anno_start	anno_end	anno_text	entity_type	sentence	section
21	25	Mep2	protein_type	Structural basis for Mep2 ammonium transceptor activation by phosphorylation	TITLE
26	46	ammonium transceptor	protein_type	Structural basis for Mep2 ammonium transceptor activation by phosphorylation	TITLE
61	76	phosphorylation	ptm	Structural basis for Mep2 ammonium transceptor activation by phosphorylation	TITLE
0	13	Mep2 proteins	protein_type	Mep2 proteins are fungal transceptors that play an important role as ammonium sensors in fungal development.	ABSTRACT
18	24	fungal	taxonomy_domain	Mep2 proteins are fungal transceptors that play an important role as ammonium sensors in fungal development.	ABSTRACT
25	37	transceptors	protein_type	Mep2 proteins are fungal transceptors that play an important role as ammonium sensors in fungal development.	ABSTRACT
69	77	ammonium	chemical	Mep2 proteins are fungal transceptors that play an important role as ammonium sensors in fungal development.	ABSTRACT
89	95	fungal	taxonomy_domain	Mep2 proteins are fungal transceptors that play an important role as ammonium sensors in fungal development.	ABSTRACT
0	4	Mep2	protein_type	Mep2 activity is tightly regulated by phosphorylation, but how this is achieved at the molecular level is not clear.	ABSTRACT
38	53	phosphorylation	ptm	Mep2 activity is tightly regulated by phosphorylation, but how this is achieved at the molecular level is not clear.	ABSTRACT
15	39	X-ray crystal structures	evidence	Here we report X-ray crystal structures of the Mep2 orthologues from Saccharomyces cerevisiae and Candida albicans and show that under nitrogen-sufficient conditions the transporters are not phosphorylated and present in closed, inactive conformations.	ABSTRACT
47	51	Mep2	protein_type	Here we report X-ray crystal structures of the Mep2 orthologues from Saccharomyces cerevisiae and Candida albicans and show that under nitrogen-sufficient conditions the transporters are not phosphorylated and present in closed, inactive conformations.	ABSTRACT
69	93	Saccharomyces cerevisiae	species	Here we report X-ray crystal structures of the Mep2 orthologues from Saccharomyces cerevisiae and Candida albicans and show that under nitrogen-sufficient conditions the transporters are not phosphorylated and present in closed, inactive conformations.	ABSTRACT
98	114	Candida albicans	species	Here we report X-ray crystal structures of the Mep2 orthologues from Saccharomyces cerevisiae and Candida albicans and show that under nitrogen-sufficient conditions the transporters are not phosphorylated and present in closed, inactive conformations.	ABSTRACT
170	182	transporters	protein_type	Here we report X-ray crystal structures of the Mep2 orthologues from Saccharomyces cerevisiae and Candida albicans and show that under nitrogen-sufficient conditions the transporters are not phosphorylated and present in closed, inactive conformations.	ABSTRACT
187	205	not phosphorylated	protein_state	Here we report X-ray crystal structures of the Mep2 orthologues from Saccharomyces cerevisiae and Candida albicans and show that under nitrogen-sufficient conditions the transporters are not phosphorylated and present in closed, inactive conformations.	ABSTRACT
221	227	closed	protein_state	Here we report X-ray crystal structures of the Mep2 orthologues from Saccharomyces cerevisiae and Candida albicans and show that under nitrogen-sufficient conditions the transporters are not phosphorylated and present in closed, inactive conformations.	ABSTRACT
229	237	inactive	protein_state	Here we report X-ray crystal structures of the Mep2 orthologues from Saccharomyces cerevisiae and Candida albicans and show that under nitrogen-sufficient conditions the transporters are not phosphorylated and present in closed, inactive conformations.	ABSTRACT
16	20	open	protein_state	Relative to the open bacterial ammonium transporters, non-phosphorylated Mep2 exhibits shifts in cytoplasmic loops and the C-terminal region (CTR) to occlude the cytoplasmic exit of the channel and to interact with His2 of the twin-His motif.	ABSTRACT
21	30	bacterial	taxonomy_domain	Relative to the open bacterial ammonium transporters, non-phosphorylated Mep2 exhibits shifts in cytoplasmic loops and the C-terminal region (CTR) to occlude the cytoplasmic exit of the channel and to interact with His2 of the twin-His motif.	ABSTRACT
31	52	ammonium transporters	protein_type	Relative to the open bacterial ammonium transporters, non-phosphorylated Mep2 exhibits shifts in cytoplasmic loops and the C-terminal region (CTR) to occlude the cytoplasmic exit of the channel and to interact with His2 of the twin-His motif.	ABSTRACT
54	72	non-phosphorylated	protein_state	Relative to the open bacterial ammonium transporters, non-phosphorylated Mep2 exhibits shifts in cytoplasmic loops and the C-terminal region (CTR) to occlude the cytoplasmic exit of the channel and to interact with His2 of the twin-His motif.	ABSTRACT
73	77	Mep2	protein_type	Relative to the open bacterial ammonium transporters, non-phosphorylated Mep2 exhibits shifts in cytoplasmic loops and the C-terminal region (CTR) to occlude the cytoplasmic exit of the channel and to interact with His2 of the twin-His motif.	ABSTRACT
97	114	cytoplasmic loops	structure_element	Relative to the open bacterial ammonium transporters, non-phosphorylated Mep2 exhibits shifts in cytoplasmic loops and the C-terminal region (CTR) to occlude the cytoplasmic exit of the channel and to interact with His2 of the twin-His motif.	ABSTRACT
123	140	C-terminal region	structure_element	Relative to the open bacterial ammonium transporters, non-phosphorylated Mep2 exhibits shifts in cytoplasmic loops and the C-terminal region (CTR) to occlude the cytoplasmic exit of the channel and to interact with His2 of the twin-His motif.	ABSTRACT
142	145	CTR	structure_element	Relative to the open bacterial ammonium transporters, non-phosphorylated Mep2 exhibits shifts in cytoplasmic loops and the C-terminal region (CTR) to occlude the cytoplasmic exit of the channel and to interact with His2 of the twin-His motif.	ABSTRACT
174	178	exit	site	Relative to the open bacterial ammonium transporters, non-phosphorylated Mep2 exhibits shifts in cytoplasmic loops and the C-terminal region (CTR) to occlude the cytoplasmic exit of the channel and to interact with His2 of the twin-His motif.	ABSTRACT
186	193	channel	site	Relative to the open bacterial ammonium transporters, non-phosphorylated Mep2 exhibits shifts in cytoplasmic loops and the C-terminal region (CTR) to occlude the cytoplasmic exit of the channel and to interact with His2 of the twin-His motif.	ABSTRACT
215	219	His2	residue_name_number	Relative to the open bacterial ammonium transporters, non-phosphorylated Mep2 exhibits shifts in cytoplasmic loops and the C-terminal region (CTR) to occlude the cytoplasmic exit of the channel and to interact with His2 of the twin-His motif.	ABSTRACT
227	241	twin-His motif	structure_element	Relative to the open bacterial ammonium transporters, non-phosphorylated Mep2 exhibits shifts in cytoplasmic loops and the C-terminal region (CTR) to occlude the cytoplasmic exit of the channel and to interact with His2 of the twin-His motif.	ABSTRACT
4	24	phosphorylation site	site	The phosphorylation site in the CTR is solvent accessible and located in a negatively charged pocket ∼30 Å away from the channel exit.	ABSTRACT
32	35	CTR	structure_element	The phosphorylation site in the CTR is solvent accessible and located in a negatively charged pocket ∼30 Å away from the channel exit.	ABSTRACT
39	57	solvent accessible	protein_state	The phosphorylation site in the CTR is solvent accessible and located in a negatively charged pocket ∼30 Å away from the channel exit.	ABSTRACT
75	100	negatively charged pocket	site	The phosphorylation site in the CTR is solvent accessible and located in a negatively charged pocket ∼30 Å away from the channel exit.	ABSTRACT
121	133	channel exit	site	The phosphorylation site in the CTR is solvent accessible and located in a negatively charged pocket ∼30 Å away from the channel exit.	ABSTRACT
4	21	crystal structure	evidence	The crystal structure of phosphorylation-mimicking Mep2 variants from C. albicans show large conformational changes in a conserved and functionally important region of the CTR.	ABSTRACT
25	50	phosphorylation-mimicking	protein_state	The crystal structure of phosphorylation-mimicking Mep2 variants from C. albicans show large conformational changes in a conserved and functionally important region of the CTR.	ABSTRACT
51	64	Mep2 variants	mutant	The crystal structure of phosphorylation-mimicking Mep2 variants from C. albicans show large conformational changes in a conserved and functionally important region of the CTR.	ABSTRACT
70	81	C. albicans	species	The crystal structure of phosphorylation-mimicking Mep2 variants from C. albicans show large conformational changes in a conserved and functionally important region of the CTR.	ABSTRACT
121	130	conserved	protein_state	The crystal structure of phosphorylation-mimicking Mep2 variants from C. albicans show large conformational changes in a conserved and functionally important region of the CTR.	ABSTRACT
172	175	CTR	structure_element	The crystal structure of phosphorylation-mimicking Mep2 variants from C. albicans show large conformational changes in a conserved and functionally important region of the CTR.	ABSTRACT
58	68	eukaryotic	taxonomy_domain	The results allow us to propose a model for regulation of eukaryotic ammonium transport by phosphorylation.	ABSTRACT
69	77	ammonium	chemical	The results allow us to propose a model for regulation of eukaryotic ammonium transport by phosphorylation.	ABSTRACT
91	106	phosphorylation	ptm	The results allow us to propose a model for regulation of eukaryotic ammonium transport by phosphorylation.	ABSTRACT
1	14	Mep2 proteins	protein_type	 Mep2 proteins are tightly regulated fungal ammonium transporters.	ABSTRACT
37	43	fungal	taxonomy_domain	 Mep2 proteins are tightly regulated fungal ammonium transporters.	ABSTRACT
44	65	ammonium transporters	protein_type	 Mep2 proteins are tightly regulated fungal ammonium transporters.	ABSTRACT
29	47	crystal structures	evidence	Here, the authors report the crystal structures of closed states of Mep2 proteins and propose a model for their regulation by comparing them with the open ammonium transporters of bacteria.	ABSTRACT
51	57	closed	protein_state	Here, the authors report the crystal structures of closed states of Mep2 proteins and propose a model for their regulation by comparing them with the open ammonium transporters of bacteria.	ABSTRACT
68	81	Mep2 proteins	protein_type	Here, the authors report the crystal structures of closed states of Mep2 proteins and propose a model for their regulation by comparing them with the open ammonium transporters of bacteria.	ABSTRACT
123	145	by comparing them with	experimental_method	Here, the authors report the crystal structures of closed states of Mep2 proteins and propose a model for their regulation by comparing them with the open ammonium transporters of bacteria.	ABSTRACT
150	154	open	protein_state	Here, the authors report the crystal structures of closed states of Mep2 proteins and propose a model for their regulation by comparing them with the open ammonium transporters of bacteria.	ABSTRACT
155	176	ammonium transporters	protein_type	Here, the authors report the crystal structures of closed states of Mep2 proteins and propose a model for their regulation by comparing them with the open ammonium transporters of bacteria.	ABSTRACT
180	188	bacteria	taxonomy_domain	Here, the authors report the crystal structures of closed states of Mep2 proteins and propose a model for their regulation by comparing them with the open ammonium transporters of bacteria.	ABSTRACT
0	12	Transceptors	protein_type	Transceptors are membrane proteins that function not only as transporters but also as receptors/sensors during nutrient sensing to activate downstream signalling pathways.	INTRO
17	34	membrane proteins	protein_type	Transceptors are membrane proteins that function not only as transporters but also as receptors/sensors during nutrient sensing to activate downstream signalling pathways.	INTRO
20	32	transceptors	protein_type	A common feature of transceptors is that they are induced when cells are starved for their substrate.	INTRO
39	63	Saccharomyces cerevisiae	species	While most studies have focused on the Saccharomyces cerevisiae transceptors for phosphate (Pho84), amino acids (Gap1) and ammonium (Mep2), transceptors are found in higher eukaryotes as well (for example, the mammalian SNAT2 amino-acid transporter and the GLUT2 glucose transporter).	INTRO
64	76	transceptors	protein_type	While most studies have focused on the Saccharomyces cerevisiae transceptors for phosphate (Pho84), amino acids (Gap1) and ammonium (Mep2), transceptors are found in higher eukaryotes as well (for example, the mammalian SNAT2 amino-acid transporter and the GLUT2 glucose transporter).	INTRO
81	90	phosphate	chemical	While most studies have focused on the Saccharomyces cerevisiae transceptors for phosphate (Pho84), amino acids (Gap1) and ammonium (Mep2), transceptors are found in higher eukaryotes as well (for example, the mammalian SNAT2 amino-acid transporter and the GLUT2 glucose transporter).	INTRO
92	97	Pho84	protein	While most studies have focused on the Saccharomyces cerevisiae transceptors for phosphate (Pho84), amino acids (Gap1) and ammonium (Mep2), transceptors are found in higher eukaryotes as well (for example, the mammalian SNAT2 amino-acid transporter and the GLUT2 glucose transporter).	INTRO
100	111	amino acids	chemical	While most studies have focused on the Saccharomyces cerevisiae transceptors for phosphate (Pho84), amino acids (Gap1) and ammonium (Mep2), transceptors are found in higher eukaryotes as well (for example, the mammalian SNAT2 amino-acid transporter and the GLUT2 glucose transporter).	INTRO
113	117	Gap1	protein	While most studies have focused on the Saccharomyces cerevisiae transceptors for phosphate (Pho84), amino acids (Gap1) and ammonium (Mep2), transceptors are found in higher eukaryotes as well (for example, the mammalian SNAT2 amino-acid transporter and the GLUT2 glucose transporter).	INTRO
123	131	ammonium	chemical	While most studies have focused on the Saccharomyces cerevisiae transceptors for phosphate (Pho84), amino acids (Gap1) and ammonium (Mep2), transceptors are found in higher eukaryotes as well (for example, the mammalian SNAT2 amino-acid transporter and the GLUT2 glucose transporter).	INTRO
133	137	Mep2	protein	While most studies have focused on the Saccharomyces cerevisiae transceptors for phosphate (Pho84), amino acids (Gap1) and ammonium (Mep2), transceptors are found in higher eukaryotes as well (for example, the mammalian SNAT2 amino-acid transporter and the GLUT2 glucose transporter).	INTRO
140	152	transceptors	protein_type	While most studies have focused on the Saccharomyces cerevisiae transceptors for phosphate (Pho84), amino acids (Gap1) and ammonium (Mep2), transceptors are found in higher eukaryotes as well (for example, the mammalian SNAT2 amino-acid transporter and the GLUT2 glucose transporter).	INTRO
166	183	higher eukaryotes	taxonomy_domain	While most studies have focused on the Saccharomyces cerevisiae transceptors for phosphate (Pho84), amino acids (Gap1) and ammonium (Mep2), transceptors are found in higher eukaryotes as well (for example, the mammalian SNAT2 amino-acid transporter and the GLUT2 glucose transporter).	INTRO
210	219	mammalian	taxonomy_domain	While most studies have focused on the Saccharomyces cerevisiae transceptors for phosphate (Pho84), amino acids (Gap1) and ammonium (Mep2), transceptors are found in higher eukaryotes as well (for example, the mammalian SNAT2 amino-acid transporter and the GLUT2 glucose transporter).	INTRO
220	225	SNAT2	protein	While most studies have focused on the Saccharomyces cerevisiae transceptors for phosphate (Pho84), amino acids (Gap1) and ammonium (Mep2), transceptors are found in higher eukaryotes as well (for example, the mammalian SNAT2 amino-acid transporter and the GLUT2 glucose transporter).	INTRO
226	248	amino-acid transporter	protein_type	While most studies have focused on the Saccharomyces cerevisiae transceptors for phosphate (Pho84), amino acids (Gap1) and ammonium (Mep2), transceptors are found in higher eukaryotes as well (for example, the mammalian SNAT2 amino-acid transporter and the GLUT2 glucose transporter).	INTRO
257	262	GLUT2	protein	While most studies have focused on the Saccharomyces cerevisiae transceptors for phosphate (Pho84), amino acids (Gap1) and ammonium (Mep2), transceptors are found in higher eukaryotes as well (for example, the mammalian SNAT2 amino-acid transporter and the GLUT2 glucose transporter).	INTRO
263	282	glucose transporter	protein_type	While most studies have focused on the Saccharomyces cerevisiae transceptors for phosphate (Pho84), amino acids (Gap1) and ammonium (Mep2), transceptors are found in higher eukaryotes as well (for example, the mammalian SNAT2 amino-acid transporter and the GLUT2 glucose transporter).	INTRO
71	83	transceptors	protein_type	One of the most important unresolved questions in the field is how the transceptors couple to downstream signalling pathways.	INTRO
92	103	transporter	protein_type	One hypothesis is that downstream signalling is dependent on a specific conformation of the transporter.	INTRO
0	4	Mep2	protein_type	Mep2 (methylammonium (MA) permease) proteins are ammonium transceptors that are ubiquitous in fungi.	INTRO
5	44	(methylammonium (MA) permease) proteins	protein_type	Mep2 (methylammonium (MA) permease) proteins are ammonium transceptors that are ubiquitous in fungi.	INTRO
49	70	ammonium transceptors	protein_type	Mep2 (methylammonium (MA) permease) proteins are ammonium transceptors that are ubiquitous in fungi.	INTRO
94	99	fungi	taxonomy_domain	Mep2 (methylammonium (MA) permease) proteins are ammonium transceptors that are ubiquitous in fungi.	INTRO
19	52	Amt/Mep/Rh family of transporters	protein_type	They belong to the Amt/Mep/Rh family of transporters that are present in all kingdoms of life and they take up ammonium from the extracellular environment.	INTRO
73	93	all kingdoms of life	taxonomy_domain	They belong to the Amt/Mep/Rh family of transporters that are present in all kingdoms of life and they take up ammonium from the extracellular environment.	INTRO
111	119	ammonium	chemical	They belong to the Amt/Mep/Rh family of transporters that are present in all kingdoms of life and they take up ammonium from the extracellular environment.	INTRO
0	5	Fungi	taxonomy_domain	Fungi typically have more than one Mep paralogue, for example, Mep1-3 in S. cerevisiae.	INTRO
35	38	Mep	protein_type	Fungi typically have more than one Mep paralogue, for example, Mep1-3 in S. cerevisiae.	INTRO
63	69	Mep1-3	protein	Fungi typically have more than one Mep paralogue, for example, Mep1-3 in S. cerevisiae.	INTRO
73	86	S. cerevisiae	species	Fungi typically have more than one Mep paralogue, for example, Mep1-3 in S. cerevisiae.	INTRO
15	28	Mep2 proteins	protein_type	Of these, only Mep2 proteins function as ammonium receptors/sensors in fungal development.	INTRO
41	49	ammonium	chemical	Of these, only Mep2 proteins function as ammonium receptors/sensors in fungal development.	INTRO
71	77	fungal	taxonomy_domain	Of these, only Mep2 proteins function as ammonium receptors/sensors in fungal development.	INTRO
41	45	Mep2	protein	Under conditions of nitrogen limitation, Mep2 initiates a signalling cascade that results in a switch from the yeast form to filamentous (pseudohyphal) growth that may be required for fungal pathogenicity.	INTRO
184	190	fungal	taxonomy_domain	Under conditions of nitrogen limitation, Mep2 initiates a signalling cascade that results in a switch from the yeast form to filamentous (pseudohyphal) growth that may be required for fungal pathogenicity.	INTRO
25	37	transceptors	protein_type	As is the case for other transceptors, it is not clear how Mep2 interacts with downstream signalling partners, but the protein kinase A and mitogen-activated protein kinase pathways have been proposed as downstream effectors of Mep2 (refs).	INTRO
59	63	Mep2	protein	As is the case for other transceptors, it is not clear how Mep2 interacts with downstream signalling partners, but the protein kinase A and mitogen-activated protein kinase pathways have been proposed as downstream effectors of Mep2 (refs).	INTRO
228	232	Mep2	protein	As is the case for other transceptors, it is not clear how Mep2 interacts with downstream signalling partners, but the protein kinase A and mitogen-activated protein kinase pathways have been proposed as downstream effectors of Mep2 (refs).	INTRO
14	18	Mep1	protein	Compared with Mep1 and Mep3, Mep2 is highly expressed and functions as a low-capacity, high-affinity transporter in the uptake of MA.	INTRO
23	27	Mep3	protein	Compared with Mep1 and Mep3, Mep2 is highly expressed and functions as a low-capacity, high-affinity transporter in the uptake of MA.	INTRO
29	33	Mep2	protein	Compared with Mep1 and Mep3, Mep2 is highly expressed and functions as a low-capacity, high-affinity transporter in the uptake of MA.	INTRO
37	53	highly expressed	protein_state	Compared with Mep1 and Mep3, Mep2 is highly expressed and functions as a low-capacity, high-affinity transporter in the uptake of MA.	INTRO
130	132	MA	chemical	Compared with Mep1 and Mep3, Mep2 is highly expressed and functions as a low-capacity, high-affinity transporter in the uptake of MA.	INTRO
13	17	Mep2	protein	In addition, Mep2 is also important for uptake of ammonium produced by growth on other nitrogen sources.	INTRO
50	58	ammonium	chemical	In addition, Mep2 is also important for uptake of ammonium produced by growth on other nitrogen sources.	INTRO
87	95	nitrogen	chemical	In addition, Mep2 is also important for uptake of ammonium produced by growth on other nitrogen sources.	INTRO
26	31	human	species	With the exception of the human RhCG structure, no structural information is available for eukaryotic ammonium transporters.	INTRO
32	36	RhCG	protein	With the exception of the human RhCG structure, no structural information is available for eukaryotic ammonium transporters.	INTRO
37	46	structure	evidence	With the exception of the human RhCG structure, no structural information is available for eukaryotic ammonium transporters.	INTRO
91	101	eukaryotic	taxonomy_domain	With the exception of the human RhCG structure, no structural information is available for eukaryotic ammonium transporters.	INTRO
102	123	ammonium transporters	protein_type	With the exception of the human RhCG structure, no structural information is available for eukaryotic ammonium transporters.	INTRO
21	30	bacterial	taxonomy_domain	By contrast, several bacterial Amt orthologues have been characterized in detail via high-resolution crystal structures and a number of molecular dynamics (MD) studies.	INTRO
31	34	Amt	protein_type	By contrast, several bacterial Amt orthologues have been characterized in detail via high-resolution crystal structures and a number of molecular dynamics (MD) studies.	INTRO
101	119	crystal structures	evidence	By contrast, several bacterial Amt orthologues have been characterized in detail via high-resolution crystal structures and a number of molecular dynamics (MD) studies.	INTRO
136	154	molecular dynamics	experimental_method	By contrast, several bacterial Amt orthologues have been characterized in detail via high-resolution crystal structures and a number of molecular dynamics (MD) studies.	INTRO
156	158	MD	experimental_method	By contrast, several bacterial Amt orthologues have been characterized in detail via high-resolution crystal structures and a number of molecular dynamics (MD) studies.	INTRO
15	25	structures	evidence	All the solved structures including that of RhCG are very similar, establishing the basic architecture of ammonium transporters.	INTRO
44	48	RhCG	protein	All the solved structures including that of RhCG are very similar, establishing the basic architecture of ammonium transporters.	INTRO
106	127	ammonium transporters	protein_type	All the solved structures including that of RhCG are very similar, establishing the basic architecture of ammonium transporters.	INTRO
18	24	stable	protein_state	The proteins form stable trimers, with each monomer having 11 transmembrane (TM) helices and a central channel for the transport of ammonium.	INTRO
25	32	trimers	oligomeric_state	The proteins form stable trimers, with each monomer having 11 transmembrane (TM) helices and a central channel for the transport of ammonium.	INTRO
44	51	monomer	oligomeric_state	The proteins form stable trimers, with each monomer having 11 transmembrane (TM) helices and a central channel for the transport of ammonium.	INTRO
62	75	transmembrane	structure_element	The proteins form stable trimers, with each monomer having 11 transmembrane (TM) helices and a central channel for the transport of ammonium.	INTRO
77	79	TM	structure_element	The proteins form stable trimers, with each monomer having 11 transmembrane (TM) helices and a central channel for the transport of ammonium.	INTRO
81	88	helices	structure_element	The proteins form stable trimers, with each monomer having 11 transmembrane (TM) helices and a central channel for the transport of ammonium.	INTRO
95	110	central channel	site	The proteins form stable trimers, with each monomer having 11 transmembrane (TM) helices and a central channel for the transport of ammonium.	INTRO
132	140	ammonium	chemical	The proteins form stable trimers, with each monomer having 11 transmembrane (TM) helices and a central channel for the transport of ammonium.	INTRO
4	14	structures	evidence	All structures show the transporters in open conformations.	INTRO
24	36	transporters	protein_type	All structures show the transporters in open conformations.	INTRO
40	44	open	protein_state	All structures show the transporters in open conformations.	INTRO
48	55	ammonia	chemical	Where earlier studies favoured the transport of ammonia gas, recent data and theoretical considerations suggest that Amt/Mep proteins are instead active, electrogenic transporters of either NH4+ (uniport) or NH3/H+ (symport).	INTRO
117	133	Amt/Mep proteins	protein_type	Where earlier studies favoured the transport of ammonia gas, recent data and theoretical considerations suggest that Amt/Mep proteins are instead active, electrogenic transporters of either NH4+ (uniport) or NH3/H+ (symport).	INTRO
146	152	active	protein_state	Where earlier studies favoured the transport of ammonia gas, recent data and theoretical considerations suggest that Amt/Mep proteins are instead active, electrogenic transporters of either NH4+ (uniport) or NH3/H+ (symport).	INTRO
154	179	electrogenic transporters	protein_type	Where earlier studies favoured the transport of ammonia gas, recent data and theoretical considerations suggest that Amt/Mep proteins are instead active, electrogenic transporters of either NH4+ (uniport) or NH3/H+ (symport).	INTRO
190	194	NH4+	chemical	Where earlier studies favoured the transport of ammonia gas, recent data and theoretical considerations suggest that Amt/Mep proteins are instead active, electrogenic transporters of either NH4+ (uniport) or NH3/H+ (symport).	INTRO
208	211	NH3	chemical	Where earlier studies favoured the transport of ammonia gas, recent data and theoretical considerations suggest that Amt/Mep proteins are instead active, electrogenic transporters of either NH4+ (uniport) or NH3/H+ (symport).	INTRO
212	214	H+	chemical	Where earlier studies favoured the transport of ammonia gas, recent data and theoretical considerations suggest that Amt/Mep proteins are instead active, electrogenic transporters of either NH4+ (uniport) or NH3/H+ (symport).	INTRO
2	18	highly conserved	protein_state	A highly conserved pair of channel-lining histidine residues dubbed the twin-His motif may serve as a proton relay system while NH3 moves through the channel during NH3/H+ symport.	INTRO
27	34	channel	site	A highly conserved pair of channel-lining histidine residues dubbed the twin-His motif may serve as a proton relay system while NH3 moves through the channel during NH3/H+ symport.	INTRO
42	51	histidine	residue_name	A highly conserved pair of channel-lining histidine residues dubbed the twin-His motif may serve as a proton relay system while NH3 moves through the channel during NH3/H+ symport.	INTRO
72	86	twin-His motif	structure_element	A highly conserved pair of channel-lining histidine residues dubbed the twin-His motif may serve as a proton relay system while NH3 moves through the channel during NH3/H+ symport.	INTRO
128	131	NH3	chemical	A highly conserved pair of channel-lining histidine residues dubbed the twin-His motif may serve as a proton relay system while NH3 moves through the channel during NH3/H+ symport.	INTRO
150	157	channel	site	A highly conserved pair of channel-lining histidine residues dubbed the twin-His motif may serve as a proton relay system while NH3 moves through the channel during NH3/H+ symport.	INTRO
165	168	NH3	chemical	A highly conserved pair of channel-lining histidine residues dubbed the twin-His motif may serve as a proton relay system while NH3 moves through the channel during NH3/H+ symport.	INTRO
169	171	H+	chemical	A highly conserved pair of channel-lining histidine residues dubbed the twin-His motif may serve as a proton relay system while NH3 moves through the channel during NH3/H+ symport.	INTRO
0	8	Ammonium	chemical	Ammonium transport is tightly regulated.	INTRO
3	10	animals	taxonomy_domain	In animals, this is due to toxicity of elevated intracellular ammonium levels, whereas for microorganisms ammonium is a preferred nitrogen source.	INTRO
62	70	ammonium	chemical	In animals, this is due to toxicity of elevated intracellular ammonium levels, whereas for microorganisms ammonium is a preferred nitrogen source.	INTRO
91	105	microorganisms	taxonomy_domain	In animals, this is due to toxicity of elevated intracellular ammonium levels, whereas for microorganisms ammonium is a preferred nitrogen source.	INTRO
106	114	ammonium	chemical	In animals, this is due to toxicity of elevated intracellular ammonium levels, whereas for microorganisms ammonium is a preferred nitrogen source.	INTRO
3	11	bacteria	taxonomy_domain	In bacteria, amt genes are present in an operon with glnK, encoding a PII-like signal transduction class protein.	INTRO
13	16	amt	gene	In bacteria, amt genes are present in an operon with glnK, encoding a PII-like signal transduction class protein.	INTRO
53	57	glnK	gene	In bacteria, amt genes are present in an operon with glnK, encoding a PII-like signal transduction class protein.	INTRO
70	112	PII-like signal transduction class protein	protein_type	In bacteria, amt genes are present in an operon with glnK, encoding a PII-like signal transduction class protein.	INTRO
22	34	Amt proteins	protein_type	By binding tightly to Amt proteins without inducing a conformational change in the transporter, GlnK sterically blocks ammonium conductance when nitrogen levels are sufficient.	INTRO
83	94	transporter	protein_type	By binding tightly to Amt proteins without inducing a conformational change in the transporter, GlnK sterically blocks ammonium conductance when nitrogen levels are sufficient.	INTRO
96	100	GlnK	protein_type	By binding tightly to Amt proteins without inducing a conformational change in the transporter, GlnK sterically blocks ammonium conductance when nitrogen levels are sufficient.	INTRO
119	127	ammonium	chemical	By binding tightly to Amt proteins without inducing a conformational change in the transporter, GlnK sterically blocks ammonium conductance when nitrogen levels are sufficient.	INTRO
20	28	nitrogen	chemical	Under conditions of nitrogen limitation, GlnK becomes uridylated, blocking its ability to bind and inhibit Amt proteins.	INTRO
41	45	GlnK	protein_type	Under conditions of nitrogen limitation, GlnK becomes uridylated, blocking its ability to bind and inhibit Amt proteins.	INTRO
54	64	uridylated	protein_state	Under conditions of nitrogen limitation, GlnK becomes uridylated, blocking its ability to bind and inhibit Amt proteins.	INTRO
107	119	Amt proteins	protein_type	Under conditions of nitrogen limitation, GlnK becomes uridylated, blocking its ability to bind and inhibit Amt proteins.	INTRO
13	23	eukaryotes	taxonomy_domain	Importantly, eukaryotes do not have GlnK orthologues and have a different mechanism for regulation of ammonium transport activity.	INTRO
36	40	GlnK	protein_type	Importantly, eukaryotes do not have GlnK orthologues and have a different mechanism for regulation of ammonium transport activity.	INTRO
102	110	ammonium	chemical	Importantly, eukaryotes do not have GlnK orthologues and have a different mechanism for regulation of ammonium transport activity.	INTRO
3	9	plants	taxonomy_domain	In plants, transporter phosphorylation and dephosphorylation are known to regulate activity.	INTRO
11	22	transporter	protein_type	In plants, transporter phosphorylation and dephosphorylation are known to regulate activity.	INTRO
23	38	phosphorylation	ptm	In plants, transporter phosphorylation and dephosphorylation are known to regulate activity.	INTRO
43	60	dephosphorylation	ptm	In plants, transporter phosphorylation and dephosphorylation are known to regulate activity.	INTRO
3	16	S. cerevisiae	species	In S. cerevisiae, phosphorylation of Ser457 within the C-terminal region (CTR) in the cytoplasm was recently proposed to cause Mep2 opening, possibly via inducing a conformational change.	INTRO
18	33	phosphorylation	ptm	In S. cerevisiae, phosphorylation of Ser457 within the C-terminal region (CTR) in the cytoplasm was recently proposed to cause Mep2 opening, possibly via inducing a conformational change.	INTRO
37	43	Ser457	residue_name_number	In S. cerevisiae, phosphorylation of Ser457 within the C-terminal region (CTR) in the cytoplasm was recently proposed to cause Mep2 opening, possibly via inducing a conformational change.	INTRO
55	72	C-terminal region	structure_element	In S. cerevisiae, phosphorylation of Ser457 within the C-terminal region (CTR) in the cytoplasm was recently proposed to cause Mep2 opening, possibly via inducing a conformational change.	INTRO
74	77	CTR	structure_element	In S. cerevisiae, phosphorylation of Ser457 within the C-terminal region (CTR) in the cytoplasm was recently proposed to cause Mep2 opening, possibly via inducing a conformational change.	INTRO
127	131	Mep2	protein_type	In S. cerevisiae, phosphorylation of Ser457 within the C-terminal region (CTR) in the cytoplasm was recently proposed to cause Mep2 opening, possibly via inducing a conformational change.	INTRO
30	34	Mep2	protein_type	To elucidate the mechanism of Mep2 transport regulation, we present here X-ray crystal structures of the Mep2 transceptors from S. cerevisiae and C. albicans.	INTRO
73	97	X-ray crystal structures	evidence	To elucidate the mechanism of Mep2 transport regulation, we present here X-ray crystal structures of the Mep2 transceptors from S. cerevisiae and C. albicans.	INTRO
105	122	Mep2 transceptors	protein_type	To elucidate the mechanism of Mep2 transport regulation, we present here X-ray crystal structures of the Mep2 transceptors from S. cerevisiae and C. albicans.	INTRO
128	141	S. cerevisiae	species	To elucidate the mechanism of Mep2 transport regulation, we present here X-ray crystal structures of the Mep2 transceptors from S. cerevisiae and C. albicans.	INTRO
146	157	C. albicans	species	To elucidate the mechanism of Mep2 transport regulation, we present here X-ray crystal structures of the Mep2 transceptors from S. cerevisiae and C. albicans.	INTRO
4	14	structures	evidence	The structures are similar to each other but show considerable differences to all other ammonium transporter structures.	INTRO
88	108	ammonium transporter	protein_type	The structures are similar to each other but show considerable differences to all other ammonium transporter structures.	INTRO
109	119	structures	evidence	The structures are similar to each other but show considerable differences to all other ammonium transporter structures.	INTRO
50	63	Mep2 proteins	protein_type	The most striking difference is the fact that the Mep2 proteins have closed conformations.	INTRO
69	75	closed	protein_state	The most striking difference is the fact that the Mep2 proteins have closed conformations.	INTRO
13	33	phosphorylation site	site	The putative phosphorylation site is solvent accessible and located in a negatively charged pocket ∼30 Å away from the channel exit.	INTRO
37	55	solvent accessible	protein_state	The putative phosphorylation site is solvent accessible and located in a negatively charged pocket ∼30 Å away from the channel exit.	INTRO
73	98	negatively charged pocket	site	The putative phosphorylation site is solvent accessible and located in a negatively charged pocket ∼30 Å away from the channel exit.	INTRO
119	131	channel exit	site	The putative phosphorylation site is solvent accessible and located in a negatively charged pocket ∼30 Å away from the channel exit.	INTRO
4	12	channels	site	The channels of phosphorylation-mimicking mutants of C. albicans Mep2 are still closed but show large conformational changes within a conserved part of the CTR.	INTRO
16	49	phosphorylation-mimicking mutants	protein_state	The channels of phosphorylation-mimicking mutants of C. albicans Mep2 are still closed but show large conformational changes within a conserved part of the CTR.	INTRO
53	64	C. albicans	species	The channels of phosphorylation-mimicking mutants of C. albicans Mep2 are still closed but show large conformational changes within a conserved part of the CTR.	INTRO
65	69	Mep2	protein	The channels of phosphorylation-mimicking mutants of C. albicans Mep2 are still closed but show large conformational changes within a conserved part of the CTR.	INTRO
80	86	closed	protein_state	The channels of phosphorylation-mimicking mutants of C. albicans Mep2 are still closed but show large conformational changes within a conserved part of the CTR.	INTRO
134	143	conserved	protein_state	The channels of phosphorylation-mimicking mutants of C. albicans Mep2 are still closed but show large conformational changes within a conserved part of the CTR.	INTRO
156	159	CTR	structure_element	The channels of phosphorylation-mimicking mutants of C. albicans Mep2 are still closed but show large conformational changes within a conserved part of the CTR.	INTRO
16	25	structure	evidence	Together with a structure of a C-terminal Mep2 variant lacking the segment containing the phosphorylation site, the results allow us to propose a structural model for phosphorylation-based regulation of eukaryotic ammonium transport.	INTRO
42	54	Mep2 variant	mutant	Together with a structure of a C-terminal Mep2 variant lacking the segment containing the phosphorylation site, the results allow us to propose a structural model for phosphorylation-based regulation of eukaryotic ammonium transport.	INTRO
55	62	lacking	protein_state	Together with a structure of a C-terminal Mep2 variant lacking the segment containing the phosphorylation site, the results allow us to propose a structural model for phosphorylation-based regulation of eukaryotic ammonium transport.	INTRO
67	74	segment	structure_element	Together with a structure of a C-terminal Mep2 variant lacking the segment containing the phosphorylation site, the results allow us to propose a structural model for phosphorylation-based regulation of eukaryotic ammonium transport.	INTRO
90	110	phosphorylation site	site	Together with a structure of a C-terminal Mep2 variant lacking the segment containing the phosphorylation site, the results allow us to propose a structural model for phosphorylation-based regulation of eukaryotic ammonium transport.	INTRO
203	213	eukaryotic	taxonomy_domain	Together with a structure of a C-terminal Mep2 variant lacking the segment containing the phosphorylation site, the results allow us to propose a structural model for phosphorylation-based regulation of eukaryotic ammonium transport.	INTRO
214	222	ammonium	chemical	Together with a structure of a C-terminal Mep2 variant lacking the segment containing the phosphorylation site, the results allow us to propose a structural model for phosphorylation-based regulation of eukaryotic ammonium transport.	INTRO
24	28	Mep2	protein_type	General architecture of Mep2 ammonium transceptors	RESULTS
29	50	ammonium transceptors	protein_type	General architecture of Mep2 ammonium transceptors	RESULTS
4	8	Mep2	protein	The Mep2 protein of S. cerevisiae (ScMep2) was overexpressed in S. cerevisiae in high yields, enabling structure determination by X-ray crystallography using data to 3.2 Å resolution by molecular replacement (MR) with the archaebacterial Amt-1 structure (see Methods section).	RESULTS
20	33	S. cerevisiae	species	The Mep2 protein of S. cerevisiae (ScMep2) was overexpressed in S. cerevisiae in high yields, enabling structure determination by X-ray crystallography using data to 3.2 Å resolution by molecular replacement (MR) with the archaebacterial Amt-1 structure (see Methods section).	RESULTS
35	41	ScMep2	protein	The Mep2 protein of S. cerevisiae (ScMep2) was overexpressed in S. cerevisiae in high yields, enabling structure determination by X-ray crystallography using data to 3.2 Å resolution by molecular replacement (MR) with the archaebacterial Amt-1 structure (see Methods section).	RESULTS
47	60	overexpressed	experimental_method	The Mep2 protein of S. cerevisiae (ScMep2) was overexpressed in S. cerevisiae in high yields, enabling structure determination by X-ray crystallography using data to 3.2 Å resolution by molecular replacement (MR) with the archaebacterial Amt-1 structure (see Methods section).	RESULTS
64	77	S. cerevisiae	species	The Mep2 protein of S. cerevisiae (ScMep2) was overexpressed in S. cerevisiae in high yields, enabling structure determination by X-ray crystallography using data to 3.2 Å resolution by molecular replacement (MR) with the archaebacterial Amt-1 structure (see Methods section).	RESULTS
103	126	structure determination	experimental_method	The Mep2 protein of S. cerevisiae (ScMep2) was overexpressed in S. cerevisiae in high yields, enabling structure determination by X-ray crystallography using data to 3.2 Å resolution by molecular replacement (MR) with the archaebacterial Amt-1 structure (see Methods section).	RESULTS
130	151	X-ray crystallography	experimental_method	The Mep2 protein of S. cerevisiae (ScMep2) was overexpressed in S. cerevisiae in high yields, enabling structure determination by X-ray crystallography using data to 3.2 Å resolution by molecular replacement (MR) with the archaebacterial Amt-1 structure (see Methods section).	RESULTS
186	207	molecular replacement	experimental_method	The Mep2 protein of S. cerevisiae (ScMep2) was overexpressed in S. cerevisiae in high yields, enabling structure determination by X-ray crystallography using data to 3.2 Å resolution by molecular replacement (MR) with the archaebacterial Amt-1 structure (see Methods section).	RESULTS
209	211	MR	experimental_method	The Mep2 protein of S. cerevisiae (ScMep2) was overexpressed in S. cerevisiae in high yields, enabling structure determination by X-ray crystallography using data to 3.2 Å resolution by molecular replacement (MR) with the archaebacterial Amt-1 structure (see Methods section).	RESULTS
222	237	archaebacterial	taxonomy_domain	The Mep2 protein of S. cerevisiae (ScMep2) was overexpressed in S. cerevisiae in high yields, enabling structure determination by X-ray crystallography using data to 3.2 Å resolution by molecular replacement (MR) with the archaebacterial Amt-1 structure (see Methods section).	RESULTS
238	243	Amt-1	protein	The Mep2 protein of S. cerevisiae (ScMep2) was overexpressed in S. cerevisiae in high yields, enabling structure determination by X-ray crystallography using data to 3.2 Å resolution by molecular replacement (MR) with the archaebacterial Amt-1 structure (see Methods section).	RESULTS
244	253	structure	evidence	The Mep2 protein of S. cerevisiae (ScMep2) was overexpressed in S. cerevisiae in high yields, enabling structure determination by X-ray crystallography using data to 3.2 Å resolution by molecular replacement (MR) with the archaebacterial Amt-1 structure (see Methods section).	RESULTS
40	49	structure	evidence	Given that the modest resolution of the structure and the limited detergent stability of ScMep2 would likely complicate structure–function studies, several other fungal Mep2 orthologues were subsequently overexpressed and screened for diffraction-quality crystals.	RESULTS
89	95	ScMep2	protein	Given that the modest resolution of the structure and the limited detergent stability of ScMep2 would likely complicate structure–function studies, several other fungal Mep2 orthologues were subsequently overexpressed and screened for diffraction-quality crystals.	RESULTS
120	146	structure–function studies	experimental_method	Given that the modest resolution of the structure and the limited detergent stability of ScMep2 would likely complicate structure–function studies, several other fungal Mep2 orthologues were subsequently overexpressed and screened for diffraction-quality crystals.	RESULTS
162	168	fungal	taxonomy_domain	Given that the modest resolution of the structure and the limited detergent stability of ScMep2 would likely complicate structure–function studies, several other fungal Mep2 orthologues were subsequently overexpressed and screened for diffraction-quality crystals.	RESULTS
169	173	Mep2	protein_type	Given that the modest resolution of the structure and the limited detergent stability of ScMep2 would likely complicate structure–function studies, several other fungal Mep2 orthologues were subsequently overexpressed and screened for diffraction-quality crystals.	RESULTS
204	234	overexpressed and screened for	experimental_method	Given that the modest resolution of the structure and the limited detergent stability of ScMep2 would likely complicate structure–function studies, several other fungal Mep2 orthologues were subsequently overexpressed and screened for diffraction-quality crystals.	RESULTS
255	263	crystals	evidence	Given that the modest resolution of the structure and the limited detergent stability of ScMep2 would likely complicate structure–function studies, several other fungal Mep2 orthologues were subsequently overexpressed and screened for diffraction-quality crystals.	RESULTS
10	14	Mep2	protein	Of these, Mep2 from C. albicans (CaMep2) showed superior stability in relatively harsh detergents such as nonyl-glucoside, allowing structure determination in two different crystal forms to high resolution (up to 1.5 Å).	RESULTS
20	31	C. albicans	species	Of these, Mep2 from C. albicans (CaMep2) showed superior stability in relatively harsh detergents such as nonyl-glucoside, allowing structure determination in two different crystal forms to high resolution (up to 1.5 Å).	RESULTS
33	39	CaMep2	protein	Of these, Mep2 from C. albicans (CaMep2) showed superior stability in relatively harsh detergents such as nonyl-glucoside, allowing structure determination in two different crystal forms to high resolution (up to 1.5 Å).	RESULTS
132	155	structure determination	experimental_method	Of these, Mep2 from C. albicans (CaMep2) showed superior stability in relatively harsh detergents such as nonyl-glucoside, allowing structure determination in two different crystal forms to high resolution (up to 1.5 Å).	RESULTS
173	186	crystal forms	evidence	Of these, Mep2 from C. albicans (CaMep2) showed superior stability in relatively harsh detergents such as nonyl-glucoside, allowing structure determination in two different crystal forms to high resolution (up to 1.5 Å).	RESULTS
67	73	CaMep2	protein	Despite different crystal packing (Supplementary Table 1), the two CaMep2 structures are identical to each other and very similar to ScMep2 (Cα r.m.s.d.	RESULTS
74	84	structures	evidence	Despite different crystal packing (Supplementary Table 1), the two CaMep2 structures are identical to each other and very similar to ScMep2 (Cα r.m.s.d.	RESULTS
133	139	ScMep2	protein	Despite different crystal packing (Supplementary Table 1), the two CaMep2 structures are identical to each other and very similar to ScMep2 (Cα r.m.s.d.	RESULTS
144	152	r.m.s.d.	evidence	Despite different crystal packing (Supplementary Table 1), the two CaMep2 structures are identical to each other and very similar to ScMep2 (Cα r.m.s.d.	RESULTS
1	27	root mean square deviation	evidence	(root mean square deviation)=0.7 Å for 434 residues), with the main differences confined to the N terminus and the CTR (Fig. 1).	RESULTS
115	118	CTR	structure_element	(root mean square deviation)=0.7 Å for 434 residues), with the main differences confined to the N terminus and the CTR (Fig. 1).	RESULTS
0	16	Electron density	evidence	Electron density is visible for the entire polypeptide chains, with the exception of the C-terminal 43 (ScMep2) and 25 residues (CaMep2), which are poorly conserved and presumably disordered.	RESULTS
100	102	43	residue_range	Electron density is visible for the entire polypeptide chains, with the exception of the C-terminal 43 (ScMep2) and 25 residues (CaMep2), which are poorly conserved and presumably disordered.	RESULTS
104	110	ScMep2	protein	Electron density is visible for the entire polypeptide chains, with the exception of the C-terminal 43 (ScMep2) and 25 residues (CaMep2), which are poorly conserved and presumably disordered.	RESULTS
116	118	25	residue_range	Electron density is visible for the entire polypeptide chains, with the exception of the C-terminal 43 (ScMep2) and 25 residues (CaMep2), which are poorly conserved and presumably disordered.	RESULTS
129	135	CaMep2	protein	Electron density is visible for the entire polypeptide chains, with the exception of the C-terminal 43 (ScMep2) and 25 residues (CaMep2), which are poorly conserved and presumably disordered.	RESULTS
148	164	poorly conserved	protein_state	Electron density is visible for the entire polypeptide chains, with the exception of the C-terminal 43 (ScMep2) and 25 residues (CaMep2), which are poorly conserved and presumably disordered.	RESULTS
180	190	disordered	protein_state	Electron density is visible for the entire polypeptide chains, with the exception of the C-terminal 43 (ScMep2) and 25 residues (CaMep2), which are poorly conserved and presumably disordered.	RESULTS
5	18	Mep2 proteins	protein_type	Both Mep2 proteins show the archetypal trimeric assemblies in which each monomer consists of 11 TM helices surrounding a central pore.	RESULTS
39	47	trimeric	oligomeric_state	Both Mep2 proteins show the archetypal trimeric assemblies in which each monomer consists of 11 TM helices surrounding a central pore.	RESULTS
73	80	monomer	oligomeric_state	Both Mep2 proteins show the archetypal trimeric assemblies in which each monomer consists of 11 TM helices surrounding a central pore.	RESULTS
96	106	TM helices	structure_element	Both Mep2 proteins show the archetypal trimeric assemblies in which each monomer consists of 11 TM helices surrounding a central pore.	RESULTS
121	133	central pore	structure_element	Both Mep2 proteins show the archetypal trimeric assemblies in which each monomer consists of 11 TM helices surrounding a central pore.	RESULTS
56	77	ammonium binding site	site	Important functional features such as the extracellular ammonium binding site, the Phe gate and the twin-His motif within the hydrophobic channel are all very similar to those present in the bacterial transporters and RhCG.	RESULTS
83	91	Phe gate	site	Important functional features such as the extracellular ammonium binding site, the Phe gate and the twin-His motif within the hydrophobic channel are all very similar to those present in the bacterial transporters and RhCG.	RESULTS
100	114	twin-His motif	structure_element	Important functional features such as the extracellular ammonium binding site, the Phe gate and the twin-His motif within the hydrophobic channel are all very similar to those present in the bacterial transporters and RhCG.	RESULTS
126	145	hydrophobic channel	site	Important functional features such as the extracellular ammonium binding site, the Phe gate and the twin-His motif within the hydrophobic channel are all very similar to those present in the bacterial transporters and RhCG.	RESULTS
191	200	bacterial	taxonomy_domain	Important functional features such as the extracellular ammonium binding site, the Phe gate and the twin-His motif within the hydrophobic channel are all very similar to those present in the bacterial transporters and RhCG.	RESULTS
201	213	transporters	protein_type	Important functional features such as the extracellular ammonium binding site, the Phe gate and the twin-His motif within the hydrophobic channel are all very similar to those present in the bacterial transporters and RhCG.	RESULTS
218	222	RhCG	protein	Important functional features such as the extracellular ammonium binding site, the Phe gate and the twin-His motif within the hydrophobic channel are all very similar to those present in the bacterial transporters and RhCG.	RESULTS
65	71	CaMep2	protein	In the remainder of the manuscript, we will specifically discuss CaMep2 due to the superior resolution of the structure.	RESULTS
110	119	structure	evidence	In the remainder of the manuscript, we will specifically discuss CaMep2 due to the superior resolution of the structure.	RESULTS
64	70	ScMep2	protein	Unless specifically stated, the drawn conclusions also apply to ScMep2.	RESULTS
34	38	Mep2	protein	While the overall architecture of Mep2 is similar to that of the prokaryotic transporters (Cα r.m.s.d. with Amt-1=1.4 Å for 361 residues), there are large differences within the N terminus, intracellular loops (ICLs) ICL1 and ICL3, and the CTR.	RESULTS
65	76	prokaryotic	taxonomy_domain	While the overall architecture of Mep2 is similar to that of the prokaryotic transporters (Cα r.m.s.d. with Amt-1=1.4 Å for 361 residues), there are large differences within the N terminus, intracellular loops (ICLs) ICL1 and ICL3, and the CTR.	RESULTS
77	89	transporters	protein_type	While the overall architecture of Mep2 is similar to that of the prokaryotic transporters (Cα r.m.s.d. with Amt-1=1.4 Å for 361 residues), there are large differences within the N terminus, intracellular loops (ICLs) ICL1 and ICL3, and the CTR.	RESULTS
94	102	r.m.s.d.	evidence	While the overall architecture of Mep2 is similar to that of the prokaryotic transporters (Cα r.m.s.d. with Amt-1=1.4 Å for 361 residues), there are large differences within the N terminus, intracellular loops (ICLs) ICL1 and ICL3, and the CTR.	RESULTS
108	113	Amt-1	protein	While the overall architecture of Mep2 is similar to that of the prokaryotic transporters (Cα r.m.s.d. with Amt-1=1.4 Å for 361 residues), there are large differences within the N terminus, intracellular loops (ICLs) ICL1 and ICL3, and the CTR.	RESULTS
190	209	intracellular loops	structure_element	While the overall architecture of Mep2 is similar to that of the prokaryotic transporters (Cα r.m.s.d. with Amt-1=1.4 Å for 361 residues), there are large differences within the N terminus, intracellular loops (ICLs) ICL1 and ICL3, and the CTR.	RESULTS
211	215	ICLs	structure_element	While the overall architecture of Mep2 is similar to that of the prokaryotic transporters (Cα r.m.s.d. with Amt-1=1.4 Å for 361 residues), there are large differences within the N terminus, intracellular loops (ICLs) ICL1 and ICL3, and the CTR.	RESULTS
217	221	ICL1	structure_element	While the overall architecture of Mep2 is similar to that of the prokaryotic transporters (Cα r.m.s.d. with Amt-1=1.4 Å for 361 residues), there are large differences within the N terminus, intracellular loops (ICLs) ICL1 and ICL3, and the CTR.	RESULTS
226	230	ICL3	structure_element	While the overall architecture of Mep2 is similar to that of the prokaryotic transporters (Cα r.m.s.d. with Amt-1=1.4 Å for 361 residues), there are large differences within the N terminus, intracellular loops (ICLs) ICL1 and ICL3, and the CTR.	RESULTS
240	243	CTR	structure_element	While the overall architecture of Mep2 is similar to that of the prokaryotic transporters (Cα r.m.s.d. with Amt-1=1.4 Å for 361 residues), there are large differences within the N terminus, intracellular loops (ICLs) ICL1 and ICL3, and the CTR.	RESULTS
21	34	Mep2 proteins	protein_type	The N termini of the Mep2 proteins are ∼20–25 residues longer compared with their bacterial counterparts (Figs 1 and 2), substantially increasing the size of the extracellular domain.	RESULTS
40	45	20–25	residue_range	The N termini of the Mep2 proteins are ∼20–25 residues longer compared with their bacterial counterparts (Figs 1 and 2), substantially increasing the size of the extracellular domain.	RESULTS
82	91	bacterial	taxonomy_domain	The N termini of the Mep2 proteins are ∼20–25 residues longer compared with their bacterial counterparts (Figs 1 and 2), substantially increasing the size of the extracellular domain.	RESULTS
162	182	extracellular domain	structure_element	The N termini of the Mep2 proteins are ∼20–25 residues longer compared with their bacterial counterparts (Figs 1 and 2), substantially increasing the size of the extracellular domain.	RESULTS
32	39	monomer	oligomeric_state	Moreover, the N terminus of one monomer interacts with the extended extracellular loop ECL5 of a neighbouring monomer.	RESULTS
68	86	extracellular loop	structure_element	Moreover, the N terminus of one monomer interacts with the extended extracellular loop ECL5 of a neighbouring monomer.	RESULTS
87	91	ECL5	structure_element	Moreover, the N terminus of one monomer interacts with the extended extracellular loop ECL5 of a neighbouring monomer.	RESULTS
110	117	monomer	oligomeric_state	Moreover, the N terminus of one monomer interacts with the extended extracellular loop ECL5 of a neighbouring monomer.	RESULTS
55	74	extracellular loops	structure_element	Together with additional, smaller differences in other extracellular loops, these changes generate a distinct vestibule leading to the ammonium binding site that is much more pronounced than in the bacterial proteins.	RESULTS
110	119	vestibule	structure_element	Together with additional, smaller differences in other extracellular loops, these changes generate a distinct vestibule leading to the ammonium binding site that is much more pronounced than in the bacterial proteins.	RESULTS
135	156	ammonium binding site	site	Together with additional, smaller differences in other extracellular loops, these changes generate a distinct vestibule leading to the ammonium binding site that is much more pronounced than in the bacterial proteins.	RESULTS
198	207	bacterial	taxonomy_domain	Together with additional, smaller differences in other extracellular loops, these changes generate a distinct vestibule leading to the ammonium binding site that is much more pronounced than in the bacterial proteins.	RESULTS
15	24	vestibule	structure_element	The N-terminal vestibule and the resulting inter-monomer interactions likely increase the stability of the Mep2 trimer, in support of data for plant AMT proteins.	RESULTS
49	56	monomer	oligomeric_state	The N-terminal vestibule and the resulting inter-monomer interactions likely increase the stability of the Mep2 trimer, in support of data for plant AMT proteins.	RESULTS
107	111	Mep2	protein	The N-terminal vestibule and the resulting inter-monomer interactions likely increase the stability of the Mep2 trimer, in support of data for plant AMT proteins.	RESULTS
112	118	trimer	oligomeric_state	The N-terminal vestibule and the resulting inter-monomer interactions likely increase the stability of the Mep2 trimer, in support of data for plant AMT proteins.	RESULTS
143	148	plant	taxonomy_domain	The N-terminal vestibule and the resulting inter-monomer interactions likely increase the stability of the Mep2 trimer, in support of data for plant AMT proteins.	RESULTS
149	161	AMT proteins	protein_type	The N-terminal vestibule and the resulting inter-monomer interactions likely increase the stability of the Mep2 trimer, in support of data for plant AMT proteins.	RESULTS
34	49	deletion mutant	protein_state	However, given that an N-terminal deletion mutant (2-27Δ) grows as well as wild-type (WT) Mep2 on minimal ammonium medium (Fig. 3 and Supplementary Fig. 1), the importance of the N terminus for Mep2 activity is not clear.	RESULTS
51	56	2-27Δ	mutant	However, given that an N-terminal deletion mutant (2-27Δ) grows as well as wild-type (WT) Mep2 on minimal ammonium medium (Fig. 3 and Supplementary Fig. 1), the importance of the N terminus for Mep2 activity is not clear.	RESULTS
75	84	wild-type	protein_state	However, given that an N-terminal deletion mutant (2-27Δ) grows as well as wild-type (WT) Mep2 on minimal ammonium medium (Fig. 3 and Supplementary Fig. 1), the importance of the N terminus for Mep2 activity is not clear.	RESULTS
86	88	WT	protein_state	However, given that an N-terminal deletion mutant (2-27Δ) grows as well as wild-type (WT) Mep2 on minimal ammonium medium (Fig. 3 and Supplementary Fig. 1), the importance of the N terminus for Mep2 activity is not clear.	RESULTS
90	94	Mep2	protein	However, given that an N-terminal deletion mutant (2-27Δ) grows as well as wild-type (WT) Mep2 on minimal ammonium medium (Fig. 3 and Supplementary Fig. 1), the importance of the N terminus for Mep2 activity is not clear.	RESULTS
106	114	ammonium	chemical	However, given that an N-terminal deletion mutant (2-27Δ) grows as well as wild-type (WT) Mep2 on minimal ammonium medium (Fig. 3 and Supplementary Fig. 1), the importance of the N terminus for Mep2 activity is not clear.	RESULTS
194	198	Mep2	protein	However, given that an N-terminal deletion mutant (2-27Δ) grows as well as wild-type (WT) Mep2 on minimal ammonium medium (Fig. 3 and Supplementary Fig. 1), the importance of the N terminus for Mep2 activity is not clear.	RESULTS
0	4	Mep2	protein	Mep2 channels are closed by a two-tier channel block	RESULTS
5	13	channels	site	Mep2 channels are closed by a two-tier channel block	RESULTS
18	24	closed	protein_state	Mep2 channels are closed by a two-tier channel block	RESULTS
39	52	channel block	structure_element	Mep2 channels are closed by a two-tier channel block	RESULTS
36	40	Mep2	protein	The largest differences between the Mep2 structures and the other known ammonium transporter structures are located on the intracellular side of the membrane.	RESULTS
41	51	structures	evidence	The largest differences between the Mep2 structures and the other known ammonium transporter structures are located on the intracellular side of the membrane.	RESULTS
72	92	ammonium transporter	protein_type	The largest differences between the Mep2 structures and the other known ammonium transporter structures are located on the intracellular side of the membrane.	RESULTS
93	103	structures	evidence	The largest differences between the Mep2 structures and the other known ammonium transporter structures are located on the intracellular side of the membrane.	RESULTS
23	27	Mep2	protein	In the vicinity of the Mep2 channel exit, the cytoplasmic end of TM2 has unwound, generating a longer ICL1 even though there are no insertions in this region compared to the bacterial proteins (Figs 2 and 4).	RESULTS
28	40	channel exit	site	In the vicinity of the Mep2 channel exit, the cytoplasmic end of TM2 has unwound, generating a longer ICL1 even though there are no insertions in this region compared to the bacterial proteins (Figs 2 and 4).	RESULTS
65	68	TM2	structure_element	In the vicinity of the Mep2 channel exit, the cytoplasmic end of TM2 has unwound, generating a longer ICL1 even though there are no insertions in this region compared to the bacterial proteins (Figs 2 and 4).	RESULTS
102	106	ICL1	structure_element	In the vicinity of the Mep2 channel exit, the cytoplasmic end of TM2 has unwound, generating a longer ICL1 even though there are no insertions in this region compared to the bacterial proteins (Figs 2 and 4).	RESULTS
174	183	bacterial	taxonomy_domain	In the vicinity of the Mep2 channel exit, the cytoplasmic end of TM2 has unwound, generating a longer ICL1 even though there are no insertions in this region compared to the bacterial proteins (Figs 2 and 4).	RESULTS
0	4	ICL1	structure_element	ICL1 has also moved inwards relative to its position in the bacterial Amts.	RESULTS
60	69	bacterial	taxonomy_domain	ICL1 has also moved inwards relative to its position in the bacterial Amts.	RESULTS
70	74	Amts	protein_type	ICL1 has also moved inwards relative to its position in the bacterial Amts.	RESULTS
61	65	ICL1	structure_element	The largest backbone movements of equivalent residues within ICL1 are ∼10 Å, markedly affecting the conserved basic RxK motif (Fig. 4).	RESULTS
100	109	conserved	protein_state	The largest backbone movements of equivalent residues within ICL1 are ∼10 Å, markedly affecting the conserved basic RxK motif (Fig. 4).	RESULTS
110	115	basic	protein_state	The largest backbone movements of equivalent residues within ICL1 are ∼10 Å, markedly affecting the conserved basic RxK motif (Fig. 4).	RESULTS
116	125	RxK motif	structure_element	The largest backbone movements of equivalent residues within ICL1 are ∼10 Å, markedly affecting the conserved basic RxK motif (Fig. 4).	RESULTS
18	23	Arg54	residue_name_number	The head group of Arg54 has moved ∼11 Å relative to that in Amt-1, whereas the shift of the head group of the variable Lys55 residue is almost 20 Å. The side chain of Lys56 in the basic motif points in an opposite direction in the Mep2 structures compared with that of, for example, Amt-1 (Fig. 4).	RESULTS
60	65	Amt-1	protein	The head group of Arg54 has moved ∼11 Å relative to that in Amt-1, whereas the shift of the head group of the variable Lys55 residue is almost 20 Å. The side chain of Lys56 in the basic motif points in an opposite direction in the Mep2 structures compared with that of, for example, Amt-1 (Fig. 4).	RESULTS
119	124	Lys55	residue_name_number	The head group of Arg54 has moved ∼11 Å relative to that in Amt-1, whereas the shift of the head group of the variable Lys55 residue is almost 20 Å. The side chain of Lys56 in the basic motif points in an opposite direction in the Mep2 structures compared with that of, for example, Amt-1 (Fig. 4).	RESULTS
167	172	Lys56	residue_name_number	The head group of Arg54 has moved ∼11 Å relative to that in Amt-1, whereas the shift of the head group of the variable Lys55 residue is almost 20 Å. The side chain of Lys56 in the basic motif points in an opposite direction in the Mep2 structures compared with that of, for example, Amt-1 (Fig. 4).	RESULTS
180	185	basic	protein_state	The head group of Arg54 has moved ∼11 Å relative to that in Amt-1, whereas the shift of the head group of the variable Lys55 residue is almost 20 Å. The side chain of Lys56 in the basic motif points in an opposite direction in the Mep2 structures compared with that of, for example, Amt-1 (Fig. 4).	RESULTS
186	191	motif	structure_element	The head group of Arg54 has moved ∼11 Å relative to that in Amt-1, whereas the shift of the head group of the variable Lys55 residue is almost 20 Å. The side chain of Lys56 in the basic motif points in an opposite direction in the Mep2 structures compared with that of, for example, Amt-1 (Fig. 4).	RESULTS
231	235	Mep2	protein	The head group of Arg54 has moved ∼11 Å relative to that in Amt-1, whereas the shift of the head group of the variable Lys55 residue is almost 20 Å. The side chain of Lys56 in the basic motif points in an opposite direction in the Mep2 structures compared with that of, for example, Amt-1 (Fig. 4).	RESULTS
236	246	structures	evidence	The head group of Arg54 has moved ∼11 Å relative to that in Amt-1, whereas the shift of the head group of the variable Lys55 residue is almost 20 Å. The side chain of Lys56 in the basic motif points in an opposite direction in the Mep2 structures compared with that of, for example, Amt-1 (Fig. 4).	RESULTS
283	288	Amt-1	protein	The head group of Arg54 has moved ∼11 Å relative to that in Amt-1, whereas the shift of the head group of the variable Lys55 residue is almost 20 Å. The side chain of Lys56 in the basic motif points in an opposite direction in the Mep2 structures compared with that of, for example, Amt-1 (Fig. 4).	RESULTS
28	37	RxK motif	structure_element	In addition to changing the RxK motif, the movement of ICL1 has another, crucial functional consequence.	RESULTS
55	59	ICL1	structure_element	In addition to changing the RxK motif, the movement of ICL1 has another, crucial functional consequence.	RESULTS
25	28	TM1	structure_element	At the C-terminal end of TM1, the side-chain hydroxyl group of the relatively conserved Tyr49 (Tyr53 in ScMep2) makes a strong hydrogen bond with the ɛ2 nitrogen atom of the absolutely conserved His342 of the twin-His motif (His348 in ScMep2), closing the channel (Figs 4 and 5).	RESULTS
67	87	relatively conserved	protein_state	At the C-terminal end of TM1, the side-chain hydroxyl group of the relatively conserved Tyr49 (Tyr53 in ScMep2) makes a strong hydrogen bond with the ɛ2 nitrogen atom of the absolutely conserved His342 of the twin-His motif (His348 in ScMep2), closing the channel (Figs 4 and 5).	RESULTS
88	93	Tyr49	residue_name_number	At the C-terminal end of TM1, the side-chain hydroxyl group of the relatively conserved Tyr49 (Tyr53 in ScMep2) makes a strong hydrogen bond with the ɛ2 nitrogen atom of the absolutely conserved His342 of the twin-His motif (His348 in ScMep2), closing the channel (Figs 4 and 5).	RESULTS
95	100	Tyr53	residue_name_number	At the C-terminal end of TM1, the side-chain hydroxyl group of the relatively conserved Tyr49 (Tyr53 in ScMep2) makes a strong hydrogen bond with the ɛ2 nitrogen atom of the absolutely conserved His342 of the twin-His motif (His348 in ScMep2), closing the channel (Figs 4 and 5).	RESULTS
104	110	ScMep2	protein	At the C-terminal end of TM1, the side-chain hydroxyl group of the relatively conserved Tyr49 (Tyr53 in ScMep2) makes a strong hydrogen bond with the ɛ2 nitrogen atom of the absolutely conserved His342 of the twin-His motif (His348 in ScMep2), closing the channel (Figs 4 and 5).	RESULTS
127	140	hydrogen bond	bond_interaction	At the C-terminal end of TM1, the side-chain hydroxyl group of the relatively conserved Tyr49 (Tyr53 in ScMep2) makes a strong hydrogen bond with the ɛ2 nitrogen atom of the absolutely conserved His342 of the twin-His motif (His348 in ScMep2), closing the channel (Figs 4 and 5).	RESULTS
174	194	absolutely conserved	protein_state	At the C-terminal end of TM1, the side-chain hydroxyl group of the relatively conserved Tyr49 (Tyr53 in ScMep2) makes a strong hydrogen bond with the ɛ2 nitrogen atom of the absolutely conserved His342 of the twin-His motif (His348 in ScMep2), closing the channel (Figs 4 and 5).	RESULTS
195	201	His342	residue_name_number	At the C-terminal end of TM1, the side-chain hydroxyl group of the relatively conserved Tyr49 (Tyr53 in ScMep2) makes a strong hydrogen bond with the ɛ2 nitrogen atom of the absolutely conserved His342 of the twin-His motif (His348 in ScMep2), closing the channel (Figs 4 and 5).	RESULTS
209	223	twin-His motif	structure_element	At the C-terminal end of TM1, the side-chain hydroxyl group of the relatively conserved Tyr49 (Tyr53 in ScMep2) makes a strong hydrogen bond with the ɛ2 nitrogen atom of the absolutely conserved His342 of the twin-His motif (His348 in ScMep2), closing the channel (Figs 4 and 5).	RESULTS
225	231	His348	residue_name_number	At the C-terminal end of TM1, the side-chain hydroxyl group of the relatively conserved Tyr49 (Tyr53 in ScMep2) makes a strong hydrogen bond with the ɛ2 nitrogen atom of the absolutely conserved His342 of the twin-His motif (His348 in ScMep2), closing the channel (Figs 4 and 5).	RESULTS
235	241	ScMep2	protein	At the C-terminal end of TM1, the side-chain hydroxyl group of the relatively conserved Tyr49 (Tyr53 in ScMep2) makes a strong hydrogen bond with the ɛ2 nitrogen atom of the absolutely conserved His342 of the twin-His motif (His348 in ScMep2), closing the channel (Figs 4 and 5).	RESULTS
256	263	channel	site	At the C-terminal end of TM1, the side-chain hydroxyl group of the relatively conserved Tyr49 (Tyr53 in ScMep2) makes a strong hydrogen bond with the ɛ2 nitrogen atom of the absolutely conserved His342 of the twin-His motif (His348 in ScMep2), closing the channel (Figs 4 and 5).	RESULTS
3	12	bacterial	taxonomy_domain	In bacterial Amt proteins, this Tyr side chain is rotated ∼4 Å away as a result of the different conformation of TM1, leaving the channel open and the histidine available for its putative role in substrate transport (Supplementary Fig. 2).	RESULTS
13	25	Amt proteins	protein_type	In bacterial Amt proteins, this Tyr side chain is rotated ∼4 Å away as a result of the different conformation of TM1, leaving the channel open and the histidine available for its putative role in substrate transport (Supplementary Fig. 2).	RESULTS
32	35	Tyr	residue_name	In bacterial Amt proteins, this Tyr side chain is rotated ∼4 Å away as a result of the different conformation of TM1, leaving the channel open and the histidine available for its putative role in substrate transport (Supplementary Fig. 2).	RESULTS
113	116	TM1	structure_element	In bacterial Amt proteins, this Tyr side chain is rotated ∼4 Å away as a result of the different conformation of TM1, leaving the channel open and the histidine available for its putative role in substrate transport (Supplementary Fig. 2).	RESULTS
130	137	channel	site	In bacterial Amt proteins, this Tyr side chain is rotated ∼4 Å away as a result of the different conformation of TM1, leaving the channel open and the histidine available for its putative role in substrate transport (Supplementary Fig. 2).	RESULTS
138	142	open	protein_state	In bacterial Amt proteins, this Tyr side chain is rotated ∼4 Å away as a result of the different conformation of TM1, leaving the channel open and the histidine available for its putative role in substrate transport (Supplementary Fig. 2).	RESULTS
151	160	histidine	residue_name	In bacterial Amt proteins, this Tyr side chain is rotated ∼4 Å away as a result of the different conformation of TM1, leaving the channel open and the histidine available for its putative role in substrate transport (Supplementary Fig. 2).	RESULTS
14	18	ICL1	structure_element	Compared with ICL1, the backbone conformational changes observed for the neighbouring ICL2 are smaller, but large shifts are nevertheless observed for the conserved residues Glu140 and Arg141 (Fig. 4).	RESULTS
86	90	ICL2	structure_element	Compared with ICL1, the backbone conformational changes observed for the neighbouring ICL2 are smaller, but large shifts are nevertheless observed for the conserved residues Glu140 and Arg141 (Fig. 4).	RESULTS
155	164	conserved	protein_state	Compared with ICL1, the backbone conformational changes observed for the neighbouring ICL2 are smaller, but large shifts are nevertheless observed for the conserved residues Glu140 and Arg141 (Fig. 4).	RESULTS
174	180	Glu140	residue_name_number	Compared with ICL1, the backbone conformational changes observed for the neighbouring ICL2 are smaller, but large shifts are nevertheless observed for the conserved residues Glu140 and Arg141 (Fig. 4).	RESULTS
185	191	Arg141	residue_name_number	Compared with ICL1, the backbone conformational changes observed for the neighbouring ICL2 are smaller, but large shifts are nevertheless observed for the conserved residues Glu140 and Arg141 (Fig. 4).	RESULTS
23	27	ICL3	structure_element	Finally, the important ICL3 linking the pseudo-symmetrical halves (TM1-5 and TM6-10) of the transporter is also shifted up to ∼10 Å and forms an additional barrier that closes the channel on the cytoplasmic side (Fig. 5).	RESULTS
40	65	pseudo-symmetrical halves	structure_element	Finally, the important ICL3 linking the pseudo-symmetrical halves (TM1-5 and TM6-10) of the transporter is also shifted up to ∼10 Å and forms an additional barrier that closes the channel on the cytoplasmic side (Fig. 5).	RESULTS
67	72	TM1-5	structure_element	Finally, the important ICL3 linking the pseudo-symmetrical halves (TM1-5 and TM6-10) of the transporter is also shifted up to ∼10 Å and forms an additional barrier that closes the channel on the cytoplasmic side (Fig. 5).	RESULTS
77	83	TM6-10	structure_element	Finally, the important ICL3 linking the pseudo-symmetrical halves (TM1-5 and TM6-10) of the transporter is also shifted up to ∼10 Å and forms an additional barrier that closes the channel on the cytoplasmic side (Fig. 5).	RESULTS
92	103	transporter	protein_type	Finally, the important ICL3 linking the pseudo-symmetrical halves (TM1-5 and TM6-10) of the transporter is also shifted up to ∼10 Å and forms an additional barrier that closes the channel on the cytoplasmic side (Fig. 5).	RESULTS
180	187	channel	site	Finally, the important ICL3 linking the pseudo-symmetrical halves (TM1-5 and TM6-10) of the transporter is also shifted up to ∼10 Å and forms an additional barrier that closes the channel on the cytoplasmic side (Fig. 5).	RESULTS
14	27	channel block	structure_element	This two-tier channel block likely ensures that very little ammonium transport will take place under nitrogen-sufficient conditions.	RESULTS
60	68	ammonium	chemical	This two-tier channel block likely ensures that very little ammonium transport will take place under nitrogen-sufficient conditions.	RESULTS
101	109	nitrogen	chemical	This two-tier channel block likely ensures that very little ammonium transport will take place under nitrogen-sufficient conditions.	RESULTS
4	10	closed	protein_state	The closed state of the channel might also explain why no density, which could correspond to ammonium (or water), is observed in the hydrophobic part of the Mep2 channel close to the twin-His motif.	RESULTS
24	31	channel	site	The closed state of the channel might also explain why no density, which could correspond to ammonium (or water), is observed in the hydrophobic part of the Mep2 channel close to the twin-His motif.	RESULTS
55	65	no density	evidence	The closed state of the channel might also explain why no density, which could correspond to ammonium (or water), is observed in the hydrophobic part of the Mep2 channel close to the twin-His motif.	RESULTS
93	101	ammonium	chemical	The closed state of the channel might also explain why no density, which could correspond to ammonium (or water), is observed in the hydrophobic part of the Mep2 channel close to the twin-His motif.	RESULTS
106	111	water	chemical	The closed state of the channel might also explain why no density, which could correspond to ammonium (or water), is observed in the hydrophobic part of the Mep2 channel close to the twin-His motif.	RESULTS
157	161	Mep2	protein	The closed state of the channel might also explain why no density, which could correspond to ammonium (or water), is observed in the hydrophobic part of the Mep2 channel close to the twin-His motif.	RESULTS
162	169	channel	site	The closed state of the channel might also explain why no density, which could correspond to ammonium (or water), is observed in the hydrophobic part of the Mep2 channel close to the twin-His motif.	RESULTS
183	197	twin-His motif	structure_element	The closed state of the channel might also explain why no density, which could correspond to ammonium (or water), is observed in the hydrophobic part of the Mep2 channel close to the twin-His motif.	RESULTS
37	43	ScMep2	protein	Significantly, this is also true for ScMep2, which was crystallized in the presence of 0.2 M ammonium ions (see Methods section).	RESULTS
55	67	crystallized	experimental_method	Significantly, this is also true for ScMep2, which was crystallized in the presence of 0.2 M ammonium ions (see Methods section).	RESULTS
93	101	ammonium	chemical	Significantly, this is also true for ScMep2, which was crystallized in the presence of 0.2 M ammonium ions (see Methods section).	RESULTS
20	24	Mep2	protein	The final region in Mep2 that shows large differences compared with the bacterial transporters is the CTR.	RESULTS
72	81	bacterial	taxonomy_domain	The final region in Mep2 that shows large differences compared with the bacterial transporters is the CTR.	RESULTS
82	94	transporters	protein_type	The final region in Mep2 that shows large differences compared with the bacterial transporters is the CTR.	RESULTS
102	105	CTR	structure_element	The final region in Mep2 that shows large differences compared with the bacterial transporters is the CTR.	RESULTS
3	7	Mep2	protein	In Mep2, the CTR has moved away and makes relatively few contacts with the main body of the transporter, generating a more elongated protein (Figs 1 and 4).	RESULTS
13	16	CTR	structure_element	In Mep2, the CTR has moved away and makes relatively few contacts with the main body of the transporter, generating a more elongated protein (Figs 1 and 4).	RESULTS
75	84	main body	structure_element	In Mep2, the CTR has moved away and makes relatively few contacts with the main body of the transporter, generating a more elongated protein (Figs 1 and 4).	RESULTS
92	103	transporter	protein_type	In Mep2, the CTR has moved away and makes relatively few contacts with the main body of the transporter, generating a more elongated protein (Figs 1 and 4).	RESULTS
123	132	elongated	protein_state	In Mep2, the CTR has moved away and makes relatively few contacts with the main body of the transporter, generating a more elongated protein (Figs 1 and 4).	RESULTS
20	30	structures	evidence	By contrast, in the structures of bacterial proteins, the CTR is docked tightly onto the N-terminal half of the transporters (corresponding to TM1-5), resulting in a more compact structure.	RESULTS
34	43	bacterial	taxonomy_domain	By contrast, in the structures of bacterial proteins, the CTR is docked tightly onto the N-terminal half of the transporters (corresponding to TM1-5), resulting in a more compact structure.	RESULTS
58	61	CTR	structure_element	By contrast, in the structures of bacterial proteins, the CTR is docked tightly onto the N-terminal half of the transporters (corresponding to TM1-5), resulting in a more compact structure.	RESULTS
89	104	N-terminal half	structure_element	By contrast, in the structures of bacterial proteins, the CTR is docked tightly onto the N-terminal half of the transporters (corresponding to TM1-5), resulting in a more compact structure.	RESULTS
112	124	transporters	protein_type	By contrast, in the structures of bacterial proteins, the CTR is docked tightly onto the N-terminal half of the transporters (corresponding to TM1-5), resulting in a more compact structure.	RESULTS
143	148	TM1-5	structure_element	By contrast, in the structures of bacterial proteins, the CTR is docked tightly onto the N-terminal half of the transporters (corresponding to TM1-5), resulting in a more compact structure.	RESULTS
171	178	compact	protein_state	By contrast, in the structures of bacterial proteins, the CTR is docked tightly onto the N-terminal half of the transporters (corresponding to TM1-5), resulting in a more compact structure.	RESULTS
179	188	structure	evidence	By contrast, in the structures of bacterial proteins, the CTR is docked tightly onto the N-terminal half of the transporters (corresponding to TM1-5), resulting in a more compact structure.	RESULTS
49	70	universally conserved	protein_state	This is illustrated by the positions of the five universally conserved residues within the CTR, that is, Arg415(370), Glu421(376), Gly424(379), Asp426(381) and Tyr 435(390) in CaMep2(Amt-1) (Fig. 2).	RESULTS
91	94	CTR	structure_element	This is illustrated by the positions of the five universally conserved residues within the CTR, that is, Arg415(370), Glu421(376), Gly424(379), Asp426(381) and Tyr 435(390) in CaMep2(Amt-1) (Fig. 2).	RESULTS
105	111	Arg415	residue_name_number	This is illustrated by the positions of the five universally conserved residues within the CTR, that is, Arg415(370), Glu421(376), Gly424(379), Asp426(381) and Tyr 435(390) in CaMep2(Amt-1) (Fig. 2).	RESULTS
112	115	370	residue_number	This is illustrated by the positions of the five universally conserved residues within the CTR, that is, Arg415(370), Glu421(376), Gly424(379), Asp426(381) and Tyr 435(390) in CaMep2(Amt-1) (Fig. 2).	RESULTS
118	124	Glu421	residue_name_number	This is illustrated by the positions of the five universally conserved residues within the CTR, that is, Arg415(370), Glu421(376), Gly424(379), Asp426(381) and Tyr 435(390) in CaMep2(Amt-1) (Fig. 2).	RESULTS
125	128	376	residue_number	This is illustrated by the positions of the five universally conserved residues within the CTR, that is, Arg415(370), Glu421(376), Gly424(379), Asp426(381) and Tyr 435(390) in CaMep2(Amt-1) (Fig. 2).	RESULTS
131	137	Gly424	residue_name_number	This is illustrated by the positions of the five universally conserved residues within the CTR, that is, Arg415(370), Glu421(376), Gly424(379), Asp426(381) and Tyr 435(390) in CaMep2(Amt-1) (Fig. 2).	RESULTS
138	141	379	residue_number	This is illustrated by the positions of the five universally conserved residues within the CTR, that is, Arg415(370), Glu421(376), Gly424(379), Asp426(381) and Tyr 435(390) in CaMep2(Amt-1) (Fig. 2).	RESULTS
144	150	Asp426	residue_name_number	This is illustrated by the positions of the five universally conserved residues within the CTR, that is, Arg415(370), Glu421(376), Gly424(379), Asp426(381) and Tyr 435(390) in CaMep2(Amt-1) (Fig. 2).	RESULTS
151	154	381	residue_number	This is illustrated by the positions of the five universally conserved residues within the CTR, that is, Arg415(370), Glu421(376), Gly424(379), Asp426(381) and Tyr 435(390) in CaMep2(Amt-1) (Fig. 2).	RESULTS
160	167	Tyr 435	residue_name_number	This is illustrated by the positions of the five universally conserved residues within the CTR, that is, Arg415(370), Glu421(376), Gly424(379), Asp426(381) and Tyr 435(390) in CaMep2(Amt-1) (Fig. 2).	RESULTS
168	171	390	residue_number	This is illustrated by the positions of the five universally conserved residues within the CTR, that is, Arg415(370), Glu421(376), Gly424(379), Asp426(381) and Tyr 435(390) in CaMep2(Amt-1) (Fig. 2).	RESULTS
176	182	CaMep2	protein	This is illustrated by the positions of the five universally conserved residues within the CTR, that is, Arg415(370), Glu421(376), Gly424(379), Asp426(381) and Tyr 435(390) in CaMep2(Amt-1) (Fig. 2).	RESULTS
183	188	Amt-1	protein	This is illustrated by the positions of the five universally conserved residues within the CTR, that is, Arg415(370), Glu421(376), Gly424(379), Asp426(381) and Tyr 435(390) in CaMep2(Amt-1) (Fig. 2).	RESULTS
36	50	‘ExxGxD' motif	structure_element	These residues include those of the ‘ExxGxD' motif, which when mutated generate inactive transporters.	RESULTS
63	70	mutated	experimental_method	These residues include those of the ‘ExxGxD' motif, which when mutated generate inactive transporters.	RESULTS
80	88	inactive	protein_state	These residues include those of the ‘ExxGxD' motif, which when mutated generate inactive transporters.	RESULTS
89	101	transporters	protein_type	These residues include those of the ‘ExxGxD' motif, which when mutated generate inactive transporters.	RESULTS
3	8	Amt-1	protein	In Amt-1 and other bacterial ammonium transporters, these CTR residues interact with residues within the N-terminal half of the protein.	RESULTS
19	28	bacterial	taxonomy_domain	In Amt-1 and other bacterial ammonium transporters, these CTR residues interact with residues within the N-terminal half of the protein.	RESULTS
29	50	ammonium transporters	protein_type	In Amt-1 and other bacterial ammonium transporters, these CTR residues interact with residues within the N-terminal half of the protein.	RESULTS
58	61	CTR	structure_element	In Amt-1 and other bacterial ammonium transporters, these CTR residues interact with residues within the N-terminal half of the protein.	RESULTS
105	120	N-terminal half	structure_element	In Amt-1 and other bacterial ammonium transporters, these CTR residues interact with residues within the N-terminal half of the protein.	RESULTS
17	23	Tyr390	residue_name_number	On one side, the Tyr390 hydroxyl in Amt-1 is hydrogen bonded with the side chain of the conserved His185 at the C-terminal end of loop ICL3.	RESULTS
36	41	Amt-1	protein	On one side, the Tyr390 hydroxyl in Amt-1 is hydrogen bonded with the side chain of the conserved His185 at the C-terminal end of loop ICL3.	RESULTS
45	60	hydrogen bonded	bond_interaction	On one side, the Tyr390 hydroxyl in Amt-1 is hydrogen bonded with the side chain of the conserved His185 at the C-terminal end of loop ICL3.	RESULTS
88	97	conserved	protein_state	On one side, the Tyr390 hydroxyl in Amt-1 is hydrogen bonded with the side chain of the conserved His185 at the C-terminal end of loop ICL3.	RESULTS
98	104	His185	residue_name_number	On one side, the Tyr390 hydroxyl in Amt-1 is hydrogen bonded with the side chain of the conserved His185 at the C-terminal end of loop ICL3.	RESULTS
130	134	loop	structure_element	On one side, the Tyr390 hydroxyl in Amt-1 is hydrogen bonded with the side chain of the conserved His185 at the C-terminal end of loop ICL3.	RESULTS
135	139	ICL3	structure_element	On one side, the Tyr390 hydroxyl in Amt-1 is hydrogen bonded with the side chain of the conserved His185 at the C-terminal end of loop ICL3.	RESULTS
20	24	ICL3	structure_element	At the other end of ICL3, the backbone carbonyl groups of Gly172 and Lys173 are hydrogen bonded to the side chain of Arg370.	RESULTS
58	64	Gly172	residue_name_number	At the other end of ICL3, the backbone carbonyl groups of Gly172 and Lys173 are hydrogen bonded to the side chain of Arg370.	RESULTS
69	75	Lys173	residue_name_number	At the other end of ICL3, the backbone carbonyl groups of Gly172 and Lys173 are hydrogen bonded to the side chain of Arg370.	RESULTS
80	95	hydrogen bonded	bond_interaction	At the other end of ICL3, the backbone carbonyl groups of Gly172 and Lys173 are hydrogen bonded to the side chain of Arg370.	RESULTS
117	123	Arg370	residue_name_number	At the other end of ICL3, the backbone carbonyl groups of Gly172 and Lys173 are hydrogen bonded to the side chain of Arg370.	RESULTS
31	39	modelled	experimental_method	Similar interactions were also modelled in the active, non-phosphorylated plant AtAmt-1;1 structure (for example, Y467-H239 and D458-K71).	RESULTS
47	53	active	protein_state	Similar interactions were also modelled in the active, non-phosphorylated plant AtAmt-1;1 structure (for example, Y467-H239 and D458-K71).	RESULTS
55	73	non-phosphorylated	protein_state	Similar interactions were also modelled in the active, non-phosphorylated plant AtAmt-1;1 structure (for example, Y467-H239 and D458-K71).	RESULTS
74	79	plant	taxonomy_domain	Similar interactions were also modelled in the active, non-phosphorylated plant AtAmt-1;1 structure (for example, Y467-H239 and D458-K71).	RESULTS
80	89	AtAmt-1;1	protein	Similar interactions were also modelled in the active, non-phosphorylated plant AtAmt-1;1 structure (for example, Y467-H239 and D458-K71).	RESULTS
90	99	structure	evidence	Similar interactions were also modelled in the active, non-phosphorylated plant AtAmt-1;1 structure (for example, Y467-H239 and D458-K71).	RESULTS
114	118	Y467	residue_name_number	Similar interactions were also modelled in the active, non-phosphorylated plant AtAmt-1;1 structure (for example, Y467-H239 and D458-K71).	RESULTS
119	123	H239	residue_name_number	Similar interactions were also modelled in the active, non-phosphorylated plant AtAmt-1;1 structure (for example, Y467-H239 and D458-K71).	RESULTS
128	132	D458	residue_name_number	Similar interactions were also modelled in the active, non-phosphorylated plant AtAmt-1;1 structure (for example, Y467-H239 and D458-K71).	RESULTS
133	136	K71	residue_name_number	Similar interactions were also modelled in the active, non-phosphorylated plant AtAmt-1;1 structure (for example, Y467-H239 and D458-K71).	RESULTS
45	48	CTR	structure_element	The result of these interactions is that the CTR ‘hugs' the N-terminal half of the transporters (Fig. 4).	RESULTS
60	75	N-terminal half	structure_element	The result of these interactions is that the CTR ‘hugs' the N-terminal half of the transporters (Fig. 4).	RESULTS
83	95	transporters	protein_type	The result of these interactions is that the CTR ‘hugs' the N-terminal half of the transporters (Fig. 4).	RESULTS
19	25	Asp381	residue_name_number	Also noteworthy is Asp381, the side chain of which interacts strongly with the positive dipole on the N-terminal end of TM2.	RESULTS
120	123	TM2	structure_element	Also noteworthy is Asp381, the side chain of which interacts strongly with the positive dipole on the N-terminal end of TM2.	RESULTS
93	97	open	protein_state	This interaction in the centre of the protein may be particularly important to stabilize the open conformations of ammonium transporters.	RESULTS
115	136	ammonium transporters	protein_type	This interaction in the centre of the protein may be particularly important to stabilize the open conformations of ammonium transporters.	RESULTS
7	11	Mep2	protein	In the Mep2 structures, none of the interactions mentioned above are present.	RESULTS
12	22	structures	evidence	In the Mep2 structures, none of the interactions mentioned above are present.	RESULTS
0	27	Phosphorylation target site	site	Phosphorylation target site is at the periphery of Mep2	RESULTS
51	55	Mep2	protein	Phosphorylation target site is at the periphery of Mep2	RESULTS
51	57	Ser457	residue_name_number	Recently Boeckstaens et al. provided evidence that Ser457 in ScMep2 (corresponding to Ser453 in CaMep2) is phosphorylated by the TORC1 effector kinase Npr1 under nitrogen-limiting conditions.	RESULTS
61	67	ScMep2	protein	Recently Boeckstaens et al. provided evidence that Ser457 in ScMep2 (corresponding to Ser453 in CaMep2) is phosphorylated by the TORC1 effector kinase Npr1 under nitrogen-limiting conditions.	RESULTS
86	92	Ser453	residue_name_number	Recently Boeckstaens et al. provided evidence that Ser457 in ScMep2 (corresponding to Ser453 in CaMep2) is phosphorylated by the TORC1 effector kinase Npr1 under nitrogen-limiting conditions.	RESULTS
96	102	CaMep2	protein	Recently Boeckstaens et al. provided evidence that Ser457 in ScMep2 (corresponding to Ser453 in CaMep2) is phosphorylated by the TORC1 effector kinase Npr1 under nitrogen-limiting conditions.	RESULTS
107	121	phosphorylated	protein_state	Recently Boeckstaens et al. provided evidence that Ser457 in ScMep2 (corresponding to Ser453 in CaMep2) is phosphorylated by the TORC1 effector kinase Npr1 under nitrogen-limiting conditions.	RESULTS
129	150	TORC1 effector kinase	protein_type	Recently Boeckstaens et al. provided evidence that Ser457 in ScMep2 (corresponding to Ser453 in CaMep2) is phosphorylated by the TORC1 effector kinase Npr1 under nitrogen-limiting conditions.	RESULTS
151	155	Npr1	protein	Recently Boeckstaens et al. provided evidence that Ser457 in ScMep2 (corresponding to Ser453 in CaMep2) is phosphorylated by the TORC1 effector kinase Npr1 under nitrogen-limiting conditions.	RESULTS
162	170	nitrogen	chemical	Recently Boeckstaens et al. provided evidence that Ser457 in ScMep2 (corresponding to Ser453 in CaMep2) is phosphorylated by the TORC1 effector kinase Npr1 under nitrogen-limiting conditions.	RESULTS
7	17	absence of	protein_state	In the absence of Npr1, plasmid-encoded WT Mep2 in a S. cerevisiae mep1-3Δ strain (triple mepΔ) does not allow growth on low concentrations of ammonium, suggesting that the transporter is inactive (Fig. 3 and Supplementary Fig. 1).	RESULTS
18	22	Npr1	protein	In the absence of Npr1, plasmid-encoded WT Mep2 in a S. cerevisiae mep1-3Δ strain (triple mepΔ) does not allow growth on low concentrations of ammonium, suggesting that the transporter is inactive (Fig. 3 and Supplementary Fig. 1).	RESULTS
24	39	plasmid-encoded	experimental_method	In the absence of Npr1, plasmid-encoded WT Mep2 in a S. cerevisiae mep1-3Δ strain (triple mepΔ) does not allow growth on low concentrations of ammonium, suggesting that the transporter is inactive (Fig. 3 and Supplementary Fig. 1).	RESULTS
40	42	WT	protein_state	In the absence of Npr1, plasmid-encoded WT Mep2 in a S. cerevisiae mep1-3Δ strain (triple mepΔ) does not allow growth on low concentrations of ammonium, suggesting that the transporter is inactive (Fig. 3 and Supplementary Fig. 1).	RESULTS
43	47	Mep2	protein	In the absence of Npr1, plasmid-encoded WT Mep2 in a S. cerevisiae mep1-3Δ strain (triple mepΔ) does not allow growth on low concentrations of ammonium, suggesting that the transporter is inactive (Fig. 3 and Supplementary Fig. 1).	RESULTS
53	66	S. cerevisiae	species	In the absence of Npr1, plasmid-encoded WT Mep2 in a S. cerevisiae mep1-3Δ strain (triple mepΔ) does not allow growth on low concentrations of ammonium, suggesting that the transporter is inactive (Fig. 3 and Supplementary Fig. 1).	RESULTS
67	74	mep1-3Δ	mutant	In the absence of Npr1, plasmid-encoded WT Mep2 in a S. cerevisiae mep1-3Δ strain (triple mepΔ) does not allow growth on low concentrations of ammonium, suggesting that the transporter is inactive (Fig. 3 and Supplementary Fig. 1).	RESULTS
83	94	triple mepΔ	mutant	In the absence of Npr1, plasmid-encoded WT Mep2 in a S. cerevisiae mep1-3Δ strain (triple mepΔ) does not allow growth on low concentrations of ammonium, suggesting that the transporter is inactive (Fig. 3 and Supplementary Fig. 1).	RESULTS
143	151	ammonium	chemical	In the absence of Npr1, plasmid-encoded WT Mep2 in a S. cerevisiae mep1-3Δ strain (triple mepΔ) does not allow growth on low concentrations of ammonium, suggesting that the transporter is inactive (Fig. 3 and Supplementary Fig. 1).	RESULTS
173	184	transporter	protein_type	In the absence of Npr1, plasmid-encoded WT Mep2 in a S. cerevisiae mep1-3Δ strain (triple mepΔ) does not allow growth on low concentrations of ammonium, suggesting that the transporter is inactive (Fig. 3 and Supplementary Fig. 1).	RESULTS
188	196	inactive	protein_state	In the absence of Npr1, plasmid-encoded WT Mep2 in a S. cerevisiae mep1-3Δ strain (triple mepΔ) does not allow growth on low concentrations of ammonium, suggesting that the transporter is inactive (Fig. 3 and Supplementary Fig. 1).	RESULTS
16	41	phosphorylation-mimicking	protein_state	Conversely, the phosphorylation-mimicking S457D variant is active both in the triple mepΔ background and in a triple mepΔ npr1Δ strain (Fig. 3).	RESULTS
42	47	S457D	mutant	Conversely, the phosphorylation-mimicking S457D variant is active both in the triple mepΔ background and in a triple mepΔ npr1Δ strain (Fig. 3).	RESULTS
59	65	active	protein_state	Conversely, the phosphorylation-mimicking S457D variant is active both in the triple mepΔ background and in a triple mepΔ npr1Δ strain (Fig. 3).	RESULTS
78	89	triple mepΔ	mutant	Conversely, the phosphorylation-mimicking S457D variant is active both in the triple mepΔ background and in a triple mepΔ npr1Δ strain (Fig. 3).	RESULTS
110	127	triple mepΔ npr1Δ	mutant	Conversely, the phosphorylation-mimicking S457D variant is active both in the triple mepΔ background and in a triple mepΔ npr1Δ strain (Fig. 3).	RESULTS
0	8	Mutation	experimental_method	Mutation of other potential phosphorylation sites in the CTR did not support growth in the npr1Δ background.	RESULTS
28	49	phosphorylation sites	site	Mutation of other potential phosphorylation sites in the CTR did not support growth in the npr1Δ background.	RESULTS
57	60	CTR	structure_element	Mutation of other potential phosphorylation sites in the CTR did not support growth in the npr1Δ background.	RESULTS
91	96	npr1Δ	mutant	Mutation of other potential phosphorylation sites in the CTR did not support growth in the npr1Δ background.	RESULTS
38	53	phosphorylation	ptm	Collectively, these data suggest that phosphorylation of Ser457 opens the Mep2 channel to allow ammonium uptake.	RESULTS
57	63	Ser457	residue_name_number	Collectively, these data suggest that phosphorylation of Ser457 opens the Mep2 channel to allow ammonium uptake.	RESULTS
57	63	Ser457	residue_name_number	Collectively, these data suggest that phosphorylation of Ser457 opens the Mep2 channel to allow ammonium uptake.	RESULTS
74	78	Mep2	protein	Collectively, these data suggest that phosphorylation of Ser457 opens the Mep2 channel to allow ammonium uptake.	RESULTS
79	86	channel	site	Collectively, these data suggest that phosphorylation of Ser457 opens the Mep2 channel to allow ammonium uptake.	RESULTS
96	104	ammonium	chemical	Collectively, these data suggest that phosphorylation of Ser457 opens the Mep2 channel to allow ammonium uptake.	RESULTS
0	6	Ser457	residue_name_number	Ser457 is located in a part of the CTR that is conserved in a subgroup of Mep2 proteins, but which is not present in bacterial proteins (Fig. 2).	RESULTS
35	38	CTR	structure_element	Ser457 is located in a part of the CTR that is conserved in a subgroup of Mep2 proteins, but which is not present in bacterial proteins (Fig. 2).	RESULTS
47	56	conserved	protein_state	Ser457 is located in a part of the CTR that is conserved in a subgroup of Mep2 proteins, but which is not present in bacterial proteins (Fig. 2).	RESULTS
74	87	Mep2 proteins	protein_type	Ser457 is located in a part of the CTR that is conserved in a subgroup of Mep2 proteins, but which is not present in bacterial proteins (Fig. 2).	RESULTS
117	126	bacterial	taxonomy_domain	Ser457 is located in a part of the CTR that is conserved in a subgroup of Mep2 proteins, but which is not present in bacterial proteins (Fig. 2).	RESULTS
5	12	segment	structure_element	This segment (residues 450–457 in ScMep2 and 446–453 in CaMep2) was dubbed an autoinhibitory (AI) region based on the fact that its removal generates an active transporter in the absence of Npr1 (Fig. 3).	RESULTS
23	30	450–457	residue_range	This segment (residues 450–457 in ScMep2 and 446–453 in CaMep2) was dubbed an autoinhibitory (AI) region based on the fact that its removal generates an active transporter in the absence of Npr1 (Fig. 3).	RESULTS
34	40	ScMep2	protein	This segment (residues 450–457 in ScMep2 and 446–453 in CaMep2) was dubbed an autoinhibitory (AI) region based on the fact that its removal generates an active transporter in the absence of Npr1 (Fig. 3).	RESULTS
45	52	446–453	residue_range	This segment (residues 450–457 in ScMep2 and 446–453 in CaMep2) was dubbed an autoinhibitory (AI) region based on the fact that its removal generates an active transporter in the absence of Npr1 (Fig. 3).	RESULTS
56	62	CaMep2	protein	This segment (residues 450–457 in ScMep2 and 446–453 in CaMep2) was dubbed an autoinhibitory (AI) region based on the fact that its removal generates an active transporter in the absence of Npr1 (Fig. 3).	RESULTS
78	104	autoinhibitory (AI) region	structure_element	This segment (residues 450–457 in ScMep2 and 446–453 in CaMep2) was dubbed an autoinhibitory (AI) region based on the fact that its removal generates an active transporter in the absence of Npr1 (Fig. 3).	RESULTS
132	139	removal	experimental_method	This segment (residues 450–457 in ScMep2 and 446–453 in CaMep2) was dubbed an autoinhibitory (AI) region based on the fact that its removal generates an active transporter in the absence of Npr1 (Fig. 3).	RESULTS
153	159	active	protein_state	This segment (residues 450–457 in ScMep2 and 446–453 in CaMep2) was dubbed an autoinhibitory (AI) region based on the fact that its removal generates an active transporter in the absence of Npr1 (Fig. 3).	RESULTS
160	171	transporter	protein_type	This segment (residues 450–457 in ScMep2 and 446–453 in CaMep2) was dubbed an autoinhibitory (AI) region based on the fact that its removal generates an active transporter in the absence of Npr1 (Fig. 3).	RESULTS
179	189	absence of	protein_state	This segment (residues 450–457 in ScMep2 and 446–453 in CaMep2) was dubbed an autoinhibitory (AI) region based on the fact that its removal generates an active transporter in the absence of Npr1 (Fig. 3).	RESULTS
190	194	Npr1	protein	This segment (residues 450–457 in ScMep2 and 446–453 in CaMep2) was dubbed an autoinhibitory (AI) region based on the fact that its removal generates an active transporter in the absence of Npr1 (Fig. 3).	RESULTS
13	22	AI region	structure_element	Where is the AI region and the Npr1 phosphorylation site located? Our structures reveal that surprisingly, the AI region is folded back onto the CTR and is not located near the centre of the trimer as expected from the bacterial structures (Fig. 4).	RESULTS
31	35	Npr1	protein	Where is the AI region and the Npr1 phosphorylation site located? Our structures reveal that surprisingly, the AI region is folded back onto the CTR and is not located near the centre of the trimer as expected from the bacterial structures (Fig. 4).	RESULTS
36	56	phosphorylation site	site	Where is the AI region and the Npr1 phosphorylation site located? Our structures reveal that surprisingly, the AI region is folded back onto the CTR and is not located near the centre of the trimer as expected from the bacterial structures (Fig. 4).	RESULTS
70	80	structures	evidence	Where is the AI region and the Npr1 phosphorylation site located? Our structures reveal that surprisingly, the AI region is folded back onto the CTR and is not located near the centre of the trimer as expected from the bacterial structures (Fig. 4).	RESULTS
111	120	AI region	structure_element	Where is the AI region and the Npr1 phosphorylation site located? Our structures reveal that surprisingly, the AI region is folded back onto the CTR and is not located near the centre of the trimer as expected from the bacterial structures (Fig. 4).	RESULTS
145	148	CTR	structure_element	Where is the AI region and the Npr1 phosphorylation site located? Our structures reveal that surprisingly, the AI region is folded back onto the CTR and is not located near the centre of the trimer as expected from the bacterial structures (Fig. 4).	RESULTS
191	197	trimer	oligomeric_state	Where is the AI region and the Npr1 phosphorylation site located? Our structures reveal that surprisingly, the AI region is folded back onto the CTR and is not located near the centre of the trimer as expected from the bacterial structures (Fig. 4).	RESULTS
219	228	bacterial	taxonomy_domain	Where is the AI region and the Npr1 phosphorylation site located? Our structures reveal that surprisingly, the AI region is folded back onto the CTR and is not located near the centre of the trimer as expected from the bacterial structures (Fig. 4).	RESULTS
229	239	structures	evidence	Where is the AI region and the Npr1 phosphorylation site located? Our structures reveal that surprisingly, the AI region is folded back onto the CTR and is not located near the centre of the trimer as expected from the bacterial structures (Fig. 4).	RESULTS
4	13	AI region	structure_element	The AI region packs against the cytoplasmic ends of TM2 and TM4, physically linking the main body of the transporter with the CTR via main chain interactions and side-chain interactions of Val447, Asp449, Pro450 and Arg452 (Fig. 6).	RESULTS
52	55	TM2	structure_element	The AI region packs against the cytoplasmic ends of TM2 and TM4, physically linking the main body of the transporter with the CTR via main chain interactions and side-chain interactions of Val447, Asp449, Pro450 and Arg452 (Fig. 6).	RESULTS
60	63	TM4	structure_element	The AI region packs against the cytoplasmic ends of TM2 and TM4, physically linking the main body of the transporter with the CTR via main chain interactions and side-chain interactions of Val447, Asp449, Pro450 and Arg452 (Fig. 6).	RESULTS
88	97	main body	structure_element	The AI region packs against the cytoplasmic ends of TM2 and TM4, physically linking the main body of the transporter with the CTR via main chain interactions and side-chain interactions of Val447, Asp449, Pro450 and Arg452 (Fig. 6).	RESULTS
105	116	transporter	protein_type	The AI region packs against the cytoplasmic ends of TM2 and TM4, physically linking the main body of the transporter with the CTR via main chain interactions and side-chain interactions of Val447, Asp449, Pro450 and Arg452 (Fig. 6).	RESULTS
126	129	CTR	structure_element	The AI region packs against the cytoplasmic ends of TM2 and TM4, physically linking the main body of the transporter with the CTR via main chain interactions and side-chain interactions of Val447, Asp449, Pro450 and Arg452 (Fig. 6).	RESULTS
189	195	Val447	residue_name_number	The AI region packs against the cytoplasmic ends of TM2 and TM4, physically linking the main body of the transporter with the CTR via main chain interactions and side-chain interactions of Val447, Asp449, Pro450 and Arg452 (Fig. 6).	RESULTS
197	203	Asp449	residue_name_number	The AI region packs against the cytoplasmic ends of TM2 and TM4, physically linking the main body of the transporter with the CTR via main chain interactions and side-chain interactions of Val447, Asp449, Pro450 and Arg452 (Fig. 6).	RESULTS
205	211	Pro450	residue_name_number	The AI region packs against the cytoplasmic ends of TM2 and TM4, physically linking the main body of the transporter with the CTR via main chain interactions and side-chain interactions of Val447, Asp449, Pro450 and Arg452 (Fig. 6).	RESULTS
216	222	Arg452	residue_name_number	The AI region packs against the cytoplasmic ends of TM2 and TM4, physically linking the main body of the transporter with the CTR via main chain interactions and side-chain interactions of Val447, Asp449, Pro450 and Arg452 (Fig. 6).	RESULTS
4	14	AI regions	structure_element	The AI regions have very similar conformations in CaMep2 and ScMep2, despite considerable differences in the rest of the CTR (Fig. 6).	RESULTS
50	56	CaMep2	protein	The AI regions have very similar conformations in CaMep2 and ScMep2, despite considerable differences in the rest of the CTR (Fig. 6).	RESULTS
61	67	ScMep2	protein	The AI regions have very similar conformations in CaMep2 and ScMep2, despite considerable differences in the rest of the CTR (Fig. 6).	RESULTS
121	124	CTR	structure_element	The AI regions have very similar conformations in CaMep2 and ScMep2, despite considerable differences in the rest of the CTR (Fig. 6).	RESULTS
16	34	Npr1 target serine	site	Strikingly, the Npr1 target serine residue is located at the periphery of the trimer, far away (∼30 Å) from any channel exit (Fig. 6).	RESULTS
78	84	trimer	oligomeric_state	Strikingly, the Npr1 target serine residue is located at the periphery of the trimer, far away (∼30 Å) from any channel exit (Fig. 6).	RESULTS
112	124	channel exit	site	Strikingly, the Npr1 target serine residue is located at the periphery of the trimer, far away (∼30 Å) from any channel exit (Fig. 6).	RESULTS
45	51	trimer	oligomeric_state	Despite its location at the periphery of the trimer, the electron density for the serine is well defined in both Mep2 structures and corresponds to the non-phosphorylated state (Fig. 6).	RESULTS
57	73	electron density	evidence	Despite its location at the periphery of the trimer, the electron density for the serine is well defined in both Mep2 structures and corresponds to the non-phosphorylated state (Fig. 6).	RESULTS
82	88	serine	residue_name	Despite its location at the periphery of the trimer, the electron density for the serine is well defined in both Mep2 structures and corresponds to the non-phosphorylated state (Fig. 6).	RESULTS
113	117	Mep2	protein	Despite its location at the periphery of the trimer, the electron density for the serine is well defined in both Mep2 structures and corresponds to the non-phosphorylated state (Fig. 6).	RESULTS
118	128	structures	evidence	Despite its location at the periphery of the trimer, the electron density for the serine is well defined in both Mep2 structures and corresponds to the non-phosphorylated state (Fig. 6).	RESULTS
152	170	non-phosphorylated	protein_state	Despite its location at the periphery of the trimer, the electron density for the serine is well defined in both Mep2 structures and corresponds to the non-phosphorylated state (Fig. 6).	RESULTS
132	150	non-phosphorylated	protein_state	This makes sense since the proteins were expressed in rich medium and confirms the recent suggestion by Boeckstaens et al. that the non-phosphorylated form of Mep2 corresponds to the inactive state.	RESULTS
159	163	Mep2	protein	This makes sense since the proteins were expressed in rich medium and confirms the recent suggestion by Boeckstaens et al. that the non-phosphorylated form of Mep2 corresponds to the inactive state.	RESULTS
183	191	inactive	protein_state	This makes sense since the proteins were expressed in rich medium and confirms the recent suggestion by Boeckstaens et al. that the non-phosphorylated form of Mep2 corresponds to the inactive state.	RESULTS
4	10	ScMep2	protein	For ScMep2, Ser457 is the most C-terminal residue for which electron density is visible, indicating that the region beyond Ser457 is disordered.	RESULTS
12	18	Ser457	residue_name_number	For ScMep2, Ser457 is the most C-terminal residue for which electron density is visible, indicating that the region beyond Ser457 is disordered.	RESULTS
60	76	electron density	evidence	For ScMep2, Ser457 is the most C-terminal residue for which electron density is visible, indicating that the region beyond Ser457 is disordered.	RESULTS
123	129	Ser457	residue_name_number	For ScMep2, Ser457 is the most C-terminal residue for which electron density is visible, indicating that the region beyond Ser457 is disordered.	RESULTS
133	143	disordered	protein_state	For ScMep2, Ser457 is the most C-terminal residue for which electron density is visible, indicating that the region beyond Ser457 is disordered.	RESULTS
3	9	CaMep2	protein	In CaMep2, the visible part of the sequence extends for two residues beyond Ser453 (Fig. 6).	RESULTS
76	82	Ser453	residue_name_number	In CaMep2, the visible part of the sequence extends for two residues beyond Ser453 (Fig. 6).	RESULTS
28	36	disorder	protein_state	The peripheral location and disorder of the CTR beyond the kinase target site should facilitate the phosphorylation by Npr1.	RESULTS
44	47	CTR	structure_element	The peripheral location and disorder of the CTR beyond the kinase target site should facilitate the phosphorylation by Npr1.	RESULTS
59	77	kinase target site	site	The peripheral location and disorder of the CTR beyond the kinase target site should facilitate the phosphorylation by Npr1.	RESULTS
100	115	phosphorylation	ptm	The peripheral location and disorder of the CTR beyond the kinase target site should facilitate the phosphorylation by Npr1.	RESULTS
119	123	Npr1	protein	The peripheral location and disorder of the CTR beyond the kinase target site should facilitate the phosphorylation by Npr1.	RESULTS
4	14	disordered	protein_state	The disordered part of the CTR is not conserved in ammonium transporters (Fig. 2), suggesting that it is not important for transport.	RESULTS
27	30	CTR	structure_element	The disordered part of the CTR is not conserved in ammonium transporters (Fig. 2), suggesting that it is not important for transport.	RESULTS
34	47	not conserved	protein_state	The disordered part of the CTR is not conserved in ammonium transporters (Fig. 2), suggesting that it is not important for transport.	RESULTS
51	72	ammonium transporters	protein_type	The disordered part of the CTR is not conserved in ammonium transporters (Fig. 2), suggesting that it is not important for transport.	RESULTS
17	23	ScMep2	protein	Interestingly, a ScMep2 457Δ truncation mutant in which a His-tag directly follows Ser457 is highly expressed but has low activity (Fig. 3 and Supplementary Fig. 1b), suggesting that the His-tag interferes with phosphorylation by Npr1.	RESULTS
24	28	457Δ	mutant	Interestingly, a ScMep2 457Δ truncation mutant in which a His-tag directly follows Ser457 is highly expressed but has low activity (Fig. 3 and Supplementary Fig. 1b), suggesting that the His-tag interferes with phosphorylation by Npr1.	RESULTS
29	46	truncation mutant	protein_state	Interestingly, a ScMep2 457Δ truncation mutant in which a His-tag directly follows Ser457 is highly expressed but has low activity (Fig. 3 and Supplementary Fig. 1b), suggesting that the His-tag interferes with phosphorylation by Npr1.	RESULTS
83	89	Ser457	residue_name_number	Interestingly, a ScMep2 457Δ truncation mutant in which a His-tag directly follows Ser457 is highly expressed but has low activity (Fig. 3 and Supplementary Fig. 1b), suggesting that the His-tag interferes with phosphorylation by Npr1.	RESULTS
118	130	low activity	protein_state	Interestingly, a ScMep2 457Δ truncation mutant in which a His-tag directly follows Ser457 is highly expressed but has low activity (Fig. 3 and Supplementary Fig. 1b), suggesting that the His-tag interferes with phosphorylation by Npr1.	RESULTS
211	226	phosphorylation	ptm	Interestingly, a ScMep2 457Δ truncation mutant in which a His-tag directly follows Ser457 is highly expressed but has low activity (Fig. 3 and Supplementary Fig. 1b), suggesting that the His-tag interferes with phosphorylation by Npr1.	RESULTS
230	234	Npr1	protein	Interestingly, a ScMep2 457Δ truncation mutant in which a His-tag directly follows Ser457 is highly expressed but has low activity (Fig. 3 and Supplementary Fig. 1b), suggesting that the His-tag interferes with phosphorylation by Npr1.	RESULTS
9	15	mutant	mutant	The same mutant lacking the His-tag has WT properties (Supplementary Fig. 1b), confirming that the region following the phosphorylation site is dispensable for function.	RESULTS
16	35	lacking the His-tag	protein_state	The same mutant lacking the His-tag has WT properties (Supplementary Fig. 1b), confirming that the region following the phosphorylation site is dispensable for function.	RESULTS
40	42	WT	protein_state	The same mutant lacking the His-tag has WT properties (Supplementary Fig. 1b), confirming that the region following the phosphorylation site is dispensable for function.	RESULTS
120	140	phosphorylation site	site	The same mutant lacking the His-tag has WT properties (Supplementary Fig. 1b), confirming that the region following the phosphorylation site is dispensable for function.	RESULTS
0	4	Mep2	protein	Mep2 lacking the AI region is conformationally heterogeneous	RESULTS
5	12	lacking	protein_state	Mep2 lacking the AI region is conformationally heterogeneous	RESULTS
17	26	AI region	structure_element	Mep2 lacking the AI region is conformationally heterogeneous	RESULTS
30	60	conformationally heterogeneous	protein_state	Mep2 lacking the AI region is conformationally heterogeneous	RESULTS
11	17	Ser457	residue_name_number	Given that Ser457/453 is far from any channel exit (Fig. 6), the crucial question is how phosphorylation opens the Mep2 channel to generate an active transporter.	RESULTS
18	21	453	residue_number	Given that Ser457/453 is far from any channel exit (Fig. 6), the crucial question is how phosphorylation opens the Mep2 channel to generate an active transporter.	RESULTS
38	50	channel exit	site	Given that Ser457/453 is far from any channel exit (Fig. 6), the crucial question is how phosphorylation opens the Mep2 channel to generate an active transporter.	RESULTS
89	104	phosphorylation	ptm	Given that Ser457/453 is far from any channel exit (Fig. 6), the crucial question is how phosphorylation opens the Mep2 channel to generate an active transporter.	RESULTS
115	119	Mep2	protein	Given that Ser457/453 is far from any channel exit (Fig. 6), the crucial question is how phosphorylation opens the Mep2 channel to generate an active transporter.	RESULTS
120	127	channel	site	Given that Ser457/453 is far from any channel exit (Fig. 6), the crucial question is how phosphorylation opens the Mep2 channel to generate an active transporter.	RESULTS
143	149	active	protein_state	Given that Ser457/453 is far from any channel exit (Fig. 6), the crucial question is how phosphorylation opens the Mep2 channel to generate an active transporter.	RESULTS
150	161	transporter	protein_type	Given that Ser457/453 is far from any channel exit (Fig. 6), the crucial question is how phosphorylation opens the Mep2 channel to generate an active transporter.	RESULTS
33	48	phosphorylation	ptm	Boeckstaens et al. proposed that phosphorylation does not affect channel activity directly, but instead relieves inhibition by the AI region.	RESULTS
131	140	AI region	structure_element	Boeckstaens et al. proposed that phosphorylation does not affect channel activity directly, but instead relieves inhibition by the AI region.	RESULTS
58	64	ScMep2	protein	The data behind this hypothesis is the observation that a ScMep2 449-485Δ deletion mutant lacking the AI region is highly active in MA uptake both in the triple mepΔ and triple mepΔ npr1Δ backgrounds, implying that this Mep2 variant has a constitutively open channel.	RESULTS
65	73	449-485Δ	mutant	The data behind this hypothesis is the observation that a ScMep2 449-485Δ deletion mutant lacking the AI region is highly active in MA uptake both in the triple mepΔ and triple mepΔ npr1Δ backgrounds, implying that this Mep2 variant has a constitutively open channel.	RESULTS
74	89	deletion mutant	protein_state	The data behind this hypothesis is the observation that a ScMep2 449-485Δ deletion mutant lacking the AI region is highly active in MA uptake both in the triple mepΔ and triple mepΔ npr1Δ backgrounds, implying that this Mep2 variant has a constitutively open channel.	RESULTS
90	97	lacking	protein_state	The data behind this hypothesis is the observation that a ScMep2 449-485Δ deletion mutant lacking the AI region is highly active in MA uptake both in the triple mepΔ and triple mepΔ npr1Δ backgrounds, implying that this Mep2 variant has a constitutively open channel.	RESULTS
102	111	AI region	structure_element	The data behind this hypothesis is the observation that a ScMep2 449-485Δ deletion mutant lacking the AI region is highly active in MA uptake both in the triple mepΔ and triple mepΔ npr1Δ backgrounds, implying that this Mep2 variant has a constitutively open channel.	RESULTS
115	128	highly active	protein_state	The data behind this hypothesis is the observation that a ScMep2 449-485Δ deletion mutant lacking the AI region is highly active in MA uptake both in the triple mepΔ and triple mepΔ npr1Δ backgrounds, implying that this Mep2 variant has a constitutively open channel.	RESULTS
132	134	MA	chemical	The data behind this hypothesis is the observation that a ScMep2 449-485Δ deletion mutant lacking the AI region is highly active in MA uptake both in the triple mepΔ and triple mepΔ npr1Δ backgrounds, implying that this Mep2 variant has a constitutively open channel.	RESULTS
154	165	triple mepΔ	mutant	The data behind this hypothesis is the observation that a ScMep2 449-485Δ deletion mutant lacking the AI region is highly active in MA uptake both in the triple mepΔ and triple mepΔ npr1Δ backgrounds, implying that this Mep2 variant has a constitutively open channel.	RESULTS
170	187	triple mepΔ npr1Δ	mutant	The data behind this hypothesis is the observation that a ScMep2 449-485Δ deletion mutant lacking the AI region is highly active in MA uptake both in the triple mepΔ and triple mepΔ npr1Δ backgrounds, implying that this Mep2 variant has a constitutively open channel.	RESULTS
220	232	Mep2 variant	mutant	The data behind this hypothesis is the observation that a ScMep2 449-485Δ deletion mutant lacking the AI region is highly active in MA uptake both in the triple mepΔ and triple mepΔ npr1Δ backgrounds, implying that this Mep2 variant has a constitutively open channel.	RESULTS
239	258	constitutively open	protein_state	The data behind this hypothesis is the observation that a ScMep2 449-485Δ deletion mutant lacking the AI region is highly active in MA uptake both in the triple mepΔ and triple mepΔ npr1Δ backgrounds, implying that this Mep2 variant has a constitutively open channel.	RESULTS
259	266	channel	site	The data behind this hypothesis is the observation that a ScMep2 449-485Δ deletion mutant lacking the AI region is highly active in MA uptake both in the triple mepΔ and triple mepΔ npr1Δ backgrounds, implying that this Mep2 variant has a constitutively open channel.	RESULTS
56	60	446Δ	mutant	We obtained a similar result for ammonium uptake by the 446Δ mutant (Fig. 3), supporting the data from Marini et al. We then constructed and purified the analogous CaMep2 442Δ truncation mutant and determined the crystal structure using data to 3.4 Å resolution.	RESULTS
61	67	mutant	protein_state	We obtained a similar result for ammonium uptake by the 446Δ mutant (Fig. 3), supporting the data from Marini et al. We then constructed and purified the analogous CaMep2 442Δ truncation mutant and determined the crystal structure using data to 3.4 Å resolution.	RESULTS
125	149	constructed and purified	experimental_method	We obtained a similar result for ammonium uptake by the 446Δ mutant (Fig. 3), supporting the data from Marini et al. We then constructed and purified the analogous CaMep2 442Δ truncation mutant and determined the crystal structure using data to 3.4 Å resolution.	RESULTS
164	170	CaMep2	protein	We obtained a similar result for ammonium uptake by the 446Δ mutant (Fig. 3), supporting the data from Marini et al. We then constructed and purified the analogous CaMep2 442Δ truncation mutant and determined the crystal structure using data to 3.4 Å resolution.	RESULTS
171	175	442Δ	mutant	We obtained a similar result for ammonium uptake by the 446Δ mutant (Fig. 3), supporting the data from Marini et al. We then constructed and purified the analogous CaMep2 442Δ truncation mutant and determined the crystal structure using data to 3.4 Å resolution.	RESULTS
176	193	truncation mutant	protein_state	We obtained a similar result for ammonium uptake by the 446Δ mutant (Fig. 3), supporting the data from Marini et al. We then constructed and purified the analogous CaMep2 442Δ truncation mutant and determined the crystal structure using data to 3.4 Å resolution.	RESULTS
198	208	determined	experimental_method	We obtained a similar result for ammonium uptake by the 446Δ mutant (Fig. 3), supporting the data from Marini et al. We then constructed and purified the analogous CaMep2 442Δ truncation mutant and determined the crystal structure using data to 3.4 Å resolution.	RESULTS
213	230	crystal structure	evidence	We obtained a similar result for ammonium uptake by the 446Δ mutant (Fig. 3), supporting the data from Marini et al. We then constructed and purified the analogous CaMep2 442Δ truncation mutant and determined the crystal structure using data to 3.4 Å resolution.	RESULTS
4	13	structure	evidence	The structure shows that removal of the AI region markedly increases the dynamics of the cytoplasmic parts of the transporter.	RESULTS
25	35	removal of	experimental_method	The structure shows that removal of the AI region markedly increases the dynamics of the cytoplasmic parts of the transporter.	RESULTS
40	49	AI region	structure_element	The structure shows that removal of the AI region markedly increases the dynamics of the cytoplasmic parts of the transporter.	RESULTS
89	106	cytoplasmic parts	structure_element	The structure shows that removal of the AI region markedly increases the dynamics of the cytoplasmic parts of the transporter.	RESULTS
114	125	transporter	protein_type	The structure shows that removal of the AI region markedly increases the dynamics of the cytoplasmic parts of the transporter.	RESULTS
47	56	AI region	structure_element	This is not unexpected given the fact that the AI region bridges the CTR and the main body of Mep2 (Fig. 6).	RESULTS
69	72	CTR	structure_element	This is not unexpected given the fact that the AI region bridges the CTR and the main body of Mep2 (Fig. 6).	RESULTS
81	90	main body	structure_element	This is not unexpected given the fact that the AI region bridges the CTR and the main body of Mep2 (Fig. 6).	RESULTS
94	98	Mep2	protein	This is not unexpected given the fact that the AI region bridges the CTR and the main body of Mep2 (Fig. 6).	RESULTS
0	7	Density	evidence	Density for ICL3 and the CTR beyond residue Arg415 is missing in the 442Δ mutant, and the density for the other ICLs including ICL1 is generally poor with visible parts of the structure having high B-factors (Fig. 7).	RESULTS
12	16	ICL3	structure_element	Density for ICL3 and the CTR beyond residue Arg415 is missing in the 442Δ mutant, and the density for the other ICLs including ICL1 is generally poor with visible parts of the structure having high B-factors (Fig. 7).	RESULTS
25	28	CTR	structure_element	Density for ICL3 and the CTR beyond residue Arg415 is missing in the 442Δ mutant, and the density for the other ICLs including ICL1 is generally poor with visible parts of the structure having high B-factors (Fig. 7).	RESULTS
44	50	Arg415	residue_name_number	Density for ICL3 and the CTR beyond residue Arg415 is missing in the 442Δ mutant, and the density for the other ICLs including ICL1 is generally poor with visible parts of the structure having high B-factors (Fig. 7).	RESULTS
69	73	442Δ	mutant	Density for ICL3 and the CTR beyond residue Arg415 is missing in the 442Δ mutant, and the density for the other ICLs including ICL1 is generally poor with visible parts of the structure having high B-factors (Fig. 7).	RESULTS
74	80	mutant	protein_state	Density for ICL3 and the CTR beyond residue Arg415 is missing in the 442Δ mutant, and the density for the other ICLs including ICL1 is generally poor with visible parts of the structure having high B-factors (Fig. 7).	RESULTS
90	97	density	evidence	Density for ICL3 and the CTR beyond residue Arg415 is missing in the 442Δ mutant, and the density for the other ICLs including ICL1 is generally poor with visible parts of the structure having high B-factors (Fig. 7).	RESULTS
112	116	ICLs	structure_element	Density for ICL3 and the CTR beyond residue Arg415 is missing in the 442Δ mutant, and the density for the other ICLs including ICL1 is generally poor with visible parts of the structure having high B-factors (Fig. 7).	RESULTS
127	131	ICL1	structure_element	Density for ICL3 and the CTR beyond residue Arg415 is missing in the 442Δ mutant, and the density for the other ICLs including ICL1 is generally poor with visible parts of the structure having high B-factors (Fig. 7).	RESULTS
176	185	structure	evidence	Density for ICL3 and the CTR beyond residue Arg415 is missing in the 442Δ mutant, and the density for the other ICLs including ICL1 is generally poor with visible parts of the structure having high B-factors (Fig. 7).	RESULTS
28	33	Tyr49	residue_name_number	Interestingly, however, the Tyr49-His342 hydrogen bond that closes the channel in the WT protein is still present (Fig. 7 and Supplementary Fig. 2).	RESULTS
34	40	His342	residue_name_number	Interestingly, however, the Tyr49-His342 hydrogen bond that closes the channel in the WT protein is still present (Fig. 7 and Supplementary Fig. 2).	RESULTS
41	54	hydrogen bond	bond_interaction	Interestingly, however, the Tyr49-His342 hydrogen bond that closes the channel in the WT protein is still present (Fig. 7 and Supplementary Fig. 2).	RESULTS
86	88	WT	protein_state	Interestingly, however, the Tyr49-His342 hydrogen bond that closes the channel in the WT protein is still present (Fig. 7 and Supplementary Fig. 2).	RESULTS
54	60	active	protein_state	Why then does this mutant appear to be constitutively active? We propose two possibilities.	RESULTS
26	30	open	protein_state	The first one is that the open state is disfavoured by crystallization because of lower stability or due to crystal packing constraints.	RESULTS
55	70	crystallization	experimental_method	The first one is that the open state is disfavoured by crystallization because of lower stability or due to crystal packing constraints.	RESULTS
35	56	Tyr–His hydrogen bond	site	The second possibility is that the Tyr–His hydrogen bond has to be disrupted by the incoming substrate to open the channel.	RESULTS
106	110	open	protein_state	The second possibility is that the Tyr–His hydrogen bond has to be disrupted by the incoming substrate to open the channel.	RESULTS
41	44	NH3	chemical	The latter model would fit well with the NH3/H+ symport model in which the proton is relayed by the twin-His motif.	RESULTS
45	47	H+	chemical	The latter model would fit well with the NH3/H+ symport model in which the proton is relayed by the twin-His motif.	RESULTS
100	114	twin-His motif	structure_element	The latter model would fit well with the NH3/H+ symport model in which the proton is relayed by the twin-His motif.	RESULTS
22	43	Tyr–His hydrogen bond	site	The importance of the Tyr–His hydrogen bond is underscored by the fact that its removal in the ScMep2 Y53A mutant results in a constitutively active transporter (Fig. 3).	RESULTS
80	87	removal	experimental_method	The importance of the Tyr–His hydrogen bond is underscored by the fact that its removal in the ScMep2 Y53A mutant results in a constitutively active transporter (Fig. 3).	RESULTS
95	101	ScMep2	protein	The importance of the Tyr–His hydrogen bond is underscored by the fact that its removal in the ScMep2 Y53A mutant results in a constitutively active transporter (Fig. 3).	RESULTS
102	106	Y53A	mutant	The importance of the Tyr–His hydrogen bond is underscored by the fact that its removal in the ScMep2 Y53A mutant results in a constitutively active transporter (Fig. 3).	RESULTS
107	113	mutant	protein_state	The importance of the Tyr–His hydrogen bond is underscored by the fact that its removal in the ScMep2 Y53A mutant results in a constitutively active transporter (Fig. 3).	RESULTS
127	148	constitutively active	protein_state	The importance of the Tyr–His hydrogen bond is underscored by the fact that its removal in the ScMep2 Y53A mutant results in a constitutively active transporter (Fig. 3).	RESULTS
149	160	transporter	protein_type	The importance of the Tyr–His hydrogen bond is underscored by the fact that its removal in the ScMep2 Y53A mutant results in a constitutively active transporter (Fig. 3).	RESULTS
0	15	Phosphorylation	ptm	Phosphorylation causes a conformational change in the CTR	RESULTS
54	57	CTR	structure_element	Phosphorylation causes a conformational change in the CTR	RESULTS
7	11	Mep2	protein	Do the Mep2 structures provide any clues regarding the potential effect of phosphorylation?	RESULTS
12	22	structures	evidence	Do the Mep2 structures provide any clues regarding the potential effect of phosphorylation?	RESULTS
75	90	phosphorylation	ptm	Do the Mep2 structures provide any clues regarding the potential effect of phosphorylation?	RESULTS
27	33	Ser457	residue_name_number	The side-chain hydroxyl of Ser457/453 is located in a well-defined electronegative pocket that is solvent accessible (Fig. 6).	RESULTS
34	37	453	residue_number	The side-chain hydroxyl of Ser457/453 is located in a well-defined electronegative pocket that is solvent accessible (Fig. 6).	RESULTS
67	89	electronegative pocket	site	The side-chain hydroxyl of Ser457/453 is located in a well-defined electronegative pocket that is solvent accessible (Fig. 6).	RESULTS
98	116	solvent accessible	protein_state	The side-chain hydroxyl of Ser457/453 is located in a well-defined electronegative pocket that is solvent accessible (Fig. 6).	RESULTS
25	31	serine	residue_name	The closest atoms to the serine hydroxyl group are the backbone carbonyl atoms of Asp419, Glu420 and Glu421, which are 3–4 Å away.	RESULTS
82	88	Asp419	residue_name_number	The closest atoms to the serine hydroxyl group are the backbone carbonyl atoms of Asp419, Glu420 and Glu421, which are 3–4 Å away.	RESULTS
90	96	Glu420	residue_name_number	The closest atoms to the serine hydroxyl group are the backbone carbonyl atoms of Asp419, Glu420 and Glu421, which are 3–4 Å away.	RESULTS
101	107	Glu421	residue_name_number	The closest atoms to the serine hydroxyl group are the backbone carbonyl atoms of Asp419, Glu420 and Glu421, which are 3–4 Å away.	RESULTS
26	41	phosphorylation	ptm	We therefore predict that phosphorylation of Ser453 will result in steric clashes as well as electrostatic repulsion, which in turn might cause substantial conformational changes within the CTR.	RESULTS
45	51	Ser453	residue_name_number	We therefore predict that phosphorylation of Ser453 will result in steric clashes as well as electrostatic repulsion, which in turn might cause substantial conformational changes within the CTR.	RESULTS
190	193	CTR	structure_element	We therefore predict that phosphorylation of Ser453 will result in steric clashes as well as electrostatic repulsion, which in turn might cause substantial conformational changes within the CTR.	RESULTS
28	38	determined	experimental_method	To test this hypothesis, we determined the structure of the phosphorylation-mimicking R452D/S453D protein (hereafter termed ‘DD mutant'), using data to a resolution of 2.4 Å. The additional mutation of the arginine preceding the phosphorylation site was introduced (i) to increase the negative charge density and make it more comparable to a phosphate at neutral pH, and (ii) to further destabilize the interactions of the AI region with the main body of the transporter (Fig. 6).	RESULTS
43	52	structure	evidence	To test this hypothesis, we determined the structure of the phosphorylation-mimicking R452D/S453D protein (hereafter termed ‘DD mutant'), using data to a resolution of 2.4 Å. The additional mutation of the arginine preceding the phosphorylation site was introduced (i) to increase the negative charge density and make it more comparable to a phosphate at neutral pH, and (ii) to further destabilize the interactions of the AI region with the main body of the transporter (Fig. 6).	RESULTS
60	85	phosphorylation-mimicking	protein_state	To test this hypothesis, we determined the structure of the phosphorylation-mimicking R452D/S453D protein (hereafter termed ‘DD mutant'), using data to a resolution of 2.4 Å. The additional mutation of the arginine preceding the phosphorylation site was introduced (i) to increase the negative charge density and make it more comparable to a phosphate at neutral pH, and (ii) to further destabilize the interactions of the AI region with the main body of the transporter (Fig. 6).	RESULTS
86	97	R452D/S453D	mutant	To test this hypothesis, we determined the structure of the phosphorylation-mimicking R452D/S453D protein (hereafter termed ‘DD mutant'), using data to a resolution of 2.4 Å. The additional mutation of the arginine preceding the phosphorylation site was introduced (i) to increase the negative charge density and make it more comparable to a phosphate at neutral pH, and (ii) to further destabilize the interactions of the AI region with the main body of the transporter (Fig. 6).	RESULTS
125	134	DD mutant	mutant	To test this hypothesis, we determined the structure of the phosphorylation-mimicking R452D/S453D protein (hereafter termed ‘DD mutant'), using data to a resolution of 2.4 Å. The additional mutation of the arginine preceding the phosphorylation site was introduced (i) to increase the negative charge density and make it more comparable to a phosphate at neutral pH, and (ii) to further destabilize the interactions of the AI region with the main body of the transporter (Fig. 6).	RESULTS
179	201	additional mutation of	experimental_method	To test this hypothesis, we determined the structure of the phosphorylation-mimicking R452D/S453D protein (hereafter termed ‘DD mutant'), using data to a resolution of 2.4 Å. The additional mutation of the arginine preceding the phosphorylation site was introduced (i) to increase the negative charge density and make it more comparable to a phosphate at neutral pH, and (ii) to further destabilize the interactions of the AI region with the main body of the transporter (Fig. 6).	RESULTS
206	214	arginine	residue_name	To test this hypothesis, we determined the structure of the phosphorylation-mimicking R452D/S453D protein (hereafter termed ‘DD mutant'), using data to a resolution of 2.4 Å. The additional mutation of the arginine preceding the phosphorylation site was introduced (i) to increase the negative charge density and make it more comparable to a phosphate at neutral pH, and (ii) to further destabilize the interactions of the AI region with the main body of the transporter (Fig. 6).	RESULTS
229	249	phosphorylation site	site	To test this hypothesis, we determined the structure of the phosphorylation-mimicking R452D/S453D protein (hereafter termed ‘DD mutant'), using data to a resolution of 2.4 Å. The additional mutation of the arginine preceding the phosphorylation site was introduced (i) to increase the negative charge density and make it more comparable to a phosphate at neutral pH, and (ii) to further destabilize the interactions of the AI region with the main body of the transporter (Fig. 6).	RESULTS
342	351	phosphate	chemical	To test this hypothesis, we determined the structure of the phosphorylation-mimicking R452D/S453D protein (hereafter termed ‘DD mutant'), using data to a resolution of 2.4 Å. The additional mutation of the arginine preceding the phosphorylation site was introduced (i) to increase the negative charge density and make it more comparable to a phosphate at neutral pH, and (ii) to further destabilize the interactions of the AI region with the main body of the transporter (Fig. 6).	RESULTS
423	432	AI region	structure_element	To test this hypothesis, we determined the structure of the phosphorylation-mimicking R452D/S453D protein (hereafter termed ‘DD mutant'), using data to a resolution of 2.4 Å. The additional mutation of the arginine preceding the phosphorylation site was introduced (i) to increase the negative charge density and make it more comparable to a phosphate at neutral pH, and (ii) to further destabilize the interactions of the AI region with the main body of the transporter (Fig. 6).	RESULTS
442	451	main body	structure_element	To test this hypothesis, we determined the structure of the phosphorylation-mimicking R452D/S453D protein (hereafter termed ‘DD mutant'), using data to a resolution of 2.4 Å. The additional mutation of the arginine preceding the phosphorylation site was introduced (i) to increase the negative charge density and make it more comparable to a phosphate at neutral pH, and (ii) to further destabilize the interactions of the AI region with the main body of the transporter (Fig. 6).	RESULTS
459	470	transporter	protein_type	To test this hypothesis, we determined the structure of the phosphorylation-mimicking R452D/S453D protein (hereafter termed ‘DD mutant'), using data to a resolution of 2.4 Å. The additional mutation of the arginine preceding the phosphorylation site was introduced (i) to increase the negative charge density and make it more comparable to a phosphate at neutral pH, and (ii) to further destabilize the interactions of the AI region with the main body of the transporter (Fig. 6).	RESULTS
4	12	ammonium	chemical	The ammonium uptake activity of the S. cerevisiae version of the DD mutant is the same as that of WT Mep2 and the S453D mutant, indicating that the mutations do not affect transporter functionality in the triple mepΔ background (Fig. 3).	RESULTS
36	49	S. cerevisiae	species	The ammonium uptake activity of the S. cerevisiae version of the DD mutant is the same as that of WT Mep2 and the S453D mutant, indicating that the mutations do not affect transporter functionality in the triple mepΔ background (Fig. 3).	RESULTS
65	74	DD mutant	mutant	The ammonium uptake activity of the S. cerevisiae version of the DD mutant is the same as that of WT Mep2 and the S453D mutant, indicating that the mutations do not affect transporter functionality in the triple mepΔ background (Fig. 3).	RESULTS
98	100	WT	protein_state	The ammonium uptake activity of the S. cerevisiae version of the DD mutant is the same as that of WT Mep2 and the S453D mutant, indicating that the mutations do not affect transporter functionality in the triple mepΔ background (Fig. 3).	RESULTS
101	105	Mep2	protein	The ammonium uptake activity of the S. cerevisiae version of the DD mutant is the same as that of WT Mep2 and the S453D mutant, indicating that the mutations do not affect transporter functionality in the triple mepΔ background (Fig. 3).	RESULTS
114	119	S453D	mutant	The ammonium uptake activity of the S. cerevisiae version of the DD mutant is the same as that of WT Mep2 and the S453D mutant, indicating that the mutations do not affect transporter functionality in the triple mepΔ background (Fig. 3).	RESULTS
120	126	mutant	protein_state	The ammonium uptake activity of the S. cerevisiae version of the DD mutant is the same as that of WT Mep2 and the S453D mutant, indicating that the mutations do not affect transporter functionality in the triple mepΔ background (Fig. 3).	RESULTS
205	216	triple mepΔ	mutant	The ammonium uptake activity of the S. cerevisiae version of the DD mutant is the same as that of WT Mep2 and the S453D mutant, indicating that the mutations do not affect transporter functionality in the triple mepΔ background (Fig. 3).	RESULTS
18	28	AI segment	structure_element	Unexpectedly, the AI segment containing the mutated residues has only undergone a slight shift compared with the WT protein (Fig. 8 and Supplementary Fig. 3).	RESULTS
113	115	WT	protein_state	Unexpectedly, the AI segment containing the mutated residues has only undergone a slight shift compared with the WT protein (Fig. 8 and Supplementary Fig. 3).	RESULTS
17	26	conserved	protein_state	By contrast, the conserved part of the CTR has undergone a large conformational change involving formation of a 12-residue-long α-helix from Leu427 to Asp438.	RESULTS
39	42	CTR	structure_element	By contrast, the conserved part of the CTR has undergone a large conformational change involving formation of a 12-residue-long α-helix from Leu427 to Asp438.	RESULTS
112	135	12-residue-long α-helix	structure_element	By contrast, the conserved part of the CTR has undergone a large conformational change involving formation of a 12-residue-long α-helix from Leu427 to Asp438.	RESULTS
141	157	Leu427 to Asp438	residue_range	By contrast, the conserved part of the CTR has undergone a large conformational change involving formation of a 12-residue-long α-helix from Leu427 to Asp438.	RESULTS
22	35	Glu420-Leu423	residue_range	In addition, residues Glu420-Leu423 including Glu421 of the ExxGxD motif are now disordered (Fig. 8 and Supplementary Fig. 3).	RESULTS
46	52	Glu421	residue_name_number	In addition, residues Glu420-Leu423 including Glu421 of the ExxGxD motif are now disordered (Fig. 8 and Supplementary Fig. 3).	RESULTS
60	72	ExxGxD motif	structure_element	In addition, residues Glu420-Leu423 including Glu421 of the ExxGxD motif are now disordered (Fig. 8 and Supplementary Fig. 3).	RESULTS
81	91	disordered	protein_state	In addition, residues Glu420-Leu423 including Glu421 of the ExxGxD motif are now disordered (Fig. 8 and Supplementary Fig. 3).	RESULTS
77	97	ammonium transporter	protein_type	This is the first time a large conformational change has been observed in an ammonium transporter as a result of a mutation, and confirms previous hypotheses that phosphorylation causes structural changes in the CTR.	RESULTS
115	123	mutation	experimental_method	This is the first time a large conformational change has been observed in an ammonium transporter as a result of a mutation, and confirms previous hypotheses that phosphorylation causes structural changes in the CTR.	RESULTS
163	178	phosphorylation	ptm	This is the first time a large conformational change has been observed in an ammonium transporter as a result of a mutation, and confirms previous hypotheses that phosphorylation causes structural changes in the CTR.	RESULTS
212	215	CTR	structure_element	This is the first time a large conformational change has been observed in an ammonium transporter as a result of a mutation, and confirms previous hypotheses that phosphorylation causes structural changes in the CTR.	RESULTS
47	52	R452D	mutant	To exclude the possibility that the additional R452D mutation is responsible for the observed changes, we also determined the structure of the ‘single D' S453D mutant.	RESULTS
111	121	determined	experimental_method	To exclude the possibility that the additional R452D mutation is responsible for the observed changes, we also determined the structure of the ‘single D' S453D mutant.	RESULTS
126	135	structure	evidence	To exclude the possibility that the additional R452D mutation is responsible for the observed changes, we also determined the structure of the ‘single D' S453D mutant.	RESULTS
144	152	single D	mutant	To exclude the possibility that the additional R452D mutation is responsible for the observed changes, we also determined the structure of the ‘single D' S453D mutant.	RESULTS
154	159	S453D	mutant	To exclude the possibility that the additional R452D mutation is responsible for the observed changes, we also determined the structure of the ‘single D' S453D mutant.	RESULTS
160	166	mutant	protein_state	To exclude the possibility that the additional R452D mutation is responsible for the observed changes, we also determined the structure of the ‘single D' S453D mutant.	RESULTS
57	65	single D	mutant	As shown in Supplementary Fig. 4, the consequence of the single D mutation is very similar to that of the DD substitution, with conformational changes and increased dynamics confined to the conserved part of the CTR (Supplementary Fig. 4).	RESULTS
66	74	mutation	experimental_method	As shown in Supplementary Fig. 4, the consequence of the single D mutation is very similar to that of the DD substitution, with conformational changes and increased dynamics confined to the conserved part of the CTR (Supplementary Fig. 4).	RESULTS
106	121	DD substitution	mutant	As shown in Supplementary Fig. 4, the consequence of the single D mutation is very similar to that of the DD substitution, with conformational changes and increased dynamics confined to the conserved part of the CTR (Supplementary Fig. 4).	RESULTS
190	199	conserved	protein_state	As shown in Supplementary Fig. 4, the consequence of the single D mutation is very similar to that of the DD substitution, with conformational changes and increased dynamics confined to the conserved part of the CTR (Supplementary Fig. 4).	RESULTS
212	215	CTR	structure_element	As shown in Supplementary Fig. 4, the consequence of the single D mutation is very similar to that of the DD substitution, with conformational changes and increased dynamics confined to the conserved part of the CTR (Supplementary Fig. 4).	RESULTS
18	36	crystal structures	evidence	To supplement the crystal structures, we also performed modelling and MD studies of WT CaMep2, the DD mutant and phosphorylated protein (S453J).	RESULTS
56	65	modelling	experimental_method	To supplement the crystal structures, we also performed modelling and MD studies of WT CaMep2, the DD mutant and phosphorylated protein (S453J).	RESULTS
70	72	MD	experimental_method	To supplement the crystal structures, we also performed modelling and MD studies of WT CaMep2, the DD mutant and phosphorylated protein (S453J).	RESULTS
84	86	WT	protein_state	To supplement the crystal structures, we also performed modelling and MD studies of WT CaMep2, the DD mutant and phosphorylated protein (S453J).	RESULTS
87	93	CaMep2	protein	To supplement the crystal structures, we also performed modelling and MD studies of WT CaMep2, the DD mutant and phosphorylated protein (S453J).	RESULTS
99	108	DD mutant	mutant	To supplement the crystal structures, we also performed modelling and MD studies of WT CaMep2, the DD mutant and phosphorylated protein (S453J).	RESULTS
113	127	phosphorylated	protein_state	To supplement the crystal structures, we also performed modelling and MD studies of WT CaMep2, the DD mutant and phosphorylated protein (S453J).	RESULTS
137	142	S453J	mutant	To supplement the crystal structures, we also performed modelling and MD studies of WT CaMep2, the DD mutant and phosphorylated protein (S453J).	RESULTS
7	9	WT	protein_state	In the WT structure, the acidic residues Asp419, Glu420 and Glu421 are within hydrogen bonding distance of Ser453.	RESULTS
10	19	structure	evidence	In the WT structure, the acidic residues Asp419, Glu420 and Glu421 are within hydrogen bonding distance of Ser453.	RESULTS
41	47	Asp419	residue_name_number	In the WT structure, the acidic residues Asp419, Glu420 and Glu421 are within hydrogen bonding distance of Ser453.	RESULTS
49	55	Glu420	residue_name_number	In the WT structure, the acidic residues Asp419, Glu420 and Glu421 are within hydrogen bonding distance of Ser453.	RESULTS
60	66	Glu421	residue_name_number	In the WT structure, the acidic residues Asp419, Glu420 and Glu421 are within hydrogen bonding distance of Ser453.	RESULTS
78	94	hydrogen bonding	bond_interaction	In the WT structure, the acidic residues Asp419, Glu420 and Glu421 are within hydrogen bonding distance of Ser453.	RESULTS
107	113	Ser453	residue_name_number	In the WT structure, the acidic residues Asp419, Glu420 and Glu421 are within hydrogen bonding distance of Ser453.	RESULTS
16	18	MD	experimental_method	After 200 ns of MD simulation, the interactions between these residues and Ser453 remain intact.	RESULTS
19	29	simulation	experimental_method	After 200 ns of MD simulation, the interactions between these residues and Ser453 remain intact.	RESULTS
75	81	Ser453	residue_name_number	After 200 ns of MD simulation, the interactions between these residues and Ser453 remain intact.	RESULTS
36	44	r.m.s.d.	evidence	The protein backbone has an average r.m.s.d. of only ∼3 Å during the 200-ns simulation, indicating that the protein is stable.	RESULTS
76	86	simulation	experimental_method	The protein backbone has an average r.m.s.d. of only ∼3 Å during the 200-ns simulation, indicating that the protein is stable.	RESULTS
119	125	stable	protein_state	The protein backbone has an average r.m.s.d. of only ∼3 Å during the 200-ns simulation, indicating that the protein is stable.	RESULTS
93	99	stable	protein_state	There is flexibility in the side chains of the acidic residues so that they are able to form stable hydrogen bonds with Ser453.	RESULTS
100	114	hydrogen bonds	bond_interaction	There is flexibility in the side chains of the acidic residues so that they are able to form stable hydrogen bonds with Ser453.	RESULTS
120	126	Ser453	residue_name_number	There is flexibility in the side chains of the acidic residues so that they are able to form stable hydrogen bonds with Ser453.	RESULTS
26	40	hydrogen bonds	bond_interaction	In particular, persistent hydrogen bonds are observed between the Ser453 hydroxyl group and the acidic group of Glu420, and also between the amine group of Ser453 and the backbone carbonyl of Glu420 (Supplementary Fig. 5).	RESULTS
66	72	Ser453	residue_name_number	In particular, persistent hydrogen bonds are observed between the Ser453 hydroxyl group and the acidic group of Glu420, and also between the amine group of Ser453 and the backbone carbonyl of Glu420 (Supplementary Fig. 5).	RESULTS
112	118	Glu420	residue_name_number	In particular, persistent hydrogen bonds are observed between the Ser453 hydroxyl group and the acidic group of Glu420, and also between the amine group of Ser453 and the backbone carbonyl of Glu420 (Supplementary Fig. 5).	RESULTS
156	162	Ser453	residue_name_number	In particular, persistent hydrogen bonds are observed between the Ser453 hydroxyl group and the acidic group of Glu420, and also between the amine group of Ser453 and the backbone carbonyl of Glu420 (Supplementary Fig. 5).	RESULTS
192	198	Glu420	residue_name_number	In particular, persistent hydrogen bonds are observed between the Ser453 hydroxyl group and the acidic group of Glu420, and also between the amine group of Ser453 and the backbone carbonyl of Glu420 (Supplementary Fig. 5).	RESULTS
4	13	DD mutant	mutant	The DD mutant is also stable during the simulations, but the average backbone r.m.s.d of ∼3.6 Å suggests slightly more conformational flexibility than WT.	RESULTS
22	28	stable	protein_state	The DD mutant is also stable during the simulations, but the average backbone r.m.s.d of ∼3.6 Å suggests slightly more conformational flexibility than WT.	RESULTS
40	51	simulations	experimental_method	The DD mutant is also stable during the simulations, but the average backbone r.m.s.d of ∼3.6 Å suggests slightly more conformational flexibility than WT.	RESULTS
78	85	r.m.s.d	evidence	The DD mutant is also stable during the simulations, but the average backbone r.m.s.d of ∼3.6 Å suggests slightly more conformational flexibility than WT.	RESULTS
151	153	WT	protein_state	The DD mutant is also stable during the simulations, but the average backbone r.m.s.d of ∼3.6 Å suggests slightly more conformational flexibility than WT.	RESULTS
7	17	simulation	experimental_method	As the simulation proceeds, the side chains of the acidic residues move away from Asp452 and Asp453, presumably to avoid electrostatic repulsion.	RESULTS
82	88	Asp452	residue_name_number	As the simulation proceeds, the side chains of the acidic residues move away from Asp452 and Asp453, presumably to avoid electrostatic repulsion.	RESULTS
93	99	Asp453	residue_name_number	As the simulation proceeds, the side chains of the acidic residues move away from Asp452 and Asp453, presumably to avoid electrostatic repulsion.	RESULTS
17	25	distance	evidence	For example, the distance between the Asp453 acidic oxygens and the Glu420 acidic oxygens increases from ∼7 to >22 Å after 200 ns simulations, and thus these residues are not interacting.	RESULTS
38	44	Asp453	residue_name_number	For example, the distance between the Asp453 acidic oxygens and the Glu420 acidic oxygens increases from ∼7 to >22 Å after 200 ns simulations, and thus these residues are not interacting.	RESULTS
68	74	Glu420	residue_name_number	For example, the distance between the Asp453 acidic oxygens and the Glu420 acidic oxygens increases from ∼7 to >22 Å after 200 ns simulations, and thus these residues are not interacting.	RESULTS
130	141	simulations	experimental_method	For example, the distance between the Asp453 acidic oxygens and the Glu420 acidic oxygens increases from ∼7 to >22 Å after 200 ns simulations, and thus these residues are not interacting.	RESULTS
15	34	structurally stable	protein_state	The protein is structurally stable throughout the simulation with little deviation in the other parts of the protein.	RESULTS
50	60	simulation	experimental_method	The protein is structurally stable throughout the simulation with little deviation in the other parts of the protein.	RESULTS
13	18	S453J	mutant	Finally, the S453J mutant is also stable throughout the 200-ns simulation and has an average backbone deviation of ∼3.8 Å, which is similar to the DD mutant.	RESULTS
19	25	mutant	protein_state	Finally, the S453J mutant is also stable throughout the 200-ns simulation and has an average backbone deviation of ∼3.8 Å, which is similar to the DD mutant.	RESULTS
34	40	stable	protein_state	Finally, the S453J mutant is also stable throughout the 200-ns simulation and has an average backbone deviation of ∼3.8 Å, which is similar to the DD mutant.	RESULTS
63	73	simulation	experimental_method	Finally, the S453J mutant is also stable throughout the 200-ns simulation and has an average backbone deviation of ∼3.8 Å, which is similar to the DD mutant.	RESULTS
147	156	DD mutant	mutant	Finally, the S453J mutant is also stable throughout the 200-ns simulation and has an average backbone deviation of ∼3.8 Å, which is similar to the DD mutant.	RESULTS
46	52	Arg452	residue_name_number	The movement of the acidic residues away from Arg452 and Sep453 is more pronounced in this simulation in comparison with the movement away from Asp452 and Asp453 in the DD mutant.	RESULTS
57	63	Sep453	residue_name_number	The movement of the acidic residues away from Arg452 and Sep453 is more pronounced in this simulation in comparison with the movement away from Asp452 and Asp453 in the DD mutant.	RESULTS
91	101	simulation	experimental_method	The movement of the acidic residues away from Arg452 and Sep453 is more pronounced in this simulation in comparison with the movement away from Asp452 and Asp453 in the DD mutant.	RESULTS
144	150	Asp452	residue_name_number	The movement of the acidic residues away from Arg452 and Sep453 is more pronounced in this simulation in comparison with the movement away from Asp452 and Asp453 in the DD mutant.	RESULTS
155	161	Asp453	residue_name_number	The movement of the acidic residues away from Arg452 and Sep453 is more pronounced in this simulation in comparison with the movement away from Asp452 and Asp453 in the DD mutant.	RESULTS
169	178	DD mutant	mutant	The movement of the acidic residues away from Arg452 and Sep453 is more pronounced in this simulation in comparison with the movement away from Asp452 and Asp453 in the DD mutant.	RESULTS
4	12	distance	evidence	The distance between the phosphate of Sep453 and the acidic oxygen atoms of Glu420 is initially ∼11 Å, but increases to >30 Å after 200 ns.	RESULTS
25	34	phosphate	chemical	The distance between the phosphate of Sep453 and the acidic oxygen atoms of Glu420 is initially ∼11 Å, but increases to >30 Å after 200 ns.	RESULTS
38	44	Sep453	residue_name_number	The distance between the phosphate of Sep453 and the acidic oxygen atoms of Glu420 is initially ∼11 Å, but increases to >30 Å after 200 ns.	RESULTS
76	82	Glu420	residue_name_number	The distance between the phosphate of Sep453 and the acidic oxygen atoms of Glu420 is initially ∼11 Å, but increases to >30 Å after 200 ns.	RESULTS
4	15	short helix	structure_element	The short helix formed by residues Leu427 to Asp438 unravels during the simulations to a disordered state.	RESULTS
35	51	Leu427 to Asp438	residue_range	The short helix formed by residues Leu427 to Asp438 unravels during the simulations to a disordered state.	RESULTS
72	83	simulations	experimental_method	The short helix formed by residues Leu427 to Asp438 unravels during the simulations to a disordered state.	RESULTS
89	99	disordered	protein_state	The short helix formed by residues Leu427 to Asp438 unravels during the simulations to a disordered state.	RESULTS
10	12	MD	experimental_method	Thus, the MD simulations support the notion from the crystal structures that phosphorylation generates conformational changes in the conserved part of the CTR.	RESULTS
13	24	simulations	experimental_method	Thus, the MD simulations support the notion from the crystal structures that phosphorylation generates conformational changes in the conserved part of the CTR.	RESULTS
53	71	crystal structures	evidence	Thus, the MD simulations support the notion from the crystal structures that phosphorylation generates conformational changes in the conserved part of the CTR.	RESULTS
77	92	phosphorylation	ptm	Thus, the MD simulations support the notion from the crystal structures that phosphorylation generates conformational changes in the conserved part of the CTR.	RESULTS
133	142	conserved	protein_state	Thus, the MD simulations support the notion from the crystal structures that phosphorylation generates conformational changes in the conserved part of the CTR.	RESULTS
155	158	CTR	structure_element	Thus, the MD simulations support the notion from the crystal structures that phosphorylation generates conformational changes in the conserved part of the CTR.	RESULTS
44	66	phosphomimetic mutants	mutant	However, the conformational changes for the phosphomimetic mutants in the crystals are confined to the CTR (Fig. 8), and the channels are still closed (Supplementary Fig. 2).	RESULTS
74	82	crystals	evidence	However, the conformational changes for the phosphomimetic mutants in the crystals are confined to the CTR (Fig. 8), and the channels are still closed (Supplementary Fig. 2).	RESULTS
103	106	CTR	structure_element	However, the conformational changes for the phosphomimetic mutants in the crystals are confined to the CTR (Fig. 8), and the channels are still closed (Supplementary Fig. 2).	RESULTS
125	133	channels	site	However, the conformational changes for the phosphomimetic mutants in the crystals are confined to the CTR (Fig. 8), and the channels are still closed (Supplementary Fig. 2).	RESULTS
144	150	closed	protein_state	However, the conformational changes for the phosphomimetic mutants in the crystals are confined to the CTR (Fig. 8), and the channels are still closed (Supplementary Fig. 2).	RESULTS
37	44	mutants	mutant	One possible explanation is that the mutants do not accurately mimic a phosphoserine, but the observation that the S453D and DD mutants are fully active in the absence of Npr1 suggests that the mutations do mimic the effect of phosphorylation (Fig. 3).	RESULTS
71	84	phosphoserine	residue_name	One possible explanation is that the mutants do not accurately mimic a phosphoserine, but the observation that the S453D and DD mutants are fully active in the absence of Npr1 suggests that the mutations do mimic the effect of phosphorylation (Fig. 3).	RESULTS
115	120	S453D	mutant	One possible explanation is that the mutants do not accurately mimic a phosphoserine, but the observation that the S453D and DD mutants are fully active in the absence of Npr1 suggests that the mutations do mimic the effect of phosphorylation (Fig. 3).	RESULTS
125	135	DD mutants	mutant	One possible explanation is that the mutants do not accurately mimic a phosphoserine, but the observation that the S453D and DD mutants are fully active in the absence of Npr1 suggests that the mutations do mimic the effect of phosphorylation (Fig. 3).	RESULTS
140	152	fully active	protein_state	One possible explanation is that the mutants do not accurately mimic a phosphoserine, but the observation that the S453D and DD mutants are fully active in the absence of Npr1 suggests that the mutations do mimic the effect of phosphorylation (Fig. 3).	RESULTS
160	170	absence of	protein_state	One possible explanation is that the mutants do not accurately mimic a phosphoserine, but the observation that the S453D and DD mutants are fully active in the absence of Npr1 suggests that the mutations do mimic the effect of phosphorylation (Fig. 3).	RESULTS
171	175	Npr1	protein	One possible explanation is that the mutants do not accurately mimic a phosphoserine, but the observation that the S453D and DD mutants are fully active in the absence of Npr1 suggests that the mutations do mimic the effect of phosphorylation (Fig. 3).	RESULTS
194	203	mutations	experimental_method	One possible explanation is that the mutants do not accurately mimic a phosphoserine, but the observation that the S453D and DD mutants are fully active in the absence of Npr1 suggests that the mutations do mimic the effect of phosphorylation (Fig. 3).	RESULTS
227	242	phosphorylation	ptm	One possible explanation is that the mutants do not accurately mimic a phosphoserine, but the observation that the S453D and DD mutants are fully active in the absence of Npr1 suggests that the mutations do mimic the effect of phosphorylation (Fig. 3).	RESULTS
18	23	S453D	mutant	The fact that the S453D structure was obtained in the presence of 10 mM ammonium ions suggests that the crystallization process favours closed states of the Mep2 channels.	RESULTS
24	33	structure	evidence	The fact that the S453D structure was obtained in the presence of 10 mM ammonium ions suggests that the crystallization process favours closed states of the Mep2 channels.	RESULTS
72	80	ammonium	chemical	The fact that the S453D structure was obtained in the presence of 10 mM ammonium ions suggests that the crystallization process favours closed states of the Mep2 channels.	RESULTS
104	119	crystallization	experimental_method	The fact that the S453D structure was obtained in the presence of 10 mM ammonium ions suggests that the crystallization process favours closed states of the Mep2 channels.	RESULTS
136	142	closed	protein_state	The fact that the S453D structure was obtained in the presence of 10 mM ammonium ions suggests that the crystallization process favours closed states of the Mep2 channels.	RESULTS
157	161	Mep2	protein	The fact that the S453D structure was obtained in the presence of 10 mM ammonium ions suggests that the crystallization process favours closed states of the Mep2 channels.	RESULTS
162	170	channels	site	The fact that the S453D structure was obtained in the presence of 10 mM ammonium ions suggests that the crystallization process favours closed states of the Mep2 channels.	RESULTS
16	36	ammonium transporter	protein_type	Knowledge about ammonium transporter structure has been obtained from experimental and theoretical studies on bacterial family members.	DISCUSS
37	46	structure	evidence	Knowledge about ammonium transporter structure has been obtained from experimental and theoretical studies on bacterial family members.	DISCUSS
110	119	bacterial	taxonomy_domain	Knowledge about ammonium transporter structure has been obtained from experimental and theoretical studies on bacterial family members.	DISCUSS
25	56	biochemical and genetic studies	experimental_method	In addition, a number of biochemical and genetic studies are available for bacterial, fungal and plant proteins.	DISCUSS
75	84	bacterial	taxonomy_domain	In addition, a number of biochemical and genetic studies are available for bacterial, fungal and plant proteins.	DISCUSS
86	92	fungal	taxonomy_domain	In addition, a number of biochemical and genetic studies are available for bacterial, fungal and plant proteins.	DISCUSS
97	102	plant	taxonomy_domain	In addition, a number of biochemical and genetic studies are available for bacterial, fungal and plant proteins.	DISCUSS
159	167	ammonium	chemical	These efforts have advanced our knowledge considerably but have not yet yielded atomic-level answers to several important mechanistic questions, including how ammonium transport is regulated in eukaryotes and the mechanism of ammonium signalling.	DISCUSS
194	204	eukaryotes	taxonomy_domain	These efforts have advanced our knowledge considerably but have not yet yielded atomic-level answers to several important mechanistic questions, including how ammonium transport is regulated in eukaryotes and the mechanism of ammonium signalling.	DISCUSS
226	234	ammonium	chemical	These efforts have advanced our knowledge considerably but have not yet yielded atomic-level answers to several important mechanistic questions, including how ammonium transport is regulated in eukaryotes and the mechanism of ammonium signalling.	DISCUSS
3	23	Arabidopsis thaliana	species	In Arabidopsis thaliana Amt-1;1, phosphorylation of the CTR residue T460 under conditions of high ammonium inhibits transport activity, that is, the default (non-phosphorylated) state of the plant transporter is open.	DISCUSS
24	31	Amt-1;1	protein	In Arabidopsis thaliana Amt-1;1, phosphorylation of the CTR residue T460 under conditions of high ammonium inhibits transport activity, that is, the default (non-phosphorylated) state of the plant transporter is open.	DISCUSS
33	48	phosphorylation	ptm	In Arabidopsis thaliana Amt-1;1, phosphorylation of the CTR residue T460 under conditions of high ammonium inhibits transport activity, that is, the default (non-phosphorylated) state of the plant transporter is open.	DISCUSS
56	59	CTR	structure_element	In Arabidopsis thaliana Amt-1;1, phosphorylation of the CTR residue T460 under conditions of high ammonium inhibits transport activity, that is, the default (non-phosphorylated) state of the plant transporter is open.	DISCUSS
68	72	T460	residue_name_number	In Arabidopsis thaliana Amt-1;1, phosphorylation of the CTR residue T460 under conditions of high ammonium inhibits transport activity, that is, the default (non-phosphorylated) state of the plant transporter is open.	DISCUSS
98	106	ammonium	chemical	In Arabidopsis thaliana Amt-1;1, phosphorylation of the CTR residue T460 under conditions of high ammonium inhibits transport activity, that is, the default (non-phosphorylated) state of the plant transporter is open.	DISCUSS
158	176	non-phosphorylated	protein_state	In Arabidopsis thaliana Amt-1;1, phosphorylation of the CTR residue T460 under conditions of high ammonium inhibits transport activity, that is, the default (non-phosphorylated) state of the plant transporter is open.	DISCUSS
191	196	plant	taxonomy_domain	In Arabidopsis thaliana Amt-1;1, phosphorylation of the CTR residue T460 under conditions of high ammonium inhibits transport activity, that is, the default (non-phosphorylated) state of the plant transporter is open.	DISCUSS
197	208	transporter	protein_type	In Arabidopsis thaliana Amt-1;1, phosphorylation of the CTR residue T460 under conditions of high ammonium inhibits transport activity, that is, the default (non-phosphorylated) state of the plant transporter is open.	DISCUSS
212	216	open	protein_state	In Arabidopsis thaliana Amt-1;1, phosphorylation of the CTR residue T460 under conditions of high ammonium inhibits transport activity, that is, the default (non-phosphorylated) state of the plant transporter is open.	DISCUSS
15	39	phosphomimetic mutations	mutant	Interestingly, phosphomimetic mutations introduced into one monomer inactivate the entire trimer, indicating that (i) heterotrimerization occurs and (ii) the CTR mediates allosteric regulation of ammonium transport activity via phosphorylation.	DISCUSS
60	67	monomer	oligomeric_state	Interestingly, phosphomimetic mutations introduced into one monomer inactivate the entire trimer, indicating that (i) heterotrimerization occurs and (ii) the CTR mediates allosteric regulation of ammonium transport activity via phosphorylation.	DISCUSS
90	96	trimer	oligomeric_state	Interestingly, phosphomimetic mutations introduced into one monomer inactivate the entire trimer, indicating that (i) heterotrimerization occurs and (ii) the CTR mediates allosteric regulation of ammonium transport activity via phosphorylation.	DISCUSS
158	161	CTR	structure_element	Interestingly, phosphomimetic mutations introduced into one monomer inactivate the entire trimer, indicating that (i) heterotrimerization occurs and (ii) the CTR mediates allosteric regulation of ammonium transport activity via phosphorylation.	DISCUSS
196	204	ammonium	chemical	Interestingly, phosphomimetic mutations introduced into one monomer inactivate the entire trimer, indicating that (i) heterotrimerization occurs and (ii) the CTR mediates allosteric regulation of ammonium transport activity via phosphorylation.	DISCUSS
228	243	phosphorylation	ptm	Interestingly, phosphomimetic mutations introduced into one monomer inactivate the entire trimer, indicating that (i) heterotrimerization occurs and (ii) the CTR mediates allosteric regulation of ammonium transport activity via phosphorylation.	DISCUSS
48	53	plant	taxonomy_domain	Owing to the lack of structural information for plant AMTs, the details of channel closure and inter-monomer crosstalk are not yet clear.	DISCUSS
54	58	AMTs	protein_type	Owing to the lack of structural information for plant AMTs, the details of channel closure and inter-monomer crosstalk are not yet clear.	DISCUSS
75	82	channel	site	Owing to the lack of structural information for plant AMTs, the details of channel closure and inter-monomer crosstalk are not yet clear.	DISCUSS
21	26	plant	taxonomy_domain	Contrasting with the plant transporters, the inactive states of Mep2 proteins under conditions of high ammonium are non-phosphorylated, with channels that are closed on the cytoplasmic side.	DISCUSS
27	39	transporters	protein_type	Contrasting with the plant transporters, the inactive states of Mep2 proteins under conditions of high ammonium are non-phosphorylated, with channels that are closed on the cytoplasmic side.	DISCUSS
45	53	inactive	protein_state	Contrasting with the plant transporters, the inactive states of Mep2 proteins under conditions of high ammonium are non-phosphorylated, with channels that are closed on the cytoplasmic side.	DISCUSS
64	77	Mep2 proteins	protein_type	Contrasting with the plant transporters, the inactive states of Mep2 proteins under conditions of high ammonium are non-phosphorylated, with channels that are closed on the cytoplasmic side.	DISCUSS
103	111	ammonium	chemical	Contrasting with the plant transporters, the inactive states of Mep2 proteins under conditions of high ammonium are non-phosphorylated, with channels that are closed on the cytoplasmic side.	DISCUSS
116	134	non-phosphorylated	protein_state	Contrasting with the plant transporters, the inactive states of Mep2 proteins under conditions of high ammonium are non-phosphorylated, with channels that are closed on the cytoplasmic side.	DISCUSS
141	149	channels	site	Contrasting with the plant transporters, the inactive states of Mep2 proteins under conditions of high ammonium are non-phosphorylated, with channels that are closed on the cytoplasmic side.	DISCUSS
159	165	closed	protein_state	Contrasting with the plant transporters, the inactive states of Mep2 proteins under conditions of high ammonium are non-phosphorylated, with channels that are closed on the cytoplasmic side.	DISCUSS
23	35	transporters	protein_type	The reason why similar transporters such as A. thaliana Amt-1;1 and Mep2 are regulated in opposite ways by phosphorylation (inactivation in plants and activation in fungi) is not known.	DISCUSS
44	55	A. thaliana	species	The reason why similar transporters such as A. thaliana Amt-1;1 and Mep2 are regulated in opposite ways by phosphorylation (inactivation in plants and activation in fungi) is not known.	DISCUSS
56	63	Amt-1;1	protein	The reason why similar transporters such as A. thaliana Amt-1;1 and Mep2 are regulated in opposite ways by phosphorylation (inactivation in plants and activation in fungi) is not known.	DISCUSS
68	72	Mep2	protein	The reason why similar transporters such as A. thaliana Amt-1;1 and Mep2 are regulated in opposite ways by phosphorylation (inactivation in plants and activation in fungi) is not known.	DISCUSS
107	122	phosphorylation	ptm	The reason why similar transporters such as A. thaliana Amt-1;1 and Mep2 are regulated in opposite ways by phosphorylation (inactivation in plants and activation in fungi) is not known.	DISCUSS
124	136	inactivation	protein_state	The reason why similar transporters such as A. thaliana Amt-1;1 and Mep2 are regulated in opposite ways by phosphorylation (inactivation in plants and activation in fungi) is not known.	DISCUSS
140	146	plants	taxonomy_domain	The reason why similar transporters such as A. thaliana Amt-1;1 and Mep2 are regulated in opposite ways by phosphorylation (inactivation in plants and activation in fungi) is not known.	DISCUSS
151	161	activation	protein_state	The reason why similar transporters such as A. thaliana Amt-1;1 and Mep2 are regulated in opposite ways by phosphorylation (inactivation in plants and activation in fungi) is not known.	DISCUSS
165	170	fungi	taxonomy_domain	The reason why similar transporters such as A. thaliana Amt-1;1 and Mep2 are regulated in opposite ways by phosphorylation (inactivation in plants and activation in fungi) is not known.	DISCUSS
3	8	fungi	taxonomy_domain	In fungi, preventing ammonium entry via channel closure in ammonium transporters would be one way to alleviate ammonium toxicity, in addition to ammonium excretion via Ato transporters and amino-acid secretion.	DISCUSS
21	29	ammonium	chemical	In fungi, preventing ammonium entry via channel closure in ammonium transporters would be one way to alleviate ammonium toxicity, in addition to ammonium excretion via Ato transporters and amino-acid secretion.	DISCUSS
59	80	ammonium transporters	protein_type	In fungi, preventing ammonium entry via channel closure in ammonium transporters would be one way to alleviate ammonium toxicity, in addition to ammonium excretion via Ato transporters and amino-acid secretion.	DISCUSS
111	119	ammonium	chemical	In fungi, preventing ammonium entry via channel closure in ammonium transporters would be one way to alleviate ammonium toxicity, in addition to ammonium excretion via Ato transporters and amino-acid secretion.	DISCUSS
145	153	ammonium	chemical	In fungi, preventing ammonium entry via channel closure in ammonium transporters would be one way to alleviate ammonium toxicity, in addition to ammonium excretion via Ato transporters and amino-acid secretion.	DISCUSS
168	171	Ato	protein_type	In fungi, preventing ammonium entry via channel closure in ammonium transporters would be one way to alleviate ammonium toxicity, in addition to ammonium excretion via Ato transporters and amino-acid secretion.	DISCUSS
172	184	transporters	protein_type	In fungi, preventing ammonium entry via channel closure in ammonium transporters would be one way to alleviate ammonium toxicity, in addition to ammonium excretion via Ato transporters and amino-acid secretion.	DISCUSS
25	35	structures	evidence	By determining the first structures of closed ammonium transporters and comparing those structures with the permanently open bacterial proteins, we demonstrate that Mep2 channel closure is likely due to movements of the CTR and ICL1 and ICL3.	DISCUSS
39	45	closed	protein_state	By determining the first structures of closed ammonium transporters and comparing those structures with the permanently open bacterial proteins, we demonstrate that Mep2 channel closure is likely due to movements of the CTR and ICL1 and ICL3.	DISCUSS
46	67	ammonium transporters	protein_type	By determining the first structures of closed ammonium transporters and comparing those structures with the permanently open bacterial proteins, we demonstrate that Mep2 channel closure is likely due to movements of the CTR and ICL1 and ICL3.	DISCUSS
72	81	comparing	experimental_method	By determining the first structures of closed ammonium transporters and comparing those structures with the permanently open bacterial proteins, we demonstrate that Mep2 channel closure is likely due to movements of the CTR and ICL1 and ICL3.	DISCUSS
88	98	structures	evidence	By determining the first structures of closed ammonium transporters and comparing those structures with the permanently open bacterial proteins, we demonstrate that Mep2 channel closure is likely due to movements of the CTR and ICL1 and ICL3.	DISCUSS
108	124	permanently open	protein_state	By determining the first structures of closed ammonium transporters and comparing those structures with the permanently open bacterial proteins, we demonstrate that Mep2 channel closure is likely due to movements of the CTR and ICL1 and ICL3.	DISCUSS
125	134	bacterial	taxonomy_domain	By determining the first structures of closed ammonium transporters and comparing those structures with the permanently open bacterial proteins, we demonstrate that Mep2 channel closure is likely due to movements of the CTR and ICL1 and ICL3.	DISCUSS
165	169	Mep2	protein_type	By determining the first structures of closed ammonium transporters and comparing those structures with the permanently open bacterial proteins, we demonstrate that Mep2 channel closure is likely due to movements of the CTR and ICL1 and ICL3.	DISCUSS
170	177	channel	site	By determining the first structures of closed ammonium transporters and comparing those structures with the permanently open bacterial proteins, we demonstrate that Mep2 channel closure is likely due to movements of the CTR and ICL1 and ICL3.	DISCUSS
220	223	CTR	structure_element	By determining the first structures of closed ammonium transporters and comparing those structures with the permanently open bacterial proteins, we demonstrate that Mep2 channel closure is likely due to movements of the CTR and ICL1 and ICL3.	DISCUSS
228	232	ICL1	structure_element	By determining the first structures of closed ammonium transporters and comparing those structures with the permanently open bacterial proteins, we demonstrate that Mep2 channel closure is likely due to movements of the CTR and ICL1 and ICL3.	DISCUSS
237	241	ICL3	structure_element	By determining the first structures of closed ammonium transporters and comparing those structures with the permanently open bacterial proteins, we demonstrate that Mep2 channel closure is likely due to movements of the CTR and ICL1 and ICL3.	DISCUSS
54	57	CTR	structure_element	More specifically, the close interactions between the CTR and ICL1/ICL3 present in open transporters are disrupted, causing ICL3 to move outwards and block the channel (Figs 4 and 9a).	DISCUSS
62	66	ICL1	structure_element	More specifically, the close interactions between the CTR and ICL1/ICL3 present in open transporters are disrupted, causing ICL3 to move outwards and block the channel (Figs 4 and 9a).	DISCUSS
67	71	ICL3	structure_element	More specifically, the close interactions between the CTR and ICL1/ICL3 present in open transporters are disrupted, causing ICL3 to move outwards and block the channel (Figs 4 and 9a).	DISCUSS
83	87	open	protein_state	More specifically, the close interactions between the CTR and ICL1/ICL3 present in open transporters are disrupted, causing ICL3 to move outwards and block the channel (Figs 4 and 9a).	DISCUSS
88	100	transporters	protein_type	More specifically, the close interactions between the CTR and ICL1/ICL3 present in open transporters are disrupted, causing ICL3 to move outwards and block the channel (Figs 4 and 9a).	DISCUSS
124	128	ICL3	structure_element	More specifically, the close interactions between the CTR and ICL1/ICL3 present in open transporters are disrupted, causing ICL3 to move outwards and block the channel (Figs 4 and 9a).	DISCUSS
160	167	channel	site	More specifically, the close interactions between the CTR and ICL1/ICL3 present in open transporters are disrupted, causing ICL3 to move outwards and block the channel (Figs 4 and 9a).	DISCUSS
13	17	ICL1	structure_element	In addition, ICL1 has shifted inwards to contribute to the channel closure by engaging His2 from the twin-His motif via hydrogen bonding with a highly conserved tyrosine hydroxyl group.	DISCUSS
59	66	channel	site	In addition, ICL1 has shifted inwards to contribute to the channel closure by engaging His2 from the twin-His motif via hydrogen bonding with a highly conserved tyrosine hydroxyl group.	DISCUSS
87	91	His2	residue_name_number	In addition, ICL1 has shifted inwards to contribute to the channel closure by engaging His2 from the twin-His motif via hydrogen bonding with a highly conserved tyrosine hydroxyl group.	DISCUSS
101	115	twin-His motif	structure_element	In addition, ICL1 has shifted inwards to contribute to the channel closure by engaging His2 from the twin-His motif via hydrogen bonding with a highly conserved tyrosine hydroxyl group.	DISCUSS
120	136	hydrogen bonding	bond_interaction	In addition, ICL1 has shifted inwards to contribute to the channel closure by engaging His2 from the twin-His motif via hydrogen bonding with a highly conserved tyrosine hydroxyl group.	DISCUSS
144	160	highly conserved	protein_state	In addition, ICL1 has shifted inwards to contribute to the channel closure by engaging His2 from the twin-His motif via hydrogen bonding with a highly conserved tyrosine hydroxyl group.	DISCUSS
161	169	tyrosine	residue_name	In addition, ICL1 has shifted inwards to contribute to the channel closure by engaging His2 from the twin-His motif via hydrogen bonding with a highly conserved tyrosine hydroxyl group.	DISCUSS
5	20	phosphorylation	ptm	Upon phosphorylation by the Npr1 kinase in response to nitrogen limitation, the region around the conserved ExxGxD motif undergoes a conformational change that opens the channel (Fig. 9).	DISCUSS
28	32	Npr1	protein	Upon phosphorylation by the Npr1 kinase in response to nitrogen limitation, the region around the conserved ExxGxD motif undergoes a conformational change that opens the channel (Fig. 9).	DISCUSS
33	39	kinase	protein_type	Upon phosphorylation by the Npr1 kinase in response to nitrogen limitation, the region around the conserved ExxGxD motif undergoes a conformational change that opens the channel (Fig. 9).	DISCUSS
55	63	nitrogen	chemical	Upon phosphorylation by the Npr1 kinase in response to nitrogen limitation, the region around the conserved ExxGxD motif undergoes a conformational change that opens the channel (Fig. 9).	DISCUSS
98	107	conserved	protein_state	Upon phosphorylation by the Npr1 kinase in response to nitrogen limitation, the region around the conserved ExxGxD motif undergoes a conformational change that opens the channel (Fig. 9).	DISCUSS
108	120	ExxGxD motif	structure_element	Upon phosphorylation by the Npr1 kinase in response to nitrogen limitation, the region around the conserved ExxGxD motif undergoes a conformational change that opens the channel (Fig. 9).	DISCUSS
170	177	channel	site	Upon phosphorylation by the Npr1 kinase in response to nitrogen limitation, the region around the conserved ExxGxD motif undergoes a conformational change that opens the channel (Fig. 9).	DISCUSS
17	40	structural similarities	evidence	Importantly, the structural similarities in the TM parts of Mep2 and AfAmt-1 (Fig. 5a) suggest that channel opening/closure does not require substantial changes in the residues lining the channel.	DISCUSS
48	56	TM parts	structure_element	Importantly, the structural similarities in the TM parts of Mep2 and AfAmt-1 (Fig. 5a) suggest that channel opening/closure does not require substantial changes in the residues lining the channel.	DISCUSS
60	64	Mep2	protein	Importantly, the structural similarities in the TM parts of Mep2 and AfAmt-1 (Fig. 5a) suggest that channel opening/closure does not require substantial changes in the residues lining the channel.	DISCUSS
69	76	AfAmt-1	protein	Importantly, the structural similarities in the TM parts of Mep2 and AfAmt-1 (Fig. 5a) suggest that channel opening/closure does not require substantial changes in the residues lining the channel.	DISCUSS
100	107	channel	site	Importantly, the structural similarities in the TM parts of Mep2 and AfAmt-1 (Fig. 5a) suggest that channel opening/closure does not require substantial changes in the residues lining the channel.	DISCUSS
188	195	channel	site	Importantly, the structural similarities in the TM parts of Mep2 and AfAmt-1 (Fig. 5a) suggest that channel opening/closure does not require substantial changes in the residues lining the channel.	DISCUSS
16	23	channel	site	How exactly the channel opens and whether opening is intra-monomeric are still open questions; it is possible that the change in the CTR may disrupt its interactions with ICL3 of the neighbouring monomer (Fig. 9b), which could result in opening of the neighbouring channel via inward movement of its ICL3.	DISCUSS
79	83	open	protein_state	How exactly the channel opens and whether opening is intra-monomeric are still open questions; it is possible that the change in the CTR may disrupt its interactions with ICL3 of the neighbouring monomer (Fig. 9b), which could result in opening of the neighbouring channel via inward movement of its ICL3.	DISCUSS
133	136	CTR	structure_element	How exactly the channel opens and whether opening is intra-monomeric are still open questions; it is possible that the change in the CTR may disrupt its interactions with ICL3 of the neighbouring monomer (Fig. 9b), which could result in opening of the neighbouring channel via inward movement of its ICL3.	DISCUSS
171	175	ICL3	structure_element	How exactly the channel opens and whether opening is intra-monomeric are still open questions; it is possible that the change in the CTR may disrupt its interactions with ICL3 of the neighbouring monomer (Fig. 9b), which could result in opening of the neighbouring channel via inward movement of its ICL3.	DISCUSS
196	203	monomer	oligomeric_state	How exactly the channel opens and whether opening is intra-monomeric are still open questions; it is possible that the change in the CTR may disrupt its interactions with ICL3 of the neighbouring monomer (Fig. 9b), which could result in opening of the neighbouring channel via inward movement of its ICL3.	DISCUSS
265	272	channel	site	How exactly the channel opens and whether opening is intra-monomeric are still open questions; it is possible that the change in the CTR may disrupt its interactions with ICL3 of the neighbouring monomer (Fig. 9b), which could result in opening of the neighbouring channel via inward movement of its ICL3.	DISCUSS
300	304	ICL3	structure_element	How exactly the channel opens and whether opening is intra-monomeric are still open questions; it is possible that the change in the CTR may disrupt its interactions with ICL3 of the neighbouring monomer (Fig. 9b), which could result in opening of the neighbouring channel via inward movement of its ICL3.	DISCUSS
31	39	monomers	oligomeric_state	Owing to the crosstalk between monomers, a single phosphorylation event might lead to opening of the entire trimer, although this has not yet been tested (Fig. 9b).	DISCUSS
50	65	phosphorylation	ptm	Owing to the crosstalk between monomers, a single phosphorylation event might lead to opening of the entire trimer, although this has not yet been tested (Fig. 9b).	DISCUSS
108	114	trimer	oligomeric_state	Owing to the crosstalk between monomers, a single phosphorylation event might lead to opening of the entire trimer, although this has not yet been tested (Fig. 9b).	DISCUSS
15	19	Mep2	protein_type	Whether or not Mep2 channel opening requires, in addition to phosphorylation, disruption of the Tyr–His2 interaction by the ammonium substrate is not yet clear.	DISCUSS
20	27	channel	site	Whether or not Mep2 channel opening requires, in addition to phosphorylation, disruption of the Tyr–His2 interaction by the ammonium substrate is not yet clear.	DISCUSS
61	76	phosphorylation	ptm	Whether or not Mep2 channel opening requires, in addition to phosphorylation, disruption of the Tyr–His2 interaction by the ammonium substrate is not yet clear.	DISCUSS
96	116	Tyr–His2 interaction	site	Whether or not Mep2 channel opening requires, in addition to phosphorylation, disruption of the Tyr–His2 interaction by the ammonium substrate is not yet clear.	DISCUSS
124	132	ammonium	chemical	Whether or not Mep2 channel opening requires, in addition to phosphorylation, disruption of the Tyr–His2 interaction by the ammonium substrate is not yet clear.	DISCUSS
40	44	Mep2	protein	Is our model for opening and closing of Mep2 channels valid for other eukaryotic ammonium transporters? Our structural data support previous studies and clarify the central role of the CTR and cytoplasmic loops in the transition between closed and open states.	DISCUSS
45	53	channels	site	Is our model for opening and closing of Mep2 channels valid for other eukaryotic ammonium transporters? Our structural data support previous studies and clarify the central role of the CTR and cytoplasmic loops in the transition between closed and open states.	DISCUSS
70	80	eukaryotic	taxonomy_domain	Is our model for opening and closing of Mep2 channels valid for other eukaryotic ammonium transporters? Our structural data support previous studies and clarify the central role of the CTR and cytoplasmic loops in the transition between closed and open states.	DISCUSS
81	102	ammonium transporters	protein_type	Is our model for opening and closing of Mep2 channels valid for other eukaryotic ammonium transporters? Our structural data support previous studies and clarify the central role of the CTR and cytoplasmic loops in the transition between closed and open states.	DISCUSS
108	123	structural data	evidence	Is our model for opening and closing of Mep2 channels valid for other eukaryotic ammonium transporters? Our structural data support previous studies and clarify the central role of the CTR and cytoplasmic loops in the transition between closed and open states.	DISCUSS
185	188	CTR	structure_element	Is our model for opening and closing of Mep2 channels valid for other eukaryotic ammonium transporters? Our structural data support previous studies and clarify the central role of the CTR and cytoplasmic loops in the transition between closed and open states.	DISCUSS
193	210	cytoplasmic loops	structure_element	Is our model for opening and closing of Mep2 channels valid for other eukaryotic ammonium transporters? Our structural data support previous studies and clarify the central role of the CTR and cytoplasmic loops in the transition between closed and open states.	DISCUSS
237	243	closed	protein_state	Is our model for opening and closing of Mep2 channels valid for other eukaryotic ammonium transporters? Our structural data support previous studies and clarify the central role of the CTR and cytoplasmic loops in the transition between closed and open states.	DISCUSS
248	252	open	protein_state	Is our model for opening and closing of Mep2 channels valid for other eukaryotic ammonium transporters? Our structural data support previous studies and clarify the central role of the CTR and cytoplasmic loops in the transition between closed and open states.	DISCUSS
43	56	Mep2 proteins	protein_type	However, even the otherwise highly similar Mep2 proteins of S. cerevisiae and C. albicans have different structures for their CTRs (Fig. 1 and Supplementary Fig. 6).	DISCUSS
60	73	S. cerevisiae	species	However, even the otherwise highly similar Mep2 proteins of S. cerevisiae and C. albicans have different structures for their CTRs (Fig. 1 and Supplementary Fig. 6).	DISCUSS
78	89	C. albicans	species	However, even the otherwise highly similar Mep2 proteins of S. cerevisiae and C. albicans have different structures for their CTRs (Fig. 1 and Supplementary Fig. 6).	DISCUSS
105	115	structures	evidence	However, even the otherwise highly similar Mep2 proteins of S. cerevisiae and C. albicans have different structures for their CTRs (Fig. 1 and Supplementary Fig. 6).	DISCUSS
126	130	CTRs	structure_element	However, even the otherwise highly similar Mep2 proteins of S. cerevisiae and C. albicans have different structures for their CTRs (Fig. 1 and Supplementary Fig. 6).	DISCUSS
17	26	AI region	structure_element	In addition, the AI region of the CTR containing the Npr1 kinase site is conserved in only a subset of fungal transporters, suggesting that the details of the structural changes underpinning regulation vary.	DISCUSS
34	37	CTR	structure_element	In addition, the AI region of the CTR containing the Npr1 kinase site is conserved in only a subset of fungal transporters, suggesting that the details of the structural changes underpinning regulation vary.	DISCUSS
53	69	Npr1 kinase site	site	In addition, the AI region of the CTR containing the Npr1 kinase site is conserved in only a subset of fungal transporters, suggesting that the details of the structural changes underpinning regulation vary.	DISCUSS
73	82	conserved	protein_state	In addition, the AI region of the CTR containing the Npr1 kinase site is conserved in only a subset of fungal transporters, suggesting that the details of the structural changes underpinning regulation vary.	DISCUSS
103	109	fungal	taxonomy_domain	In addition, the AI region of the CTR containing the Npr1 kinase site is conserved in only a subset of fungal transporters, suggesting that the details of the structural changes underpinning regulation vary.	DISCUSS
110	122	transporters	protein_type	In addition, the AI region of the CTR containing the Npr1 kinase site is conserved in only a subset of fungal transporters, suggesting that the details of the structural changes underpinning regulation vary.	DISCUSS
40	60	absolutely conserved	protein_state	Nevertheless, given the central role of absolutely conserved residues within the ICL1-ICL3-CTR interaction network (Fig. 4), we propose that the structural basics of fungal ammonium transporter activation are conserved.	DISCUSS
81	114	ICL1-ICL3-CTR interaction network	site	Nevertheless, given the central role of absolutely conserved residues within the ICL1-ICL3-CTR interaction network (Fig. 4), we propose that the structural basics of fungal ammonium transporter activation are conserved.	DISCUSS
166	172	fungal	taxonomy_domain	Nevertheless, given the central role of absolutely conserved residues within the ICL1-ICL3-CTR interaction network (Fig. 4), we propose that the structural basics of fungal ammonium transporter activation are conserved.	DISCUSS
173	181	ammonium	chemical	Nevertheless, given the central role of absolutely conserved residues within the ICL1-ICL3-CTR interaction network (Fig. 4), we propose that the structural basics of fungal ammonium transporter activation are conserved.	DISCUSS
209	218	conserved	protein_state	Nevertheless, given the central role of absolutely conserved residues within the ICL1-ICL3-CTR interaction network (Fig. 4), we propose that the structural basics of fungal ammonium transporter activation are conserved.	DISCUSS
14	18	Mep2	protein_type	The fact that Mep2 orthologues of distantly related fungi are fully functional in ammonium transport and signalling in S. cerevisiae supports this notion.	DISCUSS
52	57	fungi	taxonomy_domain	The fact that Mep2 orthologues of distantly related fungi are fully functional in ammonium transport and signalling in S. cerevisiae supports this notion.	DISCUSS
82	90	ammonium	chemical	The fact that Mep2 orthologues of distantly related fungi are fully functional in ammonium transport and signalling in S. cerevisiae supports this notion.	DISCUSS
119	132	S. cerevisiae	species	The fact that Mep2 orthologues of distantly related fungi are fully functional in ammonium transport and signalling in S. cerevisiae supports this notion.	DISCUSS
33	41	tyrosine	residue_name	It should also be noted that the tyrosine residue interacting with His2 is highly conserved in fungal Mep2 orthologues, suggesting that the Tyr–His2 hydrogen bond might be a general way to close Mep2 proteins.	DISCUSS
67	71	His2	residue_name_number	It should also be noted that the tyrosine residue interacting with His2 is highly conserved in fungal Mep2 orthologues, suggesting that the Tyr–His2 hydrogen bond might be a general way to close Mep2 proteins.	DISCUSS
75	91	highly conserved	protein_state	It should also be noted that the tyrosine residue interacting with His2 is highly conserved in fungal Mep2 orthologues, suggesting that the Tyr–His2 hydrogen bond might be a general way to close Mep2 proteins.	DISCUSS
95	101	fungal	taxonomy_domain	It should also be noted that the tyrosine residue interacting with His2 is highly conserved in fungal Mep2 orthologues, suggesting that the Tyr–His2 hydrogen bond might be a general way to close Mep2 proteins.	DISCUSS
102	106	Mep2	protein_type	It should also be noted that the tyrosine residue interacting with His2 is highly conserved in fungal Mep2 orthologues, suggesting that the Tyr–His2 hydrogen bond might be a general way to close Mep2 proteins.	DISCUSS
140	162	Tyr–His2 hydrogen bond	site	It should also be noted that the tyrosine residue interacting with His2 is highly conserved in fungal Mep2 orthologues, suggesting that the Tyr–His2 hydrogen bond might be a general way to close Mep2 proteins.	DISCUSS
189	194	close	protein_state	It should also be noted that the tyrosine residue interacting with His2 is highly conserved in fungal Mep2 orthologues, suggesting that the Tyr–His2 hydrogen bond might be a general way to close Mep2 proteins.	DISCUSS
195	208	Mep2 proteins	protein_type	It should also be noted that the tyrosine residue interacting with His2 is highly conserved in fungal Mep2 orthologues, suggesting that the Tyr–His2 hydrogen bond might be a general way to close Mep2 proteins.	DISCUSS
16	21	plant	taxonomy_domain	With regards to plant AMTs, it has been proposed that phosphorylation at T460 generates conformational changes that would close the neighbouring pore via the C terminus.	DISCUSS
22	26	AMTs	protein_type	With regards to plant AMTs, it has been proposed that phosphorylation at T460 generates conformational changes that would close the neighbouring pore via the C terminus.	DISCUSS
54	69	phosphorylation	ptm	With regards to plant AMTs, it has been proposed that phosphorylation at T460 generates conformational changes that would close the neighbouring pore via the C terminus.	DISCUSS
73	77	T460	residue_name_number	With regards to plant AMTs, it has been proposed that phosphorylation at T460 generates conformational changes that would close the neighbouring pore via the C terminus.	DISCUSS
145	149	pore	site	With regards to plant AMTs, it has been proposed that phosphorylation at T460 generates conformational changes that would close the neighbouring pore via the C terminus.	DISCUSS
158	168	C terminus	structure_element	With regards to plant AMTs, it has been proposed that phosphorylation at T460 generates conformational changes that would close the neighbouring pore via the C terminus.	DISCUSS
38	52	homology model	experimental_method	This assumption was based partly on a homology model for Amt-1;1 based on the (open) archaebacterial AfAmt-1 structure, which suggested that the C terminus of Amt-1;1 would extend further to the neighbouring monomer.	DISCUSS
57	64	Amt-1;1	protein	This assumption was based partly on a homology model for Amt-1;1 based on the (open) archaebacterial AfAmt-1 structure, which suggested that the C terminus of Amt-1;1 would extend further to the neighbouring monomer.	DISCUSS
79	83	open	protein_state	This assumption was based partly on a homology model for Amt-1;1 based on the (open) archaebacterial AfAmt-1 structure, which suggested that the C terminus of Amt-1;1 would extend further to the neighbouring monomer.	DISCUSS
85	100	archaebacterial	taxonomy_domain	This assumption was based partly on a homology model for Amt-1;1 based on the (open) archaebacterial AfAmt-1 structure, which suggested that the C terminus of Amt-1;1 would extend further to the neighbouring monomer.	DISCUSS
101	108	AfAmt-1	protein	This assumption was based partly on a homology model for Amt-1;1 based on the (open) archaebacterial AfAmt-1 structure, which suggested that the C terminus of Amt-1;1 would extend further to the neighbouring monomer.	DISCUSS
109	118	structure	evidence	This assumption was based partly on a homology model for Amt-1;1 based on the (open) archaebacterial AfAmt-1 structure, which suggested that the C terminus of Amt-1;1 would extend further to the neighbouring monomer.	DISCUSS
145	155	C terminus	structure_element	This assumption was based partly on a homology model for Amt-1;1 based on the (open) archaebacterial AfAmt-1 structure, which suggested that the C terminus of Amt-1;1 would extend further to the neighbouring monomer.	DISCUSS
159	166	Amt-1;1	protein	This assumption was based partly on a homology model for Amt-1;1 based on the (open) archaebacterial AfAmt-1 structure, which suggested that the C terminus of Amt-1;1 would extend further to the neighbouring monomer.	DISCUSS
208	215	monomer	oligomeric_state	This assumption was based partly on a homology model for Amt-1;1 based on the (open) archaebacterial AfAmt-1 structure, which suggested that the C terminus of Amt-1;1 would extend further to the neighbouring monomer.	DISCUSS
4	8	Mep2	protein	Our Mep2 structures show that this assumption may not be correct (Fig. 4 and Supplementary Fig. 6).	DISCUSS
9	19	structures	evidence	Our Mep2 structures show that this assumption may not be correct (Fig. 4 and Supplementary Fig. 6).	DISCUSS
72	75	CTR	structure_element	In addition, the considerable differences between structurally resolved CTR domains means that the exact environment of T460 in Amt-1;1 is also not known (Supplementary Fig. 6).	DISCUSS
120	124	T460	residue_name_number	In addition, the considerable differences between structurally resolved CTR domains means that the exact environment of T460 in Amt-1;1 is also not known (Supplementary Fig. 6).	DISCUSS
128	135	Amt-1;1	protein	In addition, the considerable differences between structurally resolved CTR domains means that the exact environment of T460 in Amt-1;1 is also not known (Supplementary Fig. 6).	DISCUSS
23	45	structural information	evidence	Based on the available structural information, we consider it more likely that phosphorylation-mediated pore closure in Amt-1;1 is intra-monomeric, via disruption of the interactions between the CTR and ICL1/ICL3 (for example, Y467-H239 and D458-K71).	DISCUSS
120	127	Amt-1;1	protein	Based on the available structural information, we consider it more likely that phosphorylation-mediated pore closure in Amt-1;1 is intra-monomeric, via disruption of the interactions between the CTR and ICL1/ICL3 (for example, Y467-H239 and D458-K71).	DISCUSS
195	198	CTR	structure_element	Based on the available structural information, we consider it more likely that phosphorylation-mediated pore closure in Amt-1;1 is intra-monomeric, via disruption of the interactions between the CTR and ICL1/ICL3 (for example, Y467-H239 and D458-K71).	DISCUSS
203	207	ICL1	structure_element	Based on the available structural information, we consider it more likely that phosphorylation-mediated pore closure in Amt-1;1 is intra-monomeric, via disruption of the interactions between the CTR and ICL1/ICL3 (for example, Y467-H239 and D458-K71).	DISCUSS
208	212	ICL3	structure_element	Based on the available structural information, we consider it more likely that phosphorylation-mediated pore closure in Amt-1;1 is intra-monomeric, via disruption of the interactions between the CTR and ICL1/ICL3 (for example, Y467-H239 and D458-K71).	DISCUSS
227	231	Y467	residue_name_number	Based on the available structural information, we consider it more likely that phosphorylation-mediated pore closure in Amt-1;1 is intra-monomeric, via disruption of the interactions between the CTR and ICL1/ICL3 (for example, Y467-H239 and D458-K71).	DISCUSS
232	236	H239	residue_name_number	Based on the available structural information, we consider it more likely that phosphorylation-mediated pore closure in Amt-1;1 is intra-monomeric, via disruption of the interactions between the CTR and ICL1/ICL3 (for example, Y467-H239 and D458-K71).	DISCUSS
241	245	D458	residue_name_number	Based on the available structural information, we consider it more likely that phosphorylation-mediated pore closure in Amt-1;1 is intra-monomeric, via disruption of the interactions between the CTR and ICL1/ICL3 (for example, Y467-H239 and D458-K71).	DISCUSS
246	249	K71	residue_name_number	Based on the available structural information, we consider it more likely that phosphorylation-mediated pore closure in Amt-1;1 is intra-monomeric, via disruption of the interactions between the CTR and ICL1/ICL3 (for example, Y467-H239 and D458-K71).	DISCUSS
37	43	CaMep2	protein	There is generally no equivalent for CaMep2 Tyr49 in plant AMTs, indicating that a Tyr–His2 hydrogen bond as observed in Mep2 may not contribute to the closed state in plant transporters.	DISCUSS
44	49	Tyr49	residue_name_number	There is generally no equivalent for CaMep2 Tyr49 in plant AMTs, indicating that a Tyr–His2 hydrogen bond as observed in Mep2 may not contribute to the closed state in plant transporters.	DISCUSS
53	58	plant	taxonomy_domain	There is generally no equivalent for CaMep2 Tyr49 in plant AMTs, indicating that a Tyr–His2 hydrogen bond as observed in Mep2 may not contribute to the closed state in plant transporters.	DISCUSS
59	63	AMTs	protein_type	There is generally no equivalent for CaMep2 Tyr49 in plant AMTs, indicating that a Tyr–His2 hydrogen bond as observed in Mep2 may not contribute to the closed state in plant transporters.	DISCUSS
83	105	Tyr–His2 hydrogen bond	site	There is generally no equivalent for CaMep2 Tyr49 in plant AMTs, indicating that a Tyr–His2 hydrogen bond as observed in Mep2 may not contribute to the closed state in plant transporters.	DISCUSS
121	125	Mep2	protein	There is generally no equivalent for CaMep2 Tyr49 in plant AMTs, indicating that a Tyr–His2 hydrogen bond as observed in Mep2 may not contribute to the closed state in plant transporters.	DISCUSS
152	158	closed	protein_state	There is generally no equivalent for CaMep2 Tyr49 in plant AMTs, indicating that a Tyr–His2 hydrogen bond as observed in Mep2 may not contribute to the closed state in plant transporters.	DISCUSS
168	173	plant	taxonomy_domain	There is generally no equivalent for CaMep2 Tyr49 in plant AMTs, indicating that a Tyr–His2 hydrogen bond as observed in Mep2 may not contribute to the closed state in plant transporters.	DISCUSS
174	186	transporters	protein_type	There is generally no equivalent for CaMep2 Tyr49 in plant AMTs, indicating that a Tyr–His2 hydrogen bond as observed in Mep2 may not contribute to the closed state in plant transporters.	DISCUSS
16	58	intra-monomeric CTR-ICL1/ICL3 interactions	site	We propose that intra-monomeric CTR-ICL1/ICL3 interactions lie at the basis of regulation of both fungal and plant ammonium transporters; close interactions generate open channels, whereas the lack of ‘intra-' interactions leads to inactive states.	DISCUSS
98	104	fungal	taxonomy_domain	We propose that intra-monomeric CTR-ICL1/ICL3 interactions lie at the basis of regulation of both fungal and plant ammonium transporters; close interactions generate open channels, whereas the lack of ‘intra-' interactions leads to inactive states.	DISCUSS
109	114	plant	taxonomy_domain	We propose that intra-monomeric CTR-ICL1/ICL3 interactions lie at the basis of regulation of both fungal and plant ammonium transporters; close interactions generate open channels, whereas the lack of ‘intra-' interactions leads to inactive states.	DISCUSS
115	136	ammonium transporters	protein_type	We propose that intra-monomeric CTR-ICL1/ICL3 interactions lie at the basis of regulation of both fungal and plant ammonium transporters; close interactions generate open channels, whereas the lack of ‘intra-' interactions leads to inactive states.	DISCUSS
166	170	open	protein_state	We propose that intra-monomeric CTR-ICL1/ICL3 interactions lie at the basis of regulation of both fungal and plant ammonium transporters; close interactions generate open channels, whereas the lack of ‘intra-' interactions leads to inactive states.	DISCUSS
171	179	channels	site	We propose that intra-monomeric CTR-ICL1/ICL3 interactions lie at the basis of regulation of both fungal and plant ammonium transporters; close interactions generate open channels, whereas the lack of ‘intra-' interactions leads to inactive states.	DISCUSS
193	200	lack of	protein_state	We propose that intra-monomeric CTR-ICL1/ICL3 interactions lie at the basis of regulation of both fungal and plant ammonium transporters; close interactions generate open channels, whereas the lack of ‘intra-' interactions leads to inactive states.	DISCUSS
232	240	inactive	protein_state	We propose that intra-monomeric CTR-ICL1/ICL3 interactions lie at the basis of regulation of both fungal and plant ammonium transporters; close interactions generate open channels, whereas the lack of ‘intra-' interactions leads to inactive states.	DISCUSS
64	85	phosphorylation sites	site	The need to regulate in opposite ways may be the reason why the phosphorylation sites are in different parts of the CTR, that is, centrally located close to the ExxGxD motif in AMTs and peripherally in Mep2.	DISCUSS
116	119	CTR	structure_element	The need to regulate in opposite ways may be the reason why the phosphorylation sites are in different parts of the CTR, that is, centrally located close to the ExxGxD motif in AMTs and peripherally in Mep2.	DISCUSS
161	173	ExxGxD motif	structure_element	The need to regulate in opposite ways may be the reason why the phosphorylation sites are in different parts of the CTR, that is, centrally located close to the ExxGxD motif in AMTs and peripherally in Mep2.	DISCUSS
177	181	AMTs	protein_type	The need to regulate in opposite ways may be the reason why the phosphorylation sites are in different parts of the CTR, that is, centrally located close to the ExxGxD motif in AMTs and peripherally in Mep2.	DISCUSS
202	206	Mep2	protein	The need to regulate in opposite ways may be the reason why the phosphorylation sites are in different parts of the CTR, that is, centrally located close to the ExxGxD motif in AMTs and peripherally in Mep2.	DISCUSS
13	28	phosphorylation	ptm	In this way, phosphorylation can either lead to channel closing (in the case of AMTs) or channel opening in the case of Mep2.	DISCUSS
48	55	channel	site	In this way, phosphorylation can either lead to channel closing (in the case of AMTs) or channel opening in the case of Mep2.	DISCUSS
80	84	AMTs	protein_type	In this way, phosphorylation can either lead to channel closing (in the case of AMTs) or channel opening in the case of Mep2.	DISCUSS
89	96	channel	site	In this way, phosphorylation can either lead to channel closing (in the case of AMTs) or channel opening in the case of Mep2.	DISCUSS
120	124	Mep2	protein	In this way, phosphorylation can either lead to channel closing (in the case of AMTs) or channel opening in the case of Mep2.	DISCUSS
64	81	certain mutations	mutant	Our model also provides an explanation for the observation that certain mutations within the CTR completely abolish transport activity.	DISCUSS
93	96	CTR	structure_element	Our model also provides an explanation for the observation that certain mutations within the CTR completely abolish transport activity.	DISCUSS
45	52	glycine	residue_name	An example of an inactivating residue is the glycine of the ExxGxD motif of the CTR.	DISCUSS
60	72	ExxGxD motif	structure_element	An example of an inactivating residue is the glycine of the ExxGxD motif of the CTR.	DISCUSS
80	83	CTR	structure_element	An example of an inactivating residue is the glycine of the ExxGxD motif of the CTR.	DISCUSS
0	8	Mutation	experimental_method	Mutation of this residue (G393 in EcAmtB; G456 in AtAmt-1;1) inactivates transporters as diverse as Escherichia coli AmtB and A. thaliana Amt-1;1 (refs).	DISCUSS
26	30	G393	residue_name_number	Mutation of this residue (G393 in EcAmtB; G456 in AtAmt-1;1) inactivates transporters as diverse as Escherichia coli AmtB and A. thaliana Amt-1;1 (refs).	DISCUSS
34	40	EcAmtB	protein	Mutation of this residue (G393 in EcAmtB; G456 in AtAmt-1;1) inactivates transporters as diverse as Escherichia coli AmtB and A. thaliana Amt-1;1 (refs).	DISCUSS
42	46	G456	residue_name_number	Mutation of this residue (G393 in EcAmtB; G456 in AtAmt-1;1) inactivates transporters as diverse as Escherichia coli AmtB and A. thaliana Amt-1;1 (refs).	DISCUSS
50	59	AtAmt-1;1	protein	Mutation of this residue (G393 in EcAmtB; G456 in AtAmt-1;1) inactivates transporters as diverse as Escherichia coli AmtB and A. thaliana Amt-1;1 (refs).	DISCUSS
73	85	transporters	protein_type	Mutation of this residue (G393 in EcAmtB; G456 in AtAmt-1;1) inactivates transporters as diverse as Escherichia coli AmtB and A. thaliana Amt-1;1 (refs).	DISCUSS
100	116	Escherichia coli	species	Mutation of this residue (G393 in EcAmtB; G456 in AtAmt-1;1) inactivates transporters as diverse as Escherichia coli AmtB and A. thaliana Amt-1;1 (refs).	DISCUSS
117	121	AmtB	protein	Mutation of this residue (G393 in EcAmtB; G456 in AtAmt-1;1) inactivates transporters as diverse as Escherichia coli AmtB and A. thaliana Amt-1;1 (refs).	DISCUSS
126	137	A. thaliana	species	Mutation of this residue (G393 in EcAmtB; G456 in AtAmt-1;1) inactivates transporters as diverse as Escherichia coli AmtB and A. thaliana Amt-1;1 (refs).	DISCUSS
138	145	Amt-1;1	protein	Mutation of this residue (G393 in EcAmtB; G456 in AtAmt-1;1) inactivates transporters as diverse as Escherichia coli AmtB and A. thaliana Amt-1;1 (refs).	DISCUSS
54	57	CTR	structure_element	Such mutations likely cause structural changes in the CTR that prevent close contacts between the CTR and ICL1/ICL3, thereby stabilizing a closed state that may be similar to that observed in Mep2.	DISCUSS
98	101	CTR	structure_element	Such mutations likely cause structural changes in the CTR that prevent close contacts between the CTR and ICL1/ICL3, thereby stabilizing a closed state that may be similar to that observed in Mep2.	DISCUSS
106	110	ICL1	structure_element	Such mutations likely cause structural changes in the CTR that prevent close contacts between the CTR and ICL1/ICL3, thereby stabilizing a closed state that may be similar to that observed in Mep2.	DISCUSS
111	115	ICL3	structure_element	Such mutations likely cause structural changes in the CTR that prevent close contacts between the CTR and ICL1/ICL3, thereby stabilizing a closed state that may be similar to that observed in Mep2.	DISCUSS
139	145	closed	protein_state	Such mutations likely cause structural changes in the CTR that prevent close contacts between the CTR and ICL1/ICL3, thereby stabilizing a closed state that may be similar to that observed in Mep2.	DISCUSS
192	196	Mep2	protein	Such mutations likely cause structural changes in the CTR that prevent close contacts between the CTR and ICL1/ICL3, thereby stabilizing a closed state that may be similar to that observed in Mep2.	DISCUSS
51	66	phosphorylation	ptm	Regulation and modulation of membrane transport by phosphorylation is known to occur in, for example, aquaporins and urea transporters, and is likely to be a common theme for eukaryotic channels and transporters.	DISCUSS
102	112	aquaporins	protein_type	Regulation and modulation of membrane transport by phosphorylation is known to occur in, for example, aquaporins and urea transporters, and is likely to be a common theme for eukaryotic channels and transporters.	DISCUSS
117	134	urea transporters	protein_type	Regulation and modulation of membrane transport by phosphorylation is known to occur in, for example, aquaporins and urea transporters, and is likely to be a common theme for eukaryotic channels and transporters.	DISCUSS
175	185	eukaryotic	taxonomy_domain	Regulation and modulation of membrane transport by phosphorylation is known to occur in, for example, aquaporins and urea transporters, and is likely to be a common theme for eukaryotic channels and transporters.	DISCUSS
186	194	channels	protein_type	Regulation and modulation of membrane transport by phosphorylation is known to occur in, for example, aquaporins and urea transporters, and is likely to be a common theme for eukaryotic channels and transporters.	DISCUSS
199	211	transporters	protein_type	Regulation and modulation of membrane transport by phosphorylation is known to occur in, for example, aquaporins and urea transporters, and is likely to be a common theme for eukaryotic channels and transporters.	DISCUSS
10	25	phosphorylation	ptm	Recently, phosphorylation was also shown to modulate substrate affinity in nitrate transporters.	DISCUSS
75	95	nitrate transporters	protein_type	Recently, phosphorylation was also shown to modulate substrate affinity in nitrate transporters.	DISCUSS
16	24	ammonium	chemical	With respect to ammonium transport, phosphorylation has thus far only been shown for A. thaliana AMTs and for S. cerevisiae Mep2 (refs).	DISCUSS
36	51	phosphorylation	ptm	With respect to ammonium transport, phosphorylation has thus far only been shown for A. thaliana AMTs and for S. cerevisiae Mep2 (refs).	DISCUSS
85	96	A. thaliana	species	With respect to ammonium transport, phosphorylation has thus far only been shown for A. thaliana AMTs and for S. cerevisiae Mep2 (refs).	DISCUSS
97	101	AMTs	protein_type	With respect to ammonium transport, phosphorylation has thus far only been shown for A. thaliana AMTs and for S. cerevisiae Mep2 (refs).	DISCUSS
110	123	S. cerevisiae	species	With respect to ammonium transport, phosphorylation has thus far only been shown for A. thaliana AMTs and for S. cerevisiae Mep2 (refs).	DISCUSS
124	128	Mep2	protein	With respect to ammonium transport, phosphorylation has thus far only been shown for A. thaliana AMTs and for S. cerevisiae Mep2 (refs).	DISCUSS
13	23	absence of	protein_state	However, the absence of GlnK proteins in eukaryotes suggests that phosphorylation-based regulation of ammonium transport may be widespread.	DISCUSS
24	37	GlnK proteins	protein_type	However, the absence of GlnK proteins in eukaryotes suggests that phosphorylation-based regulation of ammonium transport may be widespread.	DISCUSS
41	51	eukaryotes	taxonomy_domain	However, the absence of GlnK proteins in eukaryotes suggests that phosphorylation-based regulation of ammonium transport may be widespread.	DISCUSS
66	81	phosphorylation	ptm	However, the absence of GlnK proteins in eukaryotes suggests that phosphorylation-based regulation of ammonium transport may be widespread.	DISCUSS
102	110	ammonium	chemical	However, the absence of GlnK proteins in eukaryotes suggests that phosphorylation-based regulation of ammonium transport may be widespread.	DISCUSS
16	20	Mep2	protein_type	With respect to Mep2-mediated signalling to induce pseudohyphal growth, two models have been put forward as to how this occurs and why it is specific to Mep2 proteins.	DISCUSS
153	166	Mep2 proteins	protein_type	With respect to Mep2-mediated signalling to induce pseudohyphal growth, two models have been put forward as to how this occurs and why it is specific to Mep2 proteins.	DISCUSS
142	163	ammonium transporters	protein_type	In one model, signalling is proposed to depend on the nature of the transported substrate, which might be different in certain subfamilies of ammonium transporters (for example, Mep1/Mep3 versus Mep2).	DISCUSS
178	182	Mep1	protein	In one model, signalling is proposed to depend on the nature of the transported substrate, which might be different in certain subfamilies of ammonium transporters (for example, Mep1/Mep3 versus Mep2).	DISCUSS
183	187	Mep3	protein	In one model, signalling is proposed to depend on the nature of the transported substrate, which might be different in certain subfamilies of ammonium transporters (for example, Mep1/Mep3 versus Mep2).	DISCUSS
195	199	Mep2	protein	In one model, signalling is proposed to depend on the nature of the transported substrate, which might be different in certain subfamilies of ammonium transporters (for example, Mep1/Mep3 versus Mep2).	DISCUSS
13	16	NH3	chemical	For example, NH3 uniport or symport of NH3/H+ might result in changes in local pH, but NH4+ uniport might not, and this difference might determine signalling.	DISCUSS
39	42	NH3	chemical	For example, NH3 uniport or symport of NH3/H+ might result in changes in local pH, but NH4+ uniport might not, and this difference might determine signalling.	DISCUSS
43	45	H+	chemical	For example, NH3 uniport or symport of NH3/H+ might result in changes in local pH, but NH4+ uniport might not, and this difference might determine signalling.	DISCUSS
87	91	NH4+	chemical	For example, NH3 uniport or symport of NH3/H+ might result in changes in local pH, but NH4+ uniport might not, and this difference might determine signalling.	DISCUSS
84	88	Mep2	protein	In the other model, signalling is thought to require a distinct conformation of the Mep2 transporter occurring during the transport cycle.	DISCUSS
89	100	transporter	protein_type	In the other model, signalling is thought to require a distinct conformation of the Mep2 transporter occurring during the transport cycle.	DISCUSS
118	128	structures	evidence	While the current study does not specifically address the mechanism of signalling underlying pseudohyphal growth, our structures do show that Mep2 proteins can assume different conformations.	DISCUSS
142	155	Mep2 proteins	protein_type	While the current study does not specifically address the mechanism of signalling underlying pseudohyphal growth, our structures do show that Mep2 proteins can assume different conformations.	DISCUSS
17	25	ammonium	chemical	It is clear that ammonium transport across biomembranes remains a fascinating and challenging field in large part due to the unique properties of the substrate.	DISCUSS
4	8	Mep2	protein	Our Mep2 structural work now provides a foundation for future studies to uncover the details of the structural changes that occur during eukaryotic ammonium transport and signaling, and to assess the possibility to utilize small molecules to shut down ammonium sensing and downstream signalling pathways in pathogenic fungi.	DISCUSS
137	147	eukaryotic	taxonomy_domain	Our Mep2 structural work now provides a foundation for future studies to uncover the details of the structural changes that occur during eukaryotic ammonium transport and signaling, and to assess the possibility to utilize small molecules to shut down ammonium sensing and downstream signalling pathways in pathogenic fungi.	DISCUSS
148	156	ammonium	chemical	Our Mep2 structural work now provides a foundation for future studies to uncover the details of the structural changes that occur during eukaryotic ammonium transport and signaling, and to assess the possibility to utilize small molecules to shut down ammonium sensing and downstream signalling pathways in pathogenic fungi.	DISCUSS
252	260	ammonium	chemical	Our Mep2 structural work now provides a foundation for future studies to uncover the details of the structural changes that occur during eukaryotic ammonium transport and signaling, and to assess the possibility to utilize small molecules to shut down ammonium sensing and downstream signalling pathways in pathogenic fungi.	DISCUSS
318	323	fungi	taxonomy_domain	Our Mep2 structural work now provides a foundation for future studies to uncover the details of the structural changes that occur during eukaryotic ammonium transport and signaling, and to assess the possibility to utilize small molecules to shut down ammonium sensing and downstream signalling pathways in pathogenic fungi.	DISCUSS
0	24	X-ray crystal structures	evidence	X-ray crystal structures of Mep2 transceptors.	FIG
28	32	Mep2	protein	X-ray crystal structures of Mep2 transceptors.	FIG
33	45	transceptors	protein_type	X-ray crystal structures of Mep2 transceptors.	FIG
4	11	Monomer	oligomeric_state	(a) Monomer cartoon models viewed from the side for (left) A. fulgidus Amt-1 (PDB ID 2B2H), S. cerevisiae Mep2 (middle) and C. albicans Mep2 (right).	FIG
71	76	Amt-1	protein	(a) Monomer cartoon models viewed from the side for (left) A. fulgidus Amt-1 (PDB ID 2B2H), S. cerevisiae Mep2 (middle) and C. albicans Mep2 (right).	FIG
92	105	S. cerevisiae	species	(a) Monomer cartoon models viewed from the side for (left) A. fulgidus Amt-1 (PDB ID 2B2H), S. cerevisiae Mep2 (middle) and C. albicans Mep2 (right).	FIG
106	110	Mep2	protein	(a) Monomer cartoon models viewed from the side for (left) A. fulgidus Amt-1 (PDB ID 2B2H), S. cerevisiae Mep2 (middle) and C. albicans Mep2 (right).	FIG
124	135	C. albicans	species	(a) Monomer cartoon models viewed from the side for (left) A. fulgidus Amt-1 (PDB ID 2B2H), S. cerevisiae Mep2 (middle) and C. albicans Mep2 (right).	FIG
136	140	Mep2	protein	(a) Monomer cartoon models viewed from the side for (left) A. fulgidus Amt-1 (PDB ID 2B2H), S. cerevisiae Mep2 (middle) and C. albicans Mep2 (right).	FIG
19	23	ICL1	structure_element	The region showing ICL1 (blue), ICL3 (green) and the CTR (red) is boxed for comparison.	FIG
32	36	ICL3	structure_element	The region showing ICL1 (blue), ICL3 (green) and the CTR (red) is boxed for comparison.	FIG
53	56	CTR	structure_element	The region showing ICL1 (blue), ICL3 (green) and the CTR (red) is boxed for comparison.	FIG
4	10	CaMep2	protein	(b) CaMep2 trimer viewed from the intracellular side (right).	FIG
11	17	trimer	oligomeric_state	(b) CaMep2 trimer viewed from the intracellular side (right).	FIG
4	11	monomer	oligomeric_state	One monomer is coloured as in a and one monomer is coloured by B-factor (blue, low; red; high).	FIG
40	47	monomer	oligomeric_state	One monomer is coloured as in a and one monomer is coloured by B-factor (blue, low; red; high).	FIG
4	7	CTR	structure_element	The CTR is boxed.	FIG
5	12	Overlay	experimental_method	 (c) Overlay of ScMep2 (grey) and CaMep2 (rainbow), illustrating the differences in the CTRs.	FIG
16	22	ScMep2	protein	 (c) Overlay of ScMep2 (grey) and CaMep2 (rainbow), illustrating the differences in the CTRs.	FIG
34	40	CaMep2	protein	 (c) Overlay of ScMep2 (grey) and CaMep2 (rainbow), illustrating the differences in the CTRs.	FIG
88	92	CTRs	structure_element	 (c) Overlay of ScMep2 (grey) and CaMep2 (rainbow), illustrating the differences in the CTRs.	FIG
0	21	Sequence conservation	evidence	Sequence conservation in ammonium transporters.	FIG
25	46	ammonium transporters	protein_type	Sequence conservation in ammonium transporters.	FIG
0	18	ClustalW alignment	experimental_method	ClustalW alignment of CaMep2, ScMep2, A. fulgidus Amt-1, E. coli AmtB and A. thaliana Amt-1;1.	FIG
22	28	CaMep2	protein	ClustalW alignment of CaMep2, ScMep2, A. fulgidus Amt-1, E. coli AmtB and A. thaliana Amt-1;1.	FIG
30	36	ScMep2	protein	ClustalW alignment of CaMep2, ScMep2, A. fulgidus Amt-1, E. coli AmtB and A. thaliana Amt-1;1.	FIG
38	49	A. fulgidus	species	ClustalW alignment of CaMep2, ScMep2, A. fulgidus Amt-1, E. coli AmtB and A. thaliana Amt-1;1.	FIG
50	55	Amt-1	protein	ClustalW alignment of CaMep2, ScMep2, A. fulgidus Amt-1, E. coli AmtB and A. thaliana Amt-1;1.	FIG
65	69	AmtB	protein	ClustalW alignment of CaMep2, ScMep2, A. fulgidus Amt-1, E. coli AmtB and A. thaliana Amt-1;1.	FIG
74	85	A. thaliana	species	ClustalW alignment of CaMep2, ScMep2, A. fulgidus Amt-1, E. coli AmtB and A. thaliana Amt-1;1.	FIG
86	93	Amt-1;1	protein	ClustalW alignment of CaMep2, ScMep2, A. fulgidus Amt-1, E. coli AmtB and A. thaliana Amt-1;1.	FIG
46	52	CaMep2	protein	The secondary structure elements observed for CaMep2 are indicated, with the numbers corresponding to the centre of the TM segment.	FIG
120	130	TM segment	structure_element	The secondary structure elements observed for CaMep2 are indicated, with the numbers corresponding to the centre of the TM segment.	FIG
4	13	conserved	protein_state	The conserved RxK motif in ICL1 is boxed in blue, the ER motif in ICL2 in cyan, the conserved ExxGxD motif of the CTR in red and the AI region in yellow.	FIG
14	23	RxK motif	structure_element	The conserved RxK motif in ICL1 is boxed in blue, the ER motif in ICL2 in cyan, the conserved ExxGxD motif of the CTR in red and the AI region in yellow.	FIG
27	31	ICL1	structure_element	The conserved RxK motif in ICL1 is boxed in blue, the ER motif in ICL2 in cyan, the conserved ExxGxD motif of the CTR in red and the AI region in yellow.	FIG
54	62	ER motif	structure_element	The conserved RxK motif in ICL1 is boxed in blue, the ER motif in ICL2 in cyan, the conserved ExxGxD motif of the CTR in red and the AI region in yellow.	FIG
66	70	ICL2	structure_element	The conserved RxK motif in ICL1 is boxed in blue, the ER motif in ICL2 in cyan, the conserved ExxGxD motif of the CTR in red and the AI region in yellow.	FIG
84	93	conserved	protein_state	The conserved RxK motif in ICL1 is boxed in blue, the ER motif in ICL2 in cyan, the conserved ExxGxD motif of the CTR in red and the AI region in yellow.	FIG
94	106	ExxGxD motif	structure_element	The conserved RxK motif in ICL1 is boxed in blue, the ER motif in ICL2 in cyan, the conserved ExxGxD motif of the CTR in red and the AI region in yellow.	FIG
114	117	CTR	structure_element	The conserved RxK motif in ICL1 is boxed in blue, the ER motif in ICL2 in cyan, the conserved ExxGxD motif of the CTR in red and the AI region in yellow.	FIG
133	142	AI region	structure_element	The conserved RxK motif in ICL1 is boxed in blue, the ER motif in ICL2 in cyan, the conserved ExxGxD motif of the CTR in red and the AI region in yellow.	FIG
77	85	Phe gate	site	 Coloured residues are functionally important and correspond to those of the Phe gate (blue), the binding site Trp residue (magenta) and the twin-His motif (red).	FIG
98	110	binding site	site	 Coloured residues are functionally important and correspond to those of the Phe gate (blue), the binding site Trp residue (magenta) and the twin-His motif (red).	FIG
111	114	Trp	residue_name	 Coloured residues are functionally important and correspond to those of the Phe gate (blue), the binding site Trp residue (magenta) and the twin-His motif (red).	FIG
4	20	Npr1 kinase site	site	The Npr1 kinase site in the AI region is highlighted pink.	FIG
28	37	AI region	structure_element	The Npr1 kinase site in the AI region is highlighted pink.	FIG
39	45	CaMep2	protein	The grey sequences at the C termini of CaMep2 and ScMep2 are not visible in the structures and are likely disordered.	FIG
50	56	ScMep2	protein	The grey sequences at the C termini of CaMep2 and ScMep2 are not visible in the structures and are likely disordered.	FIG
80	90	structures	evidence	The grey sequences at the C termini of CaMep2 and ScMep2 are not visible in the structures and are likely disordered.	FIG
99	116	likely disordered	protein_state	The grey sequences at the C termini of CaMep2 and ScMep2 are not visible in the structures and are likely disordered.	FIG
0	6	Growth	experimental_method	Growth of ScMep2 variants on low ammonium medium.	FIG
10	25	ScMep2 variants	mutant	Growth of ScMep2 variants on low ammonium medium.	FIG
8	19	triple mepΔ	mutant	(a) The triple mepΔ strain (black) and triple mepΔ npr1Δ strain (grey) containing plasmids expressing WT and variant ScMep2 were grown on minimal medium containing 1 mM ammonium sulphate.	FIG
102	104	WT	protein_state	(a) The triple mepΔ strain (black) and triple mepΔ npr1Δ strain (grey) containing plasmids expressing WT and variant ScMep2 were grown on minimal medium containing 1 mM ammonium sulphate.	FIG
109	123	variant ScMep2	mutant	(a) The triple mepΔ strain (black) and triple mepΔ npr1Δ strain (grey) containing plasmids expressing WT and variant ScMep2 were grown on minimal medium containing 1 mM ammonium sulphate.	FIG
129	152	grown on minimal medium	experimental_method	(a) The triple mepΔ strain (black) and triple mepΔ npr1Δ strain (grey) containing plasmids expressing WT and variant ScMep2 were grown on minimal medium containing 1 mM ammonium sulphate.	FIG
169	186	ammonium sulphate	chemical	(a) The triple mepΔ strain (black) and triple mepΔ npr1Δ strain (grey) containing plasmids expressing WT and variant ScMep2 were grown on minimal medium containing 1 mM ammonium sulphate.	FIG
15	27	cell density	evidence	The quantified cell density reflects logarithmic growth after 24 h. Error bars are the s.d. for three replicates of each strain (b) The strains used in a were also serially diluted and spotted onto minimal agar plates containing glutamate (0.1%) or ammonium sulphate (1 mM), and grown for 3 days at 30 °C.	FIG
229	238	glutamate	chemical	The quantified cell density reflects logarithmic growth after 24 h. Error bars are the s.d. for three replicates of each strain (b) The strains used in a were also serially diluted and spotted onto minimal agar plates containing glutamate (0.1%) or ammonium sulphate (1 mM), and grown for 3 days at 30 °C.	FIG
249	266	ammonium sulphate	chemical	The quantified cell density reflects logarithmic growth after 24 h. Error bars are the s.d. for three replicates of each strain (b) The strains used in a were also serially diluted and spotted onto minimal agar plates containing glutamate (0.1%) or ammonium sulphate (1 mM), and grown for 3 days at 30 °C.	FIG
31	35	Mep2	protein	Structural differences between Mep2 and bacterial ammonium transporters.	FIG
40	49	bacterial	taxonomy_domain	Structural differences between Mep2 and bacterial ammonium transporters.	FIG
4	8	ICL1	structure_element	(a) ICL1 in AfAmt-1 (light blue) and CaMep2 (dark blue), showing unwinding and inward movement in the fungal protein. (b) Stereo diagram viewed from the cytosol of ICL1, ICL3 (green) and the CTR (red) in AfAmt-1 (light colours) and CaMep2 (dark colours).	FIG
12	19	AfAmt-1	protein	(a) ICL1 in AfAmt-1 (light blue) and CaMep2 (dark blue), showing unwinding and inward movement in the fungal protein. (b) Stereo diagram viewed from the cytosol of ICL1, ICL3 (green) and the CTR (red) in AfAmt-1 (light colours) and CaMep2 (dark colours).	FIG
37	43	CaMep2	protein	(a) ICL1 in AfAmt-1 (light blue) and CaMep2 (dark blue), showing unwinding and inward movement in the fungal protein. (b) Stereo diagram viewed from the cytosol of ICL1, ICL3 (green) and the CTR (red) in AfAmt-1 (light colours) and CaMep2 (dark colours).	FIG
102	108	fungal	taxonomy_domain	(a) ICL1 in AfAmt-1 (light blue) and CaMep2 (dark blue), showing unwinding and inward movement in the fungal protein. (b) Stereo diagram viewed from the cytosol of ICL1, ICL3 (green) and the CTR (red) in AfAmt-1 (light colours) and CaMep2 (dark colours).	FIG
164	168	ICL1	structure_element	(a) ICL1 in AfAmt-1 (light blue) and CaMep2 (dark blue), showing unwinding and inward movement in the fungal protein. (b) Stereo diagram viewed from the cytosol of ICL1, ICL3 (green) and the CTR (red) in AfAmt-1 (light colours) and CaMep2 (dark colours).	FIG
170	174	ICL3	structure_element	(a) ICL1 in AfAmt-1 (light blue) and CaMep2 (dark blue), showing unwinding and inward movement in the fungal protein. (b) Stereo diagram viewed from the cytosol of ICL1, ICL3 (green) and the CTR (red) in AfAmt-1 (light colours) and CaMep2 (dark colours).	FIG
191	194	CTR	structure_element	(a) ICL1 in AfAmt-1 (light blue) and CaMep2 (dark blue), showing unwinding and inward movement in the fungal protein. (b) Stereo diagram viewed from the cytosol of ICL1, ICL3 (green) and the CTR (red) in AfAmt-1 (light colours) and CaMep2 (dark colours).	FIG
204	211	AfAmt-1	protein	(a) ICL1 in AfAmt-1 (light blue) and CaMep2 (dark blue), showing unwinding and inward movement in the fungal protein. (b) Stereo diagram viewed from the cytosol of ICL1, ICL3 (green) and the CTR (red) in AfAmt-1 (light colours) and CaMep2 (dark colours).	FIG
232	238	CaMep2	protein	(a) ICL1 in AfAmt-1 (light blue) and CaMep2 (dark blue), showing unwinding and inward movement in the fungal protein. (b) Stereo diagram viewed from the cytosol of ICL1, ICL3 (green) and the CTR (red) in AfAmt-1 (light colours) and CaMep2 (dark colours).	FIG
35	44	RxK motif	structure_element	The side chains of residues in the RxK motif as well as those of Tyr49 and His342 are labelled.	FIG
65	70	Tyr49	residue_name_number	The side chains of residues in the RxK motif as well as those of Tyr49 and His342 are labelled.	FIG
75	81	His342	residue_name_number	The side chains of residues in the RxK motif as well as those of Tyr49 and His342 are labelled.	FIG
22	28	CaMep2	protein	 The numbering is for CaMep2.	FIG
4	13	Conserved	protein_state	(c) Conserved residues in ICL1-3 and the CTR.	FIG
26	32	ICL1-3	structure_element	(c) Conserved residues in ICL1-3 and the CTR.	FIG
41	44	CTR	structure_element	(c) Conserved residues in ICL1-3 and the CTR.	FIG
27	33	CaMep2	protein	Views from the cytosol for CaMep2 (left) and AfAmt-1, highlighting the large differences in conformation of the conserved residues in ICL1 (RxK motif; blue), ICL2 (ER motif; cyan), ICL3 (green) and the CTR (red).	FIG
45	52	AfAmt-1	protein	Views from the cytosol for CaMep2 (left) and AfAmt-1, highlighting the large differences in conformation of the conserved residues in ICL1 (RxK motif; blue), ICL2 (ER motif; cyan), ICL3 (green) and the CTR (red).	FIG
112	121	conserved	protein_state	Views from the cytosol for CaMep2 (left) and AfAmt-1, highlighting the large differences in conformation of the conserved residues in ICL1 (RxK motif; blue), ICL2 (ER motif; cyan), ICL3 (green) and the CTR (red).	FIG
134	138	ICL1	structure_element	Views from the cytosol for CaMep2 (left) and AfAmt-1, highlighting the large differences in conformation of the conserved residues in ICL1 (RxK motif; blue), ICL2 (ER motif; cyan), ICL3 (green) and the CTR (red).	FIG
158	162	ICL2	structure_element	Views from the cytosol for CaMep2 (left) and AfAmt-1, highlighting the large differences in conformation of the conserved residues in ICL1 (RxK motif; blue), ICL2 (ER motif; cyan), ICL3 (green) and the CTR (red).	FIG
164	172	ER motif	structure_element	Views from the cytosol for CaMep2 (left) and AfAmt-1, highlighting the large differences in conformation of the conserved residues in ICL1 (RxK motif; blue), ICL2 (ER motif; cyan), ICL3 (green) and the CTR (red).	FIG
181	185	ICL3	structure_element	Views from the cytosol for CaMep2 (left) and AfAmt-1, highlighting the large differences in conformation of the conserved residues in ICL1 (RxK motif; blue), ICL2 (ER motif; cyan), ICL3 (green) and the CTR (red).	FIG
202	205	CTR	structure_element	Views from the cytosol for CaMep2 (left) and AfAmt-1, highlighting the large differences in conformation of the conserved residues in ICL1 (RxK motif; blue), ICL2 (ER motif; cyan), ICL3 (green) and the CTR (red).	FIG
48	58	structures	evidence	The labelled residues are analogous within both structures.	FIG
30	36	trimer	oligomeric_state	In b and c, the centre of the trimer is at top.	FIG
20	24	Mep2	protein	Channel closures in Mep2.	FIG
11	24	superposition	experimental_method	(a) Stereo superposition of AfAmt-1 and CaMep2 showing the residues of the Phe gate, His2 of the twin-His motif and the tyrosine residue Y49 in TM1 that forms a hydrogen bond with His2 in CaMep2. (b) Surface views from the side in rainbow colouring, showing the two-tier channel block (indicated by the arrows) in CaMep2.	FIG
28	35	AfAmt-1	protein	(a) Stereo superposition of AfAmt-1 and CaMep2 showing the residues of the Phe gate, His2 of the twin-His motif and the tyrosine residue Y49 in TM1 that forms a hydrogen bond with His2 in CaMep2. (b) Surface views from the side in rainbow colouring, showing the two-tier channel block (indicated by the arrows) in CaMep2.	FIG
40	46	CaMep2	protein	(a) Stereo superposition of AfAmt-1 and CaMep2 showing the residues of the Phe gate, His2 of the twin-His motif and the tyrosine residue Y49 in TM1 that forms a hydrogen bond with His2 in CaMep2. (b) Surface views from the side in rainbow colouring, showing the two-tier channel block (indicated by the arrows) in CaMep2.	FIG
75	83	Phe gate	site	(a) Stereo superposition of AfAmt-1 and CaMep2 showing the residues of the Phe gate, His2 of the twin-His motif and the tyrosine residue Y49 in TM1 that forms a hydrogen bond with His2 in CaMep2. (b) Surface views from the side in rainbow colouring, showing the two-tier channel block (indicated by the arrows) in CaMep2.	FIG
85	89	His2	residue_name_number	(a) Stereo superposition of AfAmt-1 and CaMep2 showing the residues of the Phe gate, His2 of the twin-His motif and the tyrosine residue Y49 in TM1 that forms a hydrogen bond with His2 in CaMep2. (b) Surface views from the side in rainbow colouring, showing the two-tier channel block (indicated by the arrows) in CaMep2.	FIG
97	111	twin-His motif	structure_element	(a) Stereo superposition of AfAmt-1 and CaMep2 showing the residues of the Phe gate, His2 of the twin-His motif and the tyrosine residue Y49 in TM1 that forms a hydrogen bond with His2 in CaMep2. (b) Surface views from the side in rainbow colouring, showing the two-tier channel block (indicated by the arrows) in CaMep2.	FIG
120	128	tyrosine	residue_name	(a) Stereo superposition of AfAmt-1 and CaMep2 showing the residues of the Phe gate, His2 of the twin-His motif and the tyrosine residue Y49 in TM1 that forms a hydrogen bond with His2 in CaMep2. (b) Surface views from the side in rainbow colouring, showing the two-tier channel block (indicated by the arrows) in CaMep2.	FIG
137	140	Y49	residue_name_number	(a) Stereo superposition of AfAmt-1 and CaMep2 showing the residues of the Phe gate, His2 of the twin-His motif and the tyrosine residue Y49 in TM1 that forms a hydrogen bond with His2 in CaMep2. (b) Surface views from the side in rainbow colouring, showing the two-tier channel block (indicated by the arrows) in CaMep2.	FIG
144	147	TM1	structure_element	(a) Stereo superposition of AfAmt-1 and CaMep2 showing the residues of the Phe gate, His2 of the twin-His motif and the tyrosine residue Y49 in TM1 that forms a hydrogen bond with His2 in CaMep2. (b) Surface views from the side in rainbow colouring, showing the two-tier channel block (indicated by the arrows) in CaMep2.	FIG
161	174	hydrogen bond	bond_interaction	(a) Stereo superposition of AfAmt-1 and CaMep2 showing the residues of the Phe gate, His2 of the twin-His motif and the tyrosine residue Y49 in TM1 that forms a hydrogen bond with His2 in CaMep2. (b) Surface views from the side in rainbow colouring, showing the two-tier channel block (indicated by the arrows) in CaMep2.	FIG
180	184	His2	residue_name_number	(a) Stereo superposition of AfAmt-1 and CaMep2 showing the residues of the Phe gate, His2 of the twin-His motif and the tyrosine residue Y49 in TM1 that forms a hydrogen bond with His2 in CaMep2. (b) Surface views from the side in rainbow colouring, showing the two-tier channel block (indicated by the arrows) in CaMep2.	FIG
188	194	CaMep2	protein	(a) Stereo superposition of AfAmt-1 and CaMep2 showing the residues of the Phe gate, His2 of the twin-His motif and the tyrosine residue Y49 in TM1 that forms a hydrogen bond with His2 in CaMep2. (b) Surface views from the side in rainbow colouring, showing the two-tier channel block (indicated by the arrows) in CaMep2.	FIG
271	284	channel block	structure_element	(a) Stereo superposition of AfAmt-1 and CaMep2 showing the residues of the Phe gate, His2 of the twin-His motif and the tyrosine residue Y49 in TM1 that forms a hydrogen bond with His2 in CaMep2. (b) Surface views from the side in rainbow colouring, showing the two-tier channel block (indicated by the arrows) in CaMep2.	FIG
314	320	CaMep2	protein	(a) Stereo superposition of AfAmt-1 and CaMep2 showing the residues of the Phe gate, His2 of the twin-His motif and the tyrosine residue Y49 in TM1 that forms a hydrogen bond with His2 in CaMep2. (b) Surface views from the side in rainbow colouring, showing the two-tier channel block (indicated by the arrows) in CaMep2.	FIG
4	8	Npr1	protein	The Npr1 kinase target Ser453 is dephosphorylated and located in an electronegative pocket.	FIG
9	15	kinase	protein_type	The Npr1 kinase target Ser453 is dephosphorylated and located in an electronegative pocket.	FIG
23	29	Ser453	residue_name_number	The Npr1 kinase target Ser453 is dephosphorylated and located in an electronegative pocket.	FIG
33	49	dephosphorylated	protein_state	The Npr1 kinase target Ser453 is dephosphorylated and located in an electronegative pocket.	FIG
68	90	electronegative pocket	site	The Npr1 kinase target Ser453 is dephosphorylated and located in an electronegative pocket.	FIG
19	25	CaMep2	protein	(a) Stereoviews of CaMep2 showing 2Fo–Fc electron density (contoured at 1.0 σ) for CTR residues Asp419-Met422 and for Tyr446-Thr455 of the AI region.	FIG
83	86	CTR	structure_element	(a) Stereoviews of CaMep2 showing 2Fo–Fc electron density (contoured at 1.0 σ) for CTR residues Asp419-Met422 and for Tyr446-Thr455 of the AI region.	FIG
96	109	Asp419-Met422	residue_range	(a) Stereoviews of CaMep2 showing 2Fo–Fc electron density (contoured at 1.0 σ) for CTR residues Asp419-Met422 and for Tyr446-Thr455 of the AI region.	FIG
118	131	Tyr446-Thr455	residue_range	(a) Stereoviews of CaMep2 showing 2Fo–Fc electron density (contoured at 1.0 σ) for CTR residues Asp419-Met422 and for Tyr446-Thr455 of the AI region.	FIG
139	148	AI region	structure_element	(a) Stereoviews of CaMep2 showing 2Fo–Fc electron density (contoured at 1.0 σ) for CTR residues Asp419-Met422 and for Tyr446-Thr455 of the AI region.	FIG
4	19	phosphorylation	ptm	The phosphorylation target residue Ser453 is labelled in bold.	FIG
35	41	Ser453	residue_name_number	The phosphorylation target residue Ser453 is labelled in bold.	FIG
4	11	Overlay	experimental_method	(b) Overlay of the CTRs of ScMep2 (grey) and CaMep2 (green), showing the similar electronegative environment surrounding the phosphorylation site (P).	FIG
19	23	CTRs	structure_element	(b) Overlay of the CTRs of ScMep2 (grey) and CaMep2 (green), showing the similar electronegative environment surrounding the phosphorylation site (P).	FIG
27	33	ScMep2	protein	(b) Overlay of the CTRs of ScMep2 (grey) and CaMep2 (green), showing the similar electronegative environment surrounding the phosphorylation site (P).	FIG
45	51	CaMep2	protein	(b) Overlay of the CTRs of ScMep2 (grey) and CaMep2 (green), showing the similar electronegative environment surrounding the phosphorylation site (P).	FIG
125	145	phosphorylation site	site	(b) Overlay of the CTRs of ScMep2 (grey) and CaMep2 (green), showing the similar electronegative environment surrounding the phosphorylation site (P).	FIG
4	14	AI regions	structure_element	The AI regions are coloured magenta.	FIG
28	32	Mep2	protein	(c) Cytoplasmic view of the Mep2 trimer indicating the large distance between Ser453 and the channel exits (circles; Ile52 lining the channel exit is shown).	FIG
33	39	trimer	oligomeric_state	(c) Cytoplasmic view of the Mep2 trimer indicating the large distance between Ser453 and the channel exits (circles; Ile52 lining the channel exit is shown).	FIG
78	84	Ser453	residue_name_number	(c) Cytoplasmic view of the Mep2 trimer indicating the large distance between Ser453 and the channel exits (circles; Ile52 lining the channel exit is shown).	FIG
93	106	channel exits	site	(c) Cytoplasmic view of the Mep2 trimer indicating the large distance between Ser453 and the channel exits (circles; Ile52 lining the channel exit is shown).	FIG
117	122	Ile52	residue_name_number	(c) Cytoplasmic view of the Mep2 trimer indicating the large distance between Ser453 and the channel exits (circles; Ile52 lining the channel exit is shown).	FIG
134	146	channel exit	site	(c) Cytoplasmic view of the Mep2 trimer indicating the large distance between Ser453 and the channel exits (circles; Ile52 lining the channel exit is shown).	FIG
10	17	removal	experimental_method	Effect of removal of the AI region on Mep2 structure.	FIG
25	34	AI region	structure_element	Effect of removal of the AI region on Mep2 structure.	FIG
38	42	Mep2	protein	Effect of removal of the AI region on Mep2 structure.	FIG
43	52	structure	evidence	Effect of removal of the AI region on Mep2 structure.	FIG
19	21	WT	protein_state	(a) Side views for WT CaMep2 (left) and the truncation mutant 442Δ (right).	FIG
22	28	CaMep2	protein	(a) Side views for WT CaMep2 (left) and the truncation mutant 442Δ (right).	FIG
44	61	truncation mutant	protein_state	(a) Side views for WT CaMep2 (left) and the truncation mutant 442Δ (right).	FIG
62	66	442Δ	mutant	(a) Side views for WT CaMep2 (left) and the truncation mutant 442Δ (right).	FIG
78	86	disorder	protein_state	The latter is shown as a putty model according to B-factors to illustrate the disorder in the protein on the cytoplasmic side.	FIG
42	56	superpositions	experimental_method	 Missing regions are labelled. (b) Stereo superpositions of WT CaMep2 and the truncation mutant.	FIG
60	62	WT	protein_state	 Missing regions are labelled. (b) Stereo superpositions of WT CaMep2 and the truncation mutant.	FIG
63	69	CaMep2	protein	 Missing regions are labelled. (b) Stereo superpositions of WT CaMep2 and the truncation mutant.	FIG
78	95	truncation mutant	protein_state	 Missing regions are labelled. (b) Stereo superpositions of WT CaMep2 and the truncation mutant.	FIG
58	63	Tyr49	residue_name_number	2Fo–Fc electron density (contoured at 1.0 σ) for residues Tyr49 and His342 is shown for the truncation mutant.	FIG
68	74	His342	residue_name_number	2Fo–Fc electron density (contoured at 1.0 σ) for residues Tyr49 and His342 is shown for the truncation mutant.	FIG
92	109	truncation mutant	protein_state	2Fo–Fc electron density (contoured at 1.0 σ) for residues Tyr49 and His342 is shown for the truncation mutant.	FIG
0	15	Phosphorylation	ptm	Phosphorylation causes conformational changes in the CTR.	FIG
53	56	CTR	structure_element	Phosphorylation causes conformational changes in the CTR.	FIG
28	37	DD mutant	mutant	(a) Cytoplasmic view of the DD mutant trimer, with WT CaMep2 superposed in grey for one of the monomers.	FIG
38	44	trimer	oligomeric_state	(a) Cytoplasmic view of the DD mutant trimer, with WT CaMep2 superposed in grey for one of the monomers.	FIG
51	53	WT	protein_state	(a) Cytoplasmic view of the DD mutant trimer, with WT CaMep2 superposed in grey for one of the monomers.	FIG
54	60	CaMep2	protein	(a) Cytoplasmic view of the DD mutant trimer, with WT CaMep2 superposed in grey for one of the monomers.	FIG
61	71	superposed	experimental_method	(a) Cytoplasmic view of the DD mutant trimer, with WT CaMep2 superposed in grey for one of the monomers.	FIG
95	103	monomers	oligomeric_state	(a) Cytoplasmic view of the DD mutant trimer, with WT CaMep2 superposed in grey for one of the monomers.	FIG
24	44	phosphorylation site	site	The arrow indicates the phosphorylation site.	FIG
4	13	AI region	structure_element	The AI region is coloured magenta.	FIG
4	11	Monomer	oligomeric_state	(b) Monomer side-view superposition of WT CaMep2 and the DD mutant, showing the conformational change and disorder around the ExxGxD motif.	FIG
22	35	superposition	experimental_method	(b) Monomer side-view superposition of WT CaMep2 and the DD mutant, showing the conformational change and disorder around the ExxGxD motif.	FIG
39	41	WT	protein_state	(b) Monomer side-view superposition of WT CaMep2 and the DD mutant, showing the conformational change and disorder around the ExxGxD motif.	FIG
42	48	CaMep2	protein	(b) Monomer side-view superposition of WT CaMep2 and the DD mutant, showing the conformational change and disorder around the ExxGxD motif.	FIG
57	66	DD mutant	mutant	(b) Monomer side-view superposition of WT CaMep2 and the DD mutant, showing the conformational change and disorder around the ExxGxD motif.	FIG
126	138	ExxGxD motif	structure_element	(b) Monomer side-view superposition of WT CaMep2 and the DD mutant, showing the conformational change and disorder around the ExxGxD motif.	FIG
25	28	452	residue_number	Side chains for residues 452 and 453 are shown as stick models.	FIG
33	36	453	residue_number	Side chains for residues 452 and 453 are shown as stick models.	FIG
56	60	Mep2	protein	Schematic model for phosphorylation-based regulation of Mep2 ammonium transporters.	FIG
11	17	closed	protein_state	(a) In the closed, non-phosphorylated state (i), the CTR (magenta) and ICL3 (green) are far apart with the latter blocking the intracellular channel exit (indicated with a hatched circle).	FIG
19	37	non-phosphorylated	protein_state	(a) In the closed, non-phosphorylated state (i), the CTR (magenta) and ICL3 (green) are far apart with the latter blocking the intracellular channel exit (indicated with a hatched circle).	FIG
53	56	CTR	structure_element	(a) In the closed, non-phosphorylated state (i), the CTR (magenta) and ICL3 (green) are far apart with the latter blocking the intracellular channel exit (indicated with a hatched circle).	FIG
71	75	ICL3	structure_element	(a) In the closed, non-phosphorylated state (i), the CTR (magenta) and ICL3 (green) are far apart with the latter blocking the intracellular channel exit (indicated with a hatched circle).	FIG
141	153	channel exit	site	(a) In the closed, non-phosphorylated state (i), the CTR (magenta) and ICL3 (green) are far apart with the latter blocking the intracellular channel exit (indicated with a hatched circle).	FIG
5	20	phosphorylation	ptm	Upon phosphorylation and mimicked by the CaMep2 S453D and DD mutants (ii), the region around the ExxGxD motif undergoes a conformational change that results in the CTR interacting with the inward-moving ICL3, opening the channel (full circle) (iii).	FIG
25	33	mimicked	protein_state	Upon phosphorylation and mimicked by the CaMep2 S453D and DD mutants (ii), the region around the ExxGxD motif undergoes a conformational change that results in the CTR interacting with the inward-moving ICL3, opening the channel (full circle) (iii).	FIG
41	47	CaMep2	protein	Upon phosphorylation and mimicked by the CaMep2 S453D and DD mutants (ii), the region around the ExxGxD motif undergoes a conformational change that results in the CTR interacting with the inward-moving ICL3, opening the channel (full circle) (iii).	FIG
48	53	S453D	mutant	Upon phosphorylation and mimicked by the CaMep2 S453D and DD mutants (ii), the region around the ExxGxD motif undergoes a conformational change that results in the CTR interacting with the inward-moving ICL3, opening the channel (full circle) (iii).	FIG
58	68	DD mutants	mutant	Upon phosphorylation and mimicked by the CaMep2 S453D and DD mutants (ii), the region around the ExxGxD motif undergoes a conformational change that results in the CTR interacting with the inward-moving ICL3, opening the channel (full circle) (iii).	FIG
97	109	ExxGxD motif	structure_element	Upon phosphorylation and mimicked by the CaMep2 S453D and DD mutants (ii), the region around the ExxGxD motif undergoes a conformational change that results in the CTR interacting with the inward-moving ICL3, opening the channel (full circle) (iii).	FIG
164	167	CTR	structure_element	Upon phosphorylation and mimicked by the CaMep2 S453D and DD mutants (ii), the region around the ExxGxD motif undergoes a conformational change that results in the CTR interacting with the inward-moving ICL3, opening the channel (full circle) (iii).	FIG
203	207	ICL3	structure_element	Upon phosphorylation and mimicked by the CaMep2 S453D and DD mutants (ii), the region around the ExxGxD motif undergoes a conformational change that results in the CTR interacting with the inward-moving ICL3, opening the channel (full circle) (iii).	FIG
221	228	channel	site	Upon phosphorylation and mimicked by the CaMep2 S453D and DD mutants (ii), the region around the ExxGxD motif undergoes a conformational change that results in the CTR interacting with the inward-moving ICL3, opening the channel (full circle) (iii).	FIG
4	8	open	protein_state	The open-channel Mep2 structure is represented by archaebacterial Amt-1 and shown in lighter colours consistent with Fig. 4.	FIG
9	16	channel	site	The open-channel Mep2 structure is represented by archaebacterial Amt-1 and shown in lighter colours consistent with Fig. 4.	FIG
17	21	Mep2	protein	The open-channel Mep2 structure is represented by archaebacterial Amt-1 and shown in lighter colours consistent with Fig. 4.	FIG
22	31	structure	evidence	The open-channel Mep2 structure is represented by archaebacterial Amt-1 and shown in lighter colours consistent with Fig. 4.	FIG
50	65	archaebacterial	taxonomy_domain	The open-channel Mep2 structure is represented by archaebacterial Amt-1 and shown in lighter colours consistent with Fig. 4.	FIG
66	71	Amt-1	protein	The open-channel Mep2 structure is represented by archaebacterial Amt-1 and shown in lighter colours consistent with Fig. 4.	FIG
71	76	plant	taxonomy_domain	As discussed in the text, similar structural arrangements may occur in plant AMTs.	FIG
77	81	AMTs	protein_type	As discussed in the text, similar structural arrangements may occur in plant AMTs.	FIG
26	30	open	protein_state	In this case however, the open channel corresponds to the non-phosphorylated state; phosphorylation breaks the CTR–ICL3 interactions leading to channel closure. (b) Model based on AMT transporter analogy showing how phosphorylation of a Mep2 monomer might allosterically open channels in the entire trimer via disruption of the interactions between the CTR and ICL3 of a neighbouring monomer (arrow).	FIG
31	38	channel	site	In this case however, the open channel corresponds to the non-phosphorylated state; phosphorylation breaks the CTR–ICL3 interactions leading to channel closure. (b) Model based on AMT transporter analogy showing how phosphorylation of a Mep2 monomer might allosterically open channels in the entire trimer via disruption of the interactions between the CTR and ICL3 of a neighbouring monomer (arrow).	FIG
58	76	non-phosphorylated	protein_state	In this case however, the open channel corresponds to the non-phosphorylated state; phosphorylation breaks the CTR–ICL3 interactions leading to channel closure. (b) Model based on AMT transporter analogy showing how phosphorylation of a Mep2 monomer might allosterically open channels in the entire trimer via disruption of the interactions between the CTR and ICL3 of a neighbouring monomer (arrow).	FIG
84	99	phosphorylation	ptm	In this case however, the open channel corresponds to the non-phosphorylated state; phosphorylation breaks the CTR–ICL3 interactions leading to channel closure. (b) Model based on AMT transporter analogy showing how phosphorylation of a Mep2 monomer might allosterically open channels in the entire trimer via disruption of the interactions between the CTR and ICL3 of a neighbouring monomer (arrow).	FIG
144	151	channel	site	In this case however, the open channel corresponds to the non-phosphorylated state; phosphorylation breaks the CTR–ICL3 interactions leading to channel closure. (b) Model based on AMT transporter analogy showing how phosphorylation of a Mep2 monomer might allosterically open channels in the entire trimer via disruption of the interactions between the CTR and ICL3 of a neighbouring monomer (arrow).	FIG
216	231	phosphorylation	ptm	In this case however, the open channel corresponds to the non-phosphorylated state; phosphorylation breaks the CTR–ICL3 interactions leading to channel closure. (b) Model based on AMT transporter analogy showing how phosphorylation of a Mep2 monomer might allosterically open channels in the entire trimer via disruption of the interactions between the CTR and ICL3 of a neighbouring monomer (arrow).	FIG
237	241	Mep2	protein	In this case however, the open channel corresponds to the non-phosphorylated state; phosphorylation breaks the CTR–ICL3 interactions leading to channel closure. (b) Model based on AMT transporter analogy showing how phosphorylation of a Mep2 monomer might allosterically open channels in the entire trimer via disruption of the interactions between the CTR and ICL3 of a neighbouring monomer (arrow).	FIG
242	249	monomer	oligomeric_state	In this case however, the open channel corresponds to the non-phosphorylated state; phosphorylation breaks the CTR–ICL3 interactions leading to channel closure. (b) Model based on AMT transporter analogy showing how phosphorylation of a Mep2 monomer might allosterically open channels in the entire trimer via disruption of the interactions between the CTR and ICL3 of a neighbouring monomer (arrow).	FIG
271	275	open	protein_state	In this case however, the open channel corresponds to the non-phosphorylated state; phosphorylation breaks the CTR–ICL3 interactions leading to channel closure. (b) Model based on AMT transporter analogy showing how phosphorylation of a Mep2 monomer might allosterically open channels in the entire trimer via disruption of the interactions between the CTR and ICL3 of a neighbouring monomer (arrow).	FIG
276	284	channels	site	In this case however, the open channel corresponds to the non-phosphorylated state; phosphorylation breaks the CTR–ICL3 interactions leading to channel closure. (b) Model based on AMT transporter analogy showing how phosphorylation of a Mep2 monomer might allosterically open channels in the entire trimer via disruption of the interactions between the CTR and ICL3 of a neighbouring monomer (arrow).	FIG
299	305	trimer	oligomeric_state	In this case however, the open channel corresponds to the non-phosphorylated state; phosphorylation breaks the CTR–ICL3 interactions leading to channel closure. (b) Model based on AMT transporter analogy showing how phosphorylation of a Mep2 monomer might allosterically open channels in the entire trimer via disruption of the interactions between the CTR and ICL3 of a neighbouring monomer (arrow).	FIG
353	356	CTR	structure_element	In this case however, the open channel corresponds to the non-phosphorylated state; phosphorylation breaks the CTR–ICL3 interactions leading to channel closure. (b) Model based on AMT transporter analogy showing how phosphorylation of a Mep2 monomer might allosterically open channels in the entire trimer via disruption of the interactions between the CTR and ICL3 of a neighbouring monomer (arrow).	FIG
361	365	ICL3	structure_element	In this case however, the open channel corresponds to the non-phosphorylated state; phosphorylation breaks the CTR–ICL3 interactions leading to channel closure. (b) Model based on AMT transporter analogy showing how phosphorylation of a Mep2 monomer might allosterically open channels in the entire trimer via disruption of the interactions between the CTR and ICL3 of a neighbouring monomer (arrow).	FIG
384	391	monomer	oligomeric_state	In this case however, the open channel corresponds to the non-phosphorylated state; phosphorylation breaks the CTR–ICL3 interactions leading to channel closure. (b) Model based on AMT transporter analogy showing how phosphorylation of a Mep2 monomer might allosterically open channels in the entire trimer via disruption of the interactions between the CTR and ICL3 of a neighbouring monomer (arrow).	FIG