
C	O
and	O
D	O
,	O
indicate	O
unidirectional	O
competition	O
for	O
Cdc42	B-protein
binding	O
in	O
which	O
the	O
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
displaces	O
TOCA1	B-protein
HR1	B-structure_element
but	O
not	O
vice	O
versa	O
.	O

To	O
extend	O
these	O
studies	O
to	O
a	O
more	O
complex	O
system	O
and	O
to	O
assess	O
the	O
ability	O
of	O
TOCA1	B-protein
HR1	B-structure_element
to	O
compete	O
with	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
N	B-protein
-	I-protein
WASP	I-protein
,	O
pyrene	B-experimental_method
actin	I-experimental_method
assays	I-experimental_method
were	O
employed	O
.	O

These	O
assays	O
,	O
described	O
in	O
detail	O
elsewhere	O
,	O
were	O
carried	O
out	O
using	O
pyrene	B-chemical
actin	I-chemical
-	O
supplemented	O
Xenopus	B-taxonomy_domain
extracts	O
into	O
which	O
exogenous	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
or	O
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
was	O
added	O
,	O
to	O
assess	O
their	O
effects	O
on	O
actin	B-protein_type
polymerization	O
.	O

Actin	B-protein_type
polymerization	O
in	O
all	O
cases	O
was	O
initiated	O
by	O
the	O
addition	O
of	O
PI	B-chemical
(	I-chemical
4	I-chemical
,	I-chemical
5	I-chemical
)	I-chemical
P2	I-chemical
-	O
containing	O
liposomes	O
.	O

Actin	B-protein_type
polymerization	O
triggered	O
by	O
the	O
addition	O
of	O
PI	B-chemical
(	I-chemical
4	I-chemical
,	I-chemical
5	I-chemical
)	I-chemical
P2	I-chemical
-	O
containing	O
liposomes	O
has	O
previously	O
been	O
shown	O
to	O
depend	O
on	O
TOCA1	B-protein
and	O
N	B-protein
-	I-protein
WASP	I-protein
.	O

Endogenous	O
N	B-protein
-	I-protein
WASP	I-protein
is	O
present	O
at	O
∼	O
100	O
nm	O
in	O
Xenopus	B-taxonomy_domain
extracts	O
,	O
whereas	O
TOCA1	B-protein
is	O
present	O
at	O
a	O
10	O
-	O
fold	O
lower	O
concentration	O
than	O
N	B-protein
-	I-protein
WASP	I-protein
.	O

The	O
addition	B-experimental_method
of	O
the	O
isolated	O
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
significantly	O
inhibited	O
the	O
polymerization	O
of	O
actin	B-protein_type
at	O
concentrations	O
as	O
low	O
as	O
100	O
nm	O
and	O
completely	O
abolished	O
polymerization	O
at	O
higher	O
concentrations	O
(	O
Fig	O
.	O
8	O
).	O

The	O
GBD	B-structure_element
presumably	O
acts	O
as	O
a	O
dominant	O
negative	O
,	O
sequestering	O
endogenous	O
Cdc42	B-protein
and	O
preventing	O
endogenous	B-protein_state
full	B-protein_state
-	I-protein_state
length	I-protein_state
N	B-protein
-	I-protein
WASP	I-protein
from	O
binding	O
and	O
becoming	O
activated	O
.	O

The	O
addition	B-experimental_method
of	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
to	O
100	O
μm	O
had	O
no	O
significant	O
effect	O
on	O
the	O
rate	O
of	O
actin	B-protein_type
polymerization	O
or	O
maximum	B-evidence
fluorescence	I-evidence
.	O

This	O
is	O
consistent	O
with	O
endogenous	B-protein_state
N	B-protein
-	I-protein
WASP	I-protein
,	O
activated	O
by	O
other	O
components	O
of	O
the	O
assay	O
,	O
outcompeting	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
for	O
Cdc42	B-protein
binding	O
.	O

Actin	O
polymerization	O
downstream	O
of	O
Cdc42	B-complex_assembly
·	I-complex_assembly
N	I-complex_assembly
-	I-complex_assembly
WASP	I-complex_assembly
·	I-complex_assembly
TOCA1	I-complex_assembly
is	O
inhibited	B-protein_state
by	O
excess	O
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
but	O
not	O
by	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
.	O

Fluorescence	B-evidence
curves	I-evidence
show	O
actin	O
polymerization	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
increasing	B-experimental_method
concentrations	I-experimental_method
of	O
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
or	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
as	O
indicated	O
.	O

The	O
Cdc42	B-protein
-	O
TOCA1	B-protein
Interaction	O

The	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
alone	B-protein_state
is	O
sufficient	O
for	O
Cdc42	B-protein
binding	O
in	O
vitro	O
,	O
yet	O
the	O
affinity	B-evidence
of	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
for	O
Cdc42	B-protein
is	O
remarkably	O
low	O
(	O
Kd	B-evidence
≈	O
5	O
μm	O
).	O

This	O
is	O
over	O
100	O
times	O
lower	O
than	O
that	O
of	O
the	O
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
(	O
Kd	B-evidence
=	O
37	O
nm	O
)	O
and	O
considerably	O
lower	O
than	O
other	O
known	O
G	B-protein_type
protein	I-protein_type
-	O
HR1	B-structure_element
domain	O
interactions	O
.	O

The	O
polybasic	O
tract	O
within	O
the	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
region	I-structure_element
of	O
Cdc42	B-protein
does	O
not	O
appear	O
to	O
be	O
required	O
for	O
binding	O
to	O
TOCA1	B-protein
,	O
which	O
is	O
in	O
contrast	O
to	O
the	O
interaction	O
between	O
Rac1	B-protein
and	O
the	O
HR1b	B-structure_element
domain	O
of	O
PRK1	B-protein
but	O
more	O
similar	O
to	O
the	O
PRK1	B-protein
HR1a	B-structure_element
-	O
RhoA	B-protein
interaction	O
.	O

A	O
single	O
binding	B-site
interface	I-site
on	O
both	O
the	O
HR1	B-structure_element
domain	O
and	O
Cdc42	B-protein
can	O
be	O
concluded	O
from	O
the	O
data	O
presented	O
here	O
.	O

Furthermore	O
,	O
the	O
interfaces	B-site
are	O
comparable	O
with	O
those	O
of	O
other	O
G	B-protein_type
protein	I-protein_type
-	O
HR1	B-structure_element
interactions	O
(	O
Fig	O
.	O
4	O
),	O
and	O
the	O
lowest	O
energy	O
model	B-evidence
produced	O
in	O
rigid	B-experimental_method
body	I-experimental_method
docking	I-experimental_method
resembles	O
previously	O
studied	O
G	B-complex_assembly
protein	I-complex_assembly
·	I-complex_assembly
HR1	I-complex_assembly
complexes	O
(	O
Fig	O
.	O
6	O
).	O

It	O
seems	O
,	O
therefore	O
,	O
that	O
the	O
interaction	O
,	O
despite	O
its	O
relatively	O
low	O
affinity	O
,	O
is	O
specific	O
and	O
sterically	O
similar	O
to	O
other	O
HR1	B-structure_element
domain	O
-	O
G	B-protein_type
protein	I-protein_type
interactions	O
.	O

The	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
is	O
a	O
left	O
-	O
handed	O
coiled	B-structure_element
-	I-structure_element
coil	I-structure_element
comparable	O
with	O
other	O
known	O
HR1	B-structure_element
domains	O
.	O

A	O
short	O
region	O
N	O
-	O
terminal	O
to	O
the	O
coiled	B-structure_element
-	I-structure_element
coil	I-structure_element
exhibits	O
a	O
series	O
of	O
turns	O
and	O
contacts	O
residues	O
of	O
both	O
helices	O
of	O
the	O
coiled	B-structure_element
-	I-structure_element
coil	I-structure_element
(	O
Fig	O
.	O
3	O
).	O

The	O
corresponding	O
sequence	O
in	O
CIP4	B-protein
also	O
includes	O
a	O
series	O
of	O
turns	O
but	O
is	O
flexible	O
,	O
whereas	O
in	O
the	O
HR1a	B-structure_element
domain	O
of	O
PRK1	B-protein
,	O
the	O
equivalent	O
region	O
adopts	O
an	O
α	B-structure_element
-	I-structure_element
helical	I-structure_element
structure	I-structure_element
that	O
packs	O
against	O
the	O
coiled	B-structure_element
-	I-structure_element
coil	I-structure_element
.	O

The	O
contacts	O
between	O
the	O
N	O
-	O
terminal	O
region	O
and	O
the	O
coiled	B-structure_element
-	I-structure_element
coil	I-structure_element
are	O
predominantly	O
hydrophobic	O
in	O
both	O
cases	O
,	O
but	O
sequence	O
-	O
specific	O
contacts	O
do	O
not	O
appear	O
to	O
be	O
conserved	O
.	O

This	O
region	O
is	O
distant	O
from	O
the	O
G	B-site
protein	I-site
-	I-site
binding	I-site
interface	I-site
of	O
the	O
HR1	B-structure_element
domains	O
,	O
so	O
the	O
structural	O
differences	O
may	O
relate	O
to	O
the	O
structure	O
and	O
regulation	O
of	O
these	O
domains	O
rather	O
than	O
their	O
G	B-protein_type
protein	I-protein_type
interactions	O
.	O

The	O
interhelical	B-structure_element
loops	I-structure_element
of	O
TOCA1	B-protein
and	O
CIP4	B-protein
differ	O
from	O
the	O
same	O
region	O
in	O
the	O
HR1	B-structure_element
domains	O
of	O
PRK1	B-protein
in	O
that	O
they	O
are	O
longer	O
and	O
contain	O
two	O
short	O
stretches	O
of	O
310	B-structure_element
-	I-structure_element
helix	I-structure_element
.	O

This	O
region	O
lies	O
within	O
the	O
G	B-site
protein	I-site
-	I-site
binding	I-site
surface	I-site
of	O
all	O
of	O
the	O
HR1	B-structure_element
domains	O
(	O
Fig	O
.	O
4D	O
).	O

TOCA1	B-protein
and	O
CIP4	B-protein
both	O
bind	O
weakly	O
to	O
Cdc42	B-protein
,	O
whereas	O
the	O
HR1a	B-structure_element
domain	O
of	O
PRK1	B-protein
binds	O
tightly	O
to	O
RhoA	B-protein
and	O
Rac1	B-protein
,	O
and	O
the	O
HR1b	B-structure_element
domain	O
binds	O
to	O
Rac1	B-protein
.	O

The	O
structural	O
features	O
shared	O
by	O
TOCA1	B-protein
and	O
CIP4	B-protein
may	O
therefore	O
be	O
related	O
to	O
Cdc42	B-protein
binding	O
specificity	O
and	O
the	O
low	O
affinities	O
.	O

In	O
free	B-protein_state
TOCA1	B-protein
,	O
the	O
side	O
chains	O
of	O
the	O
interhelical	B-structure_element
region	I-structure_element
make	O
extensive	O
contacts	O
with	O
residues	O
in	O
helix	B-structure_element
1	I-structure_element
.	O

Many	O
of	O
these	O
residues	O
are	O
significantly	O
affected	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
Cdc42	B-protein
,	O
so	O
it	O
is	O
likely	O
that	O
the	O
conformation	O
of	O
this	O
loop	B-structure_element
is	O
altered	O
in	O
the	O
Cdc42	B-protein
complex	O
.	O

These	O
observations	O
therefore	O
provide	O
a	O
molecular	O
mechanism	O
whereby	O
mutation	B-experimental_method
of	O
Met383	B-residue_name_number
-	O
Gly384	B-residue_name_number
-	O
Asp385	B-residue_name_number
to	O
Ile383	B-residue_name_number
-	O
Ser384	B-residue_name_number
-	O
Thr385	B-residue_name_number
abolishes	O
TOCA1	B-protein
binding	O
to	O
Cdc42	B-protein
.	O

The	O
lowest	O
energy	O
model	B-evidence
produced	O
by	O
HADDOCK	B-experimental_method
using	O
ambiguous	O
interaction	O
restraints	O
from	O
the	O
titration	B-evidence
data	O
resembled	O
the	O
NMR	B-experimental_method
structures	B-evidence
of	O
RhoA	B-protein
and	O
Rac1	B-protein
in	B-protein_state
complex	I-protein_state
with	I-protein_state
their	O
HR1	B-structure_element
domain	O
partners	O
.	O

For	O
example	O
,	O
Phe	B-residue_name_number
-	I-residue_name_number
56Cdc42	I-residue_name_number
,	O
which	O
is	O
not	O
visible	O
in	O
free	B-protein_state
Cdc42	B-protein
or	O
Cdc42	B-complex_assembly
·	I-complex_assembly
HR1TOCA1	I-complex_assembly
,	O
is	O
close	O
to	O
the	O
TOCA1	B-protein
HR1	B-structure_element
(	O
Fig	O
.	O
6A	O
).	O

Phe	B-residue_name_number
-	I-residue_name_number
56Cdc42	I-residue_name_number
,	O
which	O
is	O
a	O
Trp	B-residue_name
in	O
both	O
Rac1	B-protein
and	O
RhoA	B-protein
(	O
Fig	O
.	O
6C	O
),	O
is	O
thought	O
to	O
pack	O
behind	O
switch	B-site
I	I-site
when	O
Cdc42	B-protein
interacts	O
with	O
ACK	B-protein
,	O
maintaining	O
the	O
switch	O
in	O
a	O
binding	O
-	O
competent	O
orientation	O
.	O

This	O
residue	O
has	O
also	O
been	O
identified	O
as	O
important	O
for	O
Cdc42	B-protein
-	O
WASP	B-protein
binding	O
.	O

Phe	B-residue_name_number
-	I-residue_name_number
56Cdc42	I-residue_name_number
is	O
therefore	O
likely	O
to	O
be	O
involved	O
in	O
the	O
Cdc42	B-protein
-	O
TOCA1	B-protein
interaction	O
,	O
probably	O
by	O
stabilizing	O
the	O
position	O
of	O
switch	B-site
I	I-site
.	O

Some	O
residues	O
that	O
are	O
affected	O
in	O
the	O
Cdc42	B-complex_assembly
·	I-complex_assembly
HR1TOCA1	I-complex_assembly
complex	O
but	O
do	O
not	O
correspond	O
to	O
contact	O
residues	O
of	O
RhoA	B-protein
or	O
Rac1	B-protein
(	O
Fig	O
.	O
6C	O
)	O
may	O
contact	O
HR1TOCA1	B-structure_element
directly	O
(	O
Fig	O
.	O
6D	O
).	O

Gln	B-residue_name_number
-	I-residue_name_number
2Cdc42	I-residue_name_number
,	O
which	O
has	O
also	O
been	O
identified	O
as	O
a	O
contact	O
residue	O
in	O
the	O
Cdc42	B-complex_assembly
·	I-complex_assembly
ACK	I-complex_assembly
complex	O
,	O
contacts	O
Val	B-residue_name_number
-	I-residue_name_number
376TOCA1	I-residue_name_number
and	O
Asn	B-residue_name_number
-	I-residue_name_number
380TOCA1	I-residue_name_number
in	O
the	O
model	O
and	O
disrupts	O
the	O
contacts	O
between	O
the	O
interhelical	B-structure_element
loop	I-structure_element
and	O
the	O
first	B-structure_element
helix	I-structure_element
of	O
the	O
TOCA1	B-protein
coiled	B-structure_element
-	I-structure_element
coil	I-structure_element
.	O

Thr	B-residue_name_number
-	I-residue_name_number
52Cdc42	I-residue_name_number
,	O
which	O
has	O
also	O
been	O
identified	O
as	O
making	O
minor	O
contacts	O
with	O
ACK	B-protein
,	O
falls	O
near	O
the	O
side	O
chains	O
of	O
HR1TOCA1	B-structure_element
helix	B-structure_element
1	I-structure_element
,	O
particularly	O
Lys	B-residue_name_number
-	I-residue_name_number
372TOCA1	I-residue_name_number
,	O
whereas	O
the	O
equivalent	O
position	O
in	O
Rac1	B-protein
is	O
Asn	B-residue_name_number
-	I-residue_name_number
52Rac1	I-residue_name_number
.	O

N52T	B-mutant
is	O
one	O
of	O
a	O
combination	O
of	O
seven	O
residues	O
found	O
to	O
confer	O
ACK	B-protein
binding	O
on	O
Rac1	B-protein
and	O
so	O
may	O
represent	O
a	O
specific	O
Cdc42	B-protein
-	O
effector	O
contact	O
residue	O
.	O

The	O
position	O
equivalent	O
to	O
Lys	B-residue_name_number
-	I-residue_name_number
372TOCA1	I-residue_name_number
in	O
PRK1	B-protein
is	O
Glu	B-residue_name_number
-	I-residue_name_number
58HR1a	I-residue_name_number
or	O
Gln	B-residue_name_number
-	I-residue_name_number
151HR1b	I-residue_name_number
.	O

Thr	B-residue_name_number
-	I-residue_name_number
52Cdc42	I-residue_name_number
-	O
Lys	B-residue_name_number
-	I-residue_name_number
372TOCA1	I-residue_name_number
may	O
therefore	O
represent	O
a	O
specific	O
Cdc42	B-protein
-	O
HR1TOCA1	B-structure_element
contact	O
.	O

Arg	B-residue_name_number
-	I-residue_name_number
68Cdc42	I-residue_name_number
of	O
switch	B-site
II	I-site
is	O
positioned	O
close	O
to	O
Glu	B-residue_name_number
-	I-residue_name_number
395TOCA1	I-residue_name_number
(	O
Fig	O
.	O
6D	O
),	O
suggesting	O
a	O
direct	O
electrostatic	O
contact	O
between	O
switch	B-site
II	I-site
of	O
Cdc42	B-protein
and	O
helix	B-structure_element
2	I-structure_element
of	O
the	O
HR1	B-structure_element
domain	O
.	O

The	O
equivalent	O
Arg	B-residue_name
in	O
Rac1	B-protein
and	O
RhoA	B-protein
is	O
pointing	O
away	O
from	O
the	O
HR1	B-structure_element
domains	O
of	O
PRK1	B-protein
.	O

The	O
importance	O
of	O
this	O
residue	O
in	O
the	O
Cdc42	B-protein
-	O
TOCA1	B-protein
interaction	O
remains	O
unclear	O
,	O
although	O
its	O
mutation	B-experimental_method
reduces	O
binding	O
to	O
RhoGAP	B-protein
,	O
suggesting	O
that	O
it	O
can	O
be	O
involved	O
in	O
Cdc42	B-protein
interactions	O
.	O

The	O
solution	B-evidence
structure	I-evidence
of	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
presented	O
here	O
,	O
along	O
with	O
the	O
model	O
of	O
the	O
HR1TOCA1	B-complex_assembly
·	I-complex_assembly
Cdc42	I-complex_assembly
complex	O
is	O
consistent	O
with	O
a	O
conserved	O
mode	O
of	O
binding	O
across	O
the	O
known	O
HR1	B-structure_element
domain	O
-	O
Rho	O
family	O
interactions	O
,	O
despite	O
their	O
differing	O
affinities	O
.	O

The	O
weak	O
binding	O
prevented	O
detailed	O
structural	B-experimental_method
and	I-experimental_method
thermodynamic	I-experimental_method
studies	I-experimental_method
of	O
the	O
complex	O
.	O

Nonetheless	O
,	O
structural	B-experimental_method
studies	I-experimental_method
of	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
,	O
combined	O
with	O
chemical	B-experimental_method
shift	I-experimental_method
mapping	I-experimental_method
,	O
have	O
highlighted	O
some	O
potentially	O
interesting	O
differences	O
between	O
Cdc42	B-protein
-	O
HR1TOCA1	B-structure_element
and	O
RhoA	B-protein
/	O
Rac1	B-protein
-	O
HR1PRK1	B-structure_element
binding	O
.	O

We	O
have	O
previously	O
postulated	O
that	O
the	O
inherent	O
flexibility	O
of	O
HR1	B-structure_element
domains	O
contributes	O
to	O
their	O
ability	O
to	O
bind	O
to	O
different	O
Rho	B-protein_type
family	I-protein_type
G	I-protein_type
proteins	I-protein_type
,	O
with	O
Rho	O
-	O
binding	O
HR1	B-structure_element
domains	O
displaying	O
increased	O
flexibility	O
,	O
reflected	O
in	O
their	O
lower	O
melting	B-evidence
temperatures	I-evidence
(	O
Tm	B-evidence
)	O
and	O
Rac	B-protein_type
binders	O
being	O
more	O
rigid	O
.	O

The	O
Tm	B-evidence
of	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
is	O
61	O
.	O
9	O
°	O
C	O
(	O
data	O
not	O
shown	O
),	O
which	O
is	O
the	O
highest	O
Tm	B-evidence
that	O
we	O
have	O
measured	O
for	O
an	O
HR1	B-structure_element
domain	O
thus	O
far	O
.	O

As	O
such	O
,	O
the	O
ability	O
of	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
to	O
bind	O
to	O
Cdc42	B-protein
(	O
a	O
close	O
relative	O
of	O
Rac1	B-protein
rather	O
than	O
RhoA	B-protein
)	O
fits	O
this	O
trend	O
.	O

An	O
investigation	O
into	O
the	O
local	O
motions	O
,	O
particularly	O
in	O
the	O
G	B-site
protein	I-site
-	I-site
binding	I-site
regions	I-site
,	O
may	O
offer	O
further	O
insight	O
into	O
the	O
differential	O
specificities	O
and	O
affinities	O
of	O
G	B-protein_type
protein	I-protein_type
-	O
HR1	B-structure_element
domain	O
interactions	O
.	O

The	O
low	O
affinity	O
of	O
the	O
Cdc42	B-protein
-	O
HR1TOCA1	B-structure_element
interaction	O
is	O
consistent	O
with	O
a	O
tightly	O
spatially	O
and	O
temporally	O
regulated	O
pathway	O
,	O
requiring	O
combinatorial	O
signals	O
leading	O
to	O
a	O
series	O
of	O
coincident	O
weak	O
interactions	O
that	O
elicit	O
full	O
activation	O
.	O

The	O
HR1	B-structure_element
domains	O
from	O
other	O
TOCA	B-protein_type
family	I-protein_type
members	I-protein_type
,	O
CIP4	B-protein
and	O
FBP17	B-protein
,	O
also	O
bind	O
at	O
low	O
micromolar	O
affinities	O
to	O
Cdc42	B-protein
,	O
so	O
the	O
low	O
affinity	O
interaction	O
appears	O
to	O
be	O
commonplace	O
among	O
this	O
family	O
of	O
HR1	B-protein_type
domain	I-protein_type
proteins	I-protein_type
,	O
in	O
contrast	O
to	O
the	O
PRK	B-protein_type
family	I-protein_type
.	O

The	O
low	O
affinity	O
of	O
the	O
HR1TOCA1	B-structure_element
-	O
Cdc42	B-protein
interaction	O
in	O
the	O
context	O
of	O
the	O
physiological	O
concentration	O
of	O
TOCA1	B-protein
in	O
Xenopus	B-taxonomy_domain
extracts	O
(∼	O
10	O
nm	O
)	O
suggests	O
that	O
binding	O
between	O
TOCA1	B-protein
and	O
Cdc42	B-protein
is	O
likely	O
to	O
occur	O
in	O
vivo	O
only	O
when	O
TOCA1	B-protein
is	O
at	O
high	O
local	O
concentrations	O
and	O
membrane	O
-	O
localized	O
and	O
therefore	O
in	O
close	O
proximity	O
to	O
activated	B-protein_state
Cdc42	B-protein
.	O

Evidence	O
suggests	O
that	O
the	O
TOCA	B-protein_type
family	I-protein_type
of	O
proteins	O
are	O
recruited	O
to	O
the	O
membrane	O
via	O
an	O
interaction	O
between	O
their	O
F	B-structure_element
-	I-structure_element
BAR	I-structure_element
domain	O
and	O
specific	O
signaling	O
lipids	O
.	O

For	O
example	O
,	O
electrostatic	O
interactions	O
between	O
the	O
F	B-structure_element
-	I-structure_element
BAR	I-structure_element
domain	O
and	O
the	O
membrane	O
are	O
required	O
for	O
TOCA1	B-protein
recruitment	O
to	O
membrane	O
vesicles	O
and	O
tubules	O
,	O
and	O
TOCA1	B-protein
-	O
dependent	O
actin	O
polymerization	O
is	O
known	O
to	O
depend	O
specifically	O
on	O
PI	B-chemical
(	I-chemical
4	I-chemical
,	I-chemical
5	I-chemical
)	I-chemical
P2	I-chemical
.	O

Furthermore	O
,	O
the	O
isolated	B-experimental_method
F	B-structure_element
-	I-structure_element
BAR	I-structure_element
domain	O
of	O
FBP17	B-protein
has	O
been	O
shown	O
to	O
induce	O
membrane	O
tubulation	O
of	O
brain	O
liposomes	O
and	O
BAR	B-structure_element
domain	O
proteins	O
that	O
promote	O
tubulation	O
cluster	O
on	O
membranes	O
at	O
high	O
densities	O
.	O

Once	O
at	O
the	O
membrane	O
,	O
high	O
local	O
concentrations	O
of	O
TOCA1	B-protein
could	O
exceed	O
the	O
Kd	B-evidence
of	O
F	B-structure_element
-	I-structure_element
BAR	I-structure_element
dimerization	B-oligomeric_state
(	O
likely	O
to	O
be	O
comparable	O
with	O
that	O
of	O
the	O
FCHo2	B-protein
F	B-structure_element
-	I-structure_element
BAR	I-structure_element
domain	O
(	O
2	O
.	O
5	O
μm	O
))	O
and	O
that	O
of	O
the	O
Cdc42	B-protein
-	O
HR1TOCA1	B-structure_element
interaction	O
.	O

Cdc42	B-protein
-	O
HR1TOCA1	B-structure_element
binding	O
would	O
then	O
be	O
favorable	O
,	O
as	O
long	O
as	O
coincident	O
activation	O
of	O
Cdc42	B-protein
had	O
occurred	O
,	O
leading	O
to	O
stabilization	O
of	O
TOCA1	B-protein
at	O
the	O
membrane	O
and	O
downstream	O
activation	O
of	O
N	B-protein
-	I-protein
WASP	I-protein
.	O

It	O
has	O
been	O
postulated	O
that	O
WASP	B-protein_type
and	O
N	B-protein
-	I-protein
WASP	I-protein
exist	O
in	O
equilibrium	O
between	O
folded	B-protein_state
(	O
inactive	B-protein_state
)	O
and	O
unfolded	B-protein_state
(	O
active	B-protein_state
)	O
forms	O
,	O
and	O
the	O
affinity	B-evidence
of	O
Cdc42	B-protein
for	O
the	O
unfolded	B-protein_state
WASP	B-protein_type
proteins	O
is	O
significantly	O
enhanced	O
.	O

The	O
unfolded	B-protein_state
,	O
high	O
affinity	O
state	O
of	O
WASP	B-protein_type
is	O
represented	O
by	O
a	O
short	O
peptide	B-chemical
,	O
the	O
GBD	B-structure_element
,	O
which	O
binds	O
with	O
a	O
low	O
nanomolar	O
affinity	O
to	O
Cdc42	B-protein
.	O

In	O
contrast	O
,	O
the	O
best	O
estimate	O
of	O
the	O
affinity	B-evidence
of	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
WASP	B-protein_type
for	O
Cdc42	B-protein
is	O
low	O
micromolar	O
.	O

In	O
the	O
inactive	B-protein_state
state	O
of	O
WASP	B-protein_type
,	O
the	O
actin	O
-	O
and	O
Arp2	B-complex_assembly
/	I-complex_assembly
3	I-complex_assembly
-	O
binding	O
VCA	B-structure_element
domain	O
contacts	O
the	O
GBD	B-structure_element
,	O
competing	O
for	O
Cdc42	B-protein
binding	O
.	O

The	O
high	O
affinity	O
of	O
Cdc42	B-protein
for	O
the	O
unfolded	B-protein_state
,	O
active	B-protein_state
form	O
pushes	O
the	O
equilibrium	O
in	O
favor	O
of	O
(	B-protein
N	I-protein
-)	I-protein
WASP	I-protein
activation	O
.	O

Binding	O
of	O
PI	B-chemical
(	I-chemical
4	I-chemical
,	I-chemical
5	I-chemical
)	I-chemical
P2	I-chemical
to	O
the	O
basic	O
region	O
just	O
N	O
-	O
terminal	O
to	O
the	O
GBD	B-structure_element
further	O
favors	O
the	O
active	B-protein_state
conformation	O
.	O

A	O
substantial	O
body	O
of	O
data	O
has	O
illuminated	O
the	O
complex	O
regulation	O
of	O
WASP	B-protein_type
/	I-protein_type
N	I-protein_type
-	I-protein_type
WASP	I-protein_type
proteins	I-protein_type
,	O
and	O
current	O
evidence	O
suggests	O
that	O
these	O
allosteric	O
activation	O
mechanisms	O
and	O
oligomerization	O
combine	O
to	O
regulate	O
WASP	B-protein_type
activity	O
,	O
allowing	O
the	O
synchronization	O
and	O
integration	O
of	O
multiple	O
potential	O
activation	O
signals	O
(	O
reviewed	O
in	O
Ref	O
.).	O

We	O
envisage	O
that	O
TOCA1	B-protein
is	O
first	O
recruited	O
to	O
the	O
appropriate	O
membrane	O
in	O
response	O
to	O
PI	B-chemical
(	I-chemical
4	I-chemical
,	I-chemical
5	I-chemical
)	I-chemical
P2	I-chemical
via	O
its	O
F	B-structure_element
-	I-structure_element
BAR	I-structure_element
domain	O
,	O
where	O
the	O
local	O
increase	O
in	O
concentration	O
favors	O
F	B-structure_element
-	I-structure_element
BAR	I-structure_element
-	O
mediated	O
dimerization	B-oligomeric_state
of	O
TOCA1	B-protein
.	O

Cdc42	B-protein
is	O
activated	O
in	O
response	O
to	O
co	O
-	O
incident	O
signals	O
and	O
can	O
then	O
bind	O
to	O
TOCA1	B-protein
,	O
further	O
stabilizing	O
TOCA1	B-protein
at	O
the	O
membrane	O
.	O

TOCA1	B-protein
can	O
then	O
recruit	O
N	B-protein
-	I-protein
WASP	I-protein
via	O
an	O
interaction	O
between	O
its	O
SH3	B-structure_element
domain	O
and	O
the	O
N	B-protein
-	I-protein
WASP	I-protein
proline	B-structure_element
-	I-structure_element
rich	I-structure_element
region	I-structure_element
.	O

The	O
recruitment	O
of	O
N	B-protein
-	I-protein
WASP	I-protein
alone	B-protein_state
and	O
of	O
the	O
N	B-complex_assembly
-	I-complex_assembly
WASP	I-complex_assembly
·	I-complex_assembly
WIP	I-complex_assembly
complex	O
by	O
TOCA1	B-protein
and	O
FBP17	B-protein
has	O
been	O
demonstrated	O
.	O

WIP	B-protein
inhibits	O
the	O
activation	O
of	O
N	B-protein
-	I-protein
WASP	I-protein
by	O
Cdc42	B-protein
,	O
an	O
effect	O
that	O
is	O
reversed	O
by	O
TOCA1	B-protein
.	O

It	O
may	O
therefore	O
be	O
envisaged	O
that	O
WIP	B-protein
and	O
TOCA1	B-protein
exert	O
opposing	O
allosteric	O
effects	O
on	O
N	B-protein
-	I-protein
WASP	I-protein
,	O
with	O
TOCA1	B-protein
favoring	O
the	O
unfolded	B-protein_state
,	O
active	B-protein_state
conformation	O
of	O
N	B-protein
-	I-protein
WASP	I-protein
and	O
increasing	O
its	O
affinity	O
for	O
Cdc42	B-protein
.	O

TOCA1	B-protein
may	O
also	O
activate	O
N	B-protein
-	I-protein
WASP	I-protein
by	O
effective	O
oligomerization	O
because	O
clustering	O
of	O
TOCA1	B-protein
at	O
the	O
membrane	O
following	O
coincident	O
interactions	O
with	O
PI	B-chemical
(	I-chemical
4	I-chemical
,	I-chemical
5	I-chemical
)	I-chemical
P2	I-chemical
and	O
Cdc42	B-protein
would	O
in	O
turn	O
lead	O
to	O
clustering	O
of	O
N	B-protein
-	I-protein
WASP	I-protein
,	O
in	O
addition	O
to	O
pushing	O
the	O
equilibrium	O
toward	O
the	O
unfolded	B-protein_state
,	O
active	B-protein_state
state	O
.	O

In	O
a	O
cellular	O
context	O
,	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
TOCA1	B-protein
and	O
N	B-protein
-	I-protein
WASP	I-protein
are	O
likely	O
to	O
have	O
similar	O
affinities	B-evidence
for	O
active	B-protein_state
Cdc42	B-protein
,	O
but	O
in	O
the	O
unfolded	B-protein_state
,	O
active	B-protein_state
conformation	O
,	O
the	O
affinity	B-evidence
of	O
N	B-protein
-	I-protein
WASP	I-protein
for	O
Cdc42	B-protein
dramatically	O
increases	O
.	O

Our	O
binding	B-evidence
data	I-evidence
suggest	O
that	O
TOCA1	B-protein
HR1	B-structure_element
binding	O
is	O
not	O
allosterically	O
regulated	O
,	O
and	O
our	O
NMR	B-experimental_method
data	O
,	O
along	O
with	O
the	O
high	O
stability	B-protein_state
of	O
TOCA1	B-protein
HR1	B-structure_element
,	O
suggest	O
that	O
there	O
is	O
no	O
widespread	O
conformational	O
change	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
Cdc42	B-protein
.	O

As	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
TOCA1	B-protein
and	O
the	O
isolated	B-protein_state
HR1	B-structure_element
domain	O
bind	O
Cdc42	B-protein
with	O
similar	O
affinities	O
,	O
the	O
N	B-protein
-	I-protein
WASP	I-protein
-	O
Cdc42	B-protein
interaction	O
will	O
be	O
favored	O
because	O
the	O
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
can	O
easily	O
outcompete	O
the	O
TOCA1	B-protein
HR1	B-structure_element
for	O
Cdc42	B-protein
.	O

A	O
combination	O
of	O
allosteric	O
activation	O
by	O
PI	B-chemical
(	I-chemical
4	I-chemical
,	I-chemical
5	I-chemical
)	I-chemical
P2	I-chemical
,	O
activated	B-protein_state
Cdc42	B-protein
and	O
TOCA1	B-protein
,	O
and	O
oligomeric	O
activation	O
implemented	O
by	O
TOCA1	B-protein
would	O
lead	O
to	O
full	B-protein_state
activation	I-protein_state
of	O
N	B-protein
-	I-protein
WASP	I-protein
and	O
downstream	O
actin	O
polymerization	O
.	O

In	O
such	O
an	O
array	O
of	O
molecules	O
localized	O
to	O
a	O
discrete	O
region	O
of	O
the	O
membrane	O
,	O
it	O
is	O
plausible	O
that	O
WASP	B-protein
could	O
bind	O
to	O
a	O
second	O
Cdc42	B-protein
molecule	O
rather	O
than	O
displacing	O
TOCA1	B-protein
from	O
its	O
cognate	O
Cdc42	B-protein
.	O

Our	O
NMR	B-experimental_method
and	O
affinity	B-evidence
data	I-evidence
,	O
however	O
,	O
are	O
consistent	O
with	O
displacement	O
of	O
the	O
TOCA1	B-protein
HR1	B-structure_element
by	O
the	O
N	B-protein
-	I-protein
WASP	I-protein
GBD	B-structure_element
.	O

Furthermore	O
,	O
TOCA1	B-protein
is	O
required	O
for	O
Cdc42	B-protein
-	O
mediated	O
activation	O
of	O
N	B-complex_assembly
-	I-complex_assembly
WASP	I-complex_assembly
·	I-complex_assembly
WIP	I-complex_assembly
,	O
implying	O
that	O
it	O
may	O
not	O
be	O
possible	O
for	O
Cdc42	B-protein
to	O
bind	O
and	O
activate	O
N	B-protein
-	I-protein
WASP	I-protein
prior	O
to	O
TOCA1	B-protein
-	O
Cdc42	B-protein
binding	O
.	O

The	O
commonly	O
used	O
MGD	B-mutant
→	I-mutant
IST	I-mutant
(	O
Cdc42	B-protein_state
-	I-protein_state
binding	I-protein_state
deficient	I-protein_state
)	O
mutant	O
of	O
TOCA1	B-protein
has	O
a	O
reduced	O
ability	O
to	O
activate	O
the	O
N	B-complex_assembly
-	I-complex_assembly
WASP	I-complex_assembly
·	I-complex_assembly
WIP	I-complex_assembly
complex	O
,	O
further	O
indicating	O
the	O
importance	O
of	O
the	O
Cdc42	B-protein
-	O
HR1TOCA1	B-structure_element
interaction	O
prior	O
to	O
downstream	O
activation	O
of	O
N	B-protein
-	I-protein
WASP	I-protein
.	O

In	O
light	O
of	O
this	O
,	O
we	O
favor	O
an	O
“	O
effector	O
handover	O
”	O
scheme	O
whereby	O
TOCA1	B-protein
interacts	O
with	O
Cdc42	B-protein
prior	O
to	O
N	B-protein
-	I-protein
WASP	I-protein
activation	O
,	O
after	O
which	O
N	B-protein
-	I-protein
WASP	I-protein
displaces	O
TOCA1	B-protein
from	O
its	O
bound	B-protein_state
Cdc42	B-protein
in	O
order	O
to	O
be	O
fully	B-protein_state
activated	I-protein_state
rather	O
than	O
binding	O
a	O
second	O
Cdc42	B-protein
molecule	O
.	O

Potentially	O
,	O
the	O
TOCA1	B-protein
-	O
Cdc42	B-protein
interaction	O
functions	O
to	O
position	O
N	B-protein
-	I-protein
WASP	I-protein
and	O
Cdc42	B-protein
such	O
that	O
they	O
are	O
poised	O
to	O
interact	O
with	O
high	O
affinity	O
.	O

The	O
concomitant	O
release	O
of	O
TOCA1	B-protein
from	O
Cdc42	B-protein
while	O
still	O
bound	B-protein_state
to	I-protein_state
N	B-protein
-	I-protein
WASP	I-protein
presumably	O
enhances	O
the	O
ability	O
of	O
TOCA1	B-protein
to	O
further	O
activate	O
N	B-complex_assembly
-	I-complex_assembly
WASP	I-complex_assembly
·	I-complex_assembly
WIP	I-complex_assembly
-	O
induced	O
actin	O
polymerization	O
.	O

There	O
is	O
an	O
advantage	O
to	O
such	O
an	O
effector	O
handover	O
,	O
in	O
that	O
N	B-protein
-	I-protein
WASP	I-protein
would	O
only	O
be	O
robustly	O
recruited	O
when	O
F	B-structure_element
-	I-structure_element
BAR	I-structure_element
domains	O
are	O
already	O
present	O
.	O

Hence	O
,	O
actin	O
polymerization	O
cannot	O
occur	O
until	O
F	B-structure_element
-	I-structure_element
BAR	I-structure_element
domains	O
are	O
poised	O
for	O
membrane	O
distortion	O
.	O

Our	O
model	O
of	O
the	O
Cdc42	B-complex_assembly
·	I-complex_assembly
HR1TOCA1	I-complex_assembly
complex	O
indicates	O
a	O
mechanism	O
by	O
which	O
such	O
a	O
handover	O
could	O
take	O
place	O
(	O
Fig	O
.	O
9	O
)	O
because	O
it	O
shows	O
that	O
the	O
effector	B-site
binding	I-site
sites	I-site
only	O
partially	O
overlap	O
on	O
Cdc42	B-protein
.	O

The	O
lysine	B-residue_name
residues	O
thought	O
to	O
be	O
involved	O
in	O
an	O
electrostatic	O
steering	O
mechanism	O
in	O
WASP	B-protein
-	O
Cdc42	B-protein
binding	O
are	O
conserved	O
in	O
N	B-protein
-	I-protein
WASP	I-protein
and	O
would	O
be	O
able	O
to	O
interact	O
with	O
Cdc42	B-protein
even	O
when	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
is	O
already	O
bound	B-protein_state
.	O

It	O
has	O
been	O
postulated	O
that	O
the	O
initial	O
interactions	O
between	O
this	O
basic	O
region	O
and	O
Cdc42	B-protein
could	O
stabilize	O
the	O
active	B-protein_state
conformation	O
of	O
WASP	B-protein
,	O
leading	O
to	O
high	O
affinity	O
binding	O
between	O
the	O
core	O
CRIB	B-structure_element
and	O
Cdc42	B-protein
.	O

The	O
region	O
C	O
-	O
terminal	O
to	O
the	O
core	O
CRIB	B-structure_element
,	O
required	O
for	O
maximal	O
affinity	O
binding	O
,	O
would	O
then	O
fully	O
displace	O
the	O
TOCA1	B-protein
HR1	B-structure_element
.	O

A	O
simplified	O
model	O
of	O
the	O
early	O
stages	O
of	O
Cdc42	B-complex_assembly
·	I-complex_assembly
N	I-complex_assembly
-	I-complex_assembly
WASP	I-complex_assembly
·	I-complex_assembly
TOCA1	I-complex_assembly
-	O
dependent	O
actin	O
polymerization	O
.	O

Step	O
1	O
,	O
TOCA1	B-protein
is	O
recruited	O
to	O
the	O
membrane	O
via	O
its	O
F	B-structure_element
-	I-structure_element
BAR	I-structure_element
domain	O
and	O
/	O
or	O
Cdc42	B-protein
interactions	O
.	O

F	O
-	O
BAR	O
oligomerization	O
is	O
expected	O
to	O
occur	O
following	O
membrane	O
binding	O
,	O
but	O
a	O
single	O
monomer	B-oligomeric_state
is	O
shown	O
for	O
clarity	O
.	O

Step	O
2	O
,	O
N	B-protein
-	I-protein
WASP	I-protein
exists	O
in	O
an	O
inactive	B-protein_state
,	O
folded	B-protein_state
conformation	O
.	O

The	O
TOCA1	B-protein
SH3	B-structure_element
domain	O
interacts	O
with	O
N	B-protein
-	I-protein
WASP	I-protein
,	O
causing	O
an	O
activatory	O
allosteric	O
effect	O
.	O

The	O
HR1TOCA1	B-structure_element
-	O
Cdc42	O
and	O
SH3TOCA1	B-structure_element
-	O
N	O
-	O
WASP	O
interactions	O
position	O
Cdc42	B-protein
and	O
N	B-protein
-	I-protein
WASP	I-protein
for	O
binding	O
.	O

Step	O
3	O
,	O
electrostatic	O
interactions	O
between	O
Cdc42	B-protein
and	O
the	O
basic	O
region	O
upstream	O
of	O
the	O
CRIB	B-structure_element
initiate	O
Cdc42	B-complex_assembly
·	I-complex_assembly
N	I-complex_assembly
-	I-complex_assembly
WASP	I-complex_assembly
binding	O
.	O

Step	O
4	O
,	O
the	O
core	O
CRIB	B-structure_element
binds	O
with	O
high	O
affinity	O
while	O
the	O
region	O
C	O
-	O
terminal	O
to	O
the	O
CRIB	B-structure_element
displaces	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
and	O
increases	O
the	O
affinity	O
of	O
the	O
N	B-protein
-	I-protein
WASP	I-protein
-	O
Cdc42	O
interaction	O
further	O
.	O

The	O
VCA	B-structure_element
domain	O
is	O
released	O
for	O
downstream	O
interactions	O
,	O
and	O
actin	O
polymerization	O
proceeds	O
.	O

WH1	O
,	O
WASP	B-structure_element
homology	I-structure_element
1	I-structure_element
domain	I-structure_element
;	O
PP	B-structure_element
,	O
proline	B-structure_element
-	I-structure_element
rich	I-structure_element
region	I-structure_element
;	O
VCA	B-structure_element
,	O
verprolin	B-structure_element
homology	I-structure_element
,	I-structure_element
cofilin	I-structure_element
homology	I-structure_element
,	I-structure_element
acidic	I-structure_element
region	I-structure_element
.	O

In	O
conclusion	O
,	O
the	O
data	O
presented	O
here	O
show	O
that	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
is	O
sufficient	O
for	O
Cdc42	B-protein
binding	O
in	O
vitro	O
and	O
that	O
the	O
interaction	O
is	O
of	O
micromolar	O
affinity	O
,	O
lower	O
than	O
that	O
of	O
other	O
G	B-protein_type
protein	I-protein_type
-	O
HR1	B-structure_element
domain	O
interactions	O
.	O

The	O
analogous	O
HR1	B-structure_element
domains	O
from	O
other	O
TOCA1	B-protein_type
family	I-protein_type
members	O
,	O
FBP17	B-protein
and	O
CIP4	B-protein
,	O
also	O
exhibit	O
micromolar	O
affinity	O
for	O
Cdc42	B-protein
.	O

A	O
role	O
for	O
the	O
TOCA1	B-protein
-,	O
FBP17	B-protein
-,	O
and	O
CIP4	B-protein
-	O
Cdc42	B-protein
interactions	O
in	O
the	O
recruitment	O
of	O
these	O
proteins	O
to	O
the	O
membrane	O
therefore	O
appears	O
unlikely	O
.	O

Instead	O
,	O
our	O
findings	O
agree	O
with	O
earlier	O
suggestions	O
that	O
the	O
F	B-structure_element
-	I-structure_element
BAR	I-structure_element
domain	O
is	O
responsible	O
for	O
membrane	O
recruitment	O
.	O

The	O
role	O
of	O
the	O
Cdc42	B-protein
-	O
TOCA1	B-protein
interaction	O
remains	O
somewhat	O
elusive	O
,	O
but	O
it	O
may	O
serve	O
to	O
position	O
activated	B-protein_state
Cdc42	B-protein
and	O
N	B-protein
-	I-protein
WASP	I-protein
to	O
allow	O
full	B-protein_state
activation	I-protein_state
of	O
N	B-protein
-	I-protein
WASP	I-protein
and	O
as	O
such	O
serve	O
to	O
couple	O
F	B-structure_element
-	I-structure_element
BAR	I-structure_element
-	O
mediated	O
membrane	O
deformation	O
with	O
N	B-protein
-	I-protein
WASP	I-protein
activation	O
.	O

We	O
envisage	O
a	O
complex	O
interplay	O
of	O
equilibria	O
between	O
free	B-protein_state
and	O
bound	B-protein_state
,	O
active	B-protein_state
and	O
inactive	B-protein_state
Cdc42	B-protein
,	O
TOCA	B-protein_type
family	I-protein_type
,	O
and	O
WASP	B-protein_type
family	O
proteins	O
,	O
facilitating	O
a	O
tightly	O
spatially	O
and	O
temporally	O
regulated	O
pathway	O
requiring	O
numerous	O
simultaneous	O
events	O
in	O
order	O
to	O
achieve	O
appropriate	O
and	O
robust	O
activation	O
of	O
the	O
downstream	O
pathway	O
.	O

Our	O
data	O
are	O
therefore	O
easily	O
reconciled	O
with	O
the	O
dynamic	O
instability	O
models	O
described	O
in	O
relation	O
to	O
the	O
formation	O
of	O
endocytic	O
vesicles	O
and	O
with	O
the	O
current	O
data	O
pertaining	O
to	O
the	O
complex	O
activation	O
of	O
WASP	B-protein_type
/	O
N	B-protein
-	I-protein
WASP	I-protein
pathways	O
by	O
allosteric	O
and	O
oligomeric	O
effects	O
.	O

It	O
is	O
clear	O
from	O
the	O
data	O
presented	O
here	O
that	O
TOCA1	B-protein
and	O
N	B-protein
-	I-protein
WASP	I-protein
do	O
not	O
bind	O
Cdc42	B-protein
simultaneously	O
and	O
that	O
N	B-protein
-	I-protein
WASP	I-protein
is	O
likely	O
to	O
outcompete	O
TOCA1	B-protein
for	O
Cdc42	B-protein
binding	O
.	O

We	O
therefore	O
postulate	O
an	O
effector	O
handover	O
mechanism	O
based	O
on	O
current	O
evidence	O
surrounding	O
WASP	B-protein
/	O
N	B-protein
-	I-protein
WASP	I-protein
activation	O
and	O
our	O
model	O
of	O
the	O
Cdc42	B-complex_assembly
·	I-complex_assembly
HR1TOCA1	I-complex_assembly
complex	O
.	O

The	O
displacement	O
of	O
the	O
TOCA1	B-protein
HR1	B-structure_element
domain	O
from	O
Cdc42	B-protein
by	O
N	B-protein
-	I-protein
WASP	I-protein
may	O
represent	O
a	O
unidirectional	O
step	O
in	O
the	O
pathway	O
of	O
Cdc42	B-complex_assembly
·	I-complex_assembly
N	I-complex_assembly
-	I-complex_assembly
WASP	I-complex_assembly
·	I-complex_assembly
TOCA1	I-complex_assembly
-	O
dependent	O
actin	O
assembly	O
.	O

The	O
dynamic	B-protein_state
organization	O
of	O
fungal	B-taxonomy_domain
acetyl	B-protein_type
-	I-protein_type
CoA	I-protein_type
carboxylase	I-protein_type

Acetyl	B-protein_type
-	I-protein_type
CoA	I-protein_type
carboxylases	I-protein_type
(	O
ACCs	B-protein_type
)	O
catalyse	O
the	O
committed	O
step	O
in	O
fatty	O
-	O
acid	O
biosynthesis	O
:	O
the	O
ATP	B-chemical
-	O
dependent	O
carboxylation	O
of	O
acetyl	B-chemical
-	I-chemical
CoA	I-chemical
to	O
malonyl	B-chemical
-	I-chemical
CoA	I-chemical
.	O
They	O
are	O
important	O
regulatory	O
hubs	O
for	O
metabolic	O
control	O
and	O
relevant	O
drug	O
targets	O
for	O
the	O
treatment	O
of	O
the	O
metabolic	O
syndrome	O
and	O
cancer	O
.	O

Eukaryotic	B-taxonomy_domain
ACCs	B-protein_type
are	O
single	B-protein_type
-	I-protein_type
chain	I-protein_type
multienzymes	I-protein_type
characterized	O
by	O
a	O
large	O
,	O
non	B-protein_state
-	I-protein_state
catalytic	I-protein_state
central	B-structure_element
domain	I-structure_element
(	O
CD	B-structure_element
),	O
whose	O
role	O
in	O
ACC	B-protein_type
regulation	O
remains	O
poorly	O
characterized	O
.	O

Here	O
we	O
report	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
yeast	B-taxonomy_domain
ACC	B-protein_type
CD	B-structure_element
,	O
revealing	O
a	O
unique	O
four	O
-	O
domain	O
organization	O
.	O

A	O
regulatory	B-structure_element
loop	I-structure_element
,	O
which	O
is	O
phosphorylated	B-protein_state
at	O
the	O
key	O
functional	O
phosphorylation	B-site
site	I-site
of	O
fungal	B-taxonomy_domain
ACC	B-protein_type
,	O
wedges	O
into	O
a	O
crevice	O
between	O
two	O
domains	O
of	O
CD	B-structure_element
.	O

Combining	O
the	O
yeast	B-taxonomy_domain
CD	B-structure_element
structure	B-evidence
with	O
intermediate	O
and	O
low	O
-	O
resolution	O
data	O
of	O
larger	B-mutant
fragments	I-mutant
up	O
to	O
intact	B-protein_state
ACCs	B-protein_type
provides	O
a	O
comprehensive	O
characterization	O
of	O
the	O
dynamic	B-protein_state
fungal	B-taxonomy_domain
ACC	B-protein_type
architecture	O
.	O

In	O
contrast	O
to	O
related	O
carboxylases	B-protein_type
,	O
large	O
-	O
scale	O
conformational	O
changes	O
are	O
required	O
for	O
substrate	O
turnover	O
,	O
and	O
are	O
mediated	O
by	O
the	O
CD	B-structure_element
under	O
phosphorylation	B-ptm
control	O
.	O

Acetyl	B-protein_type
-	I-protein_type
CoA	I-protein_type
carboxylases	I-protein_type
are	O
central	O
regulatory	O
hubs	O
of	O
fatty	O
acid	O
metabolism	O
and	O
are	O
important	O
targets	O
for	O
drug	O
development	O
in	O
obesity	O
and	O
cancer	O
.	O

Here	O
,	O
the	O
authors	O
demonstrate	O
that	O
the	O
regulation	O
of	O
these	O
highly	B-protein_state
dynamic	I-protein_state
enzymes	B-protein_type
in	O
fungi	B-taxonomy_domain
is	O
governed	O
by	O
a	O
mechanism	O
based	O
on	O
phosphorylation	B-ptm
-	O
dependent	O
conformational	O
variability	O
.	O

Biotin	B-protein_type
-	I-protein_type
dependent	I-protein_type
acetyl	I-protein_type
-	I-protein_type
CoA	I-protein_type
carboxylases	I-protein_type
(	O
ACCs	B-protein_type
)	O
are	O
essential	O
enzymes	O
that	O
catalyse	O
the	O
ATP	B-chemical
-	O
dependent	O
carboxylation	O
of	O
acetyl	B-chemical
-	I-chemical
CoA	I-chemical
to	O
malonyl	B-chemical
-	I-chemical
CoA	I-chemical
.	O
This	O
reaction	O
provides	O
the	O
committed	O
activated	O
substrate	O
for	O
the	O
biosynthesis	O
of	O
fatty	B-chemical
acids	I-chemical
via	O
fatty	B-protein_type
-	I-protein_type
acid	I-protein_type
synthase	I-protein_type
.	O

By	O
catalysing	O
this	O
rate	O
-	O
limiting	O
step	O
in	O
fatty	O
-	O
acid	O
biosynthesis	O
,	O
ACC	B-protein_type
plays	O
a	O
key	O
role	O
in	O
anabolic	O
metabolism	O
.	O

ACC	B-experimental_method
inhibition	I-experimental_method
and	I-experimental_method
knock	I-experimental_method
-	I-experimental_method
out	I-experimental_method
studies	I-experimental_method
show	O
the	O
potential	O
of	O
targeting	O
ACC	B-protein_type
for	O
treatment	O
of	O
the	O
metabolic	O
syndrome	O
.	O

Furthermore	O
,	O
elevated	O
ACC	B-protein_type
activity	O
is	O
observed	O
in	O
malignant	O
tumours	O
.	O

A	O
direct	O
link	O
between	O
ACC	B-protein_type
and	O
cancer	O
is	O
provided	O
by	O
cancer	O
-	O
associated	O
mutations	B-mutant
in	O
the	O
breast	B-protein
cancer	I-protein
susceptibility	I-protein
gene	I-protein
1	I-protein
(	O
BRCA1	B-protein
),	O
which	O
relieve	O
inhibitory	O
interactions	O
of	O
BRCA1	B-protein
with	O
ACC	B-protein_type
.	O

Thus	O
,	O
ACC	B-protein_type
is	O
a	O
relevant	O
drug	O
target	O
for	O
type	O
2	O
diabetes	O
and	O
cancer	O
.	O

Microbial	B-taxonomy_domain
ACCs	B-protein_type
are	O
also	O
the	O
principal	O
target	O
of	O
antifungal	O
and	O
antibiotic	O
compounds	O
,	O
such	O
as	O
Soraphen	B-chemical
A	I-chemical
.	O

The	O
principal	O
functional	O
protein	O
components	O
of	O
ACCs	B-protein_type
have	O
been	O
described	O
already	O
in	O
the	O
late	O
1960s	O
for	O
Escherichia	B-species
coli	I-species
(	O
E	B-species
.	I-species
coli	I-species
)	O
ACC	B-protein_type
:	O
Biotin	B-protein_type
carboxylase	I-protein_type
(	O
BC	B-protein_type
)	O
catalyses	O
the	O
ATP	B-chemical
-	O
dependent	O
carboxylation	O
of	O
a	O
biotin	B-chemical
moiety	O
,	O
which	O
is	O
covalently	O
linked	O
to	O
the	O
biotin	B-protein_type
carboxyl	I-protein_type
carrier	I-protein_type
protein	I-protein_type
(	O
BCCP	B-protein_type
).	O

Carboxyltransferase	B-protein_type
(	O
CT	B-protein_type
)	O
transfers	O
the	O
activated	O
carboxyl	B-chemical
group	O
from	O
carboxybiotin	B-chemical
to	O
acetyl	B-chemical
-	I-chemical
CoA	I-chemical
to	O
yield	O
malonyl	B-chemical
-	I-chemical
CoA	I-chemical
.	O
Prokaryotic	B-taxonomy_domain
ACCs	B-protein_type
are	O
transient	B-protein_state
assemblies	O
of	O
individual	O
BC	B-protein_type
,	O
CT	B-protein_type
and	O
BCCP	B-protein_type
subunits	O
.	O

Eukaryotic	B-taxonomy_domain
ACCs	B-protein_type
,	O
instead	O
,	O
are	O
multienzymes	B-protein_type
,	O
which	O
integrate	O
all	O
functional	O
components	O
into	O
a	O
single	O
polypeptide	O
chain	O
of	O
∼	O
2	O
,	O
300	O
amino	O
acids	O
.	O

Human	B-species
ACC	B-protein_type
occurs	O
in	O
two	O
closely	O
related	O
isoforms	B-protein_state
,	O
ACC1	B-protein
and	O
2	B-protein
,	O
located	O
in	O
the	O
cytosol	O
and	O
at	O
the	O
outer	O
mitochondrial	O
membrane	O
,	O
respectively	O
.	O

In	O
addition	O
to	O
the	O
canonical	O
ACC	B-structure_element
components	I-structure_element
,	O
eukaryotic	B-taxonomy_domain
ACCs	B-protein_type
contain	O
two	O
non	B-protein_state
-	I-protein_state
catalytic	I-protein_state
regions	B-structure_element
,	O
the	O
large	O
central	B-structure_element
domain	I-structure_element
(	O
CD	B-structure_element
)	O
and	O
the	O
BC	B-structure_element
–	I-structure_element
CT	I-structure_element
interaction	I-structure_element
domain	I-structure_element
(	O
BT	B-structure_element
).	O

The	O
CD	B-structure_element
comprises	O
one	O
-	O
third	O
of	O
the	O
protein	O
and	O
is	O
a	O
unique	B-protein_state
feature	I-protein_state
of	I-protein_state
eukaryotic	B-taxonomy_domain
ACCs	B-protein_type
without	O
homologues	O
in	O
other	O
proteins	O
.	O

The	O
function	O
of	O
this	O
domain	O
remains	O
poorly	O
characterized	O
,	O
although	O
phosphorylation	B-ptm
of	O
several	O
serine	B-residue_name
residues	O
in	O
the	O
CD	B-structure_element
regulates	O
ACC	B-protein_type
activity	O
.	O

The	O
BT	B-structure_element
domain	O
has	O
been	O
visualized	O
in	O
bacterial	B-taxonomy_domain
carboxylases	B-protein_type
,	O
where	O
it	O
mediates	O
contacts	O
between	O
α	B-structure_element
-	I-structure_element
and	O
β	B-structure_element
-	I-structure_element
subunits	I-structure_element
.	O

Structural	B-experimental_method
studies	I-experimental_method
on	O
the	O
functional	O
architecture	O
of	O
intact	B-protein_state
ACCs	B-protein_type
have	O
been	O
hindered	O
by	O
their	O
huge	O
size	O
and	O
pronounced	O
dynamics	O
,	O
as	O
well	O
as	O
the	O
transient	B-protein_state
assembly	O
mode	O
of	O
bacterial	B-taxonomy_domain
ACCs	B-protein_type
.	O

However	O
,	O
crystal	B-evidence
structures	I-evidence
of	O
individual	O
components	O
or	O
domains	O
from	O
prokaryotic	B-taxonomy_domain
and	O
eukaryotic	B-taxonomy_domain
ACCs	B-protein_type
,	O
respectively	O
,	O
have	O
been	O
solved	O
.	O

The	O
structure	B-experimental_method
determination	I-experimental_method
of	O
the	O
holoenzymes	B-protein_state
of	O
bacterial	B-taxonomy_domain
biotin	B-protein_type
-	I-protein_type
dependent	I-protein_type
carboxylases	I-protein_type
,	O
which	O
lack	B-protein_state
the	O
characteristic	O
CD	B-structure_element
,	O
such	O
as	O
the	O
pyruvate	B-protein_type
carboxylase	I-protein_type
(	O
PC	B-protein_type
),	O
propionyl	B-protein_type
-	I-protein_type
CoA	I-protein_type
carboxylase	I-protein_type
,	O
3	B-protein_type
-	I-protein_type
methyl	I-protein_type
-	I-protein_type
crotonyl	I-protein_type
-	I-protein_type
CoA	I-protein_type
carboxylase	I-protein_type
and	O
a	O
long	B-protein_type
-	I-protein_type
chain	I-protein_type
acyl	I-protein_type
-	I-protein_type
CoA	I-protein_type
carboxylase	I-protein_type
revealed	O
strikingly	O
divergent	O
architectures	O
despite	O
a	O
general	O
conservation	O
of	O
all	O
functional	O
components	O
.	O

In	O
these	O
structures	B-evidence
,	O
the	O
BC	B-protein_type
and	O
CT	B-protein_type
active	B-site
sites	I-site
are	O
at	O
distances	O
between	O
40	O
and	O
80	O
Å	O
,	O
such	O
that	O
substrate	O
transfer	O
could	O
be	O
mediated	O
solely	O
by	O
the	O
mobility	O
of	O
the	O
flexibly	B-protein_state
tethered	I-protein_state
BCCP	B-protein_type
.	O

Human	B-species
ACC1	B-protein
is	O
regulated	B-protein_state
allosterically	I-protein_state
,	O
via	O
specific	O
protein	O
–	O
protein	O
interactions	O
,	O
and	O
by	O
reversible	O
phosphorylation	B-ptm
.	O

Dynamic	O
polymerization	O
of	O
human	B-species
ACC1	B-protein
is	O
linked	O
to	O
increased	O
activity	O
and	O
is	O
regulated	B-protein_state
allosterically	I-protein_state
by	O
the	O
activator	O
citrate	B-chemical
and	O
the	O
inhibitor	O
palmitate	B-chemical
,	O
or	O
by	O
binding	O
of	O
the	O
small	O
protein	O
MIG	B-protein
-	I-protein
12	I-protein
(	O
ref	O
.).	O

Human	B-species
ACC1	B-protein
is	O
further	O
regulated	O
by	O
specific	O
phosphorylation	B-ptm
-	O
dependent	O
binding	O
of	O
BRCA1	B-protein
to	O
Ser1263	B-residue_name_number
in	O
the	O
CD	B-structure_element
.	O

BRCA1	B-protein
binds	O
only	O
to	O
the	O
phosphorylated	B-protein_state
form	O
of	O
ACC1	B-protein
and	O
prevents	O
ACC	B-protein_type
activation	O
by	O
phosphatase	B-protein_type
-	O
mediated	O
dephosphorylation	O
.	O

Furthermore	O
,	O
phosphorylation	B-ptm
by	O
AMP	B-protein
-	I-protein
activated	I-protein
protein	I-protein
kinase	I-protein
(	O
AMPK	B-protein
)	O
and	O
cAMP	B-protein
-	I-protein
dependent	I-protein
protein	I-protein
kinase	I-protein
(	O
PKA	B-protein
)	O
leads	O
to	O
a	O
decrease	O
in	O
ACC1	B-protein
activity	O
.	O

AMPK	B-protein
phosphorylates	O
ACC1	B-protein
in	O
vitro	O
at	O
Ser80	B-residue_name_number
,	O
Ser1201	B-residue_name_number
and	O
Ser1216	B-residue_name_number
and	O
PKA	B-protein
at	O
Ser78	B-residue_name_number
and	O
Ser1201	B-residue_name_number
.	O

However	O
,	O
regulatory	O
effects	O
on	O
ACC1	B-protein
activity	O
are	O
mainly	O
mediated	O
by	O
phosphorylation	B-ptm
of	O
Ser80	B-residue_name_number
and	O
Ser1201	B-residue_name_number
(	O
refs	O
).	O

Phosphorylated	B-protein_state
Ser80	B-residue_name_number
,	O
which	O
is	O
highly	B-protein_state
conserved	I-protein_state
only	O
in	O
higher	B-taxonomy_domain
eukaryotes	I-taxonomy_domain
,	O
presumably	O
binds	O
into	O
the	O
Soraphen	B-site
A	I-site
-	I-site
binding	I-site
pocket	I-site
.	O

The	O
regulatory	O
Ser1201	B-residue_name_number
shows	O
only	O
moderate	B-protein_state
conservation	I-protein_state
across	O
higher	B-taxonomy_domain
eukaryotes	I-taxonomy_domain
,	O
while	O
the	O
phosphorylated	B-protein_state
Ser1216	B-residue_name_number
is	O
highly	B-protein_state
conserved	I-protein_state
across	O
all	O
eukaryotes	B-taxonomy_domain
.	O

However	O
,	O
no	O
effect	O
of	O
Ser1216	B-residue_name_number
phosphorylation	B-ptm
on	O
ACC	B-protein_type
activity	O
has	O
been	O
reported	O
in	O
higher	B-taxonomy_domain
eukaryotes	I-taxonomy_domain
.	O

For	O
fungal	B-taxonomy_domain
ACC	B-protein_type
,	O
neither	O
spontaneous	O
nor	O
inducible	O
polymerization	O
has	O
been	O
detected	O
despite	O
considerable	O
sequence	O
conservation	O
to	O
human	B-species
ACC1	B-protein
.	O

The	O
BRCA1	B-protein
-	O
interacting	O
phosphoserine	B-residue_name
position	O
is	O
not	B-protein_state
conserved	I-protein_state
in	O
fungal	B-taxonomy_domain
ACC	B-protein_type
,	O
and	O
no	O
other	O
phospho	O
-	O
dependent	O
protein	O
–	O
protein	O
interactions	O
of	O
fungal	B-taxonomy_domain
ACC	B-protein_type
have	O
been	O
described	O
.	O

In	O
yeast	B-taxonomy_domain
ACC	B-protein_type
,	O
phosphorylation	B-site
sites	I-site
have	O
been	O
identified	O
at	O
Ser2	B-residue_name_number
,	O
Ser735	B-residue_name_number
,	O
Ser1148	B-residue_name_number
,	O
Ser1157	B-residue_name_number
and	O
Ser1162	B-residue_name_number
(	O
ref	O
.).	O

Of	O
these	O
,	O
only	O
Ser1157	B-residue_name_number
is	O
highly	B-protein_state
conserved	I-protein_state
in	O
fungal	B-taxonomy_domain
ACC	B-protein_type
and	O
aligns	B-experimental_method
to	I-experimental_method
Ser1216	B-residue_name_number
in	O
human	B-species
ACC1	B-protein
.	O

Its	O
phosphorylation	B-ptm
by	O
the	O
AMPK	B-protein
homologue	O
SNF1	B-protein
results	O
in	O
strongly	O
reduced	O
ACC	B-protein_type
activity	O
.	O

Despite	O
the	O
outstanding	O
relevance	O
of	O
ACC	B-protein_type
in	O
primary	O
metabolism	O
and	O
disease	O
,	O
the	O
dynamic	O
organization	O
and	O
regulation	O
of	O
the	O
giant	O
eukaryotic	B-taxonomy_domain
,	O
and	O
in	O
particular	O
fungal	B-taxonomy_domain
ACC	B-protein_type
,	O
remain	O
poorly	O
characterized	O
.	O

Here	O
we	O
provide	O
the	O
structure	B-evidence
of	O
Saccharomyces	B-species
cerevisiae	I-species
(	O
Sce	B-species
)	O
ACC	B-protein_type
CD	B-structure_element
,	O
intermediate	O
-	O
and	O
low	O
-	O
resolution	O
structures	B-evidence
of	O
human	B-species
(	O
Hsa	B-species
)	O
ACC	B-protein_type
CD	B-structure_element
and	O
larger	B-mutant
fragments	I-mutant
of	O
fungal	B-taxonomy_domain
ACC	B-protein_type
from	O
Chaetomium	B-species
thermophilum	I-species
(	O
Cth	B-species
;	O
Fig	O
.	O
1a	O
).	O

Integrating	O
these	O
data	O
with	O
small	B-experimental_method
-	I-experimental_method
angle	I-experimental_method
X	I-experimental_method
-	I-experimental_method
ray	I-experimental_method
scattering	I-experimental_method
(	O
SAXS	B-experimental_method
)	O
and	O
electron	B-experimental_method
microscopy	I-experimental_method
(	O
EM	B-experimental_method
)	O
observations	O
yield	O
a	O
comprehensive	O
representation	O
of	O
the	O
dynamic	O
structure	O
and	O
regulation	O
of	O
fungal	B-taxonomy_domain
ACC	B-protein_type
.	O

The	O
organization	O
of	O
the	O
yeast	B-taxonomy_domain
ACC	B-protein_type
CD	B-structure_element

First	O
,	O
we	O
focused	O
on	O
structure	B-experimental_method
determination	I-experimental_method
of	O
the	O
82	O
-	O
kDa	O
CD	B-structure_element
.	O

The	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
CD	B-structure_element
of	O
SceACC	B-protein
(	O
SceCD	B-species
)	O
was	O
determined	O
at	O
3	O
.	O
0	O
Å	O
resolution	O
by	O
experimental	B-experimental_method
phasing	I-experimental_method
and	O
refined	B-experimental_method
to	O
Rwork	B-evidence
/	O
Rfree	B-evidence
=	O
0	O
.	O
20	O
/	O
0	O
.	O
24	O
(	O
Table	O
1	O
).	O

The	O
overall	O
extent	O
of	O
the	O
SceCD	B-species
is	O
70	O
by	O
75	O
Å	O
(	O
Fig	O
.	O
1b	O
and	O
Supplementary	O
Fig	O
.	O
1a	O
,	O
b	O
),	O
and	O
the	O
attachment	O
points	O
of	O
the	O
N	O
-	O
terminal	O
26	B-structure_element
-	I-structure_element
residue	I-structure_element
linker	I-structure_element
to	O
the	O
BCCP	B-structure_element
domain	O
and	O
the	O
C	O
-	O
terminal	O
CT	B-structure_element
domain	O
are	O
separated	O
by	O
46	O
Å	O
(	O
the	O
N	O
-	O
and	O
C	O
termini	O
are	O
indicated	O
with	O
spheres	O
in	O
Fig	O
.	O
1b	O
).	O

SceCD	B-species
comprises	O
four	O
distinct	O
domains	O
,	O
an	O
N	O
-	O
terminal	O
α	B-structure_element
-	I-structure_element
helical	I-structure_element
domain	I-structure_element
(	O
CDN	B-structure_element
),	O
and	O
a	O
central	O
four	B-structure_element
-	I-structure_element
helix	I-structure_element
bundle	I-structure_element
linker	I-structure_element
domain	I-structure_element
(	O
CDL	B-structure_element
),	O
followed	O
by	O
two	O
α	B-structure_element
–	I-structure_element
β	I-structure_element
-	I-structure_element
fold	I-structure_element
C	I-structure_element
-	I-structure_element
terminal	I-structure_element
domains	I-structure_element
(	O
CDC1	B-structure_element
/	O
CDC2	B-structure_element
).	O

CDN	B-structure_element
adopts	O
a	O
letter	O
C	B-protein_state
shape	I-protein_state
,	O
where	O
one	O
of	O
the	O
ends	O
is	O
a	O
regular	B-structure_element
four	I-structure_element
-	I-structure_element
helix	I-structure_element
bundle	I-structure_element
(	O
Nα3	B-structure_element
-	I-structure_element
6	I-structure_element
),	O
the	O
other	O
end	O
is	O
a	O
helical	B-structure_element
hairpin	I-structure_element
(	O
Nα8	B-structure_element
,	I-structure_element
9	I-structure_element
)	O
and	O
the	O
bridging	B-structure_element
region	I-structure_element
comprises	O
six	O
helices	B-structure_element
(	O
Nα1	B-structure_element
,	I-structure_element
2	I-structure_element
,	I-structure_element
7	I-structure_element
,	I-structure_element
10	I-structure_element
–	I-structure_element
12	I-structure_element
).	O

CDL	B-structure_element
is	O
composed	O
of	O
a	O
small	B-structure_element
,	I-structure_element
irregular	I-structure_element
four	I-structure_element
-	I-structure_element
helix	I-structure_element
bundle	I-structure_element
(	O
Lα1	B-structure_element
–	I-structure_element
4	I-structure_element
)	O
and	O
tightly	O
interacts	O
with	O
the	O
open	O
face	O
of	O
CDC1	B-structure_element
via	O
an	O
interface	B-site
of	O
1	O
,	O
300	O
Å2	O
involving	O
helices	B-structure_element
Lα3	B-structure_element
and	O
Lα4	B-structure_element
.	O

CDL	B-structure_element
does	O
not	O
interact	O
with	O
CDN	B-structure_element
apart	O
from	O
the	O
covalent	O
linkage	O
and	O
forms	O
only	O
a	O
small	O
contact	O
to	O
CDC2	B-structure_element
via	O
a	O
loop	B-structure_element
between	O
Lα2	B-structure_element
/	I-structure_element
α3	I-structure_element
and	O
the	O
N	O
-	O
terminal	O
end	O
of	O
Lα1	B-structure_element
,	O
with	O
an	O
interface	B-site
area	O
of	O
400	O
Å2	O
.	O

CDC1	B-structure_element
/	O
CDC2	B-structure_element
share	O
a	O
common	O
fold	O
;	O
they	O
are	O
composed	O
of	O
six	B-structure_element
-	I-structure_element
stranded	I-structure_element
β	I-structure_element
-	I-structure_element
sheets	I-structure_element
flanked	O
on	O
one	O
side	O
by	O
two	O
long	B-structure_element
,	I-structure_element
bent	I-structure_element
helices	I-structure_element
inserted	O
between	O
strands	B-structure_element
β3	B-structure_element
/	I-structure_element
β4	I-structure_element
and	O
β4	B-structure_element
/	I-structure_element
β5	I-structure_element
.	O

CDC2	B-structure_element
is	O
extended	B-protein_state
at	O
its	O
C	O
terminus	O
by	O
an	O
additional	O
β	B-structure_element
-	I-structure_element
strand	I-structure_element
and	O
an	O
irregular	B-structure_element
β	I-structure_element
-	I-structure_element
hairpin	I-structure_element
.	O

On	O
the	O
basis	O
of	O
a	O
root	B-evidence
mean	I-evidence
square	I-evidence
deviation	I-evidence
of	O
main	O
chain	O
atom	O
positions	O
of	O
2	O
.	O
2	O
Å	O
,	O
CDC1	B-structure_element
/	O
CDC2	B-structure_element
are	O
structurally	O
more	O
closely	O
related	O
to	O
each	O
other	O
than	O
to	O
any	O
other	O
protein	O
(	O
Fig	O
.	O
1c	O
);	O
they	O
may	O
thus	O
have	O
evolved	O
by	O
duplication	O
.	O

Close	O
structural	O
homologues	O
could	O
not	O
be	O
found	O
for	O
the	O
CDN	B-structure_element
or	O
the	O
CDC	B-structure_element
domains	O
.	O

A	O
regulatory	B-structure_element
loop	I-structure_element
mediates	O
interdomain	O
interactions	O

To	O
define	O
the	O
functional	O
state	O
of	O
insect	B-experimental_method
-	I-experimental_method
cell	I-experimental_method
-	I-experimental_method
expressed	I-experimental_method
ACC	B-protein_type
variants	O
,	O
we	O
employed	O
mass	B-experimental_method
spectrometry	I-experimental_method
(	O
MS	B-experimental_method
)	O
for	O
phosphorylation	B-experimental_method
site	I-experimental_method
detection	I-experimental_method
.	O

In	O
insect	B-experimental_method
-	I-experimental_method
cell	I-experimental_method
-	I-experimental_method
expressed	I-experimental_method
full	B-protein_state
-	I-protein_state
length	I-protein_state
SceACC	B-protein
,	O
the	O
highly	B-protein_state
conserved	I-protein_state
Ser1157	B-residue_name_number
is	O
the	O
only	O
fully	B-protein_state
occupied	I-protein_state
phosphorylation	B-site
site	I-site
with	O
functional	O
relevance	O
in	O
S	B-species
.	I-species
cerevisiae	I-species
.	O

Additional	O
phosphorylation	B-ptm
was	O
detected	O
for	O
Ser2101	B-residue_name_number
and	O
Tyr2179	B-residue_name_number
;	O
however	O
,	O
these	O
sites	O
are	O
neither	B-protein_state
conserved	I-protein_state
across	O
fungal	B-taxonomy_domain
ACC	B-protein_type
nor	B-protein_state
natively	I-protein_state
phosphorylated	I-protein_state
in	O
yeast	B-taxonomy_domain
.	O

MS	B-experimental_method
analysis	O
of	O
dissolved	B-experimental_method
crystals	I-experimental_method
confirmed	O
the	O
phosphorylated	B-protein_state
state	O
of	O
Ser1157	B-residue_name_number
also	O
in	O
SceCD	B-species
crystals	B-evidence
.	O

The	O
SceCD	B-species
structure	B-evidence
thus	O
authentically	O
represents	O
the	O
state	O
of	O
SceACC	B-protein
,	O
where	O
the	O
enzyme	B-protein
is	O
inhibited	B-protein_state
by	O
SNF1	B-ptm
-	I-ptm
dependent	I-ptm
phosphorylation	I-ptm
.	O

In	O
the	O
SceCD	B-species
crystal	B-evidence
structure	I-evidence
,	O
the	O
phosphorylated	B-protein_state
Ser1157	B-residue_name_number
resides	O
in	O
a	O
regulatory	B-structure_element
36	I-structure_element
-	I-structure_element
amino	I-structure_element
-	I-structure_element
acid	I-structure_element
loop	I-structure_element
between	O
strands	B-structure_element
β2	B-structure_element
and	O
β3	B-structure_element
of	O
CDC1	B-structure_element
(	O
Fig	O
.	O
1b	O
,	O
d	O
),	O
which	O
contains	O
two	O
additional	O
less	B-protein_state
-	I-protein_state
conserved	I-protein_state
phosphorylation	B-site
sites	I-site
(	O
Ser1148	B-residue_name_number
and	O
Ser1162	B-residue_name_number
)	O
confirmed	O
in	O
yeast	B-taxonomy_domain
,	O
but	O
not	O
occupied	O
here	O
.	O

This	O
regulatory	B-structure_element
loop	I-structure_element
wedges	O
between	O
the	O
CDC1	B-structure_element
and	O
CDC2	B-structure_element
domains	O
and	O
provides	O
the	O
largest	O
contribution	O
to	O
the	O
interdomain	B-site
interface	I-site
.	O

The	O
N	O
-	O
terminal	O
region	O
of	O
the	O
regulatory	B-structure_element
loop	I-structure_element
also	O
directly	O
contacts	O
the	O
C	O
-	O
terminal	O
region	O
of	O
CDC2	B-structure_element
leading	O
into	O
CT	B-structure_element
.	O

Phosphoserine	B-residue_name_number
1157	I-residue_name_number
is	O
tightly	O
bound	O
by	O
two	O
highly	B-protein_state
conserved	I-protein_state
arginines	B-residue_name
(	O
Arg1173	B-residue_name_number
and	O
Arg1260	B-residue_name_number
)	O
of	O
CDC1	B-structure_element
(	O
Fig	O
.	O
1d	O
).	O

Already	O
the	O
binding	O
of	O
phosphorylated	B-protein_state
Ser1157	B-residue_name_number
apparently	O
stabilizes	O
the	O
regulatory	B-structure_element
loop	I-structure_element
conformation	O
;	O
the	O
accessory	O
phosphorylation	B-site
sites	I-site
Ser1148	B-residue_name_number
and	O
Ser1162	B-residue_name_number
in	O
the	O
same	B-structure_element
loop	I-structure_element
may	O
further	O
modulate	O
the	O
strength	O
of	O
interaction	O
between	O
the	O
regulatory	B-structure_element
loop	I-structure_element
and	O
the	O
CDC1	B-structure_element
and	O
CDC2	B-structure_element
domains	O
.	O

Phosphorylation	B-ptm
of	O
the	O
regulatory	B-structure_element
loop	I-structure_element
thus	O
determines	O
interdomain	O
interactions	O
of	O
CDC1	B-structure_element
and	O
CDC2	B-structure_element
,	O
suggesting	O
that	O
it	O
may	O
exert	O
its	O
regulatory	O
function	O
by	O
modifying	O
the	O
overall	O
structure	O
and	O
dynamics	O
of	O
the	O
CD	B-structure_element
.	O

The	O
functional	O
role	O
of	O
Ser1157	B-residue_name_number
was	O
confirmed	O
by	O
an	O
activity	B-experimental_method
assay	I-experimental_method
based	O
on	O
the	O
incorporation	O
of	O
radioactive	O
carbonate	O
into	O
acid	O
non	O
-	O
volatile	O
material	O
.	O

Phosphorylated	B-protein_state
SceACC	B-protein
shows	O
only	O
residual	O
activity	O
(	O
kcat	B-evidence
=	O
0	O
.	O
4	O
±	O
0	O
.	O
2	O
s	O
−	O
1	O
,	O
s	O
.	O
d	O
.	O
based	O
on	O
five	O
replicate	O
measurements	O
),	O
which	O
increases	O
16	O
-	O
fold	O
(	O
kcat	B-evidence
=	O
6	O
.	O
5	O
±	O
0	O
.	O
3	O
s	O
−	O
1	O
)	O
after	O
dephosphorylation	O
with	O
λ	B-protein_type
protein	I-protein_type
phosphatase	I-protein_type
.	O

The	O
values	O
obtained	O
for	O
dephosphorylated	B-protein_state
SceACC	B-protein
are	O
comparable	O
to	O
earlier	O
measurements	O
of	O
non	B-protein_state
-	I-protein_state
phosphorylated	I-protein_state
yeast	B-taxonomy_domain
ACC	B-protein_type
expressed	B-experimental_method
in	I-experimental_method
E	B-species
.	I-species
coli	I-species
.	O

The	O
variable	O
CD	B-structure_element
is	O
conserved	B-protein_state
between	O
yeast	B-taxonomy_domain
and	O
human	B-species

To	O
compare	O
the	O
organization	O
of	O
fungal	B-taxonomy_domain
and	O
human	B-species
ACC	B-protein_type
CD	B-structure_element
,	O
we	O
determined	B-experimental_method
the	I-experimental_method
structure	I-experimental_method
of	O
a	O
human	B-species
ACC1	B-mutant
fragment	I-mutant
that	O
comprises	O
the	O
BT	B-structure_element
and	O
CD	B-structure_element
domains	O
(	O
HsaBT	B-mutant
-	I-mutant
CD	I-mutant
),	O
but	O
lacks	B-protein_state
the	O
mobile	O
BCCP	B-structure_element
in	O
between	O
(	O
Fig	O
.	O
1a	O
).	O

An	O
experimentally	B-evidence
phased	I-evidence
map	I-evidence
was	O
obtained	O
at	O
3	O
.	O
7	O
Å	O
resolution	O
for	O
a	O
cadmium	B-chemical
-	O
derivatized	O
crystal	O
and	O
was	O
interpreted	O
by	O
a	O
poly	O
-	O
alanine	O
model	O
(	O
Fig	O
.	O
1e	O
and	O
Table	O
1	O
).	O

Each	O
of	O
the	O
four	O
CD	B-structure_element
domains	O
in	O
HsaBT	B-mutant
-	I-mutant
CD	I-mutant
individually	O
resembles	O
the	O
corresponding	O
SceCD	B-species
domain	O
;	O
however	O
,	O
human	B-species
and	O
yeast	B-taxonomy_domain
CDs	B-structure_element
exhibit	O
distinct	O
overall	O
structures	B-evidence
.	O

In	O
agreement	O
with	O
their	O
tight	O
interaction	O
in	O
SceCD	B-species
,	O
the	O
relative	O
spatial	O
arrangement	O
of	O
CDL	B-structure_element
and	O
CDC1	B-structure_element
is	O
preserved	O
in	O
HsaBT	B-mutant
-	I-mutant
CD	I-mutant
,	O
but	O
the	O
human	B-species
CDL	B-structure_element
/	O
CDC1	B-structure_element
didomain	O
is	O
tilted	O
by	O
30	O
°	O
based	O
on	O
a	O
superposition	B-experimental_method
of	O
human	B-species
and	O
yeast	B-taxonomy_domain
CDC2	B-structure_element
(	O
Supplementary	O
Fig	O
.	O
1c	O
).	O

As	O
a	O
result	O
,	O
the	O
N	O
terminus	O
of	O
CDL	B-structure_element
at	O
helix	B-structure_element
Lα1	B-structure_element
,	O
which	O
connects	O
to	O
CDN	B-structure_element
,	O
is	O
shifted	O
by	O
12	O
Å	O
.	O
Remarkably	O
,	O
CDN	B-structure_element
of	O
HsaBT	B-mutant
-	I-mutant
CD	I-mutant
adopts	O
a	O
completely	O
different	O
orientation	O
compared	O
with	O
SceCD	B-species
.	O

With	O
CDL	B-structure_element
/	O
CDC1	B-structure_element
superposed	B-experimental_method
,	O
CDN	B-structure_element
in	O
HsaBT	B-mutant
-	I-mutant
CD	I-mutant
is	O
rotated	O
by	O
160	O
°	O
around	O
a	O
hinge	B-structure_element
at	O
the	O
connection	O
of	O
CDN	B-structure_element
/	O
CDL	B-structure_element
(	O
Supplementary	O
Fig	O
.	O
1d	O
).	O

This	O
rotation	O
displaces	O
the	O
N	O
terminus	O
of	O
CDN	B-structure_element
in	O
HsaBT	B-mutant
-	I-mutant
CD	I-mutant
by	O
51	O
Å	O
compared	O
with	O
SceCD	B-species
,	O
resulting	O
in	O
a	O
separation	O
of	O
the	O
attachment	O
points	O
of	O
the	O
N	O
-	O
terminal	O
linker	B-structure_element
to	O
the	O
BCCP	B-structure_element
domain	I-structure_element
and	O
the	O
C	O
-	O
terminal	O
CT	B-structure_element
domain	O
by	O
67	O
Å	O
(	O
the	O
attachment	O
points	O
are	O
indicated	O
with	O
spheres	O
in	O
Fig	O
.	O
1e	O
).	O

The	O
BT	B-structure_element
domain	O
of	O
HsaBT	B-mutant
-	I-mutant
CD	I-mutant
consists	O
of	O
a	O
helix	B-structure_element
that	O
is	O
surrounded	O
at	O
its	O
N	O
terminus	O
by	O
an	O
antiparallel	B-structure_element
eight	I-structure_element
-	I-structure_element
stranded	I-structure_element
β	I-structure_element
-	I-structure_element
barrel	I-structure_element
.	O

It	O
resembles	O
the	O
BT	B-structure_element
of	O
propionyl	B-protein_type
-	I-protein_type
CoA	I-protein_type
carboxylase	I-protein_type
;	O
only	O
the	O
four	O
C	O
-	O
terminal	O
strands	B-structure_element
of	I-structure_element
the	I-structure_element
β	I-structure_element
-	I-structure_element
barrel	I-structure_element
are	O
slightly	O
tilted	O
.	O

On	O
the	O
basis	O
of	O
MS	B-experimental_method
analysis	O
of	O
insect	B-experimental_method
-	I-experimental_method
cell	I-experimental_method
-	I-experimental_method
expressed	I-experimental_method
human	B-species
full	B-protein_state
-	I-protein_state
length	I-protein_state
ACC	B-protein_type
,	O
Ser80	B-residue_name_number
shows	O
the	O
highest	O
degree	O
of	O
phosphorylation	B-ptm
(	O
90	O
%).	O

Ser29	B-residue_name_number
and	O
Ser1263	B-residue_name_number
,	O
implicated	O
in	O
insulin	B-ptm
-	I-ptm
dependent	I-ptm
phosphorylation	I-ptm
and	O
BRCA1	B-protein
binding	O
,	O
respectively	O
,	O
are	O
phosphorylated	B-protein_state
at	O
intermediate	O
levels	O
(	O
40	O
%).	O

The	O
highly	B-protein_state
conserved	I-protein_state
Ser1216	B-residue_name_number
(	O
corresponding	O
to	O
S	B-species
.	I-species
cerevisiae	I-species
Ser1157	B-residue_name_number
),	O
as	O
well	O
as	O
Ser1201	B-residue_name_number
,	O
both	O
in	O
the	O
regulatory	B-structure_element
loop	I-structure_element
discussed	O
above	O
,	O
are	O
not	B-protein_state
phosphorylated	I-protein_state
.	O

However	O
,	O
residual	O
phosphorylation	B-ptm
levels	O
were	O
detected	O
for	O
Ser1204	B-residue_name_number
(	O
7	O
%)	O
and	O
Ser1218	B-residue_name_number
(	O
7	O
%)	O
in	O
the	O
same	B-structure_element
loop	I-structure_element
.	O

MS	B-experimental_method
analysis	O
of	O
the	O
HsaBT	B-mutant
-	I-mutant
CD	I-mutant
crystallization	B-evidence
sample	I-evidence
reveals	O
partial	O
proteolytic	O
digestion	O
of	O
the	O
regulatory	B-structure_element
loop	I-structure_element
.	O

Accordingly	O
,	O
most	O
of	O
this	B-structure_element
loop	I-structure_element
is	O
not	O
represented	O
in	O
the	O
HsaBT	B-mutant
-	I-mutant
CD	I-mutant
crystal	B-evidence
structure	I-evidence
.	O

The	O
absence	B-protein_state
of	I-protein_state
the	O
regulatory	B-structure_element
loop	I-structure_element
might	O
be	O
linked	O
to	O
the	O
less	B-protein_state
-	I-protein_state
restrained	I-protein_state
interface	B-site
of	O
CDL	B-structure_element
/	O
CDC1	B-structure_element
and	O
CDC2	B-structure_element
and	O
altered	O
relative	O
orientations	O
of	O
these	O
domains	B-structure_element
.	O

Besides	O
the	O
regulatory	B-structure_element
loop	I-structure_element
,	O
also	O
the	O
phosphopeptide	B-site
target	I-site
region	I-site
for	O
BRCA1	B-protein
interaction	O
is	O
not	O
resolved	O
presumably	O
because	O
of	O
pronounced	O
flexibility	O
.	O

At	O
the	O
level	O
of	O
isolated	B-experimental_method
yeast	B-taxonomy_domain
and	O
human	B-species
CD	B-structure_element
,	O
the	O
structural	B-experimental_method
analysis	I-experimental_method
indicates	O
the	O
presence	O
of	O
at	O
least	O
two	O
hinges	B-structure_element
,	O
one	O
with	O
large	O
-	O
scale	O
flexibility	O
at	O
the	O
CDN	B-structure_element
/	I-structure_element
CDL	I-structure_element
connection	I-structure_element
,	O
and	O
one	O
with	O
tunable	O
plasticity	O
between	O
CDL	B-structure_element
/	O
CDC1	B-structure_element
and	O
CDC2	B-structure_element
,	O
plausibly	O
affected	O
by	O
phosphorylation	B-ptm
in	O
the	O
regulatory	B-structure_element
loop	I-structure_element
region	O
.	O

The	O
integration	O
of	O
CD	B-structure_element
into	O
the	O
fungal	B-taxonomy_domain
ACC	B-protein_type
multienzyme	I-protein_type

To	O
further	O
obtain	O
insights	O
into	O
the	O
functional	O
architecture	O
of	O
fungal	B-taxonomy_domain
ACC	B-protein_type
,	O
we	O
characterized	O
larger	B-mutant
multidomain	I-mutant
fragments	I-mutant
up	O
to	O
the	O
intact	B-protein_state
enzymes	B-protein
.	O

Using	O
molecular	B-experimental_method
replacement	I-experimental_method
based	O
on	O
fungal	B-taxonomy_domain
ACC	B-protein_type
CD	B-structure_element
and	O
CT	B-structure_element
models	O
,	O
we	O
obtained	O
structures	B-evidence
of	O
a	O
variant	B-mutant
comprising	O
CthCT	B-species
and	O
CDC1	B-structure_element
/	O
CDC2	B-structure_element
in	O
two	B-evidence
crystal	I-evidence
forms	I-evidence
at	O
resolutions	O
of	O
3	O
.	O
6	O
and	O
4	O
.	O
5	O
Å	O
(	O
CthCD	B-mutant
-	I-mutant
CTCter1	I-mutant
/	I-mutant
2	I-mutant
),	O
respectively	O
,	O
as	O
well	O
as	O
of	O
a	O
CthCT	B-species
linked	O
to	O
the	O
entire	O
CD	B-structure_element
at	O
7	O
.	O
2	O
Å	O
resolution	O
(	O
CthCD	B-mutant
-	I-mutant
CT	I-mutant
;	O
Figs	O
1a	O
and	O
2	O
,	O
Table	O
1	O
).	O

No	O
crystals	O
diffracting	O
to	O
sufficient	O
resolution	O
were	O
obtained	O
for	O
larger	B-mutant
BC	I-mutant
-	I-mutant
containing	I-mutant
fragments	I-mutant
,	O
or	O
for	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
Cth	B-species
or	O
SceACC	B-protein
.	O

To	O
improve	B-experimental_method
crystallizability	I-experimental_method
,	O
we	O
generated	B-experimental_method
ΔBCCP	B-mutant
variants	I-mutant
of	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
ACC	B-protein_type
,	O
which	O
,	O
based	O
on	O
SAXS	B-experimental_method
analysis	I-experimental_method
,	O
preserve	O
properties	O
of	O
intact	B-protein_state
ACC	B-protein_type
(	O
Supplementary	O
Table	O
1	O
and	O
Supplementary	O
Fig	O
.	O
2a	O
–	O
c	O
).	O

For	O
CthΔBCCP	B-mutant
,	O
crystals	B-evidence
diffracting	O
to	O
8	O
.	O
4	O
Å	O
resolution	O
were	O
obtained	O
.	O

However	O
,	O
molecular	B-experimental_method
replacement	I-experimental_method
did	O
not	O
reveal	O
a	O
unique	O
positioning	O
of	O
the	O
BC	B-structure_element
domain	O
.	O

Owing	O
to	O
the	O
limited	O
resolution	O
the	O
discussion	O
of	O
structures	B-evidence
of	O
CthCD	B-mutant
-	I-mutant
CT	I-mutant
and	O
CthΔBCCP	B-mutant
is	O
restricted	O
to	O
the	O
analysis	O
of	O
domain	O
localization	O
.	O

Still	O
,	O
these	B-evidence
structures	I-evidence
contribute	O
considerably	O
to	O
the	O
visualization	O
of	O
an	O
intrinsically	O
dynamic	B-protein_state
fungal	B-taxonomy_domain
ACC	B-protein_type
.	O

In	O
all	O
these	O
crystal	B-evidence
structures	I-evidence
,	O
the	O
CT	B-structure_element
domains	O
build	O
a	O
canonical	O
head	B-protein_state
-	I-protein_state
to	I-protein_state
-	I-protein_state
tail	I-protein_state
dimer	B-oligomeric_state
,	O
with	O
active	B-site
sites	I-site
formed	O
by	O
contributions	O
from	O
both	O
protomers	B-oligomeric_state
(	O
Fig	O
.	O
2	O
and	O
Supplementary	O
Fig	O
.	O
3a	O
).	O

The	O
connection	B-structure_element
of	O
CD	B-structure_element
and	O
CT	B-structure_element
is	O
provided	O
by	O
a	O
10	B-residue_range
-	I-residue_range
residue	I-residue_range
peptide	I-residue_range
stretch	I-residue_range
,	O
which	O
links	O
the	O
N	O
terminus	O
of	O
CT	B-structure_element
to	O
the	O
irregular	B-structure_element
β	I-structure_element
-	I-structure_element
hairpin	I-structure_element
/	I-structure_element
β	I-structure_element
-	I-structure_element
strand	I-structure_element
extension	I-structure_element
of	O
CDC2	B-structure_element
(	O
Supplementary	O
Fig	O
.	O
3b	O
).	O

The	O
connecting	B-structure_element
region	I-structure_element
is	O
remarkably	O
similar	O
in	O
isolated	B-protein_state
CD	B-structure_element
and	O
CthCD	B-mutant
-	I-mutant
CTCter	I-mutant
structures	B-evidence
,	O
indicating	O
inherent	O
conformational	O
stability	O
.	O

CD	B-structure_element
/	O
CT	B-structure_element
contacts	O
are	O
only	O
formed	O
in	O
direct	O
vicinity	O
of	O
the	O
covalent	O
linkage	O
and	O
involve	O
the	O
β	B-structure_element
-	I-structure_element
hairpin	I-structure_element
extension	I-structure_element
of	O
CDC2	B-structure_element
as	O
well	O
as	O
the	O
loop	B-structure_element
between	O
strands	B-structure_element
β2	I-structure_element
/	I-structure_element
β3	I-structure_element
of	O
the	O
CT	B-structure_element
N	I-structure_element
-	I-structure_element
lobe	I-structure_element
,	O
which	O
contains	O
a	O
conserved	B-protein_state
RxxGxN	B-structure_element
motif	I-structure_element
.	O

The	O
neighbouring	O
loop	B-structure_element
on	O
the	O
CT	B-structure_element
side	O
(	O
between	O
CT	B-structure_element
β1	B-structure_element
/	O
β2	B-structure_element
)	O
is	O
displaced	O
by	O
2	O
.	O
5	O
Å	O
compared	O
to	O
isolated	B-protein_state
CT	B-structure_element
structures	B-evidence
(	O
Supplementary	O
Fig	O
.	O
3c	O
).	O

On	O
the	O
basis	O
of	O
an	O
interface	O
area	O
of	O
∼	O
600	O
Å2	O
and	O
its	O
edge	O
-	O
to	O
-	O
edge	O
connection	O
characteristics	O
,	O
the	O
interface	B-site
between	O
CT	B-structure_element
and	O
CD	B-structure_element
might	O
be	O
classified	O
as	O
conformationally	O
variable	O
.	O

Indeed	O
,	O
the	O
comparison	O
of	O
the	O
positioning	O
of	O
eight	O
instances	O
of	O
the	O
C	O
-	O
terminal	O
part	O
of	O
CD	B-structure_element
relative	O
to	O
CT	B-structure_element
in	O
crystal	B-evidence
structures	I-evidence
determined	B-experimental_method
here	O
,	O
reveals	O
flexible	O
interdomain	O
linking	O
(	O
Fig	O
.	O
3a	O
).	O

The	O
CDC2	B-site
/	I-site
CT	I-site
interface	I-site
acts	O
as	O
a	O
true	B-structure_element
hinge	I-structure_element
with	O
observed	O
rotation	O
up	O
to	O
16	O
°,	O
which	O
results	O
in	O
a	O
translocation	O
of	O
the	O
distal	O
end	O
of	O
CDC2	B-structure_element
by	O
8	O
Å	O
.	O

The	O
interface	B-site
between	O
CDC2	B-structure_element
and	O
CDL	B-structure_element
/	O
CDC1	B-structure_element
,	O
which	O
is	O
mediated	O
by	O
the	O
phosphorylated	B-protein_state
regulatory	B-structure_element
loop	I-structure_element
in	O
the	O
SceCD	B-species
structure	B-evidence
,	O
is	O
less	O
variable	O
than	O
the	O
CD	B-structure_element
–	I-structure_element
CT	I-structure_element
junction	I-structure_element
,	O
and	O
permits	O
only	O
limited	O
rotation	O
and	O
tilting	O
(	O
Fig	O
.	O
3b	O
).	O

Analysis	O
of	O
the	O
impact	O
of	O
phosphorylation	B-ptm
on	O
the	O
interface	B-site
between	O
CDC2	B-structure_element
and	O
CDL	B-structure_element
/	O
CDC1	B-structure_element
in	O
CthACC	B-mutant
variant	I-mutant
structures	B-evidence
is	O
precluded	O
by	O
the	O
limited	O
crystallographic	O
resolution	O
.	O

However	O
,	O
MS	B-experimental_method
analysis	O
of	O
CthCD	B-mutant
-	I-mutant
CT	I-mutant
and	O
CthΔBCCP	B-mutant
constructs	O
revealed	O
between	O
60	O
and	O
70	O
%	O
phosphorylation	B-ptm
of	O
Ser1170	B-residue_name_number
(	O
corresponding	O
to	O
SceACC	B-protein
Ser1157	B-residue_name_number
).	O

The	O
CDN	B-structure_element
domain	O
positioning	O
relative	O
to	O
CDL	B-structure_element
/	O
CDC1	B-structure_element
is	O
highly	O
variable	O
with	O
three	O
main	O
orientations	O
observed	O
in	O
the	O
structures	B-evidence
of	O
SceCD	B-species
and	O
the	O
larger	B-mutant
CthACC	I-mutant
fragments	I-mutant
:	O
CDN	B-structure_element
tilts	O
,	O
resulting	O
in	O
a	O
displacement	O
of	O
its	O
N	O
terminus	O
by	O
23	O
Å	O
(	O
Fig	O
.	O
4a	O
,	O
observed	O
in	O
both	O
protomers	B-oligomeric_state
of	O
CthCD	B-mutant
-	I-mutant
CT	I-mutant
and	O
one	O
protomer	B-oligomeric_state
of	O
CthΔBCCP	B-mutant
,	O
denoted	O
as	O
CthCD	B-mutant
-	I-mutant
CT1	I-mutant
/	I-mutant
2	I-mutant
and	O
CthΔBCCP1	B-mutant
,	O
respectively	O
).	O

In	O
addition	O
,	O
CDN	B-structure_element
can	O
rotate	O
around	O
hinges	B-structure_element
in	O
the	O
connection	O
between	O
CDN	B-structure_element
/	O
CDL	B-structure_element
by	O
70	O
°	O
(	O
Fig	O
.	O
4b	O
,	O
observed	O
in	O
the	O
second	O
protomer	B-oligomeric_state
of	O
CthΔBCCP	B-mutant
,	O
denoted	O
as	O
CthΔBCCP2	B-mutant
)	O
and	O
160	O
°	O
(	O
Fig	O
.	O
4c	O
,	O
observed	O
in	O
SceCD	B-species
)	O
leading	O
to	O
displacement	O
of	O
the	O
anchor	B-site
site	I-site
for	O
the	O
BCCP	B-structure_element
linker	I-structure_element
by	O
up	O
to	O
33	O
and	O
40	O
Å	O
,	O
respectively	O
.	O

Conformational	O
variability	O
in	O
the	O
CD	B-structure_element
thus	O
contributes	O
considerably	O
to	O
variations	O
in	O
the	O
spacing	O
between	O
the	O
BC	B-structure_element
and	O
CT	B-structure_element
domains	O
,	O
and	O
may	O
extend	O
to	O
distance	O
variations	O
beyond	O
the	O
mobility	O
range	O
of	O
the	O
flexibly	B-protein_state
tethered	I-protein_state
BCCP	B-structure_element
.	O

On	O
the	O
basis	O
of	O
the	O
occurrence	O
of	O
related	O
conformational	O
changes	O
between	O
fungal	B-taxonomy_domain
and	O
human	B-species
ACC	B-mutant
fragments	I-mutant
,	O
the	O
observed	O
set	O
of	O
conformations	O
may	O
well	O
represent	O
general	O
states	O
present	O
in	O
all	O
eukaryotic	B-taxonomy_domain
ACCs	B-protein_type
.	O

Large	O
-	O
scale	O
conformational	O
variability	O
of	O
fungal	B-taxonomy_domain
ACC	B-protein_type

To	O
obtain	O
a	O
comprehensive	O
view	O
of	O
fungal	B-taxonomy_domain
ACC	B-protein_type
dynamics	O
in	B-protein_state
solution	I-protein_state
,	O
we	O
employed	O
SAXS	B-experimental_method
and	O
EM	B-experimental_method
.	O

SAXS	B-experimental_method
analysis	O
of	O
CthACC	B-protein
agrees	O
with	O
a	O
dimeric	B-oligomeric_state
state	O
and	O
an	O
elongated	B-protein_state
shape	I-protein_state
with	O
a	O
maximum	O
extent	O
of	O
350	O
Å	O
(	O
Supplementary	O
Table	O
1	O
).	O

The	O
smooth	O
appearance	O
of	O
scattering	B-evidence
curves	I-evidence
and	O
derived	B-evidence
distance	I-evidence
distributions	I-evidence
might	O
indicate	O
substantial	O
interdomain	O
flexibility	O
(	O
Supplementary	O
Fig	O
.	O
2a	O
–	O
c	O
).	O

Direct	O
observation	O
of	O
individual	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
CthACC	B-protein
particles	B-evidence
,	O
according	O
to	O
MS	B-experimental_method
results	O
predominantly	O
in	O
a	O
phosphorylated	B-protein_state
low	B-protein_state
-	I-protein_state
activity	I-protein_state
state	I-protein_state
,	O
in	O
negative	B-experimental_method
stain	I-experimental_method
EM	I-experimental_method
reveals	O
a	O
large	O
set	O
of	O
conformations	O
from	O
rod	B-protein_state
-	I-protein_state
like	I-protein_state
extended	I-protein_state
to	O
U	B-protein_state
-	I-protein_state
shaped	I-protein_state
particles	B-evidence
.	O

Class	B-evidence
averages	I-evidence
,	O
obtained	O
by	O
maximum	B-experimental_method
-	I-experimental_method
likelihood	I-experimental_method
-	I-experimental_method
based	I-experimental_method
two	I-experimental_method
-	I-experimental_method
dimensional	I-experimental_method
(	I-experimental_method
2D	I-experimental_method
)	I-experimental_method
classification	I-experimental_method
,	O
are	O
focused	O
on	O
the	O
dimeric	B-oligomeric_state
CT	B-structure_element
domain	O
and	O
the	O
full	B-protein_state
BC	B-mutant
–	I-mutant
BCCP	I-mutant
–	I-mutant
CD	I-mutant
domain	O
of	O
only	O
one	O
protomer	B-oligomeric_state
,	O
due	O
to	O
the	O
non	O
-	O
coordinated	O
motions	O
of	O
the	O
lateral	O
BC	B-structure_element
/	O
CD	B-structure_element
regions	O
relative	O
to	O
the	O
CT	B-structure_element
dimer	B-oligomeric_state
.	O

They	O
identify	O
the	O
connections	O
between	O
CDN	B-structure_element
/	O
CDL	B-structure_element
and	O
between	O
CDC2	B-structure_element
/	O
CT	B-structure_element
as	O
major	O
contributors	O
to	O
conformational	O
heterogeneity	O
(	O
Supplementary	O
Fig	O
.	O
4a	O
,	O
b	O
).	O

The	O
flexibility	O
in	O
the	O
CDC2	B-structure_element
/	I-structure_element
CT	I-structure_element
hinge	I-structure_element
appears	O
substantially	O
larger	O
than	O
the	O
variations	O
observed	O
in	O
the	O
set	O
of	O
crystal	B-evidence
structures	I-evidence
.	O

The	O
BC	B-structure_element
domain	O
is	O
not	O
completely	O
disordered	O
,	O
but	O
laterally	O
attached	O
to	O
BT	B-structure_element
/	O
CDN	B-structure_element
in	O
a	O
generally	B-protein_state
conserved	I-protein_state
position	I-protein_state
,	O
albeit	O
with	O
increased	O
flexibility	O
.	O

Surprisingly	O
,	O
in	O
both	O
the	O
linear	B-protein_state
and	I-protein_state
U	I-protein_state
-	I-protein_state
shaped	I-protein_state
conformations	I-protein_state
,	O
the	O
approximate	O
distances	O
between	O
the	O
BC	B-structure_element
and	O
CT	B-structure_element
active	B-site
sites	I-site
would	O
remain	O
larger	O
than	O
110	O
Å	O
.	O
These	O
observed	O
distances	O
are	O
considerably	O
larger	O
than	O
in	O
static	B-protein_state
structures	B-evidence
of	O
any	O
other	O
related	O
biotin	B-protein_type
-	I-protein_type
dependent	I-protein_type
carboxylase	I-protein_type
.	O

Furthermore	O
,	O
based	O
on	O
an	O
average	O
length	O
of	O
the	O
BCCP	B-structure_element
–	I-structure_element
CD	I-structure_element
linker	I-structure_element
in	O
fungal	B-taxonomy_domain
ACC	B-protein_type
of	O
26	B-residue_range
amino	I-residue_range
acids	I-residue_range
,	O
mobility	O
of	O
the	O
BCCP	B-structure_element
alone	O
would	O
not	O
be	O
sufficient	O
to	O
bridge	O
the	O
active	B-site
sites	I-site
of	O
BC	B-structure_element
and	O
CT	B-structure_element
.	O

The	O
most	O
relevant	O
candidate	O
site	O
for	O
mediating	O
such	O
additional	O
flexibility	O
and	O
permitting	O
an	O
extended	O
set	O
of	O
conformations	O
is	O
the	O
CDC1	B-site
/	I-site
CDC2	I-site
interface	I-site
,	O
which	O
is	O
rigidified	O
by	O
the	O
Ser1157	B-residue_name_number
-	O
phosphorylated	B-protein_state
regulatory	B-structure_element
loop	I-structure_element
,	O
as	O
depicted	O
in	O
the	O
SceCD	B-species
crystal	B-evidence
structure	I-evidence
.	O

Altogether	O
,	O
the	O
architecture	O
of	O
fungal	B-taxonomy_domain
ACC	B-protein_type
is	O
based	O
on	O
the	O
central	O
dimeric	B-oligomeric_state
CT	B-structure_element
domain	O
(	O
Fig	O
.	O
4d	O
).	O

The	O
CD	B-structure_element
consists	O
of	O
four	O
distinct	O
subdomains	B-structure_element
and	O
acts	O
as	O
a	O
tether	O
from	O
the	O
CT	B-structure_element
to	O
the	O
mobile	B-protein_state
BCCP	B-structure_element
and	O
an	O
oriented	B-protein_state
BC	B-structure_element
domain	O
.	O

The	O
CD	B-structure_element
has	O
no	O
direct	O
role	O
in	O
substrate	O
recognition	O
or	O
catalysis	O
but	O
contributes	O
to	O
the	O
regulation	O
of	O
all	O
eukaryotic	B-taxonomy_domain
ACCs	B-protein_type
.	O

In	O
higher	B-taxonomy_domain
eukaryotic	I-taxonomy_domain
ACCs	B-protein_type
,	O
regulation	O
via	O
phosphorylation	B-ptm
is	O
achieved	O
by	O
combining	O
the	O
effects	O
of	O
phosphorylation	B-ptm
at	O
Ser80	B-residue_name_number
,	O
Ser1201	B-residue_name_number
and	O
Ser1263	B-residue_name_number
.	O

In	O
fungal	B-taxonomy_domain
ACC	B-protein_type
,	O
however	O
,	O
Ser1157	B-residue_name_number
in	O
the	O
regulatory	B-structure_element
loop	I-structure_element
of	O
the	O
CD	B-structure_element
is	O
the	O
only	O
phosphorylation	B-site
site	I-site
that	O
has	O
been	O
demonstrated	O
to	O
be	O
both	O
phosphorylated	B-protein_state
in	O
vivo	O
and	O
involved	O
in	O
the	O
regulation	O
of	O
ACC	B-protein_type
activity	O
.	O

In	O
its	O
phosphorylated	B-protein_state
state	O
,	O
the	O
regulatory	B-structure_element
loop	I-structure_element
containing	O
Ser1157	B-residue_name_number
wedges	O
between	O
CDC1	B-structure_element
/	O
CDC2	B-structure_element
and	O
presumably	O
limits	O
the	O
conformational	B-protein_state
freedom	I-protein_state
at	O
this	O
interdomain	B-site
interface	I-site
.	O

However	O
,	O
flexibility	O
at	O
this	O
hinge	B-structure_element
may	O
be	O
required	O
for	O
full	B-protein_state
ACC	I-protein_state
activity	I-protein_state
,	O
as	O
the	O
distances	O
between	O
the	O
BCCP	B-structure_element
anchor	I-structure_element
points	I-structure_element
and	O
the	O
active	B-site
sites	I-site
of	O
BC	B-structure_element
and	O
CT	B-structure_element
observed	O
here	O
are	O
such	O
large	O
that	O
mobility	O
of	O
the	O
BCCP	B-structure_element
alone	O
is	O
not	O
sufficient	O
for	O
substrate	O
transfer	O
.	O

The	O
current	O
data	O
thus	O
suggest	O
that	O
regulation	O
of	O
fungal	B-taxonomy_domain
ACC	B-protein_type
is	O
mediated	O
by	O
controlling	O
the	O
dynamics	O
of	O
the	O
unique	B-protein_state
CD	B-structure_element
,	O
rather	O
than	O
directly	O
affecting	O
catalytic	O
turnover	O
at	O
the	O
active	B-site
sites	I-site
of	O
BC	B-structure_element
and	O
CT	B-structure_element
.	O

A	O
comparison	O
between	O
fungal	B-taxonomy_domain
and	O
human	B-species
ACC	B-protein_type
will	O
help	O
to	O
further	O
discriminate	O
mechanistic	O
differences	O
that	O
contribute	O
to	O
the	O
extended	O
control	O
and	O
polymerization	O
of	O
human	B-species
ACC	B-protein_type
.	O

Most	O
recently	O
,	O
a	O
crystal	B-evidence
structure	I-evidence
of	O
near	B-protein_state
full	I-protein_state
-	I-protein_state
length	I-protein_state
non	B-protein_state
-	I-protein_state
phosphorylated	I-protein_state
ACC	B-protein_type
from	O
S	B-species
.	I-species
cerevisae	I-species
(	O
lacking	B-protein_state
only	I-protein_state
21	B-residue_range
N	O
-	O
terminal	O
amino	O
acids	O
,	O
here	O
denoted	O
as	O
flACC	B-mutant
)	O
was	O
published	O
by	O
Wei	O
and	O
Tong	O
.	O

In	O
flACC	B-mutant
,	O
the	O
ACC	B-protein_type
dimer	B-oligomeric_state
obeys	O
twofold	O
symmetry	O
and	O
assembles	O
in	O
a	O
triangular	B-protein_state
architecture	I-protein_state
with	O
dimeric	B-oligomeric_state
BC	B-structure_element
domains	O
(	O
Supplementary	O
Fig	O
.	O
5a	O
).	O

In	O
their	O
study	O
,	O
mutational	B-experimental_method
data	I-experimental_method
indicate	O
a	O
requirement	O
for	O
BC	O
dimerization	O
for	O
catalytic	O
activity	O
.	O

The	O
transition	O
from	O
the	O
elongated	B-protein_state
open	I-protein_state
shape	I-protein_state
,	O
observed	O
in	O
our	O
experiments	O
,	O
towards	O
a	O
compact	B-protein_state
triangular	I-protein_state
shape	I-protein_state
is	O
based	O
on	O
an	O
intricate	O
interplay	O
of	O
several	O
hinge	O
-	O
bending	O
motions	O
in	O
the	O
CD	B-structure_element
(	O
Fig	O
.	O
4d	O
).	O

Comparison	B-experimental_method
of	O
flACC	B-mutant
with	O
our	O
CthΔBCCP	B-mutant
structure	B-evidence
reveals	O
the	O
CDC2	B-structure_element
/	I-structure_element
CT	I-structure_element
hinge	I-structure_element
as	O
a	O
major	O
contributor	O
to	O
conformational	O
flexibility	O
(	O
Supplementary	O
Fig	O
.	O
5b	O
,	O
c	O
).	O

In	O
flACC	B-mutant
,	O
CDC2	B-structure_element
rotates	O
∼	O
120	O
°	O
with	O
respect	O
to	O
the	O
CT	B-structure_element
domain	O
.	O

A	O
second	B-structure_element
hinge	I-structure_element
can	O
be	O
identified	O
between	O
CDC1	B-structure_element
/	O
CDC2	B-structure_element
.	O

On	O
the	O
basis	O
of	O
a	O
superposition	B-experimental_method
of	O
CDC2	B-structure_element
,	O
CDC1	B-structure_element
of	O
the	O
phosphorylated	B-protein_state
SceCD	B-species
is	O
rotated	O
by	O
30	O
°	O
relative	O
to	O
CDC1	B-structure_element
of	O
the	O
non	B-protein_state
-	I-protein_state
phosphorylated	I-protein_state
flACC	B-mutant
(	O
Supplementary	O
Fig	O
.	O
5d	O
),	O
similar	O
to	O
what	O
we	O
have	O
observed	O
for	O
the	O
non	B-protein_state
-	I-protein_state
phosphorylated	I-protein_state
HsaBT	B-mutant
-	I-mutant
CD	I-mutant
(	O
Supplementary	O
Fig	O
.	O
1d	O
).	O

When	O
inspecting	B-experimental_method
all	O
individual	O
protomer	B-oligomeric_state
and	O
fragment	B-mutant
structures	B-evidence
in	O
their	O
study	O
,	O
Wei	O
and	O
Tong	O
also	O
identify	O
the	O
CDN	B-structure_element
/	I-structure_element
CDC1	I-structure_element
connection	I-structure_element
as	O
a	O
highly	B-protein_state
flexible	I-protein_state
hinge	B-structure_element
,	O
in	O
agreement	O
with	O
our	O
observations	O
.	O

The	O
only	O
bona	O
fide	O
regulatory	B-protein_state
phophorylation	B-site
site	I-site
of	O
fungal	B-taxonomy_domain
ACC	B-protein_type
in	O
the	O
regulatory	B-structure_element
loop	I-structure_element
is	O
directly	O
participating	O
in	O
CDC1	B-structure_element
/	O
CDC2	B-structure_element
domain	O
interactions	O
and	O
thus	O
stabilizes	O
the	O
hinge	B-structure_element
conformation	I-structure_element
.	O

In	O
flACC	B-mutant
,	O
the	O
regulatory	B-structure_element
loop	I-structure_element
is	O
mostly	B-protein_state
disordered	I-protein_state
,	O
illustrating	O
the	O
increased	O
flexibility	O
due	O
to	O
the	O
absence	O
of	O
the	O
phosphoryl	B-chemical
group	O
.	O

Only	O
in	O
three	O
out	O
of	O
eight	O
observed	O
protomers	B-oligomeric_state
a	O
short	B-structure_element
peptide	I-structure_element
stretch	O
(	O
including	O
Ser1157	B-residue_name_number
)	O
was	O
modelled	B-evidence
.	O

In	O
those	O
instances	O
the	O
Ser1157	B-residue_name_number
residue	O
is	O
located	O
at	O
a	O
distance	O
of	O
14	O
–	O
20	O
Å	O
away	O
from	O
the	O
location	O
of	O
the	O
phosphorylated	B-protein_state
serine	B-residue_name
observed	O
here	O
,	O
based	O
on	O
superposition	B-experimental_method
of	O
either	O
CDC1	B-structure_element
or	O
CDC2	B-structure_element
.	O

Applying	B-experimental_method
the	O
conformation	O
of	O
the	O
CDC1	B-structure_element
/	I-structure_element
CDC2	I-structure_element
hinge	I-structure_element
observed	O
in	O
SceCD	B-species
on	O
flACC	B-mutant
leads	O
to	O
CDN	B-structure_element
sterically	O
clashing	O
with	O
CDC2	B-structure_element
and	O
BT	B-structure_element
/	O
CDN	B-structure_element
clashing	O
with	O
CT	B-structure_element
(	O
Supplementary	O
Fig	O
.	O
6a	O
,	O
b	O
).	O

Thus	O
,	O
in	O
accordance	O
with	O
the	O
results	O
presented	O
here	O
,	O
phosphorylation	B-ptm
of	O
Ser1157	B-residue_name_number
in	O
SceACC	B-protein
most	O
likely	O
limits	O
flexibility	O
in	O
the	O
CDC1	B-structure_element
/	I-structure_element
CDC2	I-structure_element
hinge	I-structure_element
such	O
that	O
activation	O
through	O
BC	B-structure_element
dimerization	O
is	O
not	O
possible	O
(	O
Fig	O
.	O
4d	O
),	O
which	O
however	O
does	O
not	O
exclude	O
intermolecular	O
dimerization	O
.	O

In	O
addition	O
,	O
EM	B-experimental_method
micrographs	B-evidence
of	O
phosphorylated	B-protein_state
and	O
dephosphorylated	B-protein_state
SceACC	B-protein
display	O
for	O
both	O
samples	O
mainly	O
elongated	B-protein_state
and	I-protein_state
U	I-protein_state
-	I-protein_state
shaped	I-protein_state
conformations	I-protein_state
and	O
reveal	O
no	O
apparent	O
differences	O
in	O
particle	B-evidence
shape	I-evidence
distributions	I-evidence
(	O
Supplementary	O
Fig	O
.	O
7	O
).	O

This	O
implicates	O
that	O
the	O
triangular	B-protein_state
shape	I-protein_state
with	O
dimeric	B-oligomeric_state
BC	B-structure_element
domains	O
has	O
a	O
low	O
population	O
also	O
in	O
the	O
active	B-protein_state
form	I-protein_state
,	O
even	O
though	O
a	O
biasing	O
influence	O
of	O
grid	O
preparation	O
cannot	O
be	O
excluded	O
completely	O
.	O

Large	O
-	O
scale	O
conformational	O
variability	O
has	O
also	O
been	O
observed	O
in	O
most	O
other	O
carrier	B-protein_type
protein	I-protein_type
-	I-protein_type
based	I-protein_type
multienzymes	I-protein_type
,	O
including	O
polyketide	B-protein_type
and	I-protein_type
fatty	I-protein_type
-	I-protein_type
acid	I-protein_type
synthases	I-protein_type
(	O
with	O
the	O
exception	O
of	O
fungal	B-protein_type
-	I-protein_type
type	I-protein_type
fatty	I-protein_type
-	I-protein_type
acid	I-protein_type
synthases	I-protein_type
),	O
non	B-protein_type
-	I-protein_type
ribosomal	I-protein_type
peptide	I-protein_type
synthetases	I-protein_type
and	O
the	O
pyruvate	B-protein_type
dehydrogenase	I-protein_type
complexes	I-protein_type
,	O
although	O
based	O
on	O
completely	O
different	O
architectures	O
.	O

Together	O
,	O
this	O
structural	B-evidence
information	I-evidence
suggests	O
that	O
variable	O
carrier	O
protein	O
tethering	O
is	O
not	O
sufficient	O
for	O
efficient	O
substrate	O
transfer	O
and	O
catalysis	O
in	O
any	O
of	O
these	O
systems	O
.	O

The	O
determination	B-experimental_method
of	I-experimental_method
a	I-experimental_method
set	I-experimental_method
of	I-experimental_method
crystal	B-evidence
structures	I-evidence
of	O
SceACC	B-protein
in	O
two	O
states	O
,	O
unphosphorylated	B-protein_state
and	O
phosphorylated	B-protein_state
at	O
the	O
major	B-site
regulatory	I-site
site	I-site
Ser1157	B-residue_name_number
,	O
provides	O
a	O
unique	O
depiction	O
of	O
multienzyme	O
regulation	O
by	O
post	O
-	O
translational	O
modification	O
(	O
Fig	O
.	O
4d	O
).	O

The	O
phosphorylated	B-protein_state
regulatory	B-structure_element
loop	I-structure_element
binds	O
to	O
an	O
allosteric	B-site
site	I-site
at	O
the	O
interface	B-site
of	O
two	O
non	B-protein_state
-	I-protein_state
catalytic	I-protein_state
domains	O
and	O
restricts	O
conformational	O
freedom	O
at	O
several	O
hinges	B-structure_element
in	O
the	O
dynamic	B-protein_state
ACC	B-protein_type
.	O

It	O
disfavours	O
the	O
adoption	O
of	O
a	O
rare	B-protein_state
,	I-protein_state
compact	I-protein_state
conformation	I-protein_state
,	O
in	O
which	O
intramolecular	O
dimerization	O
of	O
the	O
BC	B-structure_element
domains	O
results	O
in	O
catalytic	O
turnover	O
.	O

The	O
regulation	O
of	O
activity	O
thus	O
results	O
from	O
restrained	O
large	O
-	O
scale	O
conformational	O
dynamics	O
rather	O
than	O
a	O
direct	O
or	O
indirect	O
influence	O
on	O
active	B-site
site	I-site
structure	I-site
.	O

To	O
our	O
best	O
knowledge	O
,	O
ACC	B-protein_type
is	O
the	O
first	O
multienzyme	B-protein_type
for	O
which	O
such	O
a	O
phosphorylation	B-ptm
-	O
dependent	O
mechanical	O
control	O
mechanism	O
has	O
been	O
visualized	O
.	O

However	O
,	O
the	O
example	O
of	O
ACC	B-protein_type
now	O
demonstrates	O
the	O
possibility	O
of	O
regulating	O
activity	O
by	O
controlled	O
dynamics	O
of	O
non	B-structure_element
-	I-structure_element
enzymatic	I-structure_element
linker	I-structure_element
regions	I-structure_element
also	O
in	O
other	O
families	O
of	O
carrier	B-protein_type
-	I-protein_type
dependent	I-protein_type
multienzymes	I-protein_type
.	O

The	O
phosphorylated	B-protein_state
central	B-structure_element
domain	I-structure_element
of	O
yeast	B-taxonomy_domain
ACC	B-protein_type
.	O

(	O
a	O
)	O
Schematic	O
overview	O
of	O
the	O
domain	O
organization	O
of	O
eukaryotic	B-taxonomy_domain
ACCs	B-protein_type
.	O

Crystallized	B-evidence
constructs	I-evidence
are	O
indicated	O
.	O

(	O
b	O
)	O
Cartoon	O
representation	O
of	O
the	O
SceCD	B-species
crystal	B-evidence
structure	I-evidence
.	O

CDN	B-structure_element
is	O
linked	O
by	O
a	O
four	B-structure_element
-	I-structure_element
helix	I-structure_element
bundle	I-structure_element
(	O
CDL	B-structure_element
)	O
to	O
two	B-structure_element
α	I-structure_element
–	I-structure_element
β	I-structure_element
-	I-structure_element
fold	I-structure_element
domains	I-structure_element
(	O
CDC1	B-structure_element
and	O
CDC2	B-structure_element
).	O

The	O
regulatory	B-structure_element
loop	I-structure_element
is	O
shown	O
as	O
bold	O
cartoon	O
,	O
and	O
the	O
phosphorylated	B-protein_state
Ser1157	B-residue_name_number
is	O
marked	O
by	O
a	O
red	O
triangle	O
.	O

(	O
c	O
)	O
Superposition	B-experimental_method
of	O
CDC1	B-structure_element
and	O
CDC2	B-structure_element
reveals	O
highly	B-protein_state
conserved	I-protein_state
folds	B-structure_element
.	O
(	O
d	O
)	O
The	O
regulatory	B-structure_element
loop	I-structure_element
with	O
the	O
phosphorylated	B-protein_state
Ser1157	B-residue_name_number
is	O
bound	O
into	O
a	O
crevice	O
between	O
CDC1	B-structure_element
and	O
CDC2	B-structure_element
,	O
the	O
conserved	B-protein_state
residues	O
Arg1173	B-residue_name_number
and	O
Arg1260	B-residue_name_number
coordinate	O
the	O
phosphoryl	B-chemical
-	O
group	O
.	O

(	O
e	O
)	O
Structural	O
overview	O
of	O
HsaBT	B-mutant
-	I-mutant
CD	I-mutant
.	O

The	O
attachment	O
points	O
to	O
the	O
N	O
-	O
terminal	O
BCCP	B-structure_element
domain	O
and	O
the	O
C	O
-	O
terminal	O
CT	B-structure_element
domain	O
are	O
indicated	O
with	O
spheres	O
.	O

Architecture	O
of	O
the	O
CD	B-structure_element
–	O
CT	B-structure_element
core	O
of	O
fungal	B-taxonomy_domain
ACC	B-protein_type
.	O

Cartoon	O
representation	O
of	O
crystal	B-evidence
structures	I-evidence
of	O
multidomain	B-mutant
constructs	I-mutant
of	O
CthACC	B-protein
.	O

One	O
protomer	B-oligomeric_state
is	O
shown	O
in	O
colour	O
and	O
one	O
in	O
grey	O
.	O

Individual	O
domains	O
are	O
labelled	O
;	O
the	O
active	B-site
site	I-site
of	O
CT	B-structure_element
and	O
the	O
position	O
of	O
the	O
conserved	B-protein_state
regulatory	B-protein_state
phosphoserine	B-site
site	I-site
based	O
on	O
SceCD	B-species
are	O
indicated	O
by	O
an	O
asterisk	O
and	O
a	O
triangle	O
,	O
respectively	O
.	O

Variability	O
of	O
the	O
connections	O
of	O
CDC2	B-structure_element
to	O
CT	B-structure_element
and	O
CDC1	B-structure_element
in	O
fungal	B-taxonomy_domain
ACC	B-protein_type
.	O

(	O
a	O
)	O
Hinge	B-structure_element
properties	O
of	O
the	O
CDC2	B-structure_element
–	I-structure_element
CT	I-structure_element
connection	I-structure_element
analysed	O
by	O
a	O
CT	B-experimental_method
-	I-experimental_method
based	I-experimental_method
superposition	I-experimental_method
of	O
eight	O
instances	O
of	O
the	O
CDC2	B-mutant
-	I-mutant
CT	I-mutant
segment	I-mutant
.	O

For	O
clarity	O
,	O
only	O
one	O
protomer	B-oligomeric_state
of	O
CthCD	B-mutant
-	I-mutant
CTCter1	I-mutant
is	O
shown	O
in	O
full	O
colour	O
as	O
reference	O
.	O

For	O
other	O
instances	O
,	O
CDC2	B-structure_element
domains	O
are	O
shown	O
in	O
transparent	O
tube	O
representation	O
with	O
only	O
one	O
helix	O
each	O
highlighted	O
.	O

The	O
range	O
of	O
hinge	O
bending	O
is	O
indicated	O
and	O
the	O
connection	O
points	O
between	O
CDC2	B-structure_element
and	O
CT	B-structure_element
(	O
blue	O
)	O
as	O
well	O
as	O
between	O
CDC1	B-structure_element
and	O
CDC2	B-structure_element
(	O
green	O
and	O
grey	O
)	O
are	O
marked	O
as	O
spheres	O
.	O

(	O
b	O
)	O
The	O
interdomain	B-site
interface	I-site
of	O
CDC1	B-structure_element
and	O
CDC2	B-structure_element
exhibits	O
only	O
limited	O
plasticity	O
.	O

Representation	O
as	O
in	O
a	O
,	O
but	O
the	O
CDC1	B-structure_element
and	O
CDC2	B-structure_element
are	O
superposed	B-experimental_method
based	O
on	O
CDC2	B-structure_element
.	O

One	O
protomer	B-oligomeric_state
of	O
CthΔBCCP	B-mutant
is	O
shown	O
in	O
colour	O
,	O
the	O
CDL	B-structure_element
domains	O
are	O
omitted	O
for	O
clarity	O
and	O
the	O
position	O
of	O
the	O
phosphorylated	B-protein_state
serine	B-residue_name
based	O
on	O
SceCD	B-species
is	O
indicated	O
with	O
a	O
red	O
triangle	O
.	O

The	O
connection	O
points	O
from	O
CDC1	B-structure_element
to	O
CDC2	B-structure_element
and	O
to	O
CDL	B-structure_element
are	O
represented	O
by	O
green	O
spheres	O
.	O

The	O
conformational	O
dynamics	O
of	O
fungal	B-taxonomy_domain
ACC	B-protein_type
.	O

(	O
a	O
–	O
c	O
)	O
Large	O
-	O
scale	O
conformational	O
variability	O
of	O
the	O
CDN	B-structure_element
domain	O
relative	O
to	O
the	O
CDL	B-structure_element
/	O
CDC1	B-structure_element
domain	O
.	O

CthCD	B-mutant
-	I-mutant
CT1	I-mutant
(	O
in	O
colour	O
)	O
serves	O
as	O
reference	O
,	O
the	O
compared	B-experimental_method
structures	I-experimental_method
(	O
as	O
indicated	O
,	O
numbers	O
after	O
construct	O
name	O
differentiate	O
between	O
individual	O
protomers	B-oligomeric_state
)	O
are	O
shown	O
in	O
grey	O
.	O

Domains	O
other	O
than	O
CDN	B-structure_element
and	O
CDL	B-structure_element
/	O
CDC1	B-structure_element
are	O
omitted	O
for	O
clarity	O
.	O

The	O
domains	O
are	O
labelled	O
and	O
the	O
distances	O
between	O
the	O
N	O
termini	O
of	O
CDN	B-structure_element
(	O
spheres	O
)	O
in	O
the	O
compared	O
structures	O
are	O
indicated	O
.	O

(	O
d	O
)	O
Schematic	O
model	O
of	O
fungal	B-taxonomy_domain
ACC	B-protein_type
showing	O
the	O
intrinsic	O
,	O
regulated	O
flexibility	O
of	O
CD	B-structure_element
in	O
the	O
phosphorylated	B-protein_state
inhibited	B-protein_state
or	O
the	O
non	B-protein_state
-	I-protein_state
phosphorylated	I-protein_state
activated	B-protein_state
state	O
.	O

Flexibility	O
of	O
the	O
CDC2	B-structure_element
/	O
CT	B-structure_element
and	O
CDN	B-structure_element
/	O
CDL	B-structure_element
hinges	B-structure_element
is	O
illustrated	O
by	O
arrows	O
.	O

The	O
Ser1157	B-residue_name_number
phosphorylation	B-ptm
site	O
and	O
the	O
regulatory	B-structure_element
loop	I-structure_element
are	O
schematically	O
indicated	O
in	O
magenta	O
.	O

Structural	O
insights	O
into	O
the	O
Escherichia	B-species
coli	I-species
lysine	B-protein_type
decarboxylases	I-protein_type
and	O
molecular	O
determinants	O
of	O
interaction	O
with	O
the	O
AAA	B-protein_type
+	I-protein_type
ATPase	I-protein_type
RavA	B-protein

The	O
inducible	B-protein_state
lysine	B-protein_type
decarboxylase	I-protein_type
LdcI	B-protein
is	O
an	O
important	O
enterobacterial	B-taxonomy_domain
acid	B-protein_type
stress	I-protein_type
response	I-protein_type
enzyme	I-protein_type
whereas	O
LdcC	B-protein
is	O
its	O
close	O
paralogue	O
thought	O
to	O
play	O
mainly	O
a	O
metabolic	O
role	O
.	O

A	O
unique	O
macromolecular	O
cage	O
formed	O
by	O
two	O
decamers	B-oligomeric_state
of	O
the	O
Escherichia	B-species
coli	I-species
LdcI	B-protein
and	O
five	O
hexamers	B-oligomeric_state
of	O
the	O
AAA	B-protein_type
+	I-protein_type
ATPase	I-protein_type
RavA	B-protein
was	O
shown	O
to	O
counteract	O
acid	O
stress	O
under	O
starvation	O
.	O

Previously	O
,	O
we	O
proposed	O
a	O
pseudoatomic	B-evidence
model	I-evidence
of	O
the	O
LdcI	B-complex_assembly
-	I-complex_assembly
RavA	I-complex_assembly
cage	O
based	O
on	O
its	O
cryo	B-experimental_method
-	I-experimental_method
electron	I-experimental_method
microscopy	I-experimental_method
map	B-evidence
and	O
crystal	B-evidence
structures	I-evidence
of	O
an	O
inactive	B-protein_state
LdcI	B-protein
decamer	B-oligomeric_state
and	O
a	O
RavA	B-protein
monomer	B-oligomeric_state
.	O

We	O
now	O
present	O
cryo	B-experimental_method
-	I-experimental_method
electron	I-experimental_method
microscopy	I-experimental_method
3D	B-evidence
reconstructions	I-evidence
of	O
the	O
E	B-species
.	I-species
coli	I-species
LdcI	B-protein
and	O
LdcC	B-protein
,	O
and	O
an	O
improved	B-evidence
map	I-evidence
of	O
the	O
LdcI	B-protein
bound	B-protein_state
to	I-protein_state
the	O
LARA	B-structure_element
domain	I-structure_element
of	O
RavA	B-protein
,	O
at	O
pH	B-protein_state
optimal	I-protein_state
for	O
their	O
enzymatic	O
activity	O
.	O

Comparison	B-experimental_method
with	O
each	O
other	O
and	O
with	O
available	O
structures	B-evidence
uncovers	O
differences	O
between	O
LdcI	B-protein
and	O
LdcC	B-protein
explaining	O
why	O
only	O
the	O
acid	B-protein_type
stress	I-protein_type
response	I-protein_type
enzyme	I-protein_type
is	O
capable	O
of	O
binding	O
RavA	B-protein
.	O
We	O
identify	O
interdomain	O
movements	O
associated	O
with	O
the	O
pH	B-protein_state
-	I-protein_state
dependent	I-protein_state
enzyme	O
activation	O
and	O
with	O
the	O
RavA	B-protein
binding	O
.	O

Multiple	B-experimental_method
sequence	I-experimental_method
alignment	I-experimental_method
coupled	O
to	O
a	O
phylogenetic	B-experimental_method
analysis	I-experimental_method
reveals	O
that	O
certain	O
enterobacteria	B-taxonomy_domain
exert	O
evolutionary	O
pressure	O
on	O
the	O
lysine	B-protein_type
decarboxylase	I-protein_type
towards	O
the	O
cage	O
-	O
like	O
assembly	O
with	O
RavA	B-protein
,	O
implying	O
that	O
this	O
complex	O
may	O
have	O
an	O
important	O
function	O
under	O
particular	O
stress	O
conditions	O
.	O

Enterobacterial	B-taxonomy_domain
inducible	B-protein_state
decarboxylases	B-protein_type
of	O
basic	B-protein_state
amino	B-chemical
acids	I-chemical
lysine	B-residue_name
,	O
arginine	B-residue_name
and	O
ornithine	B-residue_name
have	O
a	O
common	O
evolutionary	O
origin	O
and	O
belong	O
to	O
the	O
α	B-protein_type
-	I-protein_type
family	I-protein_type
of	O
pyridoxal	B-chemical
-	I-chemical
5	I-chemical
′-	I-chemical
phosphate	I-chemical
(	O
PLP	B-chemical
)-	O
dependent	O
enzymes	O
.	O

They	O
counteract	O
acid	O
stress	O
experienced	O
by	O
the	O
bacterium	B-taxonomy_domain
in	O
the	O
host	O
digestive	O
and	O
urinary	O
tract	O
,	O
and	O
in	O
particular	O
in	O
the	O
extremely	O
acidic	O
stomach	O
.	O

Each	O
decarboxylase	B-protein_type
is	O
induced	O
by	O
an	O
excess	O
of	O
the	O
target	O
amino	B-chemical
acid	I-chemical
and	O
a	O
specific	O
range	O
of	O
extracellular	O
pH	O
,	O
and	O
works	O
in	O
conjunction	O
with	O
a	O
cognate	O
inner	B-protein_type
membrane	I-protein_type
antiporter	I-protein_type
.	O

Decarboxylation	O
of	O
the	O
amino	B-chemical
acid	I-chemical
into	O
a	O
polyamine	B-chemical
is	O
catalysed	O
by	O
a	O
PLP	B-chemical
cofactor	O
in	O
a	O
multistep	O
reaction	O
that	O
consumes	O
a	O
cytoplasmic	O
proton	B-chemical
and	O
produces	O
a	O
CO2	B-chemical
molecule	O
passively	O
diffusing	O
out	O
of	O
the	O
cell	O
,	O
while	O
the	O
polyamine	B-chemical
is	O
excreted	O
by	O
the	O
antiporter	B-protein_type
in	O
exchange	O
for	O
a	O
new	O
amino	B-chemical
acid	I-chemical
substrate	O
.	O

Consequently	O
,	O
these	O
enzymes	O
buffer	O
both	O
the	O
bacterial	B-taxonomy_domain
cytoplasm	O
and	O
the	O
local	O
extracellular	O
environment	O
.	O

These	O
amino	B-protein_type
acid	I-protein_type
decarboxylases	I-protein_type
are	O
therefore	O
called	O
acid	O
stress	O
inducible	B-protein_state
or	O
biodegradative	B-protein_state
to	O
distinguish	O
them	O
from	O
their	O
biosynthetic	B-protein_state
lysine	B-protein_type
and	I-protein_type
ornithine	I-protein_type
decarboxylase	I-protein_type
paralogs	O
catalysing	O
the	O
same	O
reaction	O
but	O
responsible	O
for	O
the	O
polyamine	B-chemical
production	O
at	O
neutral	B-protein_state
pH	I-protein_state
.	O

Inducible	B-protein_state
enterobacterial	B-taxonomy_domain
amino	B-protein_type
acid	I-protein_type
decarboxylases	I-protein_type
have	O
been	O
intensively	O
studied	O
since	O
the	O
early	O
1940	O
because	O
the	O
ability	O
of	O
bacteria	B-taxonomy_domain
to	O
withstand	O
acid	O
stress	O
can	O
be	O
linked	O
to	O
their	O
pathogenicity	O
in	O
humans	B-species
.	O

In	O
particular	O
,	O
the	O
inducible	B-protein_state
lysine	B-protein_type
decarboxylase	I-protein_type
LdcI	B-protein
(	O
or	O
CadA	B-protein
)	O
attracts	O
attention	O
due	O
to	O
its	O
broad	B-protein_state
pH	I-protein_state
range	I-protein_state
of	O
activity	O
and	O
its	O
capacity	O
to	O
promote	O
survival	O
and	O
growth	O
of	O
pathogenic	O
enterobacteria	B-taxonomy_domain
such	O
as	O
Salmonella	B-species
enterica	I-species
serovar	I-species
Typhimurium	I-species
,	O
Vibrio	B-species
cholerae	I-species
and	O
Vibrio	B-species
vulnificus	I-species
under	O
acidic	O
conditions	O
.	O

Furthermore	O
,	O
both	O
LdcI	B-protein
and	O
the	O
biosynthetic	B-protein_state
lysine	B-protein_type
decarboxylase	I-protein_type
LdcC	B-protein
of	O
uropathogenic	B-species
Escherichia	I-species
coli	I-species
(	O
UPEC	B-species
)	O
appear	O
to	O
play	O
an	O
important	O
role	O
in	O
increased	O
resistance	O
of	O
this	O
pathogen	O
to	O
nitrosative	O
stress	O
produced	O
by	O
nitric	B-chemical
oxide	I-chemical
and	O
other	O
damaging	O
reactive	O
nitrogen	O
intermediates	O
accumulating	O
during	O
the	O
course	O
of	O
urinary	O
tract	O
infections	O
(	O
UTI	O
).	O

This	O
effect	O
is	O
attributed	O
to	O
cadaverine	B-chemical
,	O
the	O
diamine	O
produced	O
by	O
decarboxylation	O
of	O
lysine	B-residue_name
by	O
LdcI	B-protein
and	O
LdcC	B-protein
,	O
that	O
was	O
shown	O
to	O
enhance	O
UPEC	B-species
colonisation	O
of	O
the	O
bladder	O
.	O

In	O
addition	O
,	O
the	O
biosynthetic	B-protein_state
E	B-species
.	I-species
coli	I-species
lysine	B-protein_type
decarboxylase	I-protein_type
LdcC	B-protein
,	O
long	O
thought	O
to	O
be	O
constitutively	O
expressed	O
in	O
low	O
amounts	O
,	O
was	O
demonstrated	O
to	O
be	O
strongly	O
upregulated	O
by	O
fluoroquinolones	B-chemical
via	O
their	O
induction	O
of	O
RpoS	B-protein
.	O
A	O
direct	O
correlation	O
between	O
the	O
level	O
of	O
cadaverine	B-chemical
and	O
the	O
resistance	O
of	O
E	B-species
.	I-species
coli	I-species
to	O
these	O
antibiotics	O
commonly	O
used	O
as	O
a	O
first	O
-	O
line	O
treatment	O
of	O
UTI	O
could	O
be	O
established	O
.	O

Both	O
acid	B-protein_state
pH	I-protein_state
and	O
cadaverine	B-chemical
induce	O
closure	O
of	O
outer	O
membrane	O
porins	B-protein_type
thereby	O
contributing	O
to	O
bacterial	B-taxonomy_domain
protection	O
from	O
acid	O
stress	O
,	O
but	O
also	O
from	O
certain	O
antibiotics	O
,	O
by	O
reduction	O
in	O
membrane	O
permeability	O
.	O

The	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
E	B-species
.	I-species
coli	I-species
LdcI	B-protein
as	O
well	O
as	O
its	O
low	O
resolution	O
characterisation	O
by	O
electron	B-experimental_method
microscopy	I-experimental_method
(	O
EM	B-experimental_method
)	O
showed	O
that	O
it	O
is	O
a	O
decamer	B-oligomeric_state
made	O
of	O
two	O
pentameric	B-oligomeric_state
rings	B-structure_element
.	O

Each	O
monomer	B-oligomeric_state
is	O
composed	O
of	O
three	O
domains	O
–	O
an	O
N	O
-	O
terminal	O
wing	B-structure_element
domain	I-structure_element
(	O
residues	O
1	B-residue_range
–	I-residue_range
129	I-residue_range
),	O
a	O
PLP	B-structure_element
-	I-structure_element
binding	I-structure_element
core	I-structure_element
domain	I-structure_element
(	O
residues	O
130	B-residue_range
–	I-residue_range
563	I-residue_range
),	O
and	O
a	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
domain	I-structure_element
(	O
CTD	B-structure_element
,	O
residues	O
564	B-residue_range
–	I-residue_range
715	I-residue_range
).	O

Monomers	B-oligomeric_state
tightly	O
associate	O
via	O
their	O
core	B-structure_element
domains	I-structure_element
into	O
2	B-protein_state
-	I-protein_state
fold	I-protein_state
symmetrical	I-protein_state
dimers	B-oligomeric_state
with	O
two	O
complete	O
active	B-site
sites	I-site
,	O
and	O
further	O
build	O
a	O
toroidal	B-structure_element
D5	I-structure_element
-	I-structure_element
symmetrical	I-structure_element
structure	I-structure_element
held	O
by	O
the	O
wing	B-structure_element
and	O
core	B-structure_element
domain	I-structure_element
interactions	O
around	O
the	O
central	B-structure_element
pore	I-structure_element
,	O
with	O
the	O
CTDs	B-structure_element
at	O
the	O
periphery	O
.	O

Ten	O
years	O
ago	O
we	O
showed	O
that	O
the	O
E	B-species
.	I-species
coli	I-species
AAA	B-protein_type
+	I-protein_type
ATPase	I-protein_type
RavA	B-protein
,	O
involved	O
in	O
multiple	O
stress	O
response	O
pathways	O
,	O
tightly	O
interacted	O
with	O
LdcI	B-protein
but	O
was	O
not	O
capable	O
of	O
binding	O
to	O
LdcC	B-protein
.	O
We	O
described	O
how	O
two	O
double	O
pentameric	B-oligomeric_state
rings	B-structure_element
of	O
the	O
LdcI	B-protein
tightly	O
associate	O
with	O
five	O
hexameric	B-oligomeric_state
rings	B-structure_element
of	O
RavA	B-protein
to	O
form	O
a	O
unique	O
cage	O
-	O
like	O
architecture	O
that	O
enables	O
the	O
bacterium	B-taxonomy_domain
to	O
withstand	O
acid	O
stress	O
even	O
under	O
conditions	O
of	O
nutrient	O
deprivation	O
eliciting	O
stringent	O
response	O
.	O

Furthermore	O
,	O
we	O
recently	O
solved	B-experimental_method
the	I-experimental_method
structure	I-experimental_method
of	O
the	O
E	B-species
.	I-species
coli	I-species
LdcI	B-complex_assembly
-	I-complex_assembly
RavA	I-complex_assembly
complex	O
by	O
cryo	B-experimental_method
-	I-experimental_method
electron	I-experimental_method
microscopy	I-experimental_method
(	O
cryoEM	B-experimental_method
)	O
and	O
combined	O
it	O
with	O
the	O
crystal	B-evidence
structures	I-evidence
of	O
the	O
individual	O
proteins	O
.	O

This	O
allowed	O
us	O
to	O
make	O
a	O
pseudoatomic	B-evidence
model	I-evidence
of	O
the	O
whole	O
assembly	O
,	O
underpinned	O
by	O
a	O
cryoEM	B-experimental_method
map	B-evidence
of	O
the	O
LdcI	B-complex_assembly
-	I-complex_assembly
LARA	I-complex_assembly
complex	O
(	O
with	O
LARA	B-structure_element
standing	O
for	O
LdcI	B-structure_element
associating	I-structure_element
domain	I-structure_element
of	I-structure_element
RavA	I-structure_element
),	O
and	O
to	O
identify	O
conformational	O
rearrangements	O
and	O
specific	O
elements	O
essential	O
for	O
complex	O
formation	O
.	O

The	O
main	O
determinants	O
of	O
the	O
LdcI	B-complex_assembly
-	I-complex_assembly
RavA	I-complex_assembly
cage	O
assembly	O
appeared	O
to	O
be	O
the	O
N	O
-	O
terminal	O
loop	B-structure_element
of	O
the	O
LARA	B-structure_element
domain	I-structure_element
of	O
RavA	B-protein
and	O
the	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
of	O
LdcI	B-protein
.	O

In	O
spite	O
of	O
this	O
wealth	O
of	O
structural	B-evidence
information	I-evidence
,	O
the	O
fact	O
that	O
LdcC	B-protein
does	O
not	O
interact	O
with	O
RavA	B-protein
,	O
although	O
the	O
two	O
lysine	B-protein_type
decarboxylases	I-protein_type
are	O
69	O
%	O
identical	O
and	O
84	O
%	O
similar	O
,	O
and	O
the	O
physiological	O
significance	O
of	O
the	O
absence	O
of	O
this	O
interaction	O
remained	O
unexplored	O
.	O

To	O
solve	O
this	O
discrepancy	O
,	O
in	O
the	O
present	O
work	O
we	O
provided	O
a	O
three	O
-	O
dimensional	O
(	O
3D	O
)	O
cryoEM	B-experimental_method
reconstruction	B-evidence
of	O
LdcC	B-protein
and	O
compared	O
it	O
with	O
the	O
available	O
LdcI	B-protein
and	O
LdcI	B-complex_assembly
-	I-complex_assembly
RavA	I-complex_assembly
structures	B-evidence
.	O

Given	O
that	O
the	O
LdcI	B-protein
crystal	B-evidence
structures	I-evidence
were	O
obtained	O
at	O
high	B-protein_state
pH	I-protein_state
where	O
the	O
enzyme	O
is	O
inactive	B-protein_state
(	O
LdcIi	B-protein
,	O
pH	B-protein_state
8	I-protein_state
.	I-protein_state
5	I-protein_state
),	O
whereas	O
the	O
cryoEM	B-experimental_method
reconstructions	B-evidence
of	O
LdcI	B-complex_assembly
-	I-complex_assembly
RavA	I-complex_assembly
and	O
LdcI	B-complex_assembly
-	I-complex_assembly
LARA	I-complex_assembly
were	O
done	O
at	O
acidic	B-protein_state
pH	I-protein_state
optimal	I-protein_state
for	O
the	O
enzymatic	O
activity	O
,	O
for	O
a	O
meaningful	O
comparison	O
,	O
we	O
also	O
produced	O
a	O
3D	B-evidence
reconstruction	I-evidence
of	O
the	O
LdcI	B-protein
at	O
active	B-protein_state
pH	I-protein_state
(	O
LdcIa	B-protein
,	O
pH	B-protein_state
6	I-protein_state
.	I-protein_state
2	I-protein_state
).	O

This	O
comparison	O
pinpointed	O
differences	O
between	O
the	O
biodegradative	B-protein_state
and	O
the	O
biosynthetic	B-protein_state
lysine	B-protein_type
decarboxylases	I-protein_type
and	O
brought	O
to	O
light	O
interdomain	O
movements	O
associated	O
to	O
pH	B-protein_state
-	I-protein_state
dependent	I-protein_state
enzyme	O
activation	O
and	O
RavA	B-protein
binding	O
,	O
notably	O
at	O
the	O
predicted	O
RavA	B-site
binding	I-site
site	I-site
at	O
the	O
level	O
of	O
the	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
of	O
LdcI	B-protein
.	O
Consequently	O
,	O
we	O
tested	O
the	O
capacity	O
of	O
cage	O
formation	O
by	O
LdcI	B-mutant
-	I-mutant
LdcC	I-mutant
chimeras	I-mutant
where	O
we	O
interchanged	B-experimental_method
the	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
sheets	I-structure_element
in	O
question	O
.	O

Finally	O
,	O
we	O
performed	O
multiple	B-experimental_method
sequence	I-experimental_method
alignment	I-experimental_method
of	O
22	O
lysine	B-protein_type
decarboxylases	I-protein_type
from	O
Enterobacteriaceae	B-taxonomy_domain
containing	O
the	O
ravA	B-gene
-	I-gene
viaA	I-gene
operon	I-gene
in	O
their	O
genome	O
.	O

Remarkably	O
,	O
this	O
analysis	O
revealed	O
that	O
several	O
specific	B-structure_element
residues	I-structure_element
in	O
the	O
above	O
-	O
mentioned	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
,	O
independently	O
of	O
the	O
rest	O
of	O
the	O
protein	O
sequence	O
,	O
are	O
sufficient	O
to	O
define	O
if	O
a	O
particular	O
lysine	B-protein_type
decarboxylase	I-protein_type
should	O
be	O
classified	O
as	O
an	O
“	O
LdcC	B-protein_type
-	I-protein_type
like	I-protein_type
”	O
or	O
an	O
“	O
LdcI	B-protein_type
-	I-protein_type
like	I-protein_type
”.	O

This	O
fascinating	O
parallelism	O
between	O
the	O
propensity	O
for	O
RavA	B-protein
binding	O
and	O
the	O
genetic	O
environment	O
of	O
an	O
enterobacterial	B-taxonomy_domain
lysine	B-protein_type
decarboxylase	I-protein_type
,	O
as	O
well	O
as	O
the	O
high	B-protein_state
degree	I-protein_state
of	I-protein_state
conservation	I-protein_state
of	O
this	O
small	B-structure_element
structural	I-structure_element
motif	I-structure_element
,	O
emphasize	O
the	O
functional	O
importance	O
of	O
the	O
interaction	O
between	O
biodegradative	B-protein_state
enterobacterial	B-taxonomy_domain
lysine	B-protein_type
decarboxylases	I-protein_type
and	O
the	O
AAA	B-protein_type
+	I-protein_type
ATPase	I-protein_type
RavA	B-protein
.	O

CryoEM	B-experimental_method
3D	B-evidence
reconstructions	I-evidence
of	O
LdcC	B-protein
,	O
LdcIa	B-protein
and	O
LdcI	B-complex_assembly
-	I-complex_assembly
LARA	I-complex_assembly

In	O
the	O
frame	O
of	O
this	O
work	O
,	O
we	O
produced	O
two	O
novel	O
subnanometer	O
resolution	O
cryoEM	B-experimental_method
reconstructions	B-evidence
of	O
the	O
E	B-species
.	I-species
coli	I-species
lysine	B-protein_type
decarboxylases	I-protein_type
at	O
pH	B-protein_state
optimal	I-protein_state
for	O
their	O
enzymatic	O
activity	O
–	O
a	O
5	O
.	O
5	O
Å	O
resolution	O
cryoEM	B-experimental_method
map	B-evidence
of	O
the	O
LdcC	B-protein
(	O
pH	B-protein_state
7	I-protein_state
.	I-protein_state
5	I-protein_state
)	O
for	O
which	O
no	O
3D	O
structural	O
information	O
has	O
been	O
previously	O
available	O
(	O
Figs	O
1A	O
,	O
B	O
and	O
S1	O
),	O
and	O
a	O
6	O
.	O
1	O
Å	O
resolution	O
cryoEM	B-experimental_method
map	B-evidence
of	O
the	O
LdcIa	B-protein
,	O
(	O
pH	B-protein_state
6	I-protein_state
.	I-protein_state
2	I-protein_state
)	O
(	O
Figs	O
1C	O
,	O
D	O
and	O
S2	O
).	O

In	O
addition	O
,	O
we	O
improved	O
our	O
earlier	O
cryoEM	B-experimental_method
map	B-evidence
of	O
the	O
LdcI	B-complex_assembly
-	I-complex_assembly
LARA	I-complex_assembly
complex	O
from	O
7	O
.	O
5	O
Å	O
to	O
6	O
.	O
2	O
Å	O
resolution	O
(	O
Figs	O
1E	O
,	O
F	O
and	O
S3	O
).	O

Based	O
on	O
these	O
reconstructions	B-evidence
,	O
reliable	O
pseudoatomic	B-evidence
models	I-evidence
of	O
the	O
three	O
assemblies	O
were	O
obtained	O
by	O
flexible	B-experimental_method
fitting	I-experimental_method
of	I-experimental_method
either	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
LdcIi	B-protein
or	O
a	O
derived	O
structural	B-experimental_method
homology	I-experimental_method
model	I-experimental_method
of	O
LdcC	B-protein
(	O
Table	O
S1	O
).	O

Significant	O
differences	O
between	O
these	O
pseudoatomic	B-evidence
models	I-evidence
can	O
be	O
interpreted	O
as	O
movements	O
between	O
specific	O
biological	O
states	O
of	O
the	O
proteins	O
as	O
described	O
below	O
.	O

The	O
wing	B-structure_element
domains	I-structure_element
as	O
a	O
stable	O
anchor	O
at	O
the	O
center	O
of	O
the	O
double	B-structure_element
-	I-structure_element
ring	I-structure_element

As	O
a	O
first	O
step	O
of	O
a	O
comparative	O
analysis	O
,	O
we	O
superimposed	B-experimental_method
the	O
three	O
cryoEM	B-experimental_method
reconstructions	B-evidence
(	O
LdcIa	B-protein
,	O
LdcI	B-complex_assembly
-	I-complex_assembly
LARA	I-complex_assembly
and	O
LdcC	B-protein
)	O
and	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
LdcIi	B-protein
decamer	B-oligomeric_state
(	O
Fig	O
.	O
2	O
and	O
Movie	O
S1	O
).	O

This	O
superposition	B-experimental_method
reveals	O
that	O
the	O
densities	B-evidence
lining	O
the	O
central	B-structure_element
hole	I-structure_element
of	O
the	O
toroid	B-structure_element
are	O
roughly	O
at	O
the	O
same	O
location	O
,	O
while	O
the	O
rest	O
of	O
the	O
structure	B-evidence
exhibits	O
noticeable	O
changes	O
.	O

Specifically	O
,	O
at	O
the	O
center	O
of	O
the	O
double	B-structure_element
-	I-structure_element
ring	I-structure_element
the	O
wing	B-structure_element
domains	I-structure_element
of	O
the	O
subunits	O
provide	O
the	O
conserved	B-protein_state
basis	O
for	O
the	O
assembly	O
with	O
the	O
lowest	B-evidence
root	I-evidence
mean	I-evidence
square	I-evidence
deviation	I-evidence
(	O
RMSD	B-evidence
)	O
(	O
between	O
1	O
.	O
4	O
and	O
2	O
Å	O
for	O
the	O
Cα	O
atoms	O
only	O
),	O
whereas	O
the	O
peripheral	O
CTDs	B-structure_element
containing	O
the	O
RavA	B-site
binding	I-site
interface	I-site
manifest	O
the	O
highest	O
RMSD	B-evidence
(	O
up	O
to	O
4	O
.	O
2	O
Å	O
)	O
(	O
Table	O
S2	O
).	O

In	O
addition	O
,	O
the	O
wing	B-structure_element
domains	I-structure_element
of	O
all	O
structures	B-evidence
are	O
very	O
similar	O
,	O
with	O
the	O
RMSD	B-evidence
after	O
optimal	O
rigid	O
body	O
alignment	O
(	O
RMSDmin	B-evidence
)	O
less	O
than	O
1	O
.	O
1	O
Å	O
.	O
Thus	O
,	O
taking	O
the	O
limited	O
resolution	O
of	O
the	O
cryoEM	B-experimental_method
maps	B-evidence
into	O
account	O
,	O
we	O
consider	O
that	O
the	O
wing	B-structure_element
domains	I-structure_element
of	O
all	O
the	O
four	O
structures	B-evidence
are	O
essentially	O
identical	O
and	O
that	O
in	O
the	O
present	O
study	O
the	O
RMSD	B-evidence
of	O
less	O
than	O
2	O
Å	O
can	O
serve	O
as	O
a	O
baseline	O
below	O
which	O
differences	O
may	O
be	O
assumed	O
as	O
insignificant	O
.	O

This	O
preservation	O
of	O
the	O
central	B-structure_element
part	I-structure_element
of	O
the	O
double	O
-	O
ring	O
assembly	O
may	O
help	O
the	O
enzymes	O
to	O
maintain	O
their	O
decameric	B-oligomeric_state
state	O
upon	O
activation	O
and	O
incorporation	O
into	O
the	O
LdcI	B-complex_assembly
-	I-complex_assembly
RavA	I-complex_assembly
cage	O
.	O

The	O
core	B-structure_element
domain	I-structure_element
and	O
the	O
active	B-site
site	I-site
rearrangements	O
upon	O
pH	B-protein_state
-	I-protein_state
dependent	I-protein_state
enzyme	O
activation	O
and	O
LARA	O
binding	O

Both	O
visual	B-experimental_method
inspection	I-experimental_method
(	O
Fig	O
.	O
2	O
)	O
and	O
RMSD	B-experimental_method
calculations	I-experimental_method
(	O
Table	O
S2	O
)	O
show	O
that	O
globally	O
the	O
three	O
structures	B-evidence
at	O
active	B-protein_state
pH	I-protein_state
(	O
LdcIa	B-protein
,	O
LdcI	B-complex_assembly
-	I-complex_assembly
LARA	I-complex_assembly
and	O
LdcC	B-protein
)	O
are	O
more	O
similar	O
to	O
each	O
other	O
than	O
to	O
the	O
structure	O
determined	O
at	O
high	B-protein_state
pH	I-protein_state
conditions	O
(	O
LdcIi	B-protein
).	O

The	O
decameric	B-oligomeric_state
enzyme	O
is	O
built	O
of	O
five	O
dimers	B-oligomeric_state
associating	O
into	O
a	O
5	B-structure_element
-	I-structure_element
fold	I-structure_element
symmetrical	I-structure_element
double	I-structure_element
-	I-structure_element
ring	I-structure_element
(	O
two	O
monomers	B-oligomeric_state
making	O
a	O
dimer	B-oligomeric_state
are	O
delineated	O
in	O
Fig	O
.	O
1	O
).	O

As	O
common	O
for	O
the	O
α	B-protein_type
family	I-protein_type
of	O
the	O
PLP	B-protein_type
-	I-protein_type
dependent	I-protein_type
decarboxylases	I-protein_type
,	O
dimerization	O
is	O
required	O
for	O
the	O
enzymatic	O
activity	O
because	O
the	O
active	B-site
site	I-site
is	O
buried	O
in	O
the	O
dimer	B-site
interface	I-site
(	O
Fig	O
.	O
3A	O
,	O
B	O
).	O

This	O
interface	B-site
is	O
formed	O
essentially	O
by	O
the	O
core	B-structure_element
domains	I-structure_element
with	O
some	O
contribution	O
of	O
the	O
CTDs	B-structure_element
.	O

The	O
core	B-structure_element
domain	I-structure_element
is	O
built	O
by	O
the	O
PLP	B-structure_element
-	I-structure_element
binding	I-structure_element
subdomain	I-structure_element
(	O
PLP	B-structure_element
-	I-structure_element
SD	I-structure_element
,	O
residues	O
184	B-residue_range
–	I-residue_range
417	I-residue_range
)	O
flanked	O
by	O
two	O
smaller	O
subdomains	B-structure_element
rich	O
in	O
partly	B-protein_state
disordered	I-protein_state
loops	B-structure_element
–	O
the	O
linker	B-structure_element
region	I-structure_element
(	O
residues	O
130	B-residue_range
–	I-residue_range
183	I-residue_range
)	O
and	O
the	O
subdomain	B-structure_element
4	I-structure_element
(	O
residues	O
418	B-residue_range
–	I-residue_range
563	I-residue_range
).	O

Zooming	O
in	O
the	O
variations	O
in	O
the	O
PLP	B-structure_element
-	I-structure_element
SD	I-structure_element
shows	O
that	O
most	O
of	O
the	O
structural	O
changes	O
concern	O
displacements	O
in	O
the	O
active	B-site
site	I-site
(	O
Fig	O
.	O
3C	O
–	O
F	O
).	O

The	O
most	O
conspicuous	O
differences	O
between	O
the	O
PLP	B-structure_element
-	I-structure_element
SDs	I-structure_element
can	O
be	O
linked	O
to	O
the	O
pH	B-protein_state
-	I-protein_state
dependent	I-protein_state
activation	O
of	O
the	O
enzymes	O
.	O

The	O
resolution	O
of	O
the	O
cryoEM	B-experimental_method
maps	B-evidence
does	O
not	O
allow	O
modeling	O
the	O
position	O
of	O
the	O
PLP	B-chemical
moiety	O
and	O
calls	O
for	O
caution	O
in	O
detailed	O
mechanistic	O
interpretations	O
in	O
terms	O
of	O
individual	O
amino	B-chemical
acids	I-chemical
.	O

In	O
particular	O
,	O
transition	O
from	O
LdcIi	B-protein
to	O
LdcI	B-complex_assembly
-	I-complex_assembly
LARA	I-complex_assembly
involves	O
~	O
3	O
.	O
5	O
Å	O
and	O
~	O
4	O
.	O
5	O
Å	O
shifts	O
away	O
from	O
the	O
5	O
-	O
fold	O
axis	O
in	O
the	O
active	B-site
site	I-site
α	B-structure_element
-	I-structure_element
helices	I-structure_element
spanning	O
residues	O
218	B-residue_range
–	I-residue_range
232	I-residue_range
and	O
246	B-residue_range
–	I-residue_range
254	I-residue_range
respectively	O
(	O
Fig	O
.	O
3C	O
–	O
E	O
).	O

Between	O
these	O
two	O
extremes	O
,	O
the	O
PLP	B-structure_element
-	I-structure_element
SDs	I-structure_element
of	O
LdcIa	B-protein
and	O
LdcC	B-protein
are	O
similar	O
both	O
in	O
the	O
context	O
of	O
the	O
decamer	B-oligomeric_state
(	O
Fig	O
.	O
3F	O
)	O
and	O
in	O
terms	O
of	O
RMSDmin	B-evidence
=	O
0	O
.	O
9	O
Å	O
,	O
which	O
probably	O
reflects	O
the	O
fact	O
that	O
,	O
at	O
the	O
optimal	B-protein_state
pH	I-protein_state
,	O
these	O
lysine	B-protein_type
decarboxylases	I-protein_type
have	O
a	O
similar	O
enzymatic	O
activity	O
.	O

In	O
addition	O
,	O
our	O
earlier	O
biochemical	B-experimental_method
observation	I-experimental_method
that	O
the	O
enzymatic	O
activity	O
of	O
LdcIa	B-protein
is	O
unaffected	O
by	O
RavA	B-protein
binding	O
is	O
consistent	O
with	O
the	O
relatively	O
small	O
changes	O
undergone	O
by	O
the	O
active	B-site
site	I-site
upon	O
transition	O
from	O
LdcIa	B-protein
to	O
LdcI	B-complex_assembly
-	I-complex_assembly
LARA	I-complex_assembly
.	O

Worthy	O
of	O
note	O
,	O
our	O
previous	O
comparison	O
of	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
LdcIi	B-protein
with	O
that	O
of	O
the	O
inducible	B-protein_state
arginine	B-protein_type
decarboxylase	I-protein_type
AdiA	B-protein
revealed	O
high	B-protein_state
conservation	I-protein_state
of	O
the	O
PLP	B-site
-	I-site
coordinating	I-site
residues	I-site
and	O
identified	O
a	O
patch	B-site
of	I-site
negatively	I-site
charged	I-site
residues	I-site
lining	O
the	O
active	B-site
site	I-site
channel	I-site
as	O
a	O
potential	O
binding	B-site
site	I-site
for	O
the	O
target	O
amino	B-chemical
acid	I-chemical
substrate	O
(	O
Figs	O
S3	O
and	O
S4	O
in	O
ref	O
.).	O

Rearrangements	O
of	O
the	O
ppGpp	B-site
binding	I-site
pocket	I-site
upon	O
pH	B-protein_state
-	I-protein_state
dependent	I-protein_state
enzyme	O
activation	O
and	O
LARA	B-structure_element
binding	O

An	O
inhibitor	O
of	O
the	O
LdcI	B-protein
and	O
LdcC	B-protein
activity	O
,	O
the	O
stringent	B-chemical
response	I-chemical
alarmone	I-chemical
ppGpp	B-chemical
,	O
is	O
known	O
to	O
bind	O
at	O
the	O
interface	B-site
between	O
neighboring	O
monomers	B-oligomeric_state
within	O
each	O
ring	B-structure_element
(	O
Fig	O
.	O
S4	O
).	O

The	O
ppGpp	B-site
binding	I-site
pocket	I-site
is	O
made	O
up	O
by	O
residues	O
from	O
all	O
domains	O
and	O
is	O
located	O
approximately	O
30	O
Å	O
away	O
from	O
the	O
PLP	B-chemical
moiety	O
.	O

Whereas	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
ppGpp	B-complex_assembly
-	I-complex_assembly
LdcIi	I-complex_assembly
was	O
solved	B-experimental_method
to	O
2	O
Å	O
resolution	O
,	O
only	O
a	O
4	O
.	O
1	O
Å	O
resolution	O
structure	B-evidence
of	O
the	O
ppGpp	B-protein_state
-	I-protein_state
free	I-protein_state
LdcIi	B-protein
could	O
be	O
obtained	O
.	O

At	O
this	O
resolution	O
,	O
the	O
apo	B-protein_state
-	O
LdcIi	B-protein
and	O
ppGpp	B-complex_assembly
-	I-complex_assembly
LdcIi	I-complex_assembly
structures	B-evidence
(	O
both	O
solved	O
at	O
pH	B-protein_state
8	I-protein_state
.	I-protein_state
5	I-protein_state
)	O
appeared	O
indistinguishable	O
except	O
for	O
the	O
presence	O
of	O
ppGpp	B-chemical
(	O
Fig	O
.	O
S11	O
in	O
ref	O
.	O
).	O

Thus	O
,	O
we	O
speculated	O
that	O
inhibition	O
of	O
LdcI	B-protein
by	O
ppGpp	B-chemical
would	O
be	O
accompanied	O
by	O
a	O
transduction	O
of	O
subtle	O
structural	O
changes	O
at	O
the	O
level	O
of	O
individual	O
amino	B-chemical
acid	I-chemical
side	O
chains	O
between	O
the	O
ppGpp	B-site
binding	I-site
pocket	I-site
and	O
the	O
active	B-site
site	I-site
of	O
the	O
enzyme	O
.	O

All	O
our	O
current	O
cryoEM	B-experimental_method
reconstructions	B-evidence
of	O
the	O
lysine	B-protein_type
decarboxylases	I-protein_type
were	O
obtained	O
in	O
the	O
absence	B-protein_state
of	I-protein_state
ppGpp	B-chemical
in	O
order	O
to	O
be	O
closer	O
to	O
the	O
active	B-protein_state
state	O
of	O
the	O
enzymes	O
under	O
study	O
.	O

While	O
differences	O
in	O
the	O
ppGpp	B-site
binding	I-site
site	I-site
could	O
indeed	O
be	O
visualized	O
(	O
Fig	O
.	O
S4	O
),	O
the	O
level	O
of	O
resolution	O
warns	O
against	O
speculations	O
about	O
their	O
significance	O
.	O

The	O
fact	O
that	O
interaction	O
with	O
RavA	B-protein
reduces	O
the	O
ppGpp	B-chemical
affinity	O
for	O
LdcI	B-protein
despite	O
the	O
long	O
distance	O
of	O
~	O
30	O
Å	O
between	O
the	O
LARA	B-site
domain	I-site
binding	I-site
site	I-site
and	O
the	O
closest	O
ppGpp	B-site
binding	I-site
pocket	I-site
(	O
Fig	O
.	O
S5	O
)	O
seems	O
to	O
favor	O
an	O
allosteric	O
regulation	O
mechanism	O
.	O

Interestingly	O
,	O
although	O
a	O
number	O
of	O
ppGpp	B-site
binding	I-site
residues	I-site
are	O
strictly	B-protein_state
conserved	I-protein_state
between	O
LdcI	B-protein
and	O
AdiA	B-protein
that	O
also	O
forms	O
decamers	B-oligomeric_state
at	O
low	B-protein_state
pH	I-protein_state
optimal	I-protein_state
for	O
its	O
arginine	B-protein_type
decarboxylase	I-protein_type
activity	O
,	O
no	O
ppGpp	B-chemical
regulation	O
of	O
AdiA	B-protein
could	O
be	O
demonstrated	O
.	O

Swinging	O
and	O
stretching	O
of	O
the	O
CTDs	B-structure_element
upon	O
pH	B-protein_state
-	I-protein_state
dependent	I-protein_state
LdcI	B-protein
activation	O
and	O
LARA	B-structure_element
binding	O

Inspection	O
of	O
the	O
superimposed	B-experimental_method
decameric	B-oligomeric_state
structures	B-evidence
(	O
Figs	O
2	O
and	O
S6	O
)	O
suggests	O
a	O
depiction	O
of	O
the	O
wing	B-structure_element
domains	I-structure_element
as	O
an	O
anchor	O
around	O
which	O
the	O
peripheral	O
CTDs	B-structure_element
swing	O
.	O

This	O
swinging	O
movement	O
seems	O
to	O
be	O
mediated	O
by	O
the	O
core	B-structure_element
domains	I-structure_element
and	O
is	O
accompanied	O
by	O
a	O
stretching	O
of	O
the	O
whole	O
LdcI	B-protein
subunits	B-structure_element
attracted	O
by	O
the	O
RavA	B-protein
magnets	O
.	O

Indeed	O
,	O
all	O
CTDs	B-structure_element
have	O
very	O
similar	O
structures	O
(	O
RMSDmin	B-evidence
<	O
1	O
Å	O
).	O

Yet	O
the	O
superposition	B-experimental_method
of	O
the	O
decamers	B-oligomeric_state
lays	O
bare	O
a	O
progressive	O
movement	O
of	O
the	O
CTD	B-structure_element
as	O
a	O
whole	O
upon	O
enzyme	O
activation	O
by	O
pH	O
and	O
the	O
binding	O
of	O
LARA	B-structure_element
.	O

The	O
LdcIi	B-protein
monomer	B-oligomeric_state
is	O
the	O
most	B-protein_state
compact	I-protein_state
,	O
whereas	O
LdcIa	B-protein
and	O
especially	O
LdcI	B-complex_assembly
-	I-complex_assembly
LARA	I-complex_assembly
gradually	B-protein_state
extend	I-protein_state
their	O
CTDs	B-structure_element
towards	O
the	O
LARA	B-structure_element
domain	I-structure_element
of	O
RavA	B-protein
(	O
Figs	O
2	O
and	O
4	O
).	O

These	O
small	O
but	O
noticeable	O
swinging	O
and	O
stretching	O
(	O
up	O
to	O
~	O
4	O
Å	O
)	O
may	O
be	O
related	O
to	O
the	O
incorporation	O
of	O
the	O
LdcI	B-protein
decamer	B-oligomeric_state
into	O
the	O
LdcI	B-complex_assembly
-	I-complex_assembly
RavA	I-complex_assembly
cage	O
.	O

The	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
of	O
a	O
lysine	B-protein_type
decarboxylase	I-protein_type
as	O
a	O
major	O
determinant	O
of	O
the	O
interaction	O
with	O
RavA	B-protein

In	O
our	O
previous	O
contribution	O
,	O
based	O
on	O
the	O
fit	O
of	O
the	O
LdcIi	B-protein
and	O
the	O
LARA	B-structure_element
crystal	B-evidence
structures	I-evidence
into	O
the	O
LdcI	B-complex_assembly
-	I-complex_assembly
LARA	I-complex_assembly
cryoEM	B-experimental_method
density	B-evidence
,	O
we	O
predicted	O
that	O
the	O
LdcI	B-complex_assembly
-	I-complex_assembly
RavA	I-complex_assembly
interaction	O
should	O
involve	O
the	O
C	O
-	O
terminal	O
two	B-structure_element
-	I-structure_element
stranded	I-structure_element
β	I-structure_element
-	I-structure_element
sheet	I-structure_element
of	O
the	O
LdcI	B-protein
.	O
Our	O
present	O
cryoEM	B-experimental_method
maps	B-evidence
and	O
pseudoatomic	B-evidence
models	I-evidence
provide	O
first	O
structure	O
-	O
based	O
insights	O
into	O
the	O
differences	O
between	O
the	O
inducible	B-protein_state
and	O
the	O
constitutive	B-protein_state
lysine	B-protein_type
decarboxylases	I-protein_type
.	O

Therefore	O
,	O
we	O
wanted	O
to	O
check	O
the	O
influence	O
of	O
the	O
primary	O
sequence	O
of	O
the	O
two	O
proteins	O
in	O
this	O
region	O
on	O
their	O
ability	O
to	O
interact	O
with	O
RavA	B-protein
.	O
To	O
this	O
end	O
,	O
we	O
swapped	B-experimental_method
the	O
relevant	O
β	B-structure_element
-	I-structure_element
sheets	I-structure_element
of	O
the	O
two	O
proteins	O
and	O
produced	O
their	O
chimeras	B-mutant
,	O
namely	O
LdcIC	B-mutant
(	O
i	O
.	O
e	O
.	O
LdcI	B-protein
with	O
the	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
of	O
LdcC	B-protein
)	O
and	O
LdcCI	B-mutant
(	O
i	O
.	O
e	O
.	O
LdcC	B-protein
with	O
the	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
of	O
LdcI	B-protein
)	O
(	O
Fig	O
.	O
5A	O
–	O
C	O
).	O

Both	B-mutant
constructs	I-mutant
could	O
be	O
purified	O
and	O
could	O
form	O
decamers	B-oligomeric_state
visually	O
indistinguishable	O
from	O
the	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
proteins	O
.	O

As	O
expected	O
,	O
binding	O
of	O
LdcI	B-protein
to	O
RavA	B-protein
was	O
completely	O
abolished	O
by	O
this	O
procedure	O
and	O
no	O
LdcIC	B-complex_assembly
-	I-complex_assembly
RavA	I-complex_assembly
complex	O
could	O
be	O
detected	O
.	O

On	O
the	O
contrary	O
,	O
introduction	B-experimental_method
of	O
the	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
of	O
LdcI	B-protein
into	O
LdcC	B-protein
led	O
to	O
an	O
assembly	O
of	O
the	O
LdcCI	B-complex_assembly
-	I-complex_assembly
RavA	I-complex_assembly
complex	O
.	O

On	O
the	O
negative	B-experimental_method
stain	I-experimental_method
EM	I-experimental_method
grid	I-experimental_method
,	O
the	O
chimeric	B-protein_state
cages	O
appeared	O
less	O
rigid	O
than	O
the	O
native	B-protein_state
LdcI	B-complex_assembly
-	I-complex_assembly
RavA	I-complex_assembly
,	O
which	O
probably	O
means	O
that	O
the	O
environment	O
of	O
the	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
contributes	O
to	O
the	O
efficiency	O
of	O
the	O
interaction	O
and	O
the	O
stability	O
of	O
the	O
entire	O
architecture	O
(	O
Fig	O
.	O
5D	O
–	O
F	O
).	O

The	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
of	O
a	O
lysine	B-protein_type
decarboxylase	I-protein_type
is	O
a	O
highly	B-protein_state
conserved	I-protein_state
signature	O
allowing	O
to	O
distinguish	O
between	O
LdcI	B-protein
and	O
LdcC	B-protein

Alignment	B-experimental_method
of	I-experimental_method
the	I-experimental_method
primary	I-experimental_method
sequences	I-experimental_method
of	O
the	O
E	B-species
.	I-species
coli	I-species
LdcI	B-protein
and	O
LdcC	B-protein
shows	O
that	O
some	O
amino	O
acid	O
residues	O
of	O
the	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
are	O
the	O
same	O
in	O
the	O
two	O
proteins	O
,	O
whereas	O
others	O
are	O
notably	O
different	O
in	O
chemical	O
nature	O
.	O

Importantly	O
,	O
most	O
of	O
the	O
amino	O
acid	O
differences	O
between	O
the	O
two	O
enzymes	O
are	O
located	O
in	O
this	O
very	B-structure_element
region	I-structure_element
.	O

Thus	O
,	O
to	O
advance	O
beyond	O
our	O
experimental	O
confirmation	O
of	O
the	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
as	O
a	O
major	O
determinant	O
of	O
the	O
capacity	O
of	O
a	O
particular	O
lysine	B-protein_type
decarboxylase	I-protein_type
to	O
form	O
a	O
cage	O
with	O
RavA	B-protein
,	O
we	O
set	O
out	O
to	O
investigate	O
whether	O
certain	B-structure_element
residues	I-structure_element
in	O
this	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
are	O
conserved	B-protein_state
in	O
lysine	B-protein_type
decarboxylases	I-protein_type
of	O
different	O
enterobacteria	B-taxonomy_domain
that	O
have	O
the	O
ravA	B-gene
-	I-gene
viaA	I-gene
operon	I-gene
in	O
their	O
genome	O
.	O

We	O
inspected	B-experimental_method
the	I-experimental_method
genetic	I-experimental_method
environment	I-experimental_method
of	O
lysine	B-protein_type
decarboxylases	I-protein_type
from	O
22	O
enterobacterial	B-taxonomy_domain
species	O
referenced	O
in	O
the	O
NCBI	O
database	O
,	O
corrected	O
the	O
gene	O
annotation	O
where	O
necessary	O
(	O
Tables	O
S3	O
and	O
S4	O
),	O
and	O
performed	O
multiple	B-experimental_method
sequence	I-experimental_method
alignment	I-experimental_method
coupled	O
to	O
a	O
phylogenetic	B-experimental_method
analysis	I-experimental_method
(	O
see	O
Methods	O
).	O

First	O
of	O
all	O
,	O
consensus	B-evidence
sequence	I-evidence
for	O
the	O
entire	O
lysine	B-protein_type
decarboxylase	I-protein_type
family	O
was	O
derived	O
.	O

Second	O
,	O
the	O
phylogenetic	B-experimental_method
analysis	I-experimental_method
clearly	O
split	O
the	O
lysine	B-protein_type
decarboxylases	I-protein_type
into	O
two	O
groups	O
(	O
Fig	O
.	O
6A	O
).	O

All	O
lysine	B-protein_type
decarboxylases	I-protein_type
predicted	O
to	O
be	O
“	O
LdcI	B-protein_type
-	I-protein_type
like	I-protein_type
”	O
or	O
biodegradable	B-protein_state
based	O
on	O
their	O
genetic	O
environment	O
,	O
as	O
for	O
example	O
their	O
organization	O
in	O
an	O
operon	O
with	O
a	O
gene	O
encoding	O
the	O
CadB	B-protein
antiporter	B-protein_type
(	O
see	O
Methods	O
),	O
were	O
found	O
in	O
one	O
group	O
,	O
whereas	O
all	O
enzymes	B-protein_type
predicted	O
as	O
“	O
LdcC	B-protein_type
-	I-protein_type
like	I-protein_type
”	O
or	O
biosynthetic	B-protein_state
partitioned	O
into	O
another	O
group	O
.	O

Thus	O
,	O
consensus	B-evidence
sequences	I-evidence
could	O
also	O
be	O
determined	O
for	O
each	O
of	O
the	O
two	O
groups	O
(	O
Figs	O
6B	O
,	O
C	O
and	O
S7	O
).	O

Inspection	O
of	O
these	O
consensus	B-evidence
sequences	I-evidence
revealed	O
important	O
differences	O
between	O
the	O
groups	O
regarding	O
charge	O
,	O
size	O
and	O
hydrophobicity	O
of	O
several	O
residues	O
precisely	O
at	O
the	O
level	O
of	O
the	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
that	O
is	O
responsible	O
for	O
the	O
interaction	O
with	O
RavA	B-protein
(	O
Fig	O
.	O
6B	O
–	O
D	O
).	O

For	O
example	O
,	O
in	O
our	O
previous	O
study	O
,	O
site	B-experimental_method
-	I-experimental_method
directed	I-experimental_method
mutations	I-experimental_method
identified	O
Y697	B-residue_name_number
as	O
critically	O
required	O
for	O
the	O
RavA	B-protein
binding	O
.	O

Our	O
current	O
analysis	O
shows	O
that	O
Y697	B-residue_name_number
is	O
strictly	B-protein_state
conserved	I-protein_state
in	O
the	O
“	O
LdcI	B-protein_type
-	I-protein_type
like	I-protein_type
”	O
group	O
whereas	O
the	O
“	O
LdcC	B-protein_type
-	I-protein_type
like	I-protein_type
”	O
enzymes	O
always	B-protein_state
have	I-protein_state
a	O
lysine	B-residue_name
in	O
this	O
position	O
;	O
it	O
also	O
uncovers	O
several	O
other	O
residues	O
potentially	O
essential	O
for	O
the	O
interaction	O
with	O
RavA	B-protein
which	O
can	O
now	O
be	O
addressed	O
by	O
site	B-experimental_method
-	I-experimental_method
directed	I-experimental_method
mutagenesis	I-experimental_method
.	O

The	O
third	O
and	O
most	O
remarkable	O
finding	O
was	O
that	O
exactly	O
the	O
same	O
separation	O
into	O
“	O
LdcI	B-protein_type
-	I-protein_type
like	I-protein_type
”	O
and	O
“	O
LdcC	B-protein_type
”-	I-protein_type
like	I-protein_type
groups	O
can	O
be	O
obtained	O
based	O
on	O
a	O
comparison	O
of	O
the	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
sheets	I-structure_element
only	O
,	O
without	O
taking	O
the	O
rest	O
of	O
the	O
primary	O
sequence	O
into	O
account	O
.	O

Therefore	O
the	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
emerges	O
as	O
being	O
a	O
highly	B-protein_state
conserved	I-protein_state
signature	B-structure_element
sequence	I-structure_element
,	O
sufficient	O
to	O
unambiguously	O
discriminate	O
between	O
the	O
“	O
LdcI	B-protein_type
-	I-protein_type
like	I-protein_type
”	O
and	O
“	O
LdcC	B-protein_type
-	I-protein_type
like	I-protein_type
”	O
enterobacterial	B-taxonomy_domain
lysine	B-protein_type
decarboxylases	I-protein_type
independently	O
of	O
any	O
other	O
information	O
(	O
Figs	O
6	O
and	O
S7	O
).	O

Our	O
structures	B-evidence
show	O
that	O
this	B-structure_element
motif	I-structure_element
is	O
not	O
involved	O
in	O
the	O
enzymatic	O
activity	O
or	O
the	O
oligomeric	O
state	O
of	O
the	O
proteins	O
.	O

Thus	O
,	O
enterobacteria	B-taxonomy_domain
identified	O
here	O
(	O
Fig	O
.	O
6	O
,	O
Table	O
S4	O
)	O
appear	O
to	O
exert	O
evolutionary	O
pressure	O
on	O
the	O
biodegradative	B-protein_state
lysine	B-protein_type
decarboxylase	I-protein_type
towards	O
the	O
RavA	B-protein
binding	O
.	O

One	O
of	O
the	O
elucidated	O
roles	O
of	O
the	O
LdcI	B-complex_assembly
-	I-complex_assembly
RavA	I-complex_assembly
cage	O
is	O
to	O
maintain	O
LdcI	B-protein
activity	O
under	O
conditions	O
of	O
enterobacterial	B-taxonomy_domain
starvation	O
by	O
preventing	O
LdcI	B-protein
inhibition	O
by	O
the	O
stringent	B-chemical
response	I-chemical
alarmone	I-chemical
ppGpp	B-chemical
.	O

Furthermore	O
,	O
the	O
recently	O
documented	O
interaction	O
of	O
both	O
LdcI	B-protein
and	O
RavA	B-protein
with	O
specific	O
subunits	B-structure_element
of	O
the	O
respiratory	B-protein_type
complex	I-protein_type
I	I-protein_type
,	O
together	O
with	O
the	O
unanticipated	O
link	O
between	O
RavA	B-protein
and	O
maturation	O
of	O
numerous	O
iron	B-protein_type
-	I-protein_type
sulfur	I-protein_type
proteins	I-protein_type
,	O
tend	O
to	O
suggest	O
an	O
additional	O
intriguing	O
function	O
for	O
this	O
3	O
.	O
5	O
MDa	O
assembly	O
.	O

The	O
conformational	O
rearrangements	O
of	O
LdcI	B-protein
upon	O
enzyme	O
activation	O
and	O
RavA	B-protein
binding	O
revealed	O
in	O
this	O
work	O
,	O
and	O
our	O
amazing	O
finding	O
that	O
the	O
molecular	O
determinant	O
of	O
the	O
LdcI	B-complex_assembly
-	I-complex_assembly
RavA	I-complex_assembly
interaction	O
is	O
the	O
one	O
that	O
straightforwardly	O
determines	O
if	O
a	O
particular	O
enterobacterial	B-taxonomy_domain
lysine	B-protein_type
decarboxylase	I-protein_type
belongs	O
to	O
“	O
LdcI	B-protein_type
-	I-protein_type
like	I-protein_type
”	O
or	O
“	O
LdcC	B-protein_type
-	I-protein_type
like	I-protein_type
”	O
proteins	O
,	O
should	O
give	O
a	O
new	O
impetus	O
to	O
functional	O
studies	O
of	O
the	O
unique	O
LdcI	B-complex_assembly
-	I-complex_assembly
RavA	I-complex_assembly
cage	O
.	O

Besides	O
,	O
the	O
structures	B-evidence
and	O
the	O
pseudoatomic	B-evidence
models	I-evidence
of	O
the	O
active	B-protein_state
ppGpp	B-protein_state
-	I-protein_state
free	I-protein_state
states	O
of	O
both	O
the	O
biodegradative	B-protein_state
and	O
the	O
biosynthetic	B-protein_state
E	B-species
.	I-species
coli	I-species
lysine	B-protein_type
decarboxylases	I-protein_type
offer	O
an	O
additional	O
tool	O
for	O
analysis	O
of	O
their	O
role	O
in	O
UPEC	B-species
infectivity	O
.	O

Together	O
with	O
the	O
apo	B-protein_state
-	O
LdcI	B-protein
and	O
ppGpp	B-complex_assembly
-	I-complex_assembly
LdcIi	I-complex_assembly
crystal	B-evidence
structures	I-evidence
,	O
our	O
cryoEM	B-experimental_method
reconstructions	B-evidence
provide	O
a	O
structural	O
framework	O
for	O
future	O
studies	O
of	O
structure	O
-	O
function	O
relationships	O
of	O
lysine	B-protein_type
decarboxylases	I-protein_type
from	O
other	O
enterobacteria	B-taxonomy_domain
and	O
even	O
of	O
their	O
homologues	O
outside	O
Enterobacteriaceae	B-taxonomy_domain
.	O
For	O
example	O
,	O
the	O
lysine	B-protein_type
decarboxylase	I-protein_type
of	O
Eikenella	B-species
corrodens	I-species
is	O
thought	O
to	O
play	O
a	O
major	O
role	O
in	O
the	O
periodontal	O
disease	O
and	O
its	O
inhibitors	O
were	O
shown	O
to	O
retard	O
gingivitis	O
development	O
.	O

Finally	O
,	O
cadaverine	B-chemical
being	O
an	O
important	O
platform	O
chemical	O
for	O
the	O
production	O
of	O
industrial	O
polymers	O
such	O
as	O
nylon	O
,	O
structural	O
information	O
is	O
valuable	O
for	O
optimisation	O
of	O
bacterial	B-taxonomy_domain
lysine	B-protein_type
decarboxylases	I-protein_type
used	O
for	O
its	O
production	O
in	O
biotechnology	O
.	O

3D	O
cryoEM	B-experimental_method
reconstructions	B-evidence
of	O
LdcC	B-protein
,	O
LdcI	B-complex_assembly
-	I-complex_assembly
LARA	I-complex_assembly
and	O
LdcIa	B-protein
.	O

(	O
A	O
,	O
C	O
,	O
E	O
)	O
cryoEM	B-experimental_method
map	B-evidence
of	O
the	O
LdcC	B-protein
(	O
A	O
),	O
LdcIa	B-protein
(	O
C	O
)	O
and	O
LdcI	B-complex_assembly
-	I-complex_assembly
LARA	I-complex_assembly
(	O
E	O
)	O
decamers	B-oligomeric_state
with	O
one	O
protomer	B-oligomeric_state
in	O
light	O
grey	O
.	O

In	O
the	O
rest	O
of	O
the	O
protomers	B-oligomeric_state
,	O
the	O
wing	B-structure_element
,	O
core	B-structure_element
and	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
domains	I-structure_element
are	O
colored	O
from	O
light	O
to	O
dark	O
in	O
shades	O
of	O
green	O
for	O
LdcC	B-protein
(	O
A	O
),	O
pink	O
for	O
LdcIa	B-protein
(	O
C	O
)	O
and	O
blue	O
for	O
LdcI	B-protein
in	O
LdcI	B-complex_assembly
-	I-complex_assembly
LARA	I-complex_assembly
(	O
E	O
).	O

In	O
(	O
E	O
),	O
the	O
LARA	B-structure_element
domain	I-structure_element
density	O
is	O
shown	O
in	O
dark	O
grey	O
.	O

Two	O
monomers	B-oligomeric_state
making	O
a	O
dimer	B-oligomeric_state
are	O
delineated	O
.	O

Scale	O
bar	O
50	O
Å	O
.	O
(	O
B	O
,	O
D	O
,	O
F	O
)	O
One	O
protomer	B-oligomeric_state
from	O
the	O
cryoEM	B-experimental_method
map	B-evidence
of	O
the	O
LdcC	B-protein
(	O
B	O
),	O
LdcIa	B-protein
(	O
D	O
)	O
and	O
LdcI	B-complex_assembly
-	I-complex_assembly
LARA	I-complex_assembly
(	O
F	O
)	O
in	O
light	O
grey	O
with	O
the	O
pseudoatomic	B-evidence
model	I-evidence
represented	O
as	O
cartoons	O
and	O
colored	O
as	O
the	O
densities	O
in	O
(	O
A	O
,	O
C	O
,	O
E	O
).	O

Superposition	B-experimental_method
of	O
the	O
pseudoatomic	B-evidence
models	I-evidence
of	O
LdcC	B-protein
,	O
LdcI	B-protein
from	O
LdcI	B-complex_assembly
-	I-complex_assembly
LARA	I-complex_assembly
and	O
LdcIa	B-protein
colored	O
as	O
in	O
Fig	O
.	O
1	O
,	O
and	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
LdcIi	B-protein
in	O
shades	O
of	O
yellow	O
.	O

Only	O
one	O
of	O
the	O
two	O
rings	B-structure_element
of	O
the	O
double	B-structure_element
toroid	I-structure_element
is	O
shown	O
for	O
clarity	O
.	O

The	O
dashed	O
circle	O
indicates	O
the	O
central	O
region	B-structure_element
that	O
remains	O
virtually	O
unchanged	O
between	O
all	O
the	O
structures	B-evidence
,	O
while	O
the	O
periphery	O
undergoes	O
visible	O
movements	O
.	O

Conformational	O
rearrangements	O
in	O
the	O
enzyme	O
active	B-site
site	I-site
.	O

(	O
A	O
)	O
LdcIi	B-protein
crystal	B-evidence
structure	I-evidence
,	O
with	O
one	O
ring	B-structure_element
represented	O
as	O
a	O
grey	O
surface	O
and	O
the	O
second	O
as	O
a	O
cartoon	O
.	O

A	O
monomer	B-oligomeric_state
with	O
its	O
PLP	B-chemical
cofactor	O
is	O
delineated	O
.	O

The	O
PLP	B-chemical
moieties	O
of	O
the	O
cartoon	O
ring	B-structure_element
are	O
shown	O
in	O
red	O
.	O

(	O
B	O
)	O
The	O
LdcIi	B-protein
dimer	B-oligomeric_state
extracted	O
from	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
decamer	B-oligomeric_state
.	O

One	O
monomer	B-oligomeric_state
is	O
colored	O
in	O
shades	O
of	O
yellow	O
as	O
in	O
Figs	O
1	O
and	O
2	O
,	O
while	O
the	O
monomer	B-oligomeric_state
related	O
by	O
C2	O
symmetry	O
is	O
grey	O
.	O

The	O
PLP	B-chemical
is	O
red	O
.	O

The	O
active	B-site
site	I-site
is	O
boxed	O
.	O

Stretching	O
of	O
the	O
LdcI	B-protein
monomer	B-oligomeric_state
upon	O
pH	B-protein_state
-	I-protein_state
dependent	I-protein_state
enzyme	O
activation	O
and	O
LARA	B-structure_element
binding	O
.	O

(	O
A	O
–	O
C	O
)	O
A	O
slice	O
through	O
the	O
pseudoatomic	B-evidence
models	I-evidence
of	O
the	O
LdcI	B-protein
monomers	B-oligomeric_state
extracted	O
from	O
the	O
superimposed	B-experimental_method
decamers	B-oligomeric_state
(	O
Fig	O
.	O
2	O
)	O
The	O
rectangle	O
indicates	O
the	O
regions	O
enlarged	O
in	O
(	O
D	O
–	O
F	O
).	O

(	O
A	O
)	O
compares	O
LdcIi	B-protein
(	O
yellow	O
)	O
and	O
LdcIa	B-protein
(	O
pink	O
),	O
(	O
B	O
)	O
compares	O
LdcIa	B-protein
(	O
pink	O
)	O
and	O
LdcI	B-complex_assembly
-	I-complex_assembly
LARA	I-complex_assembly
(	O
blue	O
),	O
and	O
(	O
C	O
)	O
compares	O
LdcIi	B-protein
(	O
yellow	O
),	O
LdcIa	B-protein
(	O
pink	O
)	O
and	O
LdcI	B-complex_assembly
-	I-complex_assembly
LARA	I-complex_assembly
(	O
blue	O
)	O
simultaneously	O
in	O
order	O
to	O
show	O
the	O
progressive	O
stretching	O
described	O
in	O
the	O
text	O
.	O

The	O
cryoEM	B-experimental_method
density	B-evidence
of	O
the	O
LARA	B-structure_element
domain	I-structure_element
is	O
represented	O
as	O
a	O
grey	O
surface	O
to	O
show	O
the	O
position	O
of	O
the	O
binding	B-site
site	I-site
and	O
the	O
direction	O
of	O
the	O
movement	O
.	O

(	O
D	O
–	O
F	O
)	O
Inserts	O
zooming	O
at	O
the	O
CTD	B-structure_element
part	O
in	O
proximity	O
of	O
the	O
LARA	B-site
binding	I-site
site	I-site
.	O

Analysis	O
of	O
the	O
LdcIC	B-mutant
and	O
LdcCI	B-mutant
chimeras	B-mutant
.	O

(	O
A	O
)	O
A	O
slice	O
through	O
the	O
pseudoatomic	B-evidence
models	I-evidence
of	O
the	O
LdcIa	B-protein
(	O
purple	O
)	O
and	O
LdcC	B-protein
(	O
green	O
)	O
monomers	B-oligomeric_state
extracted	O
from	O
the	O
superimposed	B-experimental_method
decamers	B-oligomeric_state
(	O
Fig	O
.	O
2	O
).	O
(	O
B	O
)	O
The	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
in	O
LdcIa	B-protein
and	O
LdcC	B-protein
enlarged	O
from	O
(	O
A	O
,	O
C	O
)	O
Exchanged	O
primary	O
sequences	O
(	O
capital	O
letters	O
)	O
and	O
their	O
immediate	O
vicinity	O
(	O
lower	O
case	O
letters	O
)	O
colored	O
as	O
in	O
(	O
A	O
,	O
B	O
),	O
with	O
the	O
corresponding	O
secondary	O
structure	O
elements	O
and	O
the	O
amino	O
acid	O
numbering	O
shown	O
.	O

(	O
D	O
,	O
E	O
)	O
A	O
gallery	O
of	O
negative	O
stain	O
EM	O
images	O
of	O
(	O
D	O
)	O
the	O
wild	B-protein_state
type	I-protein_state
LdcI	B-complex_assembly
-	I-complex_assembly
RavA	I-complex_assembly
cage	O
and	O
(	O
E	O
)	O
the	O
LdcCI	B-mutant
-	I-mutant
RavA	I-mutant
cage	I-mutant
-	I-mutant
like	I-mutant
particles	I-mutant
.	O
(	O
F	O
)	O
Some	O
representative	O
class	O
averages	O
of	O
the	O
LdcCI	B-mutant
-	I-mutant
RavA	I-mutant
cage	I-mutant
-	I-mutant
like	I-mutant
particles	I-mutant
.	O

Sequence	B-experimental_method
analysis	I-experimental_method
of	O
enterobacterial	B-taxonomy_domain
lysine	B-protein_type
decarboxylases	I-protein_type
.	O

(	O
A	O
)	O
Maximum	B-evidence
likelihood	I-evidence
tree	I-evidence
with	O
the	O
“	O
LdcC	B-protein_type
-	I-protein_type
like	I-protein_type
”	O
and	O
the	O
“	O
LdcI	B-protein_type
-	I-protein_type
like	I-protein_type
”	O
groups	O
highlighted	O
in	O
green	O
and	O
pink	O
,	O
respectively	O
.	O

(	O
B	O
)	O
Analysis	O
of	O
consensus	O
“	O
LdcI	B-protein_type
-	I-protein_type
like	I-protein_type
”	O
and	O
“	O
LdcC	B-protein_type
-	I-protein_type
like	I-protein_type
”	O
sequences	O
around	O
the	O
first	O
and	O
second	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
strands	I-structure_element
.	O

Numbering	O
as	O
in	O
E	B-species
.	I-species
coli	I-species
.	O

(	O
C	O
)	O
Signature	O
sequences	O
of	O
LdcI	B-protein
and	O
LdcC	B-protein
in	O
the	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
.	O

Polarity	O
differences	O
are	O
highlighted	O
.	O
(	O
D	O
)	O
Position	O
and	O
nature	O
of	O
these	O
differences	O
at	O
the	O
surface	O
of	O
the	O
respective	O
cryoEM	B-experimental_method
maps	B-evidence
with	O
the	O
color	O
code	O
as	O
in	O
B	O
.	O
See	O
also	O
Fig	O
.	O
S7	O
and	O
Tables	O
S3	O
and	O
S4	O
.	O

Crystal	B-evidence
Structures	I-evidence
of	O
Putative	O
Sugar	B-protein_type
Kinases	I-protein_type
from	O
Synechococcus	B-species
Elongatus	I-species
PCC	I-species
7942	I-species
and	O
Arabidopsis	B-species
Thaliana	I-species

The	O
genome	O
of	O
the	O
Synechococcus	B-species
elongatus	I-species
strain	I-species
PCC	I-species
7942	I-species
encodes	O
a	O
putative	O
sugar	B-protein_type
kinase	I-protein_type
(	O
SePSK	B-protein
),	O
which	O
shares	O
44	O
.	O
9	O
%	O
sequence	O
identity	O
with	O
the	O
xylulose	B-protein
kinase	I-protein
-	I-protein
1	I-protein
(	O
AtXK	B-protein
-	I-protein
1	I-protein
)	O
from	O
Arabidopsis	B-species
thaliana	I-species
.	O

Sequence	B-experimental_method
alignment	I-experimental_method
suggests	O
that	O
both	O
kinases	B-protein_type
belong	O
to	O
the	O
ribulokinase	B-protein_type
-	I-protein_type
like	I-protein_type
carbohydrate	I-protein_type
kinases	I-protein_type
,	O
a	O
sub	O
-	O
family	O
of	O
FGGY	B-protein_type
family	I-protein_type
carbohydrate	I-protein_type
kinases	I-protein_type
.	O

Here	O
we	O
solved	B-experimental_method
the	O
structures	B-evidence
of	O
SePSK	B-protein
and	O
AtXK	B-protein
-	I-protein
1	I-protein
in	O
both	O
their	O
apo	B-protein_state
forms	O
and	O
in	B-protein_state
complex	I-protein_state
with	I-protein_state
nucleotide	B-chemical
substrates	O
.	O

The	O
two	O
kinases	O
exhibit	O
nearly	O
identical	O
overall	O
architecture	O
,	O
with	O
both	O
kinases	B-protein_type
possessing	O
ATP	B-chemical
hydrolysis	O
activity	O
in	O
the	O
absence	B-protein_state
of	I-protein_state
substrates	I-protein_state
.	O

In	O
addition	O
,	O
our	O
enzymatic	B-experimental_method
assays	I-experimental_method
suggested	O
that	O
SePSK	B-protein
has	O
the	O
capability	O
to	O
phosphorylate	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
.	O

In	O
order	O
to	O
understand	O
the	O
catalytic	O
mechanism	O
of	O
SePSK	B-protein
,	O
we	O
solved	B-experimental_method
the	O
structure	B-evidence
of	O
SePSK	B-protein
in	B-protein_state
complex	I-protein_state
with	I-protein_state
D	B-chemical
-	I-chemical
ribulose	I-chemical
and	O
found	O
two	O
potential	O
substrate	B-site
binding	I-site
pockets	I-site
in	O
SePSK	B-protein
.	O

Using	O
mutation	B-experimental_method
and	I-experimental_method
activity	I-experimental_method
analysis	I-experimental_method
,	O
we	O
further	O
verified	O
the	O
key	O
residues	O
important	O
for	O
its	O
catalytic	O
activity	O
.	O

Moreover	O
,	O
our	O
structural	B-experimental_method
comparison	I-experimental_method
with	O
other	O
family	O
members	O
suggests	O
that	O
there	O
are	O
major	O
conformational	O
changes	O
in	O
SePSK	B-protein
upon	O
substrate	O
binding	O
,	O
facilitating	O
the	O
catalytic	O
process	O
.	O

Together	O
,	O
these	O
results	O
provide	O
important	O
information	O
for	O
a	O
more	O
detailed	O
understanding	O
of	O
the	O
cofactor	O
and	O
substrate	O
binding	O
mode	O
as	O
well	O
as	O
the	O
catalytic	O
mechanism	O
of	O
SePSK	B-protein
,	O
and	O
possible	O
similarities	O
with	O
its	O
plant	B-taxonomy_domain
homologue	O
AtXK	B-protein
-	I-protein
1	I-protein
.	O

Carbohydrates	B-chemical
are	O
essential	O
cellular	O
compounds	O
involved	O
in	O
the	O
metabolic	O
processes	O
present	O
in	O
all	O
organisms	O
.	O

Phosphorylation	B-ptm
is	O
one	O
of	O
the	O
various	O
pivotal	O
modifications	O
of	O
carbohydrates	B-chemical
,	O
and	O
is	O
catalyzed	O
by	O
specific	O
sugar	B-protein_type
kinases	I-protein_type
.	O

These	O
kinases	B-protein_type
exhibit	O
considerable	O
differences	O
in	O
their	O
folding	O
pattern	O
and	O
substrate	O
specificity	O
.	O

Based	O
on	O
sequence	B-experimental_method
analysis	I-experimental_method
,	O
they	O
can	O
be	O
divided	O
into	O
four	O
families	O
,	O
namely	O
HSP	B-protein_type
70_NBD	I-protein_type
family	I-protein_type
,	O
FGGY	B-protein_type
family	I-protein_type
,	O
Mer_B	B-protein_type
like	I-protein_type
family	I-protein_type
and	O
Parm_like	B-protein_type
family	I-protein_type
.	O

The	O
FGGY	B-protein_type
family	I-protein_type
carbohydrate	I-protein_type
kinases	I-protein_type
contain	O
different	O
types	O
of	O
sugar	B-protein_type
kinases	I-protein_type
,	O
all	O
of	O
which	O
possess	O
different	O
catalytic	O
substrates	O
with	O
preferences	O
for	O
short	O
-	O
chained	O
sugar	B-chemical
substrates	O
,	O
ranging	O
from	O
triose	B-chemical
to	O
heptose	B-chemical
.	O

These	O
sugar	B-chemical
substrates	O
include	O
L	B-chemical
-	I-chemical
ribulose	I-chemical
,	O
erythritol	B-chemical
,	O
L	B-chemical
-	I-chemical
fuculose	I-chemical
,	O
D	B-chemical
-	I-chemical
glycerol	I-chemical
,	O
D	B-chemical
-	I-chemical
gluconate	I-chemical
,	O
L	B-chemical
-	I-chemical
xylulose	I-chemical
,	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
,	O
L	B-chemical
-	I-chemical
rhamnulose	I-chemical
and	O
D	B-chemical
-	I-chemical
xylulose	I-chemical
.	O

Structures	B-evidence
reported	O
in	O
the	O
Protein	O
Data	O
Bank	O
of	O
the	O
FGGY	B-protein_type
family	I-protein_type
carbohydrate	I-protein_type
kinases	I-protein_type
exhibit	O
a	O
similar	O
overall	O
architecture	O
containing	O
two	O
protein	O
domains	O
,	O
one	O
of	O
which	O
is	O
responsible	O
for	O
the	O
binding	O
of	O
substrate	O
,	O
while	O
the	O
second	O
is	O
used	O
for	O
binding	O
cofactor	O
ATP	B-chemical
.	O

While	O
the	O
binding	B-site
pockets	I-site
for	O
substrates	O
are	O
at	O
the	O
same	O
position	O
,	O
each	O
FGGY	B-protein_type
family	I-protein_type
carbohydrate	I-protein_type
kinases	I-protein_type
uses	O
different	O
substrate	B-site
-	I-site
binding	I-site
residues	I-site
,	O
resulting	O
in	O
high	O
substrate	O
specificity	O
.	O

Synpcc7942_2462	B-gene
from	O
the	O
cyanobacteria	B-taxonomy_domain
Synechococcus	B-species
elongatus	I-species
PCC	I-species
7942	I-species
encodes	O
a	O
putative	O
sugar	B-protein_type
kinase	I-protein_type
(	O
SePSK	B-protein
),	O
and	O
this	O
kinase	B-protein_type
contains	O
426	B-residue_range
amino	O
acids	O
.	O

The	O
At2g21370	B-gene
gene	O
product	O
from	O
Arabidopsis	B-species
thaliana	I-species
,	O
xylulose	B-protein
kinase	I-protein
-	I-protein
1	I-protein
(	O
AtXK	B-protein
-	I-protein
1	I-protein
),	O
whose	O
mature	B-protein_state
form	I-protein_state
contains	O
436	B-residue_range
amino	O
acids	O
,	O
is	O
located	O
in	O
the	O
chloroplast	O
(	O
ChloroP	O
1	O
.	O
1	O
Server	O
).	O

SePSK	B-protein
and	O
AtXK	B-protein
-	I-protein
1	I-protein
display	O
a	O
sequence	O
identity	O
of	O
44	O
.	O
9	O
%,	O
and	O
belong	O
to	O
the	O
ribulokinase	B-protein_type
-	I-protein_type
like	I-protein_type
carbohydrate	I-protein_type
kinases	I-protein_type
,	O
a	O
sub	O
-	O
family	O
of	O
FGGY	B-protein_type
family	I-protein_type
carbohydrate	I-protein_type
kinases	I-protein_type
.	O

Members	O
of	O
this	O
sub	O
-	O
family	O
are	O
responsible	O
for	O
the	O
phosphorylation	B-ptm
of	O
sugars	B-chemical
similar	O
to	O
L	B-chemical
-	I-chemical
ribulose	I-chemical
and	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
.	O

The	O
sequence	O
and	O
the	O
substrate	O
specificity	O
of	O
ribulokinase	B-protein_type
-	I-protein_type
like	I-protein_type
carbohydrate	I-protein_type
kinases	I-protein_type
are	O
different	O
,	O
but	O
they	O
share	O
the	O
common	O
folding	O
feature	O
with	O
two	O
domains	O
.	O

Domain	B-structure_element
I	I-structure_element
exhibits	O
a	O
ribonuclease	B-structure_element
H	I-structure_element
-	I-structure_element
like	I-structure_element
folding	I-structure_element
pattern	I-structure_element
,	O
and	O
is	O
responsible	O
for	O
the	O
substrate	O
binding	O
,	O
while	O
domain	B-structure_element
II	I-structure_element
possesses	O
an	O
actin	B-structure_element
-	I-structure_element
like	I-structure_element
ATPase	I-structure_element
domain	I-structure_element
that	O
binds	O
cofactor	O
ATP	B-chemical
.	O

Two	O
possible	O
xylulose	B-protein_type
kinases	I-protein_type
(	O
xylulose	B-protein
kinase	I-protein
-	I-protein
1	I-protein
:	O
XK	B-protein
-	I-protein
1	I-protein
and	O
xylulose	B-protein
kinase	I-protein
-	I-protein
2	I-protein
:	O
XK	B-protein
-	I-protein
2	I-protein
)	O
from	O
Arabidopsis	B-species
thaliana	I-species
were	O
previously	O
proposed	O
.	O

It	O
was	O
shown	O
that	O
XK	B-protein
-	I-protein
2	I-protein
(	O
At5g49650	B-gene
)	O
located	O
in	O
the	O
cytosol	O
is	O
indeed	O
xylulose	B-protein_type
kinase	I-protein_type
.	O

However	O
,	O
the	O
function	O
of	O
XK	B-protein
-	I-protein
1	I-protein
(	O
At2g21370	B-gene
)	O
inside	O
the	O
chloroplast	O
stroma	O
has	O
remained	O
unknown	O
.	O

SePSK	B-protein
from	O
Synechococcus	B-species
elongatus	I-species
strain	I-species
PCC	I-species
7942	I-species
is	O
the	O
homolog	O
of	O
AtXK	B-protein
-	I-protein
1	I-protein
,	O
though	O
its	O
physiological	O
function	O
and	O
substrates	O
remain	O
unclear	O
.	O

In	O
order	O
to	O
obtain	O
functional	O
and	O
structural	O
information	O
about	O
these	O
two	O
proteins	O
,	O
here	O
we	O
reported	O
the	O
crystal	B-evidence
structures	I-evidence
of	O
SePSK	B-protein
and	O
AtXK	B-protein
-	I-protein
1	I-protein
.	O

Our	O
findings	O
provide	O
new	O
details	O
of	O
the	O
catalytic	O
mechanism	O
of	O
SePSK	B-protein
and	O
lay	O
the	O
foundation	O
for	O
future	O
studies	O
into	O
its	O
homologs	O
in	O
eukaryotes	B-taxonomy_domain
.	O

Overall	O
structures	B-evidence
of	O
apo	B-protein_state
-	O
SePSK	B-protein
and	O
apo	B-protein_state
-	O
AtXK	B-protein
-	I-protein
1	I-protein

The	O
attempt	O
to	O
solve	O
the	O
SePSK	B-protein
structure	B-evidence
by	O
molecular	B-experimental_method
replacement	I-experimental_method
method	I-experimental_method
failed	O
with	O
ribulokinase	B-protein
from	O
Bacillus	B-species
halodurans	I-species
(	O
PDB	O
code	O
:	O
3QDK	O
,	O
15	O
.	O
7	O
%	O
sequence	O
identity	O
)	O
as	O
an	O
initial	O
model	O
.	O

We	O
therefore	O
used	O
single	B-experimental_method
isomorphous	I-experimental_method
replacement	I-experimental_method
anomalous	I-experimental_method
scattering	I-experimental_method
method	I-experimental_method
(	O
SIRAS	B-experimental_method
)	O
for	O
successful	O
solution	O
of	O
the	O
apo	B-protein_state
-	O
SePSK	B-protein
structure	B-evidence
at	O
a	O
resolution	O
of	O
2	O
.	O
3	O
Å	O
.	O
Subsequently	O
,	O
the	O
apo	B-protein_state
-	O
SePSK	B-protein
structure	B-evidence
was	O
used	O
as	O
molecular	B-experimental_method
replacement	I-experimental_method
model	I-experimental_method
to	O
solve	O
all	O
other	O
structures	B-evidence
identified	O
in	O
this	O
study	O
.	O

Our	O
structural	B-experimental_method
analysis	I-experimental_method
showed	O
that	O
apo	B-protein_state
-	O
SePSK	B-protein
consists	O
of	O
one	O
SePSK	B-protein
protein	O
molecule	O
in	O
an	O
asymmetric	O
unit	O
.	O

The	O
amino	O
-	O
acid	O
residues	O
were	O
traced	O
from	O
Val2	B-residue_name_number
to	O
His419	B-residue_name_number
,	O
except	O
for	O
the	O
Met1	B-residue_name_number
residue	O
and	O
the	O
seven	O
residues	O
at	O
the	O
C	O
-	O
termini	O
.	O

Apo	B-protein_state
-	O
SePSK	B-protein
contains	O
two	O
domains	O
referred	O
to	O
further	O
on	O
as	O
domain	B-structure_element
I	I-structure_element
and	O
domain	B-structure_element
II	I-structure_element
(	O
Fig	O
1A	O
).	O

Domain	B-structure_element
I	I-structure_element
consists	O
of	O
non	O
-	O
contiguous	O
portions	O
of	O
the	O
polypeptide	O
chains	O
(	O
aa	O
.	O

2	B-residue_range
–	I-residue_range
228	I-residue_range
and	O
aa	O
.	O

402	B-residue_range
–	I-residue_range
419	I-residue_range
),	O
exhibiting	O
11	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
and	O
11	O
β	B-structure_element
-	I-structure_element
sheets	I-structure_element
.	O

Among	O
all	O
these	O
structural	O
elements	O
,	O
α4	B-structure_element
/	O
α5	B-structure_element
/	O
α11	B-structure_element
/	O
α18	B-structure_element
,	O
β3	B-structure_element
/	O
β2	B-structure_element
/	O
β1	B-structure_element
/	O
β6	B-structure_element
/	O
β19	B-structure_element
/	O
β20	B-structure_element
/	O
β17	B-structure_element
and	O
α21	B-structure_element
/	O
α32	B-structure_element
form	O
three	O
patches	O
,	O
referred	O
to	O
as	O
A1	B-structure_element
,	O
B1	B-structure_element
and	O
A2	B-structure_element
,	O
exhibiting	O
the	O
core	B-structure_element
region	I-structure_element
.	O

In	O
addition	O
,	O
four	O
β	B-structure_element
-	I-structure_element
sheets	I-structure_element
(	O
β7	B-structure_element
,	O
β10	B-structure_element
,	O
β12	B-structure_element
and	O
β16	B-structure_element
)	O
and	O
five	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
(	O
α8	B-structure_element
,	O
α9	B-structure_element
,	O
α13	B-structure_element
,	O
α14	B-structure_element
and	O
α15	B-structure_element
)	O
flank	O
the	O
left	O
side	O
of	O
the	O
core	B-structure_element
region	I-structure_element
.	O

Domain	B-structure_element
II	I-structure_element
is	O
comprised	O
of	O
aa	O
.	O

229	B-residue_range
–	I-residue_range
401	I-residue_range
and	O
classified	O
into	O
B2	B-structure_element
(	O
β31	B-structure_element
/	O
β29	B-structure_element
/	O
β22	B-structure_element
/	O
β23	B-structure_element
/	O
β25	B-structure_element
/	O
β24	B-structure_element
)	O
and	O
A3	B-structure_element
(	O
α26	B-structure_element
/	O
α27	B-structure_element
/	O
α28	B-structure_element
/	O
α30	B-structure_element
)	O
(	O
Fig	O
1A	O
and	O
S1	O
Fig	O
).	O

In	O
the	O
SePSK	B-protein
structure	B-evidence
,	O
B1	B-structure_element
and	O
B2	B-structure_element
are	O
sandwiched	O
by	O
A1	B-structure_element
,	O
A2	B-structure_element
and	O
A3	B-structure_element
,	O
and	O
the	O
whole	O
structure	B-evidence
shows	O
the	O
A1	B-structure_element
/	O
B1	B-structure_element
/	O
A2	B-structure_element
/	O
B2	B-structure_element
/	O
A3	B-structure_element
(	O
α	B-structure_element
/	O
β	B-structure_element
/	O
α	B-structure_element
/	O
β	B-structure_element
/	O
α	B-structure_element
)	O
folding	O
pattern	O
,	O
which	O
is	O
in	O
common	O
with	O
other	O
members	O
of	O
FGGY	B-protein_type
family	I-protein_type
carbohydrate	I-protein_type
kinases	I-protein_type
(	O
S2	O
Fig	O
).	O

The	O
overall	O
folding	O
of	O
SePSK	B-protein
resembles	O
a	O
clip	O
,	O
with	O
A2	B-structure_element
of	O
domain	B-structure_element
I	I-structure_element
acting	O
as	O
a	O
hinge	B-structure_element
region	I-structure_element
.	O

Overall	O
structures	B-evidence
of	O
SePSK	B-protein
and	O
AtXK	B-protein
-	I-protein
1	I-protein
.	O

(	O
A	O
)	O
Three	O
-	O
dimensional	O
structure	B-evidence
of	O
apo	B-protein_state
-	O
SePSK	B-protein
.	O

The	O
secondary	O
structural	O
elements	O
are	O
indicated	O
(	O
α	B-structure_element
-	I-structure_element
helix	I-structure_element
:	O
cyan	O
,	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
:	O
yellow	O
).	O

(	O
B	O
)	O
Three	O
-	O
dimensional	O
structure	B-evidence
of	O
apo	B-protein_state
-	O
AtXK	B-protein
-	I-protein
1	I-protein
.	O

The	O
secondary	O
structural	O
elements	O
are	O
indicated	O
(	O
α	B-structure_element
-	I-structure_element
helix	I-structure_element
:	O
green	O
,	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
:	O
wheat	O
).	O

Apo	B-protein_state
-	O
AtXK	B-protein
-	I-protein
1	I-protein
exhibits	O
a	O
folding	O
pattern	O
similar	O
to	O
that	O
of	O
SePSK	B-protein
in	O
line	O
with	O
their	O
high	O
sequence	O
identity	O
(	O
Fig	O
1B	O
and	O
S1	O
Fig	O
).	O

However	O
,	O
superposition	B-experimental_method
of	O
structures	B-evidence
of	O
AtXK	B-protein
-	I-protein
1	I-protein
and	O
SePSK	B-protein
shows	O
some	O
differences	O
,	O
especially	O
at	O
the	O
loop	B-structure_element
regions	I-structure_element
.	O

A	O
considerable	O
difference	O
is	O
found	O
in	O
the	O
loop3	B-structure_element
linking	O
β3	B-structure_element
and	O
α4	B-structure_element
,	O
which	O
is	O
stretched	O
out	O
in	O
the	O
AtXK	B-protein
-	I-protein
1	I-protein
structure	B-evidence
,	O
while	O
in	O
the	O
SePSK	B-protein
structure	B-evidence
,	O
it	O
is	O
bent	O
back	O
towards	O
the	O
inner	O
part	O
.	O

The	O
corresponding	O
residues	O
between	O
these	O
two	O
structures	B-evidence
(	O
SePSK	B-protein
-	O
Lys35	B-residue_name_number
and	O
AtXK	B-protein
-	I-protein
1	I-protein
-	O
Lys48	B-residue_name_number
)	O
have	O
a	O
distance	O
of	O
15	O
.	O
4	O
Å	O
(	O
S3	O
Fig	O
).	O

Activity	B-experimental_method
assays	I-experimental_method
of	O
SePSK	B-protein
and	O
AtXK	B-protein
-	I-protein
1	I-protein

In	O
order	O
to	O
understand	O
the	O
function	O
of	O
these	O
two	O
kinases	O
,	O
we	O
performed	O
structural	B-experimental_method
comparison	I-experimental_method
using	O
Dali	B-experimental_method
server	I-experimental_method
.	O

The	O
structures	B-evidence
most	O
closely	O
related	O
to	O
SePSK	B-protein
are	O
xylulose	B-protein_type
kinase	I-protein_type
,	O
glycerol	B-protein_type
kinase	I-protein_type
and	O
ribulose	B-protein_type
kinase	I-protein_type
,	O
implying	O
that	O
SePSK	B-protein
and	O
AtXK	B-protein
-	I-protein
1	I-protein
might	O
function	O
similarly	O
to	O
these	O
kinases	B-protein_type
.	O

We	O
first	O
tested	O
whether	O
both	O
enzymes	O
possessed	O
ATP	B-chemical
hydrolysis	O
activity	O
in	O
the	O
absence	B-protein_state
of	I-protein_state
substrates	O
.	O

As	O
shown	O
in	O
Fig	O
2A	O
,	O
both	O
SePSK	B-protein
and	O
AtXK	B-protein
-	I-protein
1	I-protein
exhibited	O
ATP	B-chemical
hydrolysis	O
activity	O
.	O

This	O
finding	O
is	O
in	O
agreement	O
with	O
a	O
previous	O
result	O
showing	O
that	O
xylulose	B-protein_type
kinase	I-protein_type
(	O
PDB	O
code	O
:	O
2ITM	O
)	O
possessed	O
ATP	B-chemical
hydrolysis	O
activity	O
without	O
adding	O
substrate	O
.	O

To	O
further	O
identify	O
the	O
actual	O
substrate	O
of	O
SePSK	B-protein
and	O
AtXK	B-protein
-	I-protein
1	I-protein
,	O
five	O
different	O
sugar	O
molecules	O
,	O
including	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
,	O
L	B-chemical
-	I-chemical
ribulose	I-chemical
,	O
D	B-chemical
-	I-chemical
xylulose	I-chemical
,	O
L	B-chemical
-	I-chemical
xylulose	I-chemical
and	O
Glycerol	B-chemical
,	O
were	O
used	O
in	O
enzymatic	B-experimental_method
activity	I-experimental_method
assays	I-experimental_method
.	O

As	O
shown	O
in	O
Fig	O
2B	O
,	O
the	O
ATP	B-chemical
hydrolysis	O
activity	O
of	O
SePSK	B-protein
greatly	O
increased	O
upon	O
adding	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
than	O
adding	O
other	O
potential	O
substrates	O
,	O
suggesting	O
that	O
it	O
has	O
D	B-protein_type
-	I-protein_type
ribulose	I-protein_type
kinase	I-protein_type
activity	O
.	O

In	O
contrary	O
,	O
limited	O
increasing	O
of	O
ATP	B-chemical
hydrolysis	O
activity	O
was	O
detected	O
for	O
AtXK	B-protein
-	I-protein
1	I-protein
upon	O
addition	O
of	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
(	O
Fig	O
2C	O
),	O
despite	O
its	O
structural	O
similarity	O
with	O
SePSK	B-protein
.	O

The	O
enzymatic	B-experimental_method
activity	I-experimental_method
assays	I-experimental_method
of	O
SePSK	B-protein
and	O
AtXK	B-protein
-	I-protein
1	I-protein
.	O

(	O
A	O
)	O
The	O
ATP	B-chemical
hydrolysis	O
activity	O
of	O
SePSK	B-protein
and	O
AtXK	B-protein
-	I-protein
1	I-protein
.	O

Both	O
SePSK	B-protein
and	O
AtXK	B-protein
-	I-protein
1	I-protein
showed	O
ATP	B-chemical
hydrolysis	O
activity	O
in	O
the	O
absence	B-protein_state
of	I-protein_state
substrate	O
.	O

While	O
the	O
ATP	B-chemical
hydrolysis	O
activity	O
of	O
SePSK	B-protein
greatly	O
increases	O
upon	O
addition	O
of	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
(	O
DR	B-chemical
).	O

(	O
B	O
)	O
The	O
ATP	B-chemical
hydrolysis	O
activity	O
of	O
SePSK	B-protein
with	O
addition	O
of	O
five	O
different	O
substrates	O
.	O

The	O
substrates	O
are	O
DR	B-chemical
(	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
),	O
LR	B-chemical
(	O
L	B-chemical
-	I-chemical
ribulose	I-chemical
),	O
DX	B-chemical
(	O
D	B-chemical
-	I-chemical
xylulose	I-chemical
),	O
LX	B-chemical
(	O
L	B-chemical
-	I-chemical
xylulose	I-chemical
)	O
and	O
GLY	B-chemical
(	O
Glycerol	B-chemical
).	O
(	O
C	O
)	O
The	O
ATP	B-chemical
hydrolysis	O
activity	O
of	O
SePSK	B-protein
and	O
AtXK	B-protein
-	I-protein
1	I-protein
with	O
or	O
without	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
.	O
(	O
D	O
)	O
The	O
ATP	B-chemical
hydrolysis	O
activity	O
of	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
(	O
WT	B-protein_state
)	O
and	O
single	O
-	O
site	O
mutants	O
of	O
SePSK	B-protein
.	O

Three	O
single	O
-	O
site	O
mutants	O
of	O
SePSK	B-protein
are	O
D8A	B-mutant
-	O
SePSK	B-protein
,	O
T11A	B-mutant
-	O
SePSK	B-protein
and	O
D221A	B-mutant
-	O
SePSK	B-protein
.	O

The	O
ATP	B-chemical
hydrolysis	O
activity	O
measured	O
via	O
luminescent	B-experimental_method
ADP	I-experimental_method
-	I-experimental_method
Glo	I-experimental_method
assay	I-experimental_method
(	O
Promega	O
).	O

To	O
understand	O
the	O
catalytic	O
mechanism	O
of	O
SePSK	B-protein
,	O
we	O
performed	O
structural	B-experimental_method
comparisons	I-experimental_method
among	O
xylulose	B-protein_type
kinase	I-protein_type
,	O
glycerol	B-protein_type
kinase	I-protein_type
,	O
ribulose	B-protein_type
kinase	I-protein_type
and	O
SePSK	B-protein
.	O

Our	O
results	O
suggested	O
that	O
three	O
conserved	O
residues	O
(	O
D8	B-residue_name_number
,	O
T11	B-residue_name_number
and	O
D221	B-residue_name_number
of	O
SePSK	B-protein
)	O
play	O
an	O
important	O
role	O
in	O
SePSK	B-protein
function	O
.	O

Mutations	B-experimental_method
of	O
the	O
corresponding	O
residue	O
in	O
xylulose	B-protein_type
kinase	I-protein_type
and	O
glycerol	B-protein_type
kinase	I-protein_type
from	O
Escherichia	B-species
coli	I-species
greatly	O
reduced	O
their	O
activity	O
.	O

To	O
identify	O
the	O
function	O
of	O
these	O
three	O
residues	O
of	O
SePSK	B-protein
,	O
we	O
constructed	O
D8A	B-mutant
,	O
T11A	B-mutant
and	O
D221A	B-mutant
mutants	B-protein_state
.	O

Using	O
enzymatic	B-experimental_method
activity	I-experimental_method
assays	I-experimental_method
,	O
we	O
found	O
that	O
all	O
of	O
these	O
mutants	O
exhibit	O
much	O
lower	O
activity	O
of	O
ATP	B-chemical
hydrolysis	O
after	O
adding	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
than	O
that	O
of	O
wild	B-protein_state
type	I-protein_state
,	O
indicating	O
the	O
possibility	O
that	O
these	O
three	O
residues	O
are	O
involved	O
in	O
the	O
catalytic	O
process	O
of	O
phosphorylation	B-ptm
D	B-chemical
-	I-chemical
ribulose	I-chemical
and	O
are	O
vital	O
for	O
the	O
function	O
of	O
SePSK	B-protein
(	O
Fig	O
2D	O
).	O

SePSK	B-protein
and	O
AtXK	B-protein
-	I-protein
1	I-protein
possess	O
a	O
similar	O
ATP	B-site
binding	I-site
site	I-site

To	O
obtain	O
more	O
detailed	O
information	O
of	O
SePSK	B-protein
and	O
AtXK	B-protein
-	I-protein
1	I-protein
in	B-protein_state
complex	I-protein_state
with	I-protein_state
ATP	B-chemical
,	O
we	O
soaked	B-experimental_method
the	O
apo	B-protein_state
-	O
crystals	B-evidence
in	O
the	O
reservoir	O
adding	O
cofactor	O
ATP	B-chemical
,	O
and	O
obtained	O
the	O
structures	B-evidence
of	O
SePSK	B-protein
and	O
AtXK	B-protein
-	I-protein
1	I-protein
bound	B-protein_state
with	I-protein_state
ATP	B-chemical
at	O
the	O
resolution	O
of	O
2	O
.	O
3	O
Å	O
and	O
1	O
.	O
8	O
Å	O
,	O
respectively	O
.	O

In	O
both	O
structures	B-evidence
,	O
a	O
strong	O
electron	B-evidence
density	I-evidence
was	O
found	O
in	O
the	O
conserved	B-protein_state
ATP	B-site
binding	I-site
pocket	I-site
,	O
but	O
can	O
only	O
be	O
fitted	O
with	O
an	O
ADP	B-chemical
molecule	O
(	O
S4	O
Fig	O
).	O

Thus	O
the	O
two	O
structures	B-evidence
were	O
named	O
ADP	B-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
and	O
ADP	B-complex_assembly
-	I-complex_assembly
AtXK	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
,	O
respectively	O
.	O

The	O
extremely	O
weak	O
electron	B-evidence
densities	I-evidence
of	O
ATP	O
γ	O
-	O
phosphate	B-chemical
in	O
both	O
structures	B-evidence
suggest	O
that	O
the	O
γ	O
-	O
phosphate	B-chemical
group	O
of	O
ATP	B-chemical
is	O
either	O
flexible	O
or	O
hydrolyzed	O
by	O
SePSK	B-protein
and	O
AtXK	B-protein
-	I-protein
1	I-protein
.	O

This	O
result	O
was	O
consistent	O
with	O
our	O
enzymatic	B-experimental_method
activity	I-experimental_method
assays	I-experimental_method
where	O
SePSK	B-protein
and	O
AtXK	B-protein
-	I-protein
1	I-protein
showed	O
ATP	B-chemical
hydrolysis	O
activity	O
without	O
adding	O
any	O
substrates	O
(	O
Fig	O
2A	O
and	O
2C	O
).	O

To	O
avoid	O
hydrolysis	O
of	O
ATP	B-chemical
,	O
we	O
soaked	B-experimental_method
the	O
crystals	B-evidence
of	O
apo	B-protein_state
-	O
SePSK	B-protein
and	O
apo	B-protein_state
-	O
AtXK	B-protein
-	I-protein
1	I-protein
into	O
the	O
reservoir	O
adding	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
.	O

However	O
,	O
we	O
found	O
that	O
the	O
electron	B-evidence
densities	I-evidence
of	O
γ	O
-	O
phosphate	B-chemical
group	O
of	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
(	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
γ	O
-	O
phosphate	B-chemical
)	O
are	O
still	O
weak	O
in	O
the	O
AMP	B-complex_assembly
-	I-complex_assembly
PNP	I-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
and	O
AMP	B-complex_assembly
-	I-complex_assembly
PNP	I-complex_assembly
-	I-complex_assembly
AtXK	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
structures	B-evidence
,	O
suggesting	O
high	O
flexibility	O
of	O
ATP	B-chemical
-	O
γ	O
-	O
phosphate	B-chemical
.	O

The	O
γ	O
-	O
phosphate	B-chemical
group	O
of	O
ATP	B-chemical
is	O
transferred	O
to	O
the	O
sugar	B-chemical
substrate	O
during	O
the	O
reaction	O
process	O
,	O
so	O
this	O
flexibility	O
might	O
be	O
important	O
for	O
the	O
ability	O
of	O
these	O
kinases	B-protein_type
.	O

The	O
overall	O
structures	B-evidence
as	O
well	O
as	O
the	O
coordination	O
modes	O
of	O
ADP	B-chemical
and	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
in	O
the	O
AMP	B-complex_assembly
-	I-complex_assembly
PNP	I-complex_assembly
-	I-complex_assembly
AtXK	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
,	O
ADP	B-complex_assembly
-	I-complex_assembly
AtXK	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
,	O
ADP	B-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
and	O
AMP	B-complex_assembly
-	I-complex_assembly
PNP	I-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
structures	B-evidence
are	O
nearly	O
identical	O
(	O
S5	O
Fig	O
),	O
therefore	O
the	O
structure	B-evidence
of	O
AMP	B-complex_assembly
-	I-complex_assembly
PNP	I-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
is	O
used	O
here	O
to	O
describe	O
the	O
structural	O
details	O
and	O
to	O
compare	O
with	O
those	O
of	O
other	O
family	O
members	O
.	O

As	O
shown	O
in	O
Fig	O
3A	O
,	O
one	O
SePSK	B-protein
protein	O
molecule	O
is	O
in	O
an	O
asymmetric	O
unit	O
with	O
one	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
molecule	O
.	O

The	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
is	O
bound	O
at	O
the	O
domain	B-structure_element
II	I-structure_element
,	O
where	O
it	O
fits	O
well	O
inside	O
a	O
positively	B-site
charged	I-site
groove	I-site
.	O

The	O
AMP	B-site
-	I-site
PNP	I-site
binding	I-site
pocket	I-site
consists	O
of	O
four	B-structure_element
α	I-structure_element
-	I-structure_element
helices	I-structure_element
(	O
α26	B-structure_element
,	O
α28	B-structure_element
,	O
α27	B-structure_element
and	O
α30	B-structure_element
)	O
and	O
forms	O
a	O
shape	B-protein_state
resembling	I-protein_state
a	I-protein_state
half	I-protein_state
-	I-protein_state
fist	I-protein_state
(	O
Fig	O
3A	O
and	O
3B	O
).	O

The	O
head	O
group	O
of	O
the	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
is	O
embedded	O
in	O
a	O
pocket	B-site
surrounded	O
by	O
Trp383	B-residue_name_number
,	O
Asn380	B-residue_name_number
,	O
Gly376	B-residue_name_number
and	O
Gly377	B-residue_name_number
.	O

The	O
purine	O
ring	O
of	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
is	O
positioned	O
in	O
parallel	O
to	O
the	O
indole	O
ring	O
of	O
Trp383	B-residue_name_number
.	O

In	O
addition	O
,	O
it	O
is	O
hydrogen	O
-	O
bonded	O
with	O
the	O
side	O
chain	O
amide	O
of	O
Asn380	B-residue_name_number
(	O
Fig	O
3B	O
).	O

The	O
tail	O
of	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
points	O
to	O
the	O
hinge	B-structure_element
region	I-structure_element
of	O
SePSK	B-protein
,	O
and	O
its	O
α	O
-	O
phosphate	B-chemical
and	O
β	O
-	O
phosphate	B-chemical
groups	O
are	O
stabilized	O
by	O
Gly376	B-residue_name_number
and	O
Ser243	B-residue_name_number
,	O
respectively	O
.	O

Together	O
,	O
this	O
structure	B-evidence
clearly	O
shows	O
that	O
the	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
-	O
β	O
-	O
phosphate	B-chemical
is	O
sticking	O
out	O
of	O
the	O
ATP	B-site
binding	I-site
pocket	I-site
,	O
thus	O
the	O
γ	O
-	O
phosphate	B-chemical
group	O
is	O
at	O
the	O
empty	O
space	O
between	O
domain	B-structure_element
I	I-structure_element
and	O
domain	B-structure_element
II	I-structure_element
and	O
is	O
unconstrained	O
in	O
its	O
movement	O
by	O
the	O
protein	O
.	O

Structure	B-evidence
of	O
SePSK	B-protein
in	B-protein_state
complex	I-protein_state
with	I-protein_state
AMP	B-chemical
-	I-chemical
PNP	I-chemical
.	O

(	O
A	O
)	O
The	O
electron	B-evidence
density	I-evidence
of	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
.	O

The	O
SePSK	B-protein
structure	B-evidence
is	O
shown	O
in	O
the	O
electrostatic	O
potential	O
surface	O
mode	O
.	O

The	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
is	O
depicted	O
as	O
sticks	O
with	O
its	O
ǀFoǀ	B-evidence
-	I-evidence
ǀFcǀ	I-evidence
map	I-evidence
contoured	O
at	O
3	O
σ	O
shown	O
as	O
cyan	O
mesh	O
.	O

(	O
B	O
)	O
The	O
AMP	B-site
-	I-site
PNP	I-site
binding	I-site
pocket	I-site
.	O

The	O
head	O
of	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
is	O
sandwiched	O
by	O
four	O
residues	O
(	O
Leu293	B-residue_name_number
,	O
Gly376	B-residue_name_number
,	O
Gly377	B-residue_name_number
and	O
Trp383	B-residue_name_number
).	O

The	O
four	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
(	O
α26	B-structure_element
,	O
α28	B-structure_element
,	O
α27	B-structure_element
and	O
α30	B-structure_element
)	O
are	O
labeled	O
in	O
red	O
.	O

The	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
and	O
coordinated	O
residues	O
are	O
shown	O
as	O
sticks	O
.	O

The	O
potential	O
substrate	B-site
binding	I-site
site	I-site
in	O
SePSK	B-protein

The	O
results	O
from	O
our	O
activity	B-experimental_method
assays	I-experimental_method
suggested	O
that	O
SePSK	B-protein
has	O
D	B-protein_type
-	I-protein_type
ribulose	I-protein_type
kinase	I-protein_type
activity	O
.	O

To	O
better	O
understand	O
the	O
interaction	O
pattern	O
between	O
SePSK	B-protein
and	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
,	O
the	O
apo	B-protein_state
-	O
SePSK	B-protein
crystals	B-experimental_method
were	I-experimental_method
soaked	I-experimental_method
into	I-experimental_method
the	O
reservoir	B-experimental_method
with	O
10	O
mM	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
(	O
RBL	B-chemical
)	O
and	O
the	O
RBL	B-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
structure	B-evidence
was	O
solved	B-experimental_method
.	O

As	O
shown	O
in	O
S6	O
Fig	O
,	O
two	O
residual	O
electron	B-evidence
densities	I-evidence
are	O
visible	O
in	O
domain	B-structure_element
I	I-structure_element
,	O
which	O
can	O
be	O
interpreted	O
as	O
two	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
molecules	O
with	O
reasonable	O
fit	O
.	O

As	O
shown	O
in	O
Fig	O
4A	O
,	O
the	O
nearest	O
distance	O
between	O
the	O
carbon	O
skeleton	O
of	O
two	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
molecules	O
are	O
approx	O
.	O

7	O
.	O
1	O
Å	O
(	O
RBL1	B-residue_name_number
-	O
C4	O
and	O
RBL2	B-residue_name_number
-	O
C1	O
).	O

RBL1	B-residue_name_number
is	O
located	O
in	O
the	O
pocket	B-site
consisting	O
of	O
α21	B-structure_element
and	O
the	O
loop	B-structure_element
between	O
β6	B-structure_element
and	I-structure_element
β7	I-structure_element
.	O

The	O
O4	O
and	O
O5	O
of	O
RBL1	B-residue_name_number
are	O
coordinated	O
with	O
the	O
side	O
chain	O
carboxyl	O
group	O
of	O
Asp221	B-residue_name_number
.	O

Furthermore	O
,	O
the	O
O2	O
of	O
RBL1	B-residue_name_number
interacts	O
with	O
the	O
main	O
chain	O
amide	O
nitrogen	O
of	O
Ser72	B-residue_name_number
(	O
Fig	O
4B	O
).	O

This	O
pocket	B-site
is	O
at	O
a	O
similar	O
position	O
of	O
substrate	B-site
binding	I-site
site	I-site
of	O
other	O
sugar	B-protein_type
kinase	I-protein_type
,	O
such	O
as	O
L	B-protein
-	I-protein
ribulokinase	I-protein
(	O
PDB	O
code	O
:	O
3QDK	O
)	O
(	O
S7	O
Fig	O
).	O

However	O
,	O
structural	B-experimental_method
comparison	I-experimental_method
shows	O
that	O
the	O
substrate	O
ligating	O
residues	O
between	O
the	O
two	O
structures	B-evidence
are	O
not	B-protein_state
strictly	I-protein_state
conserved	I-protein_state
.	O

Based	O
on	O
the	O
structures	B-evidence
,	O
the	O
ligating	O
residues	O
of	O
RBL1	B-residue_name_number
in	O
RBL	B-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
structure	B-evidence
are	O
Ser72	B-residue_name_number
,	O
Asp221	B-residue_name_number
and	O
Ser222	B-residue_name_number
,	O
and	O
the	O
interacting	O
residues	O
of	O
L	B-chemical
-	I-chemical
ribulose	I-chemical
with	O
L	B-protein
-	I-protein
ribulokinase	I-protein
are	O
Ala96	B-residue_name_number
,	O
Lys208	B-residue_name_number
,	O
Asp274	B-residue_name_number
and	O
Glu329	B-residue_name_number
(	O
S7	O
Fig	O
).	O

Glu329	B-residue_name_number
in	O
3QDK	O
has	O
no	O
counterpart	O
in	O
RBL	B-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
structure	B-evidence
.	O

In	O
addition	O
,	O
although	O
Lys208	B-residue_name_number
of	O
L	B-protein
-	I-protein
ribulokinase	I-protein
has	O
the	O
corresponding	O
residue	O
(	O
Lys163	B-residue_name_number
)	O
in	O
RBL	B-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
structure	B-evidence
,	O
the	O
hydrogen	O
bond	O
of	O
Lys163	B-residue_name_number
is	O
broken	O
because	O
of	O
the	O
conformational	O
change	O
of	O
two	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
(	O
α9	B-structure_element
and	O
α13	B-structure_element
)	O
of	O
SePSK	B-protein
.	O

The	O
binding	O
of	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
(	O
RBL	B-chemical
)	O
with	O
SePSK	B-protein
.	O

(	O
A	O
)	O
The	O
electrostatic	B-evidence
potential	I-evidence
surface	I-evidence
map	I-evidence
of	O
RBL	B-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
and	O
a	O
zoom	O
-	O
in	O
view	O
of	O
RBL	B-site
binding	I-site
site	I-site
.	O

The	O
RBL1	B-residue_name_number
and	O
RBL2	B-residue_name_number
are	O
depicted	O
as	O
sticks	O
.	O
(	O
B	O
)	O
Interaction	O
of	O
two	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
molecules	O
(	O
RBL1	B-residue_name_number
and	O
RBL2	B-residue_name_number
)	O
with	O
SePSK	B-protein
.	O

The	O
RBL	B-chemical
molecules	O
(	O
carbon	O
atoms	O
colored	O
yellow	O
)	O
and	O
amino	O
acid	O
residues	O
of	O
SePSK	B-protein
(	O
carbon	O
atoms	O
colored	O
green	O
)	O
involved	O
in	O
RBL	B-chemical
interaction	O
are	O
shown	O
as	O
sticks	O
.	O

The	O
hydrogen	O
bonds	O
are	O
indicated	O
by	O
the	O
black	O
dashed	O
lines	O
and	O
the	O
numbers	O
near	O
the	O
dashed	O
lines	O
are	O
the	O
distances	O
(	O
Å	O
).	O
(	O
C	O
)	O
The	O
binding	B-experimental_method
affinity	I-experimental_method
assays	I-experimental_method
of	O
SePSK	B-protein
with	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
.	O

Single	B-experimental_method
-	I-experimental_method
cycle	I-experimental_method
kinetic	I-experimental_method
data	I-experimental_method
are	O
reflecting	O
the	O
interaction	O
of	O
SePSK	B-protein
and	O
D8A	B-mutant
-	O
SePSK	B-protein
with	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
.	O

It	O
shows	O
two	O
experimental	O
sensorgrams	B-evidence
after	O
minus	O
the	O
empty	O
sensorgrams	B-evidence
.	O

The	O
original	O
data	O
is	O
shown	O
as	O
black	O
curve	O
,	O
and	O
the	O
fitted	O
data	O
is	O
shown	O
as	O
different	O
color	O
(	O
wild	B-protein_state
type	I-protein_state
SePSK	B-protein
:	O
red	O
curve	O
,	O
D8A	B-mutant
-	O
SePSK	B-protein
:	O
green	O
curve	O
).	O

Dissociation	B-evidence
rate	I-evidence
constant	I-evidence
of	O
wild	B-protein_state
type	I-protein_state
and	O
D8A	B-mutant
-	O
SePSK	B-protein
are	O
3	O
ms	O
-	O
1	O
and	O
9	O
ms	O
-	O
1	O
,	O
respectively	O
.	O

The	O
binding	B-site
pocket	I-site
of	O
RBL2	B-residue_name_number
with	O
relatively	O
weak	O
electron	B-evidence
density	I-evidence
is	O
near	O
the	O
N	O
-	O
terminal	O
region	O
of	O
SePSK	B-protein
and	O
is	O
negatively	O
charged	O
.	O

The	O
side	O
chain	O
of	O
Asp8	B-residue_name_number
interacts	O
strongly	O
with	O
O3	O
and	O
O4	O
of	O
RBL2	B-residue_name_number
.	O

The	O
hydroxyl	O
group	O
of	O
Ser12	B-residue_name_number
coordinates	O
with	O
O2	O
of	O
RBL2	B-residue_name_number
.	O

The	O
backbone	O
amide	O
nitrogens	O
of	O
Gly13	B-residue_name_number
and	O
Arg15	B-residue_name_number
also	O
keep	O
hydrogen	O
bonds	O
with	O
RBL2	B-residue_name_number
(	O
Fig	O
4B	O
).	O

Structural	B-experimental_method
comparison	I-experimental_method
of	O
SePSK	B-protein
and	O
AtXK	B-protein
-	I-protein
1	I-protein
showed	O
that	O
while	O
the	O
RBL1	B-site
binding	I-site
pocket	I-site
is	O
conserved	B-protein_state
,	O
the	O
RBL2	B-site
pocket	I-site
is	O
disrupted	O
in	O
AtXK	B-protein
-	I-protein
1	I-protein
structure	B-evidence
,	O
despite	O
the	O
fact	O
that	O
the	O
residues	O
interacting	O
with	O
RBL2	B-residue_name_number
are	O
highly	B-protein_state
conserved	I-protein_state
between	O
the	O
two	O
proteins	O
.	O

In	O
the	O
RBL	B-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
structure	B-evidence
,	O
a	O
2	O
.	O
6	O
Å	O
hydrogen	O
bond	O
is	O
present	O
between	O
RBL2	B-residue_name_number
and	O
Ser12	B-residue_name_number
(	O
Fig	O
4B	O
),	O
while	O
in	O
the	O
AtXK	B-protein
-	I-protein
1	I-protein
structure	B-evidence
this	O
hydrogen	O
bond	O
with	O
the	O
corresponding	O
residue	O
(	O
Ser22	B-residue_name_number
)	O
is	O
broken	O
.	O

This	O
break	O
is	O
probably	O
induced	O
by	O
the	O
conformational	O
change	O
of	O
the	O
two	O
β	B-structure_element
-	I-structure_element
sheets	I-structure_element
(	O
β1	B-structure_element
and	O
β2	B-structure_element
),	O
with	O
the	O
result	O
that	O
the	O
linking	B-structure_element
loop	I-structure_element
(	O
loop	B-structure_element
1	I-structure_element
)	O
is	O
located	O
further	O
away	O
from	O
the	O
RBL2	B-site
binding	I-site
site	I-site
.	O

This	O
change	O
might	O
be	O
the	O
reason	O
that	O
AtXK	B-protein
-	I-protein
1	I-protein
only	O
shows	O
limited	O
increasing	O
in	O
its	O
ATP	B-chemical
hydrolysis	O
ability	O
upon	O
adding	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
as	O
a	O
substrate	O
after	O
comparing	O
with	O
SePSK	B-protein
(	O
Fig	O
2C	O
).	O

Our	O
SePSK	B-protein
structure	B-evidence
shows	O
that	O
the	O
Asp8	B-residue_name_number
residue	O
forms	O
strong	O
hydrogen	O
bond	O
with	O
RBL2	B-residue_name_number
(	O
Fig	O
4B	O
).	O

In	O
addition	O
,	O
our	O
enzymatic	B-experimental_method
assays	I-experimental_method
indicated	O
that	O
Asp8	B-residue_name_number
is	O
important	O
for	O
the	O
activity	O
of	O
SePSK	B-protein
(	O
Fig	O
2D	O
).	O

To	O
further	O
verified	O
this	O
result	O
,	O
we	O
measured	O
the	O
binding	B-evidence
affinity	I-evidence
for	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
of	O
both	O
wild	B-protein_state
type	I-protein_state
(	O
WT	B-protein_state
)	O
and	O
D8A	B-mutant
mutant	B-protein_state
of	O
SePSK	B-protein
using	O
a	O
surface	B-experimental_method
plasmon	I-experimental_method
resonance	I-experimental_method
method	I-experimental_method
.	O

The	O
results	O
showed	O
that	O
the	O
affinity	B-evidence
of	O
D8A	B-mutant
-	O
SePSK	B-protein
with	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
is	O
weaker	O
than	O
that	O
of	O
WT	B-protein_state
with	O
a	O
reduction	O
of	O
approx	O
.	O

Dissociation	B-evidence
rate	I-evidence
constant	I-evidence
(	O
Kd	B-evidence
)	O
of	O
wild	B-protein_state
type	I-protein_state
and	O
D8A	B-mutant
-	O
SePSK	B-protein
are	O
3	O
ms	O
-	O
1	O
and	O
9	O
ms	O
-	O
1	O
,	O
respectively	O
.	O

The	O
results	O
implied	O
that	O
the	O
second	B-site
RBL	I-site
binding	I-site
site	I-site
plays	O
a	O
role	O
in	O
the	O
D	B-protein_type
-	I-protein_type
ribulose	I-protein_type
kinase	I-protein_type
function	O
of	O
SePSK	B-protein
.	O

However	O
,	O
considering	O
the	O
high	O
concentration	O
of	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
used	O
for	O
crystal	B-experimental_method
soaking	I-experimental_method
,	O
as	O
well	O
as	O
the	O
relatively	O
weak	O
electron	B-evidence
density	I-evidence
of	O
RBL2	B-residue_name_number
,	O
it	O
is	O
also	O
possible	O
that	O
the	O
second	B-site
binding	I-site
site	I-site
of	O
D	B-chemical
-	I-chemical
ribulose	I-chemical
in	O
SePSK	B-protein
is	O
an	O
artifact	O
.	O

Simulated	O
conformational	O
change	O
of	O
SePSK	B-protein
during	O
the	O
catalytic	O
process	O

It	O
was	O
reported	O
earlier	O
that	O
the	O
crossing	O
angle	O
between	O
the	O
domain	B-structure_element
I	I-structure_element
and	O
domain	B-structure_element
II	I-structure_element
in	O
FGGY	B-protein_type
family	I-protein_type
carbohydrate	I-protein_type
kinases	I-protein_type
is	O
different	O
.	O

In	O
addition	O
,	O
this	O
difference	O
may	O
be	O
caused	O
by	O
the	O
binding	O
of	O
substrates	O
and	O
/	O
or	O
ATP	B-chemical
.	O

As	O
reported	O
previously	O
,	O
members	O
of	O
the	O
sugar	B-protein_type
kinase	I-protein_type
family	O
undergo	O
a	O
conformational	O
change	O
to	O
narrow	O
the	O
crossing	O
angle	O
between	O
two	O
domains	O
and	O
reduce	O
the	O
distance	O
between	O
substrate	O
and	O
ATP	B-chemical
in	O
order	O
to	O
facilitate	O
the	O
catalytic	O
reaction	O
of	O
phosphorylation	B-ptm
of	O
sugar	O
substrates	O
.	O

After	O
comparing	O
structures	B-evidence
of	O
apo	B-protein_state
-	O
SePSK	B-protein
,	O
RBL	B-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
and	O
AMP	B-complex_assembly
-	I-complex_assembly
PNP	I-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
,	O
we	O
noticed	O
that	O
these	O
structures	B-evidence
presented	O
here	O
are	O
similar	O
.	O

Superposing	B-experimental_method
the	O
structures	B-evidence
of	O
RBL	B-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
and	O
AMP	B-complex_assembly
-	I-complex_assembly
PNP	I-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
,	O
the	O
results	O
show	O
that	O
the	O
nearest	O
distance	O
between	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
γ	O
-	O
phosphate	B-chemical
and	O
RBL1	B-residue_name_number
/	O
RBL2	B-residue_name_number
is	O
7	O
.	O
5	O
Å	O
(	O
RBL1	B-residue_name_number
-	O
O5	O
)/	O
6	O
.	O
7	O
Å	O
(	O
RBL2	B-residue_name_number
-	O
O1	O
)	O
(	O
S8	O
Fig	O
).	O

This	O
distance	O
is	O
too	O
long	O
to	O
transfer	O
the	O
γ	O
-	O
phosphate	B-chemical
group	O
from	O
ATP	B-chemical
to	O
the	O
substrate	O
.	O

Since	O
the	O
two	O
domains	O
of	O
SePSK	B-protein
are	O
widely	O
separated	O
in	O
this	O
structure	B-evidence
,	O
we	O
hypothesize	O
that	O
our	O
structures	B-evidence
of	O
SePSK	B-protein
represent	O
its	O
open	B-protein_state
form	O
,	O
and	O
that	O
a	O
conformational	O
rearrangement	O
must	O
occur	O
to	O
switch	O
to	O
the	O
closed	B-protein_state
state	O
in	O
order	O
to	O
facilitate	O
the	O
catalytic	O
process	O
of	O
phosphorylation	B-ptm
of	O
sugar	O
substrates	O
.	O

For	O
studying	O
such	O
potential	O
conformational	O
change	O
,	O
a	O
simulation	B-experimental_method
on	O
the	O
Hingeprot	B-experimental_method
Server	I-experimental_method
was	O
performed	O
to	O
predict	O
the	O
movement	O
of	O
different	O
SePSK	B-protein
domains	O
.	O

The	O
results	O
showed	O
that	O
domain	B-structure_element
I	I-structure_element
and	O
domain	B-structure_element
II	I-structure_element
are	O
closer	O
to	O
each	O
other	O
with	O
Ala228	B-residue_name_number
and	O
Thr401	B-residue_name_number
in	O
A2	B-structure_element
as	O
Hinge	B-structure_element
-	I-structure_element
residues	I-structure_element
.	O

Based	O
on	O
the	O
above	O
results	O
,	O
SePSK	B-protein
is	O
divided	O
into	O
two	O
rigid	O
parts	O
.	O

The	O
domain	B-structure_element
I	I-structure_element
of	O
RBL	B-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
(	O
aa	O
.	O
1	B-residue_range
–	I-residue_range
228	I-residue_range
,	O
aa	O
.	O
402	B-residue_range
–	I-residue_range
421	I-residue_range
)	O
and	O
the	O
domain	B-structure_element
II	I-structure_element
of	O
AMP	B-complex_assembly
-	I-complex_assembly
PNP	I-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
(	O
aa	O
.	O
229	B-residue_range
–	I-residue_range
401	I-residue_range
)	O
were	O
superposed	B-experimental_method
with	O
structures	B-evidence
,	O
including	O
apo	B-protein_state
-	O
AtXK	B-protein
-	I-protein
1	I-protein
,	O
apo	B-protein_state
-	O
SePSK	B-protein
,	O
xylulose	B-protein_type
kinase	I-protein_type
from	O
Lactobacillus	B-species
acidophilus	I-species
(	O
PDB	O
code	O
:	O
3LL3	O
)	O
and	O
the	O
S58W	B-mutant
mutant	B-protein_state
form	O
of	O
glycerol	B-protein_type
kinase	I-protein_type
from	O
Escherichia	B-species
coli	I-species
(	O
PDB	O
code	O
:	O
1GLJ	O
).	O

The	O
results	O
of	O
superposition	B-experimental_method
displayed	O
different	O
crossing	O
angle	O
between	O
these	O
two	O
domains	O
.	O

After	O
superposition	B-experimental_method
,	O
the	O
distances	O
of	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
γ	O
-	O
phosphate	B-chemical
and	O
the	O
fifth	O
hydroxyl	O
group	O
of	O
RBL1	B-residue_name_number
are	O
7	O
.	O
9	O
Å	O
(	O
superposed	B-experimental_method
with	O
AtXK	B-protein
-	I-protein
1	I-protein
),	O
7	O
.	O
4	O
Å	O
(	O
superposed	B-experimental_method
with	O
SePSK	B-protein
),	O
6	O
.	O
6	O
Å	O
(	O
superposed	B-experimental_method
with	O
3LL3	O
)	O
and	O
6	O
.	O
1	O
Å	O
(	O
superposed	B-experimental_method
with	O
1GLJ	O
).	O

Meanwhile	O
,	O
the	O
distances	O
of	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
γ	O
-	O
phosphate	B-chemical
and	O
the	O
first	O
hydroxyl	O
group	O
of	O
RBL2	B-residue_name_number
are	O
7	O
.	O
2	O
Å	O
(	O
superposed	B-experimental_method
with	O
AtXK	B-protein
-	I-protein
1	I-protein
),	O
6	O
.	O
7	O
Å	O
(	O
superposed	B-experimental_method
with	O
SePSK	B-protein
),	O
3	O
.	O
7	O
Å	O
(	O
superposed	B-experimental_method
with	O
3LL3	O
),	O
until	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
γ	O
-	O
phosphate	B-chemical
fully	O
contacts	O
RBL2	B-residue_name_number
after	O
superposition	B-experimental_method
with	O
1GLJ	O
(	O
Fig	O
5	O
).	O

This	O
distance	O
between	O
RBL2	B-residue_name_number
and	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
-	O
γ	O
-	O
phosphate	B-chemical
is	O
close	O
enough	O
to	O
facilitate	O
phosphate	B-chemical
transferring	O
.	O

Together	O
,	O
our	O
superposition	B-experimental_method
results	O
provided	O
snapshots	O
of	O
the	O
conformational	O
changes	O
at	O
different	O
catalytic	O
stages	O
of	O
SePSK	B-protein
and	O
potentially	O
revealed	O
the	O
closed	B-protein_state
form	O
of	O
SePSK	B-protein
.	O

Simulated	O
conformational	O
change	O
of	O
SePSK	B-protein
during	O
the	O
catalytic	O
process	O
.	O

The	O
structures	B-evidence
are	O
shown	O
as	O
cartoon	O
and	O
the	O
ligands	O
are	O
shown	O
as	O
sticks	O
.	O

Domain	B-structure_element
I	I-structure_element
from	O
D	B-complex_assembly
-	I-complex_assembly
ribulose	I-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
(	O
green	O
)	O
and	O
Domain	B-structure_element
II	I-structure_element
from	O
AMP	B-complex_assembly
-	I-complex_assembly
PNP	I-complex_assembly
-	I-complex_assembly
SePSK	I-complex_assembly
(	O
cyan	O
)	O
are	O
superposed	B-experimental_method
with	O
apo	B-protein_state
-	O
AtXK	B-protein
-	I-protein
1	I-protein
(	O
1st	O
),	O
apo	B-protein_state
-	O
SePSK	B-protein
(	O
2nd	O
),	O
3LL3	O
(	O
3rd	O
)	O
and	O
1GLJ	O
(	O
4th	O
),	O
respectively	O
.	O

The	O
numbers	O
near	O
the	O
black	O
dashed	O
lines	O
show	O
the	O
distances	O
(	O
Å	O
)	O
between	O
two	O
nearest	O
atoms	O
of	O
RBL	B-chemical
and	O
AMP	B-chemical
-	I-chemical
PNP	I-chemical
.	O

In	O
summary	O
,	O
our	O
structural	B-experimental_method
and	I-experimental_method
enzymatic	I-experimental_method
analyses	I-experimental_method
provide	O
evidence	O
that	O
SePSK	B-protein
shows	O
D	B-protein_type
-	I-protein_type
ribulose	I-protein_type
kinase	I-protein_type
activity	O
,	O
and	O
exhibits	O
the	O
conserved	O
features	O
of	O
FGGY	B-protein_type
family	I-protein_type
carbohydrate	I-protein_type
kinases	I-protein_type
.	O

Three	O
conserved	B-site
residues	O
in	O
SePSK	B-protein
were	O
identified	O
to	O
be	O
essential	O
for	O
this	O
function	O
.	O

Our	O
results	O
provide	O
the	O
detailed	O
information	O
about	O
the	O
interaction	O
of	O
SePSK	B-protein
with	O
ATP	B-chemical
and	O
substrates	O
.	O

Moreover	O
,	O
structural	B-experimental_method
superposition	I-experimental_method
results	O
enable	O
us	O
to	O
visualize	O
the	O
conformational	O
change	O
of	O
SePSK	B-protein
during	O
the	O
catalytic	O
process	O
.	O

In	O
conclusion	O
,	O
our	O
results	O
provide	O
important	O
information	O
for	O
a	O
more	O
detailed	O
understanding	O
of	O
the	O
mechanisms	O
of	O
SePSK	B-protein
and	O
other	O
members	O
of	O
FGGY	B-protein_type
family	I-protein_type
carbohydrate	I-protein_type
kinases	I-protein_type
.	O

Structural	O
basis	O
for	O
Mep2	B-protein_type
ammonium	B-protein_type
transceptor	I-protein_type
activation	O
by	O
phosphorylation	B-ptm

Mep2	B-protein_type
proteins	I-protein_type
are	O
fungal	B-taxonomy_domain
transceptors	B-protein_type
that	O
play	O
an	O
important	O
role	O
as	O
ammonium	B-chemical
sensors	O
in	O
fungal	B-taxonomy_domain
development	O
.	O

Mep2	B-protein_type
activity	O
is	O
tightly	O
regulated	O
by	O
phosphorylation	B-ptm
,	O
but	O
how	O
this	O
is	O
achieved	O
at	O
the	O
molecular	O
level	O
is	O
not	O
clear	O
.	O

Here	O
we	O
report	O
X	B-evidence
-	I-evidence
ray	I-evidence
crystal	I-evidence
structures	I-evidence
of	O
the	O
Mep2	B-protein_type
orthologues	O
from	O
Saccharomyces	B-species
cerevisiae	I-species
and	O
Candida	B-species
albicans	I-species
and	O
show	O
that	O
under	O
nitrogen	O
-	O
sufficient	O
conditions	O
the	O
transporters	B-protein_type
are	O
not	B-protein_state
phosphorylated	I-protein_state
and	O
present	O
in	O
closed	B-protein_state
,	O
inactive	B-protein_state
conformations	O
.	O

Relative	O
to	O
the	O
open	B-protein_state
bacterial	B-taxonomy_domain
ammonium	B-protein_type
transporters	I-protein_type
,	O
non	B-protein_state
-	I-protein_state
phosphorylated	I-protein_state
Mep2	B-protein_type
exhibits	O
shifts	O
in	O
cytoplasmic	B-structure_element
loops	I-structure_element
and	O
the	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
region	I-structure_element
(	O
CTR	B-structure_element
)	O
to	O
occlude	O
the	O
cytoplasmic	O
exit	B-site
of	O
the	O
channel	B-site
and	O
to	O
interact	O
with	O
His2	B-residue_name_number
of	O
the	O
twin	B-structure_element
-	I-structure_element
His	I-structure_element
motif	I-structure_element
.	O

The	O
phosphorylation	B-site
site	I-site
in	O
the	O
CTR	B-structure_element
is	O
solvent	B-protein_state
accessible	I-protein_state
and	O
located	O
in	O
a	O
negatively	B-site
charged	I-site
pocket	I-site
∼	O
30	O
Å	O
away	O
from	O
the	O
channel	B-site
exit	I-site
.	O

The	O
crystal	B-evidence
structure	I-evidence
of	O
phosphorylation	B-protein_state
-	I-protein_state
mimicking	I-protein_state
Mep2	B-mutant
variants	I-mutant
from	O
C	B-species
.	I-species
albicans	I-species
show	O
large	O
conformational	O
changes	O
in	O
a	O
conserved	B-protein_state
and	O
functionally	O
important	O
region	O
of	O
the	O
CTR	B-structure_element
.	O

The	O
results	O
allow	O
us	O
to	O
propose	O
a	O
model	O
for	O
regulation	O
of	O
eukaryotic	B-taxonomy_domain
ammonium	B-chemical
transport	O
by	O
phosphorylation	B-ptm
.	O

Mep2	B-protein_type
proteins	I-protein_type
are	O
tightly	O
regulated	O
fungal	B-taxonomy_domain
ammonium	B-protein_type
transporters	I-protein_type
.	O

Here	O
,	O
the	O
authors	O
report	O
the	O
crystal	B-evidence
structures	I-evidence
of	O
closed	B-protein_state
states	O
of	O
Mep2	B-protein_type
proteins	I-protein_type
and	O
propose	O
a	O
model	O
for	O
their	O
regulation	O
by	B-experimental_method
comparing	I-experimental_method
them	I-experimental_method
with	I-experimental_method
the	O
open	B-protein_state
ammonium	B-protein_type
transporters	I-protein_type
of	O
bacteria	B-taxonomy_domain
.	O

Transceptors	B-protein_type
are	O
membrane	B-protein_type
proteins	I-protein_type
that	O
function	O
not	O
only	O
as	O
transporters	O
but	O
also	O
as	O
receptors	O
/	O
sensors	O
during	O
nutrient	O
sensing	O
to	O
activate	O
downstream	O
signalling	O
pathways	O
.	O

A	O
common	O
feature	O
of	O
transceptors	B-protein_type
is	O
that	O
they	O
are	O
induced	O
when	O
cells	O
are	O
starved	O
for	O
their	O
substrate	O
.	O

While	O
most	O
studies	O
have	O
focused	O
on	O
the	O
Saccharomyces	B-species
cerevisiae	I-species
transceptors	B-protein_type
for	O
phosphate	B-chemical
(	O
Pho84	B-protein
),	O
amino	B-chemical
acids	I-chemical
(	O
Gap1	B-protein
)	O
and	O
ammonium	B-chemical
(	O
Mep2	B-protein
),	O
transceptors	B-protein_type
are	O
found	O
in	O
higher	B-taxonomy_domain
eukaryotes	I-taxonomy_domain
as	O
well	O
(	O
for	O
example	O
,	O
the	O
mammalian	B-taxonomy_domain
SNAT2	B-protein
amino	B-protein_type
-	I-protein_type
acid	I-protein_type
transporter	I-protein_type
and	O
the	O
GLUT2	B-protein
glucose	B-protein_type
transporter	I-protein_type
).	O

One	O
of	O
the	O
most	O
important	O
unresolved	O
questions	O
in	O
the	O
field	O
is	O
how	O
the	O
transceptors	B-protein_type
couple	O
to	O
downstream	O
signalling	O
pathways	O
.	O

One	O
hypothesis	O
is	O
that	O
downstream	O
signalling	O
is	O
dependent	O
on	O
a	O
specific	O
conformation	O
of	O
the	O
transporter	B-protein_type
.	O

Mep2	B-protein_type
(	B-protein_type
methylammonium	I-protein_type
(	I-protein_type
MA	I-protein_type
)	I-protein_type
permease	I-protein_type
)	I-protein_type
proteins	I-protein_type
are	O
ammonium	B-protein_type
transceptors	I-protein_type
that	O
are	O
ubiquitous	O
in	O
fungi	B-taxonomy_domain
.	O

They	O
belong	O
to	O
the	O
Amt	B-protein_type
/	I-protein_type
Mep	I-protein_type
/	I-protein_type
Rh	I-protein_type
family	I-protein_type
of	I-protein_type
transporters	I-protein_type
that	O
are	O
present	O
in	O
all	B-taxonomy_domain
kingdoms	I-taxonomy_domain
of	I-taxonomy_domain
life	I-taxonomy_domain
and	O
they	O
take	O
up	O
ammonium	B-chemical
from	O
the	O
extracellular	O
environment	O
.	O

Fungi	B-taxonomy_domain
typically	O
have	O
more	O
than	O
one	O
Mep	B-protein_type
paralogue	O
,	O
for	O
example	O
,	O
Mep1	B-protein
-	I-protein
3	I-protein
in	O
S	B-species
.	I-species
cerevisiae	I-species
.	O

Of	O
these	O
,	O
only	O
Mep2	B-protein_type
proteins	I-protein_type
function	O
as	O
ammonium	B-chemical
receptors	O
/	O
sensors	O
in	O
fungal	B-taxonomy_domain
development	O
.	O

Under	O
conditions	O
of	O
nitrogen	O
limitation	O
,	O
Mep2	B-protein
initiates	O
a	O
signalling	O
cascade	O
that	O
results	O
in	O
a	O
switch	O
from	O
the	O
yeast	O
form	O
to	O
filamentous	O
(	O
pseudohyphal	O
)	O
growth	O
that	O
may	O
be	O
required	O
for	O
fungal	B-taxonomy_domain
pathogenicity	O
.	O

As	O
is	O
the	O
case	O
for	O
other	O
transceptors	B-protein_type
,	O
it	O
is	O
not	O
clear	O
how	O
Mep2	B-protein
interacts	O
with	O
downstream	O
signalling	O
partners	O
,	O
but	O
the	O
protein	O
kinase	O
A	O
and	O
mitogen	O
-	O
activated	O
protein	O
kinase	O
pathways	O
have	O
been	O
proposed	O
as	O
downstream	O
effectors	O
of	O
Mep2	B-protein
(	O
refs	O
).	O

Compared	O
with	O
Mep1	B-protein
and	O
Mep3	B-protein
,	O
Mep2	B-protein
is	O
highly	B-protein_state
expressed	I-protein_state
and	O
functions	O
as	O
a	O
low	O
-	O
capacity	O
,	O
high	O
-	O
affinity	O
transporter	O
in	O
the	O
uptake	O
of	O
MA	B-chemical
.	O

In	O
addition	O
,	O
Mep2	B-protein
is	O
also	O
important	O
for	O
uptake	O
of	O
ammonium	B-chemical
produced	O
by	O
growth	O
on	O
other	O
nitrogen	B-chemical
sources	O
.	O

With	O
the	O
exception	O
of	O
the	O
human	B-species
RhCG	B-protein
structure	B-evidence
,	O
no	O
structural	O
information	O
is	O
available	O
for	O
eukaryotic	B-taxonomy_domain
ammonium	B-protein_type
transporters	I-protein_type
.	O

By	O
contrast	O
,	O
several	O
bacterial	B-taxonomy_domain
Amt	B-protein_type
orthologues	O
have	O
been	O
characterized	O
in	O
detail	O
via	O
high	O
-	O
resolution	O
crystal	B-evidence
structures	I-evidence
and	O
a	O
number	O
of	O
molecular	B-experimental_method
dynamics	I-experimental_method
(	O
MD	B-experimental_method
)	O
studies	O
.	O

All	O
the	O
solved	O
structures	B-evidence
including	O
that	O
of	O
RhCG	B-protein
are	O
very	O
similar	O
,	O
establishing	O
the	O
basic	O
architecture	O
of	O
ammonium	B-protein_type
transporters	I-protein_type
.	O

The	O
proteins	O
form	O
stable	B-protein_state
trimers	B-oligomeric_state
,	O
with	O
each	O
monomer	B-oligomeric_state
having	O
11	O
transmembrane	B-structure_element
(	O
TM	B-structure_element
)	O
helices	B-structure_element
and	O
a	O
central	B-site
channel	I-site
for	O
the	O
transport	O
of	O
ammonium	B-chemical
.	O

All	O
structures	B-evidence
show	O
the	O
transporters	B-protein_type
in	O
open	B-protein_state
conformations	O
.	O

Where	O
earlier	O
studies	O
favoured	O
the	O
transport	O
of	O
ammonia	B-chemical
gas	O
,	O
recent	O
data	O
and	O
theoretical	O
considerations	O
suggest	O
that	O
Amt	B-protein_type
/	I-protein_type
Mep	I-protein_type
proteins	I-protein_type
are	O
instead	O
active	B-protein_state
,	O
electrogenic	B-protein_type
transporters	I-protein_type
of	O
either	O
NH4	B-chemical
+	I-chemical
(	O
uniport	O
)	O
or	O
NH3	B-chemical
/	O
H	B-chemical
+	I-chemical
(	O
symport	O
).	O

A	O
highly	B-protein_state
conserved	I-protein_state
pair	O
of	O
channel	B-site
-	O
lining	O
histidine	B-residue_name
residues	O
dubbed	O
the	O
twin	B-structure_element
-	I-structure_element
His	I-structure_element
motif	I-structure_element
may	O
serve	O
as	O
a	O
proton	O
relay	O
system	O
while	O
NH3	B-chemical
moves	O
through	O
the	O
channel	B-site
during	O
NH3	B-chemical
/	O
H	B-chemical
+	I-chemical
symport	O
.	O

Ammonium	B-chemical
transport	O
is	O
tightly	O
regulated	O
.	O

In	O
animals	B-taxonomy_domain
,	O
this	O
is	O
due	O
to	O
toxicity	O
of	O
elevated	O
intracellular	O
ammonium	B-chemical
levels	O
,	O
whereas	O
for	O
microorganisms	B-taxonomy_domain
ammonium	B-chemical
is	O
a	O
preferred	O
nitrogen	O
source	O
.	O

In	O
bacteria	B-taxonomy_domain
,	O
amt	B-gene
genes	O
are	O
present	O
in	O
an	O
operon	O
with	O
glnK	B-gene
,	O
encoding	O
a	O
PII	B-protein_type
-	I-protein_type
like	I-protein_type
signal	I-protein_type
transduction	I-protein_type
class	I-protein_type
protein	I-protein_type
.	O

By	O
binding	O
tightly	O
to	O
Amt	B-protein_type
proteins	I-protein_type
without	O
inducing	O
a	O
conformational	O
change	O
in	O
the	O
transporter	B-protein_type
,	O
GlnK	B-protein_type
sterically	O
blocks	O
ammonium	B-chemical
conductance	O
when	O
nitrogen	O
levels	O
are	O
sufficient	O
.	O

Under	O
conditions	O
of	O
nitrogen	B-chemical
limitation	O
,	O
GlnK	B-protein_type
becomes	O
uridylated	B-protein_state
,	O
blocking	O
its	O
ability	O
to	O
bind	O
and	O
inhibit	O
Amt	B-protein_type
proteins	I-protein_type
.	O

Importantly	O
,	O
eukaryotes	B-taxonomy_domain
do	O
not	O
have	O
GlnK	B-protein_type
orthologues	O
and	O
have	O
a	O
different	O
mechanism	O
for	O
regulation	O
of	O
ammonium	B-chemical
transport	O
activity	O
.	O

In	O
plants	B-taxonomy_domain
,	O
transporter	B-protein_type
phosphorylation	B-ptm
and	O
dephosphorylation	B-ptm
are	O
known	O
to	O
regulate	O
activity	O
.	O

In	O
S	B-species
.	I-species
cerevisiae	I-species
,	O
phosphorylation	B-ptm
of	O
Ser457	B-residue_name_number
within	O
the	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
region	I-structure_element
(	O
CTR	B-structure_element
)	O
in	O
the	O
cytoplasm	O
was	O
recently	O
proposed	O
to	O
cause	O
Mep2	B-protein_type
opening	O
,	O
possibly	O
via	O
inducing	O
a	O
conformational	O
change	O
.	O

To	O
elucidate	O
the	O
mechanism	O
of	O
Mep2	B-protein_type
transport	O
regulation	O
,	O
we	O
present	O
here	O
X	B-evidence
-	I-evidence
ray	I-evidence
crystal	I-evidence
structures	I-evidence
of	O
the	O
Mep2	B-protein_type
transceptors	I-protein_type
from	O
S	B-species
.	I-species
cerevisiae	I-species
and	O
C	B-species
.	I-species
albicans	I-species
.	O

The	O
structures	B-evidence
are	O
similar	O
to	O
each	O
other	O
but	O
show	O
considerable	O
differences	O
to	O
all	O
other	O
ammonium	B-protein_type
transporter	I-protein_type
structures	B-evidence
.	O

The	O
most	O
striking	O
difference	O
is	O
the	O
fact	O
that	O
the	O
Mep2	B-protein_type
proteins	I-protein_type
have	O
closed	B-protein_state
conformations	O
.	O

The	O
putative	O
phosphorylation	B-site
site	I-site
is	O
solvent	B-protein_state
accessible	I-protein_state
and	O
located	O
in	O
a	O
negatively	B-site
charged	I-site
pocket	I-site
∼	O
30	O
Å	O
away	O
from	O
the	O
channel	B-site
exit	I-site
.	O

The	O
channels	B-site
of	O
phosphorylation	B-protein_state
-	I-protein_state
mimicking	I-protein_state
mutants	I-protein_state
of	O
C	B-species
.	I-species
albicans	I-species
Mep2	B-protein
are	O
still	O
closed	B-protein_state
but	O
show	O
large	O
conformational	O
changes	O
within	O
a	O
conserved	B-protein_state
part	O
of	O
the	O
CTR	B-structure_element
.	O

Together	O
with	O
a	O
structure	B-evidence
of	O
a	O
C	O
-	O
terminal	O
Mep2	B-mutant
variant	I-mutant
lacking	B-protein_state
the	O
segment	B-structure_element
containing	O
the	O
phosphorylation	B-site
site	I-site
,	O
the	O
results	O
allow	O
us	O
to	O
propose	O
a	O
structural	O
model	O
for	O
phosphorylation	O
-	O
based	O
regulation	O
of	O
eukaryotic	B-taxonomy_domain
ammonium	B-chemical
transport	O
.	O

General	O
architecture	O
of	O
Mep2	B-protein_type
ammonium	B-protein_type
transceptors	I-protein_type

The	O
Mep2	B-protein
protein	O
of	O
S	B-species
.	I-species
cerevisiae	I-species
(	O
ScMep2	B-protein
)	O
was	O
overexpressed	B-experimental_method
in	O
S	B-species
.	I-species
cerevisiae	I-species
in	O
high	O
yields	O
,	O
enabling	O
structure	B-experimental_method
determination	I-experimental_method
by	O
X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
using	O
data	O
to	O
3	O
.	O
2	O
Å	O
resolution	O
by	O
molecular	B-experimental_method
replacement	I-experimental_method
(	O
MR	B-experimental_method
)	O
with	O
the	O
archaebacterial	B-taxonomy_domain
Amt	B-protein
-	I-protein
1	I-protein
structure	B-evidence
(	O
see	O
Methods	O
section	O
).	O

Given	O
that	O
the	O
modest	O
resolution	O
of	O
the	O
structure	B-evidence
and	O
the	O
limited	O
detergent	O
stability	O
of	O
ScMep2	B-protein
would	O
likely	O
complicate	O
structure	B-experimental_method
–	I-experimental_method
function	I-experimental_method
studies	I-experimental_method
,	O
several	O
other	O
fungal	B-taxonomy_domain
Mep2	B-protein_type
orthologues	O
were	O
subsequently	O
overexpressed	B-experimental_method
and	I-experimental_method
screened	I-experimental_method
for	I-experimental_method
diffraction	O
-	O
quality	O
crystals	B-evidence
.	O

Of	O
these	O
,	O
Mep2	B-protein
from	O
C	B-species
.	I-species
albicans	I-species
(	O
CaMep2	B-protein
)	O
showed	O
superior	O
stability	O
in	O
relatively	O
harsh	O
detergents	O
such	O
as	O
nonyl	O
-	O
glucoside	O
,	O
allowing	O
structure	B-experimental_method
determination	I-experimental_method
in	O
two	O
different	O
crystal	B-evidence
forms	I-evidence
to	O
high	O
resolution	O
(	O
up	O
to	O
1	O
.	O
5	O
Å	O
).	O

Despite	O
different	O
crystal	O
packing	O
(	O
Supplementary	O
Table	O
1	O
),	O
the	O
two	O
CaMep2	B-protein
structures	B-evidence
are	O
identical	O
to	O
each	O
other	O
and	O
very	O
similar	O
to	O
ScMep2	B-protein
(	O
Cα	O
r	B-evidence
.	I-evidence
m	I-evidence
.	I-evidence
s	I-evidence
.	I-evidence
d	I-evidence
.	I-evidence

(	O
root	B-evidence
mean	I-evidence
square	I-evidence
deviation	I-evidence
)=	O
0	O
.	O
7	O
Å	O
for	O
434	O
residues	O
),	O
with	O
the	O
main	O
differences	O
confined	O
to	O
the	O
N	O
terminus	O
and	O
the	O
CTR	B-structure_element
(	O
Fig	O
.	O
1	O
).	O

Electron	B-evidence
density	I-evidence
is	O
visible	O
for	O
the	O
entire	O
polypeptide	O
chains	O
,	O
with	O
the	O
exception	O
of	O
the	O
C	O
-	O
terminal	O
43	B-residue_range
(	O
ScMep2	B-protein
)	O
and	O
25	B-residue_range
residues	O
(	O
CaMep2	B-protein
),	O
which	O
are	O
poorly	B-protein_state
conserved	I-protein_state
and	O
presumably	O
disordered	B-protein_state
.	O

Both	O
Mep2	B-protein_type
proteins	I-protein_type
show	O
the	O
archetypal	O
trimeric	B-oligomeric_state
assemblies	O
in	O
which	O
each	O
monomer	B-oligomeric_state
consists	O
of	O
11	O
TM	B-structure_element
helices	I-structure_element
surrounding	O
a	O
central	B-structure_element
pore	I-structure_element
.	O

Important	O
functional	O
features	O
such	O
as	O
the	O
extracellular	O
ammonium	B-site
binding	I-site
site	I-site
,	O
the	O
Phe	B-site
gate	I-site
and	O
the	O
twin	B-structure_element
-	I-structure_element
His	I-structure_element
motif	I-structure_element
within	O
the	O
hydrophobic	B-site
channel	I-site
are	O
all	O
very	O
similar	O
to	O
those	O
present	O
in	O
the	O
bacterial	B-taxonomy_domain
transporters	B-protein_type
and	O
RhCG	B-protein
.	O

In	O
the	O
remainder	O
of	O
the	O
manuscript	O
,	O
we	O
will	O
specifically	O
discuss	O
CaMep2	B-protein
due	O
to	O
the	O
superior	O
resolution	O
of	O
the	O
structure	B-evidence
.	O

Unless	O
specifically	O
stated	O
,	O
the	O
drawn	O
conclusions	O
also	O
apply	O
to	O
ScMep2	B-protein
.	O

While	O
the	O
overall	O
architecture	O
of	O
Mep2	B-protein
is	O
similar	O
to	O
that	O
of	O
the	O
prokaryotic	B-taxonomy_domain
transporters	B-protein_type
(	O
Cα	O
r	B-evidence
.	I-evidence
m	I-evidence
.	I-evidence
s	I-evidence
.	I-evidence
d	I-evidence
.	I-evidence
with	O
Amt	B-protein
-	I-protein
1	I-protein
=	O
1	O
.	O
4	O
Å	O
for	O
361	O
residues	O
),	O
there	O
are	O
large	O
differences	O
within	O
the	O
N	O
terminus	O
,	O
intracellular	B-structure_element
loops	I-structure_element
(	O
ICLs	B-structure_element
)	O
ICL1	B-structure_element
and	O
ICL3	B-structure_element
,	O
and	O
the	O
CTR	B-structure_element
.	O

The	O
N	O
termini	O
of	O
the	O
Mep2	B-protein_type
proteins	I-protein_type
are	O
∼	O
20	B-residue_range
–	I-residue_range
25	I-residue_range
residues	O
longer	O
compared	O
with	O
their	O
bacterial	B-taxonomy_domain
counterparts	O
(	O
Figs	O
1	O
and	O
2	O
),	O
substantially	O
increasing	O
the	O
size	O
of	O
the	O
extracellular	B-structure_element
domain	I-structure_element
.	O

Moreover	O
,	O
the	O
N	O
terminus	O
of	O
one	O
monomer	B-oligomeric_state
interacts	O
with	O
the	O
extended	O
extracellular	B-structure_element
loop	I-structure_element
ECL5	B-structure_element
of	O
a	O
neighbouring	O
monomer	B-oligomeric_state
.	O

Together	O
with	O
additional	O
,	O
smaller	O
differences	O
in	O
other	O
extracellular	B-structure_element
loops	I-structure_element
,	O
these	O
changes	O
generate	O
a	O
distinct	O
vestibule	B-structure_element
leading	O
to	O
the	O
ammonium	B-site
binding	I-site
site	I-site
that	O
is	O
much	O
more	O
pronounced	O
than	O
in	O
the	O
bacterial	B-taxonomy_domain
proteins	O
.	O

The	O
N	O
-	O
terminal	O
vestibule	B-structure_element
and	O
the	O
resulting	O
inter	O
-	O
monomer	O
interactions	O
likely	O
increase	O
the	O
stability	O
of	O
the	O
Mep2	B-protein
trimer	B-oligomeric_state
,	O
in	O
support	O
of	O
data	O
for	O
plant	B-taxonomy_domain
AMT	B-protein_type
proteins	I-protein_type
.	O

However	O
,	O
given	O
that	O
an	O
N	O
-	O
terminal	O
deletion	B-protein_state
mutant	I-protein_state
(	O
2	B-mutant
-	I-mutant
27Δ	I-mutant
)	O
grows	O
as	O
well	O
as	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
(	O
WT	B-protein_state
)	O
Mep2	B-protein
on	O
minimal	O
ammonium	B-chemical
medium	O
(	O
Fig	O
.	O
3	O
and	O
Supplementary	O
Fig	O
.	O
1	O
),	O
the	O
importance	O
of	O
the	O
N	O
terminus	O
for	O
Mep2	B-protein
activity	O
is	O
not	O
clear	O
.	O

Mep2	B-protein
channels	B-site
are	O
closed	B-protein_state
by	O
a	O
two	O
-	O
tier	O
channel	B-structure_element
block	I-structure_element

The	O
largest	O
differences	O
between	O
the	O
Mep2	B-protein
structures	B-evidence
and	O
the	O
other	O
known	O
ammonium	B-protein_type
transporter	I-protein_type
structures	B-evidence
are	O
located	O
on	O
the	O
intracellular	O
side	O
of	O
the	O
membrane	O
.	O

In	O
the	O
vicinity	O
of	O
the	O
Mep2	B-protein
channel	B-site
exit	I-site
,	O
the	O
cytoplasmic	O
end	O
of	O
TM2	B-structure_element
has	O
unwound	O
,	O
generating	O
a	O
longer	O
ICL1	B-structure_element
even	O
though	O
there	O
are	O
no	O
insertions	O
in	O
this	O
region	O
compared	O
to	O
the	O
bacterial	B-taxonomy_domain
proteins	O
(	O
Figs	O
2	O
and	O
4	O
).	O

ICL1	B-structure_element
has	O
also	O
moved	O
inwards	O
relative	O
to	O
its	O
position	O
in	O
the	O
bacterial	B-taxonomy_domain
Amts	B-protein_type
.	O

The	O
largest	O
backbone	O
movements	O
of	O
equivalent	O
residues	O
within	O
ICL1	B-structure_element
are	O
∼	O
10	O
Å	O
,	O
markedly	O
affecting	O
the	O
conserved	B-protein_state
basic	B-protein_state
RxK	B-structure_element
motif	I-structure_element
(	O
Fig	O
.	O
4	O
).	O

The	O
head	O
group	O
of	O
Arg54	B-residue_name_number
has	O
moved	O
∼	O
11	O
Å	O
relative	O
to	O
that	O
in	O
Amt	B-protein
-	I-protein
1	I-protein
,	O
whereas	O
the	O
shift	O
of	O
the	O
head	O
group	O
of	O
the	O
variable	O
Lys55	B-residue_name_number
residue	O
is	O
almost	O
20	O
Å	O
.	O
The	O
side	O
chain	O
of	O
Lys56	B-residue_name_number
in	O
the	O
basic	B-protein_state
motif	B-structure_element
points	O
in	O
an	O
opposite	O
direction	O
in	O
the	O
Mep2	B-protein
structures	B-evidence
compared	O
with	O
that	O
of	O
,	O
for	O
example	O
,	O
Amt	B-protein
-	I-protein
1	I-protein
(	O
Fig	O
.	O
4	O
).	O

In	O
addition	O
to	O
changing	O
the	O
RxK	B-structure_element
motif	I-structure_element
,	O
the	O
movement	O
of	O
ICL1	B-structure_element
has	O
another	O
,	O
crucial	O
functional	O
consequence	O
.	O

At	O
the	O
C	O
-	O
terminal	O
end	O
of	O
TM1	B-structure_element
,	O
the	O
side	O
-	O
chain	O
hydroxyl	O
group	O
of	O
the	O
relatively	B-protein_state
conserved	I-protein_state
Tyr49	B-residue_name_number
(	O
Tyr53	B-residue_name_number
in	O
ScMep2	B-protein
)	O
makes	O
a	O
strong	O
hydrogen	O
bond	O
with	O
the	O
ɛ2	O
nitrogen	O
atom	O
of	O
the	O
absolutely	B-protein_state
conserved	I-protein_state
His342	B-residue_name_number
of	O
the	O
twin	B-structure_element
-	I-structure_element
His	I-structure_element
motif	I-structure_element
(	O
His348	B-residue_name_number
in	O
ScMep2	B-protein
),	O
closing	O
the	O
channel	B-site
(	O
Figs	O
4	O
and	O
5	O
).	O

In	O
bacterial	B-taxonomy_domain
Amt	B-protein_type
proteins	I-protein_type
,	O
this	O
Tyr	B-residue_name
side	O
chain	O
is	O
rotated	O
∼	O
4	O
Å	O
away	O
as	O
a	O
result	O
of	O
the	O
different	O
conformation	O
of	O
TM1	B-structure_element
,	O
leaving	O
the	O
channel	B-site
open	B-protein_state
and	O
the	O
histidine	B-residue_name
available	O
for	O
its	O
putative	O
role	O
in	O
substrate	O
transport	O
(	O
Supplementary	O
Fig	O
.	O
2	O
).	O

Compared	O
with	O
ICL1	B-structure_element
,	O
the	O
backbone	O
conformational	O
changes	O
observed	O
for	O
the	O
neighbouring	O
ICL2	B-structure_element
are	O
smaller	O
,	O
but	O
large	O
shifts	O
are	O
nevertheless	O
observed	O
for	O
the	O
conserved	B-protein_state
residues	O
Glu140	B-residue_name_number
and	O
Arg141	B-residue_name_number
(	O
Fig	O
.	O
4	O
).	O

Finally	O
,	O
the	O
important	O
ICL3	B-structure_element
linking	O
the	O
pseudo	B-structure_element
-	I-structure_element
symmetrical	I-structure_element
halves	I-structure_element
(	O
TM1	B-structure_element
-	I-structure_element
5	I-structure_element
and	O
TM6	B-structure_element
-	I-structure_element
10	I-structure_element
)	O
of	O
the	O
transporter	B-protein_type
is	O
also	O
shifted	O
up	O
to	O
∼	O
10	O
Å	O
and	O
forms	O
an	O
additional	O
barrier	O
that	O
closes	O
the	O
channel	B-site
on	O
the	O
cytoplasmic	O
side	O
(	O
Fig	O
.	O
5	O
).	O

This	O
two	O
-	O
tier	O
channel	B-structure_element
block	I-structure_element
likely	O
ensures	O
that	O
very	O
little	O
ammonium	B-chemical
transport	O
will	O
take	O
place	O
under	O
nitrogen	B-chemical
-	O
sufficient	O
conditions	O
.	O

The	O
closed	B-protein_state
state	O
of	O
the	O
channel	B-site
might	O
also	O
explain	O
why	O
no	B-evidence
density	I-evidence
,	O
which	O
could	O
correspond	O
to	O
ammonium	B-chemical
(	O
or	O
water	B-chemical
),	O
is	O
observed	O
in	O
the	O
hydrophobic	O
part	O
of	O
the	O
Mep2	B-protein
channel	B-site
close	O
to	O
the	O
twin	B-structure_element
-	I-structure_element
His	I-structure_element
motif	I-structure_element
.	O

Significantly	O
,	O
this	O
is	O
also	O
true	O
for	O
ScMep2	B-protein
,	O
which	O
was	O
crystallized	B-experimental_method
in	O
the	O
presence	O
of	O
0	O
.	O
2	O
M	O
ammonium	B-chemical
ions	O
(	O
see	O
Methods	O
section	O
).	O

The	O
final	O
region	O
in	O
Mep2	B-protein
that	O
shows	O
large	O
differences	O
compared	O
with	O
the	O
bacterial	B-taxonomy_domain
transporters	B-protein_type
is	O
the	O
CTR	B-structure_element
.	O

In	O
Mep2	B-protein
,	O
the	O
CTR	B-structure_element
has	O
moved	O
away	O
and	O
makes	O
relatively	O
few	O
contacts	O
with	O
the	O
main	B-structure_element
body	I-structure_element
of	O
the	O
transporter	B-protein_type
,	O
generating	O
a	O
more	O
elongated	B-protein_state
protein	O
(	O
Figs	O
1	O
and	O
4	O
).	O

By	O
contrast	O
,	O
in	O
the	O
structures	B-evidence
of	O
bacterial	B-taxonomy_domain
proteins	O
,	O
the	O
CTR	B-structure_element
is	O
docked	O
tightly	O
onto	O
the	O
N	B-structure_element
-	I-structure_element
terminal	I-structure_element
half	I-structure_element
of	O
the	O
transporters	B-protein_type
(	O
corresponding	O
to	O
TM1	B-structure_element
-	I-structure_element
5	I-structure_element
),	O
resulting	O
in	O
a	O
more	O
compact	B-protein_state
structure	B-evidence
.	O

This	O
is	O
illustrated	O
by	O
the	O
positions	O
of	O
the	O
five	O
universally	B-protein_state
conserved	I-protein_state
residues	O
within	O
the	O
CTR	B-structure_element
,	O
that	O
is	O
,	O
Arg415	B-residue_name_number
(	O
370	B-residue_number
),	O
Glu421	B-residue_name_number
(	O
376	B-residue_number
),	O
Gly424	B-residue_name_number
(	O
379	B-residue_number
),	O
Asp426	B-residue_name_number
(	O
381	B-residue_number
)	O
and	O
Tyr	B-residue_name_number
435	I-residue_name_number
(	O
390	B-residue_number
)	O
in	O
CaMep2	B-protein
(	O
Amt	B-protein
-	I-protein
1	I-protein
)	O
(	O
Fig	O
.	O
2	O
).	O

These	O
residues	O
include	O
those	O
of	O
the	O
‘	B-structure_element
ExxGxD	I-structure_element
'	I-structure_element
motif	I-structure_element
,	O
which	O
when	O
mutated	B-experimental_method
generate	O
inactive	B-protein_state
transporters	B-protein_type
.	O

In	O
Amt	B-protein
-	I-protein
1	I-protein
and	O
other	O
bacterial	B-taxonomy_domain
ammonium	B-protein_type
transporters	I-protein_type
,	O
these	O
CTR	B-structure_element
residues	O
interact	O
with	O
residues	O
within	O
the	O
N	B-structure_element
-	I-structure_element
terminal	I-structure_element
half	I-structure_element
of	O
the	O
protein	O
.	O

On	O
one	O
side	O
,	O
the	O
Tyr390	B-residue_name_number
hydroxyl	O
in	O
Amt	B-protein
-	I-protein
1	I-protein
is	O
hydrogen	O
bonded	O
with	O
the	O
side	O
chain	O
of	O
the	O
conserved	B-protein_state
His185	B-residue_name_number
at	O
the	O
C	O
-	O
terminal	O
end	O
of	O
loop	B-structure_element
ICL3	B-structure_element
.	O

At	O
the	O
other	O
end	O
of	O
ICL3	B-structure_element
,	O
the	O
backbone	O
carbonyl	O
groups	O
of	O
Gly172	B-residue_name_number
and	O
Lys173	B-residue_name_number
are	O
hydrogen	O
bonded	O
to	O
the	O
side	O
chain	O
of	O
Arg370	B-residue_name_number
.	O

Similar	O
interactions	O
were	O
also	O
modelled	B-experimental_method
in	O
the	O
active	B-protein_state
,	O
non	B-protein_state
-	I-protein_state
phosphorylated	I-protein_state
plant	B-taxonomy_domain
AtAmt	B-protein
-	I-protein
1	I-protein
;	I-protein
1	I-protein
structure	B-evidence
(	O
for	O
example	O
,	O
Y467	B-residue_name_number
-	O
H239	B-residue_name_number
and	O
D458	B-residue_name_number
-	O
K71	B-residue_name_number
).	O

The	O
result	O
of	O
these	O
interactions	O
is	O
that	O
the	O
CTR	B-structure_element
‘	O
hugs	O
'	O
the	O
N	B-structure_element
-	I-structure_element
terminal	I-structure_element
half	I-structure_element
of	O
the	O
transporters	B-protein_type
(	O
Fig	O
.	O
4	O
).	O

Also	O
noteworthy	O
is	O
Asp381	B-residue_name_number
,	O
the	O
side	O
chain	O
of	O
which	O
interacts	O
strongly	O
with	O
the	O
positive	O
dipole	O
on	O
the	O
N	O
-	O
terminal	O
end	O
of	O
TM2	B-structure_element
.	O

This	O
interaction	O
in	O
the	O
centre	O
of	O
the	O
protein	O
may	O
be	O
particularly	O
important	O
to	O
stabilize	O
the	O
open	B-protein_state
conformations	O
of	O
ammonium	B-protein_type
transporters	I-protein_type
.	O

In	O
the	O
Mep2	B-protein
structures	B-evidence
,	O
none	O
of	O
the	O
interactions	O
mentioned	O
above	O
are	O
present	O
.	O

Phosphorylation	B-site
target	I-site
site	I-site
is	O
at	O
the	O
periphery	O
of	O
Mep2	B-protein

Recently	O
Boeckstaens	O
et	O
al	O
.	O
provided	O
evidence	O
that	O
Ser457	B-residue_name_number
in	O
ScMep2	B-protein
(	O
corresponding	O
to	O
Ser453	B-residue_name_number
in	O
CaMep2	B-protein
)	O
is	O
phosphorylated	B-protein_state
by	O
the	O
TORC1	B-protein_type
effector	I-protein_type
kinase	I-protein_type
Npr1	B-protein
under	O
nitrogen	B-chemical
-	O
limiting	O
conditions	O
.	O

In	O
the	O
absence	B-protein_state
of	I-protein_state
Npr1	B-protein
,	O
plasmid	B-experimental_method
-	I-experimental_method
encoded	I-experimental_method
WT	B-protein_state
Mep2	B-protein
in	O
a	O
S	B-species
.	I-species
cerevisiae	I-species
mep1	B-mutant
-	I-mutant
3Δ	I-mutant
strain	O
(	O
triple	B-mutant
mepΔ	I-mutant
)	O
does	O
not	O
allow	O
growth	O
on	O
low	O
concentrations	O
of	O
ammonium	B-chemical
,	O
suggesting	O
that	O
the	O
transporter	B-protein_type
is	O
inactive	B-protein_state
(	O
Fig	O
.	O
3	O
and	O
Supplementary	O
Fig	O
.	O
1	O
).	O

Conversely	O
,	O
the	O
phosphorylation	B-protein_state
-	I-protein_state
mimicking	I-protein_state
S457D	B-mutant
variant	O
is	O
active	B-protein_state
both	O
in	O
the	O
triple	B-mutant
mepΔ	I-mutant
background	O
and	O
in	O
a	O
triple	B-mutant
mepΔ	I-mutant
npr1Δ	I-mutant
strain	O
(	O
Fig	O
.	O
3	O
).	O

Mutation	B-experimental_method
of	O
other	O
potential	O
phosphorylation	B-site
sites	I-site
in	O
the	O
CTR	B-structure_element
did	O
not	O
support	O
growth	O
in	O
the	O
npr1Δ	B-mutant
background	O
.	O

Collectively	O
,	O
these	O
data	O
suggest	O
that	O
phosphorylation	B-ptm
of	O
Ser457	B-residue_name_number
opens	O
the	O
Mep2	B-protein
channel	B-site
to	O
allow	O
ammonium	B-chemical
uptake	O
.	O

Ser457	B-residue_name_number
is	O
located	O
in	O
a	O
part	O
of	O
the	O
CTR	B-structure_element
that	O
is	O
conserved	B-protein_state
in	O
a	O
subgroup	O
of	O
Mep2	B-protein_type
proteins	I-protein_type
,	O
but	O
which	O
is	O
not	O
present	O
in	O
bacterial	B-taxonomy_domain
proteins	O
(	O
Fig	O
.	O
2	O
).	O

This	O
segment	B-structure_element
(	O
residues	O
450	B-residue_range
–	I-residue_range
457	I-residue_range
in	O
ScMep2	B-protein
and	O
446	B-residue_range
–	I-residue_range
453	I-residue_range
in	O
CaMep2	B-protein
)	O
was	O
dubbed	O
an	O
autoinhibitory	B-structure_element
(	I-structure_element
AI	I-structure_element
)	I-structure_element
region	I-structure_element
based	O
on	O
the	O
fact	O
that	O
its	O
removal	B-experimental_method
generates	O
an	O
active	B-protein_state
transporter	B-protein_type
in	O
the	O
absence	B-protein_state
of	I-protein_state
Npr1	B-protein
(	O
Fig	O
.	O
3	O
).	O

Where	O
is	O
the	O
AI	B-structure_element
region	I-structure_element
and	O
the	O
Npr1	B-protein
phosphorylation	B-site
site	I-site
located	O
?	O
Our	O
structures	B-evidence
reveal	O
that	O
surprisingly	O
,	O
the	O
AI	B-structure_element
region	I-structure_element
is	O
folded	O
back	O
onto	O
the	O
CTR	B-structure_element
and	O
is	O
not	O
located	O
near	O
the	O
centre	O
of	O
the	O
trimer	B-oligomeric_state
as	O
expected	O
from	O
the	O
bacterial	B-taxonomy_domain
structures	B-evidence
(	O
Fig	O
.	O
4	O
).	O

The	O
AI	B-structure_element
region	I-structure_element
packs	O
against	O
the	O
cytoplasmic	O
ends	O
of	O
TM2	B-structure_element
and	O
TM4	B-structure_element
,	O
physically	O
linking	O
the	O
main	B-structure_element
body	I-structure_element
of	O
the	O
transporter	B-protein_type
with	O
the	O
CTR	B-structure_element
via	O
main	O
chain	O
interactions	O
and	O
side	O
-	O
chain	O
interactions	O
of	O
Val447	B-residue_name_number
,	O
Asp449	B-residue_name_number
,	O
Pro450	B-residue_name_number
and	O
Arg452	B-residue_name_number
(	O
Fig	O
.	O
6	O
).	O

The	O
AI	B-structure_element
regions	I-structure_element
have	O
very	O
similar	O
conformations	O
in	O
CaMep2	B-protein
and	O
ScMep2	B-protein
,	O
despite	O
considerable	O
differences	O
in	O
the	O
rest	O
of	O
the	O
CTR	B-structure_element
(	O
Fig	O
.	O
6	O
).	O

Strikingly	O
,	O
the	O
Npr1	B-site
target	I-site
serine	I-site
residue	O
is	O
located	O
at	O
the	O
periphery	O
of	O
the	O
trimer	B-oligomeric_state
,	O
far	O
away	O
(∼	O
30	O
Å	O
)	O
from	O
any	O
channel	B-site
exit	I-site
(	O
Fig	O
.	O
6	O
).	O

Despite	O
its	O
location	O
at	O
the	O
periphery	O
of	O
the	O
trimer	B-oligomeric_state
,	O
the	O
electron	B-evidence
density	I-evidence
for	O
the	O
serine	B-residue_name
is	O
well	O
defined	O
in	O
both	O
Mep2	B-protein
structures	B-evidence
and	O
corresponds	O
to	O
the	O
non	B-protein_state
-	I-protein_state
phosphorylated	I-protein_state
state	O
(	O
Fig	O
.	O
6	O
).	O

This	O
makes	O
sense	O
since	O
the	O
proteins	O
were	O
expressed	O
in	O
rich	O
medium	O
and	O
confirms	O
the	O
recent	O
suggestion	O
by	O
Boeckstaens	O
et	O
al	O
.	O
that	O
the	O
non	B-protein_state
-	I-protein_state
phosphorylated	I-protein_state
form	O
of	O
Mep2	B-protein
corresponds	O
to	O
the	O
inactive	B-protein_state
state	O
.	O

For	O
ScMep2	B-protein
,	O
Ser457	B-residue_name_number
is	O
the	O
most	O
C	O
-	O
terminal	O
residue	O
for	O
which	O
electron	B-evidence
density	I-evidence
is	O
visible	O
,	O
indicating	O
that	O
the	O
region	O
beyond	O
Ser457	B-residue_name_number
is	O
disordered	B-protein_state
.	O

In	O
CaMep2	B-protein
,	O
the	O
visible	O
part	O
of	O
the	O
sequence	O
extends	O
for	O
two	O
residues	O
beyond	O
Ser453	B-residue_name_number
(	O
Fig	O
.	O
6	O
).	O

The	O
peripheral	O
location	O
and	O
disorder	B-protein_state
of	O
the	O
CTR	B-structure_element
beyond	O
the	O
kinase	B-site
target	I-site
site	I-site
should	O
facilitate	O
the	O
phosphorylation	B-ptm
by	O
Npr1	B-protein
.	O

The	O
disordered	B-protein_state
part	O
of	O
the	O
CTR	B-structure_element
is	O
not	B-protein_state
conserved	I-protein_state
in	O
ammonium	B-protein_type
transporters	I-protein_type
(	O
Fig	O
.	O
2	O
),	O
suggesting	O
that	O
it	O
is	O
not	O
important	O
for	O
transport	O
.	O

Interestingly	O
,	O
a	O
ScMep2	B-protein
457Δ	B-mutant
truncation	B-protein_state
mutant	I-protein_state
in	O
which	O
a	O
His	O
-	O
tag	O
directly	O
follows	O
Ser457	B-residue_name_number
is	O
highly	O
expressed	O
but	O
has	O
low	B-protein_state
activity	I-protein_state
(	O
Fig	O
.	O
3	O
and	O
Supplementary	O
Fig	O
.	O
1b	O
),	O
suggesting	O
that	O
the	O
His	O
-	O
tag	O
interferes	O
with	O
phosphorylation	B-ptm
by	O
Npr1	B-protein
.	O

The	O
same	O
mutant	B-mutant
lacking	B-protein_state
the	I-protein_state
His	I-protein_state
-	I-protein_state
tag	I-protein_state
has	O
WT	B-protein_state
properties	O
(	O
Supplementary	O
Fig	O
.	O
1b	O
),	O
confirming	O
that	O
the	O
region	O
following	O
the	O
phosphorylation	B-site
site	I-site
is	O
dispensable	O
for	O
function	O
.	O

Mep2	B-protein
lacking	B-protein_state
the	O
AI	B-structure_element
region	I-structure_element
is	O
conformationally	B-protein_state
heterogeneous	I-protein_state

Given	O
that	O
Ser457	B-residue_name_number
/	O
453	B-residue_number
is	O
far	O
from	O
any	O
channel	B-site
exit	I-site
(	O
Fig	O
.	O
6	O
),	O
the	O
crucial	O
question	O
is	O
how	O
phosphorylation	B-ptm
opens	O
the	O
Mep2	B-protein
channel	B-site
to	O
generate	O
an	O
active	B-protein_state
transporter	B-protein_type
.	O

Boeckstaens	O
et	O
al	O
.	O
proposed	O
that	O
phosphorylation	B-ptm
does	O
not	O
affect	O
channel	O
activity	O
directly	O
,	O
but	O
instead	O
relieves	O
inhibition	O
by	O
the	O
AI	B-structure_element
region	I-structure_element
.	O

The	O
data	O
behind	O
this	O
hypothesis	O
is	O
the	O
observation	O
that	O
a	O
ScMep2	B-protein
449	B-mutant
-	I-mutant
485Δ	I-mutant
deletion	B-protein_state
mutant	I-protein_state
lacking	B-protein_state
the	O
AI	B-structure_element
region	I-structure_element
is	O
highly	B-protein_state
active	I-protein_state
in	O
MA	B-chemical
uptake	O
both	O
in	O
the	O
triple	B-mutant
mepΔ	I-mutant
and	O
triple	B-mutant
mepΔ	I-mutant
npr1Δ	I-mutant
backgrounds	O
,	O
implying	O
that	O
this	O
Mep2	B-mutant
variant	I-mutant
has	O
a	O
constitutively	B-protein_state
open	I-protein_state
channel	B-site
.	O

We	O
obtained	O
a	O
similar	O
result	O
for	O
ammonium	O
uptake	O
by	O
the	O
446Δ	B-mutant
mutant	B-protein_state
(	O
Fig	O
.	O
3	O
),	O
supporting	O
the	O
data	O
from	O
Marini	O
et	O
al	O
.	O
We	O
then	O
constructed	B-experimental_method
and	I-experimental_method
purified	I-experimental_method
the	O
analogous	O
CaMep2	B-protein
442Δ	B-mutant
truncation	B-protein_state
mutant	I-protein_state
and	O
determined	B-experimental_method
the	O
crystal	B-evidence
structure	I-evidence
using	O
data	O
to	O
3	O
.	O
4	O
Å	O
resolution	O
.	O

The	O
structure	B-evidence
shows	O
that	O
removal	B-experimental_method
of	I-experimental_method
the	O
AI	B-structure_element
region	I-structure_element
markedly	O
increases	O
the	O
dynamics	O
of	O
the	O
cytoplasmic	B-structure_element
parts	I-structure_element
of	O
the	O
transporter	B-protein_type
.	O

This	O
is	O
not	O
unexpected	O
given	O
the	O
fact	O
that	O
the	O
AI	B-structure_element
region	I-structure_element
bridges	O
the	O
CTR	B-structure_element
and	O
the	O
main	B-structure_element
body	I-structure_element
of	O
Mep2	B-protein
(	O
Fig	O
.	O
6	O
).	O

Density	B-evidence
for	O
ICL3	B-structure_element
and	O
the	O
CTR	B-structure_element
beyond	O
residue	O
Arg415	B-residue_name_number
is	O
missing	O
in	O
the	O
442Δ	B-mutant
mutant	B-protein_state
,	O
and	O
the	O
density	B-evidence
for	O
the	O
other	O
ICLs	B-structure_element
including	O
ICL1	B-structure_element
is	O
generally	O
poor	O
with	O
visible	O
parts	O
of	O
the	O
structure	B-evidence
having	O
high	O
B	O
-	O
factors	O
(	O
Fig	O
.	O
7	O
).	O

Interestingly	O
,	O
however	O
,	O
the	O
Tyr49	B-residue_name_number
-	O
His342	B-residue_name_number
hydrogen	O
bond	O
that	O
closes	O
the	O
channel	O
in	O
the	O
WT	B-protein_state
protein	O
is	O
still	O
present	O
(	O
Fig	O
.	O
7	O
and	O
Supplementary	O
Fig	O
.	O
2	O
).	O

Why	O
then	O
does	O
this	O
mutant	O
appear	O
to	O
be	O
constitutively	O
active	B-protein_state
?	O
We	O
propose	O
two	O
possibilities	O
.	O

The	O
first	O
one	O
is	O
that	O
the	O
open	B-protein_state
state	O
is	O
disfavoured	O
by	O
crystallization	B-experimental_method
because	O
of	O
lower	O
stability	O
or	O
due	O
to	O
crystal	O
packing	O
constraints	O
.	O

The	O
second	O
possibility	O
is	O
that	O
the	O
Tyr	B-site
–	I-site
His	I-site
hydrogen	I-site
bond	I-site
has	O
to	O
be	O
disrupted	O
by	O
the	O
incoming	O
substrate	O
to	O
open	B-protein_state
the	O
channel	O
.	O

The	O
latter	O
model	O
would	O
fit	O
well	O
with	O
the	O
NH3	B-chemical
/	O
H	B-chemical
+	I-chemical
symport	O
model	O
in	O
which	O
the	O
proton	O
is	O
relayed	O
by	O
the	O
twin	B-structure_element
-	I-structure_element
His	I-structure_element
motif	I-structure_element
.	O

The	O
importance	O
of	O
the	O
Tyr	B-site
–	I-site
His	I-site
hydrogen	I-site
bond	I-site
is	O
underscored	O
by	O
the	O
fact	O
that	O
its	O
removal	B-experimental_method
in	O
the	O
ScMep2	B-protein
Y53A	B-mutant
mutant	B-protein_state
results	O
in	O
a	O
constitutively	B-protein_state
active	I-protein_state
transporter	B-protein_type
(	O
Fig	O
.	O
3	O
).	O

Phosphorylation	B-ptm
causes	O
a	O
conformational	O
change	O
in	O
the	O
CTR	B-structure_element

Do	O
the	O
Mep2	B-protein
structures	B-evidence
provide	O
any	O
clues	O
regarding	O
the	O
potential	O
effect	O
of	O
phosphorylation	B-ptm
?	O

The	O
side	O
-	O
chain	O
hydroxyl	O
of	O
Ser457	B-residue_name_number
/	O
453	B-residue_number
is	O
located	O
in	O
a	O
well	O
-	O
defined	O
electronegative	B-site
pocket	I-site
that	O
is	O
solvent	B-protein_state
accessible	I-protein_state
(	O
Fig	O
.	O
6	O
).	O

The	O
closest	O
atoms	O
to	O
the	O
serine	B-residue_name
hydroxyl	O
group	O
are	O
the	O
backbone	O
carbonyl	O
atoms	O
of	O
Asp419	B-residue_name_number
,	O
Glu420	B-residue_name_number
and	O
Glu421	B-residue_name_number
,	O
which	O
are	O
3	O
–	O
4	O
Å	O
away	O
.	O

We	O
therefore	O
predict	O
that	O
phosphorylation	B-ptm
of	O
Ser453	B-residue_name_number
will	O
result	O
in	O
steric	O
clashes	O
as	O
well	O
as	O
electrostatic	O
repulsion	O
,	O
which	O
in	O
turn	O
might	O
cause	O
substantial	O
conformational	O
changes	O
within	O
the	O
CTR	B-structure_element
.	O

To	O
test	O
this	O
hypothesis	O
,	O
we	O
determined	B-experimental_method
the	O
structure	B-evidence
of	O
the	O
phosphorylation	B-protein_state
-	I-protein_state
mimicking	I-protein_state
R452D	B-mutant
/	I-mutant
S453D	I-mutant
protein	O
(	O
hereafter	O
termed	O
‘	O
DD	B-mutant
mutant	I-mutant
'),	O
using	O
data	O
to	O
a	O
resolution	O
of	O
2	O
.	O
4	O
Å	O
.	O
The	O
additional	B-experimental_method
mutation	I-experimental_method
of	I-experimental_method
the	O
arginine	B-residue_name
preceding	O
the	O
phosphorylation	B-site
site	I-site
was	O
introduced	O
(	O
i	O
)	O
to	O
increase	O
the	O
negative	O
charge	O
density	O
and	O
make	O
it	O
more	O
comparable	O
to	O
a	O
phosphate	B-chemical
at	O
neutral	O
pH	O
,	O
and	O
(	O
ii	O
)	O
to	O
further	O
destabilize	O
the	O
interactions	O
of	O
the	O
AI	B-structure_element
region	I-structure_element
with	O
the	O
main	B-structure_element
body	I-structure_element
of	O
the	O
transporter	B-protein_type
(	O
Fig	O
.	O
6	O
).	O

The	O
ammonium	B-chemical
uptake	O
activity	O
of	O
the	O
S	B-species
.	I-species
cerevisiae	I-species
version	O
of	O
the	O
DD	B-mutant
mutant	I-mutant
is	O
the	O
same	O
as	O
that	O
of	O
WT	B-protein_state
Mep2	B-protein
and	O
the	O
S453D	B-mutant
mutant	B-protein_state
,	O
indicating	O
that	O
the	O
mutations	O
do	O
not	O
affect	O
transporter	O
functionality	O
in	O
the	O
triple	B-mutant
mepΔ	I-mutant
background	O
(	O
Fig	O
.	O
3	O
).	O

Unexpectedly	O
,	O
the	O
AI	B-structure_element
segment	I-structure_element
containing	O
the	O
mutated	O
residues	O
has	O
only	O
undergone	O
a	O
slight	O
shift	O
compared	O
with	O
the	O
WT	B-protein_state
protein	O
(	O
Fig	O
.	O
8	O
and	O
Supplementary	O
Fig	O
.	O
3	O
).	O

By	O
contrast	O
,	O
the	O
conserved	B-protein_state
part	O
of	O
the	O
CTR	B-structure_element
has	O
undergone	O
a	O
large	O
conformational	O
change	O
involving	O
formation	O
of	O
a	O
12	B-structure_element
-	I-structure_element
residue	I-structure_element
-	I-structure_element
long	I-structure_element
α	I-structure_element
-	I-structure_element
helix	I-structure_element
from	O
Leu427	B-residue_range
to	I-residue_range
Asp438	I-residue_range
.	O

In	O
addition	O
,	O
residues	O
Glu420	B-residue_range
-	I-residue_range
Leu423	I-residue_range
including	O
Glu421	B-residue_name_number
of	O
the	O
ExxGxD	B-structure_element
motif	I-structure_element
are	O
now	O
disordered	B-protein_state
(	O
Fig	O
.	O
8	O
and	O
Supplementary	O
Fig	O
.	O
3	O
).	O

This	O
is	O
the	O
first	O
time	O
a	O
large	O
conformational	O
change	O
has	O
been	O
observed	O
in	O
an	O
ammonium	B-protein_type
transporter	I-protein_type
as	O
a	O
result	O
of	O
a	O
mutation	B-experimental_method
,	O
and	O
confirms	O
previous	O
hypotheses	O
that	O
phosphorylation	B-ptm
causes	O
structural	O
changes	O
in	O
the	O
CTR	B-structure_element
.	O

To	O
exclude	O
the	O
possibility	O
that	O
the	O
additional	O
R452D	B-mutant
mutation	O
is	O
responsible	O
for	O
the	O
observed	O
changes	O
,	O
we	O
also	O
determined	B-experimental_method
the	O
structure	B-evidence
of	O
the	O
‘	O
single	B-mutant
D	I-mutant
'	O
S453D	B-mutant
mutant	B-protein_state
.	O

As	O
shown	O
in	O
Supplementary	O
Fig	O
.	O
4	O
,	O
the	O
consequence	O
of	O
the	O
single	B-mutant
D	I-mutant
mutation	B-experimental_method
is	O
very	O
similar	O
to	O
that	O
of	O
the	O
DD	B-mutant
substitution	I-mutant
,	O
with	O
conformational	O
changes	O
and	O
increased	O
dynamics	O
confined	O
to	O
the	O
conserved	B-protein_state
part	O
of	O
the	O
CTR	B-structure_element
(	O
Supplementary	O
Fig	O
.	O
4	O
).	O

To	O
supplement	O
the	O
crystal	B-evidence
structures	I-evidence
,	O
we	O
also	O
performed	O
modelling	B-experimental_method
and	O
MD	B-experimental_method
studies	O
of	O
WT	B-protein_state
CaMep2	B-protein
,	O
the	O
DD	B-mutant
mutant	I-mutant
and	O
phosphorylated	B-protein_state
protein	O
(	O
S453J	B-mutant
).	O

In	O
the	O
WT	B-protein_state
structure	B-evidence
,	O
the	O
acidic	O
residues	O
Asp419	B-residue_name_number
,	O
Glu420	B-residue_name_number
and	O
Glu421	B-residue_name_number
are	O
within	O
hydrogen	O
bonding	O
distance	O
of	O
Ser453	B-residue_name_number
.	O

After	O
200	O
ns	O
of	O
MD	B-experimental_method
simulation	B-experimental_method
,	O
the	O
interactions	O
between	O
these	O
residues	O
and	O
Ser453	B-residue_name_number
remain	O
intact	O
.	O

The	O
protein	O
backbone	O
has	O
an	O
average	O
r	B-evidence
.	I-evidence
m	I-evidence
.	I-evidence
s	I-evidence
.	I-evidence
d	I-evidence
.	I-evidence
of	O
only	O
∼	O
3	O
Å	O
during	O
the	O
200	O
-	O
ns	O
simulation	B-experimental_method
,	O
indicating	O
that	O
the	O
protein	O
is	O
stable	B-protein_state
.	O

There	O
is	O
flexibility	O
in	O
the	O
side	O
chains	O
of	O
the	O
acidic	O
residues	O
so	O
that	O
they	O
are	O
able	O
to	O
form	O
stable	B-protein_state
hydrogen	O
bonds	O
with	O
Ser453	B-residue_name_number
.	O

In	O
particular	O
,	O
persistent	O
hydrogen	O
bonds	O
are	O
observed	O
between	O
the	O
Ser453	B-residue_name_number
hydroxyl	O
group	O
and	O
the	O
acidic	O
group	O
of	O
Glu420	B-residue_name_number
,	O
and	O
also	O
between	O
the	O
amine	O
group	O
of	O
Ser453	B-residue_name_number
and	O
the	O
backbone	O
carbonyl	O
of	O
Glu420	B-residue_name_number
(	O
Supplementary	O
Fig	O
.	O
5	O
).	O

The	O
DD	B-mutant
mutant	I-mutant
is	O
also	O
stable	B-protein_state
during	O
the	O
simulations	B-experimental_method
,	O
but	O
the	O
average	O
backbone	O
r	B-evidence
.	I-evidence
m	I-evidence
.	I-evidence
s	I-evidence
.	I-evidence
d	I-evidence
of	O
∼	O
3	O
.	O
6	O
Å	O
suggests	O
slightly	O
more	O
conformational	O
flexibility	O
than	O
WT	B-protein_state
.	O

As	O
the	O
simulation	B-experimental_method
proceeds	O
,	O
the	O
side	O
chains	O
of	O
the	O
acidic	O
residues	O
move	O
away	O
from	O
Asp452	B-residue_name_number
and	O
Asp453	B-residue_name_number
,	O
presumably	O
to	O
avoid	O
electrostatic	O
repulsion	O
.	O

For	O
example	O
,	O
the	O
distance	B-evidence
between	O
the	O
Asp453	B-residue_name_number
acidic	O
oxygens	O
and	O
the	O
Glu420	B-residue_name_number
acidic	O
oxygens	O
increases	O
from	O
∼	O
7	O
to	O
>	O
22	O
Å	O
after	O
200	O
ns	O
simulations	B-experimental_method
,	O
and	O
thus	O
these	O
residues	O
are	O
not	O
interacting	O
.	O

The	O
protein	O
is	O
structurally	B-protein_state
stable	I-protein_state
throughout	O
the	O
simulation	B-experimental_method
with	O
little	O
deviation	O
in	O
the	O
other	O
parts	O
of	O
the	O
protein	O
.	O

Finally	O
,	O
the	O
S453J	B-mutant
mutant	B-protein_state
is	O
also	O
stable	B-protein_state
throughout	O
the	O
200	O
-	O
ns	O
simulation	B-experimental_method
and	O
has	O
an	O
average	O
backbone	O
deviation	O
of	O
∼	O
3	O
.	O
8	O
Å	O
,	O
which	O
is	O
similar	O
to	O
the	O
DD	B-mutant
mutant	I-mutant
.	O

The	O
movement	O
of	O
the	O
acidic	O
residues	O
away	O
from	O
Arg452	B-residue_name_number
and	O
Sep453	B-residue_name_number
is	O
more	O
pronounced	O
in	O
this	O
simulation	B-experimental_method
in	O
comparison	O
with	O
the	O
movement	O
away	O
from	O
Asp452	B-residue_name_number
and	O
Asp453	B-residue_name_number
in	O
the	O
DD	B-mutant
mutant	I-mutant
.	O

The	O
distance	B-evidence
between	O
the	O
phosphate	B-chemical
of	O
Sep453	B-residue_name_number
and	O
the	O
acidic	O
oxygen	O
atoms	O
of	O
Glu420	B-residue_name_number
is	O
initially	O
∼	O
11	O
Å	O
,	O
but	O
increases	O
to	O
>	O
30	O
Å	O
after	O
200	O
ns	O
.	O

The	O
short	B-structure_element
helix	I-structure_element
formed	O
by	O
residues	O
Leu427	B-residue_range
to	I-residue_range
Asp438	I-residue_range
unravels	O
during	O
the	O
simulations	B-experimental_method
to	O
a	O
disordered	B-protein_state
state	O
.	O

Thus	O
,	O
the	O
MD	B-experimental_method
simulations	B-experimental_method
support	O
the	O
notion	O
from	O
the	O
crystal	B-evidence
structures	I-evidence
that	O
phosphorylation	B-ptm
generates	O
conformational	O
changes	O
in	O
the	O
conserved	B-protein_state
part	O
of	O
the	O
CTR	B-structure_element
.	O

However	O
,	O
the	O
conformational	O
changes	O
for	O
the	O
phosphomimetic	B-mutant
mutants	I-mutant
in	O
the	O
crystals	B-evidence
are	O
confined	O
to	O
the	O
CTR	B-structure_element
(	O
Fig	O
.	O
8	O
),	O
and	O
the	O
channels	B-site
are	O
still	O
closed	B-protein_state
(	O
Supplementary	O
Fig	O
.	O
2	O
).	O

One	O
possible	O
explanation	O
is	O
that	O
the	O
mutants	B-mutant
do	O
not	O
accurately	O
mimic	O
a	O
phosphoserine	B-residue_name
,	O
but	O
the	O
observation	O
that	O
the	O
S453D	B-mutant
and	O
DD	B-mutant
mutants	I-mutant
are	O
fully	B-protein_state
active	I-protein_state
in	O
the	O
absence	B-protein_state
of	I-protein_state
Npr1	B-protein
suggests	O
that	O
the	O
mutations	B-experimental_method
do	O
mimic	O
the	O
effect	O
of	O
phosphorylation	B-ptm
(	O
Fig	O
.	O
3	O
).	O

The	O
fact	O
that	O
the	O
S453D	B-mutant
structure	B-evidence
was	O
obtained	O
in	O
the	O
presence	O
of	O
10	O
mM	O
ammonium	B-chemical
ions	O
suggests	O
that	O
the	O
crystallization	B-experimental_method
process	O
favours	O
closed	B-protein_state
states	O
of	O
the	O
Mep2	B-protein
channels	B-site
.	O

Knowledge	O
about	O
ammonium	B-protein_type
transporter	I-protein_type
structure	B-evidence
has	O
been	O
obtained	O
from	O
experimental	O
and	O
theoretical	O
studies	O
on	O
bacterial	B-taxonomy_domain
family	O
members	O
.	O

In	O
addition	O
,	O
a	O
number	O
of	O
biochemical	B-experimental_method
and	I-experimental_method
genetic	I-experimental_method
studies	I-experimental_method
are	O
available	O
for	O
bacterial	B-taxonomy_domain
,	O
fungal	B-taxonomy_domain
and	O
plant	B-taxonomy_domain
proteins	O
.	O

These	O
efforts	O
have	O
advanced	O
our	O
knowledge	O
considerably	O
but	O
have	O
not	O
yet	O
yielded	O
atomic	O
-	O
level	O
answers	O
to	O
several	O
important	O
mechanistic	O
questions	O
,	O
including	O
how	O
ammonium	B-chemical
transport	O
is	O
regulated	O
in	O
eukaryotes	B-taxonomy_domain
and	O
the	O
mechanism	O
of	O
ammonium	B-chemical
signalling	O
.	O

In	O
Arabidopsis	B-species
thaliana	I-species
Amt	B-protein
-	I-protein
1	I-protein
;	I-protein
1	I-protein
,	O
phosphorylation	B-ptm
of	O
the	O
CTR	B-structure_element
residue	O
T460	B-residue_name_number
under	O
conditions	O
of	O
high	O
ammonium	B-chemical
inhibits	O
transport	O
activity	O
,	O
that	O
is	O
,	O
the	O
default	O
(	O
non	B-protein_state
-	I-protein_state
phosphorylated	I-protein_state
)	O
state	O
of	O
the	O
plant	B-taxonomy_domain
transporter	B-protein_type
is	O
open	B-protein_state
.	O

Interestingly	O
,	O
phosphomimetic	B-mutant
mutations	I-mutant
introduced	O
into	O
one	O
monomer	B-oligomeric_state
inactivate	O
the	O
entire	O
trimer	B-oligomeric_state
,	O
indicating	O
that	O
(	O
i	O
)	O
heterotrimerization	O
occurs	O
and	O
(	O
ii	O
)	O
the	O
CTR	B-structure_element
mediates	O
allosteric	O
regulation	O
of	O
ammonium	B-chemical
transport	O
activity	O
via	O
phosphorylation	B-ptm
.	O

Owing	O
to	O
the	O
lack	O
of	O
structural	O
information	O
for	O
plant	B-taxonomy_domain
AMTs	B-protein_type
,	O
the	O
details	O
of	O
channel	B-site
closure	O
and	O
inter	O
-	O
monomer	O
crosstalk	O
are	O
not	O
yet	O
clear	O
.	O

Contrasting	O
with	O
the	O
plant	B-taxonomy_domain
transporters	B-protein_type
,	O
the	O
inactive	B-protein_state
states	O
of	O
Mep2	B-protein_type
proteins	I-protein_type
under	O
conditions	O
of	O
high	O
ammonium	B-chemical
are	O
non	B-protein_state
-	I-protein_state
phosphorylated	I-protein_state
,	O
with	O
channels	B-site
that	O
are	O
closed	B-protein_state
on	O
the	O
cytoplasmic	O
side	O
.	O

The	O
reason	O
why	O
similar	O
transporters	B-protein_type
such	O
as	O
A	B-species
.	I-species
thaliana	I-species
Amt	B-protein
-	I-protein
1	I-protein
;	I-protein
1	I-protein
and	O
Mep2	B-protein
are	O
regulated	O
in	O
opposite	O
ways	O
by	O
phosphorylation	B-ptm
(	O
inactivation	B-protein_state
in	O
plants	B-taxonomy_domain
and	O
activation	B-protein_state
in	O
fungi	B-taxonomy_domain
)	O
is	O
not	O
known	O
.	O

In	O
fungi	B-taxonomy_domain
,	O
preventing	O
ammonium	B-chemical
entry	O
via	O
channel	O
closure	O
in	O
ammonium	B-protein_type
transporters	I-protein_type
would	O
be	O
one	O
way	O
to	O
alleviate	O
ammonium	B-chemical
toxicity	O
,	O
in	O
addition	O
to	O
ammonium	B-chemical
excretion	O
via	O
Ato	B-protein_type
transporters	B-protein_type
and	O
amino	O
-	O
acid	O
secretion	O
.	O

By	O
determining	O
the	O
first	O
structures	B-evidence
of	O
closed	B-protein_state
ammonium	B-protein_type
transporters	I-protein_type
and	O
comparing	B-experimental_method
those	O
structures	B-evidence
with	O
the	O
permanently	B-protein_state
open	I-protein_state
bacterial	B-taxonomy_domain
proteins	O
,	O
we	O
demonstrate	O
that	O
Mep2	B-protein_type
channel	B-site
closure	O
is	O
likely	O
due	O
to	O
movements	O
of	O
the	O
CTR	B-structure_element
and	O
ICL1	B-structure_element
and	O
ICL3	B-structure_element
.	O

More	O
specifically	O
,	O
the	O
close	O
interactions	O
between	O
the	O
CTR	B-structure_element
and	O
ICL1	B-structure_element
/	O
ICL3	B-structure_element
present	O
in	O
open	B-protein_state
transporters	B-protein_type
are	O
disrupted	O
,	O
causing	O
ICL3	B-structure_element
to	O
move	O
outwards	O
and	O
block	O
the	O
channel	B-site
(	O
Figs	O
4	O
and	O
9a	O
).	O

In	O
addition	O
,	O
ICL1	B-structure_element
has	O
shifted	O
inwards	O
to	O
contribute	O
to	O
the	O
channel	B-site
closure	O
by	O
engaging	O
His2	B-residue_name_number
from	O
the	O
twin	B-structure_element
-	I-structure_element
His	I-structure_element
motif	I-structure_element
via	O
hydrogen	O
bonding	O
with	O
a	O
highly	B-protein_state
conserved	I-protein_state
tyrosine	B-residue_name
hydroxyl	O
group	O
.	O

Upon	O
phosphorylation	B-ptm
by	O
the	O
Npr1	B-protein
kinase	B-protein_type
in	O
response	O
to	O
nitrogen	B-chemical
limitation	O
,	O
the	O
region	O
around	O
the	O
conserved	B-protein_state
ExxGxD	B-structure_element
motif	I-structure_element
undergoes	O
a	O
conformational	O
change	O
that	O
opens	O
the	O
channel	B-site
(	O
Fig	O
.	O
9	O
).	O

Importantly	O
,	O
the	O
structural	B-evidence
similarities	I-evidence
in	O
the	O
TM	B-structure_element
parts	I-structure_element
of	O
Mep2	B-protein
and	O
AfAmt	B-protein
-	I-protein
1	I-protein
(	O
Fig	O
.	O
5a	O
)	O
suggest	O
that	O
channel	B-site
opening	O
/	O
closure	O
does	O
not	O
require	O
substantial	O
changes	O
in	O
the	O
residues	O
lining	O
the	O
channel	B-site
.	O

How	O
exactly	O
the	O
channel	B-site
opens	O
and	O
whether	O
opening	O
is	O
intra	O
-	O
monomeric	O
are	O
still	O
open	B-protein_state
questions	O
;	O
it	O
is	O
possible	O
that	O
the	O
change	O
in	O
the	O
CTR	B-structure_element
may	O
disrupt	O
its	O
interactions	O
with	O
ICL3	B-structure_element
of	O
the	O
neighbouring	O
monomer	B-oligomeric_state
(	O
Fig	O
.	O
9b	O
),	O
which	O
could	O
result	O
in	O
opening	O
of	O
the	O
neighbouring	O
channel	B-site
via	O
inward	O
movement	O
of	O
its	O
ICL3	B-structure_element
.	O

Owing	O
to	O
the	O
crosstalk	O
between	O
monomers	B-oligomeric_state
,	O
a	O
single	O
phosphorylation	B-ptm
event	O
might	O
lead	O
to	O
opening	O
of	O
the	O
entire	O
trimer	B-oligomeric_state
,	O
although	O
this	O
has	O
not	O
yet	O
been	O
tested	O
(	O
Fig	O
.	O
9b	O
).	O

Whether	O
or	O
not	O
Mep2	B-protein_type
channel	B-site
opening	O
requires	O
,	O
in	O
addition	O
to	O
phosphorylation	B-ptm
,	O
disruption	O
of	O
the	O
Tyr	B-site
–	I-site
His2	I-site
interaction	I-site
by	O
the	O
ammonium	B-chemical
substrate	O
is	O
not	O
yet	O
clear	O
.	O

Is	O
our	O
model	O
for	O
opening	O
and	O
closing	O
of	O
Mep2	B-protein
channels	B-site
valid	O
for	O
other	O
eukaryotic	B-taxonomy_domain
ammonium	B-protein_type
transporters	I-protein_type
?	O
Our	O
structural	B-evidence
data	I-evidence
support	O
previous	O
studies	O
and	O
clarify	O
the	O
central	O
role	O
of	O
the	O
CTR	B-structure_element
and	O
cytoplasmic	B-structure_element
loops	I-structure_element
in	O
the	O
transition	O
between	O
closed	B-protein_state
and	O
open	B-protein_state
states	O
.	O

However	O
,	O
even	O
the	O
otherwise	O
highly	O
similar	O
Mep2	B-protein_type
proteins	I-protein_type
of	O
S	B-species
.	I-species
cerevisiae	I-species
and	O
C	B-species
.	I-species
albicans	I-species
have	O
different	O
structures	B-evidence
for	O
their	O
CTRs	B-structure_element
(	O
Fig	O
.	O
1	O
and	O
Supplementary	O
Fig	O
.	O
6	O
).	O

In	O
addition	O
,	O
the	O
AI	B-structure_element
region	I-structure_element
of	O
the	O
CTR	B-structure_element
containing	O
the	O
Npr1	B-site
kinase	I-site
site	I-site
is	O
conserved	B-protein_state
in	O
only	O
a	O
subset	O
of	O
fungal	B-taxonomy_domain
transporters	B-protein_type
,	O
suggesting	O
that	O
the	O
details	O
of	O
the	O
structural	O
changes	O
underpinning	O
regulation	O
vary	O
.	O

Nevertheless	O
,	O
given	O
the	O
central	O
role	O
of	O
absolutely	B-protein_state
conserved	I-protein_state
residues	O
within	O
the	O
ICL1	B-site
-	I-site
ICL3	I-site
-	I-site
CTR	I-site
interaction	I-site
network	I-site
(	O
Fig	O
.	O
4	O
),	O
we	O
propose	O
that	O
the	O
structural	O
basics	O
of	O
fungal	B-taxonomy_domain
ammonium	B-chemical
transporter	O
activation	O
are	O
conserved	B-protein_state
.	O

The	O
fact	O
that	O
Mep2	B-protein_type
orthologues	O
of	O
distantly	O
related	O
fungi	B-taxonomy_domain
are	O
fully	O
functional	O
in	O
ammonium	B-chemical
transport	O
and	O
signalling	O
in	O
S	B-species
.	I-species
cerevisiae	I-species
supports	O
this	O
notion	O
.	O

It	O
should	O
also	O
be	O
noted	O
that	O
the	O
tyrosine	B-residue_name
residue	O
interacting	O
with	O
His2	B-residue_name_number
is	O
highly	B-protein_state
conserved	I-protein_state
in	O
fungal	B-taxonomy_domain
Mep2	B-protein_type
orthologues	O
,	O
suggesting	O
that	O
the	O
Tyr	B-site
–	I-site
His2	I-site
hydrogen	I-site
bond	I-site
might	O
be	O
a	O
general	O
way	O
to	O
close	B-protein_state
Mep2	B-protein_type
proteins	I-protein_type
.	O

With	O
regards	O
to	O
plant	B-taxonomy_domain
AMTs	B-protein_type
,	O
it	O
has	O
been	O
proposed	O
that	O
phosphorylation	B-ptm
at	O
T460	B-residue_name_number
generates	O
conformational	O
changes	O
that	O
would	O
close	O
the	O
neighbouring	O
pore	B-site
via	O
the	O
C	B-structure_element
terminus	I-structure_element
.	O

This	O
assumption	O
was	O
based	O
partly	O
on	O
a	O
homology	B-experimental_method
model	I-experimental_method
for	O
Amt	B-protein
-	I-protein
1	I-protein
;	I-protein
1	I-protein
based	O
on	O
the	O
(	O
open	B-protein_state
)	O
archaebacterial	B-taxonomy_domain
AfAmt	B-protein
-	I-protein
1	I-protein
structure	B-evidence
,	O
which	O
suggested	O
that	O
the	O
C	B-structure_element
terminus	I-structure_element
of	O
Amt	B-protein
-	I-protein
1	I-protein
;	I-protein
1	I-protein
would	O
extend	O
further	O
to	O
the	O
neighbouring	O
monomer	B-oligomeric_state
.	O

Our	O
Mep2	B-protein
structures	B-evidence
show	O
that	O
this	O
assumption	O
may	O
not	O
be	O
correct	O
(	O
Fig	O
.	O
4	O
and	O
Supplementary	O
Fig	O
.	O
6	O
).	O

In	O
addition	O
,	O
the	O
considerable	O
differences	O
between	O
structurally	O
resolved	O
CTR	B-structure_element
domains	O
means	O
that	O
the	O
exact	O
environment	O
of	O
T460	B-residue_name_number
in	O
Amt	B-protein
-	I-protein
1	I-protein
;	I-protein
1	I-protein
is	O
also	O
not	O
known	O
(	O
Supplementary	O
Fig	O
.	O
6	O
).	O

Based	O
on	O
the	O
available	O
structural	B-evidence
information	I-evidence
,	O
we	O
consider	O
it	O
more	O
likely	O
that	O
phosphorylation	O
-	O
mediated	O
pore	O
closure	O
in	O
Amt	B-protein
-	I-protein
1	I-protein
;	I-protein
1	I-protein
is	O
intra	O
-	O
monomeric	O
,	O
via	O
disruption	O
of	O
the	O
interactions	O
between	O
the	O
CTR	B-structure_element
and	O
ICL1	B-structure_element
/	O
ICL3	B-structure_element
(	O
for	O
example	O
,	O
Y467	B-residue_name_number
-	O
H239	B-residue_name_number
and	O
D458	B-residue_name_number
-	O
K71	B-residue_name_number
).	O

There	O
is	O
generally	O
no	O
equivalent	O
for	O
CaMep2	B-protein
Tyr49	B-residue_name_number
in	O
plant	B-taxonomy_domain
AMTs	B-protein_type
,	O
indicating	O
that	O
a	O
Tyr	B-site
–	I-site
His2	I-site
hydrogen	I-site
bond	I-site
as	O
observed	O
in	O
Mep2	B-protein
may	O
not	O
contribute	O
to	O
the	O
closed	B-protein_state
state	O
in	O
plant	B-taxonomy_domain
transporters	B-protein_type
.	O

We	O
propose	O
that	O
intra	B-site
-	I-site
monomeric	I-site
CTR	I-site
-	I-site
ICL1	I-site
/	I-site
ICL3	I-site
interactions	I-site
lie	O
at	O
the	O
basis	O
of	O
regulation	O
of	O
both	O
fungal	B-taxonomy_domain
and	O
plant	B-taxonomy_domain
ammonium	B-protein_type
transporters	I-protein_type
;	O
close	O
interactions	O
generate	O
open	B-protein_state
channels	B-site
,	O
whereas	O
the	O
lack	B-protein_state
of	I-protein_state
‘	O
intra	O
-'	O
interactions	O
leads	O
to	O
inactive	B-protein_state
states	O
.	O

The	O
need	O
to	O
regulate	O
in	O
opposite	O
ways	O
may	O
be	O
the	O
reason	O
why	O
the	O
phosphorylation	B-site
sites	I-site
are	O
in	O
different	O
parts	O
of	O
the	O
CTR	B-structure_element
,	O
that	O
is	O
,	O
centrally	O
located	O
close	O
to	O
the	O
ExxGxD	B-structure_element
motif	I-structure_element
in	O
AMTs	B-protein_type
and	O
peripherally	O
in	O
Mep2	B-protein
.	O

In	O
this	O
way	O
,	O
phosphorylation	B-ptm
can	O
either	O
lead	O
to	O
channel	B-site
closing	O
(	O
in	O
the	O
case	O
of	O
AMTs	B-protein_type
)	O
or	O
channel	B-site
opening	O
in	O
the	O
case	O
of	O
Mep2	B-protein
.	O

Our	O
model	O
also	O
provides	O
an	O
explanation	O
for	O
the	O
observation	O
that	O
certain	B-mutant
mutations	I-mutant
within	O
the	O
CTR	B-structure_element
completely	O
abolish	O
transport	O
activity	O
.	O

An	O
example	O
of	O
an	O
inactivating	O
residue	O
is	O
the	O
glycine	B-residue_name
of	O
the	O
ExxGxD	B-structure_element
motif	I-structure_element
of	O
the	O
CTR	B-structure_element
.	O

Mutation	B-experimental_method
of	O
this	O
residue	O
(	O
G393	B-residue_name_number
in	O
EcAmtB	B-protein
;	O
G456	B-residue_name_number
in	O
AtAmt	B-protein
-	I-protein
1	I-protein
;	I-protein
1	I-protein
)	O
inactivates	O
transporters	B-protein_type
as	O
diverse	O
as	O
Escherichia	B-species
coli	I-species
AmtB	B-protein
and	O
A	B-species
.	I-species
thaliana	I-species
Amt	B-protein
-	I-protein
1	I-protein
;	I-protein
1	I-protein
(	O
refs	O
).	O

Such	O
mutations	O
likely	O
cause	O
structural	O
changes	O
in	O
the	O
CTR	B-structure_element
that	O
prevent	O
close	O
contacts	O
between	O
the	O
CTR	B-structure_element
and	O
ICL1	B-structure_element
/	O
ICL3	B-structure_element
,	O
thereby	O
stabilizing	O
a	O
closed	B-protein_state
state	O
that	O
may	O
be	O
similar	O
to	O
that	O
observed	O
in	O
Mep2	B-protein
.	O

Regulation	O
and	O
modulation	O
of	O
membrane	O
transport	O
by	O
phosphorylation	B-ptm
is	O
known	O
to	O
occur	O
in	O
,	O
for	O
example	O
,	O
aquaporins	B-protein_type
and	O
urea	B-protein_type
transporters	I-protein_type
,	O
and	O
is	O
likely	O
to	O
be	O
a	O
common	O
theme	O
for	O
eukaryotic	B-taxonomy_domain
channels	B-protein_type
and	O
transporters	B-protein_type
.	O

Recently	O
,	O
phosphorylation	B-ptm
was	O
also	O
shown	O
to	O
modulate	O
substrate	O
affinity	O
in	O
nitrate	B-protein_type
transporters	I-protein_type
.	O

With	O
respect	O
to	O
ammonium	B-chemical
transport	O
,	O
phosphorylation	B-ptm
has	O
thus	O
far	O
only	O
been	O
shown	O
for	O
A	B-species
.	I-species
thaliana	I-species
AMTs	B-protein_type
and	O
for	O
S	B-species
.	I-species
cerevisiae	I-species
Mep2	B-protein
(	O
refs	O
).	O

However	O
,	O
the	O
absence	B-protein_state
of	I-protein_state
GlnK	B-protein_type
proteins	I-protein_type
in	O
eukaryotes	B-taxonomy_domain
suggests	O
that	O
phosphorylation	B-ptm
-	O
based	O
regulation	O
of	O
ammonium	B-chemical
transport	O
may	O
be	O
widespread	O
.	O

With	O
respect	O
to	O
Mep2	B-protein_type
-	O
mediated	O
signalling	O
to	O
induce	O
pseudohyphal	O
growth	O
,	O
two	O
models	O
have	O
been	O
put	O
forward	O
as	O
to	O
how	O
this	O
occurs	O
and	O
why	O
it	O
is	O
specific	O
to	O
Mep2	B-protein_type
proteins	I-protein_type
.	O

In	O
one	O
model	O
,	O
signalling	O
is	O
proposed	O
to	O
depend	O
on	O
the	O
nature	O
of	O
the	O
transported	O
substrate	O
,	O
which	O
might	O
be	O
different	O
in	O
certain	O
subfamilies	O
of	O
ammonium	B-protein_type
transporters	I-protein_type
(	O
for	O
example	O
,	O
Mep1	B-protein
/	O
Mep3	B-protein
versus	O
Mep2	B-protein
).	O

For	O
example	O
,	O
NH3	B-chemical
uniport	O
or	O
symport	O
of	O
NH3	B-chemical
/	O
H	B-chemical
+	I-chemical
might	O
result	O
in	O
changes	O
in	O
local	O
pH	O
,	O
but	O
NH4	B-chemical
+	I-chemical
uniport	O
might	O
not	O
,	O
and	O
this	O
difference	O
might	O
determine	O
signalling	O
.	O

In	O
the	O
other	O
model	O
,	O
signalling	O
is	O
thought	O
to	O
require	O
a	O
distinct	O
conformation	O
of	O
the	O
Mep2	B-protein
transporter	B-protein_type
occurring	O
during	O
the	O
transport	O
cycle	O
.	O

While	O
the	O
current	O
study	O
does	O
not	O
specifically	O
address	O
the	O
mechanism	O
of	O
signalling	O
underlying	O
pseudohyphal	O
growth	O
,	O
our	O
structures	B-evidence
do	O
show	O
that	O
Mep2	B-protein_type
proteins	I-protein_type
can	O
assume	O
different	O
conformations	O
.	O

It	O
is	O
clear	O
that	O
ammonium	B-chemical
transport	O
across	O
biomembranes	O
remains	O
a	O
fascinating	O
and	O
challenging	O
field	O
in	O
large	O
part	O
due	O
to	O
the	O
unique	O
properties	O
of	O
the	O
substrate	O
.	O

Our	O
Mep2	B-protein
structural	O
work	O
now	O
provides	O
a	O
foundation	O
for	O
future	O
studies	O
to	O
uncover	O
the	O
details	O
of	O
the	O
structural	O
changes	O
that	O
occur	O
during	O
eukaryotic	B-taxonomy_domain
ammonium	B-chemical
transport	O
and	O
signaling	O
,	O
and	O
to	O
assess	O
the	O
possibility	O
to	O
utilize	O
small	O
molecules	O
to	O
shut	O
down	O
ammonium	B-chemical
sensing	O
and	O
downstream	O
signalling	O
pathways	O
in	O
pathogenic	O
fungi	B-taxonomy_domain
.	O

X	B-evidence
-	I-evidence
ray	I-evidence
crystal	I-evidence
structures	I-evidence
of	O
Mep2	B-protein
transceptors	B-protein_type
.	O

(	O
a	O
)	O
Monomer	B-oligomeric_state
cartoon	O
models	O
viewed	O
from	O
the	O
side	O
for	O
(	O
left	O
)	O
A	O
.	O
fulgidus	O
Amt	B-protein
-	I-protein
1	I-protein
(	O
PDB	O
ID	O
2B2H	O
),	O
S	B-species
.	I-species
cerevisiae	I-species
Mep2	B-protein
(	O
middle	O
)	O
and	O
C	B-species
.	I-species
albicans	I-species
Mep2	B-protein
(	O
right	O
).	O

The	O
region	O
showing	O
ICL1	B-structure_element
(	O
blue	O
),	O
ICL3	B-structure_element
(	O
green	O
)	O
and	O
the	O
CTR	B-structure_element
(	O
red	O
)	O
is	O
boxed	O
for	O
comparison	O
.	O

(	O
b	O
)	O
CaMep2	B-protein
trimer	B-oligomeric_state
viewed	O
from	O
the	O
intracellular	O
side	O
(	O
right	O
).	O

One	O
monomer	B-oligomeric_state
is	O
coloured	O
as	O
in	O
a	O
and	O
one	O
monomer	B-oligomeric_state
is	O
coloured	O
by	O
B	O
-	O
factor	O
(	O
blue	O
,	O
low	O
;	O
red	O
;	O
high	O
).	O

The	O
CTR	B-structure_element
is	O
boxed	O
.	O

(	O
c	O
)	O
Overlay	B-experimental_method
of	O
ScMep2	B-protein
(	O
grey	O
)	O
and	O
CaMep2	B-protein
(	O
rainbow	O
),	O
illustrating	O
the	O
differences	O
in	O
the	O
CTRs	B-structure_element
.	O

Sequence	B-evidence
conservation	I-evidence
in	O
ammonium	B-protein_type
transporters	I-protein_type
.	O

ClustalW	B-experimental_method
alignment	I-experimental_method
of	O
CaMep2	B-protein
,	O
ScMep2	B-protein
,	O
A	B-species
.	I-species
fulgidus	I-species
Amt	B-protein
-	I-protein
1	I-protein
,	O
E	O
.	O
coli	O
AmtB	B-protein
and	O
A	B-species
.	I-species
thaliana	I-species
Amt	B-protein
-	I-protein
1	I-protein
;	I-protein
1	I-protein
.	O

The	O
secondary	O
structure	O
elements	O
observed	O
for	O
CaMep2	B-protein
are	O
indicated	O
,	O
with	O
the	O
numbers	O
corresponding	O
to	O
the	O
centre	O
of	O
the	O
TM	B-structure_element
segment	I-structure_element
.	O

The	O
conserved	B-protein_state
RxK	B-structure_element
motif	I-structure_element
in	O
ICL1	B-structure_element
is	O
boxed	O
in	O
blue	O
,	O
the	O
ER	B-structure_element
motif	I-structure_element
in	O
ICL2	B-structure_element
in	O
cyan	O
,	O
the	O
conserved	B-protein_state
ExxGxD	B-structure_element
motif	I-structure_element
of	O
the	O
CTR	B-structure_element
in	O
red	O
and	O
the	O
AI	B-structure_element
region	I-structure_element
in	O
yellow	O
.	O

Coloured	O
residues	O
are	O
functionally	O
important	O
and	O
correspond	O
to	O
those	O
of	O
the	O
Phe	B-site
gate	I-site
(	O
blue	O
),	O
the	O
binding	B-site
site	I-site
Trp	B-residue_name
residue	O
(	O
magenta	O
)	O
and	O
the	O
twin	O
-	O
His	O
motif	O
(	O
red	O
).	O

The	O
Npr1	B-site
kinase	I-site
site	I-site
in	O
the	O
AI	B-structure_element
region	I-structure_element
is	O
highlighted	O
pink	O
.	O

The	O
grey	O
sequences	O
at	O
the	O
C	O
termini	O
of	O
CaMep2	B-protein
and	O
ScMep2	B-protein
are	O
not	O
visible	O
in	O
the	O
structures	B-evidence
and	O
are	O
likely	B-protein_state
disordered	I-protein_state
.	O

Growth	B-experimental_method
of	O
ScMep2	B-mutant
variants	I-mutant
on	O
low	O
ammonium	O
medium	O
.	O

(	O
a	O
)	O
The	O
triple	B-mutant
mepΔ	I-mutant
strain	O
(	O
black	O
)	O
and	O
triple	O
mepΔ	O
npr1Δ	O
strain	O
(	O
grey	O
)	O
containing	O
plasmids	O
expressing	O
WT	B-protein_state
and	O
variant	B-mutant
ScMep2	I-mutant
were	O
grown	B-experimental_method
on	I-experimental_method
minimal	I-experimental_method
medium	I-experimental_method
containing	O
1	O
mM	O
ammonium	B-chemical
sulphate	I-chemical
.	O

The	O
quantified	O
cell	B-evidence
density	I-evidence
reflects	O
logarithmic	O
growth	O
after	O
24	O
h	O
.	O
Error	O
bars	O
are	O
the	O
s	O
.	O
d	O
.	O
for	O
three	O
replicates	O
of	O
each	O
strain	O
(	O
b	O
)	O
The	O
strains	O
used	O
in	O
a	O
were	O
also	O
serially	O
diluted	O
and	O
spotted	O
onto	O
minimal	O
agar	O
plates	O
containing	O
glutamate	B-chemical
(	O
0	O
.	O
1	O
%)	O
or	O
ammonium	B-chemical
sulphate	I-chemical
(	O
1	O
mM	O
),	O
and	O
grown	O
for	O
3	O
days	O
at	O
30	O
°	O
C	O
.	O

Structural	O
differences	O
between	O
Mep2	B-protein
and	O
bacterial	B-taxonomy_domain
ammonium	O
transporters	O
.	O

(	O
a	O
)	O
ICL1	B-structure_element
in	O
AfAmt	B-protein
-	I-protein
1	I-protein
(	O
light	O
blue	O
)	O
and	O
CaMep2	B-protein
(	O
dark	O
blue	O
),	O
showing	O
unwinding	O
and	O
inward	O
movement	O
in	O
the	O
fungal	B-taxonomy_domain
protein	O
.	O
(	O
b	O
)	O
Stereo	O
diagram	O
viewed	O
from	O
the	O
cytosol	O
of	O
ICL1	B-structure_element
,	O
ICL3	B-structure_element
(	O
green	O
)	O
and	O
the	O
CTR	B-structure_element
(	O
red	O
)	O
in	O
AfAmt	B-protein
-	I-protein
1	I-protein
(	O
light	O
colours	O
)	O
and	O
CaMep2	B-protein
(	O
dark	O
colours	O
).	O

The	O
side	O
chains	O
of	O
residues	O
in	O
the	O
RxK	B-structure_element
motif	I-structure_element
as	O
well	O
as	O
those	O
of	O
Tyr49	B-residue_name_number
and	O
His342	B-residue_name_number
are	O
labelled	O
.	O

The	O
numbering	O
is	O
for	O
CaMep2	B-protein
.	O

(	O
c	O
)	O
Conserved	B-protein_state
residues	O
in	O
ICL1	B-structure_element
-	I-structure_element
3	I-structure_element
and	O
the	O
CTR	B-structure_element
.	O

Views	O
from	O
the	O
cytosol	O
for	O
CaMep2	B-protein
(	O
left	O
)	O
and	O
AfAmt	B-protein
-	I-protein
1	I-protein
,	O
highlighting	O
the	O
large	O
differences	O
in	O
conformation	O
of	O
the	O
conserved	B-protein_state
residues	O
in	O
ICL1	B-structure_element
(	O
RxK	O
motif	O
;	O
blue	O
),	O
ICL2	B-structure_element
(	O
ER	B-structure_element
motif	I-structure_element
;	O
cyan	O
),	O
ICL3	B-structure_element
(	O
green	O
)	O
and	O
the	O
CTR	B-structure_element
(	O
red	O
).	O

The	O
labelled	O
residues	O
are	O
analogous	O
within	O
both	O
structures	B-evidence
.	O

In	O
b	O
and	O
c	O
,	O
the	O
centre	O
of	O
the	O
trimer	B-oligomeric_state
is	O
at	O
top	O
.	O

Channel	O
closures	O
in	O
Mep2	B-protein
.	O

(	O
a	O
)	O
Stereo	O
superposition	B-experimental_method
of	O
AfAmt	B-protein
-	I-protein
1	I-protein
and	O
CaMep2	B-protein
showing	O
the	O
residues	O
of	O
the	O
Phe	B-site
gate	I-site
,	O
His2	B-residue_name_number
of	O
the	O
twin	B-structure_element
-	I-structure_element
His	I-structure_element
motif	I-structure_element
and	O
the	O
tyrosine	B-residue_name
residue	O
Y49	B-residue_name_number
in	O
TM1	B-structure_element
that	O
forms	O
a	O
hydrogen	O
bond	O
with	O
His2	B-residue_name_number
in	O
CaMep2	B-protein
.	O
(	O
b	O
)	O
Surface	O
views	O
from	O
the	O
side	O
in	O
rainbow	O
colouring	O
,	O
showing	O
the	O
two	O
-	O
tier	O
channel	B-structure_element
block	I-structure_element
(	O
indicated	O
by	O
the	O
arrows	O
)	O
in	O
CaMep2	B-protein
.	O

The	O
Npr1	B-protein
kinase	B-protein_type
target	O
Ser453	B-residue_name_number
is	O
dephosphorylated	B-protein_state
and	O
located	O
in	O
an	O
electronegative	B-site
pocket	I-site
.	O

(	O
a	O
)	O
Stereoviews	O
of	O
CaMep2	B-protein
showing	O
2Fo	O
–	O
Fc	O
electron	O
density	O
(	O
contoured	O
at	O
1	O
.	O
0	O
σ	O
)	O
for	O
CTR	B-structure_element
residues	O
Asp419	B-residue_range
-	I-residue_range
Met422	I-residue_range
and	O
for	O
Tyr446	B-residue_range
-	I-residue_range
Thr455	I-residue_range
of	O
the	O
AI	B-structure_element
region	I-structure_element
.	O

The	O
phosphorylation	B-ptm
target	O
residue	O
Ser453	B-residue_name_number
is	O
labelled	O
in	O
bold	O
.	O

(	O
b	O
)	O
Overlay	B-experimental_method
of	O
the	O
CTRs	B-structure_element
of	O
ScMep2	B-protein
(	O
grey	O
)	O
and	O
CaMep2	B-protein
(	O
green	O
),	O
showing	O
the	O
similar	O
electronegative	O
environment	O
surrounding	O
the	O
phosphorylation	B-site
site	I-site
(	O
P	O
).	O

The	O
AI	B-structure_element
regions	I-structure_element
are	O
coloured	O
magenta	O
.	O

(	O
c	O
)	O
Cytoplasmic	O
view	O
of	O
the	O
Mep2	B-protein
trimer	B-oligomeric_state
indicating	O
the	O
large	O
distance	O
between	O
Ser453	B-residue_name_number
and	O
the	O
channel	B-site
exits	I-site
(	O
circles	O
;	O
Ile52	B-residue_name_number
lining	O
the	O
channel	B-site
exit	I-site
is	O
shown	O
).	O

Effect	O
of	O
removal	B-experimental_method
of	O
the	O
AI	B-structure_element
region	I-structure_element
on	O
Mep2	B-protein
structure	B-evidence
.	O

(	O
a	O
)	O
Side	O
views	O
for	O
WT	B-protein_state
CaMep2	B-protein
(	O
left	O
)	O
and	O
the	O
truncation	B-protein_state
mutant	I-protein_state
442Δ	B-mutant
(	O
right	O
).	O

The	O
latter	O
is	O
shown	O
as	O
a	O
putty	O
model	O
according	O
to	O
B	O
-	O
factors	O
to	O
illustrate	O
the	O
disorder	B-protein_state
in	O
the	O
protein	O
on	O
the	O
cytoplasmic	O
side	O
.	O

Missing	O
regions	O
are	O
labelled	O
.	O
(	O
b	O
)	O
Stereo	O
superpositions	B-experimental_method
of	O
WT	B-protein_state
CaMep2	B-protein
and	O
the	O
truncation	B-protein_state
mutant	I-protein_state
.	O

2Fo	O
–	O
Fc	O
electron	O
density	O
(	O
contoured	O
at	O
1	O
.	O
0	O
σ	O
)	O
for	O
residues	O
Tyr49	B-residue_name_number
and	O
His342	B-residue_name_number
is	O
shown	O
for	O
the	O
truncation	B-protein_state
mutant	I-protein_state
.	O

Phosphorylation	B-ptm
causes	O
conformational	O
changes	O
in	O
the	O
CTR	B-structure_element
.	O

(	O
a	O
)	O
Cytoplasmic	O
view	O
of	O
the	O
DD	B-mutant
mutant	I-mutant
trimer	B-oligomeric_state
,	O
with	O
WT	B-protein_state
CaMep2	B-protein
superposed	B-experimental_method
in	O
grey	O
for	O
one	O
of	O
the	O
monomers	B-oligomeric_state
.	O

The	O
arrow	O
indicates	O
the	O
phosphorylation	B-site
site	I-site
.	O

The	O
AI	B-structure_element
region	I-structure_element
is	O
coloured	O
magenta	O
.	O

(	O
b	O
)	O
Monomer	B-oligomeric_state
side	O
-	O
view	O
superposition	B-experimental_method
of	O
WT	B-protein_state
CaMep2	B-protein
and	O
the	O
DD	B-mutant
mutant	I-mutant
,	O
showing	O
the	O
conformational	O
change	O
and	O
disorder	O
around	O
the	O
ExxGxD	B-structure_element
motif	I-structure_element
.	O

Side	O
chains	O
for	O
residues	O
452	B-residue_number
and	O
453	B-residue_number
are	O
shown	O
as	O
stick	O
models	O
.	O

Schematic	O
model	O
for	O
phosphorylation	O
-	O
based	O
regulation	O
of	O
Mep2	B-protein
ammonium	O
transporters	O
.	O

(	O
a	O
)	O
In	O
the	O
closed	B-protein_state
,	O
non	B-protein_state
-	I-protein_state
phosphorylated	I-protein_state
state	O
(	O
i	O
),	O
the	O
CTR	B-structure_element
(	O
magenta	O
)	O
and	O
ICL3	B-structure_element
(	O
green	O
)	O
are	O
far	O
apart	O
with	O
the	O
latter	O
blocking	O
the	O
intracellular	O
channel	B-site
exit	I-site
(	O
indicated	O
with	O
a	O
hatched	O
circle	O
).	O

Upon	O
phosphorylation	B-ptm
and	O
mimicked	B-protein_state
by	O
the	O
CaMep2	B-protein
S453D	B-mutant
and	O
DD	B-mutant
mutants	I-mutant
(	O
ii	O
),	O
the	O
region	O
around	O
the	O
ExxGxD	B-structure_element
motif	I-structure_element
undergoes	O
a	O
conformational	O
change	O
that	O
results	O
in	O
the	O
CTR	B-structure_element
interacting	O
with	O
the	O
inward	O
-	O
moving	O
ICL3	B-structure_element
,	O
opening	O
the	O
channel	B-site
(	O
full	O
circle	O
)	O
(	O
iii	O
).	O

The	O
open	B-protein_state
-	O
channel	B-site
Mep2	B-protein
structure	B-evidence
is	O
represented	O
by	O
archaebacterial	B-taxonomy_domain
Amt	B-protein
-	I-protein
1	I-protein
and	O
shown	O
in	O
lighter	O
colours	O
consistent	O
with	O
Fig	O
.	O
4	O
.	O

As	O
discussed	O
in	O
the	O
text	O
,	O
similar	O
structural	O
arrangements	O
may	O
occur	O
in	O
plant	B-taxonomy_domain
AMTs	B-protein_type
.	O

In	O
this	O
case	O
however	O
,	O
the	O
open	B-protein_state
channel	B-site
corresponds	O
to	O
the	O
non	B-protein_state
-	I-protein_state
phosphorylated	I-protein_state
state	O
;	O
phosphorylation	B-ptm
breaks	O
the	O
CTR	O
–	O
ICL3	O
interactions	O
leading	O
to	O
channel	B-site
closure	O
.	O
(	O
b	O
)	O
Model	O
based	O
on	O
AMT	O
transporter	O
analogy	O
showing	O
how	O
phosphorylation	B-ptm
of	O
a	O
Mep2	B-protein
monomer	B-oligomeric_state
might	O
allosterically	O
open	B-protein_state
channels	B-site
in	O
the	O
entire	O
trimer	B-oligomeric_state
via	O
disruption	O
of	O
the	O
interactions	O
between	O
the	O
CTR	B-structure_element
and	O
ICL3	B-structure_element
of	O
a	O
neighbouring	O
monomer	B-oligomeric_state
(	O
arrow	O
).	O

Visualizing	O
chaperone	B-protein_type
-	O
assisted	O
protein	O
folding	O

Challenges	O
in	O
determining	O
the	O
structures	B-evidence
of	O
heterogeneous	O
and	O
dynamic	O
protein	O
complexes	O
have	O
greatly	O
hampered	O
past	O
efforts	O
to	O
obtain	O
a	O
mechanistic	O
understanding	O
of	O
many	O
important	O
biological	O
processes	O
.	O

One	O
such	O
process	O
is	O
chaperone	B-protein_type
-	O
assisted	O
protein	O
folding	O
,	O
where	O
obtaining	O
structural	O
ensembles	O
of	O
chaperone	B-protein_type
:	O
substrate	O
complexes	O
would	O
ultimately	O
reveal	O
how	O
chaperones	B-protein_type
help	O
proteins	O
fold	O
into	O
their	O
native	O
state	O
.	O

To	O
address	O
this	O
problem	O
,	O
we	O
devised	O
a	O
novel	O
structural	O
biology	O
approach	O
based	O
on	O
X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
,	O
termed	O
Residual	B-experimental_method
Electron	I-experimental_method
and	I-experimental_method
Anomalous	I-experimental_method
Density	I-experimental_method
(	O
READ	B-experimental_method
).	O

READ	B-experimental_method
enabled	O
us	O
to	O
visualize	O
even	O
sparsely	O
populated	O
conformations	O
of	O
the	O
substrate	O
protein	O
immunity	B-protein
protein	I-protein
7	I-protein
(	O
Im7	B-protein
)	O
in	B-protein_state
complex	I-protein_state
with	I-protein_state
the	O
E	B-species
.	I-species
coli	I-species
chaperone	B-protein_type
Spy	B-protein
.	O

This	O
study	O
resulted	O
in	O
a	O
series	O
of	O
snapshots	O
depicting	O
the	O
various	O
folding	O
states	O
of	O
Im7	B-protein
while	O
bound	B-protein_state
to	I-protein_state
Spy	B-protein
.	O

The	O
ensemble	O
shows	O
that	O
Spy	B-protein_state
-	I-protein_state
associated	I-protein_state
Im7	B-protein
samples	O
conformations	O
ranging	O
from	O
unfolded	B-protein_state
to	O
partially	O
folded	B-protein_state
and	O
native	B-protein_state
-	O
like	O
states	O
,	O
and	O
reveals	O
how	O
a	O
substrate	O
can	O
explore	O
its	O
folding	O
landscape	O
while	O
bound	B-protein_state
to	I-protein_state
a	O
chaperone	B-protein_type
.	O

High	O
-	O
resolution	O
structural	B-evidence
models	I-evidence
of	O
protein	O
-	O
protein	O
interactions	O
are	O
critical	O
for	O
obtaining	O
mechanistic	O
insights	O
into	O
biological	O
processes	O
.	O

However	O
,	O
many	O
protein	O
-	O
protein	O
interactions	O
are	O
highly	B-protein_state
dynamic	I-protein_state
,	O
making	O
it	O
difficult	O
to	O
obtain	O
high	O
-	O
resolution	O
data	O
.	O

Particularly	O
challenging	O
are	O
interactions	O
of	O
intrinsically	B-protein_state
or	I-protein_state
conditionally	I-protein_state
disordered	I-protein_state
sections	O
of	O
proteins	O
with	O
their	O
partner	O
proteins	O
.	O

Recent	O
advances	O
in	O
X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
and	O
NMR	B-experimental_method
spectroscopy	I-experimental_method
continue	O
to	O
improve	O
our	O
ability	O
to	O
analyze	O
biomolecules	O
that	O
exist	O
in	O
multiple	O
conformations	O
.	O

X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
has	O
historically	O
provided	O
valuable	O
information	O
on	O
small	O
-	O
scale	O
conformational	O
changes	O
,	O
but	O
observing	O
large	O
-	O
amplitude	O
heterogeneous	O
conformational	O
changes	O
often	O
falls	O
beyond	O
the	O
reach	O
of	O
current	O
crystallographic	O
techniques	O
.	O

NMR	B-experimental_method
can	O
theoretically	O
be	O
used	O
to	O
determine	O
heterogeneous	O
ensembles	O
,	O
but	O
in	O
practice	O
,	O
this	O
proves	O
to	O
be	O
very	O
challenging	O
.	O

It	O
is	O
clear	O
that	O
molecular	O
chaperones	B-protein_type
aid	O
in	O
protein	O
folding	O
.	O

Structural	O
characterization	O
of	O
chaperone	B-protein_type
-	O
assisted	O
protein	O
folding	O
likely	O
would	O
help	O
bring	O
clarity	O
to	O
this	O
question	O
.	O

Structural	B-evidence
models	I-evidence
of	O
chaperone	B-protein_type
-	O
substrate	O
complexes	O
have	O
recently	O
begun	O
to	O
provide	O
information	O
as	O
to	O
how	O
a	O
chaperone	B-protein_type
can	O
recognize	O
its	O
substrate	O
.	O

However	O
,	O
the	O
impact	O
that	O
chaperones	B-protein_type
have	O
on	O
their	O
substrates	O
,	O
and	O
how	O
these	O
interactions	O
affect	O
the	O
folding	O
process	O
remain	O
largely	O
unknown	O
.	O

For	O
most	O
chaperones	B-protein_type
,	O
it	O
is	O
still	O
unclear	O
whether	O
the	O
chaperone	B-protein_type
actively	O
participates	O
in	O
and	O
affects	O
the	O
folding	O
of	O
the	O
substrate	O
proteins	O
,	O
or	O
merely	O
provides	O
a	O
suitable	O
microenvironment	O
enabling	O
the	O
substrate	O
to	O
fold	O
on	O
its	O
own	O
.	O

This	O
is	O
a	O
truly	O
fundamental	O
question	O
in	O
the	O
chaperone	B-protein_type
field	O
,	O
and	O
one	O
that	O
has	O
eluded	O
the	O
community	O
largely	O
because	O
of	O
the	O
highly	B-protein_state
dynamic	I-protein_state
nature	O
of	O
the	O
chaperone	B-protein_type
-	O
substrate	O
complexes	O
.	O

To	O
address	O
this	O
question	O
,	O
we	O
investigated	O
the	O
ATP	B-protein_state
-	I-protein_state
independent	I-protein_state
Escherichia	B-species
coli	I-species
periplasmic	O
chaperone	B-protein_type
Spy	B-protein
.	O

Spy	B-protein
prevents	O
protein	O
aggregation	O
and	O
aids	O
in	O
protein	O
folding	O
under	O
various	O
stress	O
conditions	O
,	O
including	O
treatment	O
with	O
tannin	B-chemical
and	O
butanol	B-chemical
.	O

We	O
originally	O
discovered	O
Spy	B-protein
by	O
its	O
ability	O
to	O
stabilize	O
the	O
protein	O
-	O
folding	O
model	O
Im7	B-protein
in	O
vivo	O
and	O
recently	O
demonstrated	O
that	O
Im7	B-protein
folds	O
while	O
associated	O
with	O
Spy	B-protein
.	O

The	O
crystal	B-evidence
structure	I-evidence
of	O
Spy	B-protein
revealed	O
that	O
it	O
forms	O
a	O
thin	O
α	O
-	O
helical	O
homodimeric	B-oligomeric_state
cradle	B-site
.	O

Crosslinking	B-experimental_method
and	I-experimental_method
genetic	I-experimental_method
experiments	I-experimental_method
suggested	O
that	O
Spy	B-protein
interacts	O
with	O
substrates	O
somewhere	O
on	O
its	O
concave	O
side	O
.	O

By	O
using	O
a	O
novel	O
X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
-	O
based	O
approach	O
to	O
model	O
disorder	O
in	O
crystal	B-evidence
structures	I-evidence
,	O
we	O
have	O
now	O
determined	O
the	O
high	O
-	O
resolution	O
ensemble	B-evidence
of	O
the	O
dynamic	B-protein_state
Spy	B-complex_assembly
:	I-complex_assembly
Im7	I-complex_assembly
complex	O
.	O

This	O
work	O
provides	O
a	O
detailed	O
view	O
of	O
chaperone	B-protein_type
-	O
mediated	O
protein	O
folding	O
and	O
shows	O
how	O
substrates	O
like	O
Im7	B-protein
find	O
their	O
native	O
fold	O
while	O
bound	B-protein_state
to	I-protein_state
their	O
chaperones	B-protein_type
.	O

Crystallizing	B-experimental_method
the	O
Spy	B-complex_assembly
:	I-complex_assembly
Im7	I-complex_assembly
complex	O

We	O
reasoned	O
that	O
to	O
obtain	O
crystals	B-evidence
of	O
complexes	O
between	O
Spy	B-protein
(	O
domain	O
boundaries	O
in	O
Supplementary	O
Fig	O
.	O
1	O
)	O
and	O
its	O
substrate	O
proteins	O
,	O
our	O
best	O
approach	O
was	O
to	O
identify	O
crystallization	B-experimental_method
conditions	I-experimental_method
that	O
yielded	O
Spy	B-protein
crystals	B-evidence
in	O
the	O
presence	B-protein_state
of	I-protein_state
protein	O
substrates	O
but	O
not	O
in	O
their	O
absence	B-protein_state
.	O

We	O
therefore	O
screened	B-experimental_method
crystallization	B-experimental_method
conditions	I-experimental_method
for	O
Spy	B-protein
with	O
four	O
different	O
substrate	O
proteins	O
:	O
a	O
fragment	O
of	O
the	O
largely	O
unfolded	B-protein_state
bovine	B-taxonomy_domain
α	B-chemical
-	I-chemical
casein	I-chemical
protein	O
,	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
(	O
WT	B-protein_state
)	O
E	B-species
.	I-species
coli	I-species
Im7	B-protein
,	O
an	O
unfolded	B-protein_state
variant	O
of	O
Im7	B-protein
(	O
L18A	B-mutant
L19A	B-mutant
L37A	B-mutant
),	O
and	O
the	O
N	B-structure_element
-	I-structure_element
terminal	I-structure_element
half	I-structure_element
of	O
Im7	B-protein
(	O
Im76	B-mutant
-	I-mutant
45	I-mutant
),	O
which	O
encompasses	O
the	O
entire	O
Spy	B-structure_element
-	I-structure_element
binding	I-structure_element
portion	I-structure_element
of	O
Im7	B-protein
.	O

We	O
found	O
conditions	O
in	O
which	O
all	O
four	O
substrates	O
co	B-experimental_method
-	I-experimental_method
crystallized	I-experimental_method
with	B-protein_state
Spy	B-protein
,	O
but	O
in	O
which	O
Spy	B-protein
alone	B-protein_state
did	O
not	O
yield	O
crystals	B-evidence
.	O

Subsequent	O
crystal	B-experimental_method
washing	I-experimental_method
and	I-experimental_method
dissolution	I-experimental_method
experiments	O
confirmed	O
the	O
presence	O
of	O
the	O
substrates	O
in	O
the	O
co	B-experimental_method
-	I-experimental_method
crystals	I-experimental_method
(	O
Supplementary	O
Fig	O
.	O
2	O
).	O

The	O
crystals	B-evidence
diffracted	O
to	O
~	O
1	O
.	O
8	O
Å	O
resolution	O
.	O

We	O
used	O
Spy	B-complex_assembly
:	I-complex_assembly
Im76	I-complex_assembly
-	I-complex_assembly
45	I-complex_assembly
selenomethionine	B-chemical
crystals	B-evidence
for	O
phasing	O
with	O
single	B-experimental_method
-	I-experimental_method
wavelength	I-experimental_method
anomalous	I-experimental_method
diffraction	I-experimental_method
(	O
SAD	B-experimental_method
)	O
experiments	O
,	O
and	O
used	O
this	O
solution	O
to	O
build	O
the	O
well	O
-	O
ordered	O
Spy	B-protein
portions	O
of	O
all	O
four	O
complexes	O
.	O

However	O
,	O
modeling	O
of	O
the	O
substrate	O
in	O
the	O
complex	O
proved	O
to	O
be	O
a	O
substantial	O
challenge	O
,	O
as	O
the	O
electron	B-evidence
density	I-evidence
of	O
the	O
substrate	O
was	O
discontinuous	O
and	O
fragmented	O
.	O

Even	O
the	O
minimal	B-structure_element
binding	I-structure_element
portion	I-structure_element
of	O
Im7	B-protein
(	O
Im76	B-mutant
-	I-mutant
45	I-mutant
)	O
showed	O
highly	O
dispersed	O
electron	B-evidence
density	I-evidence
(	O
Fig	O
.	O
1a	O
).	O

We	O
hypothesized	O
that	O
the	O
fragmented	O
density	B-evidence
was	O
due	O
to	O
multiple	O
,	O
partially	O
occupied	O
conformations	O
of	O
the	O
substrate	O
bound	O
within	O
the	O
crystal	B-evidence
.	O

Such	O
residual	O
density	O
is	O
typically	O
not	O
considered	O
usable	O
by	O
traditional	O
X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
methods	O
.	O

Thus	O
,	O
we	O
developed	O
a	O
new	O
approach	O
to	O
interpret	O
the	O
chaperone	B-protein_state
-	I-protein_state
bound	I-protein_state
substrate	O
in	O
multiple	O
conformations	O
.	O

READ	B-experimental_method
:	O
a	O
strategy	O
to	O
visualize	O
heterogeneous	O
and	O
dynamic	O
biomolecules	O

To	O
determine	O
the	O
structure	B-evidence
of	O
the	O
substrate	O
portion	O
of	O
these	O
Spy	B-protein
:	O
substrate	O
complexes	O
,	O
we	O
conceived	O
of	O
an	O
approach	O
that	O
we	O
term	O
READ	B-experimental_method
,	O
for	O
Residual	B-experimental_method
Electron	I-experimental_method
and	I-experimental_method
Anomalous	I-experimental_method
Density	I-experimental_method
.	O

We	O
split	O
this	O
approach	O
into	O
five	O
steps	O
:	O
(	O
1	O
)	O
By	O
using	O
a	O
well	O
-	O
diffracting	O
Spy	B-protein
:	O
substrate	O
co	B-evidence
-	I-evidence
crystal	I-evidence
,	O
we	O
first	O
determined	O
the	O
structure	B-evidence
of	O
the	O
folded	B-protein_state
domain	B-structure_element
of	O
Spy	B-protein
and	O
obtained	O
high	O
quality	O
residual	B-evidence
electron	I-evidence
density	I-evidence
within	O
the	O
dynamic	B-protein_state
regions	O
of	O
the	O
substrate	O
.	O

(	O
2	O
)	O
We	O
then	O
labeled	O
individual	O
residues	O
in	O
the	O
flexible	B-protein_state
regions	O
of	O
the	O
substrate	O
with	O
the	O
strong	O
anomalous	O
scatterer	O
iodine	B-chemical
,	O
which	O
serves	O
to	O
locate	O
these	O
residues	O
in	O
three	O
-	O
dimensional	O
space	O
using	O
their	O
anomalous	B-evidence
density	I-evidence
.	O

(	O
3	O
)	O
We	O
performed	O
molecular	B-experimental_method
dynamics	I-experimental_method
(	O
MD	B-experimental_method
)	O
simulations	B-experimental_method
to	O
generate	O
a	O
pool	O
of	O
energetically	O
reasonable	O
conformations	O
of	O
the	O
dynamic	B-protein_state
complex	O
and	O
(	O
4	O
)	O
applied	O
a	O
sample	B-experimental_method
-	I-experimental_method
and	I-experimental_method
-	I-experimental_method
select	I-experimental_method
algorithm	I-experimental_method
to	O
determine	O
the	O
minimal	O
set	O
of	O
substrate	O
conformations	O
that	O
fit	O
both	O
the	O
residual	B-evidence
and	I-evidence
anomalous	I-evidence
density	I-evidence
.	O

Importantly	O
,	O
even	O
though	O
we	O
only	O
labeled	O
a	O
subset	O
of	O
the	O
residues	O
in	O
the	O
flexible	B-protein_state
regions	O
of	O
the	O
substrate	O
with	O
iodine	B-chemical
,	O
the	O
residual	B-evidence
electron	I-evidence
density	I-evidence
can	O
provide	O
spatial	O
information	O
on	O
many	O
of	O
the	O
other	O
flexible	B-protein_state
residues	O
.	O

The	O
electron	B-evidence
density	I-evidence
then	O
allowed	O
us	O
to	O
connect	O
the	O
labeled	O
residues	O
of	O
the	O
substrate	O
by	O
confining	O
the	O
protein	O
chain	O
within	O
regions	O
of	O
detectable	O
density	B-evidence
.	O

In	O
this	O
way	O
,	O
the	O
two	O
forms	O
of	O
data	O
together	O
were	O
able	O
to	O
describe	O
multiple	O
conformations	O
of	O
the	O
substrate	O
within	O
the	O
crystal	B-evidence
.	O

As	O
described	O
in	O
detail	O
below	O
,	O
we	O
developed	O
the	O
READ	B-experimental_method
method	O
to	O
uncover	O
the	O
ensemble	O
of	O
conformations	O
that	O
the	O
Spy	B-structure_element
-	I-structure_element
binding	I-structure_element
domain	I-structure_element
of	O
Im7	B-protein
(	O
i	O
.	O
e	O
.,	O
Im76	B-mutant
-	I-mutant
45	I-mutant
)	O
adopts	O
while	O
bound	B-protein_state
to	I-protein_state
Spy	B-protein
.	O

However	O
,	O
we	O
believe	O
that	O
READ	B-experimental_method
will	O
prove	O
generally	O
applicable	O
to	O
visualizing	O
heterogeneous	O
and	O
dynamic	O
complexes	O
that	O
have	O
previously	O
escaped	O
detailed	O
structural	O
analysis	O
.	O

Collecting	O
READ	B-experimental_method
data	O
for	O
the	O
Spy	B-complex_assembly
:	I-complex_assembly
Im76	I-complex_assembly
-	I-complex_assembly
45	I-complex_assembly
complex	O

To	O
apply	O
the	O
READ	B-experimental_method
technique	I-experimental_method
to	O
the	O
folding	O
mechanism	O
employed	O
by	O
the	O
chaperone	B-protein_type
Spy	B-protein
,	O
we	O
selected	O
Im76	B-mutant
-	I-mutant
45	I-mutant
for	O
further	O
investigation	O
because	O
NMR	B-experimental_method
data	O
suggested	O
that	O
Im76	B-mutant
-	I-mutant
45	I-mutant
could	O
recapitulate	O
unfolded	B-protein_state
,	O
partially	O
folded	B-protein_state
,	O
and	O
native	O
-	O
like	O
states	O
of	O
Im7	B-protein
(	O
Supplementary	O
Fig	O
.	O
3	O
).	O

Moreover	O
,	O
binding	B-experimental_method
experiments	I-experimental_method
indicated	O
that	O
Im76	B-mutant
-	I-mutant
45	I-mutant
comprises	O
the	O
entire	O
Spy	B-site
-	I-site
binding	I-site
region	I-site
.	O

To	O
introduce	O
the	O
anomalous	O
scatterer	O
iodine	B-chemical
,	O
we	O
replaced	B-experimental_method
eight	O
Im76	B-mutant
-	I-mutant
45	I-mutant
residues	O
with	O
the	O
non	O
-	O
canonical	O
amino	O
acid	O
4	B-chemical
-	I-chemical
iodophenylalanine	I-chemical
(	O
pI	B-chemical
-	I-chemical
Phe	I-chemical
).	O

Its	O
strong	O
anomalous	B-evidence
scattering	I-evidence
allowed	O
us	O
to	O
track	O
the	O
positions	O
of	O
these	O
individual	O
Im76	B-mutant
-	I-mutant
45	I-mutant
residues	O
one	O
at	O
a	O
time	O
,	O
potentially	O
even	O
if	O
the	O
residue	O
was	O
found	O
in	O
several	O
locations	O
in	O
the	O
same	O
crystal	B-evidence
.	O

We	O
then	O
co	B-experimental_method
-	I-experimental_method
crystallized	I-experimental_method
Spy	B-protein
and	O
the	O
eight	O
Im76	B-mutant
-	I-mutant
45	I-mutant
peptides	O
,	O
each	O
of	O
which	O
harbored	O
an	O
individual	O
pI	B-chemical
-	I-chemical
Phe	I-chemical
substitution	B-experimental_method
at	O
one	O
distinct	O
position	O
,	O
and	O
collected	B-experimental_method
anomalous	B-evidence
data	I-evidence
for	O
all	O
eight	O
Spy	B-complex_assembly
:	I-complex_assembly
Im76	I-complex_assembly
-	I-complex_assembly
45	I-complex_assembly
complexes	O
(	O
Fig	O
.	O
1B	O
,	O
Supplementary	O
Table	O
1	O
Supplementary	O
Dataset	O
1	O
,	O
and	O
Supplementary	O
Table	O
2	O
).	O

Consistent	O
with	O
our	O
electron	B-evidence
density	I-evidence
map	I-evidence
,	O
we	O
found	O
that	O
the	O
majority	O
of	O
anomalous	B-evidence
signals	I-evidence
emerged	O
in	O
the	O
cradle	B-site
of	O
Spy	B-protein
,	O
implying	O
that	O
this	O
is	O
the	O
likely	O
Im7	B-protein
substrate	B-site
binding	I-site
site	I-site
.	O

Consistent	O
with	O
the	O
fragmented	O
density	B-evidence
,	O
however	O
,	O
we	O
observed	O
multiple	O
iodine	B-chemical
positions	O
for	O
seven	O
of	O
the	O
eight	O
substituted	O
residues	O
.	O

Together	O
,	O
these	O
results	O
indicated	O
that	O
the	O
Im7	B-protein
substrate	O
binds	O
Spy	B-protein
in	O
multiple	O
conformations	O
.	O

READ	B-experimental_method
sample	B-experimental_method
-	I-experimental_method
and	I-experimental_method
-	I-experimental_method
select	I-experimental_method
procedure	O

To	O
determine	O
the	O
structural	O
ensemble	O
that	O
Im76	B-mutant
-	I-mutant
45	I-mutant
adopts	O
while	O
bound	B-protein_state
to	I-protein_state
Spy	B-protein
,	O
we	O
combined	O
the	O
residual	B-evidence
electron	I-evidence
density	I-evidence
and	O
the	O
anomalous	B-evidence
signals	I-evidence
from	O
our	O
pI	B-chemical
-	I-chemical
Phe	I-chemical
substituted	O
Spy	B-complex_assembly
:	I-complex_assembly
Im76	I-complex_assembly
-	I-complex_assembly
45	I-complex_assembly
complexes	O
.	O

To	O
generate	O
an	O
accurate	O
depiction	O
of	O
the	O
chaperone	B-protein_type
-	O
substrate	O
interactions	O
,	O
we	O
devised	O
a	O
selection	O
protocol	O
based	O
on	O
a	O
sample	B-experimental_method
-	I-experimental_method
and	I-experimental_method
-	I-experimental_method
select	I-experimental_method
procedure	O
employed	O
in	O
NMR	B-experimental_method
spectroscopy	I-experimental_method
.	O

During	O
each	O
round	O
of	O
the	O
selection	O
,	O
a	O
genetic	B-experimental_method
algorithm	I-experimental_method
alters	O
the	O
ensemble	O
and	O
its	O
agreement	O
to	O
the	O
experimental	O
data	O
is	O
re	O
-	O
evaluated	O
.	O

If	O
successful	O
,	O
the	O
selection	O
identifies	O
the	O
smallest	O
group	O
of	O
specific	O
conformations	O
that	O
best	O
fits	O
the	O
residual	B-evidence
electron	I-evidence
density	I-evidence
and	O
anomalous	B-evidence
signals	I-evidence
.	O

The	O
READ	B-experimental_method
sample	B-experimental_method
-	I-experimental_method
and	I-experimental_method
-	I-experimental_method
select	I-experimental_method
algorithm	I-experimental_method
is	O
diagrammed	O
in	O
Fig	O
.	O
2	O
.	O

Prior	O
to	O
performing	O
the	O
selection	O
,	O
we	O
generated	O
a	O
large	O
and	O
diverse	O
pool	O
of	O
chaperone	B-protein_type
-	O
substrate	O
complexes	O
using	O
coarse	B-experimental_method
-	I-experimental_method
grained	I-experimental_method
MD	I-experimental_method
simulations	I-experimental_method
in	O
a	O
pseudo	B-experimental_method
-	I-experimental_method
crystal	I-experimental_method
environment	I-experimental_method
(	O
Fig	O
.	O
2	O
and	O
Supplementary	O
Fig	O
.	O
4	O
).	O

The	O
coarse	B-experimental_method
-	I-experimental_method
grained	I-experimental_method
simulations	I-experimental_method
are	O
based	O
on	O
a	O
single	O
-	O
residue	O
resolution	O
model	O
for	O
protein	O
folding	O
and	O
were	O
extended	O
here	O
to	O
describe	O
Spy	B-complex_assembly
-	I-complex_assembly
Im76	I-complex_assembly
-	I-complex_assembly
45	I-complex_assembly
binding	O
events	O
(	O
Online	O
Methods	O
).	O

The	O
initial	O
conditions	O
of	O
the	O
binding	B-experimental_method
simulations	I-experimental_method
are	O
not	O
biased	O
toward	O
a	O
particular	O
conformation	O
of	O
the	O
substrate	O
or	O
any	O
specific	O
chaperone	B-protein_type
-	O
substrate	O
interaction	O
(	O
Online	O
Methods	O
).	O

Im76	B-mutant
-	I-mutant
45	I-mutant
binds	O
and	O
unbinds	O
to	O
Spy	B-protein
throughout	O
the	O
simulations	B-experimental_method
.	O

This	O
strategy	O
allows	O
a	O
wide	O
range	O
of	O
substrate	O
conformations	O
to	O
interact	O
with	O
the	O
chaperone	B-protein_type
.	O

From	O
the	O
MD	B-experimental_method
simulations	B-experimental_method
,	O
we	O
extracted	O
~	O
10	O
,	O
000	O
diverse	O
Spy	B-complex_assembly
:	I-complex_assembly
Im76	I-complex_assembly
-	I-complex_assembly
45	I-complex_assembly
complexes	O
to	O
be	O
used	O
by	O
the	O
ensuing	O
selection	O
.	O

Each	O
complex	O
within	O
this	O
pool	O
comprises	O
one	O
Spy	B-protein
dimer	B-oligomeric_state
bound	B-protein_state
to	I-protein_state
a	O
single	O
Im76	B-mutant
-	I-mutant
45	I-mutant
substrate	O
.	O

This	O
pool	O
was	O
then	O
used	O
by	O
the	O
selection	O
algorithm	O
to	O
identify	O
the	O
minimal	O
ensemble	O
that	O
best	O
satisfies	O
both	O
the	O
residual	B-evidence
electron	I-evidence
and	I-evidence
anomalous	I-evidence
crystallographic	I-evidence
data	I-evidence
.	O

The	O
anomalous	B-evidence
scattering	I-evidence
portion	O
of	O
the	O
selection	O
uses	O
our	O
basic	O
knowledge	O
of	O
pI	B-chemical
-	I-chemical
Phe	I-chemical
geometry	O
:	O
the	O
iodine	B-chemical
is	O
separated	O
from	O
its	O
respective	O
Cα	O
atom	O
in	O
each	O
coarse	O
-	O
grained	O
conformer	O
by	O
6	O
.	O
5	O
Å	O
.	O
The	O
selection	O
then	O
picks	O
ensembles	O
that	O
best	O
reproduce	O
the	O
collection	O
of	O
iodine	B-chemical
anomalous	B-evidence
signals	I-evidence
.	O

Simultaneously	O
,	O
it	O
uses	O
the	O
residual	B-evidence
electron	I-evidence
density	I-evidence
to	O
help	O
choose	O
ensembles	O
.	O

To	O
make	O
the	O
electron	B-experimental_method
density	I-experimental_method
selection	I-experimental_method
practical	O
,	O
we	O
needed	O
to	O
develop	O
a	O
method	O
to	O
rapidly	O
evaluate	O
the	O
agreement	O
between	O
the	O
selected	O
sub	O
-	O
ensembles	O
and	O
the	O
experimental	O
electron	B-evidence
density	I-evidence
on	O
-	O
the	O
-	O
fly	O
during	O
the	O
selection	O
procedure	O
.	O

To	O
accomplish	O
this	O
task	O
,	O
we	O
generated	O
a	O
compressed	O
version	O
of	O
the	O
experimental	O
2mFo	B-evidence
−	I-evidence
DFc	I-evidence
electron	I-evidence
density	I-evidence
map	I-evidence
for	O
use	O
in	O
the	O
selection	O
.	O

This	O
process	O
provided	O
us	O
with	O
a	O
target	O
map	B-evidence
that	O
the	O
ensuing	O
selection	O
tried	O
to	O
recapitulate	O
.	O

To	O
reduce	O
the	O
extent	O
of	O
3D	O
space	O
to	O
be	O
explored	O
,	O
this	O
compressed	O
map	B-evidence
was	O
created	O
by	O
only	O
using	O
density	B-evidence
from	O
regions	O
of	O
space	O
significantly	O
sampled	O
by	O
Im76	B-mutant
-	I-mutant
45	I-mutant
in	O
the	O
Spy	B-complex_assembly
:	I-complex_assembly
Im76	I-complex_assembly
-	I-complex_assembly
45	I-complex_assembly
MD	B-experimental_method
simulations	B-experimental_method
.	O

For	O
each	O
of	O
the	O
~	O
10	O
,	O
000	O
complexes	O
in	O
the	O
coarse	B-experimental_method
-	I-experimental_method
grained	I-experimental_method
MD	B-experimental_method
pool	O
,	O
the	O
electron	B-evidence
density	I-evidence
at	O
the	O
Cα	O
positions	O
of	O
Im76	B-mutant
-	I-mutant
45	I-mutant
was	O
extracted	O
and	O
used	O
to	O
construct	O
an	O
electron	B-evidence
density	I-evidence
map	I-evidence
(	O
Online	O
Methods	O
).	O

These	O
individual	O
electron	B-evidence
density	I-evidence
maps	I-evidence
from	O
the	O
separate	O
conformers	O
could	O
then	O
be	O
combined	O
(	O
Fig	O
.	O
2	O
)	O
and	O
compared	O
to	O
the	O
averaged	O
experimental	O
electron	B-evidence
density	I-evidence
map	I-evidence
as	O
part	O
of	O
the	O
selection	O
algorithm	O
.	O

This	O
approach	O
allowed	O
us	O
to	O
simultaneously	O
use	O
both	O
the	O
iodine	B-chemical
anomalous	B-evidence
signals	I-evidence
and	O
the	O
residual	B-evidence
electron	I-evidence
density	I-evidence
in	O
the	O
selection	O
procedure	O
.	O

The	O
selection	O
resulted	O
in	O
small	O
ensembles	O
from	O
the	O
MD	B-experimental_method
pool	O
that	O
best	O
fit	O
the	O
READ	B-experimental_method
data	O
(	O
Fig	O
.	O
1c	O
,	O
d	O
).	O

Before	O
analyzing	O
the	O
details	O
of	O
the	O
Spy	B-complex_assembly
:	I-complex_assembly
Im76	I-complex_assembly
-	I-complex_assembly
45	I-complex_assembly
complex	O
,	O
we	O
first	O
engaged	O
in	O
a	O
series	O
of	O
validation	O
tests	O
to	O
verify	O
the	O
ensemble	O
and	O
selection	O
procedure	O
(	O
Supplementary	O
Note	O
1	O
,	O
Figures	O
1c	O
,	O
d	O
,	O
Supplemental	O
Figures	O
5	O
-	O
7	O
).	O

Of	O
note	O
,	O
the	O
final	O
six	O
-	O
membered	O
ensemble	O
was	O
the	O
largest	O
ensemble	O
that	O
could	O
simultaneously	O
decrease	O
the	O
RFree	B-evidence
and	O
pass	O
the	O
10	B-experimental_method
-	I-experimental_method
fold	I-experimental_method
cross	I-experimental_method
-	I-experimental_method
validation	I-experimental_method
test	I-experimental_method
.	O

This	O
ensemble	O
depicts	O
the	O
conformations	O
that	O
the	O
substrate	O
Im76	B-mutant
-	I-mutant
45	I-mutant
adopts	O
while	O
bound	B-protein_state
to	I-protein_state
the	O
chaperone	B-protein_type
Spy	B-protein
(	O
Fig	O
.	O
3	O
Supplementary	O
Movie	O
1	O
,	O
and	O
Table	O
1	O
).	O

Folding	O
and	O
interactions	O
of	O
Im7	B-protein
while	O
bound	B-protein_state
to	I-protein_state
Spy	B-protein

Our	O
results	O
showed	O
that	O
by	O
using	O
this	O
novel	O
READ	B-experimental_method
approach	O
,	O
we	O
were	O
able	O
to	O
obtain	O
structural	O
information	O
about	O
the	O
dynamic	O
interaction	O
of	O
a	O
chaperone	B-protein_type
with	O
its	O
substrate	O
protein	O
.	O

We	O
were	O
particularly	O
interested	O
in	O
finding	O
answers	O
to	O
one	O
of	O
the	O
most	O
fundamental	O
questions	O
in	O
chaperone	B-protein_type
biology	O
—	O
how	O
does	O
chaperone	B-protein_type
binding	O
affect	O
substrate	O
structure	O
and	O
vice	O
versa	O
.	O

By	O
analyzing	O
the	O
individual	O
structures	B-evidence
of	O
the	O
six	O
-	O
member	O
ensemble	O
of	O
Im76	B-mutant
-	I-mutant
45	I-mutant
bound	B-protein_state
to	I-protein_state
Spy	B-protein
,	O
we	O
observed	O
that	O
Im76	B-mutant
-	I-mutant
45	I-mutant
takes	O
on	O
several	O
different	O
conformations	O
while	O
bound	B-protein_state
.	O

We	O
found	O
these	O
conformations	O
to	O
be	O
highly	O
heterogeneous	O
and	O
to	O
include	O
unfolded	B-protein_state
,	O
partially	B-protein_state
folded	I-protein_state
,	O
and	O
native	B-protein_state
-	I-protein_state
like	I-protein_state
states	O
(	O
Fig	O
.	O
3	O
).	O

The	O
ensemble	O
primarily	O
encompasses	O
Im76	B-mutant
-	I-mutant
45	I-mutant
laying	O
diagonally	O
within	O
the	O
Spy	B-protein
cradle	B-site
in	O
several	O
different	O
orientations	O
,	O
but	O
some	O
conformations	O
traverse	O
as	O
far	O
as	O
the	O
tips	O
or	O
even	O
extend	O
over	O
the	O
side	O
of	O
the	O
cradle	B-site
(	O
Figs	O
.	O
3	O
,	O
4a	O
).	O

We	O
constructed	O
a	O
contact	B-evidence
map	I-evidence
of	O
the	O
complex	O
,	O
which	O
shows	O
the	O
frequency	O
of	O
interactions	O
for	O
chaperone	B-protein_type
-	O
substrate	O
residue	O
pairs	O
(	O
Fig	O
.	O
4	O
).	O

We	O
found	O
that	O
the	O
primary	O
interaction	B-site
sites	I-site
on	O
Spy	B-protein
reside	O
at	O
the	O
N	O
and	O
C	O
termini	O
(	O
Arg122	B-residue_name_number
,	O
Thr124	B-residue_name_number
,	O
and	O
Phe29	B-residue_name_number
)	O
as	O
well	O
as	O
on	O
the	O
concave	O
face	O
of	O
the	O
chaperone	B-protein_type
(	O
Arg61	B-residue_name_number
,	O
Arg43	B-residue_name_number
,	O
Lys47	B-residue_name_number
,	O
His96	B-residue_name_number
,	O
and	O
Met46	B-residue_name_number
).	O

The	O
Spy	B-site
-	I-site
contacting	I-site
residues	I-site
comprise	O
a	O
mixture	O
of	O
charged	O
,	O
polar	O
,	O
and	O
hydrophobic	O
residues	O
.	O

Surprisingly	O
,	O
we	O
noted	O
that	O
in	O
the	O
ensemble	O
,	O
Im76	B-mutant
-	I-mutant
45	I-mutant
interacts	O
with	O
only	O
38	O
%	O
of	O
the	O
hydrophobic	O
residues	O
in	O
the	O
Spy	B-protein
cradle	B-site
,	O
but	O
interacts	O
with	O
61	O
%	O
of	O
the	O
hydrophilic	O
residues	O
in	O
the	O
cradle	B-site
.	O

This	O
mixture	O
suggests	O
the	O
importance	O
of	O
both	O
electrostatic	O
and	O
hydrophobic	O
components	O
in	O
binding	O
the	O
Im76	B-mutant
-	I-mutant
45	I-mutant
ensemble	O
.	O

With	O
respect	O
to	O
the	O
substrate	O
,	O
we	O
observed	O
that	O
nearly	O
every	O
residue	O
in	O
Im76	B-mutant
-	I-mutant
45	I-mutant
is	O
in	O
contact	O
with	O
Spy	B-protein
(	O
Fig	O
.	O
4a	O
).	O

However	O
,	O
we	O
did	O
notice	O
that	O
despite	O
this	O
uniformity	O
,	O
regions	O
of	O
Im76	B-mutant
-	I-mutant
45	I-mutant
preferentially	O
interact	O
with	O
different	O
regions	O
in	O
Spy	B-protein
(	O
Fig	O
.	O
4b	O
).	O

For	O
example	O
,	O
the	O
N	B-structure_element
-	I-structure_element
terminal	I-structure_element
half	I-structure_element
of	O
Im76	B-mutant
-	I-mutant
45	I-mutant
binds	O
more	O
consistently	O
in	O
the	O
Spy	B-protein
cradle	B-site
,	O
whereas	O
the	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
half	I-structure_element
predominantly	O
binds	O
to	O
the	O
outer	O
edges	O
of	O
Spy	B-protein
’	O
s	O
concave	B-site
surface	I-site
.	O

Not	O
unexpectedly	O
,	O
we	O
found	O
that	O
as	O
Im76	B-mutant
-	I-mutant
45	I-mutant
progresses	O
from	O
the	O
unfolded	B-protein_state
to	O
the	O
native	B-protein_state
state	O
,	O
its	O
interactions	O
with	O
Spy	B-protein
shift	O
accordingly	O
.	O

Whereas	O
the	O
least	B-protein_state
-	I-protein_state
folded	I-protein_state
Im76	B-mutant
-	I-mutant
45	I-mutant
pose	O
in	O
the	O
ensemble	O
forms	O
the	O
most	O
hydrophobic	O
contacts	O
with	O
Spy	B-protein
(	O
Fig	O
.	O
3	O
),	O
the	O
two	O
most	B-protein_state
-	I-protein_state
folded	I-protein_state
conformations	O
form	O
the	O
fewest	O
hydrophobic	O
contacts	O
(	O
Fig	O
.	O
3	O
).	O

This	O
shift	O
in	O
contacts	O
is	O
likely	O
due	O
to	O
hydrophobic	O
residues	O
of	O
Im76	B-mutant
-	I-mutant
45	I-mutant
preferentially	O
forming	O
intra	O
-	O
molecular	O
contacts	O
upon	O
folding	O
(	O
i	O
.	O
e	O
.,	O
hydrophobic	O
collapse	O
),	O
effectively	O
removing	O
themselves	O
from	O
the	O
interaction	B-site
sites	I-site
.	O

The	O
diversity	O
of	O
conformations	O
and	O
binding	B-site
sites	I-site
observed	O
here	O
emphasizes	O
the	O
dynamic	O
and	O
heterogeneous	O
nature	O
of	O
the	O
chaperone	B-protein_type
-	O
substrate	O
ensemble	O
.	O

Although	O
we	O
do	O
not	O
yet	O
have	O
time	O
resolution	O
data	O
of	O
these	O
various	O
snapshots	O
of	O
Im76	B-mutant
-	I-mutant
45	I-mutant
,	O
this	O
ensemble	O
illustrates	O
how	O
a	O
substrate	O
samples	O
its	O
folding	O
landscape	O
while	O
bound	B-protein_state
to	I-protein_state
a	O
chaperone	B-protein_type
.	O

Spy	B-protein
changes	O
conformation	O
upon	O
substrate	O
binding	O

Comparing	O
the	O
structure	B-evidence
of	O
Spy	B-protein
in	O
its	O
substrate	B-protein_state
-	I-protein_state
bound	I-protein_state
and	O
apo	B-protein_state
states	O
revealed	O
that	O
the	O
Spy	B-protein
dimer	B-oligomeric_state
also	O
undergoes	O
significant	O
conformational	O
changes	O
upon	O
substrate	O
binding	O
(	O
Fig	O
.	O
5a	O
and	O
Supplementary	O
Movie	O
2	O
).	O

Upon	O
substrate	O
binding	O
,	O
the	O
Spy	B-protein
dimer	B-oligomeric_state
twists	O
9	O
°	O
about	O
its	O
center	O
relative	O
to	O
its	O
apo	B-protein_state
form	O
.	O

This	O
twist	O
yields	O
asymmetry	O
and	O
results	O
in	O
substantially	O
different	O
interaction	O
patterns	O
in	O
the	O
two	O
Spy	B-protein
monomers	B-oligomeric_state
(	O
Fig	O
.	O
4b	O
).	O

It	O
is	O
possible	O
that	O
this	O
twist	O
serves	O
to	O
increase	O
heterogeneity	O
in	O
Spy	B-protein
by	O
providing	O
more	O
binding	O
poses	O
.	O

Additionally	O
,	O
we	O
observed	O
that	O
the	O
linker	B-structure_element
region	I-structure_element
(	O
residues	O
47	B-residue_range
–	I-residue_range
57	I-residue_range
)	O
of	O
Spy	B-protein
,	O
which	O
participates	O
in	O
substrate	O
interaction	O
,	O
becomes	O
mostly	O
disordered	B-protein_state
upon	O
binding	O
the	O
substrate	O
.	O

This	O
increased	O
disorder	O
might	O
explain	O
how	O
Spy	B-protein
is	O
able	O
to	O
recognize	O
and	O
bind	O
different	O
substrates	O
and	O
/	O
or	O
differing	O
conformations	O
of	O
the	O
same	O
substrate	O
.	O

Importantly	O
,	O
we	O
observed	O
the	O
same	O
structural	O
changes	O
in	O
Spy	B-protein
regardless	O
of	O
which	O
of	O
the	O
four	O
substrates	O
was	O
bound	O
(	O
Fig	O
.	O
5b	O
,	O
Table	O
1	O
).	O

The	O
RMSD	B-evidence
between	O
the	O
well	B-protein_state
-	I-protein_state
folded	I-protein_state
sections	O
of	O
Spy	B-protein
in	O
the	O
four	O
chaperone	B-protein_type
-	O
substrate	O
complexes	O
was	O
very	O
small	O
,	O
less	O
than	O
0	O
.	O
3	O
Å	O
.	O
Combined	O
with	O
competition	B-experimental_method
experiments	I-experimental_method
showing	O
that	O
the	O
substrates	O
compete	O
in	O
solution	O
for	O
Spy	B-protein
binding	O
(	O
Fig	O
.	O
5c	O
and	O
Supplementary	O
Fig	O
.	O
8	O
),	O
we	O
conclude	O
that	O
all	O
the	O
tested	O
substrates	O
share	O
the	O
same	O
overall	O
Spy	B-site
binding	I-site
site	I-site
.	O

To	O
shed	O
light	O
on	O
how	O
chaperones	B-protein_type
interact	O
with	O
their	O
substrates	O
,	O
we	O
developed	O
a	O
novel	O
structural	O
biology	O
method	O
(	O
READ	B-experimental_method
)	O
and	O
applied	O
it	O
to	O
determine	O
a	O
conformational	B-evidence
ensemble	I-evidence
of	O
the	O
chaperone	B-protein_type
Spy	B-protein
bound	B-protein_state
to	I-protein_state
substrate	I-protein_state
.	O

As	O
a	O
substrate	O
,	O
we	O
used	O
Im76	B-mutant
-	I-mutant
45	I-mutant
,	O
the	O
chaperone	B-structure_element
-	I-structure_element
interacting	I-structure_element
portion	I-structure_element
of	O
the	O
protein	O
-	O
folding	O
model	O
protein	O
Im7	B-protein
.	O

In	O
the	O
chaperone	B-protein_state
-	I-protein_state
bound	I-protein_state
ensemble	O
,	O
Im76	B-mutant
-	I-mutant
45	I-mutant
samples	O
unfolded	B-protein_state
,	O
partially	O
folded	B-protein_state
,	O
and	O
native	B-protein_state
-	O
like	O
states	O
.	O

The	O
ensemble	O
provides	O
an	O
unprecedented	O
description	O
of	O
the	O
conformations	O
that	O
a	O
substrate	O
assumes	O
while	O
exploring	O
its	O
chaperone	B-protein_type
-	O
associated	O
folding	O
landscape	O
.	O

This	O
substrate	O
-	O
chaperone	B-protein_type
ensemble	O
helps	O
accomplish	O
the	O
longstanding	O
goal	O
of	O
obtaining	O
a	O
detailed	O
view	O
of	O
how	O
a	O
chaperone	B-protein_type
aids	O
protein	O
folding	O
.	O

We	O
recently	O
showed	O
that	O
Im7	B-protein
can	O
fold	O
while	O
remaining	O
continuously	B-protein_state
bound	I-protein_state
to	I-protein_state
Spy	B-protein
.	O

The	O
high	O
-	O
resolution	O
ensemble	B-evidence
obtained	O
here	O
now	O
provides	O
insight	O
into	O
exactly	O
how	O
this	O
occurs	O
.	O

The	O
structures	B-evidence
of	O
our	O
ensemble	B-evidence
agree	O
well	O
with	O
lower	O
-	O
resolution	O
crosslinking	O
data	O
,	O
which	O
indicate	O
that	O
chaperone	B-protein_type
-	O
substrate	O
interactions	O
primarily	O
occur	O
on	O
the	O
concave	B-site
surface	I-site
of	O
Spy	B-protein
.	O

The	O
ensemble	B-evidence
suggests	O
a	O
model	O
in	O
which	O
Spy	B-protein
provides	O
an	O
amphipathic	B-site
surface	I-site
that	O
allows	O
substrate	O
proteins	O
to	O
assume	O
different	O
conformations	O
while	O
bound	B-protein_state
to	I-protein_state
the	O
chaperone	B-protein_type
.	O

This	O
model	O
is	O
consistent	O
with	O
previous	O
studies	O
postulating	O
that	O
the	O
flexible	O
binding	O
of	O
chaperones	B-protein_type
allows	O
for	O
substrate	O
protein	O
folding	O
.	O

The	O
amphipathic	O
concave	B-site
surface	I-site
of	O
Spy	B-protein
likely	O
facilitates	O
this	O
flexible	O
binding	O
and	O
may	O
be	O
a	O
crucial	O
feature	O
for	O
Spy	B-protein
and	O
potentially	O
other	O
chaperones	B-protein_type
,	O
allowing	O
them	O
to	O
bind	O
multiple	O
conformations	O
of	O
many	O
different	O
substrates	O
.	O

In	O
contrast	O
to	O
Spy	B-protein
’	O
s	O
binding	B-site
hotspots	I-site
,	O
Im76	B-mutant
-	I-mutant
45	I-mutant
displays	O
substantially	O
less	O
specificity	O
in	O
its	O
binding	B-site
sites	I-site
.	O

Nearly	O
all	O
Im76	B-mutant
-	I-mutant
45	I-mutant
residues	O
come	O
in	O
contact	O
with	O
Spy	B-protein
.	O

Unfolded	B-protein_state
substrate	O
conformers	O
interact	O
with	O
Spy	B-protein
through	O
both	O
hydrophobic	O
and	O
hydrophilic	O
interactions	O
,	O
whereas	O
the	O
binding	O
of	O
native	B-protein_state
-	I-protein_state
like	I-protein_state
states	O
is	O
mainly	O
hydrophilic	O
.	O

This	O
trend	O
suggests	O
that	O
complex	O
formation	O
between	O
an	O
ATP	B-protein_state
-	I-protein_state
independent	I-protein_state
chaperone	B-protein_type
and	O
its	O
unfolded	B-protein_state
substrate	O
may	O
initially	O
involve	O
hydrophobic	O
interactions	O
,	O
effectively	O
shielding	O
the	O
exposed	O
aggregation	O
-	O
sensitive	O
hydrophobic	B-site
regions	I-site
in	O
the	O
substrate	O
.	O

Once	O
the	O
substrate	O
begins	O
to	O
fold	O
within	O
this	O
protected	O
environment	O
,	O
it	O
progressively	O
buries	O
its	O
own	O
hydrophobic	O
residues	O
,	O
and	O
its	O
interactions	O
with	O
the	O
chaperone	B-protein_type
shift	O
towards	O
becoming	O
more	O
electrostatic	O
.	O

Notably	O
,	O
the	O
most	O
frequent	O
contacts	O
between	O
Spy	B-protein
and	O
Im76	B-mutant
-	I-mutant
45	I-mutant
are	O
charge	O
-	O
charge	O
interactions	O
.	O

The	O
negatively	O
charged	O
Im7	B-protein
residues	O
Glu21	B-residue_name_number
,	O
Asp32	B-residue_name_number
,	O
and	O
Asp35	B-residue_name_number
reside	O
on	O
the	O
surface	O
of	O
Im7	B-protein
and	O
form	O
interactions	O
with	O
Spy	B-protein
’	O
s	O
positively	O
charged	O
cradle	B-site
in	O
both	O
the	O
unfolded	B-protein_state
and	O
native	B-protein_state
-	I-protein_state
like	I-protein_state
states	O
.	O

Residues	O
Asp32	B-residue_name_number
and	O
Asp35	B-residue_name_number
are	O
close	O
to	O
each	O
other	O
in	O
the	O
folded	B-protein_state
state	O
of	O
Im7	B-protein
.	O

This	O
proximity	O
likely	O
causes	O
electrostatic	O
repulsion	O
that	O
destabilizes	O
Im7	B-protein
’	O
s	O
native	B-protein_state
state	O
.	O

Interaction	O
with	O
Spy	B-protein
’	O
s	O
positively	O
-	O
charged	O
residues	O
likely	O
relieves	O
the	O
charge	O
repulsion	O
between	O
Asp32	B-residue_name_number
and	O
Asp35	B-residue_name_number
,	O
promoting	O
their	O
compaction	O
into	O
a	O
helical	B-protein_state
conformation	I-protein_state
.	O

As	O
inter	O
-	O
molecular	O
hydrophobic	O
interactions	O
between	O
Spy	B-protein
and	O
the	O
substrate	O
become	O
progressively	O
replaced	O
by	O
intra	O
-	O
molecular	O
interactions	O
within	O
the	O
substrate	O
,	O
the	O
affinity	O
between	O
chaperone	B-protein_type
and	O
substrates	O
could	O
decrease	O
,	O
eventually	O
leading	O
to	O
release	O
of	O
the	O
folded	B-protein_state
client	O
protein	O
.	O

Recently	O
,	O
we	O
employed	O
a	O
genetic	B-experimental_method
selection	I-experimental_method
system	I-experimental_method
to	O
improve	O
the	O
chaperone	B-protein_type
activity	O
of	O
Spy	B-protein
.	O

This	O
selection	O
resulted	O
in	O
“	O
Super	O
Spy	B-protein
”	O
variants	B-protein_state
that	O
were	O
more	O
effective	O
at	O
both	O
preventing	O
aggregation	O
and	O
promoting	O
protein	O
folding	O
.	O

In	O
conjunction	O
with	O
our	O
bound	B-protein_state
Im76	B-mutant
-	I-mutant
45	I-mutant
ensemble	B-evidence
,	O
these	O
mutants	O
now	O
allowed	O
us	O
to	O
investigate	O
structural	O
features	O
important	O
to	O
chaperone	B-protein_type
function	O
.	O

Previous	O
analysis	O
revealed	O
that	O
the	O
Super	O
Spy	B-protein
variants	B-protein_state
either	O
bound	B-protein_state
Im7	B-protein
tighter	O
than	O
WT	B-protein_state
Spy	B-protein
,	O
increased	O
chaperone	B-protein_type
flexibility	O
as	O
measured	O
via	O
H	B-experimental_method
/	I-experimental_method
D	I-experimental_method
exchange	I-experimental_method
,	O
or	O
both	O
.	O

Our	O
ensemble	B-evidence
revealed	O
that	O
two	O
of	O
the	O
Super	O
Spy	B-protein
mutations	B-protein_state
(	O
H96L	B-mutant
and	O
Q100L	B-mutant
)	O
form	O
part	O
of	O
the	O
chaperone	B-site
contact	I-site
surface	I-site
that	O
binds	O
to	O
Im76	B-mutant
-	I-mutant
45	I-mutant
(	O
Fig	O
.	O
4a	O
).	O

Moreover	O
,	O
our	O
co	B-evidence
-	I-evidence
structure	I-evidence
suggests	O
that	O
the	O
L32P	B-mutant
substitution	O
,	O
which	O
increases	O
Spy	B-protein
’	O
s	O
flexibility	O
,	O
could	O
operate	O
by	O
unhinging	O
the	O
N	B-structure_element
-	I-structure_element
terminal	I-structure_element
helix	I-structure_element
and	O
effectively	O
expanding	O
the	O
size	O
of	O
the	O
disordered	B-protein_state
linker	B-structure_element
.	O

This	O
possibility	O
is	O
supported	O
by	O
the	O
Spy	B-protein
:	O
substrate	O
structures	B-evidence
,	O
in	O
which	O
the	O
linker	B-structure_element
region	I-structure_element
becomes	O
more	O
flexible	O
compared	O
to	O
the	O
apo	B-protein_state
state	O
(	O
Fig	O
.	O
6a	O
).	O

By	O
sampling	O
multiple	O
conformations	O
,	O
this	O
linker	B-structure_element
region	I-structure_element
may	O
allow	O
diverse	O
substrate	O
conformations	O
to	O
be	O
accommodated	O
.	O

Other	O
Super	O
Spy	B-protein
mutations	B-protein_state
(	O
F115I	B-mutant
and	O
F115L	B-mutant
)	O
caused	O
increased	O
flexibility	O
but	O
not	O
tighter	O
substrate	O
binding	O
.	O

This	O
residue	O
does	O
not	O
directly	O
contact	O
Im76	B-mutant
-	I-mutant
45	I-mutant
in	O
our	O
READ	B-experimental_method
-	O
derived	O
ensemble	B-evidence
.	O

Instead	O
,	O
when	O
Spy	B-protein
is	O
bound	B-protein_state
to	I-protein_state
substrate	O
,	O
F115	B-residue_name_number
engages	O
in	O
close	O
CH	O
⋯	O
π	O
hydrogen	O
bonds	O
with	O
Tyr104	B-residue_name_number
(	O
Fig	O
.	O
6b	O
).	O

This	O
interaction	O
presumably	O
reduces	O
the	O
mobility	O
of	O
the	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
helix	I-structure_element
.	O

The	O
F115I	B-mutant
/	O
L	B-mutant
substitutions	O
would	O
replace	O
these	O
hydrogen	O
bonds	O
with	O
hydrophobic	O
interactions	O
that	O
have	O
little	O
angular	O
dependence	O
.	O

As	O
a	O
result	O
,	O
the	O
C	O
-	O
terminus	O
,	O
and	O
possibly	O
also	O
the	O
flexible	B-protein_state
linker	B-structure_element
,	O
is	O
likely	O
to	O
become	O
more	O
flexible	O
and	O
thus	O
more	O
accommodating	O
of	O
different	O
conformations	O
of	O
substrates	O
.	O

Overall	O
,	O
comparison	O
of	O
our	O
ensemble	B-evidence
to	O
the	O
Super	O
Spy	B-protein
variants	B-protein_state
provides	O
specific	O
examples	O
to	O
corroborate	O
the	O
importance	O
of	O
conformational	O
flexibility	O
in	O
chaperone	B-protein_type
-	O
substrate	O
interactions	O
.	O

Despite	O
extensive	O
studies	O
,	O
exactly	O
how	O
complex	O
chaperone	B-protein_type
machines	O
help	O
proteins	O
fold	O
remains	O
controversial	O
.	O

Our	O
study	O
indicates	O
that	O
the	O
chaperone	B-protein_type
Spy	B-protein
employs	O
a	O
simple	O
surface	O
binding	O
approach	O
that	O
allows	O
the	O
substrate	O
to	O
explore	O
various	O
conformations	O
and	O
form	O
transiently	O
favorable	O
interactions	O
while	O
being	O
protected	O
from	O
aggregation	O
.	O

We	O
speculate	O
that	O
many	O
other	O
chaperones	B-protein_type
could	O
utilize	O
a	O
similar	O
strategy	O
.	O

ATP	B-chemical
and	O
co	O
-	O
chaperone	B-protein_type
dependencies	O
may	O
have	O
emerged	O
later	O
through	O
evolution	O
to	O
better	O
modulate	O
and	O
control	O
chaperone	B-protein_type
action	O
.	O

In	O
addition	O
to	O
insights	O
into	O
chaperone	B-protein_type
function	O
,	O
this	O
work	O
presents	O
a	O
new	O
method	O
for	O
determining	O
heterogeneous	O
structural	O
ensembles	O
via	O
a	O
hybrid	O
methodology	O
of	O
X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
and	O
computational	B-experimental_method
modeling	I-experimental_method
.	O

Heterogeneous	O
dynamic	O
complexes	O
or	O
disordered	B-protein_state
regions	O
of	O
single	O
proteins	O
,	O
once	O
considered	O
solely	O
approachable	O
by	O
NMR	B-experimental_method
spectroscopy	I-experimental_method
,	O
can	O
now	O
be	O
visualized	O
through	O
X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
.	O

Crystallographic	O
data	O
and	O
ensemble	O
selection	O
.	O
(	O
a	O
)	O
2mFo	B-evidence
−	I-evidence
DFc	I-evidence
omit	I-evidence
map	I-evidence
of	O
residual	O
Im76	B-mutant
-	I-mutant
45	I-mutant
and	O
flexible	B-structure_element
linker	I-structure_element
electron	B-evidence
density	I-evidence
contoured	O
at	O
0	O
.	O
5	O
σ	O
.	O

This	O
is	O
the	O
residual	O
density	B-evidence
that	O
is	O
used	O
in	O
the	O
READ	B-experimental_method
selection	O
.	O

(	O
b	O
)	O
Composites	O
of	O
iodine	B-chemical
positions	O
detected	O
from	O
anomalous	B-evidence
signals	I-evidence
using	O
pI	B-chemical
-	I-chemical
Phe	I-chemical
substitutions	B-experimental_method
,	O
colored	O
and	O
numbered	O
by	O
sequence	O
.	O

Multiple	O
iodine	B-chemical
positions	O
were	O
detected	O
for	O
most	O
residues	O
.	O

Agreement	O
to	O
the	O
residual	O
Im76	B-mutant
-	I-mutant
45	I-mutant
electron	B-evidence
density	I-evidence
(	O
c	O
)	O
and	O
anomalous	B-evidence
iodine	I-evidence
signals	I-evidence
(	O
d	O
)	O
for	O
ensembles	O
of	O
varying	O
size	O
generated	O
by	O
randomly	O
choosing	O
from	O
the	O
MD	B-experimental_method
pool	O
(	O
blue	O
)	O
and	O
from	O
the	O
selection	O
procedure	O
(	O
black	O
).	O

The	O
cost	B-evidence
function	I-evidence
,	O
χ2	B-evidence
,	O
decreases	O
as	O
the	O
agreement	O
to	O
the	O
experimental	O
data	O
increases	O
and	O
is	O
defined	O
in	O
the	O
Online	O
Methods	O
.	O

Flowchart	O
of	O
the	O
READ	B-experimental_method
sample	B-experimental_method
-	I-experimental_method
and	I-experimental_method
-	I-experimental_method
select	I-experimental_method
process	O
.	O

Spy	B-complex_assembly
:	I-complex_assembly
Im76	I-complex_assembly
-	I-complex_assembly
45	I-complex_assembly
ensemble	O
,	O
arranged	O
by	O
RMSD	B-evidence
to	O
native	B-protein_state
state	O
of	O
Im76	B-mutant
-	I-mutant
45	I-mutant
.	O
Although	O
the	O
six	O
-	O
membered	O
ensemble	O
from	O
the	O
READ	B-experimental_method
selection	O
should	O
be	O
considered	O
only	O
as	O
an	O
ensemble	O
,	O
for	O
clarity	O
,	O
the	O
individual	O
conformers	O
are	O
shown	O
separately	O
here	O
.	O

Spy	B-protein
is	O
depicted	O
as	O
a	O
gray	O
surface	O
and	O
the	O
Im76	B-mutant
-	I-mutant
45	I-mutant
conformer	O
is	O
shown	O
as	O
orange	O
balls	O
.	O

Atoms	O
that	O
were	O
either	O
not	O
directly	O
selected	O
in	O
the	O
READ	B-experimental_method
procedure	O
,	O
or	O
whose	O
position	O
could	O
not	O
be	O
justified	O
based	O
on	O
agreement	O
with	O
the	O
residual	B-evidence
electron	I-evidence
density	I-evidence
were	O
removed	O
,	O
leading	O
to	O
non	O
-	O
contiguous	O
sections	O
.	O

Dashed	O
lines	O
connect	O
non	O
-	O
contiguous	O
segments	O
of	O
the	O
Im76	B-mutant
-	I-mutant
45	I-mutant
substrate	O
.	O

Residues	O
of	O
the	O
Spy	B-protein
flexible	O
linker	B-structure_element
region	I-structure_element
that	O
fit	O
the	O
residual	B-evidence
electron	I-evidence
density	I-evidence
are	O
shown	O
as	O
larger	O
gray	O
spheres	O
.	O

Shown	O
below	O
each	O
ensemble	O
member	O
is	O
the	O
RMSD	B-evidence
of	O
each	O
conformer	O
to	O
the	O
native	B-protein_state
state	O
of	O
Im76	B-mutant
-	I-mutant
45	I-mutant
,	O
as	O
well	O
as	O
the	O
percentage	O
of	O
contacts	O
between	O
Im76	B-mutant
-	I-mutant
45	I-mutant
and	O
Spy	B-protein
that	O
are	O
hydrophobic	O
.	O

Contact	B-evidence
maps	I-evidence
of	O
Spy	B-complex_assembly
:	I-complex_assembly
Im76	I-complex_assembly
-	I-complex_assembly
45	I-complex_assembly
complex	O
.	O

(	O
a	O
)	O
Spy	B-complex_assembly
:	I-complex_assembly
Im76	I-complex_assembly
-	I-complex_assembly
45	I-complex_assembly
contact	B-evidence
map	I-evidence
projected	O
onto	O
the	O
bound	B-protein_state
Spy	B-protein
dimer	B-oligomeric_state
(	O
above	O
)	O
and	O
Im76	B-mutant
-	I-mutant
45	I-mutant
(	O
below	O
)	O
structures	B-evidence
.	O

For	O
clarity	O
,	O
Im76	B-mutant
-	I-mutant
45	I-mutant
is	O
represented	O
with	O
a	O
single	O
conformation	O
.	O

The	O
frequency	O
plotted	O
is	O
calculated	O
as	O
the	O
average	O
contact	B-evidence
frequency	I-evidence
from	O
Spy	B-protein
to	O
every	O
residue	O
of	O
Im76	B-mutant
-	I-mutant
45	I-mutant
and	O
vice	O
-	O
versa	O
.	O

As	O
the	O
residues	O
involved	O
in	O
contacts	O
are	O
more	O
evenly	O
distributed	O
in	O
Im76	B-mutant
-	I-mutant
45	I-mutant
compared	O
to	O
Spy	B-protein
,	O
its	O
contact	B-evidence
map	I-evidence
was	O
amplified	O
.	O
(	O
b	O
)	O
Detailed	O
contact	B-evidence
maps	I-evidence
of	O
Spy	B-complex_assembly
:	I-complex_assembly
Im76	I-complex_assembly
-	I-complex_assembly
45	I-complex_assembly
.	O

Contacts	O
to	O
the	O
two	O
Spy	B-protein
monomers	B-oligomeric_state
are	O
depicted	O
separately	O
.	O

Note	O
that	O
the	O
flexible	B-protein_state
linker	B-structure_element
region	I-structure_element
of	O
Spy	B-protein
(	O
residues	O
47	B-residue_range
–	I-residue_range
57	I-residue_range
)	O
is	O
not	O
represented	O
in	O
the	O
2D	O
contact	B-evidence
maps	I-evidence
.	O

Spy	B-protein
conformation	O
changes	O
upon	O
substrate	O
binding	O
.	O

(	O
a	O
)	O
Overlay	B-experimental_method
of	O
apo	B-protein_state
Spy	B-protein
(	O
PDB	O
ID	O
:	O
3O39	O
,	O
gray	O
)	O
and	O
bound	B-protein_state
Spy	B-protein
(	O
green	O
).	O
(	O
b	O
)	O
Overlay	B-experimental_method
of	O
WT	B-protein_state
Spy	B-protein
bound	B-protein_state
to	I-protein_state
Im76	B-mutant
-	I-mutant
45	I-mutant
(	O
green	O
),	O
H96L	B-mutant
Spy	B-protein
bound	B-protein_state
to	I-protein_state
Im7	B-protein
L18A	B-mutant
L19	B-mutant
AL13A	I-mutant
(	O
blue	O
),	O
H96L	B-mutant
Spy	B-protein
bound	B-protein_state
to	I-protein_state
WT	B-protein_state
Im7	B-protein
(	O
yellow	O
),	O
and	O
WT	B-protein_state
Spy	B-protein
bound	B-protein_state
to	I-protein_state
casein	B-chemical
(	O
salmon	O
).	O
(	O
c	O
)	O
Competition	B-experimental_method
assay	I-experimental_method
showing	O
Im76	B-mutant
-	I-mutant
45	I-mutant
competes	O
with	O
Im7	B-protein
L18A	B-mutant
L19A	B-mutant
L37A	B-mutant
H40W	B-mutant
for	O
the	O
same	O
binding	B-site
site	I-site
on	O
Spy	B-protein
(	O
further	O
substrate	B-experimental_method
competition	I-experimental_method
assays	I-experimental_method
are	O
shown	O
in	O
Supplementary	O
Fig	O
.	O
8	O
).	O

Flexibility	O
of	O
Spy	B-protein
linker	B-structure_element
region	I-structure_element
and	O
effect	O
of	O
Super	O
Spy	B-protein
mutants	O
.	O
(	O
a	O
)	O
The	O
Spy	B-protein
linker	B-structure_element
region	I-structure_element
adopts	O
one	O
dominant	O
conformation	O
in	O
its	O
apo	B-protein_state
state	O
(	O
PDB	O
ID	O
3039	O
,	O
gray	O
),	O
but	O
expands	O
and	O
adopts	O
multiple	O
conformations	O
in	O
bound	B-protein_state
states	O
(	O
green	O
).	O

(	O
b	O
)	O
F115	B-residue_name_number
and	O
L32	B-residue_name_number
tether	O
Spy	B-protein
’	O
s	O
linker	B-structure_element
region	I-structure_element
to	O
its	O
cradle	B-site
,	O
decreasing	O
Spy	B-protein
activity	O
by	O
limiting	O
linker	B-structure_element
region	I-structure_element
flexibility	O
.	O

The	O
Super	O
Spy	B-protein
mutants	O
F115L	B-mutant
,	O
F115I	B-mutant
,	O
and	O
L32P	B-mutant
are	O
proposed	O
to	O
gain	O
activity	O
by	O
increasing	O
the	O
flexibility	O
or	O
size	O
of	O
this	O
linker	B-structure_element
region	I-structure_element
.	O

L32	B-residue_name_number
,	O
F115	B-residue_name_number
,	O
and	O
Y104	B-residue_name_number
are	O
rendered	O
in	O
purple	O
to	O
illustrate	O
residues	O
that	O
are	O
most	O
affected	O
by	O
Super	O
Spy	B-protein
mutations	B-protein_state
;	O
CH	O
⋯	O
π	O
hydrogen	O
bonds	O
are	O
depicted	O
by	O
orange	O
dashes	O
.	O

Structural	O
diversity	O
in	O
a	O
human	B-species
antibody	B-protein_type
germline	O
library	O

To	O
support	O
antibody	B-protein_type
therapeutic	O
development	O
,	O
the	O
crystal	B-evidence
structures	I-evidence
of	O
a	O
set	O
of	O
16	O
germline	O
variants	O
composed	O
of	O
4	O
different	O
kappa	B-structure_element
light	I-structure_element
chains	I-structure_element
paired	O
with	O
4	O
different	O
heavy	B-structure_element
chains	I-structure_element
have	O
been	O
determined	O
.	O

All	O
four	O
heavy	B-structure_element
chains	I-structure_element
of	O
the	O
antigen	B-structure_element
-	I-structure_element
binding	I-structure_element
fragments	I-structure_element
(	O
Fabs	B-structure_element
)	O
have	O
the	O
same	O
complementarity	B-structure_element
-	I-structure_element
determining	I-structure_element
region	I-structure_element
(	O
CDR	B-structure_element
)	O
H3	B-structure_element
that	O
was	O
reported	O
in	O
an	O
earlier	O
Fab	B-structure_element
structure	B-evidence
.	O

The	O
structure	B-experimental_method
analyses	I-experimental_method
include	O
comparisons	O
of	O
the	O
overall	O
structures	B-evidence
,	O
canonical	O
structures	B-evidence
of	O
the	O
CDRs	B-structure_element
and	O
the	O
VH	B-site
:	I-site
VL	I-site
packing	I-site
interactions	I-site
.	O

The	O
CDR	B-structure_element
conformations	O
for	O
the	O
most	O
part	O
are	O
tightly	O
clustered	O
,	O
especially	O
for	O
the	O
ones	O
with	O
shorter	O
lengths	O
.	O

The	O
longer	B-protein_state
CDRs	B-structure_element
with	O
tandem	O
glycines	B-residue_name
or	O
serines	B-residue_name
have	O
more	O
conformational	O
diversity	O
than	O
the	O
others	O
.	O

CDR	B-structure_element
H3	B-structure_element
,	O
despite	O
having	O
the	O
same	O
amino	O
acid	O
sequence	O
,	O
exhibits	O
the	O
largest	O
conformational	O
diversity	O
.	O

About	O
half	O
of	O
the	O
structures	B-evidence
have	O
CDR	B-structure_element
H3	B-structure_element
conformations	O
similar	O
to	O
that	O
of	O
the	O
parent	O
;	O
the	O
others	O
diverge	O
significantly	O
.	O

One	O
conclusion	O
is	O
that	O
the	O
CDR	B-structure_element
H3	B-structure_element
conformations	O
are	O
influenced	O
by	O
both	O
their	O
amino	O
acid	O
sequence	O
and	O
their	O
structural	O
environment	O
determined	O
by	O
the	O
heavy	B-structure_element
and	O
light	B-structure_element
chain	I-structure_element
pairing	O
.	O

The	O
stem	B-structure_element
regions	I-structure_element
of	O
14	O
of	O
the	O
variant	O
pairs	O
are	O
in	O
the	O
‘	O
kinked	B-protein_state
’	O
conformation	O
,	O
and	O
only	O
2	O
are	O
in	O
the	O
extended	B-protein_state
conformation	O
.	O

The	O
packing	O
of	O
the	O
VH	B-structure_element
and	O
VL	B-structure_element
domains	O
is	O
consistent	O
with	O
our	O
knowledge	O
of	O
antibody	B-protein_type
structure	B-evidence
,	O
and	O
the	O
tilt	B-evidence
angles	I-evidence
between	O
these	O
domains	O
cover	O
a	O
range	O
of	O
11	O
degrees	O
.	O

Two	O
of	O
16	O
structures	B-evidence
showed	O
particularly	O
large	O
variations	O
in	O
the	O
tilt	B-evidence
angles	I-evidence
when	O
compared	O
with	O
the	O
other	O
pairings	O
.	O

The	O
structures	B-evidence
and	O
their	O
analyses	O
provide	O
a	O
rich	O
foundation	O
for	O
future	O
antibody	B-protein_type
modeling	O
and	O
engineering	O
efforts	O
.	O

At	O
present	O
,	O
therapeutic	O
antibodies	B-protein_type
are	O
the	O
largest	O
class	O
of	O
biotherapeutic	O
proteins	O
that	O
are	O
in	O
clinical	O
trials	O
.	O

The	O
use	O
of	O
monoclonal	O
antibodies	B-protein_type
as	O
therapeutics	O
began	O
in	O
the	O
early	O
1980s	O
,	O
and	O
their	O
composition	O
has	O
transitioned	O
from	O
murine	B-taxonomy_domain
antibodies	B-protein_type
to	O
generally	O
less	O
immunogenic	O
humanized	O
and	O
human	B-species
antibodies	B-protein_type
.	O

The	O
technologies	O
currently	O
used	O
to	O
obtain	O
human	B-species
antibodies	B-protein_type
include	O
transgenic	O
mice	B-taxonomy_domain
containing	O
human	B-species
antibody	B-protein_type
repertoires	O
,	O
cloning	O
directly	O
from	O
human	B-species
B	O
cells	O
,	O
and	O
in	B-experimental_method
vitro	I-experimental_method
selection	I-experimental_method
from	O
antibody	B-experimental_method
libraries	I-experimental_method
using	O
various	O
display	O
technologies	O
.	O

Once	O
a	O
candidate	O
antibody	B-protein_type
is	O
identified	O
,	O
protein	B-experimental_method
engineering	I-experimental_method
is	O
usually	O
required	O
to	O
produce	O
a	O
molecule	O
with	O
the	O
right	O
biophysical	O
and	O
functional	O
properties	O
.	O

All	O
engineering	O
efforts	O
are	O
guided	O
by	O
our	O
understanding	O
of	O
the	O
atomic	B-evidence
structures	I-evidence
of	O
antibodies	B-protein_type
.	O

In	O
such	O
efforts	O
,	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
specific	O
antibody	B-protein_type
may	O
not	O
be	O
available	O
,	O
but	O
modeling	O
can	O
be	O
used	O
to	O
guide	O
the	O
engineering	O
efforts	O
.	O

Today	O
'	O
s	O
antibody	B-protein_type
modeling	O
approaches	O
,	O
which	O
normally	O
focus	O
on	O
the	O
variable	B-structure_element
region	I-structure_element
,	O
are	O
being	O
developed	O
by	O
the	O
application	O
of	O
structural	O
principles	O
and	O
insights	O
that	O
are	O
evolving	O
as	O
our	O
knowledge	O
of	O
antibody	B-protein_type
structures	B-evidence
continues	O
to	O
expand	O
.	O

Our	O
current	O
structural	O
knowledge	O
of	O
antibodies	B-protein_type
is	O
based	O
on	O
a	O
multitude	O
of	O
studies	O
that	O
used	O
many	O
techniques	O
to	O
gain	O
insight	O
into	O
the	O
functional	O
and	O
structural	O
properties	O
of	O
this	O
class	O
of	O
macromolecule	O
.	O

Five	O
different	O
antibody	B-protein_type
isotypes	O
occur	O
,	O
IgG	B-protein
,	O
IgD	B-protein
,	O
IgE	B-protein
,	O
IgA	B-protein
and	O
IgM	B-protein
,	O
and	O
each	O
isotype	O
has	O
a	O
unique	O
role	O
in	O
the	O
adaptive	O
immune	O
system	O
.	O

IgG	B-protein
,	O
IgD	B-protein
and	O
IgE	B-protein
isotypes	O
are	O
composed	O
of	O
2	O
heavy	B-structure_element
chains	I-structure_element
(	O
HCs	B-structure_element
)	O
and	O
2	O
light	B-structure_element
chains	I-structure_element
(	O
LCs	B-structure_element
)	O
linked	O
through	O
disulfide	B-ptm
bonds	I-ptm
,	O
while	O
IgA	B-protein
and	O
IgM	B-protein
are	O
double	O
and	O
quintuple	O
versions	O
of	O
antibodies	B-protein_type
,	O
respectively	O
.	O

Isotypes	O
IgG	B-protein
,	O
IgD	B-protein
and	O
IgA	B-protein
each	O
have	O
4	O
domains	O
,	O
one	O
variable	B-structure_element
(	O
V	B-structure_element
)	O
and	O
3	O
constant	B-structure_element
(	O
C	B-structure_element
)	O
domains	O
,	O
while	O
IgE	B-protein
and	O
IgM	B-protein
each	O
have	O
the	O
same	O
4	O
domains	O
along	O
with	O
an	O
additional	O
C	B-structure_element
domain	I-structure_element
.	O

These	O
multimeric	O
forms	O
are	O
linked	O
with	O
an	O
additional	O
J	B-structure_element
chain	O
.	O

The	O
LCs	B-structure_element
that	O
associate	O
with	O
the	O
HCs	B-structure_element
are	O
divided	O
into	O
2	O
functionally	O
indistinguishable	O
classes	O
,	O
κ	B-structure_element
and	O
λ	B-structure_element
.	O

Both	O
κ	B-structure_element
and	O
λ	B-structure_element
polypeptide	O
chains	O
are	O
composed	O
of	O
a	O
single	O
V	B-structure_element
domain	I-structure_element
and	O
a	O
single	O
C	B-structure_element
domain	I-structure_element
.	O

The	O
heavy	B-structure_element
and	O
light	B-structure_element
chains	I-structure_element
are	O
composed	O
of	O
structural	B-structure_element
domains	I-structure_element
that	O
have	O
∼	B-residue_range
110	I-residue_range
amino	I-residue_range
acid	I-residue_range
residues	I-residue_range
.	O

These	O
domains	O
have	O
a	O
common	O
folding	O
pattern	O
often	O
referred	O
to	O
as	O
the	O
“	O
immunoglobulin	B-structure_element
fold	I-structure_element
,”	O
formed	O
by	O
the	O
packing	O
together	O
of	O
2	O
anti	B-structure_element
-	I-structure_element
parallel	I-structure_element
β	I-structure_element
-	I-structure_element
sheets	I-structure_element
.	O

All	O
immunoglobulin	B-protein_type
chains	I-protein_type
have	O
an	O
N	O
-	O
terminal	O
V	B-structure_element
domain	I-structure_element
followed	O
by	O
1	O
to	O
4	O
C	B-structure_element
domains	I-structure_element
,	O
depending	O
upon	O
the	O
chain	O
type	O
.	O

In	O
antibodies	B-protein_type
,	O
the	O
heavy	B-structure_element
and	I-structure_element
light	I-structure_element
chain	I-structure_element
V	B-structure_element
domains	I-structure_element
pack	O
together	O
forming	O
the	O
antigen	B-site
combining	I-site
site	I-site
.	O

This	O
site	O
,	O
which	O
interacts	O
with	O
the	O
antigen	O
(	O
or	O
target	O
),	O
is	O
the	O
focus	O
of	O
current	O
antibody	B-protein_type
modeling	O
efforts	O
.	O

This	O
interaction	B-site
site	I-site
is	O
composed	O
of	O
6	O
complementarity	B-structure_element
-	I-structure_element
determining	I-structure_element
regions	I-structure_element
(	O
CDRs	B-structure_element
)	O
that	O
were	O
identified	O
in	O
early	O
antibody	B-experimental_method
amino	I-experimental_method
acid	I-experimental_method
sequence	I-experimental_method
analyses	I-experimental_method
to	O
be	O
hypervariable	B-protein_state
in	O
nature	O
,	O
and	O
thus	O
are	O
responsible	O
for	O
the	O
sequence	O
and	O
structural	O
diversity	O
of	O
our	O
antibody	B-protein_type
repertoire	O
.	O

The	O
sequence	O
diversity	O
of	O
the	O
CDR	B-structure_element
regions	I-structure_element
presents	O
a	O
substantial	O
challenge	O
to	O
antibody	B-protein_type
modeling	O
.	O

However	O
,	O
an	O
initial	O
structural	B-experimental_method
analysis	I-experimental_method
of	O
the	O
combining	B-site
sites	I-site
of	O
the	O
small	O
set	O
of	O
structures	B-evidence
of	O
immunoglobulin	O
fragments	O
available	O
in	O
the	O
1980s	O
found	O
that	O
5	O
of	O
the	O
6	O
hypervariable	B-structure_element
loops	I-structure_element
or	O
CDRs	B-structure_element
had	O
canonical	O
structures	O
(	O
a	O
limited	O
set	O
of	O
main	O
-	O
chain	O
conformations	O
).	O

A	O
CDR	B-structure_element
canonical	O
structure	O
is	O
defined	O
by	O
its	O
length	O
and	O
conserved	O
residues	O
located	O
in	O
the	O
hypervariable	B-structure_element
loop	I-structure_element
and	O
framework	B-structure_element
residues	I-structure_element
(	O
V	B-structure_element
-	I-structure_element
region	I-structure_element
residues	O
that	O
are	O
not	O
part	O
of	O
the	O
CDRs	B-structure_element
).	O

Furthermore	O
,	O
studies	O
of	O
antibody	B-protein_type
sequences	O
revealed	O
that	O
the	O
total	O
number	O
of	O
canonical	O
structures	O
are	O
limited	O
for	O
each	O
CDR	B-structure_element
,	O
indicating	O
possibly	O
that	O
antigen	O
recognition	O
may	O
be	O
affected	O
by	O
structural	O
restrictions	O
at	O
the	O
antigen	B-site
-	I-site
binding	I-site
site	I-site
.	O

Later	O
studies	O
found	O
that	O
the	O
CDR	B-structure_element
loop	I-structure_element
length	O
is	O
the	O
primary	O
determining	O
factor	O
of	O
antigen	B-site
-	I-site
binding	I-site
site	I-site
topography	O
because	O
it	O
is	O
the	O
primary	O
factor	O
for	O
determining	O
a	O
canonical	O
structure	O
.	O

Additional	O
efforts	O
have	O
led	O
to	O
our	O
current	O
understanding	O
that	O
the	O
LC	B-structure_element
CDRs	B-structure_element
L1	B-structure_element
,	O
L2	B-structure_element
,	O
and	O
L3	B-structure_element
have	O
preferred	O
sets	O
of	O
canonical	O
structures	O
based	O
on	O
length	O
and	O
amino	O
acid	O
sequence	O
composition	O
.	O

This	O
was	O
also	O
found	O
to	O
be	O
the	O
case	O
for	O
the	O
H1	B-structure_element
and	O
H2	B-structure_element
CDRs	B-structure_element
.	O

Classification	O
schemes	O
for	O
the	O
canonical	O
structures	O
of	O
these	O
5	O
CDRs	B-structure_element
have	O
emerged	O
and	O
evolved	O
as	O
the	O
number	O
of	O
depositions	O
in	O
the	O
Protein	O
Data	O
Bank	O
of	O
Fab	B-structure_element
fragments	O
of	O
antibodies	B-protein_type
grow	O
.	O

Recently	O
,	O
a	O
comprehensive	O
CDR	B-structure_element
classification	O
scheme	O
was	O
reported	O
identifying	O
72	O
clusters	O
of	O
conformations	O
observed	O
in	O
antibody	B-protein_type
structures	B-evidence
.	O

The	O
knowledge	O
and	O
predictability	O
of	O
these	O
CDR	B-structure_element
canonical	O
structures	B-evidence
have	O
greatly	O
advanced	O
antibody	B-protein_type
modeling	O
efforts	O
.	O

In	O
contrast	O
to	O
CDRs	B-structure_element
L1	B-structure_element
,	O
L2	B-structure_element
,	O
L3	B-structure_element
,	O
H1	B-structure_element
and	O
H2	B-structure_element
,	O
no	O
canonical	O
structures	B-evidence
have	O
been	O
observed	O
for	O
CDR	B-structure_element
H3	B-structure_element
,	O
which	O
is	O
the	O
most	O
variable	O
in	O
length	O
and	O
amino	O
acid	O
sequence	O
.	O

Some	O
clustering	O
of	O
conformations	O
was	O
observed	O
for	O
the	O
shortest	O
lengths	O
;	O
however	O
,	O
for	O
the	O
longer	O
loops	B-structure_element
,	O
only	O
the	O
portions	O
nearest	O
the	O
framework	B-structure_element
(	O
torso	B-structure_element
,	O
stem	B-structure_element
or	O
anchor	B-structure_element
region	I-structure_element
)	O
were	O
found	O
to	O
have	O
defined	O
conformations	O
.	O

In	O
the	O
torso	B-structure_element
region	I-structure_element
,	O
2	O
primary	O
groups	O
could	O
be	O
identified	O
,	O
which	O
led	O
to	O
sequence	O
-	O
based	O
rules	O
that	O
can	O
predict	O
with	O
some	O
degree	O
of	O
reliability	O
the	O
conformation	O
of	O
the	O
stem	B-structure_element
region	I-structure_element
.	O

The	O
“	O
kinked	B-protein_state
”	O
or	O
“	O
bulged	B-protein_state
”	O
conformation	O
is	O
the	O
most	O
prevalent	O
,	O
but	O
an	O
“	O
extended	B-protein_state
”	O
or	O
“	O
non	B-protein_state
-	I-protein_state
bulged	I-protein_state
”	O
conformation	O
is	O
also	O
,	O
but	O
less	O
frequently	O
,	O
observed	O
.	O

The	O
cataloging	O
and	O
development	O
of	O
the	O
rules	O
for	O
predicting	O
the	O
conformation	O
of	O
the	O
anchor	B-structure_element
region	I-structure_element
of	O
CDR	B-structure_element
H3	B-structure_element
continue	O
to	O
be	O
refined	O
,	O
producing	O
new	O
insight	O
into	O
the	O
CDR	B-structure_element
H3	B-structure_element
conformations	O
and	O
new	O
tools	O
for	O
antibody	B-protein_type
engineering	O
.	O

Current	O
antibody	B-protein_type
modeling	O
approaches	O
take	O
advantage	O
of	O
the	O
most	O
recent	O
advances	O
in	O
homology	B-experimental_method
modeling	I-experimental_method
,	O
the	O
evolving	O
understanding	O
of	O
the	O
CDR	B-structure_element
canonical	O
structures	B-evidence
,	O
the	O
emerging	O
rules	O
for	O
CDR	B-structure_element
H3	B-structure_element
modeling	O
and	O
the	O
growing	O
body	O
of	O
antibody	B-protein_type
structural	O
data	O
available	O
from	O
the	O
PDB	O
.	O

Recent	O
antibody	B-experimental_method
modeling	I-experimental_method
assessments	I-experimental_method
show	O
continued	O
improvement	O
in	O
the	O
quality	O
of	O
the	O
models	O
being	O
generated	O
by	O
a	O
variety	O
of	O
modeling	O
methods	O
.	O

Although	O
antibody	B-protein_type
modeling	O
is	O
improving	O
,	O
the	O
latest	O
assessment	O
revealed	O
a	O
number	O
of	O
challenges	O
that	O
need	O
to	O
be	O
overcome	O
to	O
provide	O
accurate	O
3	O
-	O
dimensional	O
models	O
of	O
antibody	B-protein_type
V	B-structure_element
regions	I-structure_element
,	O
including	O
accuracies	O
in	O
the	O
modeling	O
of	O
CDR	B-structure_element
H3	B-structure_element
.	O

The	O
need	O
for	O
improvement	O
in	O
this	O
area	O
was	O
also	O
highlighted	O
in	O
a	O
recent	O
study	O
reporting	O
an	O
approach	O
and	O
results	O
that	O
may	O
influence	O
future	O
antibody	B-protein_type
modeling	O
efforts	O
.	O

One	O
important	O
finding	O
of	O
the	O
antibody	B-experimental_method
modeling	I-experimental_method
assessments	I-experimental_method
was	O
that	O
errors	O
in	O
the	O
structural	O
templates	O
that	O
are	O
used	O
as	O
the	O
basis	O
for	O
homology	B-experimental_method
models	I-experimental_method
can	O
propagate	O
into	O
the	O
final	O
models	O
,	O
producing	O
inaccuracies	O
that	O
may	O
negatively	O
influence	O
the	O
predictive	O
nature	O
of	O
the	O
V	B-structure_element
region	I-structure_element
model	O
.	O

To	O
support	O
antibody	B-protein_type
engineering	O
and	O
therapeutic	O
development	O
efforts	O
,	O
a	O
phage	B-experimental_method
library	I-experimental_method
was	O
designed	O
and	O
constructed	O
based	O
on	O
a	O
limited	O
number	O
of	O
scaffolds	O
built	O
with	O
frequently	O
used	O
human	B-species
germ	O
-	O
line	O
IGV	B-structure_element
and	O
IGJ	B-structure_element
gene	O
segments	O
that	O
encode	O
antigen	B-site
combining	I-site
sites	I-site
suitable	O
for	O
recognition	O
of	O
peptides	O
and	O
proteins	O
.	O

This	O
Fab	B-structure_element
library	O
is	O
composed	O
of	O
3	O
HC	B-structure_element
germlines	O
,	O
IGHV1	B-mutant
-	I-mutant
69	I-mutant
(	O
H1	B-mutant
-	I-mutant
69	I-mutant
),	O
IGHV3	B-mutant
-	I-mutant
23	I-mutant
(	O
H3	B-mutant
-	I-mutant
23	I-mutant
)	O
and	O
IGHV5	B-mutant
-	I-mutant
51	I-mutant
(	O
H5	B-mutant
-	I-mutant
51	I-mutant
),	O
and	O
4	O
LC	B-structure_element
germlines	O
(	O
all	O
κ	B-structure_element
),	O
IGKV1	B-mutant
-	I-mutant
39	I-mutant
(	O
L1	B-mutant
-	I-mutant
39	I-mutant
),	O
IGKV3	B-mutant
-	I-mutant
11	I-mutant
(	O
L3	B-mutant
-	I-mutant
11	I-mutant
),	O
IGKV3	B-mutant
-	I-mutant
20	I-mutant
(	O
L3	B-mutant
-	I-mutant
20	I-mutant
)	O
and	O
IGKV4	B-mutant
-	I-mutant
1	I-mutant
(	O
L4	B-mutant
-	I-mutant
1	I-mutant
).	O

Selection	O
of	O
these	O
genes	O
was	O
based	O
on	O
the	O
high	O
frequency	O
of	O
their	O
use	O
and	O
their	O
cognate	O
canonical	O
structures	B-evidence
that	O
were	O
found	O
binding	O
to	O
peptides	O
and	O
proteins	O
,	O
as	O
well	O
as	O
their	O
ability	O
to	O
be	O
expressed	B-experimental_method
in	I-experimental_method
bacteria	I-experimental_method
and	O
displayed	B-experimental_method
on	I-experimental_method
filamentous	I-experimental_method
phage	I-experimental_method
.	O

The	O
implementation	O
of	O
the	O
library	O
involves	O
the	O
diversification	O
of	O
the	O
human	B-species
germline	O
genes	O
to	O
mimic	O
that	O
found	O
in	O
natural	O
human	B-species
libraries	O
.	O

The	O
crystal	B-experimental_method
structure	I-experimental_method
determinations	I-experimental_method
and	O
structural	B-experimental_method
analyses	I-experimental_method
of	O
all	O
germline	O
Fabs	B-structure_element
in	O
the	O
library	O
described	O
above	O
along	O
with	O
the	O
structures	B-evidence
of	O
a	O
fourth	O
HC	B-structure_element
germline	O
,	O
IGHV3	B-mutant
-	I-mutant
53	I-mutant
(	O
H3	B-mutant
-	I-mutant
53	I-mutant
),	O
paired	O
with	O
the	O
4	O
LCs	B-structure_element
of	O
the	O
library	O
have	O
been	O
carried	O
out	O
to	O
support	O
antibody	B-protein_type
therapeutic	O
development	O
.	O

All	O
16	O
HCs	B-structure_element
of	O
the	O
Fabs	B-structure_element
have	O
the	O
same	O
CDR	B-structure_element
H3	B-structure_element
that	O
was	O
reported	O
in	O
an	O
earlier	O
Fab	B-structure_element
structure	B-evidence
.	O

This	O
is	O
the	O
first	O
systematic	O
study	O
of	O
the	O
same	O
VH	B-structure_element
and	O
VL	B-structure_element
structures	B-evidence
in	O
the	O
context	O
of	O
different	O
pairings	O
.	O

The	O
structure	O
analyses	O
include	O
comparisons	O
of	O
the	O
overall	O
structures	B-evidence
,	O
canonical	O
structures	B-evidence
of	O
the	O
L1	B-structure_element
,	O
L2	B-structure_element
,	O
L3	B-structure_element
,	O
H1	B-structure_element
and	O
H2	B-structure_element
CDRs	B-structure_element
,	O
the	O
structures	B-evidence
of	O
all	O
CDR	B-structure_element
H3s	B-structure_element
,	O
and	O
the	O
VH	B-site
:	I-site
VL	I-site
packing	I-site
interactions	I-site
.	O

The	O
structures	B-evidence
and	O
their	O
analyses	O
provide	O
a	O
foundation	O
for	O
future	O
antibody	B-protein_type
engineering	O
and	O
structure	O
determination	O
efforts	O
.	O

Crystal	B-evidence
structures	I-evidence

Crystal	B-evidence
data	I-evidence
,	O
X	B-evidence
-	I-evidence
ray	I-evidence
data	I-evidence
,	O
and	O
refinement	B-evidence
statistics	I-evidence
.	O

(	O
Continued	O
)	O
Crystal	B-evidence
data	I-evidence
,	O
X	B-evidence
-	I-evidence
ray	I-evidence
data	I-evidence
,	O
and	O
refinement	B-evidence
statistics	I-evidence
.	O

The	O
crystal	B-evidence
structures	I-evidence
of	O
a	O
germline	B-experimental_method
library	I-experimental_method
composed	O
of	O
16	O
Fabs	B-structure_element
generated	O
by	O
combining	O
4	O
HCs	B-structure_element
(	O
H1	B-mutant
-	I-mutant
69	I-mutant
,	O
H3	B-mutant
-	I-mutant
23	I-mutant
,	O
H3	B-mutant
-	I-mutant
53	I-mutant
and	O
H5	B-mutant
-	I-mutant
51	I-mutant
)	O
and	O
4	O
LCs	B-structure_element
(	O
L1	B-mutant
-	I-mutant
39	I-mutant
,	O
L3	B-mutant
-	I-mutant
11	I-mutant
,	O
L3	B-mutant
-	I-mutant
20	I-mutant
and	O
L4	B-mutant
-	I-mutant
1	I-mutant
)	O
have	O
been	O
determined	O
.	O

The	O
Fab	B-structure_element
heavy	O
and	O
light	B-structure_element
chain	I-structure_element
sequences	O
for	O
the	O
variants	O
numbered	O
according	O
to	O
Chothia	O
are	O
shown	O
in	O
Fig	O
.	O
S1	O
.	O

The	O
four	O
different	O
HCs	B-structure_element
all	O
have	O
the	O
same	O
CDR	B-structure_element
H3	B-structure_element
sequence	O
,	O
ARYDGIYGELDF	B-structure_element
.	O

Crystallization	B-experimental_method
of	O
the	O
16	O
Fabs	B-structure_element
was	O
previously	O
reported	O
.	O

Three	O
sets	O
of	O
the	O
crystals	B-evidence
were	O
isomorphous	O
with	O
nearly	O
identical	O
unit	O
cells	O
(	O
Table	O
1	O
).	O

These	O
include	O
(	O
1	O
)	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
11	I-complex_assembly
and	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
in	O
P212121	O
,	O
(	O
2	O
)	O
H3	B-complex_assembly
-	I-complex_assembly
53	I-complex_assembly
:	I-complex_assembly
L1	I-complex_assembly
-	I-complex_assembly
39	I-complex_assembly
,	O
H3	B-complex_assembly
-	I-complex_assembly
53	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
11	I-complex_assembly
and	O
H3	B-complex_assembly
-	I-complex_assembly
53	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
in	O
P6522	O
,	O
and	O
(	O
3	O
)	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L1	I-complex_assembly
-	I-complex_assembly
39	I-complex_assembly
,	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
11	I-complex_assembly
and	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
in	O
P212121	O
.	O

Variations	O
occur	O
in	O
the	O
pH	O
(	O
buffer	O
)	O
and	O
the	O
additives	O
,	O
and	O
,	O
in	O
group	O
3	O
,	O
PEG	B-chemical
3350	I-chemical
is	O
the	O
precipitant	O
for	O
one	O
variants	O
while	O
ammonium	B-chemical
sulfate	I-chemical
is	O
the	O
precipitant	O
for	O
the	O
other	O
two	O
.	O

The	O
similarity	O
in	O
the	O
crystal	B-evidence
forms	I-evidence
is	O
attributed	O
in	O
part	O
to	O
cross	O
-	O
seeding	O
using	O
the	O
microseed	B-experimental_method
matrix	I-experimental_method
screening	I-experimental_method
for	O
groups	O
2	O
and	O
3	O
.	O

The	O
crystal	B-evidence
structures	I-evidence
of	O
the	O
16	O
Fabs	B-structure_element
have	O
been	O
determined	O
at	O
resolutions	O
ranging	O
from	O
3	O
.	O
3	O
Å	O
to	O
1	O
.	O
65	O
Å	O
(	O
Table	O
1	O
).	O

The	O
number	O
of	O
Fab	B-structure_element
molecules	O
in	O
the	O
crystallographic	O
asymmetric	O
unit	O
varies	O
from	O
1	O
(	O
for	O
12	O
Fabs	B-structure_element
)	O
to	O
2	O
(	O
for	O
4	O
Fabs	B-structure_element
).	O

Overall	O
the	O
structures	B-evidence
are	O
fairly	O
complete	O
,	O
and	O
,	O
as	O
can	O
be	O
expected	O
,	O
the	O
models	O
for	O
the	O
higher	O
resolution	O
structures	B-evidence
are	O
more	O
complete	O
than	O
those	O
for	O
the	O
lower	O
resolution	O
structures	B-evidence
(	O
Table	O
S1	O
).	O

Invariably	O
,	O
the	O
HCs	B-structure_element
have	O
more	O
disorder	B-protein_state
than	O
the	O
LCs	B-structure_element
.	O

For	O
the	O
LC	B-structure_element
,	O
the	O
disorder	B-protein_state
is	O
observed	O
at	O
2	O
of	O
the	O
C	O
-	O
terminal	O
residues	O
with	O
few	O
exceptions	O
.	O

Apart	O
from	O
the	O
C	O
-	O
terminus	O
,	O
only	O
a	O
few	O
surface	O
residues	O
in	O
LC	B-structure_element
are	O
disordered	B-protein_state
.	O

The	O
HCs	B-structure_element
feature	O
the	O
largest	O
number	O
of	O
disordered	B-protein_state
residues	O
,	O
with	O
the	O
lower	O
resolution	O
structures	B-evidence
having	O
the	O
most	O
.	O

The	O
C	O
-	O
terminal	O
residues	O
including	O
the	O
6xHis	O
tags	O
are	O
disordered	B-protein_state
in	O
all	O
16	O
structures	B-evidence
.	O

In	O
addition	O
to	O
these	O
,	O
2	O
primary	O
disordered	O
stretches	O
of	O
residues	O
are	O
observed	O
in	O
a	O
number	O
of	O
structures	B-evidence
(	O
Table	O
S1	O
).	O

One	O
involves	O
the	O
loop	B-structure_element
connecting	O
the	O
first	O
2	O
β	B-structure_element
-	I-structure_element
strands	I-structure_element
of	O
the	O
constant	B-structure_element
domain	I-structure_element
(	O
in	O
all	O
Fabs	B-structure_element
except	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L1	I-complex_assembly
-	I-complex_assembly
39	I-complex_assembly
,	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
11	I-complex_assembly
and	O
H3	B-complex_assembly
-	I-complex_assembly
53	I-complex_assembly
:	I-complex_assembly
L1	I-complex_assembly
-	I-complex_assembly
39	I-complex_assembly
).	O

The	O
other	O
is	O
located	O
in	O
CDR	B-structure_element
H3	B-structure_element
(	O
in	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
11	I-complex_assembly
,	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
and	O
in	O
one	O
of	O
2	O
copies	O
of	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
).	O

CDR	B-structure_element
H1	B-structure_element
and	O
CDR	B-structure_element
H2	B-structure_element
also	O
show	O
some	O
degree	O
of	O
disorder	B-protein_state
,	O
but	O
to	O
a	O
lesser	O
extent	O
.	O

CDR	B-structure_element
canonical	O
structures	B-evidence

Several	O
CDR	B-structure_element
definitions	O
have	O
evolved	O
over	O
decades	O
of	O
antibody	B-protein_type
research	O
.	O

Depending	O
on	O
the	O
focus	O
of	O
the	O
study	O
,	O
the	O
CDR	B-structure_element
boundaries	O
differ	O
slightly	O
between	O
various	O
definitions	O
.	O

In	O
this	O
work	O
,	O
we	O
use	O
the	O
CDR	B-structure_element
definition	O
of	O
North	O
et	O
al	O
.,	O
which	O
is	O
similar	O
to	O
that	O
of	O
Martin	O
with	O
the	O
following	O
exceptions	O
:	O
1	O
)	O
CDRs	B-structure_element
H1	B-structure_element
and	O
H3	B-structure_element
begin	O
immediately	O
after	O
the	O
Cys	B-residue_name
;	O
and	O
2	O
)	O
CDR	B-structure_element
L2	B-structure_element
includes	O
an	O
additional	O
residue	O
at	O
the	O
N	O
-	O
terminal	O
side	O
,	O
typically	O
Tyr	B-residue_name
.	O

CDR	B-structure_element
H1	B-structure_element

The	O
superposition	B-experimental_method
of	O
CDR	B-structure_element
H1	B-structure_element
backbones	O
for	O
all	O
HC	B-complex_assembly
:	I-complex_assembly
LC	I-complex_assembly
pairs	O
with	O
heavy	B-structure_element
chains	I-structure_element
:	O
(	O
A	O
)	O
H1	B-mutant
-	I-mutant
69	I-mutant
,	O
(	O
B	O
)	O
H3	B-mutant
-	I-mutant
23	I-mutant
,	O
(	O
C	O
)	O
H3	B-mutant
-	I-mutant
53	I-mutant
and	O
(	O
D	O
)	O
H5	B-mutant
-	I-mutant
51	I-mutant
.	O

CDRs	B-structure_element
are	O
defined	O
using	O
the	O
Dunbrack	O
convention	O
[	O
12	O
].	O

Assignments	O
for	O
2	O
copies	O
of	O
the	O
Fab	B-structure_element
in	O
the	O
asymmetric	O
unit	O
are	O
given	O
for	O
5	O
structures	B-evidence
.	O

No	O
assignment	O
(	O
NA	O
)	O
for	O
CDRs	B-structure_element
with	O
missing	O
residues	O
.	O

The	O
four	O
HCs	B-structure_element
feature	O
CDR	B-structure_element
H1	B-structure_element
of	O
the	O
same	O
length	O
,	O
and	O
their	O
sequences	O
are	O
highly	O
similar	O
(	O
Table	O
2	O
).	O

The	O
CDR	B-structure_element
H1	B-structure_element
backbone	O
conformations	O
for	O
all	O
variants	O
for	O
each	O
of	O
the	O
HCs	B-structure_element
are	O
shown	O
in	O
Fig	O
.	O
1	O
.	O

Three	O
of	O
the	O
HCs	B-structure_element
,	O
H3	B-mutant
-	I-mutant
23	I-mutant
,	O
H3	B-mutant
-	I-mutant
53	I-mutant
and	O
H5	B-mutant
-	I-mutant
51	I-mutant
,	O
have	O
the	O
same	O
canonical	O
structure	O
,	O
H1	B-mutant
-	I-mutant
13	I-mutant
-	I-mutant
1	I-mutant
,	O
and	O
the	O
backbone	O
conformations	O
are	O
tightly	O
clustered	O
for	O
each	O
set	O
of	O
Fab	B-structure_element
structures	B-evidence
as	O
reflected	O
in	O
the	O
rmsd	B-evidence
values	I-evidence
(	O
Fig	O
.	O
1B	O
-	O
D	O
).	O

Some	O
deviation	O
is	O
observed	O
for	O
H3	B-mutant
-	I-mutant
53	I-mutant
,	O
mostly	O
due	O
to	O
H3	B-complex_assembly
-	I-complex_assembly
53	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
,	O
which	O
exhibits	O
a	O
significant	O
degree	O
of	O
disorder	O
in	O
CDR	B-structure_element
H1	B-structure_element
.	O

The	O
electron	B-evidence
density	I-evidence
for	O
the	O
backbone	O
is	O
weak	O
and	O
discontinuous	O
,	O
and	O
completely	O
missing	O
for	O
several	O
side	O
chains	O
.	O

The	O
CDR	B-structure_element
H1	B-structure_element
structures	B-evidence
with	O
H1	B-mutant
-	I-mutant
69	I-mutant
shown	O
in	O
Fig	O
.	O
1A	O
are	O
quite	O
variable	O
,	O
both	O
for	O
the	O
structures	B-evidence
with	O
different	O
LCs	B-structure_element
and	O
for	O
the	O
copies	O
of	O
the	O
same	O
Fab	B-structure_element
in	O
the	O
asymmetric	O
unit	O
,	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
11	I-complex_assembly
and	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
.	O

In	O
total	O
,	O
6	O
independent	O
Fab	B-structure_element
structures	B-evidence
produce	O
5	O
different	O
canonical	O
structures	B-evidence
,	O
namely	O
H1	B-mutant
-	I-mutant
13	I-mutant
-	I-mutant
1	I-mutant
,	O
H1	B-mutant
-	I-mutant
13	I-mutant
-	I-mutant
3	I-mutant
,	O
H1	B-mutant
-	I-mutant
13	I-mutant
-	I-mutant
4	I-mutant
,	O
H1	B-mutant
-	I-mutant
13	I-mutant
-	I-mutant
6	I-mutant
and	O
H1	B-mutant
-	I-mutant
13	I-mutant
-	I-mutant
10	I-mutant
.	O

A	O
major	O
difference	O
of	O
H1	B-mutant
-	I-mutant
69	I-mutant
from	O
the	O
other	O
germlines	O
in	O
the	O
experimental	O
data	O
set	O
is	O
the	O
presence	O
of	O
Gly	B-residue_name
instead	O
of	O
Phe	B-residue_name
or	O
Tyr	B-residue_name
at	O
position	O
27	B-residue_number
(	O
residue	O
5	O
of	O
13	O
in	O
CDR	B-structure_element
H1	B-structure_element
).	O

Glycine	B-residue_name
introduces	O
the	O
possibility	O
of	O
a	O
higher	O
degree	O
of	O
conformational	O
flexibility	O
that	O
undoubtedly	O
translates	O
to	O
the	O
differences	O
observed	O
,	O
and	O
contributes	O
to	O
the	O
elevated	O
thermal	O
parameters	O
for	O
the	O
atoms	O
in	O
the	O
amino	O
acid	O
residues	O
in	O
this	O
region	O
.	O

CDR	B-structure_element
H2	B-structure_element

The	O
superposition	B-experimental_method
of	O
CDR	B-structure_element
H2	B-structure_element
backbones	O
for	O
all	O
HC	B-complex_assembly
:	I-complex_assembly
LC	I-complex_assembly
pairs	O
with	O
heavy	B-structure_element
chains	I-structure_element
:	O
(	O
A	O
)	O
H1	B-mutant
-	I-mutant
69	I-mutant
,	O
(	O
B	O
)	O
H3	B-mutant
-	I-mutant
23	I-mutant
,	O
(	O
C	O
)	O
H3	B-mutant
-	I-mutant
53	I-mutant
and	O
(	O
D	O
)	O
H5	B-mutant
-	I-mutant
51	I-mutant
.	O

The	O
canonical	O
structures	O
of	O
CDR	B-structure_element
H2	B-structure_element
have	O
fairly	O
consistent	O
conformations	O
(	O
Table	O
2	O
,	O
Fig	O
.	O
2	O
).	O

Each	O
of	O
the	O
4	O
HCs	B-structure_element
adopts	O
only	O
one	O
canonical	O
structure	O
regardless	O
of	O
the	O
pairing	O
LC	B-structure_element
.	O

Germlines	O
H1	B-mutant
-	I-mutant
69	I-mutant
and	O
H5	B-mutant
-	I-mutant
51	I-mutant
have	O
the	O
same	O
canonical	O
structure	O
assignment	O
H2	B-mutant
-	I-mutant
10	I-mutant
-	I-mutant
1	I-mutant
,	O
H3	B-mutant
-	I-mutant
23	I-mutant
has	O
H2	B-mutant
-	I-mutant
10	I-mutant
-	I-mutant
2	I-mutant
,	O
and	O
H3	B-mutant
-	I-mutant
53	I-mutant
has	O
H2	B-mutant
-	I-mutant
9	I-mutant
-	I-mutant
3	I-mutant
.	O

The	O
conformations	O
for	O
all	O
of	O
these	O
CDR	B-structure_element
H2s	B-structure_element
are	O
tightly	O
clustered	O
(	O
Fig	O
.	O
2	O
).	O

In	O
one	O
case	O
,	O
in	O
the	O
second	O
Fab	B-structure_element
of	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
,	O
CDR	B-structure_element
H2	B-structure_element
is	O
partially	B-protein_state
disordered	I-protein_state
(	O
Δ55	B-mutant
-	I-mutant
60	I-mutant
).	O

Although	O
three	O
of	O
the	O
germlines	O
have	O
CDR	B-structure_element
H2	B-structure_element
of	O
the	O
same	O
length	O
,	O
10	B-residue_range
residues	I-residue_range
,	O
they	O
adopt	O
2	O
distinctively	O
different	O
conformations	O
depending	O
mostly	O
on	O
the	O
residue	O
at	O
position	O
71	B-residue_number
from	O
the	O
so	O
-	O
called	O
CDR	B-structure_element
H4	B-structure_element
.	O

Arg71	B-residue_name_number
in	O
H3	B-mutant
-	I-mutant
23	I-mutant
fills	O
the	O
space	O
between	O
CDRs	B-structure_element
H2	B-structure_element
and	O
H4	B-structure_element
,	O
and	O
defines	O
the	O
conformation	O
of	O
the	O
tip	O
of	O
CDR	B-structure_element
H2	B-structure_element
so	O
that	O
residue	O
54	B-residue_number
points	O
away	O
from	O
the	O
antigen	B-site
binding	I-site
site	I-site
.	O

Germlines	O
H1	B-mutant
-	I-mutant
69	I-mutant
and	O
H5	B-mutant
-	I-mutant
51	I-mutant
are	O
unique	O
in	O
the	O
human	B-species
repertoire	O
in	O
having	O
an	O
Ala	B-residue_name
at	O
position	O
71	B-residue_number
that	O
leaves	O
enough	O
space	O
for	O
H	B-structure_element
-	O
Pro52a	B-residue_name_number
to	O
pack	O
deeper	O
against	O
CDR	B-structure_element
H4	B-structure_element
so	O
that	O
the	O
following	O
residues	O
53	B-residue_number
and	O
54	B-residue_number
point	O
toward	O
the	O
putative	O
antigen	O
.	O

Conformations	O
of	O
CDR	B-structure_element
H2	B-structure_element
in	O
H1	B-mutant
-	I-mutant
69	I-mutant
and	O
H5	B-mutant
-	I-mutant
51	I-mutant
,	O
both	O
of	O
which	O
have	O
canonical	O
structure	O
H2	B-mutant
-	I-mutant
10	I-mutant
-	I-mutant
1	I-mutant
,	O
show	O
little	O
deviation	O
within	O
each	O
set	O
of	O
4	O
structures	B-evidence
.	O

However	O
,	O
there	O
is	O
a	O
significant	O
shift	O
of	O
the	O
CDR	B-structure_element
as	O
a	O
rigid	O
body	O
when	O
the	O
2	O
sets	O
are	O
superimposed	B-experimental_method
.	O

Most	O
likely	O
this	O
is	O
the	O
result	O
of	O
interaction	O
of	O
CDR	B-structure_element
H2	B-structure_element
with	O
CDR	B-structure_element
H1	B-structure_element
,	O
namely	O
with	O
the	O
residue	O
at	O
position	O
33	B-residue_number
(	O
residue	O
11	O
of	O
13	O
in	O
CDR	B-structure_element
H1	B-structure_element
).	O

Germline	O
H1	B-mutant
-	I-mutant
69	I-mutant
has	O
Ala	B-residue_name
at	O
position	O
33	B-residue_number
whereas	O
in	O
H5	B-mutant
-	I-mutant
51	I-mutant
position	O
33	B-residue_number
is	O
occupied	O
by	O
a	O
bulky	O
Trp	B-residue_name
,	O
which	O
stacks	O
against	O
H	B-structure_element
-	O
Tyr52	B-residue_name_number
and	O
drives	O
CDR	B-structure_element
H2	B-structure_element
away	O
from	O
the	O
center	O
.	O

CDR	B-structure_element
L1	B-structure_element

The	O
superposition	B-experimental_method
of	O
CDR	B-structure_element
L1	B-structure_element
backbones	O
for	O
all	O
HC	B-complex_assembly
:	I-complex_assembly
LC	I-complex_assembly
pairs	O
with	O
light	B-structure_element
chains	I-structure_element
:	O
(	O
A	O
)	O
L1	B-mutant
-	I-mutant
39	I-mutant
,	O
(	O
B	O
)	O
L3	B-mutant
-	I-mutant
11	I-mutant
,	O
(	O
C	O
)	O
L3	B-mutant
-	I-mutant
20	I-mutant
and	O
(	O
D	O
)	O
L4	B-mutant
-	I-mutant
1	I-mutant
.	O

The	O
four	O
LC	B-structure_element
CDRs	B-structure_element
L1	B-structure_element
feature	O
3	O
different	O
lengths	O
(	O
11	B-residue_range
,	O
12	B-residue_range
and	O
17	B-residue_range
residues	O
)	O
having	O
a	O
total	O
of	O
4	O
different	O
canonical	O
structure	O
assignments	O
.	O

Of	O
these	O
LCs	B-structure_element
,	O
L1	B-mutant
-	I-mutant
39	I-mutant
and	O
L3	B-mutant
-	I-mutant
11	I-mutant
have	O
the	O
same	O
canonical	O
structure	O
,	O
L1	B-mutant
-	I-mutant
11	I-mutant
-	I-mutant
1	I-mutant
,	O
and	O
superimpose	B-experimental_method
very	O
well	O
(	O
Fig	O
.	O
3A	O
,	O
B	O
).	O

For	O
the	O
remaining	O
2	O
,	O
L3	B-mutant
-	I-mutant
20	I-mutant
has	O
2	O
different	O
assignments	O
,	O
L1	B-mutant
-	I-mutant
12	I-mutant
-	I-mutant
1	I-mutant
and	O
L1	B-mutant
-	I-mutant
12	I-mutant
-	I-mutant
2	I-mutant
,	O
while	O
L4	B-mutant
-	I-mutant
1	I-mutant
has	O
a	O
single	O
assignment	O
,	O
L1	B-mutant
-	I-mutant
17	I-mutant
-	I-mutant
1	I-mutant
.	O

L4	B-mutant
-	I-mutant
1	I-mutant
has	O
the	O
longest	O
CDR	B-structure_element
L1	B-structure_element
,	O
composed	O
of	O
17	B-residue_range
amino	I-residue_range
acid	I-residue_range
residues	I-residue_range
(	O
Fig	O
.	O
3D	O
).	O

Despite	O
this	O
,	O
the	O
conformations	O
are	O
tightly	O
clustered	O
(	O
rmsd	B-evidence
is	O
0	O
.	O
20	O
Å	O
).	O

The	O
backbone	O
conformations	O
of	O
the	O
stem	B-structure_element
regions	I-structure_element
superimpose	O
well	O
.	O

Some	O
changes	O
in	O
conformation	O
occur	O
between	O
residues	O
30a	B-residue_number
and	O
30f	B-residue_number
(	O
residues	O
8	B-residue_number
and	O
13	B-residue_number
of	O
17	B-residue_number
in	O
CDR	B-structure_element
L1	B-structure_element
).	O

This	O
is	O
the	O
tip	O
of	O
the	O
loop	B-structure_element
region	I-structure_element
,	O
which	O
appears	O
to	O
have	O
similar	O
conformations	O
that	O
fan	O
out	O
the	O
structures	B-evidence
because	O
of	O
the	O
slight	O
differences	O
in	O
torsion	O
angles	O
in	O
the	O
backbone	O
near	O
Tyr30a	B-residue_name_number
and	O
Lys30f	B-residue_name_number
.	O

L3	B-mutant
-	I-mutant
20	I-mutant
is	O
the	O
most	O
variable	O
in	O
CDR	B-structure_element
L1	B-structure_element
among	O
the	O
4	O
germlines	O
as	O
indicated	O
by	O
an	O
rmsd	B-evidence
of	O
0	O
.	O
54	O
Å	O
(	O
Fig	O
.	O
3C	O
).	O

Two	O
structures	B-evidence
,	O
H3	B-complex_assembly
-	I-complex_assembly
53	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
and	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
are	O
assigned	O
to	O
canonical	O
structure	O
L1	B-mutant
-	I-mutant
12	I-mutant
-	I-mutant
1	I-mutant
with	O
virtually	O
identical	O
backbone	O
conformations	O
.	O

The	O
third	O
structure	O
,	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
,	O
has	O
CDR	B-structure_element
L1	B-structure_element
as	O
L1	B-mutant
-	I-mutant
12	I-mutant
-	I-mutant
2	I-mutant
,	O
which	O
deviates	O
from	O
L1	B-mutant
-	I-mutant
12	I-mutant
-	I-mutant
1	I-mutant
at	O
residues	O
29	B-residue_range
-	I-residue_range
32	I-residue_range
,	O
i	O
.	O
e	O
.,	O
at	O
the	O
site	O
of	O
insertion	O
with	O
respect	O
to	O
the	O
11	B-residue_range
-	I-residue_range
residue	I-residue_range
CDR	B-structure_element
.	O

The	O
fourth	O
member	O
of	O
the	O
set	O
,	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
,	O
was	O
crystallized	B-experimental_method
with	O
2	O
Fabs	B-structure_element
in	O
the	O
asymmetric	O
unit	O
.	O

The	O
conformation	O
of	O
CDR	B-structure_element
L1	B-structure_element
in	O
these	O
2	O
Fabs	B-structure_element
is	O
slightly	O
different	O
,	O
and	O
both	O
conformations	O
fall	O
somewhere	O
between	O
L1	B-mutant
-	I-mutant
12	I-mutant
-	I-mutant
1	I-mutant
and	O
L1	B-mutant
-	I-mutant
12	I-mutant
-	I-mutant
2	I-mutant
.	O

This	O
reflects	O
the	O
lack	O
of	O
accuracy	O
in	O
the	O
structure	B-evidence
due	O
to	O
low	O
resolution	O
of	O
the	O
X	B-evidence
-	I-evidence
ray	I-evidence
data	I-evidence
(	O
3	O
.	O
3	O
Å	O
).	O

CDR	B-structure_element
L2	B-structure_element

The	O
superposition	B-experimental_method
of	O
CDR	B-structure_element
L2	B-structure_element
backbones	O
for	O
all	O
HC	B-complex_assembly
:	I-complex_assembly
LC	I-complex_assembly
pairs	O
with	O
light	B-structure_element
chains	I-structure_element
:	O
(	O
A	O
)	O
L1	B-mutant
-	I-mutant
39	I-mutant
,	O
(	O
B	O
)	O
L3	B-mutant
-	I-mutant
11	I-mutant
,	O
(	O
C	O
)	O
L3	B-mutant
-	I-mutant
20	I-mutant
and	O
(	O
D	O
)	O
L4	B-mutant
-	I-mutant
1	I-mutant
.	O

All	O
four	O
LCs	B-structure_element
have	O
CDR	B-structure_element
L2	B-structure_element
of	O
the	O
same	O
length	O
and	O
canonical	O
structure	O
,	O
L2	B-mutant
-	I-mutant
8	I-mutant
-	I-mutant
1	I-mutant
(	O
Table	O
2	O
).	O

The	O
CDR	B-structure_element
L2	B-structure_element
conformations	O
for	O
each	O
of	O
the	O
LCs	B-structure_element
paired	O
with	O
the	O
4	O
HCs	B-structure_element
are	O
clustered	O
more	O
tightly	O
than	O
any	O
of	O
the	O
other	O
CDRs	B-structure_element
(	O
rmsd	B-evidence
values	O
are	O
in	O
the	O
range	O
0	O
.	O
09	O
-	O
0	O
.	O
16	O
Å	O
),	O
and	O
all	O
4	O
sets	O
have	O
virtually	O
the	O
same	O
conformation	O
despite	O
the	O
sequence	O
diversity	O
of	O
the	O
loop	B-structure_element
.	O

CDR	B-structure_element
L3	B-structure_element

The	O
superposition	B-experimental_method
of	O
CDR	B-structure_element
L3	B-structure_element
backbones	O
for	O
all	O
HC	B-complex_assembly
:	I-complex_assembly
LC	I-complex_assembly
pairs	O
with	O
light	B-structure_element
chains	I-structure_element
:	O
(	O
A	O
)	O
L1	B-mutant
-	I-mutant
39	I-mutant
,	O
(	O
B	O
)	O
L3	B-mutant
-	I-mutant
11	I-mutant
,	O
(	O
C	O
)	O
L3	B-mutant
-	I-mutant
20	I-mutant
and	O
(	O
D	O
)	O
L4	B-mutant
-	I-mutant
1	I-mutant
.	O

As	O
with	O
CDR	B-structure_element
L2	B-structure_element
,	O
all	O
4	O
LCs	B-structure_element
have	O
CDR	B-structure_element
L3	B-structure_element
of	O
the	O
same	O
length	O
and	O
canonical	O
structure	B-evidence
,	O
L3	B-mutant
-	I-mutant
9	I-mutant
-	I-mutant
cis7	I-mutant
-	I-mutant
1	I-mutant
(	O
Table	O
2	O
).	O

The	O
conformations	O
of	O
CDR	B-structure_element
L3	B-structure_element
for	O
L1	B-mutant
-	I-mutant
39	I-mutant
,	O
L3	B-mutant
-	I-mutant
11	I-mutant
,	O
and	O
particularly	O
for	O
L320	O
,	O
are	O
not	O
as	O
tightly	O
clustered	O
as	O
those	O
of	O
L4	B-mutant
-	I-mutant
1	I-mutant
(	O
Fig	O
.	O
5	O
).	O

The	O
slight	O
conformational	O
variability	O
occurs	O
in	O
the	O
region	O
of	O
amino	O
acid	O
residues	O
90	B-residue_range
-	I-residue_range
92	I-residue_range
,	O
which	O
is	O
in	O
contact	O
with	O
CDR	B-structure_element
H3	B-structure_element
.	O

CDR	B-structure_element
H3	B-structure_element
conformational	O
diversity	O

As	O
mentioned	O
earlier	O
,	O
all	O
16	O
Fabs	B-structure_element
have	O
the	O
same	O
CDR	B-structure_element
H3	B-structure_element
,	O
for	O
which	O
the	O
amino	O
acid	O
sequence	O
is	O
derived	O
from	O
the	O
anti	O
-	O
CCL2	O
antibody	B-protein_type
CNTO	B-chemical
888	I-chemical
.	O

The	O
loop	B-structure_element
and	O
the	O
2	O
β	B-structure_element
-	I-structure_element
strands	I-structure_element
of	O
the	O
CDR	B-structure_element
H3	B-structure_element
in	O
this	O
‘	O
parent	O
’	O
structure	B-evidence
are	O
stabilized	O
by	O
H	O
-	O
bonds	O
between	O
the	O
carbonyl	O
oxygen	O
and	O
peptide	O
nitrogen	O
atoms	O
in	O
the	O
2	O
strands	O
.	O

An	O
interesting	O
feature	O
of	O
these	O
CDR	B-structure_element
H3	B-structure_element
structures	B-evidence
is	O
the	O
presence	O
of	O
a	O
water	B-chemical
molecule	O
that	O
interacts	O
with	O
the	O
peptide	O
nitrogens	O
and	O
carbonyl	O
oxygens	O
near	O
the	O
bridging	O
loop	B-structure_element
connecting	O
the	O
2	O
β	B-structure_element
-	I-structure_element
strands	I-structure_element
.	O

This	O
water	B-chemical
is	O
present	O
in	O
both	O
the	O
bound	B-protein_state
(	O
4DN4	O
)	O
and	O
unbound	B-protein_state
(	O
4DN3	O
)	O
forms	O
of	O
CNTO	B-chemical
888	I-chemical
.	O

The	O
stem	B-structure_element
region	I-structure_element
of	O
CDR	B-structure_element
H3	B-structure_element
in	O
the	O
parental	O
Fab	B-structure_element
is	O
in	O
a	O
‘	O
kinked	B-protein_state
’	O
conformation	O
,	O
in	O
which	O
the	O
indole	O
nitrogen	O
of	O
Trp103	B-residue_name_number
forms	O
a	O
hydrogen	O
bond	O
with	O
the	O
carbonyl	O
oxygen	O
of	O
Leu100b	B-residue_name_number
.	O

The	O
carboxyl	O
group	O
of	O
Asp101	B-residue_name_number
forms	O
a	O
salt	O
bridge	O
with	O
Arg94	B-residue_name_number
.	O

Ribbon	O
representations	O
of	O
(	O
A	O
)	O
the	O
superposition	B-experimental_method
of	O
all	O
CDR	B-structure_element
H3s	B-structure_element
of	O
the	O
structures	B-evidence
with	O
complete	O
backbone	O
traces	O
.	O
(	O
B	O
)	O
The	O
CDR	B-structure_element
H3s	B-structure_element
rotated	O
90	O
°	O
about	O
the	O
y	O
axis	O
of	O
the	O
page	O
.	O

The	O
structure	B-evidence
of	O
each	O
CDR	B-structure_element
H3	B-structure_element
is	O
represented	O
with	O
a	O
different	O
color	O
.	O

Despite	O
having	O
the	O
same	O
amino	O
acid	O
sequence	O
in	O
all	O
variants	O
,	O
CDR	B-structure_element
H3	B-structure_element
has	O
the	O
highest	O
degree	O
of	O
structural	O
diversity	O
and	O
disorder	O
of	O
all	O
of	O
the	O
CDRs	B-structure_element
in	O
the	O
experimental	O
set	O
.	O

Three	O
of	O
the	O
21	O
Fab	B-structure_element
structures	B-evidence
(	O
including	O
multiple	O
copies	O
in	O
the	O
asymmetric	O
unit	O
),	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
11	I-complex_assembly
,	O
H551	B-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
and	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
(	O
one	O
of	O
the	O
2	O
Fabs	B-structure_element
),	O
have	O
missing	B-protein_state
(	O
disordered	B-protein_state
)	O
residues	O
at	O
the	O
apex	O
of	O
the	O
CDR	B-structure_element
loop	I-structure_element
.	O

Another	O
four	O
of	O
the	O
Fabs	B-structure_element
,	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L1	I-complex_assembly
-	I-complex_assembly
39	I-complex_assembly
,	O
H3	B-complex_assembly
-	I-complex_assembly
53	I-complex_assembly
:	I-complex_assembly
L1	I-complex_assembly
-	I-complex_assembly
39	I-complex_assembly
,	O
H3	B-complex_assembly
-	I-complex_assembly
53	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
11	I-complex_assembly
and	O
H3	B-complex_assembly
-	I-complex_assembly
53	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
have	O
missing	O
side	O
-	O
chain	O
atoms	O
.	O

The	O
variations	O
in	O
CDR	B-structure_element
H3	B-structure_element
conformation	O
are	O
illustrated	O
in	O
Fig	O
.	O
6	O
for	O
the	O
18	O
Fab	B-structure_element
structures	B-evidence
that	O
have	O
ordered	O
backbone	O
atoms	O
.	O

A	O
comparison	O
of	O
representatives	O
of	O
the	O
“	O
kinked	B-protein_state
”	O
and	O
“	O
extended	B-protein_state
”	O
structures	B-evidence
.	O

(	O
A	O
)	O
The	O
“	O
kinked	B-protein_state
”	O
CDR	B-structure_element
H3	B-structure_element
of	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
11	I-complex_assembly
with	O
purple	O
carbon	O
atoms	O
and	O
yellow	O
dashed	O
lines	O
connecting	O
the	O
H	O
-	O
bond	O
pairs	O
for	O
Leu100b	B-residue_name_number
O	O
and	O
Trp103	B-residue_name_number
NE1	O
,	O
Arg94	B-residue_name_number
NE	O
and	O
Asp101	B-residue_name_number
OD1	O
,	O
and	O
Arg94	B-residue_name_number
NH2	O
and	O
Asp101	B-residue_name_number
OD2	O
.	O

(	O
B	O
)	O
The	O
“	O
extended	B-protein_state
”	O
CDR	B-structure_element
H3	B-structure_element
of	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
with	O
green	O
carbon	O
atoms	O
and	O
yellow	O
dashed	O
lines	O
connecting	O
the	O
H	O
-	O
bond	O
pairs	O
for	O
Asp101	B-residue_name_number
OD1	O
and	O
OD2	O
and	O
Trp103	B-residue_name_number
NE1	O
.	O

In	O
10	O
of	O
the	O
18	O
Fab	B-structure_element
structures	B-evidence
,	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L1	I-complex_assembly
-	I-complex_assembly
39	I-complex_assembly
,	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
11	I-complex_assembly
(	O
2	O
Fabs	B-structure_element
),	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
,	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
11	I-complex_assembly
(	O
2	O
Fabs	B-structure_element
),	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
,	O
H3	B-complex_assembly
-	I-complex_assembly
53	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
11	I-complex_assembly
,	O
H3	B-complex_assembly
-	I-complex_assembly
53	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
and	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L1	I-complex_assembly
-	I-complex_assembly
39	I-complex_assembly
,	O
the	O
CDRs	B-structure_element
have	O
similar	O
conformations	O
to	O
that	O
found	O
in	O
4DN3	O
.	O

The	O
bases	O
of	O
these	O
structures	B-evidence
have	O
the	O
‘	O
kinked	B-protein_state
’	O
conformation	O
with	O
the	O
H	O
-	O
bond	O
between	O
Trp103	B-residue_name_number
and	O
Leu100b	B-residue_name_number
.	O

A	O
representative	O
CDR	B-structure_element
H3	B-structure_element
structure	B-evidence
for	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L1	I-complex_assembly
-	I-complex_assembly
39	I-complex_assembly
illustrating	O
this	O
is	O
shown	O
in	O
Fig	O
.	O
7A	O
.	O

The	O
largest	O
backbone	O
conformational	O
deviation	O
for	O
the	O
set	O
is	O
at	O
Tyr99	B-residue_name_number
,	O
where	O
the	O
C	O
=	O
O	O
is	O
rotated	O
by	O
90	O
°	O
relative	O
to	O
that	O
observed	O
in	O
4DN3	O
.	O

Also	O
,	O
it	O
is	O
worth	O
noting	O
that	O
only	O
one	O
of	O
these	O
structures	B-evidence
,	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
,	O
has	O
the	O
conserved	B-protein_state
water	B-chemical
molecule	O
in	O
CDR	B-structure_element
H3	B-structure_element
observed	O
in	O
the	O
4DN3	O
and	O
4DN4	O
structures	B-evidence
.	O

In	O
fact	O
,	O
it	O
is	O
the	O
only	O
Fab	B-structure_element
in	O
the	O
set	O
that	O
has	O
a	O
water	B-chemical
molecule	O
present	O
at	O
this	O
site	O
.	O

The	O
CDR	B-structure_element
H3	B-structure_element
for	O
this	O
structure	B-evidence
is	O
shown	O
in	O
Fig	O
.	O
S3	O
.	O

The	O
remaining	O
8	O
Fabs	B-structure_element
can	O
be	O
grouped	O
into	O
5	O
different	O
conformational	O
classes	O
.	O

Three	O
of	O
the	O
Fabs	B-structure_element
,	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L1	I-complex_assembly
-	I-complex_assembly
39	I-complex_assembly
,	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
and	O
H3	B-complex_assembly
-	I-complex_assembly
53	I-complex_assembly
:	I-complex_assembly
L1	I-complex_assembly
-	I-complex_assembly
39	I-complex_assembly
,	O
have	O
distinctive	O
conformations	O
.	O

The	O
stem	B-structure_element
regions	I-structure_element
in	O
these	O
3	O
cases	O
are	O
in	O
the	O
‘	O
kinked	B-protein_state
’	O
conformation	O
consistent	O
with	O
that	O
observed	O
for	O
4DN3	O
.	O

The	O
five	O
remaining	O
Fabs	B-structure_element
,	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
(	O
2	O
copies	O
),	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
(	O
2	O
copies	O
)	O
and	O
H3	B-complex_assembly
-	I-complex_assembly
53	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
,	O
have	O
3	O
different	O
CDR	B-structure_element
H3	B-structure_element
conformations	O
(	O
Fig	O
.	O
S4	O
).	O

The	O
stem	B-structure_element
regions	I-structure_element
of	O
CDR	B-structure_element
H3	B-structure_element
for	O
the	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
Fabs	B-structure_element
are	O
in	O
the	O
‘	O
kinked	B-protein_state
’	O
conformation	O
while	O
,	O
surprisingly	O
,	O
those	O
of	O
the	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
pair	O
and	O
H3	B-complex_assembly
-	I-complex_assembly
53	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
are	O
in	O
the	O
‘	O
extended	B-protein_state
’	O
conformation	O
(	O
Fig	O
.	O
7B	O
).	O

VH	B-complex_assembly
:	I-complex_assembly
VL	I-complex_assembly
domain	O
packing	O

The	O
VH	B-structure_element
and	O
VL	B-structure_element
domains	O
have	O
a	O
β	B-structure_element
-	I-structure_element
sandwich	I-structure_element
structure	I-structure_element
(	O
also	O
often	O
referred	O
as	O
a	O
Greek	B-structure_element
key	I-structure_element
motif	I-structure_element
)	O
and	O
each	O
is	O
composed	O
of	O
a	O
4	B-structure_element
-	I-structure_element
stranded	I-structure_element
and	I-structure_element
a	I-structure_element
5	I-structure_element
-	I-structure_element
stranded	I-structure_element
antiparallel	I-structure_element
β	I-structure_element
-	I-structure_element
sheets	I-structure_element
.	O

The	O
two	O
domains	O
pack	O
together	O
such	O
that	O
the	O
5	B-structure_element
-	I-structure_element
stranded	I-structure_element
β	I-structure_element
-	I-structure_element
sheets	I-structure_element
,	O
which	O
have	O
hydrophobic	O
surfaces	O
,	O
interact	O
with	O
each	O
other	O
bringing	O
the	O
CDRs	B-structure_element
from	O
both	O
the	O
VH	B-structure_element
and	O
VL	B-structure_element
domains	O
into	O
close	O
proximity	O
.	O

The	O
domain	O
packing	O
of	O
the	O
variants	O
was	O
assessed	O
by	O
computing	O
the	O
domain	B-site
interface	I-site
interactions	O
,	O
the	O
VH	B-complex_assembly
:	I-complex_assembly
VL	I-complex_assembly
tilt	B-evidence
angles	I-evidence
,	O
the	O
buried	O
surface	O
area	O
and	O
surface	O
complementarity	O
.	O

VH	B-site
:	I-site
VL	I-site
interface	I-site
amino	O
acid	O
residue	O
interactions	O

The	O
conserved	B-protein_state
VH	B-complex_assembly
:	I-complex_assembly
VL	I-complex_assembly
interactions	O
as	O
viewed	O
along	O
the	O
VH	B-structure_element
/	O
VL	B-structure_element
axis	O
.	O

The	O
VH	B-structure_element
residues	O
are	O
in	O
blue	O
,	O
the	O
VL	B-structure_element
residues	O
are	O
in	O
orange	O
.	O

The	O
VH	B-site
:	I-site
VL	I-site
interface	I-site
is	O
pseudosymmetric	B-protein_state
,	O
and	O
involves	O
2	O
stretches	O
of	O
the	O
polypeptide	O
chain	O
from	O
each	O
domain	O
,	O
namely	O
CDR3	B-structure_element
and	O
the	O
framework	B-structure_element
region	I-structure_element
between	O
CDRs	B-structure_element
1	I-structure_element
and	I-structure_element
2	I-structure_element
.	O

These	O
stretches	O
form	O
antiparallel	B-structure_element
β	I-structure_element
-	I-structure_element
hairpins	I-structure_element
within	O
the	O
internal	O
5	B-structure_element
-	I-structure_element
stranded	I-structure_element
β	I-structure_element
-	I-structure_element
sheet	I-structure_element
.	O

There	O
are	O
a	O
few	O
principal	O
inter	O
-	O
domain	O
interactions	O
that	O
are	O
conserved	O
not	O
only	O
in	O
the	O
experimental	O
set	O
of	O
16	O
Fabs	B-structure_element
,	O
but	O
in	O
all	O
human	B-species
antibodies	B-protein_type
.	O

They	O
include	O
:	O
1	O
)	O
a	O
bidentate	O
hydrogen	O
bond	O
between	O
L	B-structure_element
-	O
Gln38	B-residue_name_number
and	O
H	B-structure_element
-	O
Gln39	B-residue_name_number
;	O
2	O
)	O
H	B-structure_element
-	O
Leu45	B-residue_name_number
in	O
a	O
hydrophobic	B-site
pocket	I-site
between	O
L	B-structure_element
-	O
Phe98	B-residue_name_number
,	O
L	B-structure_element
-	O
Tyr87	B-residue_name_number
and	O
L	B-structure_element
-	O
Pro44	B-residue_name_number
;	O
3	O
)	O
L	B-structure_element
-	O
Pro44	B-residue_name_number
stacked	O
against	O
H	B-structure_element
-	O
Trp103	B-residue_name_number
;	O
and	O
4	O
)	O
L	B-structure_element
-	O
Ala43	B-residue_name_number
opposite	O
the	O
face	O
of	O
H	B-structure_element
-	O
Tyr91	B-residue_name_number
(	O
Fig	O
.	O
8	O
).	O

With	O
the	O
exception	O
of	O
L	B-structure_element
-	O
Ala43	B-residue_name_number
,	O
all	O
other	O
residues	O
are	O
conserved	O
in	O
human	B-species
germlines	O
.	O

Position	O
43	B-residue_number
may	O
be	O
alternatively	O
occupied	O
by	O
Ser	B-residue_name
,	O
Val	B-residue_name
or	O
Pro	B-residue_name
(	O
as	O
in	O
L4	B-mutant
-	I-mutant
1	I-mutant
),	O
but	O
the	O
hydrophobic	O
interaction	O
with	O
H	B-structure_element
-	O
Tyr91	B-residue_name_number
is	O
preserved	O
.	O

These	O
core	O
interactions	O
provide	O
enough	O
stability	O
to	O
the	O
VH	B-complex_assembly
:	I-complex_assembly
VL	I-complex_assembly
dimer	B-oligomeric_state
so	O
that	O
additional	O
VH	B-site
-	I-site
VL	I-site
contacts	I-site
can	O
tolerate	O
amino	O
acid	O
sequence	O
variations	O
in	O
CDRs	B-structure_element
H3	B-structure_element
and	O
L3	B-structure_element
that	O
form	O
part	O
of	O
the	O
VH	B-site
:	I-site
VL	I-site
interface	I-site
.	O

In	O
total	O
,	O
about	O
20	B-residue_range
residues	I-residue_range
are	O
involved	O
in	O
the	O
VH	B-complex_assembly
:	I-complex_assembly
VL	I-complex_assembly
interactions	O
on	O
each	O
side	O
(	O
Fig	O
.	O
S5	O
).	O

Half	O
of	O
them	O
are	O
in	O
the	O
framework	B-structure_element
regions	I-structure_element
and	O
those	O
residues	O
(	O
except	O
residue	O
61	B-residue_number
in	O
HC	B-structure_element
,	O
which	O
is	O
actually	O
in	O
CDR2	B-structure_element
in	O
Kabat	O
'	O
s	O
definition	O
)	O
are	O
conserved	O
in	O
the	O
set	O
of	O
16	O
Fabs	B-structure_element
.	O

One	O
notable	O
exception	O
is	O
H	B-structure_element
-	O
Trp47	B-residue_name_number
,	O
which	O
exhibits	O
2	O
conformations	O
of	O
the	O
indole	O
ring	O
.	O

In	O
most	O
of	O
the	O
structures	B-evidence
,	O
it	O
has	O
the	O
χ2	B-evidence
angle	O
of	O
∼	O
80	O
°,	O
while	O
the	O
ring	O
is	O
flipped	O
over	O
(	O
χ2	B-evidence
=	O
−	O
100	O
°)	O
in	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
:	I-complex_assembly
11	I-complex_assembly
and	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
.	O

Interestingly	O
,	O
these	O
are	O
the	O
only	O
2	O
structures	B-evidence
with	O
residues	O
missing	B-protein_state
in	O
CDR	B-structure_element
H3	B-structure_element
because	O
of	O
disorder	O
,	O
although	O
both	O
structures	B-evidence
are	O
determined	O
at	O
high	O
resolution	O
and	O
the	O
rest	O
of	O
the	O
structure	B-evidence
is	O
well	O
defined	O
.	O

Apparently	O
,	O
residues	O
flanking	O
CDR	B-structure_element
H3	B-structure_element
in	O
the	O
2	O
VH	B-complex_assembly
:	I-complex_assembly
VL	I-complex_assembly
pairings	O
are	O
inconsistent	O
with	O
any	O
stable	B-protein_state
conformation	O
of	O
CDR	B-structure_element
H3	B-structure_element
,	O
which	O
translates	O
into	O
a	O
less	O
restricted	O
conformational	O
space	O
for	O
some	O
of	O
them	O
,	O
including	O
H	B-structure_element
-	O
Trp47	B-residue_name_number
.	O

VH	B-complex_assembly
:	I-complex_assembly
VL	I-complex_assembly
tilt	B-evidence
angles	I-evidence

The	O
relative	O
orientation	O
of	O
VH	B-structure_element
and	O
VL	B-structure_element
has	O
been	O
measured	O
in	O
a	O
number	O
of	O
different	O
ways	O
.	O

The	O
first	O
approach	O
uses	O
ABangles	B-experimental_method
,	O
the	O
results	O
of	O
which	O
are	O
shown	O
in	O
Table	O
S2	O
.	O

The	O
four	O
LCs	B-structure_element
all	O
are	O
classified	O
as	O
Type	O
A	O
because	O
they	O
have	O
a	O
proline	B-residue_name
at	O
position	O
44	B-residue_number
,	O
and	O
the	O
results	O
for	O
each	O
orientation	B-evidence
parameter	I-evidence
are	O
within	O
the	O
range	O
of	O
values	O
of	O
this	O
type	O
reported	O
by	O
Dunbar	O
and	O
co	O
-	O
workers	O
.	O

In	O
fact	O
,	O
the	O
parameter	O
values	O
for	O
the	O
set	O
of	O
16	O
Fabs	B-structure_element
are	O
in	O
the	O
middle	O
of	O
the	O
distribution	O
observed	O
for	O
351	O
non	O
-	O
redundant	O
antibody	B-protein_type
structures	B-evidence
determined	O
at	O
3	O
.	O
0	O
Å	O
resolution	O
or	O
better	O
.	O

The	O
only	O
exception	O
is	O
HC1	B-structure_element
,	O
which	O
is	O
shifted	O
toward	O
smaller	O
angles	O
with	O
the	O
mean	O
value	O
of	O
70	O
.	O
8	O
°	O
as	O
compared	O
to	O
the	O
distribution	O
centered	O
at	O
72	O
°	O
for	O
the	O
entire	O
PDB	O
.	O

This	O
probably	O
reflects	O
the	O
invariance	O
of	O
CDR	B-structure_element
H3	B-structure_element
in	O
the	O
current	O
set	O
as	O
opposed	O
to	O
the	O
CDR	B-structure_element
H3	B-structure_element
diversity	O
in	O
the	O
PDB	O
.	O

The	O
second	O
approach	O
used	O
for	O
comparing	O
tilt	B-evidence
angles	I-evidence
involved	O
computing	O
the	O
difference	B-evidence
in	O
the	O
tilt	B-evidence
angles	I-evidence
between	O
all	O
pairs	O
of	O
structures	B-evidence
.	O

For	O
structures	B-evidence
with	O
2	O
copies	O
of	O
the	O
Fab	B-structure_element
in	O
the	O
asymmetric	O
unit	O
,	O
only	O
one	O
structure	B-evidence
was	O
used	O
.	O

The	O
differences	O
between	O
independent	O
Fabs	B-structure_element
in	O
the	O
same	O
structure	B-evidence
are	O
4	O
.	O
9	O
°	O
for	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
,	O
1	O
.	O
6	O
°	O
for	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
11	I-complex_assembly
,	O
1	O
.	O
4	O
°	O
for	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
,	O
3	O
.	O
3	O
°	O
for	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
11	I-complex_assembly
,	O
and	O
2	O
.	O
5	O
°	O
for	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
.	O

With	O
the	O
exception	O
of	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
,	O
the	O
angles	O
are	O
within	O
the	O
range	O
of	O
2	O
-	O
3	O
°	O
as	O
are	O
observed	O
in	O
the	O
identical	O
structures	B-evidence
in	O
the	O
PDB	O
.	O

In	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
,	O
one	O
of	O
the	O
Fabs	B-structure_element
is	O
substantially	O
disordered	B-protein_state
so	O
that	O
part	O
of	O
CDR	B-structure_element
H2	B-structure_element
(	O
the	O
outer	O
β	B-structure_element
-	I-structure_element
strand	I-structure_element
,	O
residues	O
55	B-residue_range
-	I-residue_range
60	I-residue_range
)	O
is	O
completely	O
missing	O
.	O

This	O
kind	O
of	O
disorder	O
may	O
compromise	O
the	O
integrity	O
of	O
the	O
VH	B-structure_element
domain	O
and	O
its	O
interaction	O
with	O
the	O
VL	B-structure_element
.	O

Indeed	O
,	O
this	O
Fab	B-structure_element
has	O
the	O
largest	O
twist	B-evidence
angle	I-evidence
HC2	B-structure_element
within	O
the	O
experimental	O
set	O
that	O
exceeds	O
the	O
mean	O
value	O
by	O
2	O
.	O
5	O
standard	O
deviations	O
(	O
Table	O
S2	O
).	O

An	O
illustration	O
of	O
the	O
difference	O
in	O
tilt	O
angle	O
for	O
2	O
pairs	O
of	O
variants	O
by	O
the	O
superposition	B-experimental_method
of	O
the	O
VH	B-structure_element
domains	O
of	O
(	O
A	O
)	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
on	O
that	O
of	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L1	I-complex_assembly
-	I-complex_assembly
39	I-complex_assembly
(	O
the	O
VL	B-structure_element
domain	O
is	O
off	O
by	O
a	O
rigid	O
-	O
body	O
roatation	O
of	O
10	O
.	O
5	O
°)	O
and	O
(	O
B	O
)	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
on	O
that	O
of	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L1	I-complex_assembly
-	I-complex_assembly
39	I-complex_assembly
(	O
the	O
VL	B-structure_element
domain	O
is	O
off	O
by	O
a	O
rigid	O
-	O
body	O
roatation	O
of	O
1	O
.	O
6	O
°).	O

Differences	O
in	O
VH	B-complex_assembly
:	I-complex_assembly
VL	I-complex_assembly
tilt	B-evidence
angles	I-evidence
.	O

The	O
differences	B-evidence
in	O
the	O
tilt	B-evidence
angle	I-evidence
are	O
shown	O
for	O
all	O
pairs	O
of	O
V	B-structure_element
regions	I-structure_element
in	O
Table	O
3	O
.	O

The	O
smallest	O
differences	O
in	O
the	O
tilt	B-evidence
angle	I-evidence
are	O
between	O
the	O
Fabs	B-structure_element
in	O
isomorphous	O
crystal	B-evidence
forms	I-evidence
.	O

The	O
largest	O
deviations	O
in	O
the	O
tilt	B-evidence
angle	I-evidence
,	O
up	O
to	O
11	O
.	O
0	O
°,	O
are	O
found	O
for	O
2	O
structures	B-evidence
,	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
and	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
,	O
that	O
stand	O
out	O
from	O
the	O
other	O
Fabs	B-structure_element
.	O

One	O
of	O
the	O
2	O
structures	B-evidence
,	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
,	O
has	O
its	O
CDR	B-structure_element
H3	B-structure_element
in	O
the	O
‘	O
extended	B-protein_state
’	O
conformation	O
;	O
the	O
other	O
structure	O
has	O
it	O
in	O
the	O
‘	O
kinked	B-protein_state
’	O
conformation	O
.	O

Two	O
examples	O
illustrating	O
large	O
(	O
10	O
.	O
5	O
°)	O
and	O
small	O
(	O
1	O
.	O
6	O
°)	O
differences	O
in	O
the	O
tilt	B-evidence
angles	I-evidence
are	O
shown	O
in	O
Fig	O
.	O
9	O
.	O

VH	B-complex_assembly
:	I-complex_assembly
VL	I-complex_assembly
buried	O
surface	O
area	O
and	O
complementarity	O

VH	B-complex_assembly
:	I-complex_assembly
VL	I-complex_assembly
surface	O
areas	O
and	O
surface	O
complementarity	O
.	O

Some	O
side	O
chain	O
atoms	O
in	O
CDR	B-structure_element
H3	B-structure_element
are	O
missing	O
.	O

Residues	O
in	O
CDR	B-structure_element
H3	B-structure_element
are	O
missing	O
:	O
YGE	B-structure_element
in	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
11	I-complex_assembly
,	O
GIY	B-structure_element
in	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
.	O

The	O
results	O
of	O
the	O
PISA	B-experimental_method
contact	B-experimental_method
surface	I-experimental_method
calculation	I-experimental_method
and	O
surface	B-experimental_method
complementarity	I-experimental_method
calculation	I-experimental_method
are	O
shown	O
in	O
Table	O
4	O
.	O

The	O
interface	B-site
areas	O
are	O
calculated	O
as	O
the	O
average	O
of	O
the	O
VH	B-site
and	I-site
VL	I-site
contact	I-site
surfaces	I-site
.	O

Six	O
of	O
the	O
16	O
structures	B-evidence
have	O
CDR	B-structure_element
H3	B-structure_element
side	O
chains	O
or	O
complete	O
residues	O
missing	B-protein_state
,	O
and	O
therefore	O
their	O
interfaces	B-site
are	O
much	O
smaller	O
than	O
in	O
the	O
other	O
10	O
structures	B-evidence
with	O
complete	B-protein_state
CDRs	B-structure_element
(	O
the	O
results	O
are	O
provided	O
for	O
all	O
Fabs	B-structure_element
for	O
completeness	O
).	O

Among	O
the	O
complete	B-protein_state
structures	B-evidence
,	O
the	O
interface	B-site
areas	O
range	O
from	O
684	O
to	O
836	O
Å2	O
.	O

Interestingly	O
,	O
the	O
2	O
structures	B-evidence
that	O
have	O
the	O
largest	O
tilt	B-evidence
angle	I-evidence
differences	I-evidence
with	O
the	O
other	O
variants	O
,	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
and	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
,	O
have	O
the	O
smallest	O
VH	B-site
:	I-site
VL	I-site
interfaces	I-site
,	O
684	O
and	O
725	O
Å2	O
,	O
respectively	O
.	O

H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
is	O
also	O
unique	O
in	O
that	O
it	O
has	O
the	O
lowest	O
value	O
(	O
0	O
.	O
676	O
)	O
of	O
surface	B-evidence
complementarity	I-evidence
.	O

Melting	B-evidence
temperatures	I-evidence
for	O
the	O
16	O
Fabs	B-structure_element
.	O

Colors	O
:	O
blue	O
(	O
Tm	B-evidence
<	O
70	O
°	O
C	O
),	O
green	O
(	O
70	O
°	O
C	O
<	O
Tm	B-evidence
<	O
73	O
°	O
C	O
),	O
yellow	O
(	O
73	O
°	O
C	O
<	O
Tm	B-evidence
<	O
78	O
°	O
C	O
),	O
orange	O
(	O
Tm	B-evidence
>	O
78	O
°	O
C	O
).	O

Melting	B-evidence
temperatures	I-evidence
(	O
Tm	B-evidence
)	O
were	O
measured	O
for	O
all	O
Fabs	B-structure_element
using	O
differential	B-experimental_method
scanning	I-experimental_method
calorimetry	I-experimental_method
(	O
Table	O
5	O
).	O

It	O
appears	O
that	O
for	O
each	O
given	O
LC	B-structure_element
,	O
the	O
Fabs	B-structure_element
with	O
germlines	O
H1	B-mutant
-	I-mutant
69	I-mutant
and	O
H3	B-mutant
-	I-mutant
23	I-mutant
are	O
substantially	O
more	O
stable	B-protein_state
than	O
those	O
with	O
germlines	O
H3	B-mutant
-	I-mutant
53	I-mutant
and	O
H5	B-mutant
-	I-mutant
51	I-mutant
.	O

In	O
addition	O
,	O
L1	B-mutant
-	I-mutant
39	I-mutant
provides	O
a	O
much	O
higher	O
degree	O
of	O
stabilization	O
than	O
the	O
other	O
3	O
LC	B-structure_element
germlines	O
when	O
combined	O
with	O
any	O
of	O
the	O
HCs	B-structure_element
.	O

As	O
a	O
result	O
,	O
the	O
Tm	B-evidence
for	O
pairs	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L1	I-complex_assembly
-	I-complex_assembly
39	I-complex_assembly
and	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L1	I-complex_assembly
-	I-complex_assembly
39	I-complex_assembly
is	O
12	O
-	O
13	O
°	O
higher	O
than	O
for	O
pairs	O
H3	B-complex_assembly
-	I-complex_assembly
53	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
,	O
H3	B-complex_assembly
-	I-complex_assembly
53	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
,	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
and	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
.	O

These	O
findings	O
correlate	O
well	O
with	O
the	O
degree	O
of	O
conformational	O
disorder	O
observed	O
in	O
the	O
crystal	B-evidence
structures	I-evidence
.	O

Parts	O
of	O
CDR	B-structure_element
H3	B-structure_element
main	O
chain	O
are	O
completely	O
disordered	B-protein_state
,	O
and	O
were	O
not	O
modeled	O
in	O
Fabs	B-structure_element
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
and	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
11	I-complex_assembly
that	O
have	O
the	O
lowest	O
Tms	B-evidence
in	O
the	O
set	O
.	O

No	O
electron	B-evidence
density	I-evidence
is	O
observed	O
for	O
a	O
number	O
of	O
side	O
chains	O
in	O
CDRs	B-structure_element
H3	B-structure_element
and	O
L3	B-structure_element
in	O
all	O
Fabs	B-structure_element
with	O
germline	O
H3	B-mutant
-	I-mutant
53	I-mutant
,	O
which	O
indicates	O
loose	O
packing	O
of	O
the	O
variable	B-structure_element
domains	I-structure_element
.	O

All	O
those	O
molecules	O
are	O
relatively	O
unstable	O
,	O
as	O
is	O
reflected	O
in	O
their	O
low	O
Tms	B-evidence
.	O

This	O
is	O
the	O
first	O
report	O
of	O
a	O
systematic	B-experimental_method
structural	I-experimental_method
investigation	I-experimental_method
of	O
a	O
phage	B-experimental_method
germline	I-experimental_method
library	I-experimental_method
.	O

The	O
16	O
Fab	B-structure_element
structures	B-evidence
offer	O
a	O
unique	O
look	O
at	O
all	O
pairings	O
of	O
4	O
different	O
HCs	B-structure_element
(	O
H1	B-mutant
-	I-mutant
69	I-mutant
,	O
H3	B-mutant
-	I-mutant
23	I-mutant
,	O
H3	B-mutant
-	I-mutant
53	I-mutant
,	O
and	O
H5	B-mutant
-	I-mutant
51	I-mutant
)	O
and	O
4	O
different	O
LCs	B-structure_element
(	O
L1	B-mutant
-	I-mutant
39	I-mutant
,	O
L3	B-mutant
-	I-mutant
11	I-mutant
,	O
L3	B-mutant
-	I-mutant
20	I-mutant
and	O
L4	B-mutant
-	I-mutant
1	I-mutant
),	O
all	O
with	O
the	O
same	O
CDR	B-structure_element
H3	B-structure_element
.	O

The	O
structural	B-evidence
data	I-evidence
set	O
taken	O
as	O
a	O
whole	O
provides	O
insight	O
into	O
how	O
the	O
backbone	O
conformations	O
of	O
the	O
CDRs	B-structure_element
of	O
a	O
specific	O
heavy	O
or	O
light	B-structure_element
chain	I-structure_element
vary	O
when	O
it	O
is	O
paired	O
with	O
4	O
different	O
light	O
or	O
heavy	B-structure_element
chains	I-structure_element
,	O
respectively	O
.	O

A	O
large	O
variability	O
in	O
the	O
CDR	B-structure_element
conformations	O
for	O
the	O
sets	O
of	O
HCs	B-structure_element
and	O
LCs	B-structure_element
is	O
observed	O
.	O

In	O
some	O
cases	O
the	O
CDR	B-structure_element
conformations	O
for	O
all	O
members	O
of	O
a	O
set	O
are	O
virtually	O
identical	O
,	O
for	O
others	O
subtle	O
changes	O
occur	O
in	O
a	O
few	O
members	O
of	O
a	O
set	O
,	O
and	O
in	O
some	O
cases	O
larger	O
deviations	O
are	O
observed	O
within	O
a	O
set	O
.	O

The	O
five	O
variants	O
that	O
crystallized	B-experimental_method
with	O
2	O
copies	O
of	O
the	O
Fab	B-structure_element
in	O
the	O
asymmetric	O
unit	O
serve	O
somewhat	O
as	O
controls	O
for	O
the	O
influence	O
of	O
crystal	O
packing	O
on	O
the	O
conformations	O
of	O
the	O
CDRs	B-structure_element
.	O

In	O
four	O
of	O
the	O
5	O
structures	B-evidence
the	O
CDR	B-structure_element
conformations	O
are	O
consistent	O
.	O

In	O
only	O
one	O
case	O
,	O
that	O
of	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
(	O
the	O
lowest	O
resolution	O
structure	B-evidence
),	O
do	O
we	O
see	O
differences	O
in	O
the	O
conformations	O
of	O
the	O
2	O
copies	O
of	O
CDRs	B-structure_element
H1	B-structure_element
and	O
L1	B-structure_element
.	O

This	O
variability	O
is	O
likely	O
a	O
result	O
of	O
2	O
factors	O
,	O
crystal	O
packing	O
interactions	O
and	O
internal	O
instability	O
of	O
the	O
variable	B-structure_element
domain	I-structure_element
.	O

For	O
the	O
CDRs	B-structure_element
with	O
canonical	O
structures	O
,	O
the	O
largest	O
changes	O
in	O
conformation	O
occur	O
for	O
CDR	B-structure_element
H1	B-structure_element
of	O
H1	B-mutant
-	I-mutant
69	I-mutant
and	O
H3	B-mutant
-	I-mutant
53	I-mutant
.	O

The	O
other	O
2	O
HCs	B-structure_element
,	O
H3	B-mutant
-	I-mutant
23	I-mutant
and	O
H5	B-mutant
-	I-mutant
51	I-mutant
,	O
have	O
canonical	O
structures	O
that	O
are	O
remarkably	B-protein_state
well	I-protein_state
conserved	I-protein_state
(	O
Fig	O
.	O
1	O
).	O

Of	O
the	O
4	O
HCs	B-structure_element
,	O
H1	B-mutant
-	I-mutant
69	I-mutant
has	O
the	O
greatest	O
number	O
of	O
canonical	O
structure	O
assignments	O
(	O
Table	O
2	O
).	O

H1	B-mutant
-	I-mutant
69	I-mutant
is	O
unique	O
in	O
having	O
a	O
pair	O
of	O
glycine	B-residue_name
residues	O
at	O
positions	O
26	B-residue_number
and	O
27	B-residue_number
,	O
which	O
provide	O
more	O
conformational	B-protein_state
freedom	I-protein_state
in	O
CDR	B-structure_element
H1	B-structure_element
.	O

Besides	O
IGHV1	B-mutant
-	I-mutant
69	I-mutant
,	O
only	O
the	O
germlines	O
of	O
the	O
VH4	B-structure_element
family	O
possess	O
double	O
glycines	B-residue_name
in	O
CDR	B-structure_element
H1	B-structure_element
,	O
and	O
it	O
will	O
be	O
interesting	O
to	O
see	O
if	O
they	O
are	O
also	O
conformationally	B-protein_state
unstable	I-protein_state
.	O

Having	O
all	O
16	O
VH	B-complex_assembly
:	I-complex_assembly
VL	I-complex_assembly
pairs	O
with	O
the	O
same	O
CDR	B-structure_element
H3	B-structure_element
provides	O
some	O
insights	O
into	O
why	O
molecular	O
modeling	O
efforts	O
of	O
CDR	B-structure_element
H3	B-structure_element
have	O
proven	O
so	O
difficult	O
.	O

As	O
mentioned	O
in	O
the	O
Results	O
section	O
,	O
this	O
data	O
set	O
is	O
composed	O
of	O
21	O
Fabs	B-structure_element
,	O
since	O
5	O
of	O
the	O
16	O
variants	O
have	O
2	O
Fab	B-structure_element
copies	O
in	O
the	O
asymmetric	O
unit	O
.	O

For	O
the	O
18	O
Fabs	B-structure_element
with	O
complete	O
backbone	O
atoms	O
for	O
CDR	B-structure_element
H3	B-structure_element
,	O
10	O
have	O
conformations	O
similar	O
to	O
that	O
of	O
the	O
parent	O
,	O
while	O
the	O
others	O
have	O
significantly	O
different	O
conformations	O
(	O
Fig	O
.	O
6	O
).	O

Thus	O
,	O
it	O
is	O
likely	O
that	O
the	O
CDR	B-structure_element
H3	B-structure_element
conformation	O
is	O
dependent	O
upon	O
2	O
dominating	O
factors	O
:	O
1	O
)	O
amino	O
acid	O
sequence	O
;	O
and	O
2	O
)	O
VH	B-structure_element
and	O
VL	B-structure_element
context	O
.	O

More	O
than	O
half	O
of	O
the	O
variants	O
retain	O
the	O
conformation	O
of	O
the	O
parent	O
despite	O
having	O
differences	O
in	O
the	O
VH	B-complex_assembly
:	I-complex_assembly
VL	I-complex_assembly
pairing	O
.	O

This	O
subset	O
includes	O
2	O
structures	B-evidence
with	O
2	O
copies	O
of	O
the	O
Fab	B-structure_element
in	O
the	O
asymmetric	O
unit	O
,	O
all	O
of	O
which	O
are	O
nearly	O
identical	O
in	O
conformation	O
.	O

The	O
remaining	O
8	O
structures	B-evidence
exhibit	O
“	O
non	O
-	O
parental	O
”	O
conformations	O
,	O
indicating	O
that	O
the	O
VH	B-structure_element
and	O
VL	B-structure_element
context	O
can	O
also	O
be	O
a	O
dominating	O
factor	O
influencing	O
CDR	B-structure_element
H3	B-structure_element
.	O

This	O
subset	O
also	O
has	O
2	O
structures	B-evidence
with	O
2	O
Fab	B-structure_element
copies	O
in	O
the	O
asymmetric	O
unit	O
.	O

Interestingly	O
,	O
as	O
described	O
earlier	O
,	O
these	O
2	O
pairs	O
differ	O
in	O
the	O
stem	B-structure_element
regions	I-structure_element
with	O
the	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
pair	O
in	O
the	O
‘	O
extended	B-protein_state
’	O
conformation	O
and	O
H5	B-complex_assembly
-	I-complex_assembly
51	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
pair	O
in	O
the	O
‘	O
kinked	B-protein_state
’	O
conformation	O
.	O

The	O
CDR	B-structure_element
H3	B-structure_element
conformational	B-experimental_method
analysis	I-experimental_method
shows	O
that	O
,	O
for	O
each	O
set	O
of	O
variants	O
of	O
one	O
HC	B-structure_element
paired	O
with	O
the	O
4	O
different	O
LCs	B-structure_element
,	O
both	O
“	O
parental	O
”	O
and	O
“	O
non	O
-	O
parental	O
”	O
conformations	O
are	O
observed	O
.	O

The	O
same	O
variability	O
is	O
observed	O
for	O
the	O
sets	O
of	O
variants	O
composed	O
of	O
one	O
LC	B-structure_element
paired	O
with	O
each	O
of	O
the	O
4	O
HCs	B-structure_element
.	O

Thus	O
,	O
no	O
patterns	O
of	O
conformational	O
preference	O
for	O
a	O
particular	O
HC	B-structure_element
or	O
LC	B-structure_element
emerge	O
to	O
shed	O
any	O
direct	O
light	O
on	O
what	O
drives	O
the	O
conformational	O
differences	O
.	O

This	O
finding	O
supports	O
the	O
hypothesis	O
of	O
Weitzner	O
et	O
al	O
.	O
that	O
the	O
H3	B-structure_element
conformation	O
is	O
controlled	O
both	O
by	O
its	O
sequence	O
and	O
its	O
environment	O
.	O

In	O
looking	O
at	O
a	O
possible	O
correlation	O
between	O
the	O
tilt	B-evidence
angle	I-evidence
and	O
the	O
conformation	O
of	O
CDR	B-structure_element
H3	B-structure_element
,	O
no	O
clear	O
trends	O
are	O
observed	O
.	O

Two	O
variants	O
,	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
and	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
,	O
have	O
the	O
largest	O
differences	O
in	O
the	O
tilt	O
angles	O
compared	O
to	O
other	O
variants	O
as	O
seen	O
in	O
Table	O
3	O
.	O

The	O
absolute	O
VH	B-complex_assembly
:	I-complex_assembly
VL	I-complex_assembly
orientation	B-evidence
parameters	I-evidence
for	O
the	O
2	O
Fabs	B-structure_element
(	O
Table	O
S2	O
)	O
show	O
significant	O
deviation	B-evidence
in	O
HL	B-structure_element
,	O
LC1	B-structure_element
and	O
HC2	B-structure_element
values	O
(	O
2	O
-	O
3	O
standard	O
deviations	O
from	O
the	O
mean	O
).	O

One	O
of	O
the	O
variants	O
,	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
,	O
has	O
the	O
CDR	B-structure_element
H3	B-structure_element
conformation	O
similar	O
to	O
the	O
parent	O
,	O
but	O
the	O
other	O
,	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
,	O
is	O
different	O
.	O

As	O
noted	O
in	O
the	O
Results	O
section	O
,	O
the	O
2	O
variants	O
,	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
and	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
,	O
are	O
outliers	O
in	O
terms	O
of	O
the	O
tilt	B-evidence
angle	I-evidence
;	O
at	O
the	O
same	O
time	O
,	O
both	O
have	O
the	O
smallest	O
VH	B-site
:	I-site
VL	I-site
interface	I-site
.	O

These	O
smaller	O
interfaces	B-site
may	O
perhaps	O
translate	O
to	O
a	O
significant	O
deviation	O
in	O
how	O
VH	B-structure_element
is	O
oriented	O
relative	O
to	O
VL	B-structure_element
than	O
the	O
other	O
variants	O
.	O

These	O
deviations	O
from	O
the	O
other	O
variants	O
can	O
also	O
be	O
seen	O
to	O
some	O
extent	O
in	O
VH	B-complex_assembly
:	I-complex_assembly
VL	I-complex_assembly
orientation	O
parameters	O
in	O
Table	O
S2	O
,	O
as	O
well	O
as	O
in	O
the	O
smaller	O
number	O
of	O
residues	O
involved	O
in	O
the	O
VH	B-site
:	I-site
VL	I-site
interfaces	I-site
of	O
these	O
2	O
variants	O
(	O
Fig	O
.	O
S5	O
).	O

These	O
differences	O
undoubtedly	O
influence	O
the	O
conformation	O
of	O
the	O
CDRs	B-structure_element
,	O
in	O
particular	O
CDR	B-structure_element
H1	B-structure_element
(	O
Fig	O
.	O
1A	O
)	O
and	O
CDR	B-structure_element
L1	B-structure_element
(	O
Fig	O
.	O
3C	O
),	O
especially	O
with	O
the	O
tandem	O
glycines	B-residue_name
and	O
multiple	O
serines	B-residue_name
present	O
,	O
respectively	O
.	O

Pairing	O
of	O
different	O
germlines	O
yields	O
antibodies	B-protein_type
with	O
various	O
degrees	O
of	O
stability	O
.	O

As	O
indicated	O
by	O
the	O
melting	B-evidence
temperatures	I-evidence
,	O
germlines	O
H1	B-mutant
-	I-mutant
69	I-mutant
and	O
H3	B-mutant
-	I-mutant
23	I-mutant
for	O
HC	B-structure_element
and	O
germline	O
L1	B-mutant
-	I-mutant
39	I-mutant
for	O
LC	B-structure_element
produce	O
more	O
stable	B-protein_state
Fabs	B-structure_element
compared	O
to	O
the	O
other	O
germlines	O
in	O
the	O
experimental	O
set	O
.	O

One	O
possible	O
explanation	O
of	O
the	O
clear	O
preference	O
of	O
LC	B-structure_element
germline	O
L1	B-mutant
-	I-mutant
39	I-mutant
is	O
that	O
CDR	B-structure_element
L3	B-structure_element
has	O
smaller	O
residues	O
at	O
positions	O
91	B-residue_number
and	O
94	B-residue_number
,	O
allowing	O
for	O
more	O
room	O
to	O
accommodate	O
CDR	B-structure_element
H3	B-structure_element
.	O

Other	O
germlines	O
have	O
bulky	O
residues	O
,	O
Tyr	B-residue_name
,	O
Arg	B-residue_name
and	O
Trp	B-residue_name
,	O
at	O
these	O
positions	O
,	O
whereas	O
L1	B-mutant
-	I-mutant
39	I-mutant
has	O
Ser	B-residue_name
and	O
Thr	B-residue_name
.	O

Various	O
combinations	O
of	O
germline	O
sequences	O
for	O
VL	B-structure_element
and	O
VH	B-structure_element
impose	O
certain	O
constraints	O
on	O
CDR	B-structure_element
H3	B-structure_element
,	O
which	O
has	O
to	O
adapt	O
to	O
the	O
environment	O
.	O

A	O
more	O
compact	B-protein_state
CDR	B-structure_element
L3	B-structure_element
may	O
be	O
beneficial	O
in	O
this	O
situation	O
.	O

At	O
the	O
other	O
end	O
of	O
the	O
stability	O
range	O
is	O
LC	B-structure_element
germline	O
L3	B-mutant
-	I-mutant
20	I-mutant
,	O
which	O
yields	O
antibodies	B-protein_type
with	O
the	O
lowest	O
Tms	B-evidence
.	O

While	O
pairings	O
with	O
H3	B-mutant
-	I-mutant
53	I-mutant
and	O
H5	B-mutant
-	I-mutant
51	I-mutant
may	O
be	O
safely	O
called	O
a	O
mismatch	O
,	O
those	O
with	O
H1	B-mutant
-	I-mutant
69	I-mutant
and	O
H3	B-mutant
-	I-mutant
23	I-mutant
have	O
Tms	B-evidence
about	O
5	O
-	O
6	O
°	O
higher	O
.	O

Curiously	O
,	O
the	O
2	O
Fabs	B-structure_element
,	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
and	O
H3	B-complex_assembly
-	I-complex_assembly
23	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
,	O
deviate	O
markedly	O
in	O
their	O
tilt	B-evidence
angles	I-evidence
from	O
the	O
rest	O
of	O
the	O
panel	O
.	O

It	O
is	O
possible	O
that	O
by	O
adopting	O
extreme	O
tilt	B-evidence
angles	I-evidence
the	O
structure	B-evidence
modulates	O
CDR	B-structure_element
H3	B-structure_element
and	O
its	O
environment	O
,	O
which	O
apparently	O
cannot	O
be	O
achieved	O
solely	O
by	O
conformational	O
rearrangement	O
of	O
the	O
CDR	B-structure_element
.	O

Note	O
that	O
most	O
of	O
the	O
VH	B-site
:	I-site
VL	I-site
interface	I-site
residues	O
are	O
invariant	O
;	O
therefore	O
,	O
significant	O
change	O
of	O
the	O
tilt	O
angle	O
must	O
come	O
with	O
a	O
penalty	O
in	O
free	O
energy	O
.	O

Yet	O
,	O
for	O
the	O
2	O
antibodies	B-protein_type
,	O
the	O
total	O
gain	O
in	O
stability	O
merits	O
the	O
domain	O
repacking	O
.	O

Overall	O
,	O
the	O
stability	O
of	O
the	O
Fab	B-structure_element
,	O
as	O
measured	O
by	O
Tm	B-evidence
,	O
is	O
a	O
result	O
of	O
the	O
mutual	O
adjustment	O
of	O
the	O
HC	B-structure_element
and	O
LC	B-structure_element
variable	B-structure_element
domains	I-structure_element
and	O
adjustment	O
of	O
CDR	B-structure_element
H3	B-structure_element
to	O
the	O
VH	B-site
:	I-site
VL	I-site
cleft	I-site
.	O

The	O
final	O
conformation	O
represents	O
an	O
energetic	O
minimum	O
;	O
however	O
,	O
in	O
most	O
cases	O
it	O
is	O
very	O
shallow	O
,	O
so	O
that	O
a	O
single	O
mutation	O
can	O
cause	O
a	O
dramatic	O
rearrangement	O
of	O
the	O
structure	B-evidence
.	O

In	O
summary	O
,	O
the	O
analysis	O
of	O
this	O
structural	B-experimental_method
library	I-experimental_method
of	O
germline	O
variants	O
composed	O
of	O
all	O
pairs	O
of	O
4	O
HCs	B-structure_element
and	O
4LCs	O
,	O
all	O
with	O
the	O
same	O
CDR	B-structure_element
H3	B-structure_element
,	O
offers	O
some	O
unique	O
insights	O
into	O
antibody	B-protein_type
structure	B-evidence
and	O
how	O
pairing	O
and	O
sequence	O
may	O
influence	O
,	O
or	O
not	O
,	O
the	O
canonical	O
structures	O
of	O
the	O
L1	B-structure_element
,	O
L2	B-structure_element
,	O
L3	B-structure_element
,	O
H1	B-structure_element
and	O
H2	B-structure_element
CDRs	B-structure_element
.	O

Comparison	O
of	O
the	O
CDR	B-structure_element
H3s	B-structure_element
reveals	O
a	O
large	O
set	O
of	O
variants	O
with	O
conformations	O
similar	O
to	O
the	O
parent	O
,	O
while	O
a	O
second	O
set	O
has	O
significant	O
conformational	O
variability	O
,	O
indicating	O
that	O
both	O
the	O
sequence	O
and	O
the	O
structural	O
context	O
define	O
the	O
CDR	B-structure_element
H3	B-structure_element
conformation	O
.	O

Quite	O
unexpectedly	O
,	O
2	O
of	O
the	O
variants	O
,	O
H1	B-complex_assembly
-	I-complex_assembly
69	I-complex_assembly
:	I-complex_assembly
L3	I-complex_assembly
-	I-complex_assembly
20	I-complex_assembly
and	O
H3	B-complex_assembly
-	I-complex_assembly
53	I-complex_assembly
:	I-complex_assembly
L4	I-complex_assembly
-	I-complex_assembly
1	I-complex_assembly
,	O
have	O
the	O
‘	O
extended	B-protein_state
’	O
stem	B-structure_element
region	I-structure_element
differing	O
from	O
the	O
other	O
14	O
that	O
have	O
a	O
‘	O
kinked	B-protein_state
’	O
stem	B-structure_element
region	I-structure_element
.	O

These	O
data	O
reveal	O
the	O
difficulty	O
of	O
modeling	O
CDR	B-structure_element
H3	B-structure_element
accurately	O
,	O
as	O
shown	O
again	O
in	O
Antibody	O
Modeling	O
Assessment	O
II	O
.	O

Furthermore	O
,	O
antibody	B-protein_type
CDRs	B-structure_element
,	O
H3	B-structure_element
in	O
particular	O
,	O
may	O
go	O
through	O
conformational	O
changes	O
upon	O
binding	O
their	O
targets	O
,	O
making	O
structural	O
prediction	O
for	O
docking	O
purposes	O
an	O
even	O
more	O
difficult	O
task	O
.	O

Fortunately	O
,	O
for	O
most	O
applications	O
of	O
antibody	B-protein_type
modeling	O
,	O
such	O
as	O
engineering	O
affinity	O
and	O
biophysical	O
properties	O
,	O
an	O
accurate	O
CDR	B-structure_element
H3	B-structure_element
structure	B-evidence
is	O
not	O
always	O
necessary	O
.	O

For	O
those	O
applications	O
where	O
accurate	O
CDR	B-structure_element
structures	B-evidence
are	O
essential	O
,	O
such	O
as	O
docking	O
,	O
the	O
results	O
in	O
this	O
work	O
demonstrate	O
the	O
importance	O
of	O
experimental	O
structures	B-evidence
.	O

With	O
the	O
recent	O
advances	O
in	O
expression	B-experimental_method
and	I-experimental_method
crystallization	I-experimental_method
methods	I-experimental_method
,	O
Fab	B-structure_element
structures	B-evidence
can	O
be	O
obtained	O
rapidly	O
.	O

The	O
set	O
of	O
16	O
germline	O
Fab	B-structure_element
structures	B-evidence
offers	O
a	O
unique	O
dataset	O
to	O
facilitate	O
software	O
development	O
for	O
antibody	B-protein_type
modeling	O
.	O

The	O
results	O
essentially	O
support	O
the	O
underlying	O
idea	O
of	O
canonical	O
structures	B-evidence
,	O
indicating	O
that	O
most	O
CDRs	B-structure_element
with	O
germline	O
sequences	O
tend	O
to	O
adopt	O
predefined	O
conformations	O
.	O

From	O
this	O
point	O
of	O
view	O
,	O
a	O
novel	O
approach	O
to	O
design	O
combinatorial	O
antibody	B-protein_type
libraries	O
would	O
be	O
to	O
cover	O
the	O
range	O
of	O
CDR	B-structure_element
conformations	O
that	O
may	O
not	O
necessarily	O
coincide	O
with	O
the	O
germline	O
usage	O
in	O
the	O
human	B-species
repertoire	O
.	O

This	O
would	O
insure	O
more	O
structural	O
diversity	O
,	O
leading	O
to	O
a	O
more	O
diverse	O
panel	O
of	O
antibodies	B-protein_type
that	O
would	O
bind	O
to	O
a	O
broad	O
spectrum	O
of	O
targets	O
.	O

An	O
extended	B-protein_state
U2AF65	B-structure_element
–	I-structure_element
RNA	I-structure_element
-	I-structure_element
binding	I-structure_element
domain	I-structure_element
recognizes	O
the	O
3	B-site
′	I-site
splice	I-site
site	I-site
signal	O

How	O
the	O
essential	O
pre	B-protein_type
-	I-protein_type
mRNA	I-protein_type
splicing	I-protein_type
factor	I-protein_type
U2AF65	B-protein
recognizes	O
the	O
polypyrimidine	B-chemical
(	O
Py	B-chemical
)	O
signals	O
of	O
the	O
major	O
class	O
of	O
3	B-site
′	I-site
splice	I-site
sites	I-site
in	O
human	B-species
gene	O
transcripts	O
remains	O
incompletely	O
understood	O
.	O

We	O
determined	B-experimental_method
four	I-experimental_method
structures	I-experimental_method
of	O
an	O
extended	B-protein_state
U2AF65	B-structure_element
–	I-structure_element
RNA	I-structure_element
-	I-structure_element
binding	I-structure_element
domain	I-structure_element
bound	B-protein_state
to	I-protein_state
Py	B-chemical
-	I-chemical
tract	I-chemical
oligonucleotides	I-chemical
at	O
resolutions	O
between	O
2	O
.	O
0	O
and	O
1	O
.	O
5	O
Å	O
.	O
These	O
structures	B-evidence
together	O
with	O
RNA	B-experimental_method
binding	I-experimental_method
and	I-experimental_method
splicing	I-experimental_method
assays	I-experimental_method
reveal	O
unforeseen	O
roles	O
for	O
U2AF65	B-protein
inter	B-site
-	I-site
domain	I-site
residues	I-site
in	O
recognizing	O
a	O
contiguous	B-structure_element
,	O
nine	O
-	O
nucleotide	B-chemical
Py	B-chemical
tract	I-chemical
.	O

The	O
U2AF65	B-protein
linker	B-structure_element
residues	O
between	O
the	O
dual	O
RNA	B-structure_element
recognition	I-structure_element
motifs	I-structure_element
(	O
RRMs	B-structure_element
)	O
recognize	O
the	O
central	O
nucleotide	B-chemical
,	O
whereas	O
the	O
N	O
-	O
and	O
C	O
-	O
terminal	O
RRM	B-structure_element
extensions	I-structure_element
recognize	O
the	O
3	B-site
′	I-site
terminus	I-site
and	O
third	B-residue_number
nucleotide	B-chemical
.	O

Single	B-experimental_method
-	I-experimental_method
molecule	I-experimental_method
FRET	I-experimental_method
experiments	O
suggest	O
that	O
conformational	O
selection	O
and	O
induced	O
fit	O
of	O
the	O
U2AF65	B-protein
RRMs	B-structure_element
are	O
complementary	O
mechanisms	O
for	O
Py	B-chemical
-	I-chemical
tract	I-chemical
association	O
.	O

Altogether	O
,	O
these	O
results	O
advance	O
the	O
mechanistic	O
understanding	O
of	O
molecular	O
recognition	O
for	O
a	O
major	O
class	O
of	O
splice	B-site
site	I-site
signals	O
.	O

The	O
pre	B-protein_type
-	I-protein_type
mRNA	I-protein_type
splicing	I-protein_type
factor	I-protein_type
U2AF65	B-protein
recognizes	O
3	B-site
′	I-site
splice	I-site
sites	I-site
in	O
human	B-species
gene	O
transcripts	O
,	O
but	O
the	O
details	O
are	O
not	O
fully	O
understood	O
.	O

Here	O
,	O
the	O
authors	O
report	O
U2AF65	B-protein
structures	B-evidence
and	O
single	B-experimental_method
molecule	I-experimental_method
FRET	I-experimental_method
that	O
reveal	O
mechanistic	O
insights	O
into	O
splice	B-site
site	I-site
recognition	O
.	O

The	O
differential	O
skipping	O
or	O
inclusion	O
of	O
alternatively	O
spliced	O
pre	B-structure_element
-	I-structure_element
mRNA	I-structure_element
regions	I-structure_element
is	O
a	O
major	O
source	O
of	O
diversity	O
for	O
nearly	O
all	O
human	B-species
gene	O
transcripts	O
.	O

The	O
splice	B-site
sites	I-site
are	O
marked	O
by	O
relatively	O
short	B-structure_element
consensus	I-structure_element
sequences	I-structure_element
and	O
are	O
regulated	O
by	O
additional	O
pre	B-structure_element
-	I-structure_element
mRNA	I-structure_element
motifs	I-structure_element
(	O
reviewed	O
in	O
ref	O
.).	O

At	O
the	O
3	B-site
′	I-site
splice	I-site
site	I-site
of	O
the	O
major	O
intron	O
class	O
,	O
these	O
include	O
a	O
polypyrimidine	B-chemical
(	I-chemical
Py	I-chemical
)	I-chemical
tract	I-chemical
comprising	O
primarily	O
Us	B-residue_name
or	O
Cs	B-residue_name
,	O
which	O
is	O
preceded	O
by	O
a	O
branch	B-site
point	I-site
sequence	I-site
(	O
BPS	B-site
)	O
that	O
ultimately	O
serves	O
as	O
the	O
nucleophile	O
in	O
the	O
splicing	O
reaction	O
and	O
an	O
AG	B-chemical
-	I-chemical
dinucleotide	I-chemical
at	O
the	O
3	B-site
′	I-site
splice	I-site
site	I-site
junction	O
.	O

Disease	O
-	O
causing	O
mutations	O
often	O
compromise	O
pre	B-chemical
-	I-chemical
mRNA	I-chemical
splicing	O
(	O
reviewed	O
in	O
refs	O
),	O
yet	O
a	O
priori	O
predictions	O
of	O
splice	B-site
sites	I-site
and	O
the	O
consequences	O
of	O
their	O
mutations	O
are	O
challenged	O
by	O
the	O
brevity	O
and	O
degeneracy	O
of	O
known	O
splice	B-site
site	I-site
sequences	O
.	O

High	O
-	O
resolution	O
structures	B-evidence
of	O
intact	B-protein_state
splicing	B-complex_assembly
factor	I-complex_assembly
–	I-complex_assembly
RNA	I-complex_assembly
complexes	O
would	O
offer	O
key	O
insights	O
regarding	O
the	O
juxtaposition	O
of	O
the	O
distinct	O
splice	B-site
site	I-site
consensus	O
sequences	O
and	O
their	O
relationship	O
to	O
disease	O
-	O
causing	O
point	O
mutations	O
.	O

The	O
early	O
-	O
stage	O
pre	B-protein_type
-	I-protein_type
mRNA	I-protein_type
splicing	I-protein_type
factor	I-protein_type
U2AF65	B-protein
is	O
essential	O
for	O
viability	O
in	O
vertebrates	B-taxonomy_domain
and	O
other	O
model	O
organisms	O
(	O
for	O
example	O
,	O
ref	O
.).	O

A	O
tightly	O
controlled	O
assembly	B-complex_assembly
among	O
U2AF65	B-protein
,	O
the	O
pre	B-chemical
-	I-chemical
mRNA	I-chemical
,	O
and	O
partner	O
proteins	O
sequentially	O
identifies	O
the	O
3	B-site
′	I-site
splice	I-site
site	I-site
and	O
promotes	O
association	O
of	O
the	O
spliceosome	B-complex_assembly
,	O
which	O
ultimately	O
accomplishes	O
the	O
task	O
of	O
splicing	O
.	O

Initially	O
U2AF65	B-protein
recognizes	O
the	O
Py	B-chemical
-	I-chemical
tract	I-chemical
splice	B-site
site	I-site
signal	O
.	O

In	O
turn	O
,	O
the	O
ternary	B-complex_assembly
complex	I-complex_assembly
of	O
U2AF65	B-protein
with	O
SF1	B-protein
and	O
U2AF35	B-protein
identifies	O
the	O
surrounding	O
BPS	B-site
and	O
3	B-site
′	I-site
splice	I-site
site	I-site
junctions	O
.	O

Subsequently	O
U2AF65	B-protein
recruits	O
the	O
U2	B-complex_assembly
small	I-complex_assembly
nuclear	I-complex_assembly
ribonucleoprotein	I-complex_assembly
particle	I-complex_assembly
(	O
snRNP	B-complex_assembly
)	O
and	O
ultimately	O
dissociates	O
from	O
the	O
active	B-protein_state
spliceosome	B-complex_assembly
.	O

Biochemical	B-experimental_method
characterizations	I-experimental_method
of	O
U2AF65	B-protein
demonstrated	O
that	O
tandem	O
RNA	B-structure_element
recognition	I-structure_element
motifs	I-structure_element
(	O
RRM1	B-structure_element
and	O
RRM2	B-structure_element
)	O
recognize	O
the	O
Py	B-chemical
tract	I-chemical
(	O
Fig	O
.	O
1a	O
).	O

Milestone	O
crystal	B-evidence
structures	I-evidence
of	O
the	O
core	B-protein_state
U2AF65	B-protein
RRM1	B-structure_element
and	O
RRM2	B-structure_element
connected	O
by	O
a	O
shortened	B-protein_state
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
(	O
dU2AF651	B-mutant
,	I-mutant
2	I-mutant
)	O
detailed	O
a	O
subset	O
of	O
nucleotide	O
interactions	O
with	O
the	O
individual	O
U2AF65	B-protein
RRMs	B-structure_element
.	O

A	O
subsequent	O
NMR	B-experimental_method
structure	B-evidence
characterized	O
the	O
side	B-protein_state
-	I-protein_state
by	I-protein_state
-	I-protein_state
side	I-protein_state
arrangement	O
of	O
the	O
minimal	B-protein_state
U2AF65	B-protein
RRM1	B-structure_element
and	O
RRM2	B-structure_element
connected	O
by	O
a	O
linker	B-structure_element
of	O
natural	B-protein_state
length	I-protein_state
(	O
U2AF651	B-mutant
,	I-mutant
2	I-mutant
),	O
yet	O
depended	O
on	O
the	O
dU2AF651	B-mutant
,	I-mutant
2	I-mutant
crystal	B-evidence
structures	I-evidence
for	O
RNA	B-chemical
interactions	O
and	O
an	O
ab	O
initio	O
model	O
for	O
the	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
conformation	O
.	O

As	O
such	O
,	O
the	O
molecular	O
mechanisms	O
for	O
Py	B-chemical
-	I-chemical
tract	I-chemical
recognition	O
by	O
the	O
intact	B-protein_state
U2AF65	B-structure_element
–	I-structure_element
RNA	I-structure_element
-	I-structure_element
binding	I-structure_element
domain	I-structure_element
remained	O
unknown	O
.	O

Here	O
,	O
we	O
use	O
X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
and	O
biochemical	B-experimental_method
studies	I-experimental_method
to	O
reveal	O
new	O
roles	O
in	O
Py	B-chemical
-	I-chemical
tract	I-chemical
recognition	O
for	O
the	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
and	O
key	O
residues	O
surrounding	O
the	O
core	B-protein_state
U2AF65	B-protein
RRMs	B-structure_element
.	O

We	O
use	O
single	B-experimental_method
-	I-experimental_method
molecule	I-experimental_method
Förster	I-experimental_method
resonance	I-experimental_method
energy	I-experimental_method
transfer	I-experimental_method
(	O
smFRET	B-experimental_method
)	O
to	O
characterize	O
the	O
conformational	B-evidence
dynamics	I-evidence
of	O
this	O
extended	B-protein_state
U2AF65	B-structure_element
–	I-structure_element
RNA	I-structure_element
-	I-structure_element
binding	I-structure_element
domain	I-structure_element
during	O
Py	B-chemical
-	I-chemical
tract	I-chemical
recognition	O
.	O

Cognate	O
U2AF65	B-protein
–	O
Py	B-chemical
-	I-chemical
tract	I-chemical
recognition	O
requires	O
RRM	B-structure_element
extensions	I-structure_element

The	O
RNA	B-evidence
affinity	I-evidence
of	O
the	O
minimal	B-protein_state
U2AF651	B-mutant
,	I-mutant
2	I-mutant
domain	O
comprising	O
the	O
core	B-protein_state
RRM1	B-structure_element
–	O
RRM2	B-structure_element
folds	B-structure_element
(	O
U2AF651	B-mutant
,	I-mutant
2	I-mutant
,	O
residues	O
148	B-residue_range
–	I-residue_range
336	I-residue_range
)	O
is	O
relatively	O
weak	O
compared	O
with	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
U2AF65	B-protein
(	O
Fig	O
.	O
1a	O
,	O
b	O
;	O
Supplementary	O
Fig	O
.	O
1	O
).	O

Historically	O
,	O
this	O
difference	O
was	O
attributed	O
to	O
the	O
U2AF65	B-protein
arginine	B-structure_element
–	I-structure_element
serine	I-structure_element
rich	I-structure_element
domain	I-structure_element
,	O
which	O
contacts	O
pre	B-complex_assembly
-	I-complex_assembly
mRNA	I-complex_assembly
–	I-complex_assembly
U2	I-complex_assembly
snRNA	I-complex_assembly
duplexes	I-complex_assembly
outside	O
of	O
the	O
Py	B-chemical
tract	I-chemical
.	O

We	O
noticed	O
that	O
the	O
RNA	B-evidence
-	I-evidence
binding	I-evidence
affinity	I-evidence
of	O
the	O
U2AF651	B-mutant
,	I-mutant
2	I-mutant
domain	O
was	O
greatly	O
enhanced	O
by	O
the	O
addition	B-experimental_method
of	I-experimental_method
seven	I-experimental_method
and	I-experimental_method
six	I-experimental_method
residues	I-experimental_method
at	O
the	O
respective	O
N	O
and	O
C	O
termini	O
of	O
the	O
minimal	B-protein_state
RRM1	B-structure_element
and	O
RRM2	B-structure_element
(	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
,	O
residues	O
141	B-residue_range
–	I-residue_range
342	I-residue_range
;	O
Fig	O
.	O
1a	O
).	O

In	O
a	O
fluorescence	B-experimental_method
anisotropy	I-experimental_method
assay	I-experimental_method
for	O
binding	O
a	O
representative	O
Py	B-chemical
tract	I-chemical
derived	O
from	O
the	O
well	O
-	O
characterized	O
splice	B-site
site	I-site
of	O
the	O
adenovirus	B-gene
major	I-gene
late	I-gene
promoter	I-gene
(	O
AdML	B-gene
),	O
the	O
RNA	B-evidence
affinity	I-evidence
of	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
increased	O
by	O
100	O
-	O
fold	O
relative	O
to	O
U2AF651	B-mutant
,	I-mutant
2	I-mutant
to	O
comparable	O
levels	O
as	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
U2AF65	B-protein
(	O
Fig	O
.	O
1b	O
;	O
Supplementary	O
Fig	O
.	O
1a	O
–	O
d	O
).	O

Likewise	O
,	O
both	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
and	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
U2AF65	B-protein
showed	O
similar	O
sequence	B-evidence
specificity	I-evidence
for	O
U	B-structure_element
-	I-structure_element
rich	I-structure_element
stretches	I-structure_element
in	O
the	O
5	B-site
′-	I-site
region	I-site
of	O
the	O
Py	B-chemical
tract	I-chemical
and	O
promiscuity	O
for	O
C	B-structure_element
-	I-structure_element
rich	I-structure_element
regions	I-structure_element
in	O
the	O
3	B-site
′-	I-site
region	I-site
(	O
Fig	O
.	O
1c	O
,	O
Supplementary	O
Fig	O
.	O
1e	O
–	O
h	O
).	O

U2AF65	B-protein_state
-	I-protein_state
bound	I-protein_state
Py	B-chemical
tract	I-chemical
comprises	O
nine	O
contiguous	B-structure_element
nucleotides	B-chemical

To	O
investigate	O
the	O
structural	O
basis	O
for	O
cognate	O
U2AF65	B-protein
recognition	O
of	O
a	O
contiguous	B-structure_element
Py	B-chemical
tract	I-chemical
,	O
we	O
determined	B-experimental_method
four	O
crystal	B-evidence
structures	I-evidence
of	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
bound	B-protein_state
to	I-protein_state
Py	B-chemical
-	I-chemical
tract	I-chemical
oligonucleotides	I-chemical
(	O
Fig	O
.	O
2a	O
;	O
Table	O
1	O
).	O

By	O
sequential	B-experimental_method
boot	I-experimental_method
strapping	I-experimental_method
(	O
Methods	O
),	O
we	O
optimized	O
the	O
oligonucleotide	B-chemical
length	O
,	O
the	O
position	O
of	O
a	O
Br	B-chemical
-	I-chemical
dU	I-chemical
,	O
and	O
the	O
identity	O
of	O
the	O
terminal	O
nucleotide	B-chemical
(	O
rU	B-residue_name
,	O
dU	B-residue_name
and	O
rC	B-residue_name
)	O
to	O
achieve	O
full	O
views	O
of	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
bound	B-protein_state
to	I-protein_state
contiguous	B-structure_element
Py	B-chemical
tracts	I-chemical
at	O
up	O
to	O
1	O
.	O
5	O
Å	O
resolution	O
.	O

The	O
protein	O
and	O
oligonucleotide	B-chemical
conformations	O
are	O
nearly	O
identical	O
among	O
the	O
four	O
new	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
structures	B-evidence
(	O
Supplementary	O
Fig	O
.	O
2a	O
).	O

The	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
RRM1	B-structure_element
and	O
RRM2	B-structure_element
associate	O
with	O
the	O
Py	B-chemical
tract	I-chemical
in	O
a	O
parallel	B-protein_state
,	O
side	B-protein_state
-	I-protein_state
by	I-protein_state
-	I-protein_state
side	I-protein_state
arrangement	O
(	O
shown	O
for	O
representative	O
structure	O
iv	O
in	O
Fig	O
.	O
2b	O
,	O
c	O
;	O
Supplementary	O
Movie	O
1	O
).	O

An	O
extended	B-protein_state
conformation	I-protein_state
of	O
the	O
U2AF65	B-protein
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
traverses	O
across	O
the	O
α	B-structure_element
-	I-structure_element
helical	I-structure_element
surface	I-structure_element
of	O
RRM1	B-structure_element
and	O
the	O
central	O
β	B-structure_element
-	I-structure_element
strands	I-structure_element
of	O
RRM2	B-structure_element
and	O
is	O
well	O
defined	O
in	O
the	O
electron	B-evidence
density	I-evidence
(	O
Fig	O
.	O
2b	O
).	O

The	O
extensions	B-structure_element
at	O
the	O
N	O
terminus	O
of	O
RRM1	B-structure_element
and	O
C	O
terminus	O
of	O
RRM2	B-structure_element
adopt	O
well	O
-	O
ordered	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
.	O

Both	O
RRM1	B-structure_element
/	O
RRM2	B-structure_element
extensions	B-structure_element
and	O
the	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
of	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
directly	O
recognize	O
the	O
bound	B-protein_state
oligonucleotide	B-chemical
.	O

We	O
compare	O
the	O
global	O
conformation	O
of	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
structures	B-evidence
with	O
the	O
prior	O
dU2AF651	B-mutant
,	I-mutant
2	I-mutant
crystal	B-evidence
structure	I-evidence
and	O
U2AF651	B-mutant
,	I-mutant
2	I-mutant
NMR	B-experimental_method
structure	B-evidence
in	O
the	O
Supplementary	O
Discussion	O
and	O
Supplementary	O
Fig	O
.	O
2	O
.	O

The	O
discovery	O
of	O
nine	O
U2AF65	B-site
-	I-site
binding	I-site
sites	I-site
for	O
contiguous	B-structure_element
Py	B-chemical
-	I-chemical
tract	I-chemical
nucleotides	I-chemical
was	O
unexpected	O
.	O

Based	O
on	O
dU2AF651	B-mutant
,	I-mutant
2	I-mutant
structures	B-evidence
,	O
we	O
originally	O
hypothesized	O
that	O
the	O
U2AF65	B-protein
RRMs	B-structure_element
would	O
bind	O
the	O
minimal	B-protein_state
seven	O
nucleotides	B-chemical
observed	O
in	O
these	O
structures	B-evidence
.	O

Surprisingly	O
,	O
the	O
RRM2	B-structure_element
extension	I-structure_element
/	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
contribute	O
new	O
central	O
nucleotide	B-site
-	I-site
binding	I-site
sites	I-site
near	O
the	O
RRM1	B-site
/	I-site
RRM2	I-site
junction	I-site
and	O
the	O
RRM1	B-structure_element
extension	I-structure_element
recognizes	O
the	O
3	O
′-	O
terminal	O
nucleotide	B-chemical
(	O
Fig	O
.	O
2c	O
;	O
Supplementary	O
Movie	O
1	O
).	O

The	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
structures	B-evidence
characterize	O
ribose	B-chemical
(	O
r	B-chemical
)	O
nucleotides	B-chemical
at	O
all	O
of	O
the	O
binding	B-site
sites	I-site
except	O
the	O
seventh	B-residue_number
and	O
eighth	B-residue_number
deoxy	B-chemical
-(	I-chemical
d	I-chemical
)	I-chemical
U	I-chemical
,	O
which	O
are	O
likely	O
to	O
lack	O
2	O
′-	O
hydroxyl	O
contacts	O
based	O
on	O
the	O
RNA	B-protein_state
-	I-protein_state
bound	I-protein_state
dU2AF651	B-mutant
,	I-mutant
2	I-mutant
structure	B-evidence
.	O

Qualitatively	O
,	O
a	O
subset	O
of	O
the	O
U2AF651	B-site
,	I-site
2L	I-site
-	I-site
nucleotide	I-site
-	I-site
binding	I-site
sites	I-site
(	O
sites	B-site
1	I-site
–	I-site
3	I-site
and	O
7	B-site
–	I-site
9	I-site
)	O
share	O
similar	O
locations	O
to	O
those	O
of	O
the	O
dU2AF651	B-mutant
,	I-mutant
2	I-mutant
structures	B-evidence
(	O
Supplementary	O
Figs	O
2c	O
,	O
d	O
and	O
3	O
).	O

Yet	O
,	O
only	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
interactions	O
at	O
sites	B-site
1	I-site
and	I-site
7	I-site
are	O
nearly	O
identical	O
to	O
those	O
of	O
the	O
dU2AF651	B-mutant
,	I-mutant
2	I-mutant
structures	B-evidence
(	O
Supplementary	O
Fig	O
.	O
3a	O
,	O
f	O
).	O

In	O
striking	O
departures	O
from	O
prior	O
partial	O
views	O
,	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
structures	B-evidence
reveal	O
three	O
unanticipated	O
nucleotide	B-site
-	I-site
binding	I-site
sites	I-site
at	O
the	O
centre	O
of	O
the	O
Py	B-chemical
tract	I-chemical
,	O
as	O
well	O
as	O
numerous	O
new	O
interactions	O
that	O
underlie	O
cognate	O
recognition	O
of	O
the	O
Py	B-chemical
tract	I-chemical
(	O
Fig	O
.	O
3a	O
–	O
h	O
).	O

U2AF65	B-protein
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
interacts	O
with	O
the	O
Py	B-chemical
tract	I-chemical

The	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
RRM2	B-structure_element
,	O
the	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
and	O
RRM1	B-structure_element
concomitantly	O
recognize	O
the	O
three	O
central	O
nucleotides	B-chemical
of	O
the	O
Py	B-chemical
tract	I-chemical
,	O
which	O
are	O
likely	O
to	O
coordinate	O
the	O
conformational	O
arrangement	O
of	O
these	O
disparate	O
portions	O
of	O
the	O
protein	O
.	O

Residues	O
in	O
the	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
region	I-structure_element
of	O
the	O
U2AF65	B-protein
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
comprise	O
a	O
centrally	O
located	O
binding	B-site
site	I-site
for	O
the	O
fifth	B-residue_number
nucleotide	B-chemical
on	O
the	O
RRM2	B-site
surface	I-site
and	O
abutting	O
the	O
RRM1	B-site
/	I-site
RRM2	I-site
interface	I-site
(	O
Fig	O
.	O
3d	O
).	O

The	O
backbone	O
amide	O
of	O
the	O
linker	B-structure_element
V254	B-residue_name_number
and	O
the	O
carbonyl	O
of	O
T252	B-residue_name_number
engage	O
in	O
hydrogen	O
bonds	O
with	O
the	O
rU5	B-residue_name_number
-	O
O4	O
and	O
-	O
N3H	O
atoms	O
.	O

In	O
the	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
strand	I-structure_element
of	O
RRM1	B-structure_element
,	O
the	O
side	O
chains	O
of	O
K225	B-residue_name_number
and	O
R227	B-residue_name_number
donate	O
additional	O
hydrogen	O
bonds	O
to	O
the	O
rU5	B-residue_name_number
-	O
O2	O
lone	O
pair	O
electrons	O
.	O

The	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
region	I-structure_element
of	O
the	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
also	O
participates	O
in	O
the	O
preceding	O
rU4	B-site
-	I-site
binding	I-site
site	I-site
,	O
where	O
the	O
V254	B-residue_name_number
backbone	O
carbonyl	O
and	O
D256	B-residue_name_number
carboxylate	O
position	O
the	O
K260	B-residue_name_number
side	O
chain	O
to	O
hydrogen	O
bond	O
with	O
the	O
rU4	B-residue_name_number
-	O
O4	O
(	O
Fig	O
.	O
3c	O
).	O

Otherwise	O
,	O
the	O
rU4	B-residue_name_number
nucleotide	B-chemical
packs	O
against	O
F304	B-residue_name_number
in	O
the	O
signature	O
ribonucleoprotein	B-structure_element
consensus	I-structure_element
motif	I-structure_element
(	I-structure_element
RNP	I-structure_element
)-	I-structure_element
2	I-structure_element
of	O
RRM2	B-structure_element
.	O

At	O
the	O
opposite	O
side	O
of	O
the	O
central	O
fifth	B-residue_number
nucleotide	B-chemical
,	O
the	O
sixth	B-residue_number
rU6	B-residue_name_number
nucleotide	B-chemical
is	O
located	O
at	O
the	O
inter	B-site
-	I-site
RRM1	I-site
/	I-site
RRM2	I-site
interface	I-site
(	O
Fig	O
.	O
3e	O
;	O
Supplementary	O
Movie	O
1	O
).	O

This	O
nucleotide	B-chemical
twists	O
to	O
face	O
away	O
from	O
the	O
U2AF65	B-protein
linker	B-structure_element
and	O
instead	O
inserts	O
the	O
rU6	B-residue_name_number
-	O
uracil	B-residue_name
into	O
a	O
sandwich	O
between	O
the	O
β2	B-structure_element
/	I-structure_element
β3	I-structure_element
loops	I-structure_element
of	O
RRM1	B-structure_element
and	O
RRM2	B-structure_element
.	O

The	O
rU6	B-residue_name_number
base	O
edge	O
is	O
relatively	O
solvent	B-protein_state
exposed	I-protein_state
;	O
accordingly	O
,	O
the	O
rU6	B-residue_name_number
hydrogen	O
bonds	O
with	O
U2AF65	B-protein
are	O
water	B-chemical
mediated	O
apart	O
from	O
a	O
single	O
direct	O
interaction	O
by	O
the	O
RRM1	B-structure_element
-	O
N196	B-residue_name_number
side	O
chain	O
.	O

We	O
tested	B-experimental_method
the	I-experimental_method
contribution	I-experimental_method
of	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
interactions	O
with	O
the	O
new	O
central	O
nucleotide	B-chemical
to	O
Py	B-evidence
-	I-evidence
tract	I-evidence
affinity	I-evidence
(	O
Fig	O
.	O
3i	O
;	O
Supplementary	O
Fig	O
.	O
4a	O
,	O
b	O
).	O

Mutagenesis	B-experimental_method
of	O
either	O
V254	B-residue_name_number
in	O
the	O
U2AF65	B-protein
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
to	O
proline	B-residue_name
or	O
RRM1	B-structure_element
–	O
R227	B-residue_name_number
to	O
alanine	B-residue_name
,	O
which	O
remove	O
the	O
hydrogen	O
bond	O
with	O
the	O
fifth	B-residue_number
uracil	B-residue_name
-	O
O4	O
or	O
-	O
O2	O
,	O
reduced	O
the	O
affinities	B-evidence
of	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
for	O
the	O
representative	O
AdML	B-gene
Py	B-chemical
tract	I-chemical
by	O
four	O
-	O
or	O
five	O
-	O
fold	O
,	O
respectively	O
.	O

The	O
energetic	O
penalties	O
due	O
to	O
these	O
mutations	O
(	O
ΔΔG	B-evidence
0	O
.	O
8	O
–	O
0	O
.	O
9	O
kcal	O
mol	O
−	O
1	O
)	O
are	O
consistent	O
with	O
the	O
loss	O
of	O
each	O
hydrogen	O
bond	O
with	O
the	O
rU5	B-residue_name_number
base	O
and	O
support	O
the	O
relevance	O
of	O
the	O
central	O
nucleotide	O
interactions	O
observed	O
in	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
structures	B-evidence
.	O

U2AF65	B-protein
RRM	B-structure_element
extensions	I-structure_element
interact	O
with	O
the	O
Py	B-chemical
tract	I-chemical

The	O
N	B-structure_element
-	I-structure_element
and	I-structure_element
C	I-structure_element
-	I-structure_element
terminal	I-structure_element
extensions	I-structure_element
of	O
the	O
U2AF65	B-protein
RRM1	B-structure_element
and	O
RRM2	B-structure_element
directly	O
contact	O
the	O
bound	B-protein_state
Py	B-chemical
tract	I-chemical
.	O

Rather	O
than	O
interacting	O
with	O
a	O
new	O
5	O
′-	O
terminal	O
nucleotide	B-chemical
as	O
we	O
had	O
hypothesized	O
,	O
the	O
C	O
-	O
terminal	O
α	B-structure_element
-	I-structure_element
helix	I-structure_element
of	O
RRM2	B-structure_element
instead	O
folds	O
across	O
one	O
surface	O
of	O
rU3	B-residue_name_number
in	O
the	O
third	B-site
binding	I-site
site	I-site
(	O
Fig	O
.	O
3b	O
).	O

There	O
,	O
a	O
salt	O
bridge	O
between	O
the	O
K340	B-residue_name_number
side	O
chain	O
and	O
nucleotide	B-chemical
phosphate	O
,	O
as	O
well	O
as	O
G338	B-residue_name_number
-	O
base	O
stacking	O
and	O
a	O
hydrogen	O
bond	O
between	O
the	O
backbone	O
amide	O
of	O
G338	B-residue_name_number
and	O
the	O
rU3	B-residue_name_number
-	O
O4	O
,	O
secure	O
the	O
RRM2	B-structure_element
extension	I-structure_element
.	O

Indirectly	O
,	O
the	O
additional	O
contacts	O
with	O
the	O
third	B-residue_number
nucleotide	B-chemical
shift	O
the	O
rU2	B-residue_name_number
nucleotide	B-chemical
in	O
the	O
second	B-site
binding	I-site
site	I-site
closer	O
to	O
the	O
C	O
-	O
terminal	O
β	B-structure_element
-	I-structure_element
strand	I-structure_element
of	O
RRM2	B-structure_element
.	O

Consequently	O
,	O
the	O
U2AF651	B-protein_state
,	I-protein_state
2L	I-protein_state
-	I-protein_state
bound	I-protein_state
rU2	B-residue_name_number
-	O
O4	O
and	O
-	O
N3H	O
form	O
dual	O
hydrogen	O
bonds	O
with	O
the	O
K329	B-residue_name_number
backbone	O
atoms	O
(	O
Fig	O
.	O
3a	O
),	O
rather	O
than	O
a	O
single	O
hydrogen	O
bond	O
with	O
the	O
K329	B-residue_name_number
side	O
chain	O
as	O
in	O
the	O
prior	O
dU2AF651	B-mutant
,	I-mutant
2	I-mutant
structure	B-evidence
(	O
Supplementary	O
Fig	O
.	O
3b	O
).	O

At	O
the	O
N	O
terminus	O
,	O
the	O
α	B-structure_element
-	I-structure_element
helical	I-structure_element
extension	I-structure_element
of	O
U2AF65	B-protein
RRM1	B-structure_element
positions	O
the	O
Q147	B-residue_name_number
side	O
chain	O
to	O
bridge	O
the	O
eighth	B-residue_number
and	O
ninth	B-residue_number
nucleotides	B-chemical
at	O
the	O
3	B-site
′	I-site
terminus	I-site
of	O
the	O
Py	B-chemical
tract	I-chemical
(	O
Fig	O
.	O
3f	O
–	O
h	O
).	O

The	O
Q147	B-residue_name_number
residue	O
participates	O
in	O
hydrogen	O
bonds	O
with	O
the	O
-	O
N3H	O
of	O
the	O
eighth	B-residue_number
uracil	B-residue_name
and	O
-	O
O2	O
of	O
the	O
ninth	B-residue_number
pyrimidine	B-chemical
.	O

The	O
adjacent	O
R146	B-residue_name_number
guanidinium	O
group	O
donates	O
hydrogen	O
bonds	O
to	O
the	O
3	O
′-	O
terminal	O
ribose	B-chemical
-	O
O2	O
′	O
and	O
O3	O
′	O
atoms	O
,	O
where	O
it	O
could	O
form	O
a	O
salt	O
bridge	O
with	O
a	O
phospho	O
-	O
diester	O
group	O
in	O
the	O
context	O
of	O
a	O
longer	O
pre	B-chemical
-	I-chemical
mRNA	I-chemical
.	O

Consistent	O
with	O
loss	O
of	O
a	O
hydrogen	O
bond	O
with	O
the	O
ninth	B-residue_number
pyrimidine	B-chemical
-	O
O2	O
(	O
ΔΔG	B-evidence
1	O
.	O
0	O
kcal	O
mol	O
−	O
1	O
),	O
mutation	B-experimental_method
of	O
the	O
Q147	B-residue_name_number
to	O
an	O
alanine	B-residue_name
reduced	O
U2AF651	B-evidence
,	I-evidence
2L	I-evidence
affinity	I-evidence
for	O
the	O
AdML	B-gene
Py	B-chemical
tract	I-chemical
by	O
five	O
-	O
fold	O
(	O
Fig	O
.	O
3i	O
;	O
Supplementary	O
Fig	O
.	O
4c	O
).	O

We	O
compare	B-experimental_method
U2AF65	B-protein
interactions	O
with	O
uracil	B-residue_name
relative	O
to	O
cytosine	B-residue_name
pyrimidines	B-chemical
at	O
the	O
ninth	B-site
binding	I-site
site	I-site
in	O
Fig	O
.	O
3g	O
,	O
h	O
and	O
the	O
Supplementary	O
Discussion	O
.	O

Versatile	O
primary	O
sequence	O
of	O
the	O
U2AF65	B-protein
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element

The	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
structures	B-evidence
reveal	O
that	O
the	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
mediates	O
an	O
extensive	B-site
interface	I-site
with	O
the	O
second	O
α	B-structure_element
-	I-structure_element
helix	I-structure_element
of	O
RRM1	B-structure_element
,	O
the	O
β2	B-structure_element
/	I-structure_element
β3	I-structure_element
strands	I-structure_element
of	O
RRM2	B-structure_element
and	O
the	O
N	O
-	O
terminal	O
α	B-structure_element
-	I-structure_element
helical	I-structure_element
extension	I-structure_element
of	O
RRM1	B-structure_element
.	O

Altogether	O
,	O
the	O
U2AF65	B-protein
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
residues	O
(	O
R228	B-residue_range
–	I-residue_range
K260	I-residue_range
)	O
bury	O
2	O
,	O
800	O
Å2	O
of	O
surface	O
area	O
in	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
holo	B-protein_state
-	I-protein_state
protein	I-protein_state
,	O
suggestive	O
of	O
a	O
cognate	B-site
interface	I-site
compared	O
with	O
1	O
,	O
900	O
Å2	O
for	O
a	O
typical	O
protein	O
–	O
protein	O
complex	O
.	O

The	O
path	O
of	O
the	O
linker	B-structure_element
initiates	O
at	O
P229	B-residue_name_number
following	O
the	O
core	B-protein_state
RRM1	B-structure_element
β	B-structure_element
-	I-structure_element
strand	I-structure_element
,	O
in	O
a	O
kink	B-structure_element
that	O
is	O
positioned	O
by	O
intra	O
-	O
molecular	O
stacking	O
among	O
the	O
consecutive	O
R228	B-residue_name_number
,	O
Y232	B-residue_name_number
and	O
P234	B-residue_name_number
side	O
chains	O
(	O
Fig	O
.	O
4a	O
,	O
lower	O
right	O
).	O

A	O
second	B-structure_element
kink	I-structure_element
at	O
P236	B-residue_name_number
,	O
coupled	O
with	O
respective	O
packing	O
of	O
the	O
L235	B-residue_name_number
and	O
M238	B-residue_name_number
side	O
chains	O
on	O
the	O
N	O
-	O
terminal	O
α	B-structure_element
-	I-structure_element
helical	I-structure_element
RRM1	I-structure_element
extension	I-structure_element
and	O
the	O
core	B-protein_state
RRM1	B-structure_element
α2	B-structure_element
-	I-structure_element
helix	I-structure_element
,	O
reverses	O
the	O
direction	O
of	O
the	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
towards	O
the	O
RRM1	B-site
/	I-site
RRM2	I-site
interface	I-site
and	O
away	O
from	O
the	O
RNA	B-site
-	I-site
binding	I-site
site	I-site
.	O

In	O
the	O
neighbouring	O
apical	O
region	O
of	O
the	O
linker	B-structure_element
,	O
the	O
V244	B-residue_name_number
and	O
V246	B-residue_name_number
side	O
chains	O
pack	O
in	O
a	O
hydrophobic	B-site
pocket	I-site
between	O
two	O
α	B-structure_element
-	I-structure_element
helices	I-structure_element
of	O
the	O
core	B-protein_state
RRM1	B-structure_element
.	O

The	O
adjacent	O
V249	B-residue_name_number
and	O
V250	B-residue_name_number
are	O
notable	O
for	O
their	O
respective	O
interactions	O
that	O
connect	O
RRM1	B-structure_element
and	O
RRM2	B-structure_element
at	O
this	O
distal	O
interface	B-site
from	O
the	O
RNA	B-site
-	I-site
binding	I-site
site	I-site
(	O
Fig	O
.	O
4a	O
,	O
top	O
).	O

A	O
third	B-structure_element
kink	I-structure_element
stacks	O
P247	B-residue_name_number
and	O
G248	B-residue_name_number
with	O
Y245	B-residue_name_number
and	O
re	O
-	O
orients	O
the	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
region	I-structure_element
of	O
the	O
linker	B-structure_element
towards	O
the	O
RRM2	B-structure_element
and	O
bound	B-protein_state
RNA	B-chemical
.	O

At	O
the	O
RNA	B-chemical
surface	O
,	O
the	O
key	O
V254	B-residue_name_number
that	O
recognizes	O
the	O
fifth	B-residue_number
uracil	B-residue_name
is	O
secured	O
via	O
hydrophobic	O
contacts	O
between	O
its	O
side	O
chain	O
and	O
the	O
β	B-structure_element
-	I-structure_element
sheet	I-structure_element
surface	I-structure_element
of	O
RRM2	B-structure_element
,	O
chiefly	O
the	O
consensus	O
RNP1	B-structure_element
-	O
F304	B-residue_name_number
residue	O
that	O
stacks	O
with	O
the	O
fourth	B-residue_number
uracil	B-residue_name
(	O
Fig	O
.	O
4a	O
,	O
lower	O
left	O
).	O

Few	O
direct	O
contacts	O
are	O
made	O
between	O
the	O
remaining	O
residues	O
of	O
the	O
linker	B-structure_element
and	O
the	O
U2AF65	B-protein
RRM2	B-structure_element
;	O
instead	O
,	O
the	O
C	O
-	O
terminal	O
conformation	O
of	O
the	O
linker	B-structure_element
appears	O
primarily	O
RNA	B-chemical
mediated	O
(	O
Fig	O
.	O
3c	O
,	O
d	O
).	O

We	O
investigated	O
whether	O
the	O
observed	O
contacts	O
between	O
the	O
RRMs	B-structure_element
and	O
linker	B-structure_element
were	O
critical	O
for	O
RNA	O
binding	O
by	O
structure	B-experimental_method
-	I-experimental_method
guided	I-experimental_method
mutagenesis	I-experimental_method
(	O
Fig	O
.	O
4b	O
).	O

We	O
titrated	B-experimental_method
these	O
mutant	B-protein_state
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
proteins	O
into	O
fluorescein	B-chemical
-	O
labelled	O
AdML	B-gene
Py	B-chemical
-	I-chemical
tract	I-chemical
RNA	I-chemical
and	O
fit	O
the	O
fluorescence	B-evidence
anisotropy	I-evidence
changes	I-evidence
to	O
obtain	O
the	O
apparent	O
equilibrium	B-evidence
affinities	I-evidence
(	O
Supplementary	O
Fig	O
.	O
4d	O
–	O
h	O
).	O

We	O
introduced	O
glycine	B-residue_name
substitutions	B-experimental_method
to	O
maximally	O
reduce	O
the	O
buried	O
surface	O
area	O
without	O
directly	O
interfering	O
with	O
its	O
hydrogen	O
bonds	O
between	O
backbone	O
atoms	O
and	O
the	O
base	O
.	O

First	O
,	O
we	O
replaced	B-experimental_method
V249	B-residue_name_number
and	O
V250	B-residue_name_number
at	O
the	O
RRM1	B-site
/	I-site
RRM2	I-site
interface	I-site
and	O
V254	B-residue_name_number
at	O
the	O
bound	B-protein_state
RNA	B-chemical
site	O
with	O
glycine	B-residue_name
(	O
3Gly	B-mutant
).	O

However	O
,	O
the	O
resulting	O
decrease	O
in	O
the	O
AdML	B-gene
RNA	B-evidence
affinity	I-evidence
of	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
-	I-mutant
3Gly	I-mutant
mutant	B-protein_state
relative	O
to	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
protein	B-protein
was	O
not	O
significant	O
(	O
Fig	O
.	O
4b	O
).	O

In	O
parallel	O
,	O
we	O
replaced	B-experimental_method
five	O
linker	B-structure_element
residues	I-structure_element
(	O
S251	B-residue_name_number
,	O
T252	B-residue_name_number
,	O
V253	B-residue_name_number
,	O
V254	B-residue_name_number
and	O
P255	B-residue_name_number
)	O
at	O
the	O
fifth	B-site
nucleotide	I-site
-	I-site
binding	I-site
site	I-site
with	O
glycines	B-residue_name
(	O
5Gly	B-mutant
)	O
and	O
also	O
found	O
that	O
the	O
RNA	B-evidence
affinity	I-evidence
of	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
-	I-mutant
5Gly	I-mutant
mutant	B-protein_state
likewise	O
decreased	O
only	O
slightly	O
relative	O
to	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
protein	B-protein
.	O

A	O
more	O
conservative	B-experimental_method
substitution	I-experimental_method
of	O
these	O
five	O
residues	O
(	O
251	B-residue_range
–	I-residue_range
255	I-residue_range
)	O
with	O
an	O
unrelated	O
sequence	O
capable	O
of	O
backbone	O
-	O
mediated	O
hydrogen	O
bonds	O
(	O
STVVP	B-mutant
>	I-mutant
NLALA	I-mutant
)	O
confirmed	O
the	O
subtle	O
impact	O
of	O
this	O
versatile	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
sequence	I-structure_element
on	O
affinity	B-evidence
for	O
the	O
AdML	B-gene
Py	B-chemical
tract	I-chemical
.	O

Finally	O
,	O
to	O
ensure	O
that	O
these	O
selective	O
mutations	O
were	O
sufficient	O
to	O
disrupt	O
the	O
linker	B-structure_element
/	O
RRM	B-structure_element
contacts	O
,	O
we	O
substituted	B-experimental_method
glycine	B-residue_name
for	O
the	O
majority	O
of	O
buried	O
hydrophobic	O
residues	O
in	O
the	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
(	O
including	O
M144	B-residue_name_number
,	O
L235	B-residue_name_number
,	O
M238	B-residue_name_number
,	O
V244	B-residue_name_number
,	O
V246	B-residue_name_number
,	O
V249	B-residue_name_number
,	O
V250	B-residue_name_number
,	O
S251	B-residue_name_number
,	O
T252	B-residue_name_number
,	O
V253	B-residue_name_number
,	O
V254	B-residue_name_number
,	O
P255	B-residue_name_number
;	O
called	O
12Gly	B-mutant
).	O

Despite	O
12	B-experimental_method
concurrent	I-experimental_method
mutations	I-experimental_method
,	O
the	O
AdML	B-gene
RNA	B-evidence
affinity	I-evidence
of	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
-	I-mutant
12Gly	I-mutant
variant	B-protein_state
was	O
reduced	O
by	O
only	O
three	O
-	O
fold	O
relative	O
to	O
the	O
unmodified	B-protein_state
protein	B-protein
(	O
Fig	O
.	O
4b	O
),	O
which	O
is	O
less	O
than	O
the	O
penalty	O
of	O
the	O
V254P	B-mutant
mutation	O
that	O
disrupts	O
the	O
rU5	B-residue_name_number
hydrogen	O
bond	O
(	O
Fig	O
.	O
3d	O
,	O
i	O
).	O

To	O
test	O
the	O
interplay	O
of	O
the	O
U2AF65	B-protein
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
with	O
its	O
N	O
-	O
and	O
C	O
-	O
terminal	O
RRM	B-structure_element
extensions	I-structure_element
,	O
we	O
constructed	B-experimental_method
an	O
internal	O
linker	B-experimental_method
deletion	I-experimental_method
of	O
20	B-residue_range
-	I-residue_range
residues	I-residue_range
within	O
the	O
extended	B-protein_state
RNA	B-structure_element
-	I-structure_element
binding	I-structure_element
domain	I-structure_element
(	O
dU2AF651	B-mutant
,	I-mutant
2L	I-mutant
).	O

We	O
found	O
that	O
the	O
affinity	B-evidence
of	O
dU2AF651	B-mutant
,	I-mutant
2L	I-mutant
for	O
the	O
AdML	B-gene
RNA	B-chemical
was	O
significantly	O
reduced	O
relative	O
to	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
(	O
four	O
-	O
fold	O
,	O
Figs	O
1b	O
and	O
4b	O
;	O
Supplementary	O
Fig	O
.	O
4i	O
).	O

Yet	O
,	O
it	O
is	O
well	O
known	O
that	O
the	O
linker	B-experimental_method
deletion	I-experimental_method
in	O
the	O
context	O
of	O
the	O
minimal	B-protein_state
RRM1	B-structure_element
–	O
RRM2	B-structure_element
boundaries	O
has	O
no	O
detectable	O
effect	O
on	O
the	O
RNA	B-evidence
affinities	I-evidence
of	O
dU2AF651	B-mutant
,	I-mutant
2	I-mutant
compared	O
with	O
U2AF651	B-mutant
,	I-mutant
2	I-mutant
(	O
refs	O
;	O
Figs	O
1b	O
and	O
4b	O
;	O
Supplementary	O
Fig	O
.	O
4j	O
).	O

The	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
structures	B-evidence
suggest	O
that	O
an	O
extended	B-protein_state
conformation	I-protein_state
of	O
the	O
truncated	B-protein_state
dU2AF651	B-mutant
,	I-mutant
2	I-mutant
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
would	O
suffice	O
to	O
connect	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
RRM1	B-structure_element
C	O
terminus	O
to	O
the	O
N	O
terminus	O
of	O
RRM2	B-structure_element
(	O
24	O
Å	O
distance	O
between	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
R227	B-residue_name_number
-	O
Cα	O
–	O
H259	B-residue_name_number
-	O
Cα	O
atoms	O
),	O
which	O
agrees	O
with	O
the	O
greater	O
RNA	B-evidence
affinities	I-evidence
of	O
dU2AF651	B-mutant
,	I-mutant
2	I-mutant
and	O
U2AF651	B-mutant
,	I-mutant
2	I-mutant
dual	B-protein_state
RRMs	B-structure_element
compared	O
with	O
the	O
individual	B-protein_state
U2AF65	B-protein
RRMs	B-structure_element
.	O

However	O
,	O
stretching	O
of	O
the	O
truncated	B-protein_state
dU2AF651	B-mutant
,	I-mutant
2L	I-mutant
linker	B-structure_element
to	O
connect	O
the	O
RRM	B-structure_element
termini	I-structure_element
is	O
expected	O
to	O
disrupt	O
its	O
nucleotide	O
interactions	O
.	O

Likewise	O
,	O
deletion	B-experimental_method
of	O
the	O
N	O
-	O
terminal	O
RRM1	B-structure_element
extension	I-structure_element
in	O
the	O
shortened	B-protein_state
constructs	O
would	O
remove	O
packing	O
interactions	O
that	O
position	O
the	O
linker	B-structure_element
in	O
a	O
kinked	B-structure_element
turn	I-structure_element
following	O
P229	B-residue_name_number
(	O
Fig	O
.	O
4a	O
),	O
consistent	O
with	O
the	O
lower	O
RNA	B-evidence
affinities	I-evidence
of	O
dU2AF651	B-mutant
,	I-mutant
2L	I-mutant
,	O
dU2AF651	B-mutant
,	I-mutant
2	I-mutant
and	O
U2AF651	B-mutant
,	I-mutant
2	I-mutant
compared	O
with	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
.	O

To	O
further	O
test	O
cooperation	O
among	O
the	O
U2AF65	B-protein
RRM	B-structure_element
extensions	I-structure_element
and	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
for	O
RNA	O
recognition	O
,	O
we	O
tested	O
the	O
impact	O
of	O
a	O
triple	O
Q147A	B-mutant
/	O
V254P	B-mutant
/	O
R227A	B-mutant
mutation	B-experimental_method
(	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
-	I-mutant
3Mut	I-mutant
)	O
for	O
RNA	O
binding	O
(	O
Fig	O
.	O
4b	O
;	O
Supplementary	O
Fig	O
.	O
4d	O
).	O

Notably	O
,	O
the	O
Q147A	B-mutant
/	O
V254P	B-mutant
/	O
R227A	B-mutant
mutation	B-experimental_method
reduced	O
the	O
RNA	B-evidence
affinity	I-evidence
of	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
-	I-mutant
3Mut	I-mutant
protein	O
by	O
30	O
-	O
fold	O
more	O
than	O
would	O
be	O
expected	O
based	O
on	O
simple	O
addition	O
of	O
the	O
ΔΔG	B-evidence
'	O
s	O
for	O
the	O
single	O
mutations	O
.	O

This	O
difference	O
indicates	O
that	O
the	O
linearly	B-protein_state
distant	I-protein_state
regions	B-structure_element
of	O
the	O
U2AF65	B-protein
primary	O
sequence	O
,	O
including	O
Q147	B-residue_name_number
in	O
the	O
N	O
-	O
terminal	O
RRM1	B-structure_element
extension	I-structure_element
and	O
R227	B-residue_name_number
/	O
V254	B-residue_name_number
in	O
the	O
N	O
-/	O
C	O
-	O
terminal	O
linker	B-structure_element
regions	I-structure_element
at	O
the	O
fifth	B-site
nucleotide	I-site
site	I-site
,	O
cooperatively	O
recognize	O
the	O
Py	B-chemical
tract	I-chemical
.	O

Altogether	O
,	O
we	O
conclude	O
that	O
the	O
conformation	O
of	O
the	O
U2AF65	B-protein
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
is	O
key	O
for	O
recognizing	O
RNA	B-chemical
and	O
is	O
positioned	O
by	O
the	O
RRM	B-structure_element
extension	I-structure_element
but	O
otherwise	O
relatively	O
independent	O
of	O
the	O
side	O
chain	O
composition	O
.	O

The	O
non	O
-	O
additive	O
effects	O
of	O
the	O
Q147A	B-mutant
/	O
V254P	B-mutant
/	O
R227A	B-mutant
triple	B-experimental_method
mutation	I-experimental_method
,	O
coupled	O
with	O
the	O
context	O
-	O
dependent	O
penalties	O
of	O
an	O
internal	O
U2AF65	B-protein
linker	B-experimental_method
deletion	I-experimental_method
,	O
highlights	O
the	O
importance	O
of	O
the	O
structural	O
interplay	O
among	O
the	O
U2AF65	B-protein
linker	B-structure_element
and	O
the	O
N	B-structure_element
-	I-structure_element
and	I-structure_element
C	I-structure_element
-	I-structure_element
terminal	I-structure_element
extensions	I-structure_element
flanking	O
the	O
core	B-protein_state
RRMs	B-structure_element
.	O

Importance	O
of	O
U2AF65	B-complex_assembly
–	I-complex_assembly
RNA	I-complex_assembly
contacts	O
for	O
pre	B-chemical
-	I-chemical
mRNA	I-chemical
splicing	O

We	O
proceeded	O
to	O
test	O
the	O
importance	O
of	O
new	O
U2AF65	B-complex_assembly
–	I-complex_assembly
Py	I-complex_assembly
-	I-complex_assembly
tract	I-complex_assembly
interactions	O
for	O
splicing	O
of	O
a	O
model	O
pre	B-chemical
-	I-chemical
mRNA	I-chemical
substrate	O
in	O
a	O
human	B-species
cell	O
line	O
(	O
Fig	O
.	O
5	O
;	O
Supplementary	O
Fig	O
.	O
5	O
).	O

As	O
a	O
representative	O
splicing	O
substrate	O
,	O
we	O
utilized	O
a	O
well	O
-	O
characterized	O
minigene	B-chemical
splicing	I-chemical
reporter	I-chemical
(	O
called	O
pyPY	B-chemical
)	O
comprising	O
a	O
weak	O
(	O
that	O
is	O
,	O
degenerate	O
,	O
py	B-chemical
)	O
and	O
strong	O
(	O
that	O
is	O
,	O
U	B-structure_element
-	I-structure_element
rich	I-structure_element
,	O
PY	B-chemical
)	O
polypyrimidine	B-chemical
tracts	I-chemical
preceding	O
two	O
alternative	O
splice	B-site
sites	I-site
(	O
Fig	O
.	O
5a	O
).	O

When	O
transfected	B-experimental_method
into	O
HEK293T	O
cells	O
containing	O
only	O
endogenous	B-protein_state
U2AF65	B-protein
,	O
the	O
PY	B-site
splice	I-site
site	I-site
is	O
used	O
and	O
the	O
remaining	O
transcript	O
remains	O
unspliced	O
.	O

When	O
co	B-experimental_method
-	I-experimental_method
transfected	I-experimental_method
with	O
an	O
expression	B-experimental_method
plasmid	I-experimental_method
for	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
U2AF65	B-protein
,	O
use	O
of	O
the	O
py	B-site
splice	I-site
site	I-site
significantly	O
increases	O
(	O
by	O
more	O
than	O
five	O
-	O
fold	O
)	O
and	O
as	O
documented	O
converts	O
a	O
fraction	O
of	O
the	O
unspliced	O
to	O
spliced	O
transcript	O
.	O

The	O
strong	O
PY	B-site
splice	I-site
site	I-site
is	O
insensitive	O
to	O
added	O
U2AF65	B-protein
,	O
suggesting	O
that	O
endogenous	B-protein_state
U2AF65	B-protein
levels	O
are	O
sufficient	O
to	O
saturate	O
this	O
site	O
(	O
Supplementary	O
Fig	O
.	O
5b	O
).	O

We	O
introduced	O
the	O
triple	B-experimental_method
mutation	I-experimental_method
(	O
V254P	B-mutant
/	O
R227A	B-mutant
/	O
Q147A	B-mutant
)	O
that	O
significantly	O
reduced	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
association	O
with	O
the	O
Py	B-chemical
tract	I-chemical
(	O
Fig	O
.	O
4b	O
)	O
in	O
the	O
context	O
of	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
U2AF65	B-protein
(	O
U2AF65	B-mutant
-	I-mutant
3Mut	I-mutant
).	O

Co	B-experimental_method
-	I-experimental_method
transfection	I-experimental_method
of	O
the	O
U2AF65	B-mutant
-	I-mutant
3Mut	I-mutant
with	O
the	O
pyPY	B-chemical
splicing	O
substrate	O
significantly	O
reduced	O
splicing	O
of	O
the	O
weak	O
‘	B-site
py	I-site
'	I-site
splice	I-site
site	I-site
relative	O
to	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
U2AF65	B-protein
(	O
Fig	O
.	O
5b	O
,	O
c	O
).	O

We	O
conclude	O
that	O
the	O
Py	B-chemical
-	I-chemical
tract	I-chemical
interactions	O
with	O
these	O
residues	O
of	O
the	O
U2AF65	B-protein
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
and	O
RRM	B-structure_element
extensions	I-structure_element
are	O
important	O
for	O
splicing	O
as	O
well	O
as	O
for	O
binding	O
a	O
representative	O
of	O
the	O
major	B-structure_element
U2	I-structure_element
-	I-structure_element
class	I-structure_element
of	I-structure_element
splice	I-structure_element
sites	I-structure_element
.	O

Sparse	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
contacts	O
underlie	O
apo	B-protein_state
-	O
U2AF65	B-protein
dynamics	O

The	O
direct	O
interface	B-site
between	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
RRM1	B-structure_element
and	O
RRM2	B-structure_element
is	O
minor	O
,	O
burying	O
265	O
Å2	O
of	O
solvent	O
accessible	O
surface	O
area	O
compared	O
with	O
570	O
Å2	O
on	O
average	O
for	O
a	O
crystal	O
packing	O
interface	O
.	O

A	O
handful	O
of	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
hydrogen	O
bonds	O
are	O
apparent	O
between	O
the	O
side	O
chains	O
of	O
RRM1	B-structure_element
-	O
N155	B-residue_name_number
and	O
RRM2	B-structure_element
-	O
K292	B-residue_name_number
,	O
RRM1	B-structure_element
-	O
N155	B-residue_name_number
and	O
RRM2	B-structure_element
-	O
D272	B-residue_name_number
as	O
well	O
as	O
the	O
backbone	O
atoms	O
of	O
RRM1	B-structure_element
-	O
G221	B-residue_name_number
and	O
RRM2	B-structure_element
-	O
D273	B-residue_name_number
(	O
Fig	O
.	O
4c	O
).	O

This	O
minor	O
U2AF65	B-protein
RRM1	B-site
/	I-site
RRM2	I-site
interface	I-site
,	O
coupled	O
with	O
the	O
versatile	O
sequence	O
of	O
the	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
,	O
highlighted	O
the	O
potential	O
role	O
for	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
conformational	O
dynamics	O
in	O
U2AF65	B-protein
-	O
splice	O
site	O
recognition	O
.	O

Paramagnetic	B-experimental_method
resonance	I-experimental_method
enhancement	I-experimental_method
(	O
PRE	B-experimental_method
)	O
measurements	O
previously	O
had	O
suggested	O
a	O
predominant	O
back	B-protein_state
-	I-protein_state
to	I-protein_state
-	I-protein_state
back	I-protein_state
,	O
or	O
‘	O
closed	B-protein_state
'	O
conformation	O
of	O
the	O
apo	B-protein_state
-	O
U2AF651	B-mutant
,	I-mutant
2	I-mutant
RRM1	B-structure_element
and	O
RRM2	B-structure_element
in	O
equilibrium	O
with	O
a	O
minor	O
‘	O
open	B-protein_state
'	O
conformation	O
resembling	O
the	O
RNA	B-protein_state
-	I-protein_state
bound	I-protein_state
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
arrangement	O
.	O

Yet	O
,	O
small	B-experimental_method
-	I-experimental_method
angle	I-experimental_method
X	I-experimental_method
-	I-experimental_method
ray	I-experimental_method
scattering	I-experimental_method
(	O
SAXS	B-experimental_method
)	O
data	O
indicated	O
that	O
both	O
the	O
minimal	B-protein_state
U2AF651	B-mutant
,	I-mutant
2	I-mutant
and	O
longer	O
constructs	O
comprise	O
a	O
highly	B-protein_state
diverse	I-protein_state
continuum	I-protein_state
of	I-protein_state
conformations	I-protein_state
in	O
the	O
absence	B-protein_state
of	I-protein_state
RNA	B-chemical
that	O
includes	O
the	O
‘	O
closed	B-protein_state
'	O
and	O
‘	O
open	B-protein_state
'	O
conformations	O
.	O

To	O
complement	O
the	O
static	O
portraits	O
of	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
structure	B-evidence
that	O
we	O
had	O
determined	O
by	O
X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
,	O
we	O
used	O
smFRET	B-experimental_method
to	O
characterize	O
the	O
probability	B-evidence
distribution	I-evidence
functions	I-evidence
and	O
time	O
dependence	O
of	O
U2AF65	B-protein
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
conformational	O
dynamics	O
in	O
solution	O
.	O

The	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
dynamics	O
of	O
U2AF65	B-protein
were	O
followed	O
using	O
FRET	B-experimental_method
between	O
fluorophores	B-chemical
attached	O
to	O
RRM1	B-structure_element
and	O
RRM2	B-structure_element
(	O
Fig	O
.	O
6a	O
,	O
b	O
,	O
Methods	O
).	O

The	O
positions	O
of	O
single	O
cysteine	B-residue_name
mutations	B-experimental_method
for	O
fluorophore	B-chemical
attachment	O
(	O
A181C	B-mutant
in	O
RRM1	B-structure_element
and	O
Q324C	B-mutant
in	O
RRM2	B-structure_element
)	O
were	O
chosen	O
based	O
on	O
inspection	O
of	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
structures	B-evidence
and	O
the	O
‘	O
closed	B-protein_state
'	O
model	O
of	O
apo	B-protein_state
-	O
U2AF651	B-mutant
,	I-mutant
2	I-mutant
.	O

Criteria	O
included	O
(	O
i	O
)	O
residue	O
locations	O
that	O
are	O
distant	O
from	O
and	O
hence	O
not	O
expected	O
to	O
interfere	O
with	O
the	O
RRM	B-complex_assembly
/	I-complex_assembly
RNA	I-complex_assembly
or	O
inter	B-site
-	I-site
RRM	I-site
interfaces	I-site
,	O
(	O
ii	O
)	O
inter	O
-	O
dye	O
distances	O
(	O
50	O
Å	O
for	O
U2AF651	B-complex_assembly
,	I-complex_assembly
2L	I-complex_assembly
–	I-complex_assembly
Py	I-complex_assembly
tract	I-complex_assembly
and	O
30	O
Å	O
for	O
the	O
closed	B-protein_state
apo	B-protein_state
-	O
model	O
)	O
that	O
are	O
expected	O
to	O
be	O
near	O
the	O
Förster	B-experimental_method
radius	I-experimental_method
(	I-experimental_method
Ro	I-experimental_method
)	I-experimental_method
for	O
the	O
Cy3	B-chemical
/	O
Cy5	B-chemical
pair	O
(	O
56	O
Å	O
),	O
where	O
changes	O
in	O
the	O
efficiency	O
of	O
energy	O
transfer	O
are	O
most	O
sensitive	O
to	O
distance	O
,	O
and	O
(	O
iii	O
)	O
FRET	B-evidence
efficiencies	I-evidence
that	O
are	O
calculated	O
to	O
be	O
significantly	O
greater	O
for	O
the	O
‘	O
closed	B-protein_state
'	O
apo	B-protein_state
-	O
model	O
as	O
opposed	O
to	O
the	O
‘	O
open	B-protein_state
'	O
RNA	B-protein_state
-	I-protein_state
bound	I-protein_state
structures	B-evidence
(	O
by	O
∼	O
30	O
%).	O

The	O
FRET	B-evidence
efficiencies	I-evidence
of	O
either	O
of	O
these	O
structurally	O
characterized	O
conformations	O
also	O
are	O
expected	O
to	O
be	O
significantly	O
greater	O
than	O
elongated	B-protein_state
U2AF65	B-protein
conformations	O
that	O
lack	B-protein_state
inter	O
-	O
RRM	B-structure_element
contacts	O
.	O

Double	O
-	O
cysteine	B-residue_name
variant	B-protein_state
of	O
U2AF651	B-mutant
,	I-mutant
2	I-mutant
was	O
modified	B-experimental_method
with	O
equimolar	O
amount	O
of	O
Cy3	B-chemical
and	O
Cy5	B-chemical
.	O

Only	O
traces	B-evidence
that	O
showed	O
single	O
photobleaching	O
events	O
for	O
both	O
donor	O
and	O
acceptor	O
dyes	O
and	O
anti	O
-	O
correlated	O
changes	O
in	O
acceptor	O
and	O
donor	O
fluorescence	O
were	O
included	O
in	O
smFRET	B-experimental_method
data	O
analysis	O
.	O

We	O
first	O
characterized	O
the	O
conformational	O
dynamics	O
spectrum	O
of	O
U2AF65	B-protein
in	O
the	O
absence	B-protein_state
of	I-protein_state
RNA	B-chemical
(	O
Fig	O
.	O
6c	O
,	O
d	O
;	O
Supplementary	O
Fig	O
.	O
7a	O
,	O
b	O
).	O

The	O
double	O
-	O
labelled	O
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
)	O
protein	O
was	O
tethered	B-protein_state
to	O
a	O
slide	O
via	O
biotin	B-chemical
-	I-chemical
NTA	I-chemical
/	I-chemical
Ni	I-chemical
+	I-chemical
2	I-chemical
resin	I-chemical
.	O

Virtually	O
no	O
fluorescent	O
molecules	O
were	O
detected	O
in	O
the	O
absence	B-protein_state
of	I-protein_state
biotin	B-chemical
-	I-chemical
NTA	I-chemical
/	I-chemical
Ni	I-chemical
+	I-chemical
2	I-chemical
,	O
which	O
demonstrates	O
the	O
absence	B-protein_state
of	I-protein_state
detectable	O
non	O
-	O
specific	O
binding	O
of	O
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
to	O
the	O
slide	O
.	O

The	O
FRET	B-evidence
distribution	I-evidence
histogram	I-evidence
built	O
from	O
more	O
than	O
a	O
thousand	O
traces	B-evidence
of	O
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
)	O
in	O
the	O
absence	B-protein_state
of	I-protein_state
ligand	B-chemical
showed	O
an	O
extremely	O
broad	O
distribution	O
centred	O
at	O
a	O
FRET	B-evidence
efficiency	I-evidence
of	O
∼	O
0	O
.	O
4	O
(	O
Fig	O
.	O
6d	O
).	O

Approximately	O
40	O
%	O
of	O
the	O
smFRET	B-experimental_method
traces	B-evidence
showed	O
apparent	O
transitions	O
between	O
multiple	O
FRET	B-evidence
values	I-evidence
(	O
for	O
example	O
,	O
Fig	O
.	O
6c	O
).	O

Despite	O
the	O
large	O
width	O
of	O
the	O
FRET	B-evidence
-	I-evidence
distribution	I-evidence
histogram	I-evidence
,	O
the	O
majority	O
(	O
80	O
%)	O
of	O
traces	B-evidence
that	O
showed	O
fluctuations	O
sampled	O
only	O
two	O
distinct	O
FRET	B-evidence
states	I-evidence
(	O
for	O
example	O
,	O
Supplementary	O
Fig	O
.	O
7a	O
).	O

Approximately	O
70	O
%	O
of	O
observed	O
fluctuations	O
were	O
interchanges	O
between	O
the	O
∼	O
0	O
.	O
65	O
and	O
∼	O
0	O
.	O
45	O
FRET	B-evidence
values	I-evidence
(	O
Supplementary	O
Fig	O
.	O
7b	O
).	O

We	O
cannot	O
exclude	O
a	O
possibility	O
that	O
tethering	O
of	O
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
)	O
to	O
the	O
microscope	O
slide	O
introduces	O
structural	O
heterogeneity	O
into	O
the	O
protein	O
and	O
,	O
thus	O
,	O
contributes	O
to	O
the	O
breadth	O
of	O
the	O
FRET	B-evidence
distribution	I-evidence
histogram	I-evidence
.	O

However	O
,	O
the	O
presence	O
of	O
repetitive	O
fluctuations	O
between	O
particular	O
FRET	B-evidence
values	I-evidence
supports	O
the	O
hypothesis	O
that	O
RNA	B-protein_state
-	I-protein_state
free	I-protein_state
U2AF65	B-protein
samples	O
several	O
distinct	O
conformations	O
.	O

This	O
result	O
is	O
consistent	O
with	O
the	O
broad	O
ensembles	O
of	O
extended	B-protein_state
solution	O
conformations	O
that	O
best	O
fit	O
the	O
SAXS	B-experimental_method
data	O
collected	O
for	O
U2AF651	B-mutant
,	I-mutant
2	I-mutant
as	O
well	O
as	O
for	O
a	O
longer	O
construct	O
(	O
residues	O
136	B-residue_range
–	I-residue_range
347	I-residue_range
).	O

We	O
conclude	O
that	O
weak	O
contacts	O
between	O
the	O
U2AF65	B-protein
RRM1	B-structure_element
and	O
RRM2	B-structure_element
permit	O
dissociation	O
of	O
these	O
RRMs	B-structure_element
in	O
the	O
absence	B-protein_state
of	I-protein_state
RNA	B-chemical
.	O

U2AF65	B-protein
conformational	O
selection	O
and	O
induced	O
fit	O
by	O
bound	B-protein_state
RNA	B-chemical

We	O
next	O
used	O
smFRET	B-experimental_method
to	O
probe	O
the	O
conformational	O
selection	O
of	O
distinct	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
arrangements	O
following	O
association	O
of	O
U2AF65	B-protein
with	O
the	O
AdML	B-gene
Py	B-chemical
-	I-chemical
tract	I-chemical
prototype	O
.	O

Addition	O
of	O
the	O
AdML	B-gene
RNA	B-chemical
to	O
tethered	B-protein_state
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
)	O
selectively	O
increases	O
a	O
fraction	O
of	O
molecules	O
showing	O
an	O
∼	O
0	O
.	O
45	O
apparent	O
FRET	B-evidence
efficiency	I-evidence
,	O
suggesting	O
that	O
RNA	O
binding	O
stabilizes	O
a	O
single	O
conformation	O
,	O
which	O
corresponds	O
to	O
the	O
0	O
.	O
45	O
FRET	B-evidence
state	I-evidence
(	O
Fig	O
.	O
6e	O
,	O
f	O
).	O

To	O
assess	O
the	O
possible	O
contributions	O
of	O
RNA	B-protein_state
-	I-protein_state
free	I-protein_state
conformations	O
of	O
U2AF65	B-protein
and	O
/	O
or	O
structural	O
heterogeneity	O
introduced	O
by	O
tethering	B-experimental_method
of	O
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
)	O
to	O
the	O
slide	O
to	O
the	O
observed	O
distribution	B-evidence
of	I-evidence
FRET	I-evidence
values	I-evidence
,	O
we	O
reversed	B-experimental_method
the	I-experimental_method
immobilization	I-experimental_method
scheme	I-experimental_method
.	O

We	O
tethered	B-protein_state
the	O
AdML	B-gene
RNA	B-chemical
to	O
the	O
slide	O
via	O
a	O
biotinylated	B-chemical
oligonucleotide	I-chemical
DNA	I-chemical
handle	O
and	O
added	B-experimental_method
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
)	O
in	O
the	O
absence	B-protein_state
of	I-protein_state
biotin	B-chemical
-	I-chemical
NTA	I-chemical
resin	I-chemical
(	O
Fig	O
.	O
6g	O
,	O
h	O
;	O
Supplementary	O
Fig	O
.	O
7c	O
–	O
g	O
).	O

A	O
0	O
.	O
45	O
FRET	B-evidence
value	I-evidence
was	O
again	O
predominant	O
,	O
indicating	O
a	O
similar	O
RNA	B-protein_state
-	I-protein_state
bound	I-protein_state
conformation	O
and	O
structural	O
dynamics	O
for	O
the	O
untethered	B-protein_state
and	O
tethered	B-protein_state
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
).	O

We	O
examined	O
the	O
effect	O
on	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
conformations	O
of	O
purine	B-experimental_method
interruptions	I-experimental_method
that	O
often	O
occur	O
in	O
relatively	O
degenerate	O
human	B-species
Py	B-chemical
tracts	I-chemical
.	O

We	O
introduced	B-experimental_method
an	O
rArA	B-chemical
purine	B-chemical
dinucleotide	I-chemical
within	O
a	O
variant	O
of	O
the	O
AdML	B-gene
Py	B-chemical
tract	I-chemical
(	O
detailed	O
in	O
Methods	O
).	O

Insertion	B-experimental_method
of	O
adenine	B-chemical
nucleotides	I-chemical
decreased	O
binding	B-evidence
affinity	I-evidence
of	O
U2AF65	B-protein
to	O
RNA	B-chemical
by	O
approximately	O
five	O
-	O
fold	O
.	O

Nevertheless	O
,	O
in	O
the	O
presence	O
of	O
saturating	O
concentrations	O
of	O
rArA	B-chemical
-	O
interrupted	O
RNA	B-chemical
slide	B-protein_state
-	I-protein_state
tethered	I-protein_state
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
)	O
showed	O
a	O
prevalent	O
∼	O
0	O
.	O
45	O
apparent	O
FRET	B-evidence
value	I-evidence
(	O
Fig	O
.	O
6i	O
,	O
j	O
),	O
which	O
was	O
also	O
predominant	O
in	O
the	O
presence	O
of	O
continuous	O
Py	B-chemical
tract	I-chemical
.	O

Therefore	O
,	O
RRM1	B-structure_element
-	O
to	O
-	O
RRM2	B-structure_element
distance	O
remains	O
similar	O
regardless	O
of	O
whether	O
U2AF65	B-protein
is	O
bound	B-protein_state
to	I-protein_state
interrupted	O
or	O
continuous	O
Py	B-chemical
tract	I-chemical
.	O

The	O
inter	B-evidence
-	I-evidence
fluorophore	I-evidence
distances	I-evidence
derived	O
from	O
the	O
observed	O
0	O
.	O
45	O
FRET	B-evidence
state	I-evidence
agree	O
with	O
the	O
distances	O
between	O
the	O
α	O
-	O
carbon	O
atoms	O
of	O
the	O
respective	O
residues	O
in	O
the	O
crystal	B-evidence
structures	I-evidence
of	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
bound	B-protein_state
to	I-protein_state
Py	B-chemical
-	I-chemical
tract	I-chemical
oligonucleotides	I-chemical
.	O

It	O
should	O
be	O
noted	O
that	O
inferring	O
distances	O
from	O
FRET	B-evidence
values	I-evidence
is	O
prone	O
to	O
significant	O
error	O
because	O
of	O
uncertainties	O
in	O
the	O
determination	O
of	O
fluorophore	O
orientation	O
factor	O
κ2	O
and	O
Förster	O
radius	O
R0	O
,	O
the	O
parameters	O
used	O
in	O
distance	O
calculations	O
.	O

Nevertheless	O
,	O
the	O
predominant	O
0	O
.	O
45	O
FRET	B-evidence
state	I-evidence
in	O
the	O
presence	O
of	O
RNA	B-chemical
agrees	O
with	O
the	O
Py	B-protein_state
-	I-protein_state
tract	I-protein_state
-	I-protein_state
bound	I-protein_state
crystal	B-evidence
structure	I-evidence
of	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
.	O

Importantly	O
,	O
the	O
majority	O
of	O
traces	B-evidence
(∼	O
70	O
%)	O
of	O
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
)	O
bound	B-protein_state
to	I-protein_state
the	O
slide	O
-	O
tethered	O
RNA	B-chemical
lacked	O
FRET	O
fluctuations	O
and	O
predominately	O
exhibited	O
a	O
∼	O
0	O
.	O
45	O
FRET	B-evidence
value	I-evidence
(	O
for	O
example	O
,	O
Fig	O
.	O
6g	O
).	O

The	O
remaining	O
∼	O
30	O
%	O
of	O
traces	B-evidence
for	O
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
)	O
bound	B-protein_state
to	I-protein_state
the	O
slide	O
-	O
tethered	O
RNA	B-chemical
showed	O
fluctuations	O
between	O
distinct	O
FRET	B-evidence
values	I-evidence
.	O

The	O
majority	O
of	O
traces	B-evidence
that	O
show	O
fluctuations	O
began	O
at	O
high	O
(	O
0	O
.	O
65	O
–	O
0	O
.	O
8	O
)	O
FRET	B-evidence
value	I-evidence
and	O
transitioned	O
to	O
a	O
∼	O
0	O
.	O
45	O
FRET	B-evidence
value	I-evidence
(	O
Supplementary	O
Fig	O
.	O
7c	O
–	O
g	O
).	O

Hidden	B-experimental_method
Markov	I-experimental_method
modelling	I-experimental_method
analysis	I-experimental_method
of	O
smFRET	B-experimental_method
traces	B-evidence
suggests	O
that	O
RNA	B-protein_state
-	I-protein_state
bound	I-protein_state
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
can	O
sample	O
at	O
least	O
two	O
other	O
conformations	O
corresponding	O
to	O
∼	O
0	O
.	O
7	O
–	O
0	O
.	O
8	O
and	O
∼	O
0	O
.	O
3	O
FRET	B-evidence
values	I-evidence
in	O
addition	O
to	O
the	O
predominant	O
conformation	O
corresponding	O
to	O
the	O
0	O
.	O
45	O
FRET	B-evidence
state	I-evidence
.	O

Although	O
a	O
compact	O
conformation	O
(	O
or	O
multiple	O
conformations	O
)	O
of	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
corresponding	O
to	O
∼	O
0	O
.	O
7	O
–	O
0	O
.	O
8	O
FRET	B-evidence
values	I-evidence
can	O
bind	O
RNA	B-chemical
,	O
on	O
RNA	B-chemical
binding	O
,	O
these	O
compact	B-protein_state
conformations	O
of	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
transition	O
into	O
a	O
more	O
stable	O
structural	O
state	O
that	O
corresponds	O
to	O
∼	O
0	O
.	O
45	O
FRET	B-evidence
value	I-evidence
and	O
is	O
likely	O
similar	O
to	O
the	O
side	B-protein_state
-	I-protein_state
by	I-protein_state
-	I-protein_state
side	I-protein_state
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
-	O
arrangement	O
of	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
crystal	B-evidence
structures	I-evidence
.	O

Thus	O
,	O
the	O
sequence	O
of	O
structural	O
rearrangements	O
of	O
U2AF65	B-protein
observed	O
in	O
smFRET	B-experimental_method
traces	B-evidence
(	O
Supplementary	O
Fig	O
.	O
7c	O
–	O
g	O
)	O
suggests	O
that	O
a	O
‘	O
conformational	O
selection	O
'	O
mechanism	O
of	O
Py	B-chemical
-	I-chemical
tract	I-chemical
recognition	O
(	O
that	O
is	O
,	O
RNA	O
ligand	O
stabilization	O
of	O
a	O
pre	B-protein_state
-	I-protein_state
configured	I-protein_state
U2AF65	B-protein
conformation	O
)	O
is	O
complemented	O
by	O
‘	O
induced	O
fit	O
'	O
(	O
that	O
is	O
,	O
RNA	O
-	O
induced	O
rearrangement	O
of	O
the	O
U2AF65	B-protein
RRMs	B-structure_element
to	O
achieve	O
the	O
final	O
‘	O
side	B-protein_state
-	I-protein_state
by	I-protein_state
-	I-protein_state
side	I-protein_state
'	O
conformation	O
),	O
as	O
discussed	O
below	O
.	O

The	O
U2AF65	B-protein
structures	B-evidence
and	O
analyses	B-evidence
presented	O
here	O
represent	O
a	O
successful	O
step	O
towards	O
defining	O
a	O
molecular	O
map	O
of	O
the	O
3	B-site
′	I-site
splice	I-site
site	I-site
.	O

Several	O
observations	O
indicate	O
that	O
the	O
numerous	O
intramolecular	O
contacts	O
,	O
here	O
revealed	O
among	O
the	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
and	O
RRM1	B-structure_element
,	O
RRM2	B-structure_element
,	O
and	O
the	O
N	O
-	O
terminal	O
RRM1	B-structure_element
extension	I-structure_element
,	O
synergistically	O
coordinate	O
U2AF65	B-protein
–	O
Py	O
-	O
tract	O
recognition	O
.	O

Truncation	B-experimental_method
of	O
U2AF65	B-protein
to	O
the	O
core	B-protein_state
RRM1	B-structure_element
–	I-structure_element
RRM2	I-structure_element
region	I-structure_element
reduces	O
its	O
RNA	B-evidence
affinity	I-evidence
by	O
100	O
-	O
fold	O
.	O

Likewise	O
,	O
deletion	B-experimental_method
of	O
20	B-residue_range
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
residues	I-structure_element
significantly	O
reduces	O
U2AF65	B-protein
–	O
RNA	B-chemical
binding	O
only	O
when	O
introduced	O
in	O
the	O
context	O
of	O
the	O
longer	B-protein_state
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
construct	O
comprising	O
the	O
RRM	B-structure_element
extensions	I-structure_element
,	O
which	O
in	O
turn	O
position	O
the	O
linker	B-structure_element
for	O
RNA	B-chemical
interactions	O
.	O

Notably	O
,	O
a	O
triple	B-protein_state
mutation	I-protein_state
of	O
three	O
residues	O
(	O
V254P	B-mutant
,	O
Q147A	B-mutant
and	O
R227A	B-mutant
)	O
in	O
the	O
respective	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
,	O
N	B-structure_element
-	I-structure_element
and	I-structure_element
C	I-structure_element
-	I-structure_element
terminal	I-structure_element
extensions	I-structure_element
non	O
-	O
additively	O
reduce	O
RNA	B-evidence
binding	I-evidence
by	O
150	O
-	O
fold	O
.	O

Altogether	O
,	O
these	O
data	O
indicate	O
that	O
interactions	O
among	O
the	O
U2AF65	B-protein
RRM1	B-structure_element
/	O
RRM2	B-structure_element
,	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
,	O
N	B-structure_element
-	I-structure_element
and	I-structure_element
C	I-structure_element
-	I-structure_element
terminal	I-structure_element
extensions	I-structure_element
are	O
mutually	O
inter	O
-	O
dependent	O
for	O
cognate	O
Py	B-chemical
-	I-chemical
tract	I-chemical
recognition	O
.	O

The	O
implications	O
of	O
this	O
finding	O
for	O
U2AF65	B-protein
conservation	O
and	O
Py	B-chemical
-	I-chemical
tract	I-chemical
recognition	O
are	O
detailed	O
in	O
the	O
Supplementary	O
Discussion	O
.	O

Recently	O
,	O
high	B-experimental_method
-	I-experimental_method
throughput	I-experimental_method
sequencing	I-experimental_method
studies	I-experimental_method
have	O
shown	O
that	O
somatic	O
mutations	O
in	O
pre	B-protein_type
-	I-protein_type
mRNA	I-protein_type
splicing	I-protein_type
factors	I-protein_type
occur	O
in	O
the	O
majority	O
of	O
patients	O
with	O
myelodysplastic	O
syndrome	O
(	O
MDS	O
).	O

MDS	O
-	O
relevant	O
mutations	O
are	O
common	O
in	O
the	O
small	B-protein_state
U2AF	B-protein_type
subunit	I-protein_type
(	O
U2AF35	B-protein
,	O
or	O
U2AF1	B-protein
),	O
yet	O
such	O
mutations	O
are	O
rare	O
in	O
the	O
large	B-protein_state
U2AF65	B-protein
subunit	O
(	O
also	O
called	O
U2AF2	B-protein
)—	O
possibly	O
due	O
to	O
the	O
selective	O
versus	O
nearly	O
universal	O
requirements	O
of	O
these	O
factors	O
for	O
splicing	O
.	O

A	O
confirmed	O
somatic	O
mutation	O
of	O
U2AF65	B-protein
in	O
patients	O
with	O
MDS	O
,	O
L187V	B-mutant
,	O
is	O
located	O
on	O
a	O
solvent	B-site
-	I-site
exposed	I-site
surface	I-site
of	O
RRM1	B-structure_element
that	O
is	O
distinct	O
from	O
the	O
RNA	B-site
interface	I-site
(	O
Fig	O
.	O
7a	O
).	O

This	O
L187	B-residue_name_number
surface	O
is	O
oriented	O
towards	O
the	O
N	O
terminus	O
of	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
construct	O
,	O
where	O
it	O
is	O
expected	O
to	O
abut	O
the	O
U2AF35	B-site
-	I-site
binding	I-site
site	I-site
in	O
the	O
context	O
of	O
the	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
U2AF	B-protein
heterodimer	B-oligomeric_state
.	O

Likewise	O
,	O
an	O
unconfirmed	O
M144I	B-mutant
mutation	O
reported	O
by	O
the	O
same	O
group	O
corresponds	O
to	O
the	O
N	O
-	O
terminal	O
residue	O
of	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
,	O
which	O
is	O
separated	O
by	O
only	O
∼	O
20	O
residues	O
from	O
the	O
U2AF35	B-site
-	I-site
binding	I-site
site	I-site
.	O

As	O
such	O
,	O
we	O
suggest	O
that	O
the	O
MDS	O
-	O
relevant	O
U2AF65	B-protein
mutations	O
contribute	O
to	O
MDS	O
progression	O
indirectly	O
,	O
by	O
destabilizing	O
a	O
relevant	O
conformation	O
of	O
the	O
conjoined	O
U2AF35	B-protein
subunit	O
rather	O
than	O
affecting	O
U2AF65	B-protein
functions	O
in	O
RNA	B-chemical
binding	O
or	O
spliceosome	B-complex_assembly
recruitment	O
per	O
se	O
.	O

Our	O
smFRET	B-experimental_method
results	O
agree	O
with	O
prior	O
NMR	B-experimental_method
/	O
PRE	B-experimental_method
evidence	O
for	O
multi	O
-	O
domain	O
conformational	O
selection	O
as	O
one	O
mechanistic	O
basis	O
for	O
U2AF65	B-protein
–	O
RNA	B-chemical
association	O
(	O
Fig	O
.	O
7b	O
).	O

An	O
∼	O
0	O
.	O
45	O
FRET	B-evidence
value	I-evidence
is	O
likely	O
to	O
correspond	O
to	O
the	O
U2AF65	B-protein
conformation	O
visualized	O
in	O
our	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
crystal	B-evidence
structures	I-evidence
,	O
in	O
which	O
the	O
RRM1	B-structure_element
and	O
RRM2	B-structure_element
bind	O
side	B-protein_state
-	I-protein_state
by	I-protein_state
-	I-protein_state
side	I-protein_state
to	O
the	O
Py	B-chemical
-	I-chemical
tract	I-chemical
oligonucleotide	I-chemical
.	O

The	O
lesser	O
0	O
.	O
65	O
–	O
0	O
.	O
8	O
and	O
0	O
.	O
2	O
–	O
0	O
.	O
3	O
FRET	B-evidence
values	I-evidence
in	O
the	O
untethered	B-protein_state
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
)	O
experiment	O
could	O
correspond	O
to	O
respective	O
variants	O
of	O
the	O
‘	O
closed	B-protein_state
',	O
back	B-protein_state
-	I-protein_state
to	I-protein_state
-	I-protein_state
back	I-protein_state
U2AF65	B-protein
conformations	O
characterized	O
by	O
NMR	B-experimental_method
/	O
PRE	B-experimental_method
data	O
,	O
or	O
to	O
extended	B-protein_state
U2AF65	B-protein
conformations	O
,	O
in	O
which	O
the	O
intramolecular	O
RRM1	B-structure_element
/	O
RRM2	B-structure_element
interactions	O
have	O
dissociated	O
the	O
protein	B-protein
is	O
bound	B-protein_state
to	I-protein_state
RNA	B-chemical
via	O
single	B-protein_state
RRMs	B-structure_element
.	O

An	O
increased	O
prevalence	O
of	O
the	O
∼	O
0	O
.	O
45	O
FRET	B-evidence
value	I-evidence
following	O
U2AF65	B-protein
–	O
RNA	B-chemical
binding	O
,	O
coupled	O
with	O
the	O
apparent	O
absence	B-protein_state
of	I-protein_state
transitions	O
in	O
many	O
∼	O
0	O
.	O
45	O
-	O
value	O
single	O
molecule	O
traces	B-evidence
(	O
for	O
example	O
,	O
Fig	O
.	O
6e	O
),	O
suggests	O
a	O
population	O
shift	O
in	O
which	O
RNA	B-chemical
binds	O
to	O
(	O
and	O
draws	O
the	O
equilibrium	O
towards	O
)	O
a	O
pre	B-protein_state
-	I-protein_state
configured	I-protein_state
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
proximity	O
that	O
most	O
often	O
corresponds	O
to	O
the	O
∼	O
0	O
.	O
45	O
FRET	B-evidence
value	I-evidence
.	O

Notably	O
,	O
our	O
smFRET	B-experimental_method
results	O
reveal	O
that	O
U2AF65	B-protein
–	O
Py	B-chemical
-	I-chemical
tract	I-chemical
recognition	O
can	O
be	O
characterized	O
by	O
an	O
‘	O
extended	O
conformational	O
selection	O
'	O
model	O
(	O
Fig	O
.	O
7b	O
).	O

Examples	O
of	O
‘	O
extended	B-protein_state
conformational	O
selection	O
'	O
during	O
ligand	O
binding	O
have	O
been	O
characterized	O
for	O
a	O
growing	O
number	O
of	O
macromolecules	O
(	O
for	O
example	O
,	O
adenylate	B-protein_type
kinase	I-protein_type
,	O
LAO	B-protein_type
-	I-protein_type
binding	I-protein_type
protein	I-protein_type
,	O
poly	B-protein_type
-	I-protein_type
ubiquitin	I-protein_type
,	O
maltose	B-protein_type
-	I-protein_type
binding	I-protein_type
protein	I-protein_type
and	O
the	O
preQ1	B-protein_type
riboswitch	I-protein_type
,	O
among	O
others	O
).	O

Here	O
,	O
the	O
majority	O
of	O
changes	O
in	O
smFRET	B-experimental_method
traces	B-evidence
for	O
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
)	O
bound	B-protein_state
to	I-protein_state
slide	O
-	O
tethered	O
RNA	B-chemical
began	O
at	O
high	O
(	O
0	O
.	O
65	O
–	O
0	O
.	O
8	O
)	O
FRET	B-evidence
value	I-evidence
and	O
transition	O
to	O
the	O
predominant	O
0	O
.	O
45	O
FRET	B-evidence
value	I-evidence
(	O
Supplementary	O
Fig	O
.	O
7c	O
–	O
g	O
).	O

These	O
transitions	O
could	O
correspond	O
to	O
rearrangement	O
from	O
the	O
‘	O
closed	B-protein_state
'	O
NMR	B-experimental_method
/	O
PRE	B-experimental_method
-	O
based	O
U2AF65	B-protein
conformation	O
in	O
which	O
the	O
RNA	B-site
-	I-site
binding	I-site
surface	I-site
of	O
only	O
a	O
single	B-protein_state
RRM	B-structure_element
is	O
exposed	O
and	O
available	O
for	O
RNA	O
binding	O
,	O
to	O
the	O
structural	O
state	O
seen	O
in	O
the	O
side	B-protein_state
-	I-protein_state
by	I-protein_state
-	I-protein_state
side	I-protein_state
,	O
RNA	B-protein_state
-	I-protein_state
bound	I-protein_state
crystal	B-evidence
structure	I-evidence
.	O

As	O
such	O
,	O
the	O
smFRET	B-experimental_method
approach	O
reconciles	O
prior	O
inconsistencies	O
between	O
two	O
major	O
conformations	O
that	O
were	O
detected	O
by	O
NMR	B-experimental_method
/	O
PRE	B-experimental_method
experiments	O
and	O
a	O
broad	O
ensemble	O
of	O
diverse	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
arrangements	O
that	O
fit	O
the	O
SAXS	B-experimental_method
data	O
for	O
the	O
apo	B-protein_state
-	O
protein	B-protein
.	O

Similar	O
interdisciplinary	O
structural	O
approaches	O
are	O
likely	O
to	O
illuminate	O
whether	O
similar	O
mechanistic	O
bases	O
for	O
RNA	O
binding	O
are	O
widespread	O
among	O
other	O
members	O
of	O
the	O
vast	O
multi	O
-	O
RRM	B-structure_element
family	O
.	O

The	O
finding	O
that	O
U2AF65	B-protein
recognizes	O
a	O
nine	O
base	O
pair	O
Py	B-chemical
tract	I-chemical
contributes	O
to	O
an	O
elusive	O
‘	O
code	O
'	O
for	O
predicting	O
splicing	O
patterns	O
from	O
primary	O
sequences	O
in	O
the	O
post	O
-	O
genomic	O
era	O
(	O
reviewed	O
in	O
ref	O
.).	O

Based	O
on	O
(	O
i	O
)	O
similar	O
RNA	B-evidence
affinities	I-evidence
of	O
U2AF65	B-protein
and	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
,	O
(	O
ii	O
)	O
indistinguishable	O
conformations	O
among	O
four	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
structures	B-evidence
in	O
two	O
different	O
crystal	O
packing	O
arrangements	O
and	O
(	O
iii	O
)	O
penalties	B-evidence
of	O
structure	B-experimental_method
-	I-experimental_method
guided	I-experimental_method
mutations	I-experimental_method
in	O
RNA	B-experimental_method
binding	I-experimental_method
and	I-experimental_method
splicing	I-experimental_method
assays	I-experimental_method
,	O
we	O
suggest	O
that	O
the	O
extended	B-protein_state
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
regions	I-structure_element
of	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
structures	B-evidence
underlie	O
cognate	O
Py	B-chemical
-	I-chemical
tract	I-chemical
recognition	O
by	O
the	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
U2AF65	B-protein
protein	O
.	O

Further	O
research	O
will	O
be	O
needed	O
to	O
understand	O
the	O
roles	O
of	O
SF1	B-protein
and	O
U2AF35	B-protein
subunits	O
in	O
the	O
conformational	O
equilibria	O
underlying	O
U2AF65	B-protein
association	O
with	O
Py	B-chemical
tracts	I-chemical
.	O

Moreover	O
,	O
structural	O
differences	O
among	O
U2AF65	B-protein
homologues	O
and	O
paralogues	O
may	O
regulate	O
splice	B-site
site	I-site
selection	O
.	O

Ultimately	O
,	O
these	O
guidelines	O
will	O
assist	O
the	O
identification	O
of	O
3	B-site
′	I-site
splice	I-site
sites	I-site
and	O
the	O
relationship	O
of	O
disease	O
-	O
causing	O
mutations	O
to	O
penalties	O
for	O
U2AF65	B-protein
association	O
.	O

The	O
intact	B-protein_state
U2AF65	B-protein
RRM1	B-structure_element
/	O
RRM2	B-structure_element
-	O
containing	O
domain	O
and	O
flanking	O
residues	O
are	O
required	O
for	O
binding	O
contiguous	B-structure_element
Py	B-chemical
tracts	I-chemical
.	O

(	O
a	O
)	O
Domain	O
organization	O
of	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
(	O
fl	B-protein_state
)	O
U2AF65	B-protein
and	O
constructs	O
used	O
for	O
RNA	B-chemical
binding	O
and	O
structural	O
experiments	O
.	O

An	O
internal	O
deletion	O
(	O
d	B-mutant
,	O
Δ	B-mutant
)	O
of	O
residues	O
238	B-residue_range
–	I-residue_range
257	I-residue_range
removes	O
a	O
portion	O
of	O
the	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
from	O
the	O
dU2AF651	B-mutant
,	I-mutant
2	I-mutant
and	O
dU2AF651	B-mutant
,	I-mutant
2L	I-mutant
constructs	O
.	O

(	O
b	O
)	O
Comparison	O
of	O
the	O
apparent	O
equilibrium	B-evidence
affinities	I-evidence
of	O
various	O
U2AF65	B-protein
constructs	O
for	O
binding	O
the	O
prototypical	O
AdML	B-gene
Py	B-chemical
tract	I-chemical
(	O
5	B-chemical
′-	I-chemical
CCCUUUUUUUUCC	I-chemical
-	I-chemical
3	I-chemical
′).	I-chemical

The	O
flU2AF65	B-protein
protein	O
includes	O
a	O
heterodimerization	B-structure_element
domain	I-structure_element
of	O
the	O
U2AF35	B-protein
subunit	O
to	O
promote	O
solubility	O
and	O
folding	O
.	O

The	O
apparent	O
equilibrium	B-evidence
dissociation	I-evidence
constants	I-evidence
(	O
KD	B-evidence
)	O
for	O
binding	O
the	O
AdML	B-gene
13mer	O
are	O
as	O
follows	O
:	O
flU2AF65	B-protein
,	O
30	O
±	O
3	O
nM	O
;	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
,	O
35	O
±	O
6	O
nM	O
;	O
U2AF651	B-mutant
,	I-mutant
2	I-mutant
,	O
3	O
,	O
600	O
±	O
300	O
nM	O
.	O
(	O
c	O
)	O
Comparison	O
of	O
the	O
RNA	B-evidence
sequence	I-evidence
specificities	I-evidence
of	O
flU2AF65	B-protein
and	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
constructs	O
binding	O
C	B-structure_element
-	I-structure_element
rich	I-structure_element
Py	B-chemical
tracts	I-chemical
with	O
4U	O
'	O
s	O
embedded	O
in	O
either	O
the	O
5	O
′-	O
(	O
light	O
grey	O
fill	O
)	O
or	O
3	O
′-	O
(	O
dark	O
grey	O
fill	O
)	O
regions	O
.	O

The	O
KD	B-evidence
'	O
s	O
for	O
binding	O
5	B-chemical
′-	I-chemical
CCUUUUCCCCCCC	I-chemical
-	I-chemical
3	I-chemical
′	I-chemical
are	O
:	O
flU2AF65	B-protein
,	O
41	O
±	O
2	O
nM	O
;	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
,	O
31	O
±	O
3	O
nM	O
.	O
The	O
KD	B-evidence
'	O
s	O
for	O
binding	O
5	B-chemical
′-	I-chemical
CCCCCCCUUUUCC	I-chemical
-	I-chemical
3	I-chemical
′	I-chemical
are	O
:	O
flU2AF65	B-protein
,	O
414	O
±	O
12	O
nM	O
;	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
,	O
417	O
±	O
10	O
nM	O
.	O
Bar	O
graphs	O
are	O
hatched	O
to	O
match	O
the	O
constructs	O
shown	O
in	O
a	O
.	O
The	O
average	B-evidence
apparent	I-evidence
equilibrium	I-evidence
affinity	I-evidence
(	O
KA	B-evidence
)	O
and	O
s	O
.	O
e	O
.	O
m	O
.	O
for	O
three	O
independent	O
titrations	O
are	O
plotted	O
.	O

The	O
purified	O
protein	O
and	O
average	B-evidence
fitted	I-evidence
fluorescence	I-evidence
anisotropy	I-evidence
RNA	I-evidence
-	I-evidence
binding	I-evidence
curves	I-evidence
are	O
shown	O
in	O
Supplementary	O
Fig	O
.	O
1	O
.	O

RRM	B-structure_element
,	O
RNA	B-structure_element
recognition	I-structure_element
motif	I-structure_element
;	O
RS	B-structure_element
,	O
arginine	B-structure_element
-	I-structure_element
serine	I-structure_element
rich	I-structure_element
;	O
UHM	B-structure_element
,	O
U2AF	B-structure_element
homology	I-structure_element
motif	I-structure_element
;	O
ULM	B-structure_element
,	O
U2AF	B-structure_element
ligand	I-structure_element
motif	I-structure_element
.	O

Structures	B-evidence
of	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
recognizing	O
a	O
contiguous	B-structure_element
Py	B-chemical
tract	I-chemical
.	O

(	O
a	O
)	O
Alignment	B-experimental_method
of	O
oligonucleotide	B-chemical
sequences	O
that	O
were	O
co	B-experimental_method
-	I-experimental_method
crystallized	I-experimental_method
in	O
the	O
indicated	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
structures	B-evidence
.	O

The	O
regions	O
of	O
RRM1	B-structure_element
,	O
RRM2	B-structure_element
and	O
linker	B-structure_element
contacts	O
are	O
indicated	O
above	O
by	O
respective	O
black	O
and	O
blue	O
arrows	O
from	O
N	O
-	O
to	O
C	O
-	O
terminus	O
.	O

For	O
clarity	O
,	O
we	O
consistently	O
number	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
nucleotide	B-site
-	I-site
binding	I-site
sites	I-site
from	O
one	O
to	O
nine	O
,	O
although	O
in	O
some	O
cases	O
the	O
co	B-experimental_method
-	I-experimental_method
crystallized	I-experimental_method
oligonucleotide	B-chemical
comprises	O
eight	O
nucleotides	B-chemical
and	O
as	O
such	O
leaves	O
the	O
first	B-site
binding	I-site
site	I-site
empty	O
.	O

The	O
prior	O
dU2AF651	B-mutant
,	I-mutant
2	I-mutant
nucleotide	B-site
-	I-site
binding	I-site
sites	I-site
are	O
given	O
in	O
parentheses	O
(	O
site	O
4	O
'	O
interacts	O
with	O
dU2AF65	B-mutant
RRM1	B-structure_element
and	O
RRM2	B-structure_element
by	O
crystallographic	O
symmetry	O
).	O

(	O
b	O
)	O
Stereo	O
views	O
of	O
a	O
‘	O
kicked	O
'	O
2	B-evidence
|	I-evidence
Fo	I-evidence
|−|	I-evidence
Fc	I-evidence
|	I-evidence
electron	I-evidence
density	I-evidence
map	I-evidence
contoured	O
at	O
1σ	O
for	O
the	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
,	O
N	O
-	O
and	O
C	O
-	O
terminal	O
residues	O
(	O
blue	O
)	O
or	O
bound	O
oligonucleotide	B-chemical
of	O
a	O
representative	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
structure	O
(	O
structure	O
iv	O
,	O
bound	B-protein_state
to	I-protein_state
5	O
′-(	O
P	O
)	O
rUrUrUdUrUrU	O
(	O
BrdU	O
)	O
dUrC	O
)	O
(	O
magenta	O
).	O

Crystallographic	O
statistics	O
are	O
given	O
in	O
Table	O
1	O
and	O
the	O
overall	O
conformations	O
of	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
and	O
prior	O
dU2AF651	B-mutant
,	I-mutant
2	I-mutant
/	O
U2AF651	B-mutant
,	I-mutant
2	I-mutant
structures	B-evidence
are	O
compared	O
in	O
Supplementary	O
Fig	O
.	O
2	O
.	O

BrdU	B-chemical
,	O
5	B-chemical
-	I-chemical
bromo	I-chemical
-	I-chemical
deoxy	I-chemical
-	I-chemical
uridine	I-chemical
;	O
d	B-chemical
,	O
deoxy	B-chemical
-	I-chemical
ribose	I-chemical
;	O
P	B-chemical
-,	I-chemical
5	B-chemical
′-	I-chemical
phosphorylation	I-chemical
;	O
r	B-chemical
,	O
ribose	B-chemical
.	O

Representative	O
views	O
of	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
interactions	O
with	O
each	O
new	O
nucleotide	B-chemical
of	O
the	O
bound	B-protein_state
Py	B-chemical
tract	I-chemical
.	O

New	O
residues	O
of	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
structures	B-evidence
are	O
coloured	O
a	O
darker	O
shade	O
of	O
blue	O
,	O
apart	O
from	O
residues	O
that	O
were	O
tested	O
by	O
site	B-experimental_method
-	I-experimental_method
directed	I-experimental_method
mutagenesis	I-experimental_method
,	O
which	O
are	O
coloured	O
yellow	O
.	O

The	O
nucleotide	B-site
-	I-site
binding	I-site
sites	I-site
of	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
and	O
prior	O
dU2AF651	B-mutant
,	I-mutant
2	I-mutant
structure	B-evidence
are	O
compared	O
in	O
Supplementary	O
Fig	O
.	O
3a	O
–	O
h	O
.	O
The	O
first	B-site
and	I-site
seventh	I-site
U2AF651	I-site
,	I-site
2L	I-site
-	I-site
binding	I-site
sites	I-site
are	O
unchanged	O
from	O
the	O
prior	O
dU2AF651	B-complex_assembly
,	I-complex_assembly
2	I-complex_assembly
–	I-complex_assembly
RNA	I-complex_assembly
structure	B-evidence
and	O
are	O
portrayed	O
in	O
Supplementary	O
Fig	O
.	O
3a	O
,	O
f	O
.	O
The	O
four	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
structures	B-evidence
are	O
similar	O
with	O
the	O
exception	O
of	O
pH	O
-	O
dependent	O
variations	O
at	O
the	O
ninth	B-site
site	I-site
that	O
are	O
detailed	O
in	O
Supplementary	O
Fig	O
.	O
3i	O
,	O
j	O
.	O
The	O
representative	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
structure	B-evidence
shown	O
has	O
the	O
highest	O
resolution	O
and	O
/	O
or	O
ribose	B-chemical
nucleotide	I-chemical
at	O
the	O
given	O
site	O
:	O
(	O
a	O
)	O
rU2	B-residue_name_number
of	O
structure	O
iv	O
;	O
(	O
b	O
)	O
rU3	B-residue_name_number
of	O
structure	O
iii	O
;	O
(	O
c	O
)	O
rU4	B-residue_name_number
of	O
structure	O
i	O
;	O
(	O
d	O
)	O
rU5	B-residue_name_number
of	O
structure	O
iii	O
;	O
(	O
e	O
)	O
rU6	B-residue_name_number
of	O
structure	O
ii	O
;	O
(	O
f	O
)	O
dU8	B-residue_name_number
of	O
structure	O
iii	O
;	O
(	O
g	O
)	O
dU9	B-residue_name_number
of	O
structure	O
iii	O
;	O
(	O
h	O
)	O
rC9	B-residue_name_number
of	O
structure	O
iv	O
.	O

(	O
i	O
)	O
Bar	O
graph	O
of	O
apparent	O
equilibrium	B-evidence
affinities	I-evidence
(	O
KA	B-evidence
)	O
of	O
the	O
wild	B-protein_state
type	I-protein_state
(	O
blue	O
)	O
and	O
the	O
indicated	O
mutant	B-protein_state
(	O
yellow	O
)	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
proteins	O
binding	O
the	O
AdML	B-gene
Py	B-chemical
tract	I-chemical
(	O
5	B-chemical
′-	I-chemical
CCCUUUUUUUUCC	I-chemical
-	I-chemical
3	I-chemical
′).	I-chemical

The	O
apparent	O
equilibrium	B-evidence
dissociation	I-evidence
constants	I-evidence
(	O
KD	B-evidence
)	O
of	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
mutant	B-protein_state
proteins	O
are	O
:	O
wild	B-protein_state
type	I-protein_state
(	O
WT	B-protein_state
),	O
35	O
±	O
6	O
nM	O
;	O
R227A	B-mutant
,	O
166	O
±	O
2	O
nM	O
;	O
V254P	B-mutant
,	O
137	O
±	O
10	O
nM	O
;	O
Q147A	B-mutant
,	O
171	O
±	O
21	O
nM	O
.	O
The	O
average	O
KA	B-evidence
and	O
s	O
.	O
e	O
.	O
m	O
.	O
for	O
three	O
independent	O
titrations	O
are	O
plotted	O
.	O

The	O
average	O
fitted	O
fluorescence	O
anisotropy	O
RNA	B-evidence
-	I-evidence
binding	I-evidence
curves	I-evidence
are	O
shown	O
in	O
Supplementary	O
Fig	O
.	O
4a	O
–	O
c	O
.	O

The	O
U2AF65	B-protein
linker	B-structure_element
/	O
RRM	B-structure_element
and	O
inter	O
-	O
RRM	B-structure_element
interactions	O
.	O

(	O
a	O
)	O
Contacts	O
of	O
the	O
U2AF65	B-protein
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
linker	I-structure_element
with	O
the	O
RRMs	B-structure_element
.	O

A	O
semi	O
-	O
transparent	O
space	O
-	O
filling	O
surface	O
is	O
shown	O
for	O
the	O
RRM1	B-structure_element
(	O
green	O
)	O
and	O
RRM2	B-structure_element
(	O
light	O
blue	O
).	O

Residues	O
V249	B-residue_name_number
,	O
V250	B-residue_name_number
,	O
V254	B-residue_name_number
(	O
yellow	O
)	O
are	O
mutated	B-experimental_method
to	O
V249G	B-mutant
/	O
V250G	B-mutant
/	O
V254G	B-mutant
in	O
the	O
3Gly	B-mutant
mutant	I-mutant
;	O
residues	O
S251	B-residue_name_number
,	O
T252	B-residue_name_number
,	O
V253	B-residue_name_number
,	O
P255	B-residue_name_number
(	O
red	O
)	O
along	O
with	O
V254	B-residue_name_number
are	O
mutated	B-experimental_method
to	O
S251G	B-mutant
/	O
T252G	B-mutant
/	O
V253G	B-mutant
/	O
V254G	B-mutant
/	O
P255G	B-mutant
in	O
the	O
5Gly	B-mutant
mutant	I-mutant
or	O
to	O
S251N	B-mutant
/	O
T252L	B-mutant
/	O
V253A	B-mutant
/	O
V254L	B-mutant
/	O
P255A	B-mutant
in	O
the	O
NLALA	B-mutant
mutant	I-mutant
;	O
residues	O
M144	B-residue_name_number
,	O
L235	B-residue_name_number
,	O
M238	B-residue_name_number
,	O
V244	B-residue_name_number
,	O
V246	B-residue_name_number
(	O
orange	O
)	O
along	O
with	O
V249	B-residue_name_number
,	O
V250	B-residue_name_number
,	O
S251	B-residue_name_number
,	O
T252	B-residue_name_number
,	O
V253	B-residue_name_number
,	O
V254	B-residue_name_number
,	O
P255	B-residue_name_number
are	O
mutated	B-experimental_method
to	O
M144G	B-mutant
/	O
L235G	B-mutant
/	O
M238G	B-mutant
/	O
V244G	B-mutant
/	O
V246G	B-mutant
/	O
V249G	B-mutant
/	O
V250G	B-mutant
/	O
S251G	B-mutant
/	O
T252G	B-mutant
/	O
V253G	B-mutant
/	O
V254G	B-mutant
/	O
P255G	B-mutant
in	O
the	O
12Gly	B-mutant
mutant	I-mutant
.	O

Other	O
linker	B-structure_element
residues	O
are	O
coloured	O
either	O
dark	O
blue	O
for	O
new	O
residues	O
in	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
structure	O
or	O
light	O
blue	O
for	O
the	O
remaining	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
residues	O
.	O

The	O
central	O
panel	O
shows	O
an	O
overall	O
view	O
with	O
stick	O
diagrams	O
for	O
mutated	O
residues	O
;	O
boxed	O
regions	O
are	O
expanded	O
to	O
show	O
the	O
C	O
-	O
terminal	O
(	O
bottom	O
left	O
)	O
and	O
central	B-structure_element
linker	I-structure_element
regions	I-structure_element
(	O
top	O
)	O
at	O
the	O
inter	B-structure_element
-	I-structure_element
RRM	I-structure_element
interfaces	I-structure_element
,	O
and	O
N	O
-	O
terminal	O
linker	O
region	O
contacts	O
with	O
RRM1	B-structure_element
(	O
bottom	O
right	O
).	O

(	O
b	O
)	O
Bar	O
graph	O
of	O
apparent	O
equilibrium	B-evidence
affinities	I-evidence
(	O
KA	B-evidence
)	O
for	O
the	O
AdML	B-gene
Py	B-chemical
tract	I-chemical
(	O
5	B-chemical
′-	I-chemical
CCCUUUUUUUUCC	I-chemical
-	I-chemical
3	I-chemical
′)	I-chemical
of	O
the	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
(	O
blue	O
)	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
protein	O
compared	O
with	O
mutations	O
of	O
the	O
residues	O
shown	O
in	O
a	O
:	O
3Gly	B-mutant
(	O
yellow	O
),	O
5Gly	B-mutant
(	O
red	O
),	O
NLALA	B-mutant
(	O
hatched	O
red	O
),	O
12Gly	B-mutant
(	O
orange	O
)	O
and	O
the	O
linker	B-experimental_method
deletions	I-experimental_method
dU2AF651	B-mutant
,	I-mutant
2	I-mutant
in	O
the	O
minimal	B-protein_state
RRM1	B-structure_element
–	I-structure_element
RRM2	I-structure_element
region	I-structure_element
(	O
residues	O
148	B-residue_range
–	I-residue_range
237	I-residue_range
,	O
258	B-residue_range
–	I-residue_range
336	I-residue_range
)	O
or	O
dU2AF651	B-mutant
,	I-mutant
2L	I-mutant
(	O
residues	O
141	B-residue_range
–	I-residue_range
237	I-residue_range
,	O
258	B-residue_range
–	I-residue_range
342	I-residue_range
).	O

The	O
apparent	O
equilibrium	B-evidence
dissociation	I-evidence
constants	I-evidence
(	O
KD	B-evidence
)	O
of	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
mutant	B-protein_state
proteins	O
are	O
:	O
wild	B-protein_state
type	I-protein_state
(	O
WT	B-protein_state
),	O
35	O
±	O
6	O
nM	O
;	O
3Gly	B-mutant
,	O
47	O
±	O
4	O
nM	O
;	O
5Gly	B-mutant
,	O
61	O
±	O
3	O
nM	O
;	O
12Gly	B-mutant
,	O
88	O
±	O
21	O
nM	O
;	O
NLALA	B-mutant
,	O
45	O
±	O
3	O
nM	O
;	O
dU2AF651	B-mutant
,	I-mutant
2L	I-mutant
,	O
123	O
±	O
5	O
nM	O
;	O
dU2AF651	B-mutant
,	I-mutant
2	I-mutant
,	O
5000	O
±	O
100	O
nM	O
;	O
3Mut	B-mutant
,	O
5630	O
±	O
70	O
nM	O
.	O
The	O
average	O
KA	B-evidence
and	O
s	O
.	O
e	O
.	O
m	O
.	O
for	O
three	O
independent	O
titrations	O
are	O
plotted	O
.	O

The	O
fitted	O
fluorescence	O
anisotropy	O
RNA	B-evidence
-	I-evidence
binding	I-evidence
curves	I-evidence
are	O
shown	O
in	O
Supplementary	O
Fig	O
.	O
4d	O
–	O
j	O
.	O
(	O
c	O
)	O
Close	O
view	O
of	O
the	O
U2AF65	B-protein
RRM1	B-site
/	I-site
RRM2	I-site
interface	I-site
following	O
a	O
two	O
-	O
fold	O
rotation	O
about	O
the	O
x	O
-	O
axis	O
relative	O
to	O
a	O
.	O

U2AF65	B-protein
inter	O
-	O
domain	O
residues	O
are	O
important	O
for	O
splicing	O
a	O
representative	O
pre	B-chemical
-	I-chemical
mRNA	I-chemical
substrate	O
in	O
human	B-species
cells	O
.	O

(	O
a	O
)	O
Schematic	O
diagram	O
of	O
the	O
pyPY	B-chemical
reporter	O
minigene	O
construct	O
comprising	O
two	O
alternative	O
splice	B-site
sites	I-site
preceded	O
by	O
either	O
the	O
weak	O
IgM	O
Py	B-chemical
tract	I-chemical
(	O
py	B-chemical
)	O
or	O
the	O
strong	O
AdML	B-gene
Py	B-chemical
tract	I-chemical
(	O
PY	B-chemical
)	O
(	O
sequences	O
inset	O
).	O

(	O
b	O
)	O
Representative	O
RT	B-experimental_method
-	I-experimental_method
PCR	I-experimental_method
of	O
pyPY	B-chemical
transcripts	O
from	O
HEK293T	O
cells	O
co	B-experimental_method
-	I-experimental_method
transfected	I-experimental_method
with	O
constructs	O
encoding	O
the	O
pyPY	B-chemical
minigene	O
and	O
either	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
(	O
WT	B-protein_state
)	O
U2AF65	B-protein
or	O
a	O
triple	O
U2AF65	B-protein
mutant	B-protein_state
(	O
3Mut	B-mutant
)	O
of	O
Q147A	B-mutant
,	O
R227A	B-mutant
and	O
V254P	B-mutant
residues	O
.	O
(	O
c	O
)	O
A	O
bar	O
graph	O
of	O
the	O
average	O
percentage	O
of	O
the	O
py	B-chemical
-	O
spliced	O
mRNA	B-chemical
relative	O
to	O
total	O
detected	O
pyPY	B-chemical
transcripts	O
(	O
spliced	O
and	O
unspliced	O
)	O
for	O
the	O
corresponding	O
gel	O
lanes	O
(	O
black	O
,	O
no	O
U2AF65	B-protein
added	O
;	O
white	O
,	O
WT	B-protein_state
U2AF65	B-protein
;	O
grey	O
,	O
3Mut	B-mutant
U2AF65	B-protein
).	O

Protein	B-experimental_method
overexpression	I-experimental_method
and	O
qRT	B-experimental_method
-	I-experimental_method
PCR	I-experimental_method
results	O
are	O
shown	O
in	O
Supplementary	O
Fig	O
.	O
5	O
.	O

RNA	O
binding	O
stabilizes	O
the	O
side	B-protein_state
-	I-protein_state
by	I-protein_state
-	I-protein_state
side	I-protein_state
conformation	O
of	O
U2AF65	B-protein
RRMs	B-structure_element
.	O

(	O
a	O
,	O
b	O
)	O
Views	O
of	O
FRET	B-experimental_method
pairs	O
chosen	O
to	O
follow	O
the	O
relative	O
movement	O
of	O
RRM1	B-structure_element
and	O
RRM2	B-structure_element
on	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
‘	O
side	B-protein_state
-	I-protein_state
by	I-protein_state
-	I-protein_state
side	I-protein_state
'	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
RRMs	B-structure_element
bound	B-protein_state
to	I-protein_state
a	O
Py	B-chemical
-	I-chemical
tract	I-chemical
oligonucleotide	I-chemical
(	O
a	O
,	O
representative	O
structure	O
iv	O
)	O
or	O
‘	O
closed	B-protein_state
'	O
NMR	B-experimental_method
/	O
PRE	B-experimental_method
-	O
based	O
model	O
of	O
U2AF651	B-mutant
,	I-mutant
2	I-mutant
(	O
b	O
,	O
PDB	O
ID	O
2YH0	O
)	O
in	O
identical	O
orientations	O
of	O
RRM2	B-structure_element
.	O

The	O
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
proteins	O
were	O
doubly	O
labelled	O
at	O
A181C	B-mutant
/	O
Q324C	B-mutant
such	O
that	O
a	O
mixture	O
of	O
Cy3	B-chemical
/	O
Cy5	B-chemical
fluorophores	B-chemical
are	O
expected	O
to	O
be	O
present	O
at	O
each	O
site	O
.	O

(	O
c	O
–	O
f	O
,	O
i	O
,	O
j	O
)	O
The	O
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
)	O
protein	O
was	O
immobilized	O
on	O
the	O
microscope	O
slide	O
via	O
biotin	B-chemical
-	I-chemical
NTA	I-chemical
/	I-chemical
Ni	I-chemical
+	I-chemical
2	I-chemical
(	O
orange	O
line	O
)	O
on	O
a	O
neutravidin	O
(	O
black	O
X	O
)-	O
biotin	O
-	O
PEG	O
(	O
orange	O
triangle	O
)-	O
treated	O
surface	O
and	O
imaged	O
either	O
in	O
the	O
absence	B-protein_state
of	I-protein_state
ligands	B-chemical
(	O
c	O
,	O
d	O
),	O
in	O
the	O
presence	O
of	O
5	O
μM	O
AdML	B-gene
Py	B-chemical
-	I-chemical
tract	I-chemical
RNA	I-chemical
(	O
5	B-chemical
′-	I-chemical
CCUUUUUUUUCC	I-chemical
-	I-chemical
3	I-chemical
′)	I-chemical
(	O
e	O
,	O
f	O
),	O
or	O
in	O
the	O
presence	O
of	O
10	O
μM	O
adenosine	B-residue_name
-	O
interrupted	O
variant	O
RNA	B-chemical
(	O
5	B-chemical
′-	I-chemical
CUUUUUAAUUUCCA	I-chemical
-	I-chemical
3	I-chemical
′)	I-chemical
(	O
i	O
,	O
j	O
).	O

The	O
untethered	B-protein_state
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
)	O
protein	O
(	O
1	O
nM	O
)	O
was	O
added	O
to	O
AdML	B-gene
RNA	B-chemical
–	I-chemical
polyethylene	I-chemical
-	I-chemical
glycol	I-chemical
-	I-chemical
linker	I-chemical
–	I-chemical
DNA	I-chemical
oligonucleotide	I-chemical
(	O
10	O
nM	O
),	O
which	O
was	O
immobilized	O
on	O
the	O
microscope	O
slide	O
by	O
annealing	O
with	O
a	O
complementary	O
biotinyl	B-chemical
-	I-chemical
DNA	I-chemical
oligonucleotide	I-chemical
(	O
black	O
vertical	O
line	O
).	O

Typical	O
single	B-experimental_method
-	I-experimental_method
molecule	I-experimental_method
FRET	I-experimental_method
traces	B-evidence
(	O
c	O
,	O
e	O
,	O
g	O
,	O
i	O
)	O
show	O
fluorescence	O
intensities	O
from	O
Cy3	B-chemical
(	O
green	O
)	O
and	O
Cy5	B-chemical
(	O
red	O
)	O
and	O
the	O
calculated	B-evidence
apparent	I-evidence
FRET	I-evidence
efficiency	I-evidence
(	O
blue	O
).	O

Additional	O
traces	B-evidence
for	O
untethered	B-protein_state
,	O
RNA	B-protein_state
-	I-protein_state
bound	I-protein_state
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
)	O
are	O
shown	O
in	O
Supplementary	O
Fig	O
.	O
7c	O
,	O
d	O
.	O
Histograms	B-evidence
(	O
d	O
,	O
f	O
,	O
h	O
,	O
j	O
)	O
show	O
the	O
distribution	B-evidence
of	I-evidence
FRET	I-evidence
values	I-evidence
in	O
RNA	B-protein_state
-	I-protein_state
free	I-protein_state
,	O
slide	B-protein_state
-	I-protein_state
tethered	I-protein_state
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
)	O
(	O
d	O
);	O
AdML	B-gene
RNA	B-protein_state
-	I-protein_state
bound	I-protein_state
,	O
slide	B-protein_state
-	I-protein_state
tethered	I-protein_state
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
)	O
(	O
f	O
);	O
AdML	B-gene
RNA	B-protein_state
-	I-protein_state
bound	I-protein_state
,	O
untethered	B-protein_state
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
)	O
(	O
h	O
)	O
and	O
adenosine	O
-	O
interrupted	O
RNA	B-protein_state
-	I-protein_state
bound	I-protein_state
,	O
slide	B-protein_state
-	I-protein_state
tethered	I-protein_state
U2AF651	B-mutant
,	I-mutant
2LFRET	I-mutant
(	O
Cy3	B-chemical
/	O
Cy5	B-chemical
)	O
(	O
j	O
).	O

N	O
is	O
the	O
number	O
of	O
single	O
-	O
molecule	O
traces	B-evidence
compiled	O
for	O
each	O
histogram	B-evidence
.	O

Schematic	O
models	O
of	O
U2AF65	B-protein
recognizing	O
the	O
Py	B-chemical
tract	I-chemical
.	O

(	O
a	O
)	O
Diagram	O
of	O
the	O
U2AF65	B-protein
,	O
SF1	B-protein
and	O
U2AF35	B-protein
splicing	O
factors	O
bound	B-protein_state
to	I-protein_state
the	O
consensus	O
elements	O
of	O
the	O
3	B-site
′	I-site
splice	I-site
site	I-site
.	O

A	O
surface	O
representation	O
of	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
is	O
shown	O
bound	B-protein_state
to	I-protein_state
nine	O
nucleotides	B-chemical
(	O
nt	O
);	O
the	O
relative	O
distances	O
and	O
juxtaposition	O
of	O
the	O
branch	B-site
point	I-site
sequence	I-site
(	O
BPS	B-site
)	O
and	O
consensus	O
AG	B-chemical
dinucleotide	I-chemical
at	O
the	O
3	B-site
′	I-site
splice	I-site
site	I-site
are	O
unknown	O
.	O

MDS	O
-	O
relevant	O
mutated	O
residues	O
of	O
U2AF65	B-protein
are	O
shown	O
as	O
yellow	O
spheres	O
(	O
L187	B-residue_name_number
and	O
M144	B-residue_name_number
).	O

(	O
b	O
)	O
Following	O
binding	O
to	O
the	O
Py	B-chemical
-	I-chemical
tract	I-chemical
RNA	I-chemical
,	O
a	O
conformation	O
corresponding	O
to	O
high	B-evidence
FRET	I-evidence
and	O
consistent	O
with	O
the	O
‘	O
closed	B-protein_state
',	O
back	B-protein_state
-	I-protein_state
to	I-protein_state
-	I-protein_state
back	I-protein_state
apo	B-protein_state
-	O
U2AF65	B-protein
model	O
resulting	O
from	O
PRE	B-experimental_method
/	O
NMR	B-experimental_method
characterization	O
(	O
PDB	O
ID	O
2YH0	O
)	O
often	O
transitions	O
to	O
a	O
conformation	O
corresponding	O
to	O
∼	O
0	O
.	O
45	O
FRET	B-evidence
value	I-evidence
,	O
which	O
is	O
consistent	O
with	O
‘	O
open	B-protein_state
',	O
side	B-protein_state
-	I-protein_state
by	I-protein_state
-	I-protein_state
side	I-protein_state
RRMs	B-structure_element
such	O
as	O
the	O
U2AF651	B-mutant
,	I-mutant
2L	I-mutant
crystal	B-evidence
structures	I-evidence
.	O

Alternatively	O
,	O
a	O
conformation	O
of	O
U2AF65	B-protein
corresponding	O
to	O
∼	O
0	O
.	O
45	O
FRET	B-evidence
value	I-evidence
can	O
directly	O
bind	O
to	O
RNA	B-chemical
;	O
RNA	B-chemical
binding	O
stabilizes	O
the	O
‘	O
open	B-protein_state
',	O
side	B-protein_state
-	I-protein_state
by	I-protein_state
-	I-protein_state
side	I-protein_state
conformation	O
and	O
thus	O
shifts	O
the	O
U2AF65	B-protein
population	O
towards	O
the	O
∼	O
0	O
.	O
45	O
FRET	B-evidence
value	I-evidence
.	O

RRM1	B-structure_element
,	O
green	O
;	O
RRM2	B-structure_element
,	O
pale	O
blue	O
;	O
RRM	B-structure_element
extensions	I-structure_element
/	O
linker	B-structure_element
,	O
blue	O
.	O

RNA	B-chemical
protects	O
a	O
nucleoprotein	B-complex_assembly
complex	O
against	O
radiation	O
damage	O

Systematic	O
analysis	O
of	O
radiation	O
damage	O
within	O
a	O
protein	B-complex_assembly
–	I-complex_assembly
RNA	I-complex_assembly
complex	O
over	O
a	O
large	O
dose	O
range	O
(	O
1	O
.	O
3	O
–	O
25	O
MGy	O
)	O
reveals	O
significant	O
differential	O
susceptibility	O
of	O
RNA	B-chemical
and	O
protein	O
.	O

A	O
new	O
method	O
of	O
difference	B-experimental_method
electron	I-experimental_method
-	I-experimental_method
density	I-experimental_method
quantification	I-experimental_method
is	O
presented	O
.	O

Radiation	O
damage	O
during	O
macromolecular	B-experimental_method
X	I-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallographic	I-experimental_method
data	I-experimental_method
collection	I-experimental_method
is	O
still	O
the	O
main	O
impediment	O
for	O
many	O
macromolecular	B-experimental_method
structure	I-experimental_method
determinations	I-experimental_method
.	O

Although	O
this	O
has	O
been	O
well	O
characterized	O
within	O
protein	O
crystals	B-evidence
,	O
far	O
less	O
is	O
known	O
about	O
specific	O
damage	O
effects	O
within	O
the	O
larger	O
class	O
of	O
nucleoprotein	O
complexes	O
.	O

Here	O
,	O
a	O
methodology	O
has	O
been	O
developed	O
whereby	O
per	B-evidence
-	I-evidence
atom	I-evidence
density	I-evidence
changes	I-evidence
could	O
be	O
quantified	O
with	O
increasing	O
dose	O
over	O
a	O
wide	O
(	O
1	O
.	O
3	O
–	O
25	O
.	O
0	O
MGy	O
)	O
range	O
and	O
at	O
higher	O
resolution	O
(	O
1	O
.	O
98	O
Å	O
)	O
than	O
the	O
previous	O
systematic	O
specific	O
damage	O
study	O
on	O
a	O
protein	O
–	O
DNA	B-chemical
complex	O
.	O

Specific	O
damage	O
manifestations	O
were	O
determined	O
within	O
the	O
large	O
trp	B-protein_type
RNA	I-protein_type
-	I-protein_type
binding	I-protein_type
attenuation	I-protein_type
protein	I-protein_type
(	O
TRAP	B-complex_assembly
)	O
bound	B-protein_state
to	I-protein_state
a	O
single	O
-	O
stranded	O
RNA	B-chemical
that	O
forms	O
a	O
belt	O
around	O
the	O
protein	O
.	O

Over	O
a	O
large	O
dose	O
range	O
,	O
the	O
RNA	B-chemical
was	O
found	O
to	O
be	O
far	O
less	O
susceptible	O
to	O
radiation	O
-	O
induced	O
chemical	O
changes	O
than	O
the	O
protein	O
.	O

The	O
availability	O
of	O
two	O
TRAP	B-complex_assembly
molecules	O
in	O
the	O
asymmetric	O
unit	O
,	O
of	O
which	O
only	O
one	O
contained	O
bound	B-protein_state
RNA	B-chemical
,	O
allowed	O
a	O
controlled	O
investigation	O
into	O
the	O
exact	O
role	O
of	O
RNA	B-chemical
binding	O
in	O
protein	O
specific	O
damage	O
susceptibility	O
.	O

The	O
11	O
-	O
fold	O
symmetry	O
within	O
each	O
TRAP	B-complex_assembly
ring	B-structure_element
permitted	O
statistically	O
significant	O
analysis	O
of	O
the	O
Glu	B-residue_name
and	O
Asp	B-residue_name
damage	O
patterns	O
,	O
with	O
RNA	B-chemical
binding	O
unexpectedly	O
being	O
observed	O
to	O
protect	O
these	O
otherwise	O
highly	O
sensitive	O
residues	O
within	O
the	O
11	O
RNA	B-site
-	I-site
binding	I-site
pockets	I-site
distributed	O
around	O
the	O
outside	O
of	O
the	O
protein	O
molecule	O
.	O

Additionally	O
,	O
the	O
method	O
enabled	O
a	O
quantification	O
of	O
the	O
reduction	O
in	O
radiation	O
-	O
induced	O
Lys	B-residue_name
and	O
Phe	B-residue_name
disordering	O
upon	O
RNA	B-chemical
binding	O
directly	O
from	O
the	O
electron	B-evidence
density	I-evidence
.	O

With	O
the	O
wide	O
use	O
of	O
high	O
-	O
flux	O
third	O
-	O
generation	O
synchrotron	O
sources	O
,	O
radiation	O
damage	O
(	O
RD	O
)	O
has	O
once	O
again	O
become	O
a	O
dominant	O
reason	O
for	O
the	O
failure	O
of	O
structure	B-experimental_method
determination	I-experimental_method
using	O
macromolecular	B-experimental_method
crystallography	I-experimental_method
(	O
MX	B-experimental_method
)	O
in	O
experiments	O
conducted	O
both	O
at	O
room	O
temperature	O
and	O
under	O
cryocooled	O
conditions	O
(	O
100	O
K	O
).	O

Significant	O
progress	O
has	O
been	O
made	O
in	O
recent	O
years	O
in	O
understanding	O
the	O
inevitable	O
manifestations	O
of	O
X	O
-	O
ray	O
-	O
induced	O
RD	O
within	O
protein	O
crystals	B-evidence
,	O
and	O
there	O
is	O
now	O
a	O
body	O
of	O
literature	O
on	O
possible	O
strategies	O
to	O
mitigate	O
the	O
effects	O
of	O
RD	O
(	O
e	O
.	O
g	O
.	O
Zeldin	O
,	O
Brockhauser	O
et	O
al	O
.,	O
2013	O
;	O
Bourenkov	O
&	O
Popov	O
,	O
2010	O
).	O

However	O
,	O
there	O
is	O
still	O
no	O
general	O
consensus	O
within	O
the	O
field	O
on	O
how	O
to	O
minimize	O
RD	O
during	O
MX	B-experimental_method
data	O
collection	O
,	O
and	O
debates	O
on	O
the	O
dependence	O
of	O
RD	O
progression	O
on	O
incident	O
X	O
-	O
ray	O
energy	O
(	O
Shimizu	O
et	O
al	O
.,	O
2007	O
;	O
Liebschner	O
et	O
al	O
.,	O
2015	O
)	O
and	O
the	O
efficacy	O
of	O
radical	O
scavengers	O
(	O
Allan	O
et	O
al	O
.,	O
2013	O
)	O
have	O
yet	O
to	O
be	O
resolved	O
.	O

Global	O
radiation	O
damage	O
is	O
observed	O
within	O
reciprocal	O
space	O
as	O
the	O
overall	O
decay	O
of	O
the	O
summed	O
intensity	O
of	O
reflections	O
detected	O
within	O
the	O
diffraction	B-evidence
pattern	I-evidence
as	O
dose	O
increases	O
(	O
Garman	O
,	O
2010	O
;	O
Murray	O
&	O
Garman	O
,	O
2002	O
).	O

Dose	O
is	O
defined	O
as	O
the	O
absorbed	O
energy	O
per	O
unit	O
mass	O
of	O
crystal	O
in	O
grays	O
(	O
Gy	O
;	O
1	O
Gy	O
=	O
1	O
J	O
kg	O
−	O
1	O
),	O
and	O
is	O
the	O
metric	O
against	O
which	O
damage	O
progression	O
should	O
be	O
monitored	O
during	O
MX	B-experimental_method
data	O
collection	O
,	O
as	O
opposed	O
to	O
time	O
.	O

At	O
100	O
K	O
,	O
an	O
experimental	O
dose	O
limit	O
of	O
30	O
MGy	O
has	O
been	O
recommended	O
as	O
an	O
upper	O
limit	O
beyond	O
which	O
the	O
biological	O
information	O
derived	O
from	O
any	O
macromolecular	O
crystal	B-evidence
may	O
be	O
compromised	O
(	O
Owen	O
et	O
al	O
.,	O
2006	O
).	O

Specific	B-experimental_method
radiation	I-experimental_method
damage	I-experimental_method
(	O
SRD	B-experimental_method
)	O
is	O
observed	O
in	O
the	O
real	B-evidence
-	I-evidence
space	I-evidence
electron	I-evidence
density	I-evidence
,	O
and	O
has	O
been	O
detected	O
at	O
much	O
lower	O
doses	O
than	O
any	O
observable	O
decay	O
in	O
the	O
intensity	O
of	O
reflections	O
.	O

Indeed	O
,	O
the	O
C	O
—	O
Se	B-chemical
bond	O
in	O
selenomethionine	B-chemical
,	O
the	O
stability	O
of	O
which	O
is	O
key	O
for	O
the	O
success	O
of	O
experimental	O
phasing	O
methods	O
,	O
can	O
be	O
cleaved	O
at	O
a	O
dose	O
as	O
low	O
as	O
2	O
MGy	O
for	O
a	O
crystal	B-evidence
maintained	O
at	O
100	O
K	O
(	O
Holton	O
,	O
2007	O
).	O

SRD	O
has	O
been	O
well	O
characterized	O
in	O
a	O
large	O
range	O
of	O
proteins	O
,	O
and	O
is	O
seen	O
to	O
follow	O
a	O
reproducible	O
order	O
:	O
metallo	O
-	O
centre	O
reduction	O
,	O
disulfide	B-ptm
-	I-ptm
bond	I-ptm
cleavage	O
,	O
acidic	O
residue	O
decarboxylation	O
and	O
methionine	O
methylthio	O
cleavage	O
(	O
Ravelli	O
&	O
McSweeney	O
,	O
2000	O
;	O
Burmeister	O
,	O
2000	O
;	O
Weik	O
et	O
al	O
.,	O
2000	O
;	O
Yano	O
et	O
al	O
.,	O
2005	O
).	O

There	O
are	O
a	O
number	O
of	O
cases	O
where	O
SRD	O
manifestations	O
have	O
compromised	O
the	O
biological	O
information	O
extracted	O
from	O
MX	B-experimental_method
-	I-experimental_method
determined	I-experimental_method
structures	B-evidence
at	O
much	O
lower	O
doses	O
than	O
the	O
recommended	O
30	O
MGy	O
limit	O
,	O
leading	O
to	O
false	O
structural	O
interpretations	O
of	O
protein	O
mechanisms	O
.	O

Active	B-site
-	I-site
site	I-site
residues	I-site
appear	O
to	O
be	O
particularly	O
susceptible	O
,	O
particularly	O
for	O
photosensitive	O
proteins	O
and	O
in	O
instances	O
where	O
chemical	O
strain	O
is	O
an	O
intrinsic	O
feature	O
of	O
the	O
reaction	O
mechanism	O
.	O

For	O
instance	O
,	O
structure	B-experimental_method
determination	I-experimental_method
of	O
the	O
purple	O
membrane	O
protein	O
bacterio	B-protein_type
­	I-protein_type
rhodopsin	I-protein_type
required	O
careful	O
corrections	O
for	O
radiation	O
-	O
induced	O
structural	O
changes	O
before	O
the	O
correct	O
photosensitive	O
intermediate	O
states	O
could	O
be	O
isolated	O
(	O
Matsui	O
et	O
al	O
.,	O
2002	O
).	O

The	O
significant	O
chemical	O
strain	O
required	O
for	O
catalysis	O
within	O
the	O
active	B-site
site	I-site
of	O
phosphoserine	B-protein_type
aminotransferase	I-protein_type
has	O
been	O
observed	O
to	O
diminish	O
during	O
X	O
-	O
ray	O
exposure	O
(	O
Dubnovitsky	O
et	O
al	O
.,	O
2005	O
).	O

Since	O
the	O
majority	O
of	O
SRD	B-experimental_method
studies	I-experimental_method
to	O
date	O
have	O
focused	O
on	O
proteins	O
,	O
much	O
less	O
is	O
known	O
about	O
the	O
effects	O
of	O
X	O
-	O
ray	O
irradiation	O
on	O
the	O
wider	O
class	O
of	O
crystalline	O
nucleoprotein	B-complex_assembly
complexes	O
or	O
how	O
to	O
correct	O
for	O
such	O
radiation	O
-	O
induced	O
structural	O
changes	O
.	O

Understanding	O
RD	O
to	O
such	O
complexes	O
is	O
crucial	O
,	O
since	O
DNA	B-chemical
is	O
rarely	O
naked	O
within	O
a	O
cell	O
,	O
instead	O
dynamically	O
interacting	O
with	O
proteins	O
,	O
facilitating	O
replication	O
,	O
transcription	O
,	O
modification	O
and	O
DNA	B-chemical
repair	O
.	O

As	O
of	O
early	O
2016	O
,	O
>	O
5400	O
nucleoprotein	B-complex_assembly
complex	O
structures	B-evidence
have	O
been	O
deposited	O
within	O
the	O
PDB	O
,	O
with	O
91	O
%	O
solved	O
by	O
MX	B-experimental_method
.	O

It	O
is	O
essential	O
to	O
understand	O
how	O
these	O
increasingly	O
complex	O
macromolecular	O
structures	B-evidence
are	O
affected	O
by	O
the	O
radiation	O
used	O
to	O
solve	O
them	O
.	O

Nucleoproteins	B-complex_assembly
also	O
represent	O
one	O
of	O
the	O
main	O
targets	O
of	O
radiotherapy	O
,	O
and	O
an	O
insight	O
into	O
the	O
damage	O
mechanisms	O
induced	O
by	O
X	O
-	O
ray	O
irradiation	O
could	O
inform	O
innovative	O
treatments	O
.	O

Investigations	O
on	O
sub	O
-	O
ionization	O
-	O
level	O
LEEs	O
(	O
0	O
–	O
15	O
eV	O
)	O
interacting	O
with	O
both	O
dried	O
and	O
aqueous	O
oligonucleotides	O
(	O
Alizadeh	O
&	O
Sanche	O
,	O
2014	O
;	O
Simons	O
,	O
2006	O
)	O
concluded	O
that	O
resonant	O
electron	O
attachment	O
to	O
DNA	B-chemical
bases	O
and	O
the	O
sugar	O
-	O
phosphate	O
backbone	O
could	O
lead	O
to	O
the	O
preferential	O
cleavage	O
of	O
strong	O
(∼	O
4	O
eV	O
,	O
385	O
kJ	O
mol	O
−	O
1	O
)	O
sugar	O
-	O
phosphate	O
C	O
—	O
O	O
covalent	O
bonds	O
within	O
the	O
DNA	B-chemical
backbone	O
and	O
then	O
base	O
-	O
sugar	O
N1	O
—	O
C	O
bonds	O
,	O
eventually	O
leading	O
to	O
single	O
-	O
strand	O
breakages	O
(	O
SSBs	O
;	O
Ptasińska	O
&	O
Sanche	O
,	O
2007	O
).	O

Electrons	O
have	O
been	O
shown	O
to	O
be	O
mobile	O
at	O
77	O
K	O
by	O
electron	B-experimental_method
spin	I-experimental_method
resonance	I-experimental_method
spectroscopy	I-experimental_method
studies	O
(	O
Symons	O
,	O
1997	O
;	O
Jones	O
et	O
al	O
.,	O
1987	O
),	O
with	O
rapid	O
electron	O
quantum	O
tunnelling	O
and	O
positive	O
hole	O
migration	O
along	O
the	O
protein	O
backbone	O
and	O
through	O
stacked	O
DNA	B-chemical
bases	O
indicated	O
as	O
a	O
dominant	O
mechanism	O
by	O
which	O
oxidative	O
and	O
reductive	O
damage	O
localizes	O
at	O
distances	O
from	O
initial	O
ionization	B-site
sites	I-site
at	O
100	O
K	O
(	O
O	O
’	O
Neill	O
et	O
al	O
.,	O
2002	O
).	O

The	O
investigation	O
of	O
naturally	O
forming	O
nucleoprotein	O
complexes	O
circumvents	O
the	O
inherent	O
challenges	O
in	O
making	O
controlled	O
comparisons	O
of	O
damage	O
mechanisms	O
between	O
protein	O
and	O
nucleic	O
acids	O
crystallized	B-experimental_method
separately	O
.	O
Recently	O
,	O
for	O
a	O
well	O
characterized	O
bacterial	B-taxonomy_domain
protein	O
–	O
DNA	B-chemical
complex	O
(	O
C	B-complex_assembly
.	I-complex_assembly
Esp1396I	I-complex_assembly
;	O
PDB	O
entry	O
3clc	O
;	O
resolution	O
2	O
.	O
8	O
Å	O
;	O
McGeehan	O
et	O
al	O
.,	O
2008	O
)	O
it	O
was	O
concluded	O
that	O
over	O
a	O
wide	O
dose	O
range	O
(	O
2	O
.	O
1	O
–	O
44	O
.	O
6	O
MGy	O
)	O
the	O
protein	O
was	O
far	O
more	O
susceptible	O
to	O
SRD	O
than	O
the	O
DNA	B-chemical
within	O
the	O
crystal	B-evidence
(	O
Bury	O
et	O
al	O
.,	O
2015	O
).	O

Only	O
at	O
doses	O
above	O
20	O
MGy	O
were	O
precursors	O
of	O
phosphodiester	O
-	O
bond	O
cleavage	O
observed	O
within	O
AT	B-structure_element
-	I-structure_element
rich	I-structure_element
regions	I-structure_element
of	O
the	O
35	O
-	O
mer	O
DNA	B-chemical
.	O

For	O
crystalline	O
complexes	O
such	O
as	O
C	B-complex_assembly
.	I-complex_assembly
Esp1396I	I-complex_assembly
,	O
whether	O
the	O
protein	O
is	O
intrinsically	O
more	O
susceptible	O
to	O
X	O
-	O
ray	O
-	O
induced	O
damage	O
or	O
whether	O
the	O
protein	O
scavenges	O
electrons	O
to	O
protect	O
the	O
DNA	B-chemical
remains	O
unclear	O
in	O
the	O
absence	O
of	O
a	O
non	O
-	O
nucleic	O
acid	O
-	O
bound	O
protein	O
control	O
obtained	O
under	O
exactly	O
the	O
same	O
crystallization	O
and	O
data	O
-	O
collection	O
conditions	O
.	O

To	O
monitor	O
the	O
effects	O
of	O
nucleic	O
acid	O
binding	O
on	O
protein	O
damage	O
susceptibility	O
,	O
a	O
crystal	B-evidence
containing	O
two	O
protein	O
molecules	O
per	O
asymmetric	O
unit	O
,	O
only	O
one	O
of	O
which	O
was	O
bound	B-protein_state
to	I-protein_state
RNA	B-chemical
,	O
is	O
reported	O
here	O
(	O
Fig	O
.	O
1	O
▸).	O

Using	O
newly	O
developed	O
methodology	O
,	O
we	O
present	O
a	O
controlled	B-experimental_method
SRD	I-experimental_method
investigation	O
at	O
1	O
.	O
98	O
Å	O
resolution	O
using	O
a	O
large	O
(∼	O
91	O
kDa	O
)	O
crystalline	O
protein	B-complex_assembly
–	I-complex_assembly
RNA	I-complex_assembly
complex	O
:	O
trp	B-protein_type
RNA	I-protein_type
-	I-protein_type
binding	I-protein_type
attenuation	I-protein_type
protein	I-protein_type
(	O
TRAP	B-complex_assembly
)	O
bound	B-protein_state
to	I-protein_state
a	O
53	O
bp	O
RNA	B-chemical
sequence	O
(	B-chemical
GAGUU	I-chemical
)	I-chemical
10GAG	I-chemical
(	O
PDB	O
entry	O
1gtf	O
;	O
Hopcroft	O
et	O
al	O
.,	O
2002	O
).	O

TRAP	B-complex_assembly
consists	O
of	O
11	O
identical	O
subunits	B-structure_element
assembled	O
into	O
a	O
ring	B-structure_element
with	O
11	O
-	O
fold	O
rotational	O
symmetry	O
.	O

It	O
binds	O
with	O
high	O
affinity	O
(	O
K	B-evidence
d	I-evidence
≃	O
1	O
.	O
0	O
nM	O
)	O
to	O
RNA	B-chemical
segments	O
containing	O
11	O
GAG	B-structure_element
/	I-structure_element
UAG	I-structure_element
triplets	I-structure_element
separated	O
by	O
two	O
or	O
three	O
spacer	B-structure_element
nucleotides	I-structure_element
(	O
Elliott	O
et	O
al	O
.,	O
2001	O
)	O
to	O
regulate	O
the	O
transcription	O
of	O
tryptophan	B-chemical
biosynthetic	O
genes	O
in	O
Bacillus	B-species
subtilis	I-species
(	O
Antson	O
et	O
al	O
.,	O
1999	O
).	O

In	O
this	O
structure	B-evidence
,	O
the	O
bases	O
of	O
the	O
G1	B-chemical
-	I-chemical
A2	I-chemical
-	I-chemical
G3	I-chemical
nucleotides	O
form	O
direct	O
hydrogen	O
bonds	O
to	O
the	O
protein	O
,	O
unlike	O
the	O
U4	B-chemical
-	I-chemical
U5	I-chemical
nucleotides	O
,	O
which	O
appear	O
to	O
be	O
more	O
flexible	O
.	O

Ten	O
successive	O
1	O
.	O
98	O
Å	O
resolution	O
MX	B-experimental_method
data	O
sets	O
were	O
collected	O
from	O
the	O
same	O
TRAP	B-complex_assembly
–	I-complex_assembly
RNA	I-complex_assembly
crystal	B-evidence
to	O
analyse	O
X	O
-	O
ray	O
-	O
induced	O
structural	O
changes	O
over	O
a	O
large	O
dose	O
range	O
(	O
d	O
1	O
=	O
1	O
.	O
3	O
MGy	O
to	O
d	O
10	O
=	O
25	O
.	O
0	O
MGy	O
).	O

To	O
avoid	O
the	O
previous	O
necessity	O
for	O
visual	O
inspection	O
of	O
electron	B-evidence
-	I-evidence
density	I-evidence
maps	I-evidence
to	O
detect	O
SRD	B-site
sites	I-site
,	O
a	O
computational	O
approach	O
was	O
designed	O
to	O
quantify	O
the	O
electron	B-evidence
-	I-evidence
density	I-evidence
change	I-evidence
for	O
each	O
refined	O
atom	O
with	O
increasing	O
dose	O
,	O
thus	O
providing	O
a	O
rapid	O
systematic	O
method	O
for	O
SRD	O
study	O
on	O
such	O
large	O
multimeric	O
complexes	O
.	O

By	O
employing	O
the	O
high	O
11	O
-	O
fold	O
structural	O
symmetry	O
within	O
each	O
TRAP	B-complex_assembly
macromolecule	O
,	O
this	O
approach	O
permitted	O
a	O
thorough	O
statistical	O
quantification	O
of	O
the	O
RD	O
effects	O
of	O
RNA	B-chemical
binding	O
to	O
TRAP	B-complex_assembly
.	O

Per	B-experimental_method
-	I-experimental_method
atom	I-experimental_method
quantification	I-experimental_method
of	I-experimental_method
electron	I-experimental_method
density	I-experimental_method

To	O
quantify	O
the	O
exact	O
effects	O
of	O
nucleic	O
acid	O
binding	O
to	O
a	O
protein	O
on	O
SRD	O
susceptibility	O
,	O
a	O
high	O
-	O
throughput	O
and	O
automated	O
pipeline	O
was	O
created	O
to	O
systematically	O
calculate	O
the	O
electron	B-evidence
-	I-evidence
density	I-evidence
change	I-evidence
for	O
every	O
refined	O
atom	O
within	O
the	O
TRAP	B-complex_assembly
–	I-complex_assembly
RNA	I-complex_assembly
structure	B-evidence
as	O
a	O
function	O
of	O
dose	O
.	O

This	O
provides	O
an	O
atom	O
-	O
specific	O
quantification	O
of	O
density	B-evidence
–	I-evidence
dose	I-evidence
dynamics	I-evidence
,	O
which	O
was	O
previously	O
lacking	O
within	O
the	O
field	O
.	O

Previous	O
studies	O
have	O
characterized	O
SRD	B-site
sites	I-site
by	O
reporting	O
magnitudes	O
of	O
F	B-evidence
obs	I-evidence
(	I-evidence
d	I-evidence
n	I-evidence
)	I-evidence
−	I-evidence
F	I-evidence
obs	I-evidence
(	I-evidence
d	I-evidence
1	I-evidence
)	I-evidence
Fourier	I-evidence
difference	I-evidence
map	I-evidence
peaks	I-evidence
in	O
terms	O
of	O
the	O
sigma	B-evidence
(	O
σ	B-evidence
)	O
contour	O
level	O
(	O
the	O
number	O
of	O
standard	B-evidence
deviations	I-evidence
from	O
the	O
mean	B-evidence
map	I-evidence
electron	I-evidence
-	I-evidence
density	I-evidence
value	I-evidence
)	O
at	O
which	O
peaks	O
become	O
visible	O
.	O

However	O
,	O
these	O
σ	B-evidence
levels	O
depend	O
on	O
the	O
standard	B-evidence
deviation	I-evidence
values	O
of	O
the	O
map	B-evidence
,	O
which	O
can	O
deviate	O
between	O
data	O
sets	O
,	O
and	O
are	O
thus	O
unsuitable	O
for	O
quantitative	O
comparison	O
of	O
density	B-evidence
between	O
different	O
dose	O
data	O
sets	O
.	O

Instead	O
,	O
we	O
use	O
here	O
a	O
maximum	B-evidence
density	I-evidence
-	I-evidence
loss	I-evidence
metric	I-evidence
(	O
D	B-evidence
loss	I-evidence
),	O
which	O
is	O
the	O
per	O
-	O
atom	O
equivalent	O
of	O
the	O
magnitude	O
of	O
these	O
negative	B-evidence
Fourier	I-evidence
difference	I-evidence
map	I-evidence
peaks	I-evidence
in	O
units	O
of	O
e	O
Å	O
−	O
3	O
.	O

Large	O
positive	O
D	B-evidence
loss	I-evidence
values	O
indicate	O
radiation	O
-	O
induced	O
atomic	O
disordering	O
reproducibly	O
throughout	O
the	O
unit	O
cells	O
with	O
respect	O
to	O
the	O
initial	O
low	O
-	O
dose	O
data	O
set	O
.	O

For	O
each	O
TRAP	B-complex_assembly
–	I-complex_assembly
RNA	I-complex_assembly
data	O
set	O
,	O
the	O
D	B-evidence
loss	I-evidence
metric	I-evidence
successfully	O
identified	O
the	O
recognized	O
forms	O
of	O
protein	O
SRD	B-experimental_method
(	O
Fig	O
.	O
2	O
▸	O
a	O
),	O
with	O
clear	O
Glu	B-residue_name
and	O
Asp	B-residue_name
side	O
-	O
chain	O
decarboxylation	O
even	O
in	O
the	O
first	O
difference	B-evidence
map	I-evidence
calculated	O
(	O
3	O
.	O
9	O
MGy	O
;	O
Fig	O
.	O
3	O
▸	O
a	O
).	O

The	O
main	O
sequence	O
of	O
TRAP	B-complex_assembly
does	O
not	O
contain	O
any	O
Trp	B-residue_name
and	O
Cys	B-residue_name
residues	O
(	O
and	O
thus	O
contains	O
no	O
disulfide	O
bonds	O
).	O

The	O
substrate	O
Trp	B-chemical
amino	O
-	O
acid	O
ligands	O
also	O
exhibited	O
disordering	O
of	O
the	O
free	O
terminal	O
carboxyl	O
groups	O
at	O
higher	O
doses	O
(	O
Fig	O
.	O
2	O
▸	O
a	O
);	O
however	O
,	O
no	O
clear	O
Fourier	B-evidence
difference	I-evidence
peaks	I-evidence
could	O
be	O
observed	O
visually	O
.	O

Even	O
for	O
radiation	O
-	O
insensitive	O
residues	O
(	O
e	O
.	O
g	O
.	O
Gly	B-residue_name
)	O
the	O
average	O
D	B-evidence
loss	I-evidence
increases	O
with	O
dose	O
:	O
this	O
is	O
the	O
effect	O
of	O
global	O
radiation	O
damage	O
,	O
since	O
as	O
dose	O
increases	O
the	O
electron	B-evidence
density	I-evidence
associated	O
with	O
each	O
refined	O
atom	O
becomes	O
weaker	O
as	O
the	O
atomic	O
occupancy	O
decreases	O
(	O
Fig	O
.	O
2	O
▸	O
b	O
).	O

Only	O
Glu	B-residue_name
and	O
Asp	B-residue_name
residues	O
exhibit	O
a	O
rate	O
of	O
D	B-evidence
loss	I-evidence
increase	O
that	O
consistently	O
exceeds	O
the	O
average	O
decay	O
(	O
Fig	O
.	O
2	O
▸	O
b	O
,	O
dashed	O
line	O
)	O
at	O
each	O
dose	O
.	O

The	O
rate	O
of	O
D	B-evidence
loss	I-evidence
(	O
attributed	O
to	O
side	O
-	O
chain	O
decarboxylation	O
)	O
was	O
consistently	O
larger	O
for	O
Glu	B-residue_name
compared	O
with	O
Asp	B-residue_name
residues	O
over	O
the	O
large	O
dose	O
range	O
(	O
Fig	O
.	O
2	O
▸	O
b	O
and	O
Supplementary	O
Fig	O
.	O
S3	O
);	O
this	O
observation	O
is	O
consistent	O
with	O
our	O
calculations	O
on	O
model	O
systems	O
(	O
see	O
above	O
)	O
that	O
suggest	O
that	O
,	O
without	O
considering	O
differential	O
hydrogen	O
-	O
bonding	O
environments	O
,	O
CO2	B-chemical
loss	O
is	O
more	O
exothermic	O
by	O
around	O
8	O
kJ	O
mol	O
−	O
1	O
from	O
oxidized	B-protein_state
Glu	B-residue_name
residues	O
than	O
from	O
their	O
Asp	B-residue_name
counterparts	O
.	O

RNA	B-chemical
is	O
less	O
susceptible	O
to	O
electron	B-evidence
-	I-evidence
density	I-evidence
loss	O
than	O
protein	O
within	O
the	O
TRAP	B-complex_assembly
–	I-complex_assembly
RNA	I-complex_assembly
complex	O

Visual	B-experimental_method
inspection	I-experimental_method
of	I-experimental_method
Fourier	B-evidence
difference	I-evidence
maps	I-evidence
illustrated	O
the	O
clear	O
lack	O
of	O
RNA	B-chemical
electron	B-evidence
-	I-evidence
density	I-evidence
degradation	I-evidence
with	O
increasing	O
dose	O
compared	O
with	O
the	O
obvious	O
protein	O
damage	O
manifestations	O
(	O
Figs	O
.	O
3	O
▸	O
b	O
and	O
3	O
▸	O
c	O
).	O

Only	O
at	O
the	O
highest	O
doses	O
investigated	O
(>	O
20	O
MGy	O
)	O
was	O
density	O
loss	O
observed	O
at	O
the	O
RNA	B-chemical
phosphate	O
and	O
C	O
—	O
O	O
bonds	O
of	O
the	O
phosphodiester	O
backbone	O
.	O

However	O
,	O
the	O
median	O
D	B-evidence
loss	I-evidence
was	O
lower	O
by	O
a	O
factor	O
of	O
>	O
2	O
for	O
RNA	B-chemical
P	O
atoms	O
than	O
for	O
Glu	B-residue_name
and	O
Asp	B-residue_name
side	O
-	O
chain	O
groups	O
at	O
25	O
.	O
0	O
MGy	O
(	O
Supplementary	O
Fig	O
.	O
S4	O
),	O
and	O
furthermore	O
could	O
not	O
be	O
numerically	O
distinguished	O
from	O
Gly	B-residue_name
Cα	O
atoms	O
within	O
TRAP	B-complex_assembly
,	O
which	O
are	O
not	O
radiation	O
-	O
sensitive	O
at	O
the	O
doses	O
tested	O
here	O
(	O
Supplementary	O
Fig	O
.	O
S3	O
).	O

RNA	B-chemical
binding	O
protects	O
radiation	O
-	O
sensitive	O
residues	O

For	O
the	O
large	O
number	O
of	O
acidic	O
residues	O
per	O
TRAP	B-complex_assembly
ring	B-structure_element
(	O
four	O
Asp	B-residue_name
and	O
six	O
Glu	B-residue_name
residues	O
per	O
protein	O
monomer	B-oligomeric_state
),	O
a	O
strong	O
dependence	O
of	O
decarboxylation	O
susceptibility	O
on	O
local	O
environment	O
was	O
observed	O
(	O
Fig	O
.	O
4	O
▸).	O

For	O
each	O
Glu	B-residue_name
Cδ	O
or	O
Asp	B-residue_name
Cγ	O
atom	O
,	O
D	B-evidence
loss	I-evidence
provided	O
a	O
direct	O
measure	O
of	O
the	O
rate	O
of	O
side	O
-	O
chain	O
carboxyl	O
-	O
group	O
disordering	O
and	O
subsequent	O
decarboxylation	O
.	O

For	O
acidic	O
residues	O
with	O
no	O
differing	O
interactions	O
between	O
nonbound	B-protein_state
and	O
bound	B-protein_state
TRAP	B-complex_assembly
(	O
Fig	O
.	O
4	O
▸	O
a	O
),	O
similar	O
damage	O
was	O
apparent	O
between	O
the	O
two	O
rings	O
within	O
the	O
asymmetric	O
unit	O
,	O
as	O
expected	O
.	O

However	O
,	O
TRAP	B-complex_assembly
residues	O
directly	O
on	O
the	O
RNA	B-site
-	I-site
binding	I-site
interfaces	I-site
exhibited	O
greater	O
damage	O
accumulation	O
in	O
nonbound	B-protein_state
TRAP	B-complex_assembly
(	O
Fig	O
.	O
4	O
▸	O
b	O
),	O
and	O
for	O
residues	O
at	O
the	O
ring	B-site
–	I-site
ring	I-site
interfaces	I-site
(	O
where	O
crystal	O
contacts	O
were	O
detected	O
)	O
bound	B-protein_state
TRAP	B-complex_assembly
exhibited	O
enhanced	O
SRD	O
accumulation	O
(	O
Fig	O
.	O
4	O
▸	O
c	O
).	O

Three	O
acidic	O
residues	O
(	O
Glu36	B-residue_name_number
,	O
Asp39	B-residue_name_number
and	O
Glu42	B-residue_name_number
)	O
are	O
involved	O
in	O
RNA	B-chemical
interactions	O
within	O
each	O
of	O
the	O
11	O
TRAP	B-complex_assembly
ring	B-structure_element
subunits	B-structure_element
,	O
and	O
Fig	O
.	O
5	O
▸	O
shows	O
their	O
density	B-evidence
changes	I-evidence
with	O
increasing	O
dose	O
.	O

Hotelling	B-experimental_method
’	I-experimental_method
s	I-experimental_method
T	I-experimental_method
-	I-experimental_method
squared	I-experimental_method
test	I-experimental_method
(	O
the	O
multivariate	O
counterpart	O
of	O
Student	B-experimental_method
’	I-experimental_method
s	I-experimental_method
t	I-experimental_method
-	I-experimental_method
test	I-experimental_method
)	O
was	O
used	O
to	O
reject	O
the	O
null	O
hypothesis	O
that	O
the	O
means	O
of	O
the	O
D	B-evidence
loss	I-evidence
metric	I-evidence
were	O
equal	O
for	O
the	O
bound	B-protein_state
and	O
nonbound	B-protein_state
groups	O
in	O
Fig	O
.	O
5	O
▸.	O

A	O
significant	O
reduction	O
in	O
D	B-evidence
loss	I-evidence
is	O
seen	O
for	O
Glu36	B-residue_name_number
in	O
RNA	B-protein_state
-	I-protein_state
bound	I-protein_state
compared	O
with	O
nonbound	B-protein_state
TRAP	B-complex_assembly
,	O
indicative	O
of	O
a	O
lower	O
rate	O
of	O
side	O
-	O
chain	O
decarboxylation	O
(	O
Fig	O
.	O
5	O
▸	O
a	O
;	O
p	O
=	O
6	O
.	O
06	O
×	O
10	O
−	O
5	O
).	O

For	O
each	O
TRAP	B-complex_assembly
ring	B-structure_element
subunit	B-structure_element
,	O
the	O
Glu36	B-residue_name_number
side	O
-	O
chain	O
carboxyl	O
group	O
accepts	O
a	O
pair	O
of	O
hydrogen	O
bonds	O
from	O
the	O
two	O
N	O
atoms	O
of	O
the	O
G3	B-residue_name_number
RNA	B-chemical
base	O
.	O

In	O
our	O
analysis	O
,	O
Asp39	B-residue_name_number
in	O
the	O
TRAP	B-complex_assembly
–(	I-complex_assembly
GAGUU	I-complex_assembly
)	I-complex_assembly
10GAG	I-complex_assembly
structure	B-evidence
appears	O
to	O
exhibit	O
two	O
distinct	O
hydrogen	O
bonds	O
to	O
the	O
G1	B-residue_name_number
base	O
within	O
each	O
of	O
the	O
11	O
TRAP	B-site
–	I-site
RNA	I-site
interfaces	I-site
,	O
as	O
does	O
Glu36	B-residue_name_number
to	O
G3	B-residue_name_number
;	O
however	O
,	O
the	O
reduction	O
in	O
density	B-evidence
disordering	O
upon	O
RNA	B-chemical
binding	O
is	O
far	O
less	O
significant	O
for	O
Asp39	B-residue_name_number
than	O
for	O
Glu36	B-residue_name_number
(	O
Fig	O
.	O
5	O
▸	O
b	O
,	O
p	O
=	O
0	O
.	O
0925	O
).	O

RNA	B-chemical
binding	O
reduces	O
radiation	O
-	O
induced	O
disorder	O
on	O
the	O
atomic	O
scale	O

One	O
oxygen	O
(	O
O	O
∊	O
1	O
)	O
of	O
Glu42	B-residue_name_number
appears	O
to	O
form	O
a	O
hydrogen	O
bond	O
to	O
a	O
nearby	O
water	B-chemical
within	O
each	O
TRAP	B-site
RNA	I-site
-	I-site
binding	I-site
pocket	I-site
,	O
with	O
the	O
other	O
(	O
O	O
∊	O
2	O
)	O
being	O
involved	O
in	O
a	O
salt	O
-	O
bridge	O
interaction	O
with	O
Arg58	B-residue_name_number
(	O
Hopcroft	O
et	O
al	O
.,	O
2002	O
;	O
Antson	O
et	O
al	O
.,	O
1999	O
).	O

Salt	O
-	O
bridge	O
interactions	O
have	O
previously	O
been	O
suggested	O
to	O
reduce	O
the	O
glutamate	B-residue_name
decarboxylation	O
rate	O
within	O
the	O
large	O
(∼	O
62	O
.	O
4	O
kDa	O
)	O
myrosinase	B-protein_type
protein	O
structure	B-evidence
(	O
Burmeister	O
,	O
2000	O
).	O

A	O
significant	O
difference	O
was	O
observed	O
between	O
the	O
D	B-evidence
loss	I-evidence
dynamics	I-evidence
for	O
the	O
nonbound	B-protein_state
/	O
bound	B-protein_state
Glu42	B-residue_name_number
O	O
∊	O
1	O
atoms	O
(	O
Fig	O
.	O
5	O
▸	O
c	O
;	O
p	O
=	O
0	O
.	O
007	O
)	O
but	O
not	O
for	O
the	O
Glu42	B-residue_name_number
O	O
∊	O
2	O
atoms	O
(	O
Fig	O
.	O
5	O
▸	O
d	O
;	O
p	O
=	O
0	O
.	O
239	O
),	O
indicating	O
that	O
the	O
stabilizing	O
strength	O
of	O
this	O
salt	O
-	O
bridge	O
interaction	O
was	O
conserved	O
upon	O
RNA	B-chemical
binding	O
and	O
that	O
the	O
water	B-chemical
-	O
mediated	O
hydrogen	O
bond	O
had	O
a	O
greater	O
relative	O
susceptibility	O
to	O
atomic	O
disordering	O
in	O
the	O
absence	B-protein_state
of	I-protein_state
RNA	B-chemical
.	O

The	O
density	B-evidence
-	I-evidence
change	I-evidence
dynamics	I-evidence
were	O
statistically	O
indistinguishable	O
between	O
bound	B-protein_state
and	O
nonbound	B-protein_state
TRAP	B-complex_assembly
for	O
each	O
Glu42	B-residue_name_number
carboxyl	O
group	O
Cδ	O
atom	O
(	O
p	O
=	O
0	O
.	O
435	O
),	O
indicating	O
that	O
upon	O
RNA	B-chemical
binding	O
the	O
conserved	O
salt	O
-	O
bridge	O
interaction	O
ultimately	O
dictated	O
the	O
overall	O
Glu42	B-residue_name_number
decarboxylation	O
rate	O
.	O

The	O
RNA	B-chemical
-	O
stabilizing	O
effect	O
was	O
not	O
restricted	O
to	O
radiation	O
-	O
sensitive	O
acidic	O
residues	O
.	O

The	O
side	O
chain	O
of	O
Phe32	B-residue_name_number
stacks	O
against	O
the	O
G3	B-residue_name_number
base	O
within	O
the	O
11	O
TRAP	B-site
RNA	I-site
-	I-site
binding	I-site
interfaces	I-site
(	O
Antson	O
et	O
al	O
.,	O
1999	O
).	O

With	O
increasing	O
dose	O
,	O
the	O
D	B-evidence
loss	I-evidence
associated	O
with	O
the	O
Phe32	B-residue_name_number
side	O
chain	O
was	O
significantly	O
reduced	O
upon	O
RNA	B-chemical
binding	O
(	O
Fig	O
.	O
5	O
▸	O
e	O
;	O
Phe32	B-residue_name_number
Cζ	O
;	O
p	O
=	O
0	O
.	O
0014	O
),	O
an	O
indication	O
that	O
radiation	O
-	O
induced	O
conformation	O
disordering	O
of	O
Phe32	B-residue_name_number
had	O
been	O
reduced	O
.	O

The	O
extended	O
aliphatic	O
Lys37	B-residue_name_number
side	O
chain	O
stacks	O
against	O
the	O
nearby	O
G1	B-residue_name_number
base	O
,	O
making	O
a	O
series	O
of	O
nonpolar	O
contacts	O
within	O
each	O
RNA	B-site
-	I-site
binding	I-site
interface	I-site
.	O

The	O
D	B-evidence
loss	I-evidence
for	O
Lys37	B-residue_name_number
side	O
-	O
chain	O
atoms	O
was	O
also	O
reduced	O
when	O
stacked	O
against	O
the	O
G1	B-residue_name_number
base	O
(	O
Fig	O
.	O
5	O
▸	O
f	O
;	O
p	O
=	O
0	O
.	O
0243	O
for	O
Lys37	B-residue_name_number
C	O
∊	O
atoms	O
).	O

Representative	O
Phe32	B-residue_name_number
and	O
Lys37	B-residue_name_number
atoms	O
were	O
selected	O
to	O
illustrate	O
these	O
trends	O
.	O

Here	O
,	O
MX	B-experimental_method
radiation	O
-	O
induced	O
specific	O
structural	O
changes	O
within	O
the	O
large	O
TRAP	B-complex_assembly
–	I-complex_assembly
RNA	I-complex_assembly
assembly	O
over	O
a	O
large	O
dose	O
range	O
(	O
1	O
.	O
3	O
–	O
25	O
.	O
0	O
MGy	O
)	O
have	O
been	O
analysed	O
using	O
a	O
high	O
-	O
throughput	O
quantitative	O
approach	O
,	O
providing	O
a	O
measure	O
of	O
the	O
electron	B-evidence
-	I-evidence
density	I-evidence
distribution	I-evidence
for	O
each	O
refined	O
atom	O
with	O
increasing	O
dose	O
,	O
D	B-evidence
loss	I-evidence
.	O

Compared	O
with	O
previous	O
studies	O
,	O
the	O
results	O
provide	O
a	O
further	O
step	O
in	O
the	O
detailed	O
characterization	O
of	O
SRD	O
effects	O
in	O
MX	B-experimental_method
.	O

Our	O
method	O
­	O
ology	O
,	O
which	O
eliminated	O
tedious	O
and	O
error	O
-	O
prone	O
visual	O
inspection	O
,	O
permitted	O
the	O
determination	O
on	O
a	O
per	O
-	O
atom	O
basis	O
of	O
the	O
most	O
damaged	O
sites	O
,	O
as	O
characterized	O
by	O
F	B-evidence
obs	I-evidence
(	I-evidence
d	I-evidence
n	I-evidence
)	I-evidence
−	I-evidence
F	I-evidence
obs	I-evidence
(	I-evidence
d	I-evidence
1	I-evidence
)	I-evidence
Fourier	I-evidence
difference	I-evidence
map	I-evidence
peaks	I-evidence
between	O
successive	O
data	O
sets	O
collected	O
from	O
the	O
same	O
crystal	B-evidence
.	O

Here	O
,	O
it	O
provided	O
the	O
precision	O
required	O
to	O
quantify	O
the	O
role	O
of	O
RNA	B-chemical
in	O
the	O
damage	O
susceptibilities	O
of	O
equivalent	O
atoms	O
between	O
RNA	B-protein_state
-	I-protein_state
bound	I-protein_state
and	O
nonbound	B-protein_state
TRAP	B-complex_assembly
,	O
but	O
it	O
is	O
applicable	O
to	O
any	O
MX	B-experimental_method
SRD	O
study	O
.	O

The	O
RNA	B-chemical
was	O
found	O
to	O
be	O
substantially	O
more	O
radiation	B-protein_state
-	I-protein_state
resistant	I-protein_state
than	O
the	O
protein	O
,	O
even	O
at	O
the	O
highest	O
doses	O
investigated	O
(∼	O
25	O
.	O
0	O
MGy	O
),	O
which	O
is	O
in	O
strong	O
concurrence	O
with	O
our	O
previous	O
SRD	B-experimental_method
investigation	I-experimental_method
of	O
the	O
C	B-complex_assembly
.	I-complex_assembly
Esp1396I	I-complex_assembly
protein	O
–	O
DNA	B-chemical
complex	O
(	O
Bury	O
et	O
al	O
.,	O
2015	O
).	O

Consistent	O
with	O
that	O
study	O
,	O
at	O
high	O
doses	O
of	O
above	O
∼	O
20	O
MGy	O
,	O
F	B-evidence
obs	I-evidence
(	I-evidence
d	I-evidence
n	I-evidence
)	I-evidence
−	I-evidence
F	I-evidence
obs	I-evidence
(	I-evidence
d	I-evidence
1	I-evidence
)	I-evidence
map	I-evidence
density	I-evidence
was	O
detected	O
around	O
P	O
,	O
O3	O
′	O
and	O
O5	O
′	O
atoms	O
of	O
the	O
RNA	B-chemical
backbone	O
,	O
with	O
no	O
significant	O
difference	B-evidence
density	I-evidence
localized	O
to	O
RNA	B-chemical
ribose	O
and	O
basic	O
subunits	B-structure_element
.	O

RNA	B-chemical
backbone	O
disordering	O
thus	O
appears	O
to	O
be	O
the	O
main	O
radiation	O
-	O
induced	O
effect	O
in	O
RNA	B-chemical
,	O
with	O
the	O
protein	O
–	O
base	O
interactions	O
maintained	O
even	O
at	O
high	O
doses	O
(>	O
20	O
MGy	O
).	O

The	O
U4	B-residue_name_number
phosphate	B-chemical
exhibited	O
marginally	O
larger	O
D	B-evidence
loss	I-evidence
values	O
above	O
20	O
MGy	O
than	O
G1	B-residue_name_number
,	O
A2	B-residue_name_number
and	O
G3	B-residue_name_number
(	O
Supplementary	O
Fig	O
.	O
S4	O
).	O

Since	O
U4	B-residue_name_number
is	O
the	O
only	O
refined	O
nucleotide	O
not	O
to	O
exhibit	O
significant	O
base	O
–	O
protein	O
interactions	O
around	O
TRAP	B-complex_assembly
(	O
with	O
a	O
water	B-chemical
-	O
mediated	O
hydrogen	O
bond	O
detected	O
in	O
only	O
three	O
of	O
the	O
11	O
subunits	B-structure_element
and	O
a	O
single	O
Arg58	B-residue_name_number
hydrogen	O
bond	O
suggested	O
in	O
a	O
further	O
four	O
subunits	B-structure_element
),	O
this	O
increased	O
U4	B-residue_name_number
D	B-evidence
loss	I-evidence
can	O
be	O
explained	O
owing	O
to	O
its	O
greater	O
flexibility	O
.	O

At	O
25	O
.	O
0	O
MGy	O
,	O
the	O
magnitude	O
of	O
the	O
RNA	B-chemical
backbone	O
D	B-evidence
loss	I-evidence
was	O
of	O
the	O
same	O
order	O
as	O
for	O
the	O
radiation	O
-	O
insensitive	O
Gly	B-residue_name
Cα	O
atoms	O
and	O
on	O
average	O
less	O
than	O
half	O
that	O
of	O
the	O
acidic	O
residues	O
of	O
the	O
protein	O
(	O
Supplementary	O
Fig	O
.	O
S3	O
).	O

Consequently	O
,	O
no	O
clear	O
single	O
-	O
strand	O
breaks	O
could	O
be	O
located	O
,	O
and	O
since	O
RNA	B-chemical
-	O
binding	O
within	O
the	O
current	O
TRAP	B-complex_assembly
–(	I-complex_assembly
GAGUU	I-complex_assembly
)	I-complex_assembly
10GAG	I-complex_assembly
complex	O
is	O
mediated	O
predominantly	O
through	O
base	O
–	O
protein	O
interactions	O
,	O
the	O
biological	O
integrity	O
of	O
the	O
RNA	B-chemical
complex	O
was	O
dictated	O
by	O
the	O
rate	O
at	O
which	O
protein	O
decarboxylation	O
occurred	O
.	O

RNA	B-chemical
interacting	O
with	O
TRAP	B-complex_assembly
was	O
shown	O
to	O
offer	O
significant	O
protection	O
against	O
radiation	O
-	O
induced	O
structural	O
changes	O
.	O

Both	O
Glu36	B-residue_name_number
and	O
Asp39	B-residue_name_number
bind	O
directly	O
to	O
RNA	B-chemical
,	O
each	O
through	O
two	O
hydrogen	O
bonds	O
to	O
guanine	B-chemical
bases	O
(	O
G3	B-residue_name_number
and	O
G1	B-residue_name_number
,	O
respectively	O
).	O

However	O
,	O
compared	O
with	O
Asp39	B-residue_name_number
,	O
Glu36	B-residue_name_number
is	O
strikingly	O
less	O
decarboxylated	O
when	O
bound	B-protein_state
to	I-protein_state
RNA	B-chemical
(	O
Fig	O
.	O
4	O
▸).	O

This	O
is	O
in	O
good	O
agreement	O
with	O
previous	O
mutagenesis	B-experimental_method
and	I-experimental_method
nucleoside	I-experimental_method
analogue	I-experimental_method
studies	I-experimental_method
(	O
Elliott	O
et	O
al	O
.,	O
2001	O
),	O
which	O
indicated	O
that	O
the	O
G1	B-residue_name_number
nucleotide	O
does	O
not	O
bind	O
to	O
TRAP	B-complex_assembly
as	O
strongly	O
as	O
do	O
A2	B-residue_name_number
and	O
G3	B-residue_name_number
,	O
and	O
plays	O
little	O
role	O
in	O
the	O
high	O
RNA	B-evidence
-	I-evidence
binding	I-evidence
affinity	I-evidence
of	O
TRAP	B-complex_assembly
(	O
K	B-evidence
d	I-evidence
≃	O
1	O
.	O
1	O
±	O
0	O
.	O
4	O
nM	O
).	O

For	O
Glu36	B-residue_name_number
and	O
Asp39	B-residue_name_number
,	O
no	O
direct	O
quantitative	O
correlation	O
could	O
be	O
established	O
between	O
hydrogen	O
-	O
bond	O
length	O
and	O
D	B-evidence
loss	I-evidence
(	O
linear	B-evidence
R	I-evidence
2	I-evidence
of	O
<	O
0	O
.	O
23	O
for	O
all	O
doses	O
;	O
Supplementary	O
Fig	O
.	O
S5	O
).	O

Thus	O
,	O
another	O
factor	O
must	O
be	O
responsible	O
for	O
this	O
clear	O
reduction	O
in	O
Glu36	B-residue_name_number
CO2	O
decarboxyl	O
­	O
ation	O
in	O
RNA	B-protein_state
-	I-protein_state
bound	I-protein_state
TRAP	B-complex_assembly
.	O

The	O
Glu36	B-residue_name_number
carboxyl	O
side	O
chain	O
also	O
potentially	O
forms	O
hydrogen	O
bonds	O
to	O
His34	B-residue_name_number
and	O
Lys56	B-residue_name_number
,	O
but	O
since	O
these	O
interactions	O
are	O
conserved	B-protein_state
irrespective	O
of	O
G3	B-residue_name_number
nucleotide	O
binding	O
,	O
this	O
cannot	O
directly	O
account	O
for	O
the	O
stabilization	O
effect	O
on	O
Glu36	B-residue_name_number
in	O
RNA	B-protein_state
-	I-protein_state
bound	I-protein_state
TRAP	B-complex_assembly
.	O

When	O
bound	B-protein_state
to	I-protein_state
RNA	B-chemical
,	O
the	O
average	O
solvent	O
-	O
accessible	O
area	O
of	O
the	O
Glu36	B-residue_name_number
side	O
-	O
chain	O
O	O
atoms	O
is	O
reduced	O
from	O
∼	O
15	O
to	O
0	O
Å2	O
.	O

We	O
propose	O
that	O
with	O
no	O
solvent	O
accessibility	O
Glu36	B-residue_name_number
decarboxylation	O
is	O
inhibited	O
,	O
since	O
the	O
CO2	B-evidence
-	I-evidence
formation	I-evidence
rate	I-evidence
K	I-evidence
2	I-evidence
is	O
greatly	O
reduced	O
,	O
and	O
suggest	O
that	O
steric	O
hindrance	O
prevents	O
each	O
radicalized	O
Glu36	B-residue_name_number
CO2	O
group	O
from	O
achieving	O
the	O
planar	O
conformation	O
required	O
for	O
complete	O
dissociation	O
from	O
TRAP	B-complex_assembly
.	O

The	O
electron	B-evidence
-	I-evidence
recombination	I-evidence
rate	I-evidence
K	I-evidence
−	I-evidence
1	I-evidence
remains	O
high	O
,	O
however	O
,	O
owing	O
to	O
rapid	O
electron	O
migration	O
through	O
the	O
protein	B-complex_assembly
–	I-complex_assembly
RNA	I-complex_assembly
complex	O
to	O
refill	O
the	O
Glu36	B-residue_name_number
positive	B-site
hole	I-site
(	O
the	O
precursor	O
for	O
Glu	B-residue_name
decarboxylation	O
).	O

Upon	O
RNA	B-chemical
binding	O
,	O
the	O
Asp39	B-residue_name_number
side	O
-	O
chain	O
carboxyl	O
group	O
solvent	O
-	O
accessible	O
area	O
changes	O
from	O
∼	O
75	O
to	O
35	O
Å2	O
,	O
still	O
allowing	O
a	O
high	O
CO2	B-chemical
-	O
formation	O
rate	B-evidence
K	I-evidence
2	I-evidence
.	O

The	O
prevalence	O
of	O
radical	O
attack	O
from	O
solvent	O
channels	O
surrounding	O
the	O
protein	O
in	O
the	O
crystal	B-evidence
is	O
a	O
questionable	O
cause	O
,	O
considering	O
previous	O
observations	O
indicating	O
that	O
the	O
strongly	O
oxidizing	O
hydroxyl	O
radical	O
is	O
immobile	O
at	O
100	O
K	O
(	O
Allan	O
et	O
al	O
.,	O
2013	O
;	O
Owen	O
et	O
al	O
.,	O
2012	O
).	O

By	O
comparing	O
equivalent	O
acidic	O
residues	O
with	B-protein_state
and	O
without	B-protein_state
RNA	B-chemical
,	O
we	O
have	O
now	O
deconvoluted	O
the	O
role	O
of	O
solvent	O
accessibility	O
from	O
other	O
local	O
protein	O
environment	O
factors	O
,	O
and	O
thus	O
propose	O
a	O
suitable	O
mechanism	O
by	O
which	O
exceptionally	O
low	O
solvent	O
accessibility	O
can	O
reduce	O
the	O
rate	O
of	O
decarboxylation	O
.	O

Apart	O
from	O
these	O
RNA	B-site
-	I-site
binding	I-site
interfaces	I-site
,	O
RNA	B-chemical
binding	O
was	O
seen	O
to	O
enhance	O
decarboxylation	O
for	O
residues	O
Glu50	B-residue_name_number
,	O
Glu71	B-residue_name_number
and	O
Glu73	B-residue_name_number
,	O
all	O
of	O
which	O
are	O
involved	O
in	O
crystal	O
contacts	O
between	O
TRAP	B-complex_assembly
rings	B-structure_element
(	O
Fig	O
.	O
4	O
▸	O
c	O
).	O

However	O
,	O
for	O
each	O
of	O
these	O
residues	O
the	O
exact	O
crystal	O
contacts	O
are	O
not	O
preserved	O
between	O
bound	B-protein_state
and	O
nonbound	B-protein_state
TRAP	B-complex_assembly
or	O
even	O
between	O
monomers	O
within	O
one	O
TRAP	B-complex_assembly
ring	B-structure_element
.	O

For	O
example	O
,	O
in	O
bound	B-protein_state
TRAP	B-complex_assembly
,	O
Glu73	B-residue_name_number
hydrogen	O
-	O
bonds	O
to	O
a	O
nearby	O
lysine	B-residue_name
on	O
each	O
of	O
the	O
11	O
subunits	B-structure_element
,	O
whereas	O
in	O
nonbound	B-protein_state
TRAP	B-complex_assembly
no	O
such	O
interaction	O
exists	O
and	O
Glu73	B-residue_name_number
interacts	O
with	O
a	O
variable	O
number	O
of	O
refined	O
waters	B-chemical
in	O
each	O
subunit	B-structure_element
.	O

Radiation	O
-	O
induced	O
side	O
-	O
chain	O
conformational	O
changes	O
have	O
been	O
poorly	O
characterized	O
in	O
previous	O
SRD	B-experimental_method
investigations	I-experimental_method
owing	O
to	O
their	O
strong	O
dependence	O
on	O
packing	O
density	O
and	O
geometric	O
strain	O
.	O

Such	O
structural	O
changes	O
are	O
known	O
to	O
have	O
significant	O
roles	O
within	O
enzymatic	O
pathways	O
,	O
and	O
experimenters	O
must	O
be	O
aware	O
of	O
these	O
possible	O
confounding	O
factors	O
when	O
assigning	O
true	O
functional	O
mechanisms	O
using	O
MX	B-experimental_method
.	O

Our	O
results	O
show	O
that	O
RNA	B-chemical
binding	O
to	O
TRAP	B-complex_assembly
physically	O
stabilizes	O
non	O
-	O
acidic	O
residues	O
within	O
the	O
TRAP	B-complex_assembly
macromolecule	O
,	O
most	O
notably	O
Lys37	B-residue_name_number
and	O
Phe32	B-residue_name_number
,	O
which	O
stack	O
against	O
the	O
G1	B-residue_name_number
and	O
G3	B-residue_name_number
bases	O
,	O
respectively	O
.	O

It	O
has	O
been	O
suggested	O
(	O
Burmeister	O
,	O
2000	O
)	O
that	O
Tyr	B-residue_name
residues	O
can	O
lose	O
their	O
aromatic	O
–	O
OH	O
group	O
owing	O
to	O
radiation	O
-	O
induced	O
effects	O
;	O
however	O
,	O
no	O
energetically	O
favourable	O
pathway	O
for	O
–	O
OH	O
cleavage	O
exists	O
and	O
this	O
has	O
not	O
been	O
detected	O
in	O
aqueous	O
radiation	O
-	O
chemistry	O
studies	O
.	O

In	O
TRAP	B-complex_assembly
,	O
D	B-evidence
loss	I-evidence
increased	O
at	O
a	O
similar	O
rate	O
for	O
both	O
the	O
Tyr	B-residue_name
O	O
atoms	O
and	O
aromatic	O
ring	B-structure_element
atoms	O
,	O
suggesting	O
that	O
full	O
ring	B-structure_element
conformational	O
disordering	O
is	O
more	O
likely	O
.	O

Indeed	O
,	O
no	O
convincing	O
reproducible	O
Fourier	B-evidence
difference	I-evidence
peaks	I-evidence
above	O
the	O
background	O
map	B-evidence
noise	O
were	O
observed	O
around	O
any	O
Tyr	B-residue_name
terminal	O
–	O
OH	O
groups	O
.	O

The	O
RNA	B-chemical
-	O
stabilization	O
effects	O
on	O
protein	O
are	O
observed	O
at	O
short	O
ranges	O
and	O
are	O
restricted	O
to	O
within	O
the	O
RNA	B-site
-	I-site
binding	I-site
interfaces	I-site
around	O
the	O
TRAP	B-complex_assembly
ring	B-structure_element
.	O

For	O
example	O
,	O
Asp17	B-residue_name_number
is	O
located	O
∼	O
6	O
.	O
8	O
Å	O
from	O
the	O
G1	B-residue_name_number
base	O
,	O
outside	O
the	O
RNA	B-site
-	I-site
binding	I-site
interfaces	I-site
,	O
and	O
has	O
indistinguishable	O
Cγ	O
atom	O
D	O
loss	B-evidence
dose	I-evidence
-	I-evidence
dynamics	I-evidence
between	O
RNA	B-protein_state
-	I-protein_state
bound	I-protein_state
and	O
nonbound	B-protein_state
TRAP	B-complex_assembly
(	O
p	O
>	O
0	O
.	O
9	O
).	O

An	O
increase	O
in	O
the	O
dose	O
at	O
which	O
functionally	O
important	O
residues	O
remain	O
intact	O
has	O
biological	O
ramifications	O
for	O
understanding	O
the	O
mechanisms	O
at	O
which	O
ionizing	O
radiation	O
damage	O
is	O
mitigated	O
within	O
naturally	O
forming	O
DNA	B-complex_assembly
–	I-complex_assembly
protein	I-complex_assembly
and	O
RNA	B-complex_assembly
–	I-complex_assembly
protein	I-complex_assembly
complexes	O
.	O

Observations	O
of	O
lower	O
protein	O
radiation	O
-	O
sensitivity	O
in	O
DNA	B-protein_state
-	I-protein_state
bound	I-protein_state
forms	O
have	O
been	O
recorded	O
in	O
solution	O
at	O
RT	O
at	O
much	O
lower	O
doses	O
(∼	O
1	O
kGy	O
)	O
than	O
those	O
used	O
for	O
typical	O
MX	B-experimental_method
experiments	O
[	O
e	O
.	O
g	O
.	O
an	O
oestrogen	O
response	O
element	O
–	O
receptor	O
complex	O
(	O
Stísová	O
et	O
al	O
.,	O
2006	O
)	O
and	O
a	O
DNA	B-protein_type
glycosylase	I-protein_type
and	O
its	O
abasic	B-site
DNA	I-site
target	I-site
site	I-site
(	O
Gillard	O
et	O
al	O
.,	O
2004	O
)].	O

In	O
these	O
studies	O
,	O
the	O
main	O
damaging	O
species	O
is	O
predicted	O
to	O
be	O
the	O
oxidizing	O
hydroxyl	O
radical	O
produced	O
through	O
solvent	O
irradiation	O
,	O
which	O
is	O
known	O
to	O
add	O
to	O
double	O
covalent	O
bonds	O
within	O
both	O
DNA	B-chemical
and	O
RNA	B-chemical
bases	O
to	O
induce	O
strand	O
breaks	O
and	O
base	O
modification	O
(	O
Spotheim	O
-	O
Maurizot	O
&	O
Davídková	O
,	O
2011	O
;	O
Chance	O
et	O
al	O
.,	O
1997	O
).	O

It	O
was	O
suggested	O
that	O
physical	O
screening	O
of	O
DNA	B-chemical
by	O
protein	O
shielded	O
the	O
DNA	B-site
–	I-site
protein	I-site
interaction	I-site
sites	I-site
from	O
radical	O
damage	O
,	O
yielding	O
an	O
extended	O
life	O
-	O
dose	O
for	O
the	O
nucleoprotein	O
complex	O
compared	O
with	O
separate	O
protein	O
and	O
DNA	B-chemical
constituents	O
at	O
RT	O
.	O

However	O
,	O
in	O
the	O
current	O
MX	B-experimental_method
study	O
at	O
100	O
K	O
,	O
the	O
main	O
damaging	O
species	O
are	O
believed	O
to	O
be	O
migrating	O
LEEs	O
and	O
holes	O
produced	O
directly	O
within	O
the	O
protein	B-complex_assembly
–	I-complex_assembly
RNA	I-complex_assembly
components	O
or	O
in	O
closely	O
associated	O
solvent	O
.	O

The	O
results	O
presented	O
here	O
suggest	O
that	O
biologically	O
relevant	O
nucleoprotein	B-complex_assembly
complexes	O
also	O
exhibit	O
prolonged	O
life	O
-	O
doses	O
under	O
the	O
effect	O
of	O
LEE	O
-	O
induced	O
structural	O
changes	O
,	O
involving	O
direct	O
physical	O
protection	O
of	O
key	O
RNA	B-site
-	I-site
binding	I-site
residues	I-site
.	O

Such	O
reduced	O
radiation	O
-	O
sensitivity	O
in	O
this	O
case	O
ensures	O
that	O
the	O
interacting	O
protein	O
remains	O
bound	B-protein_state
long	O
enough	O
to	O
the	O
RNA	B-chemical
to	O
complete	O
its	O
function	O
,	O
even	O
whilst	O
exposed	O
to	O
ionizing	O
radiation	O
.	O

Within	O
the	O
nonbound	B-protein_state
TRAP	B-complex_assembly
macromolecule	O
,	O
the	O
acidic	O
residues	O
within	O
the	O
unoccupied	O
RNA	B-site
-	I-site
binding	I-site
interfaces	I-site
(	O
Asp39	B-residue_name_number
,	O
Glu36	B-residue_name_number
,	O
Glu42	B-residue_name_number
)	O
are	O
notably	O
amongst	O
the	O
most	O
susceptible	O
residues	O
within	O
the	O
asymmetric	O
unit	O
(	O
Fig	O
.	O
4	O
▸).	O

When	O
exposed	O
to	O
X	O
-	O
rays	O
,	O
these	O
residues	O
will	O
be	O
preferentially	O
damaged	O
by	O
X	O
-	O
rays	O
and	O
subsequently	O
reduce	O
the	O
affinity	O
with	O
which	O
TRAP	B-complex_assembly
binds	O
to	O
RNA	B-chemical
.	O

Within	O
the	O
cellular	O
environment	O
,	O
this	O
mechanism	O
could	O
reduce	O
the	O
risk	O
that	O
radiation	O
-	O
damaged	O
proteins	O
might	O
bind	O
to	O
RNA	B-chemical
,	O
thus	O
avoiding	O
the	O
detrimental	O
introduction	O
of	O
incorrect	O
DNA	B-chemical
-	O
repair	O
,	O
transcriptional	O
and	O
base	O
-	O
modification	O
pathways	O
.	O

The	O
TRAP	B-complex_assembly
–(	I-complex_assembly
GAGUU	I-complex_assembly
)	I-complex_assembly
10GAG	I-complex_assembly
complex	O
asymmetric	O
unit	O
(	O
PDB	O
entry	O
1gtf	O
;	O
Hopcroft	O
et	O
al	O
.,	O
2002	O
).	O

Bound	B-protein_state
tryptophan	B-chemical
ligands	O
are	O
represented	O
as	O
coloured	O
spheres	O
.	O

RNA	B-chemical
is	O
shown	O
is	O
yellow	O
.	O

(	O
a	O
)	O
Electron	O
-	O
density	O
loss	O
sites	O
as	O
indicated	O
by	O
D	O
loss	O
in	O
the	O
TRAP	B-complex_assembly
–	I-complex_assembly
RNA	I-complex_assembly
complex	O
crystal	B-evidence
by	O
residue	O
/	O
nucleotide	O
type	O
for	O
five	O
doses	O
[	O
sites	O
determined	O
above	O
the	O
4	O
×	O
average	O
D	O
loss	O
threshold	O
,	O
calculated	O
over	O
the	O
TRAP	B-complex_assembly
–	I-complex_assembly
RNA	I-complex_assembly
structure	B-evidence
for	O
the	O
first	O
difference	B-evidence
map	I-evidence
:	O
F	O
obs	O
(	O
d	O
2	O
)	O
−	O
F	O
obs	O
(	O
d	O
1	O
)].	O

(	O
b	O
)	O
Average	O
D	O
loss	O
for	O
each	O
residue	O
/	O
nucleotide	O
type	O
with	O
respect	O
to	O
the	O
DWD	B-evidence
(	O
diffraction	B-evidence
-	I-evidence
weighted	I-evidence
dose	I-evidence
;	O
Zeldin	O
,	O
Brock	O
­	O
hauser	O
et	O
al	O
.,	O
2013	O
).	O

Only	O
a	O
subset	O
of	O
key	O
TRAP	B-complex_assembly
residue	O
types	O
are	O
included	O
.	O

The	O
average	O
D	O
loss	O
(	O
calculated	O
over	O
the	O
whole	O
TRAP	B-complex_assembly
asymmetric	O
unit	O
)	O
is	O
shown	O
at	O
each	O
dose	O
(	O
dashed	O
line	O
).	O

In	O
(	O
a	O
)	O
clear	O
difference	B-evidence
density	I-evidence
is	O
observed	O
around	O
the	O
Glu42	B-residue_name_number
carboxyl	O
side	O
chain	O
in	O
chain	O
H	O
,	O
within	O
the	O
lowest	B-evidence
dose	I-evidence
difference	I-evidence
map	I-evidence
at	O
d	O
2	O
=	O
3	O
.	O
9	O
MGy	O
.	O

Radiation	O
-	O
induced	O
protein	O
disordering	O
is	O
evident	O
across	O
the	O
large	O
dose	O
range	O
(	O
b	O
,	O
c	O
);	O
in	O
comparison	O
,	O
no	O
clear	O
deterioration	O
of	O
the	O
RNA	B-chemical
density	B-evidence
was	O
observed	O
.	O

D	O
loss	O
calculated	O
for	O
all	O
side	O
-	O
chain	O
carboxyl	O
group	O
Glu	B-residue_name
Cδ	O
and	O
Asp	B-residue_name
Cγ	O
atoms	O
within	O
the	O
TRAP	B-complex_assembly
–	I-complex_assembly
RNA	I-complex_assembly
complex	O
for	O
a	O
dose	O
of	O
19	O
.	O
3	O
MGy	O
(	O
d	O
8	O
).	O

Residues	O
have	O
been	O
grouped	O
by	O
amino	O
-	O
acid	O
number	O
,	O
and	O
split	O
into	O
bound	B-protein_state
and	O
nonbound	B-protein_state
groupings	O
,	O
with	O
each	O
bar	O
representing	O
the	O
mean	O
calculated	O
over	O
11	O
equivalent	O
atoms	O
around	O
a	O
TRAP	B-complex_assembly
ring	B-structure_element
.	O

D	O
loss	O
against	O
dose	O
for	O
(	O
a	O
)	O
Glu36	B-residue_name_number
Cδ	O
,	O
(	O
b	O
)	O
Asp39	B-residue_name_number
Cγ	O
,	O
(	O
c	O
)	O
Glu42	B-residue_name_number
O	O
∊	O
1	O
,	O
(	O
d	O
)	O
Glu42	B-residue_name_number
O	O
∊	O
2	O
,	O
(	O
e	O
)	O
Phe32	B-residue_name_number
Cζ	O
and	O
(	O
f	O
)	O
Lys37	B-residue_name_number
C	O
∊	O
atoms	O
.	O

95	O
%	O
CI	O
are	O
included	O
for	O
each	O
set	O
of	O
11	O
equivalent	O
atoms	O
grouped	O
as	O
bound	B-protein_state
/	O
nonbound	B-protein_state
.	O

RNA	B-site
-	I-site
binding	I-site
interface	I-site
interactions	O
are	O
shown	O
for	O
TRAP	B-complex_assembly
chain	O
N	O
,	O
with	O
the	O
F	O
obs	O
(	O
d	O
7	O
)	O
−	O
F	O
obs	O
(	O
d	O
1	O
)	O
Fourier	O
difference	O
map	O
(	O
dose	O
16	O
.	O
7	O
MGy	O
)	O
overlaid	O
and	O
contoured	O
at	O
a	O
±	O
4σ	O
level	O
.	O

Mechanistic	O
insight	O
into	O
a	O
peptide	B-protein_type
hormone	I-protein_type
signaling	O
complex	O
mediating	O
floral	O
organ	O
abscission	O

Plants	B-taxonomy_domain
constantly	O
renew	O
during	O
their	O
life	O
cycle	O
and	O
thus	O
require	O
to	O
shed	O
senescent	O
and	O
damaged	O
organs	O
.	O

Floral	O
abscission	O
is	O
controlled	O
by	O
the	O
leucine	B-protein_type
-	I-protein_type
rich	I-protein_type
repeat	I-protein_type
receptor	I-protein_type
kinase	I-protein_type
(	O
LRR	B-protein_type
-	I-protein_type
RK	I-protein_type
)	O
HAESA	B-protein
and	O
the	O
peptide	B-protein_type
hormone	I-protein_type
IDA	B-protein
.	O

It	O
is	O
unknown	O
how	O
expression	O
of	O
IDA	B-protein
in	O
the	O
abscission	O
zone	O
leads	O
to	O
HAESA	B-protein
activation	O
.	O

Here	O
we	O
show	O
that	O
IDA	B-protein
is	O
sensed	O
directly	O
by	O
the	O
HAESA	B-protein
ectodomain	B-structure_element
.	O

Crystal	B-evidence
structures	I-evidence
of	O
HAESA	B-protein
in	B-protein_state
complex	I-protein_state
with	I-protein_state
IDA	B-protein
reveal	O
a	O
hormone	B-site
binding	I-site
pocket	I-site
that	O
accommodates	O
an	O
active	B-protein_state
dodecamer	B-structure_element
peptide	B-chemical
.	O

A	O
central	O
hydroxyproline	B-residue_name
residue	O
anchors	O
IDA	B-protein
to	O
the	O
receptor	O
.	O

The	O
HAESA	B-protein
co	B-protein_type
-	I-protein_type
receptor	I-protein_type
SERK1	B-protein
,	O
a	O
positive	O
regulator	O
of	O
the	O
floral	O
abscission	O
pathway	O
,	O
allows	O
for	O
high	O
-	O
affinity	O
sensing	O
of	O
the	O
peptide	B-protein_type
hormone	I-protein_type
by	O
binding	O
to	O
an	O
Arg	B-structure_element
-	I-structure_element
His	I-structure_element
-	I-structure_element
Asn	I-structure_element
motif	I-structure_element
in	O
IDA	B-protein
.	O

This	O
sequence	O
pattern	O
is	O
conserved	B-protein_state
among	O
diverse	O
plant	B-taxonomy_domain
peptides	B-chemical
,	O
suggesting	O
that	O
plant	B-taxonomy_domain
peptide	B-protein_type
hormone	I-protein_type
receptors	I-protein_type
may	O
share	O
a	O
common	O
ligand	O
binding	O
mode	O
and	O
activation	O
mechanism	O
.	O

Plants	B-taxonomy_domain
can	O
shed	O
their	O
leaves	O
,	O
flowers	O
or	O
other	O
organs	O
when	O
they	O
no	O
longer	O
need	O
them	O
.	O
But	O
how	O
does	O
a	O
leaf	O
or	O
a	O
flower	O
know	O
when	O
to	O
let	O
go	O
?	O
A	O
receptor	B-protein_type
protein	I-protein_type
called	O
HAESA	B-protein
is	O
found	O
on	O
the	O
surface	O
of	O
the	O
cells	O
that	O
surround	O
a	O
future	O
break	O
point	O
on	O
the	O
plant	O
.	O
When	O
its	O
time	O
to	O
shed	O
an	O
organ	O
,	O
a	O
hormone	B-chemical
called	O
IDA	B-protein
instructs	O
HAESA	B-protein
to	O
trigger	O
the	O
shedding	O
process	O
.	O

However	O
,	O
the	O
molecular	O
details	O
of	O
how	O
IDA	B-protein
triggers	O
organ	O
shedding	O
are	O
not	O
clear	O
.	O

The	O
shedding	O
of	O
floral	O
organs	O
(	O
or	O
leaves	O
)	O
can	O
be	O
easily	O
studied	O
in	O
a	O
model	O
plant	B-taxonomy_domain
called	O
Arabidopsis	B-taxonomy_domain
.	O

Santiago	O
et	O
al	O
.	O
used	O
protein	B-experimental_method
biochemistry	I-experimental_method
,	O
structural	B-experimental_method
biology	I-experimental_method
and	O
genetics	B-experimental_method
to	O
uncover	O
how	O
the	O
IDA	B-protein
hormone	B-chemical
activates	O
HAESA	B-protein
.	O

The	O
experiments	O
show	O
that	O
IDA	B-protein
binds	B-protein_state
directly	I-protein_state
to	I-protein_state
a	O
canyon	B-protein_state
shaped	I-protein_state
pocket	B-site
in	O
HAESA	B-protein
that	O
extends	O
out	O
from	O
the	O
surface	O
of	O
the	O
cell	O
.	O

IDA	B-protein
binding	O
to	O
HAESA	B-protein
allows	O
another	O
receptor	B-protein_type
protein	I-protein_type
called	O
SERK1	B-protein
to	B-protein_state
bind	I-protein_state
to	I-protein_state
HAESA	B-protein
,	O
which	O
results	O
in	O
the	O
release	O
of	O
signals	O
inside	O
the	O
cell	O
that	O
trigger	O
the	O
shedding	O
of	O
organs	O
.	O

The	O
next	O
step	O
following	O
on	O
from	O
this	O
work	O
is	O
to	O
understand	O
what	O
signals	O
are	O
produced	O
when	O
IDA	B-protein
activates	O
HAESA	B-protein
.	O

Another	O
challenge	O
will	O
be	O
to	O
find	O
out	O
where	O
IDA	B-protein
is	O
produced	O
in	O
the	O
plant	B-taxonomy_domain
and	O
what	O
causes	O
it	O
to	O
accumulate	O
in	O
specific	O
places	O
in	O
preparation	O
for	O
organ	O
shedding	O
.	O

The	O
HAESA	B-protein
ectodomain	B-structure_element
folds	O
into	O
a	O
superhelical	B-structure_element
assembly	I-structure_element
of	O
21	O
leucine	B-structure_element
-	I-structure_element
rich	I-structure_element
repeats	I-structure_element
.	O

(	O
A	O
)	O
SDS	B-experimental_method
PAGE	I-experimental_method
analysis	O
of	O
the	O
purified	O
Arabidopsis	B-species
thaliana	I-species
HAESA	B-protein
ectodomain	B-structure_element
(	O
residues	O
20	B-residue_range
–	I-residue_range
620	I-residue_range
)	O
obtained	O
by	O
secreted	B-experimental_method
expression	I-experimental_method
in	I-experimental_method
insect	I-experimental_method
cells	I-experimental_method
.	O

The	O
calculated	O
molecular	O
mass	O
is	O
65	O
.	O
7	O
kDa	O
,	O
the	O
actual	O
molecular	O
mass	O
obtained	O
by	O
mass	B-experimental_method
spectrometry	I-experimental_method
is	O
74	O
,	O
896	O
Da	O
,	O
accounting	O
for	O
the	O
N	B-chemical
-	I-chemical
glycans	I-chemical
.	O
(	O
B	O
)	O
Ribbon	O
diagrams	O
showing	O
front	O
(	O
left	O
panel	O
)	O
and	O
side	O
views	O
(	O
right	O
panel	O
)	O
of	O
the	O
isolated	O
HAESA	B-protein
LRR	B-structure_element
domain	I-structure_element
.	O

The	O
N	O
-	O
(	O
residues	O
20	B-residue_range
–	I-residue_range
88	I-residue_range
)	O
and	O
C	O
-	O
terminal	O
(	O
residues	O
593	B-residue_range
–	I-residue_range
615	I-residue_range
)	O
capping	B-structure_element
domains	I-structure_element
are	O
shown	O
in	O
yellow	O
,	O
the	O
central	O
21	O
LRR	B-structure_element
motifs	I-structure_element
are	O
in	O
blue	O
and	O
disulphide	B-ptm
bonds	I-ptm
are	O
highlighted	O
in	O
green	O
(	O
in	O
bonds	O
representation	O
).	O
(	O
C	O
)	O
Structure	B-experimental_method
based	I-experimental_method
sequence	I-experimental_method
alignment	I-experimental_method
of	O
the	O
21	O
leucine	B-structure_element
-	I-structure_element
rich	I-structure_element
repeats	I-structure_element
in	O
HAESA	B-protein
with	O
the	O
plant	B-taxonomy_domain
LRR	B-structure_element
consensus	O
sequence	O
shown	O
for	O
comparison	O
.	O

Conserved	B-protein_state
hydrophobic	B-protein_state
residues	B-structure_element
are	O
shaded	O
in	O
gray	O
,	O
N	B-site
-	I-site
glycosylation	I-site
sites	I-site
visible	O
in	O
our	O
structures	B-evidence
are	O
highlighted	O
in	O
blue	O
,	O
cysteine	B-residue_name
residues	O
involved	O
in	O
disulphide	B-ptm
bridge	I-ptm
formation	O
in	O
green	O
.	O
(	O
D	O
)	O
Asn	B-ptm
-	I-ptm
linked	I-ptm
glycans	I-ptm
mask	O
the	O
N	O
-	O
terminal	O
portion	O
of	O
the	O
HAESA	B-protein
ectodomain	B-structure_element
.	O

Oligomannose	B-chemical
core	O
structures	O
(	O
containing	O
two	O
N	B-chemical
-	I-chemical
actylglucosamines	I-chemical
and	O
three	O
terminal	O
mannose	B-chemical
units	O
)	O
as	O
found	O
in	O
Trichoplusia	B-species
ni	I-species
cells	O
and	O
in	O
plants	B-taxonomy_domain
were	O
modeled	O
onto	O
the	O
seven	O
glycosylation	B-site
sites	I-site
observed	O
in	O
our	O
HAESA	B-protein
structures	B-evidence
,	O
to	O
visualize	O
the	O
surface	O
areas	O
potentially	O
not	O
masked	O
by	O
carbohydrate	B-chemical
.	O

The	O
HAESA	B-protein
ectodomain	B-structure_element
is	O
shown	O
in	O
blue	O
(	O
in	O
surface	O
representation	O
),	O
the	O
glycan	B-chemical
structures	O
are	O
shown	O
in	O
yellow	O
.	O

Hydrophobic	O
contacts	O
and	O
a	O
hydrogen	B-site
-	I-site
bond	I-site
network	I-site
mediate	O
the	O
interaction	O
between	O
HAESA	B-protein
and	O
the	O
peptide	B-protein_type
hormone	I-protein_type
IDA	B-protein
.	O

(	O
A	O
)	O
Details	O
of	O
the	O
IDA	B-site
binding	I-site
pocket	I-site
.	O

HAESA	B-protein
is	O
shown	O
in	O
blue	O
(	O
ribbon	O
diagram	O
),	O
the	O
C	O
-	O
terminal	O
Arg	B-structure_element
-	I-structure_element
His	I-structure_element
-	I-structure_element
Asn	I-structure_element
motif	I-structure_element
(	O
left	O
panel	O
),	O
the	O
central	O
Hyp	B-structure_element
anchor	I-structure_element
(	O
center	O
)	O
and	O
the	O
N	O
-	O
terminal	O
Pro	B-structure_element
-	I-structure_element
rich	I-structure_element
motif	I-structure_element
in	O
IDA	B-protein
(	O
right	O
panel	O
)	O
are	O
shown	O
in	O
yellow	O
(	O
in	O
bonds	O
representation	O
).	O

HAESA	B-site
interface	I-site
residues	I-site
are	O
shown	O
as	O
sticks	O
,	O
selected	O
hydrogen	O
bond	O
interactions	O
are	O
denoted	O
as	O
dotted	O
lines	O
(	O
in	O
magenta	O
).	O
(	O
B	O
)	O
View	O
of	O
the	O
complete	O
IDA	B-protein
(	O
in	O
bonds	O
representation	O
,	O
in	O
yellow	O
)	O
binding	B-site
pocket	I-site
in	O
HAESA	B-protein
(	O
surface	O
view	O
,	O
in	O
blue	O
).	O

Orientation	O
as	O
in	O
(	O
A	O
).	O
(	O
C	O
)	O
Structure	B-experimental_method
based	I-experimental_method
sequence	I-experimental_method
alignment	I-experimental_method
of	O
leucine	B-structure_element
-	I-structure_element
rich	I-structure_element
repeats	I-structure_element
in	O
HAESA	B-protein
with	O
the	O
plant	B-taxonomy_domain
LRR	B-structure_element
consensus	B-evidence
sequence	I-evidence
shown	O
for	O
comparison	O
.	O

Residues	O
mediating	O
hydrophobic	O
interactions	O
with	O
the	O
IDA	B-chemical
peptide	I-chemical
are	O
highlighted	O
in	O
blue	O
,	O
residues	O
contributing	O
to	O
hydrogen	O
bond	O
interactions	O
and	O
/	O
or	O
salt	O
bridges	O
are	O
shown	O
in	O
red	O
.	O

The	O
IDA	B-site
binding	I-site
pocket	I-site
covers	O
LRRs	B-structure_element
2	I-structure_element
–	I-structure_element
14	I-structure_element
and	O
all	O
residues	O
originate	O
from	O
the	O
inner	O
surface	O
of	O
the	O
HAESA	B-protein
superhelix	B-structure_element
.	O

The	O
IDA	B-complex_assembly
-	I-complex_assembly
HAESA	I-complex_assembly
and	O
SERK1	B-complex_assembly
-	I-complex_assembly
HAESA	I-complex_assembly
complex	O
interfaces	B-site
are	O
conserved	B-protein_state
among	O
HAESA	B-protein
and	O
HAESA	B-protein_type
-	I-protein_type
like	I-protein_type
proteins	I-protein_type
from	O
different	O
plant	B-taxonomy_domain
species	O
.	O

Structure	B-experimental_method
-	I-experimental_method
based	I-experimental_method
sequence	I-experimental_method
alignment	I-experimental_method
of	O
the	O
HAESA	B-protein_type
family	I-protein_type
members	I-protein_type
:	O
Arabidopsis	B-species
thaliana	I-species
HAESA	B-protein
(	O
Uniprot	O
(	O
http	O
://	O
www	O
.	O
uniprot	O
.	O
org	O
)	O
ID	O
P47735	O
),	O
Arabidopsis	B-species
thaliana	I-species
HSL2	B-protein
(	O
Uniprot	O
ID	O
C0LGX3	O
),	O
Capsella	B-species
rubella	I-species
HAESA	B-protein
(	O
Uniprot	O
ID	O
R0F2U6	O
),	O
Citrus	B-species
clementina	I-species
HSL2	B-protein
(	O
Uniprot	O
ID	O
V4U227	O
),	O
Vitis	B-species
vinifera	I-species
HAESA	B-protein
(	O
Uniprot	O
ID	O
F6HM39	O
).	O

The	O
alignment	O
includes	O
a	O
secondary	O
structure	O
assignment	O
calculated	O
with	O
the	O
program	O
DSSP	O
and	O
colored	O
according	O
to	O
Figure	O
1	O
,	O
with	O
the	O
N	O
-	O
and	O
C	O
-	O
terminal	O
caps	B-structure_element
and	O
the	O
21	O
LRR	B-structure_element
motifs	I-structure_element
indicated	O
in	O
orange	O
and	O
blue	O
,	O
respectively	O
.	O

Cysteine	B-residue_name
residues	O
engaged	O
in	O
disulphide	B-ptm
bonds	I-ptm
are	O
depicted	O
in	O
green	O
.	O

HAESA	B-protein
residues	O
interacting	O
with	O
the	O
IDA	B-chemical
peptide	I-chemical
and	O
/	O
or	O
the	O
SERK1	B-protein
co	B-protein_type
-	I-protein_type
receptor	I-protein_type
kinase	I-protein_type
ectodomain	B-structure_element
are	O
highlighted	O
in	O
blue	O
and	O
orange	O
,	O
respectively	O
.	O

The	O
peptide	B-protein_type
hormone	I-protein_type
IDA	B-protein
binds	O
to	O
the	O
HAESA	B-protein
LRR	B-structure_element
ectodomain	I-structure_element
.	O

(	O
A	O
)	O
Multiple	B-experimental_method
sequence	I-experimental_method
alignment	I-experimental_method
of	O
selected	O
IDA	B-protein_type
family	I-protein_type
members	I-protein_type
.	O

The	O
conserved	B-protein_state
PIP	B-structure_element
motif	I-structure_element
is	O
highlighted	O
in	O
yellow	O
,	O
the	O
central	O
Hyp	B-residue_name
in	O
blue	O
.	O

The	O
PKGV	B-structure_element
motif	I-structure_element
present	O
in	O
our	O
N	B-protein_state
-	I-protein_state
terminally	I-protein_state
extended	I-protein_state
IDA	B-chemical
peptide	I-chemical
is	O
highlighted	O
in	O
red	O
.	O
(	O
B	O
)	O
Isothermal	B-experimental_method
titration	I-experimental_method
calorimetry	I-experimental_method
of	O
the	O
HAESA	B-protein
ectodomain	B-structure_element
vs	O
.	O
IDA	B-protein
and	O
including	O
the	O
synthetic	B-protein_state
peptide	B-chemical
sequence	O
.	O

(	O
C	O
)	O
Structure	O
of	O
the	O
HAESA	B-complex_assembly
–	I-complex_assembly
IDA	I-complex_assembly
complex	O
with	O
HAESA	B-protein
shown	O
in	O
blue	O
(	O
ribbon	O
diagram	O
).	O

IDA	B-protein
(	O
in	O
bonds	O
representation	O
,	O
surface	O
view	O
included	O
)	O
is	O
depicted	O
in	O
yellow	O
.	O

The	O
peptide	B-site
binding	I-site
pocket	I-site
covers	O
HAESA	B-protein
LRRs	B-structure_element
2	I-structure_element
–	I-structure_element
14	I-structure_element
.	O
(	O
D	O
)	O
Close	O
-	O
up	O
view	O
of	O
the	O
entire	O
IDA	B-protein
(	O
in	O
yellow	O
)	O
peptide	B-site
binding	I-site
site	I-site
in	O
HAESA	B-protein
(	O
in	O
blue	O
).	O

Details	O
of	O
the	O
interactions	O
between	O
the	O
central	O
Hyp	B-structure_element
anchor	I-structure_element
in	O
IDA	B-protein
and	O
the	O
C	O
-	O
terminal	O
Arg	B-structure_element
-	I-structure_element
His	I-structure_element
-	I-structure_element
Asn	I-structure_element
motif	I-structure_element
with	O
HAESA	B-protein
are	O
highlighted	O
in	O
(	O
E	O
)	O
and	O
(	O
F	O
),	O
respectively	O
.	O

Hydrogren	O
bonds	O
are	O
depicted	O
as	O
dotted	O
lines	O
(	O
in	O
magenta	O
),	O
a	O
water	B-chemical
molecule	O
is	O
shown	O
as	O
a	O
red	O
sphere	O
.	O

During	O
their	O
growth	O
,	O
development	O
and	O
reproduction	O
plants	B-taxonomy_domain
use	O
cell	O
separation	O
processes	O
to	O
detach	O
no	O
-	O
longer	O
required	O
,	O
damaged	O
or	O
senescent	O
organs	O
.	O

Abscission	O
of	O
floral	O
organs	O
in	O
Arabidopsis	B-taxonomy_domain
is	O
a	O
model	O
system	O
to	O
study	O
these	O
cell	O
separation	O
processes	O
in	O
molecular	O
detail	O
.	O

The	O
LRR	B-structure_element
-	I-structure_element
RKs	I-structure_element
HAESA	B-protein
(	O
greek	O
:	O
to	O
adhere	O
to	O
)	O
and	O
HAESA	B-protein
-	I-protein
LIKE	I-protein
2	I-protein
(	O
HSL2	B-protein
)	O
redundantly	O
control	O
floral	O
abscission	O
.	O

Loss	O
-	O
of	O
-	O
function	O
of	O
the	O
secreted	O
small	O
protein	O
INFLORESCENCE	B-protein
DEFICIENT	I-protein
IN	I-protein
ABSCISSION	I-protein
(	O
IDA	B-protein
)	O
causes	O
floral	O
organs	O
to	O
remain	O
attached	O
while	O
its	O
over	O
-	O
expression	O
leads	O
to	O
premature	O
shedding	O
.	O

Full	B-protein_state
-	I-protein_state
length	I-protein_state
IDA	B-protein
is	O
proteolytically	B-ptm
processed	I-ptm
and	O
a	O
conserved	B-protein_state
stretch	B-residue_range
of	I-residue_range
20	I-residue_range
amino	I-residue_range
-	I-residue_range
acids	I-residue_range
(	O
termed	O
EPIP	B-structure_element
)	O
can	O
rescue	O
the	O
IDA	B-protein
loss	O
-	O
of	O
-	O
function	O
phenotype	O
(	O
Figure	O
1A	O
).	O

It	O
has	O
been	O
demonstrated	O
that	O
a	O
dodecamer	B-structure_element
peptide	B-chemical
within	O
EPIP	B-structure_element
is	O
able	O
to	O
activate	O
HAESA	B-protein
and	O
HSL2	B-protein
in	O
transient	B-experimental_method
assays	I-experimental_method
in	O
tobacco	B-taxonomy_domain
cells	O
.	O

This	B-structure_element
sequence	I-structure_element
motif	I-structure_element
is	O
highly	B-protein_state
conserved	I-protein_state
among	O
IDA	B-protein_type
family	I-protein_type
members	I-protein_type
(	O
IDA	B-protein_type
-	I-protein_type
LIKE	I-protein_type
PROTEINS	I-protein_type
,	O
IDLs	B-protein_type
)	O
and	O
contains	O
a	O
central	O
Pro	B-residue_name
residue	O
,	O
presumed	O
to	O
be	O
post	B-protein_state
-	I-protein_state
translationally	I-protein_state
modified	I-protein_state
to	O
hydroxyproline	B-residue_name
(	O
Hyp	B-residue_name
;	O
Figure	O
1A	O
).	O

The	O
available	O
genetic	O
and	O
biochemical	O
evidence	O
suggests	O
that	O
IDA	B-protein
and	O
HAESA	B-protein
together	O
control	O
floral	O
abscission	O
,	O
but	O
it	O
is	O
poorly	O
understood	O
if	O
IDA	B-protein
is	O
directly	O
sensed	O
by	O
the	O
receptor	B-protein_type
kinase	I-protein_type
HAESA	B-protein
and	O
how	O
IDA	B-protein
binding	O
at	O
the	O
cell	O
surface	O
would	O
activate	O
the	O
receptor	O
.	O

IDA	B-protein
directly	O
binds	O
to	O
the	O
LRR	B-structure_element
domain	I-structure_element
of	O
HAESA	B-protein

Active	B-protein_state
IDA	B-protein_type
-	I-protein_type
family	I-protein_type
peptide	I-protein_type
hormones	I-protein_type
are	O
hydroxyprolinated	B-protein_state
dodecamers	B-structure_element
.	O

Close	O
-	O
up	O
views	O
of	O
(	O
A	O
)	O
IDA	B-protein
,	O
(	O
B	O
)	O
the	O
N	B-protein_state
-	I-protein_state
terminally	I-protein_state
extended	I-protein_state
PKGV	B-mutant
-	I-mutant
IDA	I-mutant
and	O
(	O
C	O
)	O
IDL1	B-protein
bound	B-protein_state
to	I-protein_state
the	O
HAESA	B-protein
hormone	B-site
binding	I-site
pocket	I-site
(	O
in	O
bonds	O
representation	O
,	O
in	O
yellow	O
)	O
and	O
including	O
simulated	B-experimental_method
annealing	I-experimental_method
2Fo	B-evidence
–	I-evidence
Fc	I-evidence
omit	I-evidence
electron	I-evidence
density	I-evidence
maps	I-evidence
contoured	O
at	O
1	O
.	O
0	O
σ	O
.	O

Note	O
that	O
Pro58IDA	B-residue_name_number
and	O
Leu67IDA	B-residue_name_number
are	O
the	O
first	O
residues	O
defined	O
by	O
electron	B-evidence
density	I-evidence
when	O
bound	B-protein_state
to	I-protein_state
the	O
HAESA	B-protein
ectodomain	B-structure_element
.	O
(	O
D	O
)	O
Table	O
summaries	O
for	O
equilibrium	B-evidence
dissociation	I-evidence
constants	I-evidence
(	O
Kd	B-evidence
),	O
binding	B-evidence
enthalpies	I-evidence
(	O
ΔH	B-evidence
),	O
binding	B-evidence
entropies	I-evidence
(	O
ΔS	B-evidence
)	O
and	O
stoichoimetries	O
(	O
N	O
)	O
for	O
different	O
IDA	B-chemical
peptides	I-chemical
binding	O
to	O
the	O
HAESA	B-protein
ectodomain	B-structure_element
(	O
±	O
fitting	O
errors	O
;	O
n	O
.	O
d	O
.	O

no	O
detectable	O
binding	O
).	O
(	O
E	O
)	O
Structural	B-experimental_method
superposition	I-experimental_method
of	O
the	O
active	B-protein_state
IDA	B-protein
(	O
in	O
bonds	O
representation	O
,	O
in	O
gray	O
)	O
and	O
IDL1	B-chemical
peptide	I-chemical
(	O
in	O
yellow	O
)	O
hormones	O
bound	B-protein_state
to	I-protein_state
the	O
HAESA	B-protein
ectodomain	B-structure_element
.	O

Root	B-evidence
mean	I-evidence
square	I-evidence
deviation	I-evidence
(	O
r	B-evidence
.	I-evidence
m	I-evidence
.	I-evidence
s	I-evidence
.	I-evidence
d	I-evidence
.)	I-evidence
is	O
1	O
.	O
0	O
Å	O
comparing	O
100	O
corresponding	O
atoms	O
.	O

The	O
receptor	B-protein_type
kinase	I-protein_type
SERK1	B-protein
acts	O
as	O
a	O
HAESA	B-protein_type
co	I-protein_type
-	I-protein_type
receptor	I-protein_type
and	O
promotes	O
high	O
-	O
affinity	O
IDA	B-protein
sensing	O
.	O

(	O
A	O
)	O
Petal	B-experimental_method
break	I-experimental_method
-	I-experimental_method
strength	I-experimental_method
assays	I-experimental_method
measure	O
the	O
force	O
(	O
expressed	O
in	O
gram	O
equivalents	O
)	O
required	O
to	O
remove	O
the	O
petals	O
from	O
the	O
flower	O
of	O
serk	B-gene
mutant	B-protein_state
plants	B-taxonomy_domain
compared	O
to	O
haesa	B-gene
/	O
hsl2	B-gene
mutant	B-protein_state
and	O
Col	O
-	O
0	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
flowers	O
.	O

Petal	O
break	O
-	O
strength	O
was	O
found	O
significantly	O
increased	O
in	O
almost	O
all	O
positions	O
(	O
indicated	O
with	O
a	O
*)	O
for	O
haesa	B-gene
/	O
hsl2	B-gene
and	O
serk1	B-gene
-	I-gene
1	I-gene
mutant	B-protein_state
plants	B-taxonomy_domain
with	O
respect	O
to	O
the	O
Col	O
-	O
0	O
control	O
.	O

(	O
B	O
)	O
Analytical	B-experimental_method
size	I-experimental_method
-	I-experimental_method
exclusion	I-experimental_method
chromatography	I-experimental_method
.	O

The	O
HAESA	B-protein
LRR	B-structure_element
domain	I-structure_element
elutes	O
as	O
a	O
monomer	B-oligomeric_state
(	O
black	O
dotted	O
line	O
),	O
as	O
does	O
the	O
isolated	O
SERK1	B-protein
ectodomain	B-structure_element
(	O
blue	O
dotted	O
line	O
).	O

A	O
HAESA	B-complex_assembly
–	I-complex_assembly
IDA	I-complex_assembly
–	I-complex_assembly
SERK1	I-complex_assembly
complex	O
elutes	O
as	O
an	O
apparent	O
heterodimer	B-oligomeric_state
(	O
red	O
line	O
),	O
while	O
a	O
mixture	O
of	O
HAESA	B-protein
and	O
SERK1	B-protein
yields	O
two	O
isolated	O
peaks	O
that	O
correspond	O
to	O
monomeric	B-oligomeric_state
HAESA	B-protein
and	O
SERK1	B-protein
,	O
respectively	O
(	O
black	O
line	O
).	O

Void	O
(	O
V0	O
)	O
volume	O
and	O
total	O
volume	O
(	O
Vt	O
)	O
are	O
shown	O
,	O
together	O
with	O
elution	O
volumes	O
for	O
molecular	O
mass	O
standards	O
(	O
A	O
,	O
Thyroglobulin	B-protein
,	O
669	O
,	O
000	O
Da	O
;	O
B	O
,	O
Ferritin	B-protein
,	O
440	O
,	O
00	O
Da	O
,	O
C	O
,	O
Aldolase	B-protein
,	O
158	O
,	O
000	O
Da	O
;	O
D	O
,	O
Conalbumin	B-protein
,	O
75	O
,	O
000	O
Da	O
;	O
E	O
,	O
Ovalbumin	B-protein
,	O
44	O
,	O
000	O
Da	O
;	O
F	O
,	O
Carbonic	B-protein
anhydrase	I-protein
,	O
29	O
,	O
000	O
Da	O
).	O

A	O
SDS	B-experimental_method
PAGE	I-experimental_method
of	O
the	O
peak	O
fractions	O
is	O
shown	O
alongside	O
.	O

Purified	O
HAESA	B-protein
and	O
SERK1	B-protein
are	O
~	O
75	O
and	O
~	O
28	O
kDa	O
,	O
respectively	O
.	O
(	O
C	O
)	O
Isothermal	B-experimental_method
titration	I-experimental_method
calorimetry	I-experimental_method
of	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
and	O
Hyp64	B-mutant
→	I-mutant
Pro	I-mutant
IDA	I-mutant
versus	O
the	O
HAESA	B-protein
and	O
SERK1	B-protein
ectodomains	B-structure_element
.	O

The	O
titration	B-experimental_method
of	O
IDA	B-protein
wild	B-protein_state
-	I-protein_state
type	I-protein_state
versus	O
the	O
isolated	O
HAESA	B-protein
ectodomain	B-structure_element
from	O
Figure	O
1B	O
is	O
shown	O
for	O
comparison	O
(	O
red	O
line	O
;	O
n	O
.	O
d	O
.	O

no	O
detectable	O
binding	O
)	O
(	O
D	O
)	O
Analytical	B-experimental_method
size	I-experimental_method
-	I-experimental_method
exclusion	I-experimental_method
chromatography	I-experimental_method
in	O
the	O
presence	B-protein_state
of	I-protein_state
the	O
IDA	B-mutant
Hyp64	I-mutant
→	I-mutant
Pro	I-mutant
mutant	B-protein_state
peptide	B-chemical
reveals	O
no	O
complex	O
formation	O
between	O
HAESA	B-protein
and	O
SERK1	B-protein
ectodomains	B-structure_element
.	O

(	O
E	O
)	O
In	B-experimental_method
vitro	I-experimental_method
kinase	I-experimental_method
assays	I-experimental_method
of	O
the	O
HAESA	B-protein
and	O
SERK1	B-protein
kinase	B-structure_element
domains	I-structure_element
.	O

Wild	B-protein_state
-	I-protein_state
type	I-protein_state
HAESA	B-protein
and	O
SERK1	B-protein
kinase	B-structure_element
domains	I-structure_element
(	O
KDs	B-structure_element
)	O
exhibit	O
auto	O
-	O
phosphorylation	O
activities	O
(	O
lanes	O
1	O
+	O
3	O
).	O

Mutant	B-protein_state
(	O
m	O
)	O
versions	O
,	O
which	O
carry	O
point	B-experimental_method
mutations	I-experimental_method
in	O
their	O
active	B-site
sites	I-site
(	O
Asp837HAESA	B-mutant
→	I-mutant
Asn	I-mutant
,	O
Asp447SERK1	B-mutant
→	I-mutant
Asn	I-mutant
)	O
possess	O
no	O
autophosphorylation	O
activity	O
(	O
lanes	O
2	O
+	O
4	O
).	O

Transphosphorylation	O
activity	O
from	O
the	O
active	B-protein_state
kinase	O
to	O
the	O
mutated	B-protein_state
form	O
can	O
be	O
observed	O
in	O
both	O
directions	O
(	O
lanes	O
5	O
+	O
6	O
).	O

We	O
purified	B-experimental_method
the	O
HAESA	B-protein
ectodomain	B-structure_element
(	O
residues	O
20	B-residue_range
–	I-residue_range
620	I-residue_range
)	O
from	O
baculovirus	B-experimental_method
-	I-experimental_method
infected	I-experimental_method
insect	I-experimental_method
cells	I-experimental_method
(	O
Figure	O
1	O
—	O
figure	O
supplement	O
1A	O
,	O
see	O
Materials	O
and	O
methods	O
)	O
and	O
quantified	O
the	O
interaction	O
of	O
the	O
~	O
75	O
kDa	O
glycoprotein	B-protein_type
with	O
synthetic	B-protein_state
IDA	B-chemical
peptides	I-chemical
using	O
isothermal	B-experimental_method
titration	I-experimental_method
calorimetry	I-experimental_method
(	O
ITC	B-experimental_method
).	O

A	O
Hyp	B-protein_state
-	I-protein_state
modified	I-protein_state
dodecamer	B-structure_element
comprising	O
the	O
highly	B-protein_state
conserved	I-protein_state
PIP	B-structure_element
motif	I-structure_element
in	O
IDA	B-protein
(	O
Figure	O
1A	O
)	O
interacts	O
with	O
HAESA	B-protein
with	O
1	O
:	O
1	O
stoichiometry	O
(	O
N	O
)	O
and	O
with	O
a	O
dissociation	B-evidence
constant	I-evidence
(	O
Kd	B-evidence
)	O
of	O
~	O
20	O
μM	O
(	O
Figure	O
1B	O
).	O

We	O
next	O
determined	O
crystal	B-evidence
structures	I-evidence
of	O
the	O
apo	B-protein_state
HAESA	B-protein
ectodomain	B-structure_element
and	O
of	O
a	O
HAESA	B-complex_assembly
-	I-complex_assembly
IDA	I-complex_assembly
complex	O
,	O
at	O
1	O
.	O
74	O
and	O
1	O
.	O
86	O
Å	O
resolution	O
,	O
respectively	O
(	O
Figure	O
1C	O
;	O
Figure	O
1	O
—	O
figure	O
supplement	O
1B	O
–	O
D	O
;	O
Tables	O
1	O
,	O
2	O
).	O

IDA	B-protein
binds	O
in	O
a	O
completely	B-protein_state
extended	I-protein_state
conformation	I-protein_state
along	O
the	O
inner	O
surface	O
of	O
the	O
HAESA	B-protein
ectodomain	B-structure_element
,	O
covering	O
LRRs	B-structure_element
2	I-structure_element
–	I-structure_element
14	I-structure_element
(	O
Figure	O
1C	O
,	O
D	O
,	O
Figure	O
1	O
—	O
figure	O
supplement	O
2	O
).	O

The	O
central	O
Hyp64IDA	B-residue_name_number
is	O
buried	O
in	O
a	O
specific	O
pocket	B-site
formed	O
by	O
HAESA	B-protein
LRRs	B-structure_element
8	I-structure_element
–	I-structure_element
10	I-structure_element
,	O
with	O
its	O
hydroxyl	O
group	O
establishing	O
hydrogen	O
bonds	O
with	O
the	O
strictly	B-protein_state
conserved	I-protein_state
Glu266HAESA	B-residue_name_number
and	O
with	O
a	O
water	B-chemical
molecule	O
,	O
which	O
in	O
turn	O
is	O
coordinated	O
by	O
the	O
main	O
chain	O
oxygens	O
of	O
Phe289HAESA	B-residue_name_number
and	O
Ser311HAESA	B-residue_name_number
(	O
Figure	O
1E	O
;	O
Figure	O
1	O
—	O
figure	O
supplement	O
3	O
).	O

The	O
restricted	O
size	O
of	O
the	O
Hyp	B-site
pocket	I-site
suggests	O
that	O
IDA	B-protein
does	O
not	O
require	O
arabinosylation	B-ptm
of	O
Hyp64IDA	B-residue_name_number
for	O
activity	O
in	O
vivo	O
,	O
a	O
modification	O
that	O
has	O
been	O
reported	O
for	O
Hyp	B-residue_name
residues	O
in	O
plant	B-taxonomy_domain
CLE	B-protein_type
peptide	I-protein_type
hormones	I-protein_type
.	O

The	O
C	O
-	O
terminal	O
Arg	B-structure_element
-	I-structure_element
His	I-structure_element
-	I-structure_element
Asn	I-structure_element
motif	I-structure_element
in	O
IDA	B-protein
maps	O
to	O
a	O
cavity	B-site
formed	O
by	O
HAESA	B-protein
LRRs	B-structure_element
11	I-structure_element
–	I-structure_element
14	I-structure_element
(	O
Figure	O
1D	O
,	O
F	O
).	O

The	O
COO	O
-	O
group	O
of	O
Asn69IDA	B-residue_name_number
is	O
in	O
direct	O
contact	O
with	O
Arg407HAESA	B-residue_name_number
and	O
Arg409HAESA	B-residue_name_number
and	O
HAESA	B-protein
cannot	O
bind	O
a	O
C	B-protein_state
-	I-protein_state
terminally	I-protein_state
extended	I-protein_state
IDA	B-mutant
-	I-mutant
SFVN	I-mutant
peptide	O
(	O
Figures	O
1D	O
,	O
F	O
,	O
2D	O
).	O

This	O
suggests	O
that	O
the	O
conserved	B-protein_state
Asn69IDA	B-residue_name_number
may	O
constitute	O
the	O
very	O
C	O
-	O
terminus	O
of	O
the	O
mature	B-protein_state
IDA	B-chemical
peptide	I-chemical
in	O
planta	B-taxonomy_domain
and	O
that	O
active	B-protein_state
IDA	B-protein
is	O
generated	O
by	O
proteolytic	O
processing	O
from	O
a	O
longer	O
pre	O
-	O
protein	O
.	O

Mutation	B-experimental_method
of	O
Arg417HSL2	B-residue_name_number
(	O
which	O
corresponds	O
to	O
Arg409HAESA	B-residue_name_number
)	O
causes	O
a	O
loss	O
-	O
of	O
-	O
function	O
phenotype	O
in	O
HSL2	B-protein
,	O
which	O
indicates	O
that	O
the	O
peptide	B-site
binding	I-site
pockets	I-site
in	O
different	O
HAESA	B-protein_type
receptors	I-protein_type
have	O
common	O
structural	O
and	O
sequence	O
features	O
.	O

Indeed	O
,	O
we	O
find	O
many	O
of	O
the	O
residues	O
contributing	O
to	O
the	O
formation	O
of	O
the	O
IDA	B-site
binding	I-site
surface	I-site
in	O
HAESA	B-protein
to	O
be	O
conserved	B-protein_state
in	O
HSL2	B-protein
and	O
in	O
other	O
HAESA	B-protein_type
-	I-protein_type
type	I-protein_type
receptors	I-protein_type
in	O
different	O
plant	B-taxonomy_domain
species	O
(	O
Figure	O
1	O
—	O
figure	O
supplement	O
3	O
).	O

A	O
N	O
-	O
terminal	O
Pro	B-structure_element
-	I-structure_element
rich	I-structure_element
motif	I-structure_element
in	O
IDA	B-protein
makes	O
contacts	O
with	O
LRRs	B-structure_element
2	I-structure_element
–	I-structure_element
6	I-structure_element
of	O
the	O
receptor	O
(	O
Figure	O
1D	O
,	O
Figure	O
1	O
—	O
figure	O
supplement	O
2A	O
–	O
C	O
).	O

Other	O
hydrophobic	O
and	O
polar	O
interactions	O
are	O
mediated	O
by	O
Ser62IDA	B-residue_name_number
,	O
Ser65IDA	B-residue_name_number
and	O
by	O
backbone	O
atoms	O
along	O
the	O
IDA	B-chemical
peptide	I-chemical
(	O
Figure	O
1D	O
,	O
Figure	O
1	O
—	O
figure	O
supplement	O
2A	O
–	O
C	O
).	O

HAESA	B-protein
specifically	O
senses	O
IDA	B-protein_type
-	I-protein_type
family	I-protein_type
dodecamer	B-structure_element
peptides	B-chemical

We	O
next	O
investigated	O
whether	O
HAESA	B-protein
binds	O
N	B-protein_state
-	I-protein_state
terminally	I-protein_state
extended	I-protein_state
versions	O
of	O
IDA	B-protein
.	O

We	O
obtained	O
a	O
structure	B-evidence
of	O
HAESA	B-protein
in	B-protein_state
complex	I-protein_state
with	I-protein_state
a	O
PKGV	B-mutant
-	I-mutant
IDA	I-mutant
peptide	B-chemical
at	O
1	O
.	O
94	O
Å	O
resolution	O
(	O
Table	O
2	O
).	O

In	O
this	O
structure	B-evidence
,	O
no	O
additional	O
electron	B-evidence
density	I-evidence
accounts	O
for	O
the	O
PKGV	B-structure_element
motif	I-structure_element
at	O
the	O
IDA	B-protein
N	O
-	O
terminus	O
(	O
Figure	O
2A	O
,	O
B	O
).	O

Consistently	O
,	O
PKGV	B-mutant
-	I-mutant
IDA	I-mutant
and	O
IDA	B-protein
have	O
similar	O
binding	B-evidence
affinities	I-evidence
in	O
our	O
ITC	B-experimental_method
assays	I-experimental_method
,	O
further	O
indicating	O
that	O
HAESA	B-protein
senses	O
a	O
dodecamer	B-structure_element
peptide	B-chemical
comprising	O
residues	O
58	B-residue_range
-	I-residue_range
69IDA	I-residue_range
(	O
Figure	O
2D	O
).	O

We	O
next	O
tested	O
if	O
HAESA	B-protein
binds	O
other	O
IDA	B-chemical
peptide	I-chemical
family	I-chemical
members	I-chemical
.	O

IDL1	B-protein
,	O
which	O
can	O
rescue	O
IDA	B-protein
loss	O
-	O
of	O
-	O
function	O
mutants	O
when	O
introduced	O
in	O
abscission	O
zone	O
cells	O
,	O
can	O
also	O
be	O
sensed	O
by	O
HAESA	B-protein
,	O
albeit	O
with	O
lower	O
affinity	B-evidence
(	O
Figure	O
2D	O
).	O

A	O
2	O
.	O
56	O
Å	O
co	B-evidence
-	I-evidence
crystal	I-evidence
structure	I-evidence
with	O
IDL1	B-protein
reveals	O
that	O
different	O
IDA	B-protein_type
family	I-protein_type
members	I-protein_type
use	O
a	O
common	O
binding	O
mode	O
to	O
interact	O
with	O
HAESA	B-protein_type
-	I-protein_type
type	I-protein_type
receptors	I-protein_type
(	O
Figure	O
2A	O
–	O
C	O
,	O
E	O
,	O
Table	O
2	O
).	O

We	O
do	O
not	O
detect	O
interaction	O
between	O
HAESA	B-protein
and	O
a	O
synthetic	B-protein_state
peptide	B-chemical
missing	B-protein_state
the	I-protein_state
C	I-protein_state
-	I-protein_state
terminal	I-protein_state
Asn69IDA	B-residue_name_number
(	O
ΔN69	B-mutant
),	O
highlighting	O
the	O
importance	O
of	O
the	O
polar	O
interactions	O
between	O
the	O
IDA	B-protein
carboxy	O
-	O
terminus	O
and	O
Arg407HAESA	B-residue_name_number
/	O
Arg409HAESA	B-residue_name_number
(	O
Figures	O
1F	O
,	O
2D	O
).	O

Replacing	B-experimental_method
Hyp64IDA	B-residue_name_number
,	O
which	O
is	O
common	O
to	O
all	O
IDLs	B-protein_type
,	O
with	O
proline	B-residue_name
impairs	O
the	O
interaction	O
with	O
the	O
receptor	O
,	O
as	O
does	O
the	O
Lys66IDA	B-mutant
/	I-mutant
Arg67IDA	I-mutant
→	I-mutant
Ala	I-mutant
double	B-protein_state
-	I-protein_state
mutant	I-protein_state
discussed	O
below	O
(	O
Figure	O
1A	O
,	O
2D	O
).	O

Notably	O
,	O
HAESA	B-protein
can	O
discriminate	O
between	O
IDLs	B-protein_type
and	O
functionally	B-protein_state
unrelated	I-protein_state
dodecamer	B-structure_element
peptides	B-chemical
with	O
Hyp	B-ptm
modifications	I-ptm
,	O
such	O
as	O
CLV3	B-protein
(	O
Figures	O
2D	O
,	O
7	O
).	O

The	O
co	B-protein_type
-	I-protein_type
receptor	I-protein_type
kinase	I-protein_type
SERK1	B-protein
allows	O
for	O
high	O
-	O
affinity	O
IDA	O
sensing	O

Our	O
binding	B-experimental_method
assays	I-experimental_method
reveal	O
that	O
IDA	B-chemical
family	I-chemical
peptides	I-chemical
are	O
sensed	O
by	O
the	O
isolated	B-protein_state
HAESA	B-protein
ectodomain	B-structure_element
with	O
relatively	O
weak	O
binding	B-evidence
affinities	I-evidence
(	O
Figures	O
1B	O
,	O
2A	O
–	O
D	O
).	O

It	O
has	O
been	O
recently	O
reported	O
that	O
SOMATIC	B-protein_type
EMBRYOGENESIS	I-protein_type
RECEPTOR	I-protein_type
KINASES	I-protein_type
(	O
SERKs	B-protein_type
)	O
are	O
positive	O
regulators	O
of	O
floral	O
abscission	O
and	O
can	O
interact	O
with	O
HAESA	B-protein
and	O
HSL2	B-protein
in	O
an	O
IDA	O
-	O
dependent	O
manner	O
.	O

As	O
all	O
five	O
SERK	B-protein_type
family	I-protein_type
members	I-protein_type
appear	O
to	O
be	O
expressed	O
in	O
the	O
Arabidopsis	B-taxonomy_domain
abscission	O
zone	O
,	O
we	O
quantified	O
their	O
relative	O
contribution	O
to	O
floral	O
abscission	O
in	O
Arabidopsis	B-taxonomy_domain
using	O
a	O
petal	B-experimental_method
break	I-experimental_method
-	I-experimental_method
strength	I-experimental_method
assay	I-experimental_method
.	O

Our	O
experiments	O
suggest	O
that	O
among	O
the	O
SERK	B-protein_type
family	I-protein_type
members	I-protein_type
,	O
SERK1	B-protein
is	O
a	O
positive	O
regulator	O
of	O
floral	O
abscission	O
.	O

We	O
found	O
that	O
the	O
force	O
required	O
to	O
remove	O
the	O
petals	O
of	O
serk1	B-gene
-	I-gene
1	I-gene
mutants	B-protein_state
is	O
significantly	O
higher	O
than	O
that	O
needed	O
for	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
plants	B-taxonomy_domain
,	O
as	O
previously	O
observed	O
for	O
haesa	B-gene
/	O
hsl2	B-gene
mutants	B-protein_state
,	O
and	O
that	O
floral	O
abscission	O
is	O
delayed	O
in	O
serk1	B-gene
-	I-gene
1	I-gene
(	O
Figure	O
3A	O
).	O

The	O
serk2	B-gene
-	I-gene
2	I-gene
,	O
serk3	B-gene
-	I-gene
1	I-gene
,	O
serk4	B-gene
-	I-gene
1	I-gene
and	O
serk5	B-gene
-	I-gene
1	I-gene
mutant	B-protein_state
lines	O
showed	O
a	O
petal	O
break	O
-	O
strength	O
profile	O
not	O
significantly	O
different	O
from	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
plants	B-taxonomy_domain
.	O

Possibly	O
because	O
SERKs	B-protein_type
have	O
additional	O
roles	O
in	O
plant	O
development	O
such	O
as	O
in	O
pollen	O
formation	O
and	O
brassinosteroid	O
signaling	O
,	O
we	O
found	O
that	O
higher	O
-	O
order	O
SERK	O
mutants	O
exhibit	O
pleiotropic	O
phenotypes	O
in	O
the	O
flower	O
,	O
rendering	O
their	O
analysis	O
and	O
comparison	O
by	O
quantitative	B-experimental_method
petal	I-experimental_method
break	I-experimental_method
-	I-experimental_method
strength	I-experimental_method
assays	I-experimental_method
difficult	O
.	O

We	O
thus	O
focused	O
on	O
analyzing	O
the	O
contribution	O
of	O
SERK1	B-protein
to	O
HAESA	B-protein
ligand	O
sensing	O
and	O
receptor	O
activation	O
.	O

In	O
vitro	O
,	O
the	O
LRR	B-structure_element
ectodomain	I-structure_element
of	O
SERK1	B-protein
(	O
residues	O
24	B-residue_range
–	I-residue_range
213	I-residue_range
)	O
forms	O
stable	B-protein_state
,	O
IDA	B-protein_state
-	I-protein_state
dependent	I-protein_state
heterodimeric	B-oligomeric_state
complexes	B-protein_state
with	I-protein_state
HAESA	B-protein
in	O
size	B-experimental_method
exclusion	I-experimental_method
chromatography	I-experimental_method
experiments	O
(	O
Figure	O
3B	O
).	O

We	O
next	O
quantified	O
the	O
contribution	O
of	O
SERK1	B-protein
to	O
IDA	B-protein
recognition	O
by	O
HAESA	B-protein
.	O

We	O
found	O
that	O
HAESA	B-protein
senses	O
IDA	B-protein
with	O
a	O
~	O
60	O
fold	O
higher	O
binding	B-evidence
affinity	I-evidence
in	O
the	O
presence	B-protein_state
of	I-protein_state
SERK1	B-protein
,	O
suggesting	O
that	O
SERK1	B-protein
is	O
involved	O
in	O
the	O
specific	O
recognition	O
of	O
the	O
peptide	B-protein_type
hormone	I-protein_type
(	O
Figure	O
3C	O
).	O

We	O
next	O
titrated	B-experimental_method
SERK1	B-protein
into	O
a	O
solution	O
containing	O
only	O
the	O
HAESA	B-protein
ectodomain	B-structure_element
.	O

In	O
this	O
case	O
,	O
there	O
was	O
no	O
detectable	O
interaction	O
between	O
receptor	O
and	O
co	O
-	O
receptor	O
,	O
while	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
IDA	B-protein
,	O
SERK1	B-protein
strongly	O
binds	O
HAESA	B-protein
with	O
a	O
dissociation	B-evidence
constant	I-evidence
in	O
the	O
mid	O
-	O
nanomolar	O
range	O
(	O
Figure	O
3C	O
).	O

This	O
suggests	O
that	O
IDA	B-protein
itself	O
promotes	O
receptor	O
–	O
co	O
-	O
receptor	O
association	O
,	O
as	O
previously	O
described	O
for	O
the	O
steroid	B-chemical
hormone	I-chemical
brassinolide	B-chemical
and	O
for	O
other	O
LRR	B-complex_assembly
-	I-complex_assembly
RK	I-complex_assembly
complexes	O
.	O

Importantly	O
,	O
hydroxyprolination	B-ptm
of	O
IDA	B-protein
is	O
critical	O
for	O
HAESA	B-complex_assembly
-	I-complex_assembly
IDA	I-complex_assembly
-	I-complex_assembly
SERK1	I-complex_assembly
complex	O
formation	O
(	O
Figure	O
3C	O
,	O
D	O
).	O

Our	O
calorimetry	B-experimental_method
experiments	O
now	O
reveal	O
that	O
SERKs	B-protein_type
may	O
render	O
HAESA	B-protein
,	O
and	O
potentially	O
other	O
receptor	B-protein_type
kinases	I-protein_type
,	O
competent	O
for	O
high	O
-	O
affinity	O
sensing	O
of	O
their	O
cognate	O
ligands	O
.	O

Upon	O
IDA	B-protein
binding	O
at	O
the	O
cell	O
surface	O
,	O
the	O
kinase	B-structure_element
domains	I-structure_element
of	O
HAESA	B-protein
and	O
SERK1	B-protein
,	O
which	O
have	O
been	O
shown	O
to	O
be	O
active	B-protein_state
protein	B-protein_type
kinases	I-protein_type
,	O
may	O
interact	O
in	O
the	O
cytoplasm	O
to	O
activate	O
each	O
other	O
.	O

Consistently	O
,	O
the	O
HAESA	B-protein
kinase	B-structure_element
domain	I-structure_element
can	O
transphosphorylate	O
SERK1	B-protein
and	O
vice	O
versa	O
in	O
in	O
vitro	O
transphosphorylation	B-experimental_method
assays	I-experimental_method
(	O
Figure	O
3E	O
).	O

Together	O
,	O
our	O
genetic	B-experimental_method
and	I-experimental_method
biochemical	I-experimental_method
experiments	I-experimental_method
implicate	O
SERK1	B-protein
as	O
a	O
HAESA	B-protein_type
co	I-protein_type
-	I-protein_type
receptor	I-protein_type
in	O
the	O
Arabidopsis	B-taxonomy_domain
abscission	O
zone	O
.	O

SERK1	B-protein
senses	O
a	O
conserved	B-protein_state
motif	B-structure_element
in	O
IDA	B-chemical
family	I-chemical
peptides	I-chemical

Crystal	B-evidence
structure	I-evidence
of	O
a	O
HAESA	B-complex_assembly
–	I-complex_assembly
IDA	I-complex_assembly
–	I-complex_assembly
SERK1	I-complex_assembly
signaling	O
complex	O
.	O

(	O
A	O
)	O
Overview	O
of	O
the	O
ternary	O
complex	O
with	O
HAESA	B-protein
in	O
blue	O
(	O
surface	O
representation	O
),	O
IDA	B-protein
in	O
yellow	O
(	O
bonds	O
representation	O
)	O
and	O
SERK1	B-protein
in	O
orange	O
(	O
surface	O
view	O
).	O
(	O
B	O
)	O
The	O
HAESA	B-protein
ectodomain	B-structure_element
undergoes	O
a	O
conformational	O
change	O
upon	O
SERK1	B-protein
co	O
-	O
receptor	O
binding	O
.	O

Shown	O
are	O
Cα	O
traces	O
of	O
a	O
structural	B-experimental_method
superposition	I-experimental_method
of	O
the	O
unbound	B-protein_state
(	O
yellow	O
)	O
and	O
SERK1	B-protein_state
-	I-protein_state
bound	I-protein_state
(	O
blue	O
)	O
HAESA	B-protein
ectodomains	B-structure_element
(	O
r	B-evidence
.	I-evidence
m	I-evidence
.	I-evidence
s	I-evidence
.	I-evidence
d	I-evidence
.	I-evidence
is	O
1	O
.	O
5	O
Å	O
between	O
572	O
corresponding	O
Cα	O
atoms	O
).	O

SERK1	B-protein
(	O
in	O
orange	O
)	O
and	O
IDA	B-protein
(	O
in	O
red	O
)	O
are	O
shown	O
alongside	O
.	O

The	O
conformational	O
change	O
in	O
the	O
C	O
-	O
terminal	O
LRRs	B-structure_element
and	O
capping	B-structure_element
domain	I-structure_element
is	O
indicated	O
by	O
an	O
arrow	O
.	O
(	O
C	O
)	O
SERK1	B-protein
forms	O
an	O
integral	O
part	O
of	O
the	O
receptor	O
'	O
s	O
peptide	B-site
binding	I-site
pocket	I-site
.	O

The	O
N	O
-	O
terminal	O
capping	B-structure_element
domain	I-structure_element
of	O
SERK1	B-protein
(	O
in	O
orange	O
)	O
directly	O
contacts	O
the	O
C	O
-	O
terminal	O
part	O
of	O
IDA	B-protein
(	O
in	O
yellow	O
,	O
in	O
bonds	O
representation	O
)	O
and	O
the	O
receptor	B-protein_type
HAESA	B-protein
(	O
in	O
blue	O
).	O

Polar	O
contacts	O
of	O
SERK1	B-protein
with	O
IDA	B-protein
are	O
shown	O
in	O
magenta	O
,	O
with	O
the	O
HAESA	B-protein
LRR	B-structure_element
domain	I-structure_element
in	O
gray	O
.	O
(	O
D	O
)	O
Details	O
of	O
the	O
zipper	B-structure_element
-	I-structure_element
like	I-structure_element
SERK1	B-site
-	I-site
HAESA	I-site
interface	I-site
.	O

Ribbon	O
diagrams	O
of	O
HAESA	B-protein
(	O
in	O
blue	O
)	O
and	O
SERK1	B-protein
(	O
in	O
orange	O
)	O
are	O
shown	O
with	O
selected	O
interface	B-site
residues	I-site
(	O
in	O
bonds	O
representation	O
).	O

To	O
understand	O
in	O
molecular	O
terms	O
how	O
SERK1	B-protein
contributes	O
to	O
high	O
-	O
affinity	O
IDA	B-protein
recognition	O
,	O
we	O
solved	O
a	O
2	O
.	O
43	O
Å	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
ternary	O
HAESA	B-complex_assembly
–	I-complex_assembly
IDA	I-complex_assembly
–	I-complex_assembly
SERK1	I-complex_assembly
complex	O
(	O
Figure	O
4A	O
,	O
Table	O
2	O
).	O

HAESA	B-protein
LRRs	B-structure_element
16	I-structure_element
–	I-structure_element
21	I-structure_element
and	O
its	O
C	O
-	O
terminal	O
capping	B-structure_element
domain	I-structure_element
undergo	O
a	O
conformational	O
change	O
upon	O
SERK1	B-protein
binding	O
(	O
Figure	O
4B	O
).	O

The	O
SERK1	B-protein
ectodomain	B-structure_element
interacts	O
with	O
the	O
IDA	B-site
peptide	I-site
binding	I-site
site	I-site
using	O
a	O
loop	B-structure_element
region	I-structure_element
(	O
residues	O
51	B-residue_range
-	I-residue_range
59SERK1	I-residue_range
)	O
from	O
its	O
N	O
-	O
terminal	O
cap	B-structure_element
(	O
Figure	O
4A	O
,	O
C	O
).	O

SERK1	B-protein
loop	B-structure_element
residues	O
establish	O
multiple	O
hydrophobic	O
and	O
polar	O
contacts	O
with	O
Lys66IDA	B-residue_name_number
and	O
the	O
C	O
-	O
terminal	O
Arg	B-structure_element
-	I-structure_element
His	I-structure_element
-	I-structure_element
Asn	I-structure_element
motif	I-structure_element
in	O
IDA	B-protein
(	O
Figure	O
4C	O
).	O

SERK1	B-protein
LRRs	B-structure_element
1	I-structure_element
–	I-structure_element
5	I-structure_element
and	O
its	O
C	O
-	O
terminal	O
capping	B-structure_element
domain	I-structure_element
form	O
an	O
additional	O
zipper	B-structure_element
-	I-structure_element
like	I-structure_element
interface	B-site
with	O
residues	O
originating	O
from	O
HAESA	B-protein
LRRs	B-structure_element
15	I-structure_element
–	I-structure_element
21	I-structure_element
and	O
from	O
the	O
HAESA	B-protein
C	O
-	O
terminal	O
cap	B-structure_element
(	O
Figure	O
4D	O
).	O

SERK1	B-protein
binds	O
HAESA	B-protein
using	O
these	O
two	O
distinct	O
interaction	B-site
surfaces	I-site
(	O
Figure	O
1	O
—	O
figure	O
supplement	O
3	O
),	O
with	O
the	O
N	B-structure_element
-	I-structure_element
cap	I-structure_element
of	O
the	O
SERK1	B-protein
LRR	B-structure_element
domain	I-structure_element
partially	O
covering	O
the	O
IDA	B-site
peptide	I-site
binding	I-site
cleft	I-site
.	O

The	O
IDA	B-protein
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
motif	I-structure_element
is	O
required	O
for	O
HAESA	B-complex_assembly
-	I-complex_assembly
SERK1	I-complex_assembly
complex	O
formation	O
and	O
for	O
IDA	O
bioactivity	O
.	O

(	O
A	O
)	O
Size	B-experimental_method
exclusion	I-experimental_method
chromatography	I-experimental_method
experiments	O
similar	O
to	O
Figure	O
3B	O
,	O
D	O
reveal	O
that	O
IDA	B-protein
mutant	B-protein_state
peptides	B-chemical
targeting	O
the	O
C	B-structure_element
-	I-structure_element
terminal	I-structure_element
motif	I-structure_element
do	O
not	O
form	O
biochemically	B-protein_state
stable	I-protein_state
HAESA	B-complex_assembly
-	I-complex_assembly
IDA	I-complex_assembly
-	I-complex_assembly
SERK1	I-complex_assembly
complexes	O
.	O

Deletion	B-experimental_method
of	O
the	O
C	O
-	O
terminal	O
Asn69IDA	B-residue_name_number
completely	O
inhibits	B-protein_state
complex	O
formation	O
.	O

Purified	B-experimental_method
HAESA	B-protein
and	O
SERK1	B-protein
are	O
~	O
75	O
and	O
~	O
28	O
kDa	O
,	O
respectively	O
.	O

Left	O
panel	O
:	O
IDA	B-mutant
K66A	I-mutant
/	I-mutant
R67A	I-mutant
;	O
center	O
:	O
IDA	B-mutant
ΔN69	I-mutant
,	O
right	O
panel	O
:	O
SDS	B-experimental_method
-	I-experimental_method
PAGE	I-experimental_method
of	O
peak	O
fractions	O
.	O

Note	O
that	O
the	O
HAESA	B-protein
and	O
SERK1	B-protein
input	O
lanes	O
have	O
already	O
been	O
shown	O
in	O
Figure	O
3D	O
.	O
(	O
B	O
)	O
Isothermal	B-evidence
titration	I-evidence
thermographs	I-evidence
of	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
and	O
mutant	B-protein_state
IDA	B-chemical
peptides	I-chemical
titrated	B-experimental_method
into	O
a	O
HAESA	B-protein
-	O
SERK1	B-protein
mixture	O
in	O
the	O
cell	O
.	O

Table	O
summaries	O
for	O
calorimetric	B-evidence
binding	I-evidence
constants	I-evidence
and	O
stoichoimetries	O
for	O
different	O
IDA	B-chemical
peptides	I-chemical
binding	O
to	O
the	O
HAESA	B-protein
–	O
SERK1	B-protein
ectodomain	B-structure_element
mixture	O
(	O
±	O
fitting	O
errors	O
;	O
n	O
.	O
d	O
.	O

(	O
C	O
)	O
Quantitative	O
petal	B-experimental_method
break	I-experimental_method
-	I-experimental_method
strength	I-experimental_method
assay	I-experimental_method
for	O
Col	O
-	O
0	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
flowers	O
and	O
35S	B-gene
::	O
IDA	B-protein
wild	B-protein_state
-	I-protein_state
type	I-protein_state
and	O
35S	B-gene
::	O
IDA	B-mutant
K66A	I-mutant
/	I-mutant
R67A	I-mutant
mutant	B-protein_state
flowers	O
.	O

35S	B-gene
::	O
IDA	B-protein
plants	B-taxonomy_domain
showed	O
significantly	O
increased	O
abscission	O
compared	O
to	O
Col	O
-	O
0	O
controls	O
in	O
inflorescence	O
positions	O
2	O
and	O
3	O
(	O
a	O
).	O

Up	O
to	O
inflorescence	O
position	O
4	O
,	O
petal	O
break	O
in	O
35S	B-gene
::	O
IDA	B-mutant
K66A	I-mutant
/	I-mutant
R67A	I-mutant
mutant	B-protein_state
plants	B-taxonomy_domain
was	O
significantly	O
increased	O
compared	O
to	O
both	O
Col	O
-	O
0	O
control	O
plants	B-taxonomy_domain
(	O
b	O
)	O
and	O
35S	B-gene
::	O
IDA	B-protein
plants	B-taxonomy_domain
(	O
c	O
)	O
(	O
D	O
)	O
Normalized	O
expression	O
levels	O
(	O
relative	O
expression	O
±	O
standard	O
error	O
;	O
ida	O
:	O
-	O
0	O
.	O
02	O
±	O
0	O
.	O
001	O
;	O
Col	O
-	O
0	O
:	O
1	O
±	O
0	O
.	O
11	O
;	O
35S	B-gene
::	O
IDA	B-protein
124	O
±	O
0	O
.	O
75	O
;	O
35S	B-gene
::	O
IDA	B-mutant
K66A	I-mutant
/	I-mutant
R67A	I-mutant
:	O
159	O
±	O
0	O
.	O
58	O
)	O
of	O
IDA	B-protein
wild	B-protein_state
-	I-protein_state
type	I-protein_state
and	O
mutant	B-protein_state
transcripts	O
in	O
the	O
35S	B-experimental_method
promoter	I-experimental_method
over	I-experimental_method
-	I-experimental_method
expression	I-experimental_method
lines	I-experimental_method
analyzed	O
in	O
(	O
C	O
).	O
(	O
E	O
)	O
Magnified	O
view	O
of	O
representative	O
abscission	O
zones	O
from	O
35S	B-gene
::	O
IDA	B-protein
,	O
Col	O
-	O
0	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
and	O
35S	B-gene
::	O
IDA	B-mutant
K66A	I-mutant
/	I-mutant
R67A	I-mutant
double	B-protein_state
-	I-protein_state
mutant	I-protein_state
T3	B-experimental_method
transgenic	I-experimental_method
lines	I-experimental_method
.	O

15	O
out	O
of	O
15	O
35S	B-gene
::	O
IDA	B-protein
plants	B-taxonomy_domain
,	O
0	O
out	O
of	O
15	O
Col	O
-	O
0	O
plants	B-taxonomy_domain
and	O
0	O
out	O
of	O
15	O
35S	B-gene
::	O
IDA	B-mutant
K66A	I-mutant
/	I-mutant
R67A	I-mutant
double	B-protein_state
-	I-protein_state
mutant	I-protein_state
plants	B-taxonomy_domain
,	O
showed	O
an	O
enlarged	O
abscission	O
zone	O
,	O
respectively	O
(	O
3	O
independent	O
lines	O
were	O
analyzed	O
).	O

The	O
four	O
C	O
-	O
terminal	O
residues	O
in	O
IDA	B-protein
(	O
Lys66IDA	B-residue_range
-	I-residue_range
Asn69IDA	I-residue_range
)	O
are	O
conserved	B-protein_state
among	O
IDA	B-protein_type
family	I-protein_type
members	I-protein_type
and	O
are	O
in	O
direct	O
contact	O
with	O
SERK1	B-protein
(	O
Figures	O
1A	O
,	O
4C	O
).	O

We	O
thus	O
assessed	O
their	O
contribution	O
to	O
HAESA	B-complex_assembly
–	I-complex_assembly
SERK1	I-complex_assembly
complex	O
formation	O
.	O

Deletion	B-experimental_method
of	O
the	O
buried	O
Asn69IDA	B-residue_name_number
completely	B-protein_state
inhibits	I-protein_state
receptor	O
–	O
co	O
-	O
receptor	O
complex	O
formation	O
and	O
HSL2	O
activation	O
(	O
Figure	O
5A	O
,	O
B	O
).	O

A	O
synthetic	B-protein_state
Lys66IDA	B-mutant
/	I-mutant
Arg67IDA	I-mutant
→	I-mutant
Ala	I-mutant
mutant	B-protein_state
peptide	B-chemical
(	O
IDA	B-mutant
K66A	I-mutant
/	I-mutant
R66A	I-mutant
)	O
showed	O
a	O
10	O
fold	O
reduced	O
binding	B-evidence
affinity	I-evidence
when	O
titrated	B-experimental_method
in	O
a	O
HAESA	B-protein
/	O
SERK1	B-protein
protein	O
solution	O
(	O
Figures	O
5A	O
,	O
B	O
,	O
2D	O
).	O

We	O
over	B-experimental_method
-	I-experimental_method
expressed	I-experimental_method
full	B-protein_state
-	I-protein_state
length	I-protein_state
wild	B-protein_state
-	I-protein_state
type	I-protein_state
IDA	B-protein
or	O
this	O
Lys66IDA	B-mutant
/	I-mutant
Arg67IDA	I-mutant
→	I-mutant
Ala	I-mutant
double	B-protein_state
-	I-protein_state
mutant	I-protein_state
to	O
similar	O
levels	O
in	O
Col	O
-	O
0	O
Arabidopsis	B-taxonomy_domain
plants	B-taxonomy_domain
(	O
Figure	O
5D	O
).	O

We	O
found	O
that	O
over	B-experimental_method
-	I-experimental_method
expression	I-experimental_method
of	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
IDA	B-protein
leads	O
to	O
early	O
floral	O
abscission	O
and	O
an	O
enlargement	O
of	O
the	O
abscission	O
zone	O
(	O
Figure	O
5C	O
–	O
E	O
).	O

In	O
contrast	O
,	O
over	B-experimental_method
-	I-experimental_method
expression	I-experimental_method
of	O
the	O
IDA	B-mutant
Lys66IDA	I-mutant
/	I-mutant
Arg67IDA	I-mutant
→	I-mutant
Ala	I-mutant
double	B-protein_state
mutant	I-protein_state
significantly	O
delays	O
floral	O
abscission	O
when	O
compared	O
to	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
control	O
plants	B-taxonomy_domain
,	O
suggesting	O
that	O
the	O
mutant	B-protein_state
IDA	B-chemical
peptide	I-chemical
has	O
reduced	O
activity	O
in	O
planta	B-taxonomy_domain
(	O
Figure	O
5C	O
–	O
E	O
).	O

Comparison	O
of	O
35S	B-gene
::	O
IDA	B-protein
wild	B-protein_state
-	I-protein_state
type	I-protein_state
and	O
mutant	B-protein_state
plants	B-taxonomy_domain
further	O
indicates	O
that	O
mutation	B-experimental_method
of	O
Lys66IDA	B-mutant
/	I-mutant
Arg67IDA	I-mutant
→	I-mutant
Ala	I-mutant
may	O
cause	O
a	O
weak	O
dominant	O
negative	O
effect	O
(	O
Figure	O
5C	O
–	O
E	O
).	O

In	O
agreement	O
with	O
our	O
structures	B-evidence
and	O
biochemical	B-experimental_method
assays	I-experimental_method
,	O
this	O
experiment	O
suggests	O
a	O
role	O
of	O
the	O
conserved	B-protein_state
IDA	B-protein
C	O
-	O
terminus	O
in	O
the	O
control	O
of	O
floral	O
abscission	O
.	O

In	O
contrast	O
to	O
animal	B-taxonomy_domain
LRR	B-protein_type
receptors	I-protein_type
,	O
plant	B-taxonomy_domain
LRR	B-structure_element
-	I-structure_element
RKs	I-structure_element
harbor	O
spiral	B-protein_state
-	I-protein_state
shaped	I-protein_state
ectodomains	B-structure_element
and	O
thus	O
they	O
require	O
shape	B-protein_state
-	I-protein_state
complementary	I-protein_state
co	B-protein_type
-	I-protein_type
receptor	I-protein_type
proteins	I-protein_type
for	O
receptor	O
activation	O
.	O

For	O
a	O
rapidly	O
growing	O
number	O
of	O
plant	B-taxonomy_domain
signaling	O
pathways	O
,	O
SERK	B-protein_type
proteins	I-protein_type
act	O
as	O
these	O
essential	O
co	B-protein_type
-	I-protein_type
receptors	I-protein_type
(;	O
).	O

SERK1	O
has	O
been	O
previously	O
reported	O
as	O
a	O
positive	O
regulator	O
in	O
plant	B-taxonomy_domain
embryogenesis	O
,	O
male	O
sporogenesis	O
,	O
brassinosteroid	O
signaling	O
and	O
in	O
phytosulfokine	O
perception	O
.	O

Recent	O
findings	O
by	O
and	O
our	O
mechanistic	O
studies	O
now	O
also	O
support	O
a	O
positive	O
role	O
for	O
SERK1	B-protein
in	O
floral	O
abscission	O
.	O

As	O
serk1	B-gene
-	I-gene
1	I-gene
mutant	B-protein_state
plants	B-taxonomy_domain
show	O
intermediate	O
abscission	O
phenotypes	O
when	O
compared	O
to	O
haesa	B-gene
/	O
hsl2	O
mutants	B-protein_state
,	O
SERK1	B-protein
likely	O
acts	O
redundantly	O
with	O
other	O
SERKs	B-protein_type
in	O
the	O
abscission	O
zone	O
(	O
Figure	O
3A	O
).	O

It	O
has	O
been	O
previously	O
suggested	O
that	O
SERK1	B-protein
can	O
inhibit	O
cell	O
separation	O
.	O

However	O
our	O
results	O
show	O
that	O
SERK1	B-protein
also	O
can	O
activate	O
this	O
process	O
upon	O
IDA	B-protein
sensing	O
,	O
indicating	O
that	O
SERKs	B-protein_type
may	O
fulfill	O
several	O
different	O
functions	O
in	O
the	O
course	O
of	O
the	O
abscission	O
process	O
.	O

While	O
the	O
sequence	O
of	O
the	O
mature	B-protein_state
IDA	B-chemical
peptide	I-chemical
has	O
not	O
been	O
experimentally	O
determined	O
in	O
planta	B-taxonomy_domain
,	O
our	O
HAESA	B-complex_assembly
-	I-complex_assembly
IDA	I-complex_assembly
complex	O
structures	B-evidence
and	O
calorimetry	B-evidence
assays	I-evidence
suggest	O
that	O
active	B-protein_state
IDLs	B-protein_type
are	O
hydroxyprolinated	B-protein_state
dodecamers	B-structure_element
.	O

It	O
will	O
be	O
thus	O
interesting	O
to	O
see	O
if	O
proteolytic	O
processing	O
of	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
IDA	B-protein
in	O
vivo	O
is	O
regulated	O
in	O
a	O
cell	O
-	O
type	O
or	O
tissue	O
-	O
specific	O
manner	O
.	O

The	O
central	O
Hyp	B-residue_name
residue	O
in	O
IDA	B-protein
is	O
found	O
buried	O
in	O
the	O
HAESA	B-protein
peptide	B-site
binding	I-site
surface	I-site
and	O
thus	O
this	O
post	O
-	O
translational	O
modification	O
may	O
regulate	O
IDA	B-protein
bioactivity	O
.	O

Our	O
comparative	B-experimental_method
structural	I-experimental_method
and	I-experimental_method
biochemical	I-experimental_method
analysis	I-experimental_method
further	O
suggests	O
that	O
IDLs	B-protein_type
share	O
a	O
common	O
receptor	O
binding	O
mode	O
,	O
but	O
may	O
preferably	O
bind	O
to	O
HAESA	B-protein
,	O
HSL1	B-protein
or	O
HSL2	B-protein
in	O
different	O
plant	B-taxonomy_domain
tissues	O
and	O
organs	O
.	O

In	O
our	O
quantitative	B-experimental_method
biochemical	I-experimental_method
assays	I-experimental_method
,	O
the	O
presence	B-protein_state
of	I-protein_state
SERK1	B-protein
dramatically	O
increases	O
the	O
HAESA	B-protein
binding	O
specificity	O
and	O
affinity	O
for	O
IDA	B-protein
.	O

This	O
observation	O
is	O
consistent	O
with	O
our	O
complex	O
structure	B-evidence
in	O
which	O
receptor	O
and	O
co	O
-	O
receptor	O
together	O
form	O
the	O
IDA	B-site
binding	I-site
pocket	I-site
.	O

The	O
fact	O
that	O
SERK1	B-protein
specifically	O
interacts	O
with	O
the	O
very	O
C	O
-	O
terminus	O
of	O
IDLs	B-protein_type
may	O
allow	O
for	O
the	O
rational	O
design	O
of	O
peptide	B-chemical
hormone	I-chemical
antagonists	I-chemical
,	O
as	O
previously	O
demonstrated	O
for	O
the	O
brassinosteroid	O
pathway	O
.	O

Importantly	O
,	O
our	O
calorimetry	B-experimental_method
assays	I-experimental_method
reveal	O
that	O
the	O
SERK1	B-protein
ectodomain	B-structure_element
binds	B-protein_state
HAESA	B-protein
with	O
nanomolar	O
affinity	O
,	O
but	O
only	O
in	O
the	O
presence	B-protein_state
of	I-protein_state
IDA	B-protein
(	O
Figure	O
3C	O
).	O

This	O
ligand	O
-	O
induced	O
formation	O
of	O
a	O
receptor	O
–	O
co	O
-	O
receptor	O
complex	O
may	O
allow	O
the	O
HAESA	B-protein
and	O
SERK1	B-protein
kinase	B-structure_element
domains	I-structure_element
to	O
efficiently	O
trans	O
-	O
phosphorylate	O
and	O
activate	O
each	O
other	O
in	O
the	O
cytoplasm	O
.	O

It	O
is	O
of	O
note	O
that	O
our	O
reported	O
binding	B-evidence
affinities	I-evidence
for	O
IDA	B-protein
and	O
SERK1	B-protein
have	O
been	O
measured	O
using	O
synthetic	B-protein_state
peptides	B-chemical
and	O
the	O
isolated	B-experimental_method
HAESA	B-protein
and	O
SERK1	B-protein
ectodomains	B-structure_element
,	O
and	O
thus	O
might	O
differ	O
in	O
the	O
context	O
of	O
the	O
full	B-protein_state
-	I-protein_state
length	I-protein_state
,	O
membrane	B-protein_state
-	I-protein_state
embedded	I-protein_state
signaling	O
complex	O
.	O

SERK1	B-protein
uses	O
partially	O
overlapping	O
surface	O
areas	O
to	O
activate	O
different	O
plant	B-taxonomy_domain
signaling	B-protein_type
receptors	I-protein_type
.	O

(	O
A	O
)	O
Structural	B-experimental_method
comparison	I-experimental_method
of	O
plant	B-taxonomy_domain
steroid	B-chemical
and	O
peptide	B-protein_type
hormone	I-protein_type
membrane	B-protein_type
signaling	I-protein_type
complexes	I-protein_type
.	O

Left	O
panel	O
:	O
Ribbon	O
diagram	O
of	O
HAESA	B-protein
(	O
in	O
blue	O
),	O
SERK1	B-protein
(	O
in	O
orange	O
)	O
and	O
IDA	B-protein
(	O
in	O
bonds	O
and	O
surface	O
represention	O
).	O

Right	O
panel	O
:	O
Ribbon	O
diagram	O
of	O
the	O
plant	B-taxonomy_domain
steroid	B-protein_type
receptor	I-protein_type
BRI1	B-protein
(	O
in	O
blue	O
)	O
bound	B-protein_state
to	I-protein_state
brassinolide	B-chemical
(	O
in	O
gray	O
,	O
in	O
bonds	O
representation	O
)	O
and	O
to	O
SERK1	B-protein
,	O
shown	O
in	O
the	O
same	O
orientation	O
(	O
PDB	O
-	O
ID	O
.	O
4lsx	O
).	O

(	O
B	O
)	O
View	O
of	O
the	O
inner	O
surface	O
of	O
the	O
SERK1	B-protein
LRR	B-structure_element
domain	I-structure_element
(	O
PDB	O
-	O
ID	O
4lsc	O
,	O
surface	O
representation	O
,	O
in	O
gray	O
).	O

A	O
ribbon	O
diagram	O
of	O
SERK1	B-protein
in	O
the	O
same	O
orientation	O
is	O
shown	O
alongside	O
.	O

Residues	O
interacting	O
with	O
the	O
HAESA	B-protein
or	O
BRI1	B-protein
LRR	B-structure_element
domains	I-structure_element
are	O
shown	O
in	O
orange	O
or	O
magenta	O
,	O
respectively	O
.	O

Comparison	B-experimental_method
of	O
our	O
HAESA	B-complex_assembly
–	I-complex_assembly
IDA	I-complex_assembly
–	I-complex_assembly
SERK1	I-complex_assembly
structure	B-evidence
with	O
the	O
brassinosteroid	O
receptor	O
signaling	O
complex	O
,	O
where	O
SERK1	B-protein
also	O
acts	O
as	O
co	B-protein_type
-	I-protein_type
receptor	I-protein_type
,	O
reveals	O
an	O
overall	O
conserved	B-protein_state
mode	O
of	O
SERK1	B-protein
binding	O
,	O
while	O
the	O
ligand	B-site
binding	I-site
pockets	I-site
map	O
to	O
very	O
different	O
areas	O
in	O
the	O
corresponding	O
receptors	O
(	O
LRRs	B-structure_element
2	I-structure_element
–	I-structure_element
14	I-structure_element
;	O
HAESA	B-protein
;	O
LRRs	B-structure_element
21	I-structure_element
–	I-structure_element
25	I-structure_element
,	O
BRI1	B-protein
)	O
and	O
may	O
involve	O
an	O
island	O
domain	O
(	O
BRI1	B-protein
)	O
or	O
not	O
(	O
HAESA	B-protein
)	O
(	O
Figure	O
6A	O
).	O

Several	O
residues	O
in	O
the	O
SERK1	B-protein
N	O
-	O
terminal	O
capping	B-structure_element
domain	I-structure_element
(	O
Thr59SERK1	B-residue_name_number
,	O
Phe61SERK1	B-residue_name_number
)	O
and	O
the	O
LRR	B-site
inner	I-site
surface	I-site
(	O
Asp75SERK1	B-residue_name_number
,	O
Tyr101SERK1	B-residue_name_number
,	O
SER121SERK1	B-residue_name_number
,	O
Phe145SERK1	B-residue_name_number
)	O
contribute	O
to	O
the	O
formation	O
of	O
both	O
complexes	O
(	O
Figures	O
4C	O
,	O
D	O
,	O
6B	O
).	O

In	O
addition	O
,	O
residues	O
53	B-residue_range
-	I-residue_range
55SERK1	I-residue_range
from	O
the	O
SERK1	B-protein
N	O
-	O
terminal	O
cap	B-structure_element
mediate	O
specific	O
interactions	O
with	O
the	O
IDA	B-chemical
peptide	I-chemical
(	O
Figures	O
4C	O
,	O
6B	O
).	O

These	O
residues	O
are	O
not	O
involved	O
in	O
the	O
sensing	O
of	O
the	O
steroid	B-chemical
hormone	I-chemical
brassinolide	B-chemical
.	O

In	O
both	O
cases	O
however	O
,	O
the	O
co	O
-	O
receptor	O
completes	O
the	O
hormone	B-site
binding	I-site
pocket	I-site
.	O

This	O
fact	O
together	O
with	O
the	O
largely	O
overlapping	O
SERK1	B-site
binding	I-site
surfaces	I-site
in	O
HAESA	B-protein
and	O
BRI1	B-protein
allows	O
us	O
to	O
speculate	O
that	O
SERK1	B-protein
may	O
promote	O
high	O
-	O
affinity	O
peptide	B-protein_type
hormone	I-protein_type
and	O
brassinosteroid	O
sensing	O
by	O
simply	O
slowing	O
down	O
dissociation	O
of	O
the	O
ligand	O
from	O
its	O
cognate	O
receptor	O
.	O

Different	O
plant	B-taxonomy_domain
peptide	B-protein_type
hormone	I-protein_type
families	I-protein_type
contain	O
a	O
C	O
-	O
terminal	O
(	B-structure_element
Arg	I-structure_element
)-	I-structure_element
His	I-structure_element
-	I-structure_element
Asn	I-structure_element
motif	I-structure_element
,	O
which	O
in	O
IDA	B-protein
represents	O
the	O
co	B-site
-	I-site
receptor	I-site
recognition	I-site
site	I-site
.	O

Structure	B-experimental_method
-	I-experimental_method
guided	I-experimental_method
multiple	I-experimental_method
sequence	I-experimental_method
alignment	I-experimental_method
of	O
IDA	B-protein
and	O
IDA	B-chemical
-	I-chemical
like	I-chemical
peptides	I-chemical
with	O
other	O
plant	B-taxonomy_domain
peptide	B-protein_type
hormone	I-protein_type
families	I-protein_type
,	O
including	O
CLAVATA3	B-protein_type
–	I-protein_type
EMBRYO	I-protein_type
SURROUNDING	I-protein_type
REGION	I-protein_type
-	I-protein_type
RELATED	I-protein_type
(	O
CLV3	B-protein_type
/	I-protein_type
CLE	I-protein_type
),	O
ROOT	B-protein_type
GROWTH	I-protein_type
FACTOR	I-protein_type
–	I-protein_type
GOLVEN	I-protein_type
(	O
RGF	B-protein_type
/	I-protein_type
GLV	I-protein_type
),	O
PRECURSOR	B-protein_type
GENE	I-protein_type
PROPEP1	I-protein_type
(	O
PEP1	B-protein_type
)	O
from	O
Arabidopsis	B-species
thaliana	I-species
.	O

The	O
conserved	B-protein_state
(	B-structure_element
Arg	I-structure_element
)-	I-structure_element
His	I-structure_element
-	I-structure_element
Asn	I-structure_element
motif	I-structure_element
is	O
highlighted	O
in	O
red	O
,	O
the	O
central	O
Hyp	B-residue_name
residue	O
in	O
IDLs	B-protein_type
and	O
CLEs	B-protein_type
is	O
marked	O
in	O
blue	O
.	O

Our	O
experiments	O
reveal	O
that	O
SERK1	B-protein
recognizes	O
a	O
C	O
-	O
terminal	O
Arg	B-structure_element
-	I-structure_element
His	I-structure_element
-	I-structure_element
Asn	I-structure_element
motif	I-structure_element
in	O
IDA	B-protein
.	O

Importantly	O
,	O
this	B-structure_element
motif	I-structure_element
can	O
also	O
be	O
found	O
in	O
other	O
peptide	B-protein_type
hormone	I-protein_type
families	I-protein_type
(	O
Figure	O
7	O
).	O

Among	O
these	O
are	O
the	O
CLE	B-chemical
peptides	I-chemical
regulating	O
stem	O
cell	O
maintenance	O
in	O
the	O
shoot	O
and	O
the	O
root	O
.	O

It	O
is	O
interesting	O
to	O
note	O
,	O
that	O
CLEs	B-protein_type
in	O
their	O
mature	B-protein_state
form	I-protein_state
are	O
also	O
hydroxyprolinated	B-protein_state
dodecamers	B-structure_element
,	O
which	O
bind	O
to	O
a	O
surface	B-site
area	I-site
in	O
the	O
BARELY	B-protein_type
ANY	I-protein_type
MERISTEM	I-protein_type
1	I-protein_type
receptor	I-protein_type
that	O
would	O
correspond	O
to	O
part	O
of	O
the	O
IDA	B-site
binding	I-site
cleft	I-site
in	O
HAESA	B-protein
.	O

Diverse	O
plant	B-taxonomy_domain
peptide	B-protein_type
hormones	I-protein_type
may	O
thus	O
also	O
bind	O
their	O
LRR	B-protein_type
-	I-protein_type
RK	I-protein_type
receptors	I-protein_type
in	O
an	O
extended	B-protein_state
conformation	I-protein_state
along	O
the	O
inner	O
surface	O
of	O
the	O
LRR	B-structure_element
domain	I-structure_element
and	O
may	O
also	O
use	O
small	B-protein_state
,	O
shape	B-protein_state
-	I-protein_state
complementary	I-protein_state
co	B-protein_type
-	I-protein_type
receptors	I-protein_type
for	O
high	O
-	O
affinity	O
ligand	O
binding	O
and	O
receptor	O
activation	O
.	O

The	O
Taf14	B-protein
YEATS	B-structure_element
domain	I-structure_element
is	O
a	O
reader	O
of	O
histone	B-protein_type
crotonylation	B-ptm

The	O
discovery	O
of	O
new	O
histone	B-protein_type
modifications	O
is	O
unfolding	O
at	O
startling	O
rates	O
,	O
however	O
,	O
the	O
identification	O
of	O
effectors	O
capable	O
of	O
interpreting	O
these	O
modifications	O
has	O
lagged	O
behind	O
.	O

Here	O
we	O
report	O
the	O
YEATS	B-structure_element
domain	I-structure_element
as	O
an	O
effective	O
reader	O
of	O
histone	B-protein_type
lysine	B-residue_name
crotonylation	B-ptm
–	O
an	O
epigenetic	O
signature	O
associated	O
with	O
active	O
transcription	O
.	O

We	O
show	O
that	O
the	O
Taf14	B-protein
YEATS	B-structure_element
domain	I-structure_element
engages	O
crotonyllysine	B-residue_name
via	O
a	O
unique	O
π	O
-	O
π	O
-	O
π	O
-	O
stacking	O
mechanism	O
and	O
that	O
other	O
YEATS	B-structure_element
domains	I-structure_element
have	O
crotonyllysine	B-residue_name
binding	O
activity	O
.	O

Crotonylation	B-ptm
of	O
lysine	B-residue_name
residues	O
(	O
crotonyllysine	B-residue_name
,	O
Kcr	B-residue_name
)	O
has	O
emerged	O
as	O
one	O
of	O
the	O
fundamental	O
histone	B-protein_type
post	O
-	O
translational	O
modifications	O
(	O
PTMs	O
)	O
found	O
in	O
mammalian	B-taxonomy_domain
chromatin	O
.	O

The	O
crotonyllysine	B-residue_name
mark	O
on	O
histone	B-protein_type
H3K18	B-protein_type
is	O
produced	O
by	O
p300	B-protein
,	O
a	O
histone	B-protein_type
acetyltransferase	I-protein_type
also	O
responsible	O
for	O
acetylation	B-ptm
of	O
histones	O
.	O

Owing	O
to	O
some	O
differences	O
in	O
their	O
genomic	O
distribution	O
,	O
the	O
crotonyllysine	B-residue_name
and	O
acetyllysine	B-residue_name
(	O
Kac	B-residue_name
)	O
modifications	O
have	O
been	O
linked	O
to	O
distinct	O
functional	O
outcomes	O
.	O

p300	B-protein
-	O
catalyzed	O
histone	B-protein_type
crotonylation	B-ptm
,	O
which	O
is	O
likely	O
metabolically	O
regulated	O
,	O
stimulates	O
transcription	O
to	O
a	O
greater	O
degree	O
than	O
p300	B-protein
-	O
catalyzed	O
acetylation	B-ptm
.	O

The	O
discovery	O
of	O
individual	O
biological	O
roles	O
for	O
the	O
crotonyllysine	B-residue_name
and	O
acetyllysine	B-residue_name
marks	O
suggests	O
that	O
these	O
PTMs	O
can	O
be	O
read	O
by	O
distinct	O
readers	O
.	O

While	O
a	O
number	O
of	O
acetyllysine	B-residue_name
readers	O
have	O
been	O
identified	O
and	O
characterized	O
,	O
a	O
specific	O
reader	O
of	O
the	O
crotonyllysine	B-residue_name
mark	O
remains	O
unknown	O
(	O
reviewed	O
in	O
).	O

A	O
recent	O
survey	O
of	O
bromodomains	B-structure_element
(	O
BDs	B-structure_element
)	O
demonstrates	O
that	O
only	O
one	O
BD	B-structure_element
associates	O
very	O
weakly	O
with	O
a	O
crotonylated	B-protein_state
peptide	O
,	O
however	O
it	O
binds	O
more	O
tightly	O
to	O
acetylated	B-protein_state
peptides	O
,	O
inferring	O
that	O
bromodomains	B-structure_element
do	O
not	O
possess	O
physiologically	O
relevant	O
crotonyllysine	B-residue_name
binding	O
activity	O
.	O

The	O
family	O
of	O
acetyllysine	B-residue_name
readers	O
has	O
been	O
expanded	O
with	O
the	O
discovery	O
that	O
the	O
YEATS	B-structure_element
(	O
Yaf9	B-protein
,	O
ENL	B-protein
,	O
AF9	B-protein
,	O
Taf14	B-protein
,	O
Sas5	B-protein
)	O
domains	O
of	O
human	B-species
AF9	B-protein
and	O
yeast	B-taxonomy_domain
Taf14	B-protein
are	O
capable	O
of	O
recognizing	O
the	O
histone	B-protein_type
mark	O
H3K9ac	B-protein_type
.	O

The	O
acetyllysine	B-residue_name
binding	O
function	O
of	O
the	O
AF9	B-protein
YEATS	B-structure_element
domain	I-structure_element
is	O
essential	O
for	O
the	O
recruitment	O
of	O
the	O
histone	B-protein_type
methyltransferase	I-protein_type
DOT1L	B-protein
to	O
H3K9ac	B-protein_type
-	O
containing	O
chromatin	O
and	O
for	O
DOT1L	B-protein
-	O
mediated	O
H3K79	B-protein_type
methylation	B-ptm
and	O
transcription	O
.	O

Similarly	O
,	O
activation	O
of	O
a	O
subset	O
of	O
genes	O
and	O
DNA	O
damage	O
repair	O
in	O
yeast	B-taxonomy_domain
require	O
the	O
acetyllysine	B-residue_name
binding	O
activity	O
of	O
the	O
Taf14	B-protein
YEATS	B-structure_element
domain	I-structure_element
.	O

Consistent	O
with	O
its	O
role	O
in	O
gene	O
regulation	O
,	O
Taf14	B-protein
was	O
identified	O
as	O
a	O
core	O
component	O
of	O
the	O
transcription	O
factor	O
complexes	O
TFIID	B-complex_assembly
and	O
TFIIF	B-complex_assembly
.	O

However	O
,	O
Taf14	B-protein
is	O
also	O
found	O
in	O
a	O
number	O
of	O
chromatin	O
-	O
remodeling	O
complexes	O
(	O
i	O
.	O
e	O
.,	O
INO80	B-complex_assembly
,	O
SWI	B-complex_assembly
/	I-complex_assembly
SNF	I-complex_assembly
and	O
RSC	B-complex_assembly
)	O
and	O
the	O
histone	B-protein_type
acetyltransferase	I-protein_type
complex	O
NuA3	B-complex_assembly
,	O
indicating	O
a	O
multifaceted	O
role	O
of	O
Taf14	B-protein
in	O
transcriptional	O
regulation	O
and	O
chromatin	O
biology	O
.	O

In	O
this	O
study	O
,	O
we	O
identified	O
the	O
Taf14	B-protein
YEATS	B-structure_element
domain	I-structure_element
as	O
a	O
reader	O
of	O
crotonyllysine	B-residue_name
that	O
binds	O
to	O
histone	B-protein_type
H3	B-protein_type
crotonylated	B-protein_state
at	O
lysine	B-residue_name_number
9	I-residue_name_number
(	O
H3K9cr	B-protein_type
)	O
via	O
a	O
distinctive	O
binding	O
mechanism	O
.	O

We	O
found	O
that	O
H3K9cr	B-protein_type
is	O
present	O
in	O
yeast	B-taxonomy_domain
and	O
is	O
dynamically	O
regulated	O
.	O

To	O
elucidate	O
the	O
molecular	O
basis	O
for	O
recognition	O
of	O
the	O
H3K9cr	B-protein_type
mark	O
,	O
we	O
obtained	O
a	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
Taf14	B-protein
YEATS	B-structure_element
domain	I-structure_element
in	B-protein_state
complex	I-protein_state
with	I-protein_state
H3K9cr5	B-chemical
-	I-chemical
13	I-chemical
(	O
residues	O
5	B-residue_range
–	I-residue_range
13	I-residue_range
of	O
H3	B-protein_type
)	O
peptide	O
(	O
Fig	O
.	O
1	O
,	O
Supplementary	O
Results	O
,	O
Supplementary	O
Fig	O
.	O
1	O
and	O
Supplementary	O
Table	O
1	O
).	O

The	O
Taf14	B-protein
YEATS	B-structure_element
domain	I-structure_element
adopts	O
an	O
immunoglobin	B-structure_element
-	I-structure_element
like	I-structure_element
β	I-structure_element
sandwich	I-structure_element
fold	I-structure_element
containing	O
eight	O
anti	B-structure_element
-	I-structure_element
parallel	I-structure_element
β	I-structure_element
strands	I-structure_element
linked	O
by	O
short	O
loops	B-structure_element
that	O
form	O
a	O
binding	B-site
site	I-site
for	O
H3K9cr	B-protein_type
(	O
Fig	O
.	O
1b	O
).	O

The	O
H3K9cr	B-protein_type
peptide	O
lays	O
in	O
an	O
extended	B-protein_state
conformation	I-protein_state
in	O
an	O
orientation	O
orthogonal	O
to	O
the	O
β	B-structure_element
strands	I-structure_element
and	O
is	O
stabilized	O
through	O
an	O
extensive	O
network	O
of	O
direct	O
and	O
water	O
-	O
mediated	O
hydrogen	O
bonds	O
and	O
a	O
salt	O
bridge	O
(	O
Fig	O
.	O
1c	O
).	O

The	O
most	O
striking	O
feature	O
of	O
the	O
crotonyllysine	B-residue_name
recognition	O
mechanism	O
is	O
the	O
unique	O
coordination	O
of	O
crotonylated	B-protein_state
lysine	B-residue_name
residue	O
.	O

The	O
fully	O
extended	O
side	O
chain	O
of	O
K9cr	B-residue_name_number
transverses	O
the	O
narrow	O
tunnel	O
,	O
crossing	O
the	O
β	B-structure_element
sandwich	I-structure_element
at	O
right	O
angle	O
in	O
a	O
corkscrew	O
-	O
like	O
manner	O
(	O
Fig	O
.	O
1b	O
and	O
Supplementary	O
Figure	O
1b	O
).	O

The	O
planar	O
crotonyl	O
group	O
is	O
inserted	O
between	O
Trp81	B-residue_name_number
and	O
Phe62	B-residue_name_number
of	O
the	O
protein	O
,	O
the	O
aromatic	O
rings	O
of	O
which	O
are	O
positioned	O
strictly	O
parallel	O
to	O
each	O
other	O
and	O
at	O
equal	O
distance	O
from	O
the	O
crotonyl	O
group	O
,	O
yielding	O
a	O
novel	O
aromatic	O
-	O
amide	O
/	O
aliphatic	O
-	O
aromatic	O
π	O
-	O
π	O
-	O
π	O
-	O
stacking	O
system	O
that	O
,	O
to	O
our	O
knowledge	O
,	O
has	O
not	O
been	O
reported	O
previously	O
for	O
any	O
protein	O
-	O
protein	O
interaction	O
(	O
Fig	O
.	O
1d	O
and	O
Supplementary	O
Fig	O
.	O
1c	O
).	O

The	O
side	O
chain	O
of	O
Trp81	B-residue_name_number
appears	O
to	O
adopt	O
two	O
conformations	O
,	O
one	O
of	O
which	O
provides	O
maximum	O
π	O
-	O
stacking	O
with	O
the	O
alkene	O
functional	O
group	O
while	O
the	O
other	O
rotamer	O
affords	O
maximum	O
π	O
-	O
stacking	O
with	O
the	O
amide	O
π	O
electrons	O
(	O
Supplementary	O
Fig	O
.	O
1c	O
).	O

The	O
dual	O
conformation	O
of	O
Trp81	B-residue_name_number
is	O
likely	O
due	O
to	O
the	O
conjugated	O
nature	O
of	O
the	O
C	O
=	O
C	O
and	O
C	O
=	O
O	O
π	O
-	O
orbitals	O
within	O
the	O
crotonyl	O
functional	O
group	O
.	O

This	O
provides	O
the	O
capability	O
for	O
the	O
alkene	O
moiety	O
to	O
form	O
electrostatic	O
contacts	O
,	O
as	O
Cα	O
and	O
Cβ	O
lay	O
within	O
electrostatic	O
interaction	O
distances	O
of	O
the	O
carbonyl	O
oxygen	O
of	O
Gln79	B-residue_name_number
and	O
of	O
the	O
hydroxyl	O
group	O
of	O
Thr61	B-residue_name_number
,	O
respectively	O
.	O

The	O
hydroxyl	O
group	O
of	O
Thr61	B-residue_name_number
also	O
participates	O
in	O
a	O
hydrogen	O
bond	O
with	O
the	O
amide	O
nitrogen	O
of	O
the	O
K9cr	B-residue_name_number
side	O
chain	O
(	O
Fig	O
.	O
1d	O
).	O

The	O
fixed	O
position	O
of	O
the	O
Thr61	B-residue_name_number
hydroxyl	O
group	O
,	O
which	O
facilitates	O
interactions	O
with	O
both	O
the	O
amide	O
and	O
Cα	O
of	O
K9cr	B-residue_name_number
,	O
is	O
achieved	O
through	O
a	O
hydrogen	O
bond	O
with	O
imidazole	O
ring	O
of	O
His59	B-residue_name_number
.	O

Extra	O
stabilization	O
of	O
K9cr	B-residue_name_number
is	O
attained	O
by	O
a	O
hydrogen	O
bond	O
formed	O
between	O
its	O
carbonyl	O
oxygen	O
and	O
the	O
backbone	O
nitrogen	O
of	O
Trp81	B-residue_name_number
,	O
as	O
well	O
as	O
a	O
water	B-chemical
-	O
mediated	O
hydrogen	O
bond	O
with	O
the	O
backbone	O
carbonyl	O
group	O
of	O
Gly82	B-residue_name_number
(	O
Fig	O
1d	O
).	O

This	O
distinctive	O
mechanism	O
was	O
corroborated	O
through	O
mapping	O
the	O
Taf14	B-protein
YEATS	B-site
-	I-site
H3K9cr	I-site
binding	I-site
interface	I-site
in	O
solution	O
using	O
NMR	B-experimental_method
chemical	I-experimental_method
shift	I-experimental_method
perturbation	I-experimental_method
analysis	I-experimental_method
(	O
Supplementary	O
Fig	O
.	O
2a	O
,	O
b	O
).	O

Binding	O
of	O
the	O
Taf14	B-protein
YEATS	B-structure_element
domain	I-structure_element
to	O
H3K9cr	B-protein_type
is	O
robust	O
.	O

The	O
dissociation	B-evidence
constant	I-evidence
(	O
Kd	B-evidence
)	O
for	O
the	O
Taf14	B-complex_assembly
YEATS	I-complex_assembly
-	I-complex_assembly
H3K9cr5	I-complex_assembly
-	I-complex_assembly
13	I-complex_assembly
complex	O
was	O
found	O
to	O
be	O
9	O
.	O
5	O
μM	O
,	O
as	O
measured	O
by	O
fluorescence	B-experimental_method
spectroscopy	I-experimental_method
(	O
Supplementary	O
Fig	O
.	O
2c	O
).	O

This	O
value	O
is	O
in	O
the	O
range	O
of	O
binding	B-evidence
affinities	I-evidence
exhibited	O
by	O
the	O
majority	O
of	O
histone	O
readers	O
,	O
thus	O
attesting	O
to	O
the	O
physiological	O
relevance	O
of	O
the	O
H3K9cr	B-protein_type
recognition	O
by	O
Taf14	B-protein
.	O

To	O
determine	O
whether	O
H3K9cr	B-protein_type
is	O
present	O
in	O
yeast	B-taxonomy_domain
,	O
we	O
generated	O
whole	B-experimental_method
cell	I-experimental_method
extracts	I-experimental_method
from	O
logarithmically	O
growing	O
yeast	B-taxonomy_domain
cells	O
and	O
subjected	O
them	O
to	O
Western	B-experimental_method
blot	I-experimental_method
analysis	I-experimental_method
using	O
antibodies	O
directed	O
towards	O
H3K9cr	B-protein_type
,	O
H3K9ac	B-protein_type
and	O
H3	B-protein_type
(	O
Fig	O
.	O
2a	O
,	O
b	O
,	O
Supplementary	O
Fig	O
.	O
3	O
and	O
Supplementary	O
Table	O
2	O
).	O

Both	O
H3K9cr	B-protein_type
and	O
H3K9ac	B-protein_type
were	O
detected	O
in	O
yeast	B-taxonomy_domain
histones	B-protein_type
;	O
to	O
our	O
knowledge	O
,	O
this	O
is	O
the	O
first	O
report	O
of	O
H3K9cr	B-protein_type
occurring	O
in	O
yeast	B-taxonomy_domain
.	O

We	O
next	O
asked	O
if	O
H3K9cr	B-protein_type
is	O
regulated	O
by	O
the	O
actions	O
of	O
histone	B-protein_type
acetyltransferases	I-protein_type
(	O
HATs	B-protein_type
)	O
and	O
histone	B-protein_type
deacetylases	I-protein_type
(	O
HDACs	B-protein_type
).	O

Towards	O
this	O
end	O
,	O
we	O
probed	O
extracts	O
derived	O
from	O
yeast	B-taxonomy_domain
cells	O
in	O
which	O
major	O
yeast	B-taxonomy_domain
HATs	B-protein_type
(	O
HAT1	B-protein
,	O
Gcn5	B-protein
,	O
and	O
Rtt109	B-protein
)	O
or	O
HDACs	B-protein_type
(	O
Rpd3	B-protein
,	O
Hos1	B-protein
,	O
and	O
Hos2	B-protein
)	O
were	O
deleted	B-experimental_method
.	O

As	O
shown	O
in	O
Figure	O
2a	O
,	O
b	O
and	O
Supplementary	O
Fig	O
.	O
3e	O
,	O
H3K9cr	B-protein_type
levels	O
were	O
abolished	O
or	O
reduced	O
considerably	O
in	O
the	O
HAT	B-protein_type
deletion	B-experimental_method
strains	O
,	O
whereas	O
they	O
were	O
dramatically	O
increased	O
in	O
the	O
HDAC	B-protein_type
deletion	B-experimental_method
strains	O
.	O

Furthermore	O
,	O
fluctuations	O
in	O
the	O
H3K9cr	B-protein_type
levels	O
were	O
more	O
substantial	O
than	O
fluctuations	O
in	O
the	O
corresponding	O
H3K9ac	B-protein_type
levels	O
.	O

Together	O
,	O
these	O
results	O
reveal	O
that	O
H3K9cr	B-protein_type
is	O
a	O
dynamic	O
mark	O
of	O
chromatin	O
in	O
yeast	B-taxonomy_domain
and	O
suggest	O
an	O
important	O
role	O
for	O
this	O
modification	O
in	O
transcription	O
as	O
it	O
is	O
regulated	O
by	O
HATs	B-protein_type
and	O
HDACs	B-protein_type
.	O

We	O
have	O
previously	O
shown	O
that	O
among	O
acetylated	B-protein_state
histone	B-protein_type
marks	O
,	O
the	O
Taf14	B-protein
YEATS	B-structure_element
domain	I-structure_element
prefers	O
acetylated	B-protein_state
H3K9	B-protein_type
(	O
also	O
see	O
Supplementary	O
Fig	O
.	O
3b	O
),	O
however	O
it	O
binds	O
to	O
H3K9cr	B-protein_type
tighter	O
.	O

The	O
selectivity	O
of	O
Taf14	B-protein
towards	O
crotonyllysine	B-residue_name
was	O
substantiated	O
by	O
1H	B-experimental_method
,	I-experimental_method
15N	I-experimental_method
HSQC	I-experimental_method
experiments	O
,	O
in	O
which	O
either	O
H3K9cr5	B-chemical
-	I-chemical
13	I-chemical
or	O
H3K9ac5	B-chemical
-	I-chemical
13	I-chemical
peptide	O
was	O
titrated	B-experimental_method
into	O
the	O
15N	B-protein_state
-	I-protein_state
labeled	I-protein_state
Taf14	B-protein
YEATS	B-structure_element
domain	I-structure_element
(	O
Fig	O
.	O
2c	O
and	O
Supplementary	O
Fig	O
.	O
4a	O
,	O
b	O
).	O

Binding	O
of	O
H3K9cr	B-protein_type
induced	O
resonance	B-evidence
changes	I-evidence
in	O
slow	O
exchange	O
regime	O
on	O
the	O
NMR	B-experimental_method
time	O
scale	O
,	O
indicative	O
of	O
strong	O
interaction	O
.	O

In	O
contrast	O
,	O
binding	O
of	O
H3K9ac	B-protein_type
resulted	O
in	O
an	O
intermediate	O
exchange	O
,	O
which	O
is	O
characteristic	O
of	O
a	O
weaker	O
association	O
.	O

Furthermore	O
,	O
crosspeaks	B-evidence
of	O
Gly80	B-residue_name_number
and	O
Trp81	B-residue_name_number
of	O
the	O
YEATS	B-structure_element
domain	I-structure_element
were	O
uniquely	O
perturbed	O
by	O
H3K9cr	B-protein_type
and	O
H3K9ac	B-protein_type
,	O
indicating	O
a	O
different	O
chemical	O
environment	O
in	O
the	O
respective	O
crotonyllysine	B-site
and	I-site
acetyllysine	I-site
binding	I-site
pockets	I-site
(	O
Supplementary	O
Fig	O
.	O
4a	O
).	O

These	O
differences	O
support	O
our	O
model	O
that	O
Trp81	B-residue_name_number
adopts	O
two	O
conformations	O
upon	O
complex	O
formation	O
with	O
the	O
H3K9cr	B-protein_type
mark	O
as	O
compared	O
to	O
H3K9ac	B-protein_type
(	O
Supplementary	O
Figs	O
.	O
1c	O
,	O
d	O
and	O
4c	O
).	O

One	O
of	O
the	O
conformations	O
,	O
characterized	O
by	O
the	O
π	O
stacking	O
involving	O
two	O
aromatic	O
residues	O
and	O
the	O
alkene	O
group	O
,	O
is	O
observed	O
only	O
in	O
the	O
YEATS	B-complex_assembly
-	I-complex_assembly
H3K9cr	I-complex_assembly
complex	O
.	O

To	O
establish	O
whether	O
the	O
Taf14	B-protein
YEATS	B-structure_element
domain	I-structure_element
is	O
able	O
to	O
recognize	O
other	O
recently	O
identified	O
acyllysine	B-residue_name
marks	O
,	O
we	O
performed	O
solution	B-experimental_method
pull	I-experimental_method
-	I-experimental_method
down	I-experimental_method
assays	I-experimental_method
using	O
H3	B-protein_type
peptides	O
acetylated	B-protein_state
,	O
propionylated	B-protein_state
,	O
butyrylated	B-protein_state
,	O
and	O
crotonylated	B-protein_state
at	O
lysine	B-residue_name_number
9	I-residue_name_number
(	O
residues	O
1	B-residue_range
–	I-residue_range
20	I-residue_range
of	O
H3	B-protein_type
).	O

As	O
shown	O
in	O
Figure	O
2d	O
and	O
Supplementary	O
Fig	O
.	O
5a	O
,	O
the	O
Taf14	B-protein
YEATS	B-structure_element
domain	I-structure_element
binds	O
more	O
strongly	O
to	O
H3K9cr1	B-chemical
-	I-chemical
20	I-chemical
,	O
as	O
compared	O
to	O
other	O
acylated	B-protein_state
histone	O
peptides	O
.	O

The	O
preference	O
for	O
H3K9cr	B-protein_type
over	O
H3K9ac	B-protein_type
,	O
H3K9pr	B-protein_type
and	O
H3K9bu	B-protein_type
was	O
supported	O
by	O
1H	B-experimental_method
,	I-experimental_method
15N	I-experimental_method
HSQC	I-experimental_method
titration	I-experimental_method
experiments	I-experimental_method
.	O

Addition	O
of	O
H3K9ac1	B-chemical
-	I-chemical
20	I-chemical
,	O
H3K9pr1	B-chemical
-	I-chemical
20	I-chemical
,	O
and	O
H3K9bu1	B-chemical
-	I-chemical
20	I-chemical
peptides	O
caused	O
chemical	B-evidence
shift	I-evidence
perturbations	I-evidence
in	O
the	O
Taf14	B-protein
YEATS	B-structure_element
domain	I-structure_element
in	O
intermediate	O
exchange	O
regime	O
,	O
implying	O
that	O
these	O
interactions	O
are	O
weaker	O
compared	O
to	O
the	O
interaction	O
with	O
the	O
H3K9cr1	B-chemical
-	I-chemical
20	I-chemical
peptide	O
(	O
Supplementary	O
Fig	O
.	O
5b	O
).	O

We	O
concluded	O
that	O
H3K9cr	B-protein_type
is	O
the	O
preferred	O
target	O
of	O
this	O
domain	O
.	O

From	O
comparative	B-experimental_method
structural	I-experimental_method
analysis	I-experimental_method
of	O
the	O
YEATS	O
complexes	O
,	O
Gly80	B-residue_name_number
emerged	O
as	O
candidate	O
residue	O
potentially	O
responsible	O
for	O
the	O
preference	O
for	O
crotonyllysine	B-residue_name
.	O

In	O
attempt	O
to	O
generate	O
a	O
mutant	O
capable	O
of	O
accommodating	O
a	O
short	O
acetyl	O
moiety	O
but	O
discriminating	O
against	O
a	O
longer	O
,	O
planar	O
crotonyl	O
moiety	O
,	O
we	O
mutated	B-protein_state
Gly80	B-residue_name_number
to	O
more	O
bulky	O
residues	O
,	O
however	O
all	O
mutants	B-protein_state
of	I-protein_state
Gly80	B-residue_name_number
lost	O
their	O
binding	O
activities	O
towards	O
either	O
acylated	B-protein_state
peptide	O
,	O
suggesting	O
that	O
Gly80	B-residue_name_number
is	O
absolutely	O
required	O
for	O
the	O
interaction	O
.	O

In	O
contrast	O
,	O
mutation	B-experimental_method
of	O
Val24	B-residue_name_number
,	O
a	O
residue	O
located	O
on	O
another	O
side	O
of	O
Trp81	B-residue_name_number
,	O
had	O
no	O
effect	O
on	O
binding	O
(	O
Fig	O
.	O
2d	O
and	O
Supplementary	O
Fig	O
.	O
5a	O
,	O
c	O
).	O

To	O
determine	O
if	O
the	O
binding	O
to	O
crotonyllysine	B-residue_name
is	O
conserved	B-protein_state
,	O
we	O
tested	O
human	B-species
YEATS	B-structure_element
domains	I-structure_element
by	O
pull	B-experimental_method
-	I-experimental_method
down	I-experimental_method
experiments	I-experimental_method
using	O
singly	O
and	O
multiply	O
acetylated	B-protein_state
,	O
propionylated	B-protein_state
,	O
butyrylated	B-protein_state
,	O
and	O
crotonylated	B-protein_state
histone	B-protein_type
peptides	O
(	O
Supplementary	O
Fig	O
.	O
6	O
).	O

We	O
found	O
that	O
all	O
YEATS	B-structure_element
domains	I-structure_element
tested	O
are	O
capable	O
of	O
binding	O
to	O
crotonyllysine	B-residue_name
peptides	O
,	O
though	O
they	O
display	O
variable	O
preferences	O
for	O
the	O
acyl	O
moieties	O
.	O

While	O
YEATS2	B-protein
and	O
ENL	B-protein
showed	O
selectivity	O
for	O
the	O
crotonylated	B-protein_state
peptides	O
,	O
GAS41	B-protein
and	O
AF9	B-protein
bound	O
acylated	B-protein_state
peptides	O
almost	O
equally	O
well	O
.	O

Unlike	O
the	O
YEATS	B-structure_element
domain	I-structure_element
,	O
a	O
known	O
acetyllysine	B-protein_type
reader	I-protein_type
,	O
bromodomain	B-structure_element
,	O
does	O
not	O
recognize	O
crotonyllysine	B-residue_name
.	O

We	O
assayed	O
a	O
large	O
set	O
of	O
BDs	B-structure_element
in	O
pull	B-experimental_method
-	I-experimental_method
down	I-experimental_method
experiments	I-experimental_method
and	O
found	O
that	O
this	O
module	O
is	O
highly	O
specific	O
for	O
acetyllysine	B-residue_name
and	O
propionyllysine	B-residue_name
containing	O
peptides	O
(	O
Supplementary	O
Fig	O
.	O
7	O
).	O

However	O
,	O
bromodomains	B-structure_element
did	O
not	O
interact	O
(	O
or	O
associated	O
very	O
weakly	O
)	O
with	O
longer	O
acyl	O
modifications	O
,	O
including	O
crotonyllysine	B-residue_name
,	O
as	O
in	O
the	O
case	O
of	O
BDs	B-structure_element
of	O
TAF1	B-protein
and	O
BRD2	B-protein
,	O
supporting	O
recent	O
reports	O
.	O

These	O
results	O
demonstrate	O
that	O
the	O
YEATS	B-structure_element
domain	I-structure_element
is	O
currently	O
the	O
sole	O
reader	O
of	O
crotonyllysine	B-residue_name
.	O

In	O
conclusion	O
,	O
we	O
have	O
identified	O
the	O
YEATS	B-structure_element
domain	I-structure_element
of	O
Taf14	B-protein
as	O
the	O
first	O
reader	O
of	O
histone	B-protein_type
crotonylation	B-ptm
.	O

We	O
further	O
demonstrate	O
that	O
H3K9cr	B-protein_type
exists	O
in	O
yeast	B-taxonomy_domain
and	O
is	O
dynamically	O
regulated	O
by	O
HATs	B-protein_type
and	O
HDACs	B-protein_type
.	O

As	O
we	O
previously	O
showed	O
the	O
importance	O
of	O
acyllysine	B-residue_name
binding	O
by	O
the	O
Taf14	B-protein
YEATS	B-structure_element
domain	I-structure_element
for	O
the	O
DNA	O
damage	O
response	O
and	O
gene	O
transcription	O
,	O
it	O
will	O
be	O
essential	O
in	O
the	O
future	O
to	O
define	O
the	O
physiological	O
role	O
of	O
crotonyllysine	B-residue_name
recognition	O
and	O
to	O
differentiate	O
the	O
activities	O
of	O
Taf14	B-protein
that	O
are	O
due	O
to	O
binding	O
to	O
crotonyllysine	B-residue_name
and	O
acetyllysine	B-residue_name
modifications	O
.	O

Furthermore	O
,	O
the	O
functional	O
significance	O
of	O
crotonyllysine	B-residue_name
recognition	O
by	O
other	O
YEATS	B-protein_type
proteins	O
will	O
be	O
of	O
great	O
importance	O
to	O
elucidate	O
and	O
compare	O
.	O

The	O
structural	O
mechanism	O
for	O
the	O
recognition	O
of	O
H3K9cr	B-protein_type

(	O
a	O
)	O
Chemical	O
structure	O
of	O
crotonyllysine	B-residue_name
.	O
(	O
b	O
)	O
The	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
Taf14	B-protein
YEATS	B-structure_element
domain	I-structure_element
(	O
wheat	O
)	O
in	B-protein_state
complex	I-protein_state
with	I-protein_state
the	O
H3K9cr5	B-chemical
-	I-chemical
13	I-chemical
peptide	O
(	O
green	O
).	O
(	O
c	O
)	O
H3K9cr	B-protein_type
is	O
stabilized	O
via	O
an	O
extensive	O
network	O
of	O
intermolecular	O
electrostatic	O
and	O
polar	O
interactions	O
with	O
the	O
Taf14	B-protein
YEATS	B-structure_element
domain	I-structure_element
.	O

(	O
d	O
)	O
The	O
π	O
-	O
π	O
-	O
π	O
stacking	O
mechanism	O
involving	O
the	O
alkene	O
moiety	O
of	O
crotonyllysine	B-residue_name
.	O

H3K9cr	B-protein_type
is	O
a	O
selective	O
target	O
of	O
the	O
Taf14	B-protein
YEATS	B-structure_element
domain	I-structure_element

(	O
a	O
,	O
b	O
)	O
Western	B-experimental_method
blot	I-experimental_method
analysis	O
comparing	O
the	O
levels	O
of	O
H3K9cr	B-protein_type
and	O
H3K9ac	B-protein_type
in	O
wild	B-protein_state
type	I-protein_state
(	O
WT	B-protein_state
),	O
HAT	O
deletion	O
,	O
or	O
HDAC	B-protein_type
deletion	B-experimental_method
yeast	B-taxonomy_domain
strains	O
.	O

Total	O
H3	B-protein_type
was	O
used	O
as	O
a	O
loading	O
control	O
.	O

(	O
c	O
)	O
Superimposed	O
1H	B-experimental_method
,	I-experimental_method
15N	I-experimental_method
HSQC	I-experimental_method
spectra	B-evidence
of	O
Taf14	B-protein
YEATS	B-structure_element
recorded	O
as	O
H3K9cr5	B-chemical
-	I-chemical
13	I-chemical
and	O
H3K9ac5	B-chemical
-	I-chemical
13	I-chemical
peptides	O
were	O
titrated	B-experimental_method
in	O
.	O

Spectra	B-evidence
are	O
color	O
coded	O
according	O
to	O
the	O
protein	O
:	O
peptide	O
molar	O
ratio	O
.	O

(	O
d	O
)	O
Western	B-experimental_method
blot	I-experimental_method
analyses	O
of	O
peptide	B-experimental_method
pull	I-experimental_method
-	I-experimental_method
down	I-experimental_method
assays	I-experimental_method
using	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
and	O
mutated	B-protein_state
Taf14	B-protein
YEATS	B-structure_element
domains	I-structure_element
and	O
indicated	O
peptides	O
.	O

A	O
unified	O
mechanism	O
for	O
proteolysis	O
and	O
autocatalytic	B-ptm
activation	I-ptm
in	O
the	O
20S	B-complex_assembly
proteasome	I-complex_assembly

Biogenesis	O
of	O
the	O
20S	B-complex_assembly
proteasome	I-complex_assembly
is	O
tightly	O
regulated	O
.	O

The	O
N	O
-	O
terminal	O
propeptides	B-structure_element
protecting	O
the	O
active	B-site
-	I-site
site	I-site
threonines	B-residue_name
are	O
autocatalytically	B-ptm
released	O
only	O
on	O
completion	O
of	O
assembly	O
.	O

However	O
,	O
the	O
trigger	O
for	O
the	O
self	O
-	O
activation	O
and	O
the	O
reason	O
for	O
the	O
strict	B-protein_state
conservation	I-protein_state
of	O
threonine	B-residue_name
as	O
the	O
active	O
site	O
nucleophile	O
remain	O
enigmatic	O
.	O

Here	O
we	O
use	O
mutagenesis	B-experimental_method
,	O
X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
and	O
biochemical	B-experimental_method
assays	I-experimental_method
to	O
suggest	O
that	O
Lys33	B-residue_name_number
initiates	O
nucleophilic	O
attack	O
of	O
the	O
propeptide	B-structure_element
by	O
deprotonating	O
the	O
Thr1	B-residue_name_number
hydroxyl	O
group	O
and	O
that	O
both	O
residues	O
together	O
with	O
Asp17	B-residue_name_number
are	O
part	O
of	O
a	O
catalytic	B-site
triad	I-site
.	O

Substitution	B-experimental_method
of	O
Thr1	B-residue_name_number
by	O
Cys	B-residue_name
disrupts	O
the	O
interaction	O
with	O
Lys33	B-residue_name_number
and	O
inactivates	B-protein_state
the	O
proteasome	B-complex_assembly
.	O

Although	O
a	O
Thr1Ser	B-mutant
mutant	B-protein_state
is	O
active	B-protein_state
,	O
it	O
is	O
less	O
efficient	O
compared	O
with	O
wild	B-protein_state
type	I-protein_state
because	O
of	O
the	O
unfavourable	O
orientation	O
of	O
Ser1	B-residue_name_number
towards	O
incoming	O
substrates	O
.	O

This	O
work	O
provides	O
insights	O
into	O
the	O
basic	O
mechanism	O
of	O
proteolysis	O
and	O
propeptide	B-ptm
autolysis	I-ptm
,	O
as	O
well	O
as	O
the	O
evolutionary	O
pressures	O
that	O
drove	O
the	O
proteasome	B-complex_assembly
to	O
become	O
a	O
threonine	B-protein_type
protease	I-protein_type
.	O

The	O
proteasome	B-complex_assembly
,	O
an	O
essential	O
molecular	O
machine	O
,	O
is	O
a	O
threonine	B-protein_type
protease	I-protein_type
,	O
but	O
the	O
evolution	O
and	O
the	O
components	O
of	O
its	O
proteolytic	O
centre	O
are	O
unclear	O
.	O

Here	O
,	O
the	O
authors	O
use	O
structural	O
biology	O
and	O
biochemistry	O
to	O
investigate	O
the	O
role	O
of	O
proteasome	B-complex_assembly
active	B-site
site	I-site
residues	O
on	O
maturation	O
and	O
activity	O
.	O

The	O
20S	B-complex_assembly
proteasome	I-complex_assembly
core	I-complex_assembly
particle	I-complex_assembly
(	O
CP	B-complex_assembly
)	O
is	O
the	O
key	O
non	B-protein_type
-	I-protein_type
lysosomal	I-protein_type
protease	I-protein_type
of	O
eukaryotic	B-taxonomy_domain
cells	O
.	O

Its	O
seven	O
different	O
α	B-protein
and	O
seven	O
different	O
β	B-protein
subunits	I-protein
assemble	O
into	O
four	O
heptameric	B-oligomeric_state
rings	B-structure_element
that	O
are	O
stacked	O
on	O
each	O
other	O
to	O
form	O
a	O
hollow	B-structure_element
cylinder	I-structure_element
.	O

While	O
the	O
inactive	B-protein_state
α	B-protein
subunits	I-protein
build	O
the	O
two	O
outer	O
rings	B-structure_element
,	O
the	O
β	B-protein
subunits	I-protein
form	O
the	O
inner	O
rings	B-structure_element
.	O

Only	O
three	O
out	O
of	O
the	O
seven	O
different	O
β	B-protein
subunits	I-protein
,	O
namely	O
β1	B-protein
,	O
β2	B-protein
and	O
β5	B-protein
,	O
bear	O
N	O
-	O
terminal	O
proteolytic	B-site
active	I-site
centres	I-site
,	O
and	O
before	O
CP	B-complex_assembly
maturation	O
these	O
are	O
protected	O
by	O
propeptides	B-structure_element
.	O

In	O
the	O
last	O
stage	O
of	O
CP	B-complex_assembly
biogenesis	O
,	O
the	O
prosegments	B-structure_element
are	O
autocatalytically	B-ptm
removed	I-ptm
through	O
nucleophilic	O
attack	O
by	O
the	O
active	B-site
site	I-site
residue	I-site
Thr1	B-residue_name_number
on	O
the	O
preceding	O
peptide	O
bond	O
involving	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
).	I-residue_name_number

Release	O
of	O
the	O
propeptides	B-structure_element
creates	O
a	O
functionally	O
active	B-protein_state
CP	B-complex_assembly
that	O
cleaves	O
proteins	O
into	O
short	O
peptides	O
.	O

Although	O
the	O
chemical	O
nature	O
of	O
the	O
substrate	B-site
-	I-site
binding	I-site
channel	I-site
and	O
hence	O
substrate	O
preferences	O
are	O
unique	O
to	O
each	O
of	O
the	O
distinct	O
active	B-protein_state
β	B-protein
subunits	I-protein
,	O
all	O
active	B-site
sites	I-site
employ	O
an	O
identical	O
reaction	O
mechanism	O
to	O
hydrolyse	O
peptide	O
bonds	O
.	O

Nucleophilic	O
attack	O
of	O
Thr1Oγ	B-residue_name_number
on	O
the	O
carbonyl	O
carbon	O
atom	O
of	O
the	O
scissile	O
peptide	O
bond	O
creates	O
a	O
first	O
cleavage	O
product	O
and	O
a	O
covalent	O
acyl	O
-	O
enzyme	O
intermediate	O
.	O

Hydrolysis	O
of	O
this	O
complex	B-complex_assembly
by	O
the	O
addition	O
of	O
a	O
nucleophilic	O
water	B-chemical
molecule	O
regenerates	O
the	O
enzyme	B-complex_assembly
and	O
releases	O
the	O
second	O
peptide	B-chemical
fragment	O
.	O

The	O
proteasome	B-complex_assembly
belongs	O
to	O
the	O
family	O
of	O
N	B-protein_type
-	I-protein_type
terminal	I-protein_type
nucleophilic	I-protein_type
(	I-protein_type
Ntn	I-protein_type
)	I-protein_type
hydrolases	I-protein_type
,	O
and	O
the	O
free	B-protein_state
N	O
-	O
terminal	O
amine	O
group	O
of	O
Thr1	B-residue_name_number
was	O
proposed	O
to	O
deprotonate	O
the	O
Thr1	B-residue_name_number
hydroxyl	O
group	O
to	O
generate	O
a	O
nucleophilic	O
Thr1Oγ	B-residue_name_number
for	O
peptide	O
-	O
bond	O
cleavage	O
.	O

This	O
mechanism	O
,	O
however	O
,	O
cannot	O
explain	O
autocatalytic	B-ptm
precursor	I-ptm
processing	I-ptm
because	O
in	O
the	O
immature	B-protein_state
active	B-site
sites	I-site
,	O
Thr1N	B-residue_name_number
is	O
part	O
of	O
the	O
peptide	O
bond	O
with	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
),	I-residue_name_number
the	O
bond	O
that	O
needs	O
to	O
be	O
hydrolysed	O
.	O

An	O
alternative	O
candidate	O
for	O
deprotonating	O
the	O
Thr1	B-residue_name_number
hydroxyl	O
group	O
is	O
the	O
side	O
chain	O
of	O
Lys33	B-residue_name_number
as	O
it	O
is	O
within	O
hydrogen	O
-	O
bonding	O
distance	O
to	O
Thr1OH	B-residue_name_number
(	O
2	O
.	O
7	O
Å	O
).	O

In	O
principle	O
it	O
could	O
function	O
as	O
the	O
general	O
base	O
during	O
both	O
autocatalytic	B-ptm
removal	I-ptm
of	O
the	O
propeptide	B-structure_element
and	O
protein	O
substrate	O
cleavage	O
.	O

Here	O
we	O
provide	O
experimental	O
evidences	O
for	O
this	O
distinct	O
view	O
of	O
the	O
proteasome	B-complex_assembly
active	B-site
-	I-site
site	I-site
mechanism	O
.	O

Data	O
from	O
biochemical	B-experimental_method
and	I-experimental_method
structural	I-experimental_method
analyses	I-experimental_method
of	O
proteasome	O
variants	O
with	O
mutations	O
in	O
the	O
β5	B-protein
propeptide	B-structure_element
and	O
the	O
active	B-site
site	I-site
strongly	O
support	O
the	O
model	O
and	O
deliver	O
novel	O
insights	O
into	O
the	O
structural	O
constraints	O
required	O
for	O
the	O
autocatalytic	B-ptm
activation	I-ptm
of	O
the	O
proteasome	B-complex_assembly
.	O

Furthermore	O
,	O
we	O
determine	O
the	O
advantages	O
of	O
Thr	B-residue_name
over	O
Cys	B-residue_name
or	O
Ser	B-residue_name
as	O
the	O
active	O
-	O
site	O
nucleophile	O
using	O
X	B-experimental_method
-	I-experimental_method
ray	I-experimental_method
crystallography	I-experimental_method
together	O
with	O
activity	B-experimental_method
and	I-experimental_method
inhibition	I-experimental_method
assays	I-experimental_method
.	O

Inactivation	O
of	O
proteasome	B-complex_assembly
subunits	B-protein
by	O
T1A	B-mutant
mutations	B-experimental_method

Proteasome	B-complex_assembly
-	O
mediated	O
degradation	O
of	O
cell	O
-	O
cycle	O
regulators	O
and	O
potentially	O
toxic	O
misfolded	O
proteins	O
is	O
required	O
for	O
the	O
viability	O
of	O
eukaryotic	B-taxonomy_domain
cells	O
.	O

Inactivation	O
of	O
the	O
active	B-site
site	I-site
Thr1	B-residue_name_number
by	O
mutation	B-experimental_method
to	I-experimental_method
Ala	B-residue_name
has	O
been	O
used	O
to	O
study	O
substrate	O
specificity	O
and	O
the	O
hierarchy	O
of	O
the	O
proteasome	B-complex_assembly
active	B-site
sites	I-site
.	O

Yeast	B-taxonomy_domain
strains	O
carrying	O
the	O
single	O
mutations	O
β1	B-mutant
-	I-mutant
T1A	I-mutant
or	O
β2	B-mutant
-	I-mutant
T1A	I-mutant
,	O
or	O
both	O
,	O
are	O
viable	O
,	O
even	O
though	O
one	O
or	O
two	O
of	O
the	O
three	O
distinct	O
catalytic	B-protein_state
β	B-protein
subunits	I-protein
are	O
disabled	B-protein_state
and	O
carry	B-protein_state
remnants	I-protein_state
of	I-protein_state
their	O
N	O
-	O
terminal	O
propeptides	B-structure_element
(	O
Table	O
1	O
).	O

These	O
results	O
indicate	O
that	O
the	O
β1	B-protein
and	O
β2	B-protein
proteolytic	O
activities	O
are	O
not	O
essential	O
for	O
cell	O
survival	O
.	O

By	O
contrast	O
,	O
the	O
T1A	B-mutant
mutation	O
in	O
subunit	O
β5	B-protein
has	O
been	O
reported	O
to	O
be	O
lethal	O
or	O
nearly	O
so	O
.	O

Viability	O
is	O
restored	O
if	O
the	O
β5	B-mutant
-	I-mutant
T1A	I-mutant
subunit	O
has	O
its	O
propeptide	B-structure_element
(	O
pp	B-chemical
)	O
deleted	B-experimental_method
but	I-experimental_method
expressed	I-experimental_method
separately	I-experimental_method
in	O
trans	B-protein_state
(	O
β5	B-mutant
-	I-mutant
T1A	I-mutant
pp	B-chemical
trans	B-protein_state
),	O
although	O
substantial	O
phenotypic	O
impairment	O
remains	O
(	O
Table	O
1	O
).	O

Our	O
present	O
crystallographic	B-experimental_method
analysis	I-experimental_method
of	O
the	O
β5	B-mutant
-	I-mutant
T1A	I-mutant
pp	B-chemical
trans	B-protein_state
mutant	B-protein_state
demonstrates	O
that	O
the	O
mutation	B-experimental_method
per	O
se	O
does	O
not	O
structurally	O
alter	O
the	O
catalytic	B-site
active	I-site
site	I-site
and	O
that	O
the	O
trans	B-experimental_method
-	I-experimental_method
expressed	I-experimental_method
β5	B-protein
propeptide	B-structure_element
is	O
not	B-protein_state
bound	I-protein_state
in	O
the	O
β5	B-protein
substrate	B-site
-	I-site
binding	I-site
channel	I-site
(	O
Supplementary	O
Fig	O
.	O
1a	O
).	O

The	O
extremely	O
weak	O
growth	O
of	O
the	O
β5	B-mutant
-	I-mutant
T1A	I-mutant
mutant	B-protein_state
pp	B-chemical
cis	B-protein_state
described	O
by	O
Chen	O
and	O
Hochstrasser	O
compared	O
with	O
the	O
inviability	O
reported	O
by	O
Heinemeyer	O
et	O
al	O
.	O
prompted	O
us	O
to	O
analyse	O
this	O
discrepancy	O
.	O

Sequencing	B-experimental_method
of	I-experimental_method
the	I-experimental_method
plasmids	I-experimental_method
,	O
testing	O
them	O
in	O
both	O
published	O
yeast	B-taxonomy_domain
strain	O
backgrounds	O
and	O
site	B-experimental_method
-	I-experimental_method
directed	I-experimental_method
mutagenesis	I-experimental_method
revealed	O
that	O
the	O
β5	B-mutant
-	I-mutant
T1A	I-mutant
mutant	B-protein_state
pp	B-chemical
cis	B-protein_state
is	O
viable	O
,	O
but	O
suffers	O
from	O
a	O
marked	O
growth	O
defect	O
that	O
requires	O
extended	O
incubation	O
of	O
4	O
–	O
5	O
days	O
for	O
initial	O
colony	O
formation	O
(	O
Table	O
1	O
and	O
Supplementary	O
Methods	O
).	O

We	O
also	O
identified	O
an	O
additional	O
point	O
mutation	O
K81R	B-mutant
in	O
subunit	O
β5	B-protein
that	O
was	O
present	O
in	O
the	O
allele	O
used	O
in	O
ref	O
..	O
This	B-experimental_method
single	I-experimental_method
amino	I-experimental_method
-	I-experimental_method
acid	I-experimental_method
exchange	I-experimental_method
is	O
located	O
at	O
the	O
interface	B-site
of	O
the	O
subunits	O
α4	B-protein
,	O
β4	B-protein
and	O
β5	B-protein
(	O
Supplementary	O
Fig	O
.	O
1b	O
)	O
and	O
might	O
weakly	O
promote	O
CP	B-complex_assembly
assembly	O
by	O
enhancing	O
inter	O
-	O
subunit	O
contacts	O
.	O

The	O
slightly	O
better	O
growth	O
of	O
the	O
β5	B-mutant
-	I-mutant
T1A	I-mutant
-	I-mutant
K81R	I-mutant
mutant	B-protein_state
allowed	O
us	O
to	O
solve	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
a	O
yeast	B-taxonomy_domain
proteasome	B-complex_assembly
(	O
yCP	B-complex_assembly
)	O
with	O
the	O
β5	B-mutant
-	I-mutant
T1A	I-mutant
mutation	O
,	O
which	O
is	O
discussed	O
in	O
the	O
following	O
section	O
(	O
for	O
details	O
see	O
Supplementary	O
Note	O
1	O
).	O

Propeptide	B-structure_element
conformation	O
and	O
triggering	O
of	O
autolysis	B-ptm

In	O
the	O
final	O
steps	O
of	O
proteasome	B-complex_assembly
biogenesis	O
,	O
the	O
propeptides	B-structure_element
are	O
autocatalytically	B-ptm
cleaved	I-ptm
from	O
the	O
mature	B-protein_state
β	B-protein
-	I-protein
subunit	I-protein
domains	I-protein
.	O

For	O
subunit	O
β1	B-protein
,	O
this	O
process	O
was	O
previously	O
inferred	O
to	O
require	O
that	O
the	O
propeptide	B-structure_element
residue	O
at	O
position	O
(-	B-residue_number
2	I-residue_number
)	I-residue_number
of	O
the	O
subunit	O
precursor	O
occupies	O
the	O
S1	B-site
specificity	I-site
pocket	I-site
of	O
the	O
substrate	B-site
-	I-site
binding	I-site
channel	I-site
formed	O
by	O
amino	O
acid	O
45	B-residue_number
(	O
for	O
details	O
see	O
Supplementary	O
Note	O
2	O
).	O

Furthermore	O
,	O
it	O
was	O
observed	O
that	O
the	O
prosegment	B-structure_element
forms	O
an	O
antiparallel	B-structure_element
β	I-structure_element
-	I-structure_element
sheet	I-structure_element
in	O
the	O
active	B-site
site	I-site
,	O
and	O
that	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
adopts	O
a	O
γ	B-structure_element
-	I-structure_element
turn	I-structure_element
conformation	I-structure_element
,	O
which	O
by	O
definition	O
is	O
characterized	O
by	O
a	O
hydrogen	O
bond	O
between	O
Leu	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
O	O
and	O
Thr1NH	B-residue_name_number
(	O
ref	O
.).	O

Here	O
we	O
again	O
analysed	O
the	O
β1	B-mutant
-	I-mutant
T1A	I-mutant
mutant	B-protein_state
crystallographically	B-experimental_method
but	O
in	O
addition	O
determined	O
the	O
structures	B-evidence
of	O
the	O
β2	B-mutant
-	I-mutant
T1A	I-mutant
single	O
and	O
β1	B-mutant
-	I-mutant
T1A	I-mutant
-	I-mutant
β2	I-mutant
-	I-mutant
T1A	I-mutant
double	O
mutants	O
(	O
Protein	O
Data	O
Bank	O
(	O
PDB	O
)	O
entry	O
codes	O
are	O
provided	O
in	O
Supplementary	O
Table	O
1	O
).	O

In	O
subunit	O
β1	B-protein
,	O
we	O
found	O
that	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
indeed	O
forms	O
a	O
sharp	B-structure_element
turn	I-structure_element
,	O
which	O
relaxes	O
on	O
prosegment	B-ptm
cleavage	I-ptm
(	O
Fig	O
.	O
1a	O
and	O
Supplementary	O
Fig	O
.	O
2a	O
).	O

However	O
,	O
the	O
γ	B-structure_element
-	I-structure_element
turn	I-structure_element
conformation	I-structure_element
and	O
the	O
associated	O
hydrogen	O
bond	O
initially	O
proposed	O
is	O
for	O
geometric	O
and	O
chemical	O
reasons	O
inappropriate	O
and	O
would	O
not	O
perfectly	O
position	O
the	O
carbonyl	O
carbon	O
atom	O
of	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
for	O
nucleophilic	O
attack	O
by	O
Thr1	B-residue_name_number
.	O

Regarding	O
the	O
β2	B-protein
propeptide	B-structure_element
,	O
Thr	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
occupies	O
the	O
S1	B-site
pocket	I-site
but	O
is	O
less	O
deeply	O
anchored	O
compared	O
with	O
Leu	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
in	O
β1	B-protein
,	O
which	O
might	O
be	O
due	O
to	O
the	O
rather	O
large	O
β2	B-protein
-	O
S1	B-site
pocket	I-site
created	O
by	O
Gly45	B-residue_name_number
.	O

Thr	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
positions	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
O	O
via	O
hydrogen	O
bonding	O
(∼	O
2	O
.	O
8	O
Å	O
)	O
in	O
a	O
perfect	O
trajectory	O
for	O
the	O
nucleophilic	O
attack	O
by	O
Thr1Oγ	B-residue_name_number
(	O
Fig	O
.	O
1b	O
and	O
Supplementary	O
Fig	O
.	O
2b	O
).	O

Next	O
,	O
we	O
examined	O
the	O
position	O
of	O
the	O
β5	B-protein
propeptide	B-structure_element
in	O
the	O
β5	B-mutant
-	I-mutant
T1A	I-mutant
-	I-mutant
K81R	I-mutant
mutant	B-protein_state
.	O

Surprisingly	O
,	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
is	O
completely	O
extended	O
and	O
forces	O
the	O
histidine	B-residue_name
side	O
chain	O
at	O
position	O
(-	B-residue_number
2	I-residue_number
)	I-residue_number
to	O
occupy	O
the	O
S2	B-site
instead	O
of	O
the	O
S1	B-site
pocket	I-site
,	O
thereby	O
disrupting	O
the	O
antiparallel	B-structure_element
β	I-structure_element
-	I-structure_element
sheet	I-structure_element
.	O

Nonetheless	O
,	O
the	O
carbonyl	O
carbon	O
of	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
would	O
be	O
ideally	O
placed	O
for	O
nucleophilic	O
attack	O
by	O
Thr1Oγ	B-residue_name_number
(	O
Fig	O
.	O
1c	O
and	O
Supplementary	O
Fig	O
.	O
2c	O
,	O
d	O
).	O

As	O
the	O
K81R	B-mutant
mutation	O
is	O
located	O
far	O
from	O
the	O
active	B-site
site	I-site
(	O
Thr1Cα	B-residue_name_number
–	O
Arg81Cα	B-residue_name_number
:	O
24	O
Å	O
),	O
any	O
influence	O
on	O
propeptide	B-structure_element
conformation	O
can	O
be	O
excluded	O
.	O

Instead	O
,	O
the	O
plasticity	O
of	O
the	O
β5	B-protein
S1	B-site
pocket	I-site
caused	O
by	O
the	O
rotational	O
flexibility	O
of	O
Met45	B-residue_name_number
might	O
prevent	O
stable	O
accommodation	O
of	O
His	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
in	O
the	O
S1	B-site
site	I-site
and	O
thus	O
also	O
promote	O
its	O
immediate	O
release	O
after	O
autolysis	B-ptm
.	O

Processing	O
of	O
β	O
-	O
subunit	O
precursors	O
requires	O
deprotonation	O
of	O
Thr1OH	B-residue_name_number
;	O
however	O
,	O
the	O
general	O
base	O
initiating	O
autolysis	B-ptm
is	O
unknown	O
.	O

Remarkably	O
,	O
eukaryotic	B-taxonomy_domain
proteasomal	O
β5	B-protein
subunits	O
bear	O
a	O
His	B-residue_name
residue	O
in	O
position	O
(-	B-residue_number
2	I-residue_number
)	I-residue_number
of	O
the	O
propeptide	B-structure_element
(	O
Supplementary	O
Fig	O
.	O
3a	O
).	O

As	O
histidine	B-residue_name
commonly	O
functions	O
as	O
a	O
proton	O
shuttle	O
in	O
the	O
catalytic	B-site
triads	I-site
of	O
serine	B-protein_type
proteases	I-protein_type
,	O
we	O
investigated	O
the	O
role	O
of	O
His	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
in	O
processing	O
of	O
the	O
β5	B-protein
propeptide	B-structure_element
by	O
exchanging	B-experimental_method
it	I-experimental_method
for	I-experimental_method
Asn	B-residue_name
,	O
Lys	B-residue_name
,	O
Phe	B-residue_name
and	O
Ala	B-residue_name
.	O
All	O
yeast	B-taxonomy_domain
mutants	O
were	O
viable	O
at	O
30	O
°	O
C	O
,	O
but	O
suffered	O
from	O
growth	O
defects	O
at	O
37	O
°	O
C	O
with	O
the	O
H	B-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
N	I-mutant
and	O
H	B-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
F	I-mutant
mutants	O
being	O
most	O
affected	O
(	O
Supplementary	O
Fig	O
.	O
3b	O
and	O
Table	O
1	O
).	O

In	O
agreement	O
,	O
the	O
chymotrypsin	O
-	O
like	O
(	O
ChT	O
-	O
L	O
)	O
activity	O
of	O
H	B-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
N	I-mutant
and	O
H	B-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
F	I-mutant
mutant	B-protein_state
yCPs	B-complex_assembly
was	O
impaired	O
in	O
situ	O
and	O
in	O
vitro	O
(	O
Supplementary	O
Fig	O
.	O
3c	O
).	O

Structural	B-experimental_method
analyses	I-experimental_method
revealed	O
that	O
the	O
propeptides	B-structure_element
of	O
all	O
mutant	B-protein_state
yCPs	B-complex_assembly
shared	O
residual	O
2FO	B-evidence
–	I-evidence
FC	I-evidence
electron	I-evidence
densities	I-evidence
.	O

Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
and	O
Phe	B-residue_name
/	O
Lys	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
were	O
visualized	O
at	O
low	O
occupancy	O
,	O
while	O
Ala	B-residue_name
/	O
Asn	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
could	O
not	O
be	O
assigned	O
.	O

This	O
observation	O
indicates	O
a	O
mixture	O
of	O
processed	B-protein_state
and	O
unprocessed	B-protein_state
β5	B-protein
subunits	O
and	O
partially	O
impaired	O
autolysis	B-ptm
,	O
thereby	O
excluding	O
any	O
essential	O
role	O
of	O
residue	O
(-	B-residue_number
2	I-residue_number
)	I-residue_number
as	O
the	O
general	O
base	O
.	O

Next	O
,	O
we	O
examined	O
the	O
effect	O
of	O
residue	O
(-	B-residue_number
2	I-residue_number
)	I-residue_number
on	O
the	O
orientation	O
of	O
the	O
propeptide	B-structure_element
by	O
creating	B-experimental_method
mutants	I-experimental_method
that	I-experimental_method
combine	I-experimental_method
the	O
T1A	B-mutant
(	O
K81R	B-mutant
)	O
mutation	B-experimental_method
(	I-experimental_method
s	I-experimental_method
)	I-experimental_method
with	O
H	B-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
L	I-mutant
,	O
H	B-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
T	I-mutant
or	O
H	B-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
A	I-mutant
substitutions	B-experimental_method
.	O

Leu	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
is	O
encoded	O
in	O
the	O
yeast	B-taxonomy_domain
β1	B-protein
subunit	O
precursor	O
(	O
Supplementary	O
Fig	O
.	O
3a	O
);	O
Thr	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
is	O
generally	O
part	O
of	O
β2	B-protein
-	O
propeptides	B-structure_element
(	O
Supplementary	O
Fig	O
.	O
3a	O
);	O
and	O
Ala	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
was	O
expected	O
to	O
fit	O
the	O
β5	B-protein
-	O
S1	B-site
pocket	I-site
without	O
inducing	O
conformational	O
changes	O
of	O
Met45	B-residue_name_number
,	O
allowing	O
it	O
to	O
accommodate	O
‘	O
β1	O
-	O
like	O
'	O
propeptide	O
positioning	O
.	O

As	O
expected	O
from	O
β5	B-mutant
-	I-mutant
T1A	I-mutant
mutants	O
,	O
the	O
yeasts	B-taxonomy_domain
show	O
severe	O
growth	O
phenotypes	O
,	O
with	O
minor	O
variations	O
(	O
Supplementary	O
Fig	O
.	O
4a	O
and	O
Table	O
1	O
).	O

We	O
determined	O
crystal	B-evidence
structures	I-evidence
of	O
the	O
β5	B-mutant
-	I-mutant
H	I-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
L	I-mutant
-	I-mutant
T1A	I-mutant
,	O
β5	B-mutant
-	I-mutant
H	I-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
T	I-mutant
-	I-mutant
T1A	I-mutant
and	O
the	O
β5	B-mutant
-	I-mutant
H	I-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
A	I-mutant
-	I-mutant
T1A	I-mutant
-	I-mutant
K81R	I-mutant
mutants	O
(	O
Supplementary	O
Table	O
1	O
).	O

For	O
the	O
β5	B-mutant
-	I-mutant
H	I-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
A	I-mutant
-	I-mutant
T1A	I-mutant
-	I-mutant
K81R	I-mutant
variant	O
,	O
only	O
the	O
residues	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
and	O
Ala	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
could	O
be	O
visualized	O
,	O
indicating	O
that	O
Ala	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
leads	O
to	O
insufficient	O
stabilization	O
of	O
the	O
propeptide	B-structure_element
in	O
the	O
substrate	B-site
-	I-site
binding	I-site
channel	I-site
(	O
Supplementary	O
Fig	O
.	O
4d	O
).	O

By	O
contrast	O
,	O
the	O
prosegments	B-structure_element
of	O
the	O
β5	B-mutant
-	I-mutant
H	I-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
L	I-mutant
-	I-mutant
T1A	I-mutant
and	O
the	O
β5	B-mutant
-	I-mutant
H	I-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
T	I-mutant
-	I-mutant
T1A	I-mutant
mutants	O
were	O
significantly	O
better	O
resolved	O
in	O
the	O
2FO	B-evidence
–	I-evidence
FC	I-evidence
electron	I-evidence
-	I-evidence
density	I-evidence
maps	I-evidence
yet	O
not	O
at	O
full	O
occupancy	O
(	O
Supplementary	O
Fig	O
.	O
4b	O
,	O
c	O
and	O
Supplementary	O
Table	O
1	O
),	O
suggesting	O
that	O
the	O
natural	O
propeptide	B-structure_element
bearing	O
His	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
is	O
most	O
favourable	O
.	O

Nevertheless	O
,	O
both	O
Leu	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
and	O
Thr	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
were	O
found	O
to	O
occupy	O
the	O
S1	B-site
specificity	I-site
pocket	I-site
formed	O
by	O
Met45	B-residue_name_number
(	O
Fig	O
.	O
2a	O
,	O
b	O
and	O
Supplementary	O
Fig	O
.	O
4f	O
–	O
h	O
).	O

This	O
result	O
proves	O
that	O
the	O
naturally	O
occurring	O
His	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
of	O
the	O
β5	B-protein
propeptide	B-structure_element
does	O
not	O
stably	O
fit	O
into	O
the	O
S1	B-site
site	I-site
.	O

Since	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
adopts	O
the	O
same	O
position	O
in	O
both	O
wild	B-protein_state
-	I-protein_state
type	I-protein_state
(	O
WT	B-protein_state
)	O
and	O
mutant	B-protein_state
β5	B-protein
propeptides	B-structure_element
,	O
and	O
since	O
in	O
all	O
cases	O
its	O
carbonyl	O
carbon	O
is	O
perfectly	O
placed	O
for	O
nucleophilic	O
attack	O
by	O
Thr1Oγ	B-residue_name_number
(	O
Fig	O
.	O
2b	O
),	O
we	O
propose	O
that	O
neither	O
binding	O
of	O
residue	O
(-	B-residue_number
2	I-residue_number
)	I-residue_number
to	O
the	O
S1	B-site
pocket	I-site
nor	O
formation	O
of	O
the	O
antiparallel	B-structure_element
β	I-structure_element
-	I-structure_element
sheet	I-structure_element
is	O
essential	O
for	O
autolysis	B-ptm
of	O
the	O
propeptide	B-structure_element
.	O

Next	O
,	O
we	O
determined	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
a	O
chimeric	B-protein_state
yCP	B-complex_assembly
having	O
the	O
yeast	B-taxonomy_domain
β1	B-protein
-	O
propeptide	B-structure_element
replaced	B-experimental_method
by	I-experimental_method
its	O
β5	B-protein
counterpart	B-structure_element
.	O

Although	O
we	O
observed	O
fragments	O
of	O
2FO	B-evidence
–	I-evidence
FC	I-evidence
electron	I-evidence
density	I-evidence
in	O
the	O
β1	B-protein
active	B-site
site	I-site
,	O
the	O
data	O
were	O
not	O
interpretable	O
.	O

Bearing	O
in	O
mind	O
that	O
in	O
contrast	O
to	O
Thr	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
in	O
β2	B-protein
,	O
Leu	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
in	O
subunit	O
β1	B-protein
is	O
not	B-protein_state
conserved	I-protein_state
among	O
species	O
(	O
Supplementary	O
Fig	O
.	O
3a	O
),	O
we	O
created	B-experimental_method
a	O
β2	B-mutant
-	I-mutant
T	I-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
V	I-mutant
proteasome	B-complex_assembly
mutant	B-protein_state
.	O

As	O
proven	O
by	O
the	O
β2	B-mutant
-	I-mutant
T1A	I-mutant
crystal	B-evidence
structures	I-evidence
,	O
Thr	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
hydrogen	O
bonds	O
to	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
O	O
.	O
Although	O
this	O
interaction	O
was	O
not	O
observed	O
for	O
the	O
β5	B-mutant
-	I-mutant
H	I-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
T	I-mutant
-	I-mutant
T1A	I-mutant
mutant	B-protein_state
(	O
Fig	O
.	O
2c	O
and	O
Supplementary	O
Fig	O
.	O
4c	O
,	O
i	O
),	O
exchange	B-experimental_method
of	O
Thr	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
by	O
Val	B-residue_name
in	O
β2	B-protein
,	O
a	O
conservative	O
mutation	O
regarding	O
size	O
but	O
drastic	O
with	O
respect	O
to	O
polarity	O
,	O
was	O
found	O
to	O
inhibit	O
maturation	O
of	O
this	O
subunit	O
(	O
Fig	O
.	O
2d	O
and	O
Supplementary	O
Fig	O
.	O
4e	O
,	O
j	O
).	O

Notably	O
,	O
the	O
2FO	B-evidence
–	I-evidence
FC	I-evidence
electron	I-evidence
-	I-evidence
density	I-evidence
map	I-evidence
displays	O
a	O
different	O
orientation	O
for	O
the	O
β2	B-protein
propeptide	B-structure_element
than	O
has	O
been	O
observed	O
for	O
the	O
β2	B-mutant
-	I-mutant
T1A	I-mutant
proteasome	B-complex_assembly
.	O

In	O
particular	O
,	O
Val	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
is	O
displaced	O
from	O
the	O
S1	B-site
site	I-site
and	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
is	O
severely	O
shifted	O
(	O
movement	O
of	O
the	O
carbonyl	O
oxygen	O
atom	O
of	O
3	O
.	O
8	O
Å	O
),	O
thereby	O
preventing	O
nucleophilic	O
attack	O
of	O
Thr1	B-residue_name_number
(	O
Fig	O
.	O
2d	O
and	O
Supplementary	O
Fig	O
.	O
4j	O
,	O
k	O
).	O

These	O
results	O
further	O
confirm	O
that	O
correct	O
positioning	O
of	O
the	O
active	B-site
-	I-site
site	I-site
residues	I-site
and	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
is	O
decisive	O
for	O
the	O
maturation	O
of	O
the	O
proteasome	B-complex_assembly
.	O

The	O
active	B-site
site	I-site
of	O
the	O
proteasome	B-complex_assembly

Proton	O
shuttling	O
from	O
the	O
proteasomal	O
active	B-site
site	I-site
Thr1OH	B-residue_name_number
to	O
Thr1NH2	B-residue_name_number
via	O
a	O
nucleophilic	O
water	B-chemical
molecule	O
was	O
suggested	O
to	O
initiate	O
peptide	O
-	O
bond	O
hydrolysis	O
.	O

However	O
,	O
in	O
the	O
immature	B-protein_state
particle	B-complex_assembly
Thr1NH2	B-residue_name_number
is	O
blocked	O
by	O
the	O
propeptide	B-structure_element
and	O
cannot	O
activate	O
Thr1Oγ	B-residue_name_number
.	O

Instead	O
,	O
Lys33NH2	B-residue_name_number
,	O
which	O
is	O
in	O
hydrogen	O
-	O
bonding	O
distance	O
to	O
Thr1Oγ	B-residue_name_number
(	O
2	O
.	O
7	O
Å	O
)	O
in	O
all	O
catalytically	B-protein_state
active	I-protein_state
β	B-protein
subunits	I-protein
(	O
Fig	O
.	O
3a	O
,	O
b	O
),	O
was	O
proposed	O
to	O
serve	O
as	O
the	O
proton	O
acceptor	O
.	O

A	O
proposed	O
catalytic	B-site
tetrad	I-site
model	O
involving	O
Thr1OH	B-residue_name_number
,	O
Thr1NH2	B-residue_name_number
,	O
Lys33NH2	B-residue_name_number
and	O
Asp17Oδ	B-residue_name_number
,	O
as	O
well	O
as	O
a	O
nucleophilic	O
water	B-chemical
molecule	O
as	O
the	O
proton	O
shuttle	O
appeared	O
to	O
accommodate	O
all	O
possible	O
views	O
of	O
the	O
proteasomal	O
active	B-site
site	I-site
.	O

Twenty	O
years	O
later	O
,	O
with	O
a	O
plethora	O
of	O
yCP	B-complex_assembly
X	B-evidence
-	I-evidence
ray	I-evidence
structures	I-evidence
in	O
hand	O
,	O
we	O
decided	O
to	O
re	O
-	O
analyse	O
the	O
active	B-site
site	I-site
of	O
the	O
proteasome	B-complex_assembly
and	O
to	O
resolve	O
the	O
uncertainty	O
regarding	O
the	O
nature	O
of	O
the	O
general	O
base	O
.	O

Mutation	B-experimental_method
of	O
β5	B-protein
-	O
Lys33	B-residue_name_number
to	O
Ala	B-residue_name
causes	O
a	O
strongly	O
deleterious	O
phenotype	O
,	O
and	O
previous	O
structural	B-experimental_method
and	I-experimental_method
biochemical	I-experimental_method
analyses	I-experimental_method
confirmed	O
that	O
this	O
is	O
caused	O
by	O
failure	O
of	O
propeptide	B-ptm
cleavage	I-ptm
,	O
and	O
consequently	O
,	O
lack	O
of	O
ChT	O
-	O
L	O
activity	O
(	O
Fig	O
.	O
4a	O
,	O
Supplementary	O
Fig	O
.	O
3b	O
and	O
Table	O
1	O
;	O
for	O
details	O
see	O
Supplementary	O
Note	O
1	O
).	O

The	O
phenotype	O
of	O
the	O
β5	B-mutant
-	I-mutant
K33A	I-mutant
mutant	B-protein_state
was	O
however	O
less	O
pronounced	O
than	O
for	O
the	O
β5	B-mutant
-	I-mutant
T1A	I-mutant
-	I-mutant
K81R	I-mutant
yeast	B-taxonomy_domain
(	O
Fig	O
.	O
4a	O
).	O

This	O
discrepancy	O
in	O
growth	O
was	O
traced	O
to	O
an	O
additional	O
point	O
mutation	O
L	B-mutant
(-	I-mutant
49	I-mutant
)	I-mutant
S	I-mutant
in	O
the	O
β5	B-protein
-	O
propeptide	B-structure_element
of	O
the	O
β5	B-mutant
-	I-mutant
K33A	I-mutant
mutant	B-protein_state
(	O
see	O
also	O
Supplementary	O
Note	O
1	O
).	O

Structural	B-experimental_method
comparison	I-experimental_method
of	O
the	O
β5	B-mutant
-	I-mutant
L	I-mutant
(-	I-mutant
49	I-mutant
)	I-mutant
S	I-mutant
-	I-mutant
K33A	I-mutant
and	O
β5	B-mutant
-	I-mutant
T1A	I-mutant
-	I-mutant
K81R	I-mutant
active	B-site
sites	I-site
revealed	O
that	O
mutation	B-experimental_method
of	O
Lys33	B-residue_name_number
to	O
Ala	B-residue_name
creates	O
a	O
cavity	O
that	O
is	O
filled	O
with	O
Thr1	B-residue_name_number
and	O
the	O
remnant	O
propeptide	B-structure_element
.	O

This	O
structural	O
alteration	O
destroys	O
active	B-site
-	I-site
site	I-site
integrity	O
and	O
abolishes	O
catalytic	O
activity	O
of	O
the	O
β5	B-protein
active	B-site
site	I-site
(	O
Supplementary	O
Fig	O
.	O
5a	O
).	O

Additional	O
proof	O
for	O
the	O
key	O
function	O
of	O
Lys33	B-residue_name_number
was	O
obtained	O
from	O
the	O
β5	B-mutant
-	I-mutant
K33A	I-mutant
mutant	B-protein_state
,	O
with	O
the	O
propeptide	B-structure_element
expressed	B-experimental_method
separately	I-experimental_method
from	O
the	O
main	O
subunit	O
(	O
pp	B-chemical
trans	B-protein_state
).	O

The	O
Thr1	B-residue_name_number
N	O
terminus	O
of	O
this	O
mutant	B-protein_state
is	O
not	O
blocked	O
by	O
the	O
propeptide	B-structure_element
,	O
yet	O
its	O
catalytic	O
activity	O
is	O
reduced	O
by	O
∼	O
83	O
%	O
(	O
Supplementary	O
Fig	O
.	O
6b	O
).	O

Consistent	O
with	O
this	O
,	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
β5	B-mutant
-	I-mutant
K33A	I-mutant
pp	B-chemical
trans	B-protein_state
mutant	B-protein_state
in	B-protein_state
complex	I-protein_state
with	I-protein_state
carfilzomib	B-chemical
only	O
showed	O
partial	O
occupancy	O
of	O
the	O
ligand	O
at	O
the	O
β5	B-protein
active	B-site
sites	I-site
(	O
Supplementary	O
Fig	O
.	O
5b	O
and	O
Supplementary	O
Table	O
1	O
).	O

Since	O
no	O
acetylation	B-ptm
of	O
the	O
Thr1	B-residue_name_number
N	O
terminus	O
was	O
observed	O
for	O
the	O
β5	B-mutant
-	I-mutant
K33A	I-mutant
pp	B-chemical
trans	B-protein_state
apo	B-protein_state
crystal	B-evidence
structure	I-evidence
,	O
the	O
reduced	O
reactivity	O
towards	O
substrates	O
and	O
inhibitors	O
indicates	O
that	O
Lys33NH2	B-residue_name_number
,	O
rather	O
than	O
Thr1NH2	B-residue_name_number
,	O
deprotonates	O
and	O
activates	O
Thr1OH	B-residue_name_number
.	O

Furthermore	O
,	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
β5	B-mutant
-	I-mutant
K33A	I-mutant
pp	B-chemical
trans	B-protein_state
mutant	B-protein_state
without	B-protein_state
inhibitor	I-protein_state
revealed	O
that	O
Thr1Oγ	B-residue_name_number
strongly	O
coordinates	O
a	O
well	O
-	O
defined	O
water	B-chemical
molecule	O
(∼	O
2	O
Å	O
;	O
Fig	O
.	O
3c	O
and	O
Supplementary	O
Fig	O
.	O
5c	O
,	O
d	O
).	O

This	O
water	B-chemical
hydrogen	O
bonds	O
also	O
to	O
Arg19O	B-residue_name_number
(∼	O
3	O
.	O
0	O
Å	O
)	O
and	O
Asp17Oδ	B-residue_name_number
(∼	O
3	O
.	O
0	O
Å	O
),	O
and	O
thereby	O
presumably	O
enables	O
residual	O
activity	O
of	O
the	O
mutant	B-protein_state
.	O

Remarkably	O
,	O
the	O
solvent	O
molecule	O
occupies	O
the	O
position	O
normally	O
taken	O
by	O
Lys33NH2	B-residue_name_number
in	O
the	O
WT	B-protein_state
proteasome	B-complex_assembly
structure	B-evidence
(	O
Fig	O
.	O
3c	O
),	O
further	O
corroborating	O
the	O
essential	O
role	O
of	O
Lys33	B-residue_name_number
as	O
the	O
general	O
base	O
for	O
autolysis	B-ptm
and	O
proteolysis	O
.	O

Conservative	B-experimental_method
substitution	I-experimental_method
of	O
Lys33	B-residue_name_number
by	O
Arg	B-residue_name
delays	O
autolysis	B-ptm
of	O
the	O
β5	B-protein
precursor	O
and	O
impairs	O
yeast	B-taxonomy_domain
growth	O
(	O
for	O
details	O
see	O
Supplementary	O
Note	O
1	O
).	O

While	O
Thr1	B-residue_name_number
occupies	O
the	O
same	O
position	O
as	O
in	O
WT	B-protein_state
yCPs	B-complex_assembly
,	O
Arg33	B-residue_name_number
is	O
unable	O
to	O
hydrogen	O
bond	O
to	O
Asp17	B-residue_name_number
,	O
thereby	O
inactivating	O
the	O
β5	B-protein
active	B-site
site	I-site
(	O
Supplementary	O
Fig	O
.	O
5e	O
).	O

The	O
conservative	B-experimental_method
mutation	I-experimental_method
of	O
Asp17	B-residue_name_number
to	O
Asn	B-residue_name
in	O
subunit	O
β5	B-protein
of	O
the	O
yCP	B-complex_assembly
also	O
provokes	O
a	O
severe	O
growth	O
defect	O
(	O
Supplementary	O
Note	O
1	O
,	O
Supplementary	O
Fig	O
.	O
6a	O
and	O
Table	O
1	O
).	O

Notably	O
,	O
only	O
with	O
the	O
additional	O
point	O
mutation	O
L	B-mutant
(-	I-mutant
49	I-mutant
)	I-mutant
S	I-mutant
present	O
in	O
the	O
β5	B-protein
propeptide	B-structure_element
could	O
we	O
purify	O
a	O
small	O
amount	O
of	O
the	O
β5	B-mutant
-	I-mutant
D17N	I-mutant
mutant	B-protein_state
yCP	B-complex_assembly
.	O

As	O
determined	O
by	O
crystallographic	B-experimental_method
analysis	I-experimental_method
,	O
this	O
mutant	B-protein_state
β5	B-protein
subunit	O
was	O
partially	B-protein_state
processed	I-protein_state
(	O
Table	O
1	O
)	O
but	O
displayed	O
impaired	O
reactivity	O
towards	O
the	O
proteasome	B-complex_assembly
inhibitor	O
carfilzomib	B-chemical
compared	O
with	O
the	O
subunits	O
β1	B-protein
and	O
β2	B-protein
,	O
and	O
with	O
WT	B-protein_state
β5	B-protein
(	O
Supplementary	O
Fig	O
.	O
7a	O
).	O

In	O
contrast	O
to	O
the	O
cis	B-protein_state
-	O
construct	O
,	O
expression	B-experimental_method
of	O
the	O
β5	B-protein
propeptide	B-structure_element
in	O
trans	B-protein_state
allowed	O
straightforward	O
isolation	B-experimental_method
and	O
crystallization	B-experimental_method
of	O
the	O
D17N	B-mutant
mutant	B-protein_state
proteasome	B-complex_assembly
.	O

The	O
ChT	O
-	O
L	O
activity	O
of	O
the	O
β5	B-mutant
-	I-mutant
D17N	I-mutant
pp	B-chemical
in	O
trans	B-protein_state
CP	B-complex_assembly
towards	O
the	O
canonical	O
β5	B-protein
model	O
substrates	O
N	B-chemical
-	I-chemical
succinyl	I-chemical
-	I-chemical
Leu	I-chemical
-	I-chemical
Leu	I-chemical
-	I-chemical
Val	I-chemical
-	I-chemical
Tyr	I-chemical
-	I-chemical
7	I-chemical
-	I-chemical
amino	I-chemical
-	I-chemical
4	I-chemical
-	I-chemical
methylcoumarin	I-chemical
(	O
Suc	B-chemical
-	I-chemical
LLVY	I-chemical
-	I-chemical
AMC	I-chemical
)	O
and	O
carboxybenzyl	B-chemical
-	I-chemical
Gly	I-chemical
-	I-chemical
Gly	I-chemical
-	I-chemical
Leu	I-chemical
-	I-chemical
para	I-chemical
-	I-chemical
nitroanilide	I-chemical
(	O
Z	B-chemical
-	I-chemical
GGL	I-chemical
-	I-chemical
pNA	I-chemical
)	O
was	O
severely	O
reduced	O
(	O
Supplementary	O
Fig	O
.	O
6b	O
),	O
confirming	O
that	O
Asp17	B-residue_name_number
is	O
of	O
fundamental	O
importance	O
for	O
the	O
catalytic	O
activity	O
of	O
the	O
mature	B-protein_state
proteasome	B-complex_assembly
.	O

Even	O
though	O
the	O
β5	B-mutant
-	I-mutant
D17N	I-mutant
pp	B-chemical
trans	B-protein_state
yCP	B-complex_assembly
crystal	B-evidence
structure	I-evidence
appeared	O
identical	O
to	O
the	O
WT	B-protein_state
yCP	B-complex_assembly
(	O
Supplementary	O
Fig	O
.	O
7b	O
),	O
the	O
co	B-evidence
-	I-evidence
crystal	I-evidence
structure	I-evidence
with	O
the	O
α	B-chemical
′,	I-chemical
β	I-chemical
′	I-chemical
epoxyketone	I-chemical
inhibitor	O
carfilzomib	B-chemical
visualized	O
only	O
partial	O
occupancy	O
of	O
the	O
ligand	O
in	O
the	O
β5	B-protein
active	B-site
site	I-site
(	O
Supplementary	O
Fig	O
.	O
7a	O
).	O

This	O
observation	O
is	O
consistent	O
with	O
a	O
strongly	O
reduced	O
reactivity	O
of	O
β5	B-protein
-	O
Thr1	B-residue_name_number
and	O
the	O
crystal	B-evidence
structure	I-evidence
of	O
the	O
β5	B-mutant
-	I-mutant
D17N	I-mutant
pp	B-chemical
cis	B-protein_state
mutant	B-protein_state
in	B-protein_state
complex	I-protein_state
with	I-protein_state
carfilzomib	B-chemical
.	O

Autolysis	B-ptm
and	O
residual	O
catalytic	O
activity	O
of	O
the	O
β5	B-mutant
-	I-mutant
D17N	I-mutant
mutants	O
may	O
originate	O
from	O
the	O
carbonyl	O
group	O
of	O
Asn17	B-residue_name_number
,	O
which	O
albeit	O
to	O
a	O
lower	O
degree	O
still	O
can	O
polarize	O
Lys33	B-residue_name_number
for	O
the	O
activation	O
of	O
Thr1	B-residue_name_number
.	O

In	O
agreement	O
,	O
an	O
E17A	B-mutant
mutant	B-protein_state
in	O
the	O
proteasomal	O
β	B-protein
-	I-protein
subunit	I-protein
of	O
the	O
archaeon	B-taxonomy_domain
Thermoplasma	B-species
acidophilum	I-species
prevents	O
autolysis	B-ptm
and	O
catalysis	O
.	O

Strikingly	O
,	O
although	O
the	O
X	B-evidence
-	I-evidence
ray	I-evidence
data	I-evidence
on	O
the	O
β5	B-mutant
-	I-mutant
D17N	I-mutant
mutant	B-protein_state
with	O
the	O
propeptide	B-structure_element
expressed	B-experimental_method
in	O
cis	B-protein_state
and	O
in	O
trans	B-protein_state
looked	O
similar	O
,	O
there	O
was	O
a	O
pronounced	O
difference	O
in	O
their	O
growth	O
phenotypes	O
observed	O
(	O
Supplementary	O
Fig	O
.	O
6a	O
and	O
Supplementary	O
Fig	O
.	O
7b	O
).	O

On	O
the	O
basis	O
of	O
these	O
results	O
,	O
we	O
propose	O
that	O
CPs	B-complex_assembly
from	O
all	O
domains	O
of	O
life	O
use	O
a	O
catalytic	B-site
triad	I-site
consisting	O
of	O
Thr1	B-residue_name_number
,	O
Lys33	B-residue_name_number
and	O
Asp	B-residue_name
/	O
Glu17	B-residue_name_number
for	O
both	O
autocatalytic	B-ptm
precursor	I-ptm
processing	I-ptm
and	O
proteolysis	O
(	O
Fig	O
.	O
3d	O
).	O

This	O
model	O
is	O
also	O
consistent	O
with	O
the	O
fact	O
that	O
no	O
defined	O
water	B-chemical
molecule	O
is	O
observed	O
in	O
the	O
mature	B-protein_state
WT	B-protein_state
proteasomal	O
active	B-site
site	I-site
that	O
could	O
shuttle	O
the	O
proton	O
from	O
Thr1Oγ	B-residue_name_number
to	O
Thr1NH2	B-residue_name_number
.	O

To	O
explore	O
this	O
active	B-site
-	I-site
site	I-site
model	O
further	O
,	O
we	O
exchanged	B-experimental_method
the	I-experimental_method
conserved	I-experimental_method
Asp166	B-residue_name_number
residue	O
for	O
Asn	B-residue_name
in	O
the	O
yeast	B-taxonomy_domain
β5	B-protein
subunit	O
.	O

Asp166Oδ	B-residue_name_number
is	O
hydrogen	O
-	O
bonded	O
to	O
Thr1NH2	B-residue_name_number
via	O
Ser129OH	B-residue_name_number
and	O
Ser169OH	B-residue_name_number
,	O
and	O
therefore	O
was	O
proposed	O
to	O
be	O
involved	O
in	O
catalysis	O
.	O

The	O
β5	B-mutant
-	I-mutant
D166N	I-mutant
pp	B-chemical
cis	B-protein_state
yeast	B-taxonomy_domain
mutant	B-protein_state
is	O
significantly	O
impaired	O
in	O
growth	O
and	O
its	O
ChT	O
-	O
L	O
activity	O
is	O
drastically	O
reduced	O
(	O
Supplementary	O
Fig	O
.	O
6a	O
,	O
b	O
and	O
Table	O
1	O
).	O

X	B-evidence
-	I-evidence
ray	I-evidence
data	I-evidence
on	O
the	O
β5	B-mutant
-	I-mutant
D166N	I-mutant
mutant	B-protein_state
indicate	O
that	O
the	O
β5	B-protein
propeptide	B-structure_element
is	O
hydrolysed	O
,	O
but	O
due	O
to	O
reorientation	O
of	O
Ser129OH	B-residue_name_number
,	O
the	O
interaction	O
with	O
Asn166Oδ	B-residue_name_number
is	O
disrupted	O
(	O
Supplementary	O
Fig	O
.	O
8a	O
).	O

Instead	O
,	O
a	O
water	B-chemical
molecule	O
is	O
bound	B-protein_state
to	I-protein_state
Ser129OH	B-residue_name_number
and	O
Thr1NH2	B-residue_name_number
(	O
Supplementary	O
Fig	O
.	O
8b	O
),	O
which	O
may	O
enable	O
precursor	B-ptm
processing	I-ptm
.	O

The	O
hydrogen	O
bonds	O
involving	O
Ser169OH	B-residue_name_number
are	O
intact	O
and	O
may	O
account	O
for	O
residual	O
substrate	O
turnover	O
.	O

Soaking	B-experimental_method
the	O
β5	B-mutant
-	I-mutant
D166N	I-mutant
crystals	B-experimental_method
with	O
carfilzomib	B-chemical
and	O
MG132	B-chemical
resulted	O
in	O
covalent	O
modification	O
of	O
Thr1	B-residue_name_number
at	O
high	O
occupancy	O
(	O
Supplementary	O
Fig	O
.	O
8c	O
).	O

In	O
the	O
carfilzomib	B-complex_assembly
complex	I-complex_assembly
structure	B-evidence
,	O
Thr1Oγ	B-residue_name_number
and	O
Thr1N	B-residue_name_number
incorporate	O
into	O
a	O
morpholine	O
ring	O
structure	O
and	O
Ser129	B-residue_name_number
adopts	O
its	O
WT	B-protein_state
-	O
like	O
orientation	O
.	O

In	O
the	O
MG132	B-protein_state
-	I-protein_state
bound	I-protein_state
state	I-protein_state
,	O
Thr1N	B-residue_name_number
is	O
unmodified	B-protein_state
,	O
and	O
we	O
again	O
observe	O
that	O
Ser129	B-residue_name_number
is	O
hydrogen	O
-	O
bonded	O
to	O
a	O
water	B-chemical
molecule	O
instead	O
of	O
Asn166	B-residue_name_number
.	O

Whereas	O
Asn	B-residue_name
can	O
to	O
some	O
degree	O
replace	O
Asp166	B-residue_name_number
due	O
to	O
its	O
carbonyl	O
group	O
in	O
the	O
side	O
chain	O
,	O
Ala	B-residue_name
at	O
this	O
position	O
was	O
found	O
to	O
prevent	O
both	O
autolysis	B-ptm
and	O
catalysis	O
.	O

These	O
results	O
suggest	O
that	O
Asp166	B-residue_name_number
and	O
Ser129	B-residue_name_number
function	O
as	O
a	O
proton	O
shuttle	O
and	O
affect	O
the	O
protonation	O
state	O
of	O
Thr1N	B-residue_name_number
during	O
autolysis	B-ptm
and	O
catalysis	O
.	O

Substitution	B-experimental_method
of	O
the	O
active	B-site
-	I-site
site	I-site
Thr1	B-residue_name_number
by	O
Cys	B-residue_name

Mutation	B-experimental_method
of	O
Thr1	B-residue_name_number
to	O
Cys	B-residue_name
inactivates	O
the	O
20S	B-complex_assembly
proteasome	I-complex_assembly
from	O
the	O
archaeon	B-taxonomy_domain
T	B-species
.	I-species
acidophilum	I-species
.	O

In	O
yeast	B-taxonomy_domain
,	O
this	O
mutation	B-experimental_method
causes	O
a	O
strong	O
growth	O
defect	O
(	O
Fig	O
.	O
4a	O
and	O
Table	O
1	O
),	O
although	O
the	O
propeptide	B-structure_element
is	O
hydrolysed	O
,	O
as	O
shown	O
here	O
by	O
its	O
X	B-evidence
-	I-evidence
ray	I-evidence
structure	I-evidence
.	O

In	O
one	O
of	O
the	O
two	O
β5	B-protein
subunits	O
,	O
however	O
,	O
we	O
found	O
the	O
cleaved	B-protein_state
propeptide	B-structure_element
still	B-protein_state
bound	I-protein_state
in	O
the	O
substrate	B-site
-	I-site
binding	I-site
channel	I-site
(	O
Fig	O
.	O
4c	O
).	O

His	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
occupies	O
the	O
S2	B-site
pocket	I-site
like	O
observed	O
for	O
the	O
β5	B-mutant
-	I-mutant
T1A	I-mutant
-	I-mutant
K81R	I-mutant
mutant	B-protein_state
,	O
but	O
in	O
contrast	O
to	O
the	O
latter	O
,	O
the	O
propeptide	B-structure_element
in	O
the	O
T1C	B-mutant
mutant	B-protein_state
adopts	O
an	O
antiparallel	B-structure_element
β	I-structure_element
-	I-structure_element
sheet	I-structure_element
conformation	O
as	O
known	O
from	O
inhibitors	O
like	O
MG132	B-chemical
(	O
Fig	O
.	O
4c	O
–	O
e	O
and	O
Supplementary	O
Fig	O
.	O
9b	O
).	O

On	O
the	O
basis	O
of	O
the	O
phenotype	O
of	O
the	O
T1C	B-mutant
mutant	B-protein_state
and	O
the	O
propeptide	B-structure_element
remnant	O
identified	O
in	O
its	O
active	B-site
site	I-site
,	O
we	O
suppose	O
that	O
autolysis	B-ptm
is	O
retarded	O
and	O
may	O
not	O
have	O
been	O
completed	O
before	O
crystallization	B-experimental_method
.	O

Owing	O
to	O
the	O
unequal	O
positions	O
of	O
the	O
two	O
β5	B-protein
subunits	O
within	O
the	O
CP	B-complex_assembly
in	O
the	O
crystal	O
lattice	O
,	O
maturation	O
and	O
propeptide	B-structure_element
displacement	O
may	O
occur	O
at	O
different	O
timescales	O
in	O
the	O
two	O
subunits	O
.	O

Despite	O
propeptide	B-ptm
hydrolysis	I-ptm
,	O
the	O
β5	B-mutant
-	I-mutant
T1C	I-mutant
active	B-site
site	I-site
is	O
catalytically	B-protein_state
inactive	I-protein_state
(	O
Fig	O
.	O
4b	O
and	O
Supplementary	O
Fig	O
.	O
9a	O
).	O

In	O
agreement	O
,	O
soaking	B-experimental_method
crystals	I-experimental_method
with	O
the	O
CP	B-complex_assembly
inhibitors	O
bortezomib	B-chemical
or	O
carfilzomib	B-chemical
modifies	O
only	O
the	O
β1	B-protein
and	O
β2	B-protein
active	B-site
sites	I-site
,	O
while	O
leaving	O
the	O
β5	B-mutant
-	I-mutant
T1C	I-mutant
proteolytic	B-site
centres	I-site
unmodified	B-protein_state
even	O
though	O
they	O
are	O
only	O
partially	O
occupied	O
by	O
the	O
cleaved	B-protein_state
propeptide	B-structure_element
remnant	O
.	O

Moreover	O
,	O
the	O
structural	B-evidence
data	I-evidence
reveal	O
that	O
the	O
thiol	O
group	O
of	O
Cys1	B-residue_name_number
is	O
rotated	O
by	O
74	O
°	O
with	O
respect	O
to	O
the	O
hydroxyl	O
side	O
chain	O
of	O
Thr1	B-residue_name_number
(	O
Fig	O
.	O
4f	O
and	O
Supplementary	O
Fig	O
.	O
9b	O
).	O

Consequently	O
,	O
the	O
hydrogen	O
bond	O
bridging	O
the	O
active	O
-	O
site	O
nucleophile	O
and	O
Lys33	B-residue_name_number
in	O
WT	B-protein_state
CPs	B-complex_assembly
is	O
broken	O
with	O
Cys1	B-residue_name_number
.	O

Notably	O
,	O
the	O
2FO	B-evidence
–	I-evidence
FC	I-evidence
electron	I-evidence
-	I-evidence
density	I-evidence
map	I-evidence
of	O
the	O
T1C	B-mutant
mutant	B-protein_state
also	O
indicates	O
that	O
Lys33NH2	B-residue_name_number
is	O
disordered	B-protein_state
.	O

Together	O
,	O
these	O
observations	O
suggest	O
that	O
efficient	O
peptide	O
-	O
bond	O
hydrolysis	O
requires	O
that	O
Lys33NH2	B-residue_name_number
hydrogen	O
bonds	O
to	O
the	O
active	O
site	O
nucleophile	O
.	O

The	O
benefit	O
of	O
Thr	B-residue_name
over	O
Ser	B-residue_name
as	O
the	O
active	O
-	O
site	O
nucleophile	O

All	O
proteasomes	B-complex_assembly
strictly	B-protein_state
employ	I-protein_state
threonine	B-residue_name
as	O
the	O
active	B-site
-	I-site
site	I-site
residue	I-site
instead	O
of	O
serine	B-residue_name
.	O

To	O
investigate	O
the	O
reason	O
for	O
this	O
singularity	O
,	O
we	O
analysed	O
a	O
β5	B-mutant
-	I-mutant
T1S	I-mutant
mutant	B-protein_state
,	O
which	O
is	O
viable	O
but	O
suffers	O
from	O
growth	O
defects	O
(	O
Fig	O
.	O
4a	O
and	O
Table	O
1	O
).	O

Activity	B-experimental_method
assays	I-experimental_method
with	O
the	O
β5	B-protein
-	O
specific	O
substrate	O
Suc	B-chemical
-	I-chemical
LLVY	I-chemical
-	I-chemical
AMC	I-chemical
demonstrated	O
that	O
the	O
ChT	O
-	O
L	O
activity	O
of	O
the	O
T1S	B-mutant
mutant	B-protein_state
is	O
reduced	O
by	O
40	O
–	O
45	O
%	O
compared	O
with	O
WT	B-protein_state
proteasomes	B-complex_assembly
depending	O
on	O
the	O
incubation	O
temperature	O
(	O
Fig	O
.	O
4b	O
and	O
Supplementary	O
Fig	O
.	O
9c	O
).	O

By	O
contrast	O
,	O
turnover	O
of	O
the	O
substrate	O
Z	B-chemical
-	I-chemical
GGL	I-chemical
-	I-chemical
pNA	I-chemical
,	O
used	O
to	O
monitor	O
ChT	O
-	O
L	O
activity	O
in	O
situ	O
but	O
in	O
a	O
less	O
quantitative	O
fashion	O
,	O
is	O
not	O
detectably	O
impaired	O
(	O
Supplementary	O
Fig	O
.	O
9a	O
).	O

Crystal	B-evidence
structure	I-evidence
analysis	O
of	O
the	O
β5	B-mutant
-	I-mutant
T1S	I-mutant
mutant	B-protein_state
confirmed	O
precursor	B-ptm
processing	I-ptm
(	O
Fig	O
.	O
4g	O
),	O
and	O
ligand	B-complex_assembly
-	I-complex_assembly
complex	I-complex_assembly
structures	B-evidence
with	O
bortezomib	B-chemical
and	O
carfilzomib	B-chemical
unambiguously	O
corroborated	O
the	O
reactivity	O
of	O
Ser1	B-residue_name_number
(	O
Fig	O
.	O
5	O
).	O

However	O
,	O
the	O
apo	B-protein_state
crystal	B-evidence
structure	I-evidence
revealed	O
that	O
Ser1Oγ	B-residue_name_number
is	O
turned	O
away	O
from	O
the	O
substrate	B-site
-	I-site
binding	I-site
channel	I-site
(	O
Fig	O
.	O
4g	O
).	O

Compared	O
with	O
Thr1Oγ	B-residue_name_number
in	O
WT	B-protein_state
CP	B-complex_assembly
structures	B-evidence
,	O
Ser1Oγ	B-residue_name_number
is	O
rotated	O
by	O
60	O
°.	O

Because	O
both	O
conformations	O
of	O
Ser1Oγ	B-residue_name_number
are	O
hydrogen	O
-	O
bonded	O
to	O
Lys33NH2	B-residue_name_number
(	O
Fig	O
.	O
4h	O
),	O
the	O
relay	O
system	O
is	O
capable	O
of	O
hydrolysing	O
peptide	O
substrates	O
,	O
albeit	O
at	O
lower	O
rates	O
compared	O
with	O
Thr1	B-residue_name_number
.	O

The	O
active	B-site
-	I-site
site	I-site
residue	I-site
Thr1	B-residue_name_number
is	O
fixed	O
in	O
its	O
position	O
,	O
as	O
its	O
methyl	O
group	O
is	O
engaged	O
in	O
hydrophobic	O
interactions	O
with	O
Thr3	B-residue_name_number
and	O
Ala46	B-residue_name_number
(	O
Fig	O
.	O
4h	O
).	O

Consequently	O
,	O
the	O
hydroxyl	O
group	O
of	O
Thr1	B-residue_name_number
requires	O
no	O
reorientation	O
before	O
substrate	O
cleavage	O
and	O
is	O
thus	O
more	O
catalytically	O
efficient	O
than	O
Ser1	B-residue_name_number
.	O

In	O
agreement	O
,	O
at	O
an	O
elevated	O
growing	O
temperature	O
of	O
37	O
°	O
C	O
the	O
T1S	B-mutant
mutant	B-protein_state
is	O
unable	O
to	O
grow	O
(	O
Fig	O
.	O
4a	O
).	O

In	O
vitro	O
,	O
the	O
mutant	B-protein_state
proteasome	B-complex_assembly
is	O
less	O
susceptible	O
to	O
proteasome	B-complex_assembly
inhibition	O
by	O
bortezomib	B-chemical
(	O
3	O
.	O
7	O
-	O
fold	O
)	O
and	O
carfilzomib	B-chemical
(	O
1	O
.	O
8	O
-	O
fold	O
;	O
Fig	O
.	O
5	O
).	O

Nevertheless	O
,	O
inhibitor	B-complex_assembly
complex	I-complex_assembly
structures	B-evidence
indicate	O
identical	O
binding	O
modes	O
compared	O
with	O
the	O
WT	B-protein_state
yCP	B-complex_assembly
structures	B-evidence
,	O
with	B-protein_state
the	I-protein_state
same	I-protein_state
inhibitors	I-protein_state
.	O

Notably	O
,	O
the	O
affinity	B-evidence
of	O
the	O
tetrapeptide	O
carfilzomib	B-chemical
is	O
less	O
impaired	O
,	O
as	O
it	O
is	O
better	O
stabilized	O
in	O
the	O
substrate	B-site
-	I-site
binding	I-site
channel	I-site
than	O
the	O
dipeptide	O
bortezomib	B-chemical
,	O
which	O
lacks	O
a	O
defined	O
P3	O
site	O
and	O
has	O
only	O
a	O
few	O
interactions	O
with	O
the	O
surrounding	O
protein	O
.	O

Hence	O
,	O
the	O
mean	B-evidence
residence	I-evidence
time	I-evidence
of	O
carfilzomib	B-chemical
at	O
the	O
active	B-site
site	I-site
is	O
prolonged	O
and	O
the	O
probability	O
to	O
covalently	O
react	O
with	O
Ser1	B-residue_name_number
is	O
increased	O
.	O

Considered	O
together	O
,	O
these	O
results	O
provide	O
a	O
plausible	O
explanation	O
for	O
the	O
invariance	O
of	O
threonine	B-residue_name
as	O
the	O
active	O
-	O
site	O
nucleophile	O
in	O
proteasomes	B-complex_assembly
in	O
all	O
three	O
domains	O
of	O
life	O
,	O
as	O
well	O
as	O
in	O
proteasome	B-protein_type
-	I-protein_type
like	I-protein_type
proteases	I-protein_type
such	O
as	O
HslV	B-protein
(	O
ref	O
.).	O

The	O
20S	B-complex_assembly
proteasome	I-complex_assembly
CP	B-complex_assembly
is	O
the	O
major	O
non	B-protein_type
-	I-protein_type
lysosomal	I-protein_type
protease	I-protein_type
in	O
eukaryotic	B-taxonomy_domain
cells	O
,	O
and	O
its	O
assembly	O
is	O
highly	O
organized	O
.	O

The	O
β	B-protein
-	I-protein
subunit	I-protein
propeptides	B-structure_element
,	O
particularly	O
that	O
of	O
β5	B-protein
,	O
are	O
key	O
factors	O
that	O
help	O
drive	O
proper	O
assembly	O
of	O
the	O
CP	B-complex_assembly
complex	O
.	O

In	O
addition	O
,	O
they	O
prevent	O
irreversible	O
inactivation	O
of	O
the	O
Thr1	B-residue_name_number
N	O
terminus	O
by	O
N	B-ptm
-	I-ptm
acetylation	I-ptm
.	O

By	O
contrast	O
,	O
the	O
prosegments	B-structure_element
of	O
β	B-protein
subunits	I-protein
are	O
dispensable	O
for	O
archaeal	B-taxonomy_domain
proteasome	B-complex_assembly
assembly	O
,	O
at	O
least	O
when	O
heterologously	B-experimental_method
expressed	I-experimental_method
in	O
Escherichia	B-species
coli	I-species
.	O

In	O
eukaryotes	B-taxonomy_domain
,	O
deletion	O
of	O
or	O
failure	O
to	O
cleave	O
the	O
β1	B-protein
and	O
β2	B-protein
propeptides	B-structure_element
is	O
well	O
tolerated	O
.	O

However	O
,	O
removal	B-experimental_method
of	I-experimental_method
the	O
β5	B-protein
prosegment	B-structure_element
or	O
any	O
interference	O
with	O
its	O
cleavage	O
causes	O
severe	O
phenotypic	O
defects	O
.	O

These	O
observations	O
highlight	O
the	O
unique	O
function	O
and	O
importance	O
of	O
the	O
β5	B-protein
propeptide	B-structure_element
as	O
well	O
as	O
the	O
β5	B-protein
active	B-site
site	I-site
for	O
maturation	O
and	O
function	O
of	O
the	O
eukaryotic	B-taxonomy_domain
CP	B-complex_assembly
.	O

Here	O
we	O
have	O
described	O
the	O
atomic	B-evidence
structures	I-evidence
of	O
various	O
β5	B-mutant
-	I-mutant
T1A	I-mutant
mutants	O
,	O
which	O
allowed	O
for	O
the	O
first	O
time	O
visualization	O
of	O
the	O
residual	O
β5	B-protein
propeptide	B-structure_element
.	O

Depending	O
on	O
the	O
(-	B-residue_number
2	I-residue_number
)	I-residue_number
residue	O
we	O
observed	O
various	O
propeptide	B-structure_element
conformations	O
,	O
but	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
is	O
in	O
all	O
structures	B-evidence
perfectly	O
located	O
for	O
the	O
nucleophilic	O
attack	O
by	O
Thr1Oγ	B-residue_name_number
,	O
although	O
it	O
does	O
not	O
adopt	O
the	O
tight	B-structure_element
turn	I-structure_element
observed	O
for	O
the	O
prosegment	B-structure_element
of	O
subunit	O
β1	B-protein
.	O

From	O
these	O
data	O
we	O
conclude	O
that	O
only	O
the	O
positioning	O
of	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
and	O
Thr1	B-residue_name_number
as	O
well	O
as	O
the	O
integrity	O
of	O
the	O
proteasomal	O
active	B-site
site	I-site
are	O
required	O
for	O
autolysis	B-ptm
.	O

In	O
this	O
regard	O
,	O
inappropriate	O
N	B-ptm
-	I-ptm
acetylation	I-ptm
of	O
the	O
Thr1	B-residue_name_number
N	O
terminus	O
cannot	O
be	O
removed	O
by	O
Thr1Oγ	B-residue_name_number
due	O
to	O
the	O
rotational	O
freedom	O
and	O
flexibility	O
of	O
the	O
acetyl	O
group	O
.	O

The	O
propeptide	B-structure_element
needs	O
some	O
anchoring	O
in	O
the	O
substrate	B-site
-	I-site
binding	I-site
channel	I-site
to	O
properly	O
position	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
),	I-residue_name_number
but	O
this	O
seems	O
to	O
be	O
independent	O
of	O
the	O
orientation	O
of	O
residue	O
(-	B-residue_number
2	I-residue_number
).	I-residue_number

Autolytic	O
activation	O
of	O
the	O
CP	B-complex_assembly
constitutes	O
one	O
of	O
the	O
final	O
steps	O
of	O
proteasome	O
biogenesis	O
,	O
but	O
the	O
trigger	O
for	O
propeptide	B-ptm
cleavage	I-ptm
had	O
remained	O
enigmatic	O
.	O

On	O
the	O
basis	O
of	O
the	O
numerous	O
CP	B-complex_assembly
:	I-complex_assembly
ligand	I-complex_assembly
complexes	O
solved	O
during	O
the	O
past	O
18	O
years	O
and	O
in	O
the	O
current	O
study	O
,	O
we	O
provide	O
a	O
revised	O
interpretation	O
of	O
proteasome	B-complex_assembly
active	B-site
-	I-site
site	I-site
architecture	I-site
.	O

We	O
propose	O
a	O
catalytic	B-site
triad	I-site
for	O
the	O
active	B-site
site	I-site
of	O
the	O
CP	B-complex_assembly
consisting	O
of	O
residues	O
Thr1	B-residue_name_number
,	O
Lys33	B-residue_name_number
and	O
Asp	B-residue_name
/	O
Glu17	B-residue_name_number
,	O
which	O
are	O
conserved	O
among	O
all	O
proteolytically	O
active	O
eukaryotic	B-taxonomy_domain
,	O
bacterial	B-taxonomy_domain
and	O
archaeal	B-taxonomy_domain
proteasome	B-complex_assembly
subunits	O
.	O

Lys33NH2	B-residue_name_number
is	O
expected	O
to	O
act	O
as	O
the	O
proton	O
acceptor	O
during	O
autocatalytic	B-ptm
removal	I-ptm
of	O
the	O
propeptides	B-structure_element
,	O
as	O
well	O
as	O
during	O
substrate	O
proteolysis	O
,	O
while	O
Asp17Oδ	B-residue_name_number
orients	O
Lys33NH2	B-residue_name_number
and	O
makes	O
it	O
more	O
prone	O
to	O
protonation	O
by	O
raising	O
its	O
pKa	O
(	O
hydrogen	O
bond	O
distance	O
:	O
Lys33NH3	B-residue_name_number
+–	O
Asp17Oδ	B-residue_name_number
:	O
2	O
.	O
9	O
Å	O
).	O

Analogously	O
to	O
the	O
proteasome	B-complex_assembly
,	O
a	O
Thr	B-site
–	I-site
Lys	I-site
–	I-site
Asp	I-site
triad	I-site
is	O
also	O
found	O
in	O
L	B-protein_type
-	I-protein_type
asparaginase	I-protein_type
.	O

Thus	O
,	O
specific	O
protein	O
surroundings	O
can	O
significantly	O
alter	O
the	O
chemical	O
properties	O
of	O
amino	O
acids	O
such	O
as	O
Lys	B-residue_name
to	O
function	O
as	O
an	O
acid	O
–	O
base	O
catalyst	O
.	O

In	O
this	O
new	O
view	O
of	O
the	O
proteasomal	O
active	B-site
site	I-site
,	O
the	O
positively	O
charged	O
Thr1NH3	B-residue_name_number
+-	O
terminus	O
hydrogen	O
bonds	O
to	O
the	O
amide	O
nitrogen	O
of	O
incoming	O
peptide	O
substrates	O
and	O
stabilizes	O
as	O
well	O
as	O
activates	O
them	O
for	O
the	O
endoproteolytic	B-ptm
cleavage	I-ptm
by	O
Thr1Oγ	B-residue_name_number
(	O
Fig	O
.	O
3d	O
).	O

Consistent	O
with	O
this	O
model	O
,	O
the	O
positively	O
charged	O
Thr1	B-residue_name_number
N	O
terminus	O
is	O
engaged	O
in	O
hydrogen	O
bonds	O
with	O
inhibitory	O
compounds	O
like	O
fellutamide	B-chemical
B	I-chemical
(	O
ref	O
.),	O
α	B-chemical
-	I-chemical
ketoamides	I-chemical
,	O
homobelactosin	B-chemical
C	I-chemical
(	O
ref	O
.)	O
and	O
salinosporamide	B-chemical
A	I-chemical
(	O
ref	O
.).	O

Furthermore	O
,	O
opening	O
of	O
the	O
β	O
-	O
lactone	O
compound	O
omuralide	B-chemical
by	O
Thr1	B-residue_name_number
creates	O
a	O
C3	O
-	O
hydroxyl	O
group	O
,	O
whose	O
proton	O
originates	O
from	O
Thr1NH3	B-residue_name_number
+.	O

The	O
resulting	O
uncharged	O
Thr1NH2	B-residue_name_number
is	O
hydrogen	O
-	O
bridged	O
to	O
the	O
C3	O
-	O
OH	O
group	O
.	O

In	O
agreement	O
,	O
acetylation	B-ptm
of	O
the	O
Thr1	B-residue_name_number
N	O
terminus	O
irreversibly	O
blocks	O
hydrolytic	O
activity	O
,	O
and	O
binding	O
of	O
substrates	O
is	O
prevented	O
for	O
steric	O
reasons	O
.	O

By	O
acting	O
as	O
a	O
proton	O
donor	O
during	O
catalysis	O
,	O
the	O
Thr1	B-residue_name_number
N	O
terminus	O
may	O
also	O
favour	O
cleavage	O
of	O
substrate	O
peptide	O
bonds	O
(	O
Fig	O
.	O
3d	O
).	O

Cleavage	O
of	O
the	O
scissile	O
peptide	O
bond	O
requires	O
protonation	O
of	O
the	O
emerging	O
free	O
amine	O
,	O
and	O
in	O
the	O
proteasome	B-complex_assembly
,	O
the	O
Thr1	B-residue_name_number
amine	O
group	O
is	O
likely	O
to	O
assume	O
this	O
function	O
.	O

Analogously	O
,	O
Thr1NH3	B-residue_name_number
+	O
might	O
promote	O
the	O
bivalent	O
reaction	O
mode	O
of	O
epoxyketone	O
inhibitors	O
by	O
protonating	O
the	O
epoxide	O
moiety	O
to	O
create	O
a	O
positively	O
charged	O
trivalent	O
oxygen	O
atom	O
that	O
is	O
subsequently	O
nucleophilically	O
attacked	O
by	O
Thr1NH2	B-residue_name_number
.	O

During	O
autolysis	B-ptm
the	O
Thr1	B-residue_name_number
N	O
terminus	O
is	O
engaged	O
in	O
a	O
hydroxyoxazolidine	O
ring	O
intermediate	O
(	O
Fig	O
.	O
3d	O
),	O
which	O
is	O
unstable	O
and	O
short	O
-	O
lived	O
.	O

Breakdown	O
of	O
this	O
tetrahedral	O
transition	O
state	O
releases	O
the	O
Thr1	B-residue_name_number
N	O
terminus	O
that	O
is	O
protonated	O
by	O
aspartic	B-residue_name_number
acid	I-residue_name_number
166	I-residue_name_number
via	O
Ser129OH	B-residue_name_number
to	O
yield	O
Thr1NH3	B-residue_name_number
+.	O

The	O
residues	O
Ser129	B-residue_name_number
and	O
Asp166	B-residue_name_number
are	O
expected	O
to	O
increase	O
the	O
pKa	O
value	O
of	O
Thr1N	B-residue_name_number
,	O
thereby	O
favouring	O
its	O
charged	O
state	O
.	O

Consistent	O
with	O
playing	O
an	O
essential	O
role	O
in	O
proton	O
shuttling	O
,	O
the	O
mutation	B-experimental_method
D166A	B-mutant
prevents	O
autolysis	B-ptm
of	O
the	O
archaeal	B-taxonomy_domain
CP	B-complex_assembly
and	O
the	O
exchange	B-experimental_method
D166N	B-mutant
impairs	O
catalytic	O
activity	O
of	O
the	O
yeast	B-taxonomy_domain
CP	B-complex_assembly
about	O
60	O
%.	O

The	O
mutation	B-experimental_method
D166N	B-mutant
lowers	O
the	O
pKa	O
of	O
Thr1N	B-residue_name_number
,	O
which	O
is	O
thus	O
more	O
likely	O
to	O
exist	O
in	O
the	O
uncharged	O
deprotonated	O
state	O
(	O
Thr1NH2	B-residue_name_number
).	O

This	O
interpretation	O
agrees	O
with	O
the	O
strongly	O
reduced	O
catalytic	O
activity	O
of	O
the	O
β5	B-mutant
-	I-mutant
D166N	I-mutant
mutant	B-protein_state
on	O
the	O
one	O
hand	O
,	O
and	O
the	O
ability	O
to	O
react	O
readily	O
with	O
carfilzomib	B-chemical
on	O
the	O
other	O
.	O

Hence	O
,	O
the	O
proteasome	B-complex_assembly
can	O
be	O
viewed	O
as	O
having	O
a	O
second	B-site
triad	I-site
that	O
is	O
essential	O
for	O
efficient	O
proteolysis	O
.	O

While	O
Lys33NH2	B-residue_name_number
and	O
Asp17Oδ	B-residue_name_number
are	O
required	O
to	O
deprotonate	O
the	O
Thr1	B-residue_name_number
hydroxyl	O
side	O
chain	O
,	O
Ser129OH	B-residue_name_number
and	O
Asp166OH	B-residue_name_number
serve	O
to	O
protonate	O
the	O
N	O
-	O
terminal	O
amine	O
group	O
of	O
Thr1	B-residue_name_number
.	O

In	O
accord	O
with	O
the	O
proposed	O
Thr1	B-residue_name_number
–	O
Lys33	B-residue_name_number
–	O
Asp17	B-residue_name_number
catalytic	B-site
triad	I-site
,	O
crystallographic	B-evidence
data	I-evidence
on	O
the	O
proteolytically	B-protein_state
inactive	I-protein_state
β5	B-mutant
-	I-mutant
T1C	I-mutant
mutant	B-protein_state
demonstrate	O
that	O
the	O
interaction	O
of	O
Lys33NH2	B-residue_name_number
and	O
Cys1	B-residue_name_number
is	O
broken	O
.	O

However	O
,	O
owing	O
to	O
Cys	B-residue_name
being	O
a	O
strong	O
nucleophile	O
,	O
the	O
propeptide	B-structure_element
can	O
still	O
be	O
cleaved	B-protein_state
off	O
over	O
time	O
.	O

While	O
only	O
one	O
single	O
turnover	O
is	O
necessary	O
for	O
autolysis	B-ptm
,	O
continuous	O
enzymatic	O
activity	O
is	O
required	O
for	O
significant	O
and	O
detectable	O
substrate	O
hydrolysis	O
.	O

Notably	O
,	O
in	O
the	O
Ntn	B-protein_type
hydrolase	I-protein_type
penicillin	B-protein_type
acylase	I-protein_type
,	O
substitution	B-experimental_method
of	O
the	O
catalytic	B-protein_state
N	O
-	O
terminal	O
Ser	B-residue_name
residue	O
by	O
Cys	B-residue_name
also	O
inactivates	B-protein_state
the	O
enzyme	B-protein_type
but	O
still	O
enables	O
precursor	B-ptm
processing	I-ptm
.	O

To	O
investigate	O
why	O
the	O
CP	B-complex_assembly
specifically	O
employs	O
threonine	B-residue_name
as	O
its	O
active	B-site
-	I-site
site	I-site
residue	I-site
,	O
we	O
used	O
a	O
β5	B-mutant
-	I-mutant
T1S	I-mutant
mutant	B-protein_state
of	O
the	O
yCP	B-complex_assembly
and	O
characterized	O
it	O
biochemically	B-experimental_method
and	I-experimental_method
structurally	I-experimental_method
.	O

Activity	B-experimental_method
assays	I-experimental_method
with	O
the	O
β5	B-mutant
-	I-mutant
T1S	I-mutant
mutant	B-protein_state
revealed	O
reduced	O
turnover	O
of	O
Suc	B-chemical
-	I-chemical
LLVY	I-chemical
-	I-chemical
AMC	I-chemical
.	O

We	O
also	O
observed	O
slightly	O
lower	O
affinity	O
of	O
the	O
β5	B-mutant
-	I-mutant
T1S	I-mutant
mutant	B-protein_state
yCP	B-complex_assembly
for	O
the	O
Food	O
and	O
Drug	O
Administration	O
-	O
approved	O
proteasome	B-complex_assembly
inhibitors	O
bortezomib	B-chemical
and	O
carfilzomib	B-chemical
.	O

Structural	B-evidence
analyses	I-evidence
support	O
these	O
findings	O
with	O
the	O
T1S	B-mutant
mutant	B-protein_state
and	O
provide	O
an	O
explanation	O
for	O
the	O
strict	B-protein_state
use	I-protein_state
of	I-protein_state
Thr	B-residue_name
residues	O
in	O
proteasomes	B-complex_assembly
.	O

Thr1	B-residue_name_number
is	O
well	O
anchored	O
in	O
the	O
active	B-site
site	I-site
by	O
hydrophobic	O
interactions	O
of	O
its	O
Cγ	O
methyl	O
group	O
with	O
Ala46	B-residue_name_number
(	O
Cβ	O
),	O
Lys33	B-residue_name_number
(	O
carbon	O
side	O
chain	O
)	O
and	O
Thr3	B-residue_name_number
(	O
Cγ	O
).	O

Notably	O
,	O
proteolytically	B-protein_state
active	I-protein_state
proteasome	B-complex_assembly
subunits	O
from	O
archaea	B-taxonomy_domain
,	O
yeast	B-taxonomy_domain
and	O
mammals	B-taxonomy_domain
,	O
including	O
constitutive	O
,	O
immuno	O
-	O
and	O
thymoproteasome	O
subunits	O
,	O
either	O
encode	O
Thr	B-residue_name
or	O
Ile	B-residue_name
at	O
position	O
3	B-residue_number
,	O
indicating	O
the	O
importance	O
of	O
the	O
Cγ	O
for	O
fixing	O
the	O
position	O
of	O
the	O
nucleophilic	O
Thr1	B-residue_name_number
.	O

In	O
contrast	O
to	O
Thr1	B-residue_name_number
,	O
the	O
hydroxyl	O
group	O
of	O
Ser1	B-residue_name_number
occupies	O
the	O
position	O
of	O
the	O
Thr1	B-residue_name_number
methyl	O
side	O
chain	O
in	O
the	O
WT	B-protein_state
enzyme	B-complex_assembly
,	O
which	O
requires	O
its	O
reorientation	O
relative	O
to	O
the	O
substrate	O
to	O
allow	O
cleavage	O
(	O
Fig	O
.	O
4g	O
,	O
h	O
).	O

Notably	O
,	O
in	O
the	O
threonine	B-protein_type
aspartase	I-protein_type
Taspase1	B-protein
,	O
mutation	B-experimental_method
of	O
the	O
active	B-site
-	I-site
site	I-site
Thr234	B-residue_name_number
to	O
Ser	B-residue_name
also	O
places	O
the	O
side	O
chain	O
in	O
the	O
position	O
of	O
the	O
methyl	O
group	O
of	O
Thr234	B-residue_name_number
in	O
the	O
WT	B-protein_state
,	O
thereby	O
reducing	O
catalytic	O
activity	O
.	O

Similarly	O
,	O
although	O
the	O
serine	B-residue_name
mutant	B-protein_state
is	O
active	B-protein_state
,	O
threonine	B-residue_name
is	O
more	O
efficient	O
in	O
the	O
context	O
of	O
the	O
proteasome	B-complex_assembly
active	B-site
site	I-site
.	O

The	O
greater	O
suitability	O
of	O
threonine	B-residue_name
for	O
the	O
proteasome	B-complex_assembly
active	B-site
site	I-site
,	O
which	O
has	O
been	O
noted	O
in	O
biochemical	O
as	O
well	O
as	O
in	O
kinetic	O
studies	O
,	O
constitutes	O
a	O
likely	O
reason	O
for	O
the	O
conservation	B-protein_state
of	O
the	O
Thr1	B-residue_name_number
residue	O
in	O
all	O
proteasomes	B-complex_assembly
from	O
bacteria	B-taxonomy_domain
to	O
eukaryotes	B-taxonomy_domain
.	O

Conformation	O
of	O
proteasomal	O
propeptides	B-structure_element
.	O

(	O
a	O
)	O
Structural	B-experimental_method
superposition	I-experimental_method
of	O
the	O
β1	B-mutant
-	I-mutant
T1A	I-mutant
propeptide	B-structure_element
and	O
the	O
matured	B-protein_state
WT	B-protein_state
β1	B-protein
active	B-site
-	I-site
site	I-site
Thr1	B-residue_name_number
.	O

Only	O
the	O
residues	O
(-	B-residue_range
5	I-residue_range
)	I-residue_range
to	I-residue_range
(-	I-residue_range
1	I-residue_range
)	I-residue_range
of	O
the	O
β1	B-mutant
-	I-mutant
T1A	I-mutant
propeptide	B-structure_element
are	O
displayed	O
.	O

The	O
major	O
determinant	O
of	O
the	O
S1	B-site
specificity	I-site
pocket	I-site
,	O
residue	O
45	B-residue_number
,	O
is	O
depicted	O
.	O

Note	O
the	O
tight	O
conformation	O
of	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
and	O
Ala1	B-residue_name_number
before	O
propeptide	B-structure_element
removal	O
(	O
G	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
turn	O
;	O
cyan	O
double	O
arrow	O
)	O
compared	O
with	O
the	O
relaxed	O
,	O
processed	B-protein_state
WT	B-protein_state
active	B-site
-	I-site
site	I-site
Thr1	B-residue_name_number
(	O
red	O
double	O
arrow	O
).	O

The	O
black	O
arrow	O
indicates	O
the	O
attack	O
of	O
Thr1Oγ	B-residue_name_number
onto	O
the	O
carbonyl	O
carbon	O
atom	O
of	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
).	I-residue_name_number

(	O
b	O
)	O
Structural	B-experimental_method
superposition	I-experimental_method
of	O
the	O
β1	B-mutant
-	I-mutant
T1A	I-mutant
propeptide	B-structure_element
and	O
the	O
β2	B-mutant
-	I-mutant
T1A	I-mutant
propeptide	B-structure_element
highlights	O
subtle	O
differences	O
in	O
their	O
conformations	O
,	O
but	O
illustrates	O
that	O
Ala1	B-residue_name_number
and	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
match	O
well	O
.	O

Thr	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
OH	O
is	O
hydrogen	O
-	O
bonded	O
to	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
O	O
(∼	O
2	O
.	O
8	O
Å	O
;	O
black	O
dashed	O
line	O
).	O

(	O
c	O
)	O
Structural	B-experimental_method
superposition	I-experimental_method
of	O
the	O
β1	B-mutant
-	I-mutant
T1A	I-mutant
,	O
the	O
β2	B-mutant
-	I-mutant
T1A	I-mutant
and	O
the	O
β5	B-mutant
-	I-mutant
T1A	I-mutant
-	I-mutant
K81R	I-mutant
propeptide	B-structure_element
remnants	O
depict	O
their	O
differences	O
in	O
conformation	O
.	O

While	O
residue	O
(-	B-residue_number
2	I-residue_number
)	I-residue_number
of	O
the	O
β1	B-protein
and	O
β2	B-protein
prosegments	B-structure_element
fit	O
the	O
S1	B-site
pocket	I-site
,	O
His	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
of	O
the	O
β5	B-protein
propeptide	B-structure_element
occupies	O
the	O
S2	B-site
pocket	I-site
.	O

Nonetheless	O
,	O
in	O
all	O
mutants	O
the	O
carbonyl	O
carbon	O
atom	O
of	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
is	O
ideally	O
placed	O
for	O
the	O
nucleophilic	O
attack	O
by	O
Thr1Oγ	B-residue_name_number
.	O

The	O
hydrogen	O
bond	O
between	O
Thr	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
OH	O
and	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
O	O
(∼	O
2	O
.	O
8	O
Å	O
)	O
is	O
indicated	O
by	O
a	O
black	O
dashed	O
line	O
.	O

Mutations	B-experimental_method
of	O
residue	O
(-	B-residue_number
2	I-residue_number
)	I-residue_number
and	O
their	O
influence	O
on	O
propeptide	B-structure_element
conformation	O
and	O
autolysis	B-ptm
.	O

(	O
a	O
)	O
Structural	B-experimental_method
superposition	I-experimental_method
of	O
the	O
β1	B-mutant
-	I-mutant
T1A	I-mutant
propeptide	B-structure_element
and	O
the	O
β5	B-mutant
-	I-mutant
H	I-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
L	I-mutant
-	I-mutant
T1A	I-mutant
mutant	B-protein_state
propeptide	B-structure_element
.	O

The	O
(-	B-residue_number
2	I-residue_number
)	I-residue_number
residues	O
of	O
both	O
prosegments	B-structure_element
point	O
into	O
the	O
S1	B-site
pocket	I-site
.	O

(	O
b	O
)	O
Structural	B-experimental_method
superposition	I-experimental_method
of	O
the	O
β5	B-protein
propeptides	B-structure_element
in	O
the	O
β5	B-mutant
-	I-mutant
H	I-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
L	I-mutant
-	I-mutant
T1A	I-mutant
,	O
β5	B-mutant
-	I-mutant
H	I-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
T	I-mutant
-	I-mutant
T1A	I-mutant
,	O
β5	B-mutant
-(	I-mutant
H	I-mutant
-	I-mutant
2	I-mutant
)	I-mutant
A	I-mutant
-	I-mutant
T1A	I-mutant
-	I-mutant
K81R	I-mutant
and	O
β5	B-mutant
-	I-mutant
T1A	I-mutant
-	I-mutant
K81R	I-mutant
mutant	B-protein_state
proteasomes	B-complex_assembly
.	O

While	O
the	O
residues	O
(-	B-residue_range
2	I-residue_range
)	I-residue_range
to	I-residue_range
(-	I-residue_range
4	I-residue_range
)	I-residue_range
vary	O
in	O
their	O
conformation	O
,	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
and	O
Ala1	B-residue_name_number
are	O
located	O
in	O
all	O
structures	B-evidence
at	O
the	O
same	O
positions	O
.	O

(	O
c	O
)	O
Structural	B-experimental_method
superposition	I-experimental_method
of	O
the	O
β2	B-mutant
-	I-mutant
T1A	I-mutant
propeptide	B-structure_element
and	O
the	O
β5	B-mutant
-	I-mutant
H	I-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
T	I-mutant
-	I-mutant
T1A	I-mutant
mutant	B-protein_state
propeptide	B-structure_element
.	O

The	O
(-	B-residue_number
2	I-residue_number
)	I-residue_number
residues	O
of	O
both	O
prosegments	B-structure_element
point	O
into	O
the	O
S1	B-site
pocket	I-site
,	O
but	O
only	O
Thr	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
OH	O
of	O
β2	B-protein
forms	O
a	O
hydrogen	O
bridge	O
to	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
O	O
(	O
black	O
dashed	O
line	O
).	O

(	O
d	O
)	O
Structural	B-experimental_method
superposition	I-experimental_method
of	O
the	O
matured	B-protein_state
β2	B-protein
active	B-site
site	I-site
,	O
the	O
WT	B-protein_state
β2	B-mutant
-	I-mutant
T1A	I-mutant
propeptide	B-structure_element
and	O
the	O
β2	B-mutant
-	I-mutant
T	I-mutant
(-	I-mutant
2	I-mutant
)	I-mutant
V	I-mutant
mutant	B-protein_state
propeptide	B-structure_element
.	O

Notably	O
,	O
Val	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
of	O
the	O
latter	O
does	O
not	O
occupy	O
the	O
S1	B-site
pocket	I-site
,	O
thereby	O
changing	O
the	O
orientation	O
of	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
)	I-residue_name_number
and	O
preventing	O
nucleophilic	O
attack	O
of	O
Thr1Oγ	B-residue_name_number
on	O
the	O
carbonyl	O
carbon	O
atom	O
of	O
Gly	B-residue_name_number
(-	I-residue_name_number
1	I-residue_name_number
).	I-residue_name_number

Architecture	O
and	O
proposed	O
reaction	O
mechanism	O
of	O
the	O
proteasomal	O
active	B-site
site	I-site
.	O

(	O
a	O
)	O
Hydrogen	B-site
-	I-site
bonding	I-site
network	I-site
at	O
the	O
mature	B-protein_state
WT	B-protein_state
β5	B-protein
proteasomal	O
active	B-site
site	I-site
(	O
dotted	O
lines	O
).	O

Thr1OH	B-residue_name_number
is	O
hydrogen	O
-	O
bonded	O
to	O
Lys33NH2	B-residue_name_number
(	O
2	O
.	O
7	O
Å	O
),	O
which	O
in	O
turn	O
interacts	O
with	O
Asp17Oδ	B-residue_name_number
.	O

The	O
Thr1	B-residue_name_number
N	O
terminus	O
is	O
engaged	O
in	O
hydrogen	O
bonds	O
with	O
Ser129Oγ	B-residue_name_number
,	O
the	O
carbonyl	O
oxygen	O
of	O
residue	O
168	B-residue_number
,	O
Ser169Oγ	B-residue_name_number
and	O
Asp166Oδ	B-residue_name_number
.	O
(	O
b	O
)	O
The	O
orientations	O
of	O
the	O
active	B-site
-	I-site
site	I-site
residues	I-site
involved	O
in	O
hydrogen	O
bonding	O
are	O
strictly	B-protein_state
conserved	I-protein_state
in	O
each	O
proteolytic	B-site
centre	I-site
,	O
as	O
shown	O
by	O
superposition	B-experimental_method
of	O
the	O
β	B-protein
subunits	I-protein
.	O

(	O
c	O
)	O
Structural	B-experimental_method
superposition	I-experimental_method
of	O
the	O
WT	B-protein_state
β5	B-protein
and	O
the	O
β5	B-mutant
-	I-mutant
K33A	I-mutant
pp	B-chemical
trans	B-protein_state
mutant	B-protein_state
active	B-site
site	I-site
.	O

In	O
the	O
latter	O
,	O
a	O
water	B-chemical
molecule	O
(	O
red	O
sphere	O
)	O
is	O
found	O
at	O
the	O
position	O
where	O
in	O
the	O
WT	B-protein_state
structure	O
the	O
side	O
chain	O
amine	O
group	O
of	O
Lys33	B-residue_name_number
is	O
located	O
.	O

Similarly	O
to	O
Lys33	B-residue_name_number
,	O
the	O
water	B-chemical
molecule	O
hydrogen	O
bonds	O
to	O
Arg19O	B-residue_name_number
,	O
Asp17Oδ	B-residue_name_number
and	O
Thr1OH	B-residue_name_number
.	O

Note	O
,	O
the	O
strong	O
interaction	O
with	O
the	O
water	B-chemical
molecule	O
causes	O
a	O
minor	O
shift	O
of	O
Thr1	B-residue_name_number
,	O
while	O
all	O
other	O
active	B-site
-	I-site
site	I-site
residues	I-site
remain	O
in	O
place	O
.	O

(	O
d	O
)	O
Proposed	O
chemical	O
reaction	O
mechanism	O
for	O
autocatalytic	B-ptm
precursor	I-ptm
processing	I-ptm
and	O
proteolysis	O
in	O
the	O
proteasome	B-complex_assembly
.	O

The	O
active	B-site
-	I-site
site	I-site
Thr1	B-residue_name_number
is	O
depicted	O
in	O
blue	O
,	O
the	O
propeptide	B-structure_element
segment	O
and	O
the	O
peptide	O
substrate	O
are	O
coloured	O
in	O
green	O
,	O
whereas	O
the	O
scissile	O
peptide	O
bond	O
is	O
highlighted	O
in	O
red	O
.	O

Autolysis	B-ptm
(	O
left	O
set	O
of	O
structures	O
)	O
is	O
initiated	O
by	O
deprotonation	O
of	O
Thr1OH	B-residue_name_number
via	O
Lys33NH2	B-residue_name_number
and	O
the	O
formation	O
of	O
a	O
tetrahedral	O
transition	O
state	O
.	O

The	O
strictly	B-protein_state
conserved	I-protein_state
oxyanion	O
hole	O
Gly47NH	B-residue_name_number
stabilizing	O
the	O
negatively	O
charged	O
intermediate	O
is	O
illustrated	O
as	O
a	O
semicircle	O
.	O

Collapse	O
of	O
the	O
transition	O
state	O
frees	O
the	O
Thr1	B-residue_name_number
N	O
terminus	O
(	O
by	O
completing	O
an	O
N	O
-	O
to	O
-	O
O	O
acyl	O
shift	O
of	O
the	O
propeptide	B-structure_element
),	O
which	O
is	O
subsequently	O
protonated	O
by	O
Asp166OH	B-residue_name_number
via	O
Ser129OH	B-residue_name_number
.	O

Next	O
,	O
Thr1NH2	B-residue_name_number
polarizes	O
a	O
water	B-chemical
molecule	O
for	O
the	O
nucleophilic	O
attack	O
of	O
the	O
acyl	O
-	O
enzyme	O
intermediate	O
.	O

On	O
hydrolysis	O
of	O
the	O
latter	O
,	O
the	O
active	B-site
-	I-site
site	I-site
Thr1	B-residue_name_number
is	O
ready	O
for	O
catalysis	O
(	O
right	O
set	O
of	O
structures	O
).	O

The	O
charged	O
Thr1	B-residue_name_number
N	O
terminus	O
may	O
engage	O
in	O
the	O
orientation	O
of	O
the	O
amide	O
moiety	O
and	O
donate	O
a	O
proton	O
to	O
the	O
emerging	O
N	O
terminus	O
of	O
the	O
C	O
-	O
terminal	O
cleavage	O
product	O
.	O

The	O
resulting	O
deprotonated	O
Thr1NH2	B-residue_name_number
finally	O
activates	O
a	O
water	B-chemical
molecule	O
for	O
hydrolysis	O
of	O
the	O
acyl	O
-	O
enzyme	O
.	O

The	O
proteasome	B-complex_assembly
favours	O
threonine	B-residue_name
as	O
the	O
active	O
-	O
site	O
nucleophile	O
.	O

(	O
a	O
)	O
Growth	B-experimental_method
tests	I-experimental_method
by	I-experimental_method
serial	I-experimental_method
dilution	I-experimental_method
of	O
WT	B-protein_state
and	O
pre2	O
(	O
β5	B-protein
)	O
mutant	B-protein_state
yeast	B-taxonomy_domain
cultures	O
reveal	O
growth	O
defects	O
of	O
the	O
active	B-site
-	I-site
site	I-site
mutants	B-experimental_method
under	O
the	O
indicated	O
conditions	O
after	O
2	O
days	O
(	O
2	O
d	O
)	O
of	O
incubation	O
.	O

(	O
b	O
)	O
Purified	O
WT	B-protein_state
and	O
mutant	B-protein_state
proteasomes	B-complex_assembly
were	O
tested	O
for	O
their	O
chymotrypsin	O
-	O
like	O
activity	O
(	O
β5	B-protein
)	O
using	O
the	O
substrate	O
Suc	B-chemical
-	I-chemical
LLVY	I-chemical
-	I-chemical
AMC	I-chemical
.	O

(	O
c	O
)	O
Illustration	O
of	O
the	O
2FO	B-evidence
–	I-evidence
FC	I-evidence
electron	I-evidence
-	I-evidence
density	I-evidence
map	I-evidence
(	O
blue	O
mesh	O
contoured	O
at	O
1σ	O
)	O
for	O
the	O
β5	B-mutant
-	I-mutant
T1C	I-mutant
propeptide	B-structure_element
fragment	O
.	O

The	O
prosegment	B-structure_element
is	O
cleaved	B-protein_state
but	O
still	B-protein_state
bound	I-protein_state
in	O
the	O
substrate	B-site
-	I-site
binding	I-site
channel	I-site
.	O

Notably	O
,	O
His	B-residue_name_number
(-	I-residue_name_number
2	I-residue_name_number
)	I-residue_name_number
does	O
not	O
occupy	O
the	O
S1	B-site
pocket	I-site
formed	O
by	O
Met45	B-residue_name_number
,	O
similar	O
to	O
what	O
was	O
observed	O
for	O
the	O
β5	B-mutant
-	I-mutant
T1A	I-mutant
-	I-mutant
K81R	I-mutant
mutant	B-protein_state
.	O

(	O
d	O
)	O
Structural	B-experimental_method
superposition	I-experimental_method
of	O
the	O
β5	B-mutant
-	I-mutant
T1A	I-mutant
-	I-mutant
K81R	I-mutant
and	O
the	O
β5	B-mutant
-	I-mutant
T1C	I-mutant
mutant	B-protein_state
subunits	O
onto	O
the	O
WT	B-protein_state
β5	B-protein
subunit	O
.	O
(	O
e	O
)	O
Structural	B-experimental_method
superposition	I-experimental_method
of	O
the	O
β5	B-mutant
-	I-mutant
T1C	I-mutant
propeptide	B-structure_element
onto	O
the	O
β1	B-mutant
-	I-mutant
T1A	I-mutant
active	B-site
site	I-site
(	O
blue	O
)	O
and	O
the	O
WT	B-protein_state
β5	B-protein
active	B-site
site	I-site
in	B-protein_state
complex	I-protein_state
with	I-protein_state
the	O
proteasome	B-complex_assembly
inhibitor	O
MG132	B-chemical
(	O
ref	O
.).	O

The	O
inhibitor	B-chemical
as	O
well	O
as	O
the	O
propeptides	B-structure_element
adopt	O
similar	O
conformations	O
in	O
the	O
substrate	B-site
-	I-site
binding	I-site
channel	I-site
.	O

(	O
f	O
)	O
Structural	B-experimental_method
superposition	I-experimental_method
of	O
the	O
WT	B-protein_state
β5	B-protein
and	O
β5	B-mutant
-	I-mutant
T1C	I-mutant
mutant	B-protein_state
active	B-site
sites	I-site
illustrates	O
the	O
different	O
orientations	O
of	O
the	O
hydroxyl	O
group	O
of	O
Thr1	B-residue_name_number
and	O
the	O
thiol	O
side	O
chain	O
of	O
Cys1	B-residue_name_number
.	O

(	O
g	O
)	O
Structural	B-experimental_method
superposition	I-experimental_method
of	O
the	O
WT	B-protein_state
β5	B-protein
and	O
β5	B-mutant
-	I-mutant
T1S	I-mutant
mutant	B-protein_state
active	B-site
sites	I-site
reveals	O
different	O
orientations	O
of	O
the	O
hydroxyl	O
groups	O
of	O
Thr1	B-residue_name_number
and	O
Ser1	B-residue_name_number
,	O
respectively	O
.	O

The	O
2FO	B-evidence
–	I-evidence
FC	I-evidence
electron	I-evidence
-	I-evidence
density	I-evidence
map	I-evidence
for	O
Ser1	B-residue_name_number
(	O
blue	O
mesh	O
contoured	O
at	O
1σ	O
)	O
is	O
illustrated	O
.	O

(	O
h	O
)	O
The	O
methyl	O
group	O
of	O
Thr1	B-residue_name_number
is	O
anchored	O
by	O
hydrophobic	O
interactions	O
with	O
Ala46Cβ	B-residue_name_number
and	O
Thr3Cγ	B-residue_name_number
.	O

Ser1	B-residue_name_number
lacks	B-protein_state
this	O
stabilization	O
and	O
is	O
therefore	O
rotated	O
by	O
60	O
°.	O

Inhibition	O
of	O
WT	B-protein_state
and	O
mutant	B-protein_state
β5	B-mutant
-	I-mutant
T1S	I-mutant
proteasomes	B-complex_assembly
by	O
bortezomib	B-chemical
and	O
carfilzomib	B-chemical
.	O

Inhibition	B-experimental_method
assays	I-experimental_method
(	O
left	O
panel	O
).	O

Purified	O
yeast	B-taxonomy_domain
proteasomes	B-complex_assembly
were	O
tested	O
for	O
the	O
susceptibility	O
of	O
their	O
ChT	O
-	O
L	O
(	O
β5	B-protein
)	O
activity	O
to	O
inhibition	O
by	O
bortezomib	B-chemical
and	O
carfilzomib	B-chemical
using	O
the	O
substrate	O
Suc	B-chemical
-	I-chemical
LLVY	I-chemical
-	I-chemical
AMC	I-chemical
.	O

IC50	B-evidence
values	I-evidence
were	O
determined	O
in	O
triplicate	O
;	O
s	O
.	O
d	O
.'	O
s	O
are	O
indicated	O
by	O
error	O
bars	O
.	O

Note	O
that	O
IC50	B-evidence
values	I-evidence
depend	O
on	O
time	O
and	O
enzyme	O
concentration	O
.	O

Proteasomes	B-complex_assembly
(	O
final	O
concentration	O
:	O
66	O
nM	O
)	O
were	O
incubated	O
with	O
inhibitor	O
for	O
45	O
min	O
before	O
substrate	O
addition	O
(	O
final	O
concentration	O
:	O
200	O
μM	O
).	O

Structures	B-evidence
of	O
the	O
β5	B-mutant
-	I-mutant
T1S	I-mutant
mutant	B-protein_state
in	O
complex	B-complex_assembly
with	I-complex_assembly
both	I-complex_assembly
ligands	I-complex_assembly
(	O
green	O
)	O
prove	O
the	O
reactivity	O
of	O
Ser1	B-residue_name_number
(	O
right	O
panel	O
).	O

The	O
2FO	B-evidence
–	I-evidence
FC	I-evidence
electron	I-evidence
-	I-evidence
density	I-evidence
maps	I-evidence
(	O
blue	O
mesh	O
)	O
for	O
Ser1	B-residue_name_number
(	O
brown	O
)	O
and	O
the	O
covalently	O
bound	O
ligands	O
(	O
green	O
;	O
only	O
the	O
P1	B-site
site	I-site
(	O
Leu1	B-residue_name_number
)	O
is	O
shown	O
)	O
are	O
contoured	O
at	O
1σ	O
.	O

The	O
WT	B-protein_state
proteasome	B-complex_assembly
:	I-complex_assembly
inhibitor	I-complex_assembly
complex	I-complex_assembly
structures	B-evidence
(	O
inhibitor	O
in	O
grey	O
;	O
Thr1	B-residue_name_number
in	O
black	O
)	O
are	O
superimposed	B-experimental_method
and	O
demonstrate	O
that	O
mutation	B-experimental_method
of	O
Thr1	B-residue_name_number
to	O
Ser	B-residue_name
does	O
not	O
affect	O
the	O
binding	O
mode	O
of	O
bortezomib	B-chemical
or	O
carfilzomib	B-chemical
.	O