diff --git "a/annotation_IOB/PMC5012862.tsv" "b/annotation_IOB/PMC5012862.tsv" new file mode 100644--- /dev/null +++ "b/annotation_IOB/PMC5012862.tsv" @@ -0,0 +1,15440 @@ +Structural B-experimental_method +characterization I-experimental_method +of O +encapsulated B-protein_state +ferritin B-protein_type +provides O +insight O +into O +iron B-chemical +storage O +in O +bacterial B-taxonomy_domain +nanocompartments B-complex_assembly + +Ferritins B-protein_type +are O +ubiquitous O +proteins O +that O +oxidise O +and O +store O +iron B-chemical +within O +a O +protein O +shell B-structure_element +to O +protect O +cells O +from O +oxidative O +damage O +. O + +We O +have O +characterized O +the O +structure B-evidence +and O +function O +of O +a O +new O +member O +of O +the O +ferritin B-protein_type +superfamily O +that O +is O +sequestered O +within O +an O +encapsulin B-protein +capsid O +. O + +We O +show O +that O +this O +encapsulated B-protein_state +ferritin B-protein_type +( O +EncFtn B-protein +) O +has O +two O +main B-structure_element +alpha I-structure_element +helices I-structure_element +, O +which O +assemble O +in O +a O +metal B-protein_state +dependent I-protein_state +manner O +to O +form O +a O +ferroxidase B-site +center I-site +at O +a O +dimer B-site +interface I-site +. O + +EncFtn B-protein +adopts O +an O +open B-protein_state +decameric B-oligomeric_state +structure B-evidence +that O +is O +topologically O +distinct O +from O +other O +ferritins B-protein_type +. O + +While O +EncFtn B-protein +acts O +as O +a O +ferroxidase B-protein_type +, O +it O +cannot O +mineralize O +iron B-chemical +. O + +Conversely O +, O +the O +encapsulin B-protein +shell B-structure_element +associates O +with O +iron B-chemical +, O +but O +is O +not B-protein_state +enzymatically I-protein_state +active I-protein_state +, O +and O +we O +demonstrate O +that O +EncFtn B-protein +must O +be O +housed O +within O +the O +encapsulin B-protein +for O +iron B-chemical +storage O +. O + +This O +encapsulin B-protein +nanocompartment B-complex_assembly +is O +widely O +distributed O +in O +bacteria B-taxonomy_domain +and O +archaea B-taxonomy_domain +and O +represents O +a O +distinct O +class O +of O +iron B-chemical +storage O +system O +, O +where O +the O +oxidation O +and O +mineralization O +of O +iron B-chemical +are O +distributed O +between O +two O +proteins O +. O + +Iron B-chemical +is O +essential O +for O +life O +as O +it O +is O +a O +key O +component O +of O +many O +different O +enzymes O +that O +participate O +in O +processes O +such O +as O +energy O +production O +and O +metabolism O +. O + +However O +, O +iron B-chemical +can O +also O +be O +highly O +toxic O +to O +cells O +because O +it O +readily O +reacts O +with O +oxygen B-chemical +. O + +To O +balance O +the O +cell O +’ O +s O +need O +for O +iron B-chemical +against O +its O +potential O +damaging O +effects O +, O +organisms O +have O +evolved O +iron B-protein_type +storage I-protein_type +proteins I-protein_type +known O +as O +ferritins B-protein_type +that O +form O +cage B-structure_element +- I-structure_element +like I-structure_element +structures I-structure_element +. O + +The O +ferritins B-protein_type +convert O +iron B-chemical +into O +a O +less O +reactive O +form O +that O +is O +mineralised O +and O +safely O +stored O +in O +the O +central B-site +cavity I-site +of O +the O +ferritin B-protein_type +cage O +and O +is O +available O +for O +cells O +when O +they O +need O +it O +. O + +Recently O +, O +a O +new O +family O +of O +ferritins B-protein_type +known O +as O +encapsulated B-protein_state +ferritins B-protein_type +have O +been O +found O +in O +some O +microorganisms B-taxonomy_domain +. O + +These O +ferritins B-protein_type +are O +found O +in O +bacterial B-taxonomy_domain +genomes O +with O +a O +gene O +that O +codes O +for O +a O +protein O +cage O +called O +an O +encapsulin B-protein +. O + +Although O +the O +structure B-evidence +of O +the O +encapsulin B-protein +cage O +is O +known O +to O +look O +like O +the O +shell B-structure_element +of O +a O +virus B-taxonomy_domain +, O +the O +structure B-evidence +that O +the O +encapsulated B-protein_state +ferritin B-protein_type +itself O +forms O +is O +not O +known O +. O + +It O +is O +also O +not O +clear O +how O +encapsulin B-protein +and O +the O +encapsulated B-protein_state +ferritin B-protein_type +work O +together O +to O +store O +iron B-chemical +. O + +He O +et O +al O +. O +have O +now O +used O +the O +techniques O +of O +X B-experimental_method +- I-experimental_method +ray I-experimental_method +crystallography I-experimental_method +and O +mass B-experimental_method +spectrometry I-experimental_method +to O +determine O +the O +structure B-evidence +of O +the O +encapsulated B-protein_state +ferritin B-protein_type +found O +in O +some O +bacteria B-taxonomy_domain +. O + +The O +encapsulated B-protein_state +ferritin B-protein_type +forms O +a O +ring B-structure_element +- I-structure_element +shaped I-structure_element +doughnut B-structure_element +in O +which O +ten O +subunits B-structure_element +of O +ferritin B-protein_type +are O +arranged O +in O +a O +ring B-structure_element +; O +this O +is O +totally O +different O +from O +the O +enclosed O +cages B-structure_element +that O +other O +ferritins B-protein_type +form O +. O + +Biochemical B-experimental_method +studies I-experimental_method +revealed O +that O +the O +encapsulated B-protein_state +ferritin B-protein_type +is O +able O +to O +convert O +iron B-chemical +into O +a O +less O +reactive O +form O +, O +but O +it O +cannot O +store O +iron B-chemical +on O +its O +own O +since O +it O +does O +not O +form O +a O +cage O +. O + +Thus O +, O +the O +encapsulated B-protein_state +ferritin B-protein_type +needs O +to O +be O +housed O +within O +the O +encapsulin B-protein +cage O +to O +store O +iron B-chemical +. O + +Further O +work O +is O +needed O +to O +investigate O +how O +iron B-chemical +moves O +into O +the O +encapsulin B-protein +cage O +to O +reach O +the O +ferritin B-protein_type +proteins O +. O + +Some O +organisms O +have O +both O +standard O +ferritin B-protein_type +cages O +and O +encapsulated B-protein_state +ferritins B-protein_type +; O +why O +this O +is O +the O +case O +also O +remains O +to O +be O +discovered O +. O + +Encapsulin B-protein_type +nanocompartments B-complex_assembly +are O +a O +family O +of O +proteinaceous O +metabolic O +compartments O +that O +are O +widely O +distributed O +in O +bacteria B-taxonomy_domain +and O +archaea B-taxonomy_domain +. O + +They O +share O +a O +common O +architecture O +, O +comprising O +an O +icosahedral B-protein_state +shell B-structure_element +formed O +by O +the O +oligomeric O +assembly O +of O +a O +protein O +, O +encapsulin B-protein_type +, O +that O +is O +structurally O +related O +to O +the O +HK97 B-taxonomy_domain +bacteriophage I-taxonomy_domain +capsid O +protein O +gp5 B-protein +. O + +Gp5 B-protein +is O +known O +to O +assemble O +as O +a O +66 O +nm O +diameter O +icosahedral B-protein_state +shell B-structure_element +of O +420 O +subunits B-structure_element +. O + +In O +contrast O +, O +both O +the O +Pyrococcus B-species +furiosus I-species +and O +Myxococcus B-species +xanthus I-species +encapsulin B-protein +shell B-structure_element +- O +proteins O +form O +32 O +nm O +icosahedra B-structure_element +with O +180 O +subunits B-structure_element +; O +while O +the O +Thermotoga B-species +maritima I-species +encapsulin B-protein +is O +smaller O +still O +with O +a O +25 O +nm O +, O +60 O +- O +subunit O +icosahedron B-structure_element +. O + +The O +high O +structural O +similarity O +of O +the O +encapsulin B-protein_type +shell B-structure_element +- O +proteins O +to O +gp5 B-protein +suggests O +a O +common O +evolutionary O +origin O +for O +these O +proteins O +. O + +The O +genes O +encoding O +encapsulin B-protein_type +proteins O +are O +found O +downstream O +of O +genes O +for O +dye B-protein_type +- I-protein_type +dependent I-protein_type +peroxidase I-protein_type +( O +DyP B-protein_type +) O +family O +enzymes O +, O +or O +encapsulin B-protein_type +- I-protein_type +associated I-protein_type +ferritins I-protein_type +( O +EncFtn B-protein_type +). O + +Enzymes O +in O +the O +DyP B-protein_type +family I-protein_type +are O +active O +against O +polyphenolic O +compounds O +such O +as O +azo O +dyes O +and O +lignin O +breakdown O +products O +; O +although O +their O +physiological O +function O +and O +natural O +substrates O +are O +not O +known O +. O + +Ferritin B-protein_type +family O +proteins O +are O +found O +in O +all O +kingdoms B-taxonomy_domain +and O +have O +a O +wide O +range O +of O +activities O +, O +including O +ribonucleotide B-protein_type +reductase I-protein_type +, O +protecting O +DNA O +from O +oxidative O +damage O +, O +and O +iron B-chemical +storage O +. O + +The O +classical B-protein_state +iron B-complex_assembly +storage I-complex_assembly +ferritin I-complex_assembly +nanocages I-complex_assembly +are O +found O +in O +all O +kingdoms B-taxonomy_domain +and O +are O +essential O +in O +eukaryotes B-taxonomy_domain +; O +they O +play O +a O +central O +role O +in O +iron B-chemical +homeostasis O +, O +where O +they O +protect O +the O +cell O +from O +toxic O +free O +Fe2 B-chemical ++ I-chemical +by O +oxidizing O +it O +and O +storing O +the O +resulting O +Fe3 B-chemical ++ I-chemical +as O +ferrihydrite B-chemical +minerals O +within O +their O +central B-site +cavity I-site +. O + +The O +encapsulin B-protein_type +- O +associated O +enzymes O +are O +sequestered O +within O +the O +icosahedral B-protein_state +shell B-structure_element +through O +interactions O +between O +the O +shell B-structure_element +’ O +s O +inner O +surface O +and O +a O +short B-structure_element +localization I-structure_element +sequence I-structure_element +( O +Gly B-structure_element +- I-structure_element +Ser I-structure_element +- I-structure_element +Leu I-structure_element +- I-structure_element +Lys I-structure_element +) O +appended O +to O +their O +C O +- O +termini O +. O + +This B-structure_element +motif I-structure_element +is O +well B-protein_state +- I-protein_state +conserved I-protein_state +, O +and O +the O +addition O +of O +this O +sequence O +to O +heterologous O +proteins O +is O +sufficient O +to O +direct O +them O +to O +the O +interior O +of O +encapsulins B-protein_type +. O + +A O +recent O +study O +of O +the O +Myxococcus B-species +xanthus I-species +encapsulin B-protein +showed O +that O +it O +sequesters O +a O +number O +of O +different O +EncFtn B-protein_type +proteins O +and O +acts O +as O +an O +‘ O +iron B-chemical +- O +megastore O +’ O +to O +protect O +these O +bacteria B-taxonomy_domain +from O +oxidative O +stress O +. O + +At O +32 O +nm O +in O +diameter O +, O +it O +is O +much O +larger O +than O +other O +members O +of O +the O +ferritin B-protein_type +superfamily O +, O +such O +as O +the O +12 O +nm O +24 O +- O +subunit O +classical B-protein_state +ferritin B-protein_type +nanocage B-complex_assembly +and O +the O +8 O +nm O +12 O +- O +subunit O +Dps B-protein_type +( O +DNA B-protein_type +- I-protein_type +binding I-protein_type +protein I-protein_type +from O +starved O +cells O +) O +complex O +; O +and O +is O +thus O +capable O +of O +sequestering O +up O +to O +ten O +times O +more O +iron B-chemical +than O +these O +ferritins B-protein_type +. O + +The O +primary O +sequences O +of O +EncFtn B-protein_type +proteins O +have O +Glu B-structure_element +- I-structure_element +X I-structure_element +- I-structure_element +X I-structure_element +- I-structure_element +His I-structure_element +metal B-site +coordination I-site +sites I-site +, O +which O +are O +shared O +features O +of O +the O +ferritin B-protein_type +family O +proteins O +. O + +Secondary B-experimental_method +structure I-experimental_method +prediction I-experimental_method +identifies O +two O +major B-structure_element +α I-structure_element +- I-structure_element +helical I-structure_element +regions I-structure_element +in O +these O +proteins O +; O +this O +is O +in O +contrast O +to O +other O +members O +of O +the O +ferritin B-protein_type +superfamily O +, O +which O +have O +four O +major B-structure_element +α I-structure_element +- I-structure_element +helices I-structure_element +( O +Supplementary O +file O +1 O +). O + +The O +‘ O +half O +- O +ferritin B-protein_type +’ O +primary O +sequence O +of O +the O +EncFtn B-protein_type +family O +and O +their O +association O +with O +encapsulin B-protein +nanocompartments B-complex_assembly +suggests O +a O +distinct O +biochemical O +and O +structural O +organization O +to O +other O +ferritin B-protein_type +family O +proteins O +. O + +The O +Rhodospirillum B-species +rubrum I-species +EncFtn B-protein +protein O +( O +Rru_A0973 B-gene +) O +shares O +33 O +% O +protein O +sequence O +identity O +with O +the O +M B-species +. I-species +xanthus I-species +( O +MXAN_4464 B-gene +), O +53 O +% O +with O +the O +T B-species +. I-species +maritima I-species +( O +Tmari_0787 B-gene +), O +and O +29 O +% O +with O +the O +P B-species +. I-species +furiosus I-species +( O +PF1192 B-gene +) O +homologues O +. O + +The O +GXXH B-structure_element +motifs O +are O +strictly B-protein_state +conserved I-protein_state +in O +each O +of O +these O +species O +( O +Supplementary O +file O +1 O +). O + +Here O +we O +investigate O +the O +structure B-evidence +and O +biochemistry O +of O +EncFtn B-protein +in O +order O +to O +understand O +iron B-chemical +storage O +within O +the O +encapsulin B-protein +nanocompartment B-complex_assembly +. O + +We O +have O +produced O +recombinant O +encapsulin B-protein +( O +Enc B-protein +) O +and O +EncFtn B-protein +from O +the O +aquatic B-taxonomy_domain +purple B-taxonomy_domain +- I-taxonomy_domain +sulfur I-taxonomy_domain +bacterium I-taxonomy_domain +R B-species +. I-species +rubrum I-species +, O +which O +serves O +as O +a O +model O +organism O +for O +the O +study O +of O +the O +control O +of O +the O +bacterial B-taxonomy_domain +nitrogen O +fixation O +machinery O +, O +in O +Escherichia B-species +coli I-species +. O + +Analysis O +by O +transmission B-experimental_method +electron I-experimental_method +microscopy I-experimental_method +( O +TEM B-experimental_method +) O +indicates O +that O +their O +co B-experimental_method +- I-experimental_method +expression I-experimental_method +leads O +to O +the O +production O +of O +an O +icosahedral B-protein_state +nanocompartment B-complex_assembly +with O +encapsulated B-protein_state +EncFtn B-protein +. O + +The O +crystal B-evidence +structure I-evidence +of O +a O +truncated B-protein_state +hexahistidine B-protein_state +- I-protein_state +tagged I-protein_state +variant O +of O +the O +EncFtn B-protein +protein O +( O +EncFtnsH B-protein +) O +shows O +that O +it O +forms O +a O +decameric B-oligomeric_state +structure B-evidence +with O +an O +annular O +‘ O +ring B-structure_element +- I-structure_element +doughnut I-structure_element +’ O +topology O +, O +which O +is O +distinct O +from O +the O +four B-structure_element +- I-structure_element +helical I-structure_element +bundles I-structure_element +of O +the O +24meric B-oligomeric_state +ferritins B-protein_type +and O +dodecahedral B-oligomeric_state +DPS B-protein_type +proteins O +. O + +We O +identify O +a O +symmetrical O +iron B-protein_state +bound I-protein_state +ferroxidase B-site +center I-site +( O +FOC B-site +) O +formed O +between O +subunits B-structure_element +in O +the O +decamer B-oligomeric_state +and O +additional O +metal B-site +- I-site +binding I-site +sites I-site +close O +to O +the O +center O +of O +the O +ring B-structure_element +and O +on O +the O +outer O +surface O +. O + +We O +also O +demonstrate O +the O +metal O +- O +dependent O +assembly O +of O +EncFtn B-protein +decamers B-oligomeric_state +using O +native B-experimental_method +PAGE I-experimental_method +, O +analytical B-experimental_method +gel I-experimental_method +- I-experimental_method +filtration I-experimental_method +, O +and O +native B-experimental_method +mass I-experimental_method +spectrometry I-experimental_method +. O + +Biochemical B-experimental_method +assays I-experimental_method +show O +that O +EncFtn B-protein +is O +active B-protein_state +as O +a O +ferroxidase B-protein_type +enzyme O +. O + +Through O +site B-experimental_method +- I-experimental_method +directed I-experimental_method +mutagenesis I-experimental_method +we O +show O +that O +the O +conserved B-protein_state +glutamic B-residue_name +acid I-residue_name +and O +histidine B-residue_name +residues O +in O +the O +FOC B-site +influence O +protein O +assembly O +and O +activity O +. O + +We O +use O +our O +combined O +structural B-evidence +and I-evidence +biochemical I-evidence +data I-evidence +to O +propose O +a O +model O +for O +the O +EncFtn B-protein +- O +catalyzed O +sequestration O +of O +iron B-chemical +within O +the O +encapsulin B-protein +shell B-structure_element +. O + +Assembly O +of O +R B-species +. I-species +rubrum I-species +EncFtn B-protein +encapsulin B-protein +nanocompartments B-complex_assembly +in O +E B-species +. I-species +coli I-species + +Full B-evidence +- I-evidence +frame I-evidence +transmission I-evidence +electron I-evidence +micrographs I-evidence +of O +R B-species +. I-species +rubrum I-species +nanocompartments B-complex_assembly +. O + +( O +A O +/ O +B O +) O +Negative B-experimental_method +stain I-experimental_method +TEM I-experimental_method +image B-evidence +of O +recombinant O +R B-species +. I-species +rubrum I-species +encapsulin B-protein +and O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +nanocompartments B-complex_assembly +. O + +All O +samples O +were O +imaged O +at O +143 O +, O +000 O +x O +magnification O +; O +the O +scale O +bar O +length O +corresponds O +to O +50 O +nm O +. O +( O +C O +) O +Histogram B-evidence +showing O +the O +distribution O +of O +nanocompartment B-complex_assembly +diameters O +. O + +A O +model O +Gaussian B-experimental_method +nonlinear I-experimental_method +least I-experimental_method +square I-experimental_method +function I-experimental_method +was O +fitted O +to O +the O +data O +to O +obtain O +a O +mean O +diameter O +of O +24 O +. O +6 O +nm O +with O +a O +standard O +deviation O +of O +2 O +. O +0 O +nm O +for O +encapsulin B-protein +( O +grey O +) O +and O +a O +mean O +value O +of O +23 O +. O +9 O +nm O +with O +a O +standard O +deviation O +of O +2 O +. O +2 O +nm O +for O +co B-experimental_method +- I-experimental_method +expressed I-experimental_method +EncFtn B-protein +and O +encapsulin B-protein +( O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +, O +black O +). O + +Purification O +of O +recombinant O +R B-species +. I-species +rubrum I-species +encapsulin B-protein +nanocompartments B-complex_assembly +. O + +( O +A O +) O +Recombinantly B-experimental_method +expressed I-experimental_method +encapsulin B-protein +( O +Enc B-protein +) O +and O +co B-experimental_method +- I-experimental_method +expressed I-experimental_method +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +were O +purified O +by O +sucrose B-experimental_method +gradient I-experimental_method +ultracentrifugation I-experimental_method +from O +E B-species +. I-species +coli I-species +B834 O +( O +DE3 O +) O +grown O +in O +SeMet B-chemical +medium O +. O + +Samples O +were O +resolved O +by O +18 O +% O +acrylamide O +SDS B-experimental_method +- I-experimental_method +PAGE I-experimental_method +; O +the O +position O +of O +the O +proteins O +found O +in O +the O +complexes O +as O +resolved O +on O +the O +gel O +are O +shown O +with O +arrows O +. O + +( O +B O +/ O +C O +) O +Negative B-experimental_method +stain I-experimental_method +TEM I-experimental_method +image O +of O +recombinant O +encapsulin B-protein +and O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +nanocompartments B-complex_assembly +. O + +Representative O +encapsulin B-protein +and O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +complexes O +are O +indicated O +with O +red O +arrows O +. O + +We O +produced O +recombinant O +R B-species +. I-species +rubrum I-species +encapsulin B-protein +nanocompartments B-complex_assembly +in O +E B-species +. I-species +coli I-species +by O +co B-experimental_method +- I-experimental_method +expression I-experimental_method +of O +the O +encapsulin B-protein +( O +Rru_A0974 B-gene +) O +and O +EncFtn B-protein +( O +Rru_A0973 B-gene +) O +proteins O +, O +and O +purified O +these O +by O +sucrose B-experimental_method +gradient I-experimental_method +ultra I-experimental_method +- I-experimental_method +centrifugation I-experimental_method +( O +Figure O +1A O +). O + +TEM B-experimental_method +imaging O +of O +uranyl O +acetate O +- O +stained O +samples O +revealed O +that O +, O +when O +expressed B-experimental_method +in I-experimental_method +isolation I-experimental_method +, O +the O +encapsulin B-protein +protein O +forms O +empty B-protein_state +compartments B-complex_assembly +with O +an O +average O +diameter O +of O +24 O +nm O +( O +Figure O +1B O +and O +Figure O +1 O +— O +figure O +supplement O +1A O +/ O +C O +), O +consistent O +with O +the O +appearance O +and O +size O +of O +the O +T B-species +. I-species +maritima I-species +encapsulin B-protein +. O + +We O +were O +not O +able O +to O +resolve O +any O +higher O +- O +order O +structures O +of O +EncFtn B-protein +by O +TEM B-experimental_method +. O + +Protein O +purified O +from O +co B-experimental_method +- I-experimental_method +expression I-experimental_method +of O +the O +encapsulin B-protein +and O +EncFtn B-protein +resulted O +in O +24 O +nm O +compartments O +with O +regions O +in O +the O +center O +that O +exclude O +stain O +, O +consistent O +with O +the O +presence B-protein_state +of I-protein_state +the O +EncFtn B-protein +within O +the O +encapsulin B-protein +shell B-structure_element +( O +Figure O +1C O +and O +Figure O +1 O +— O +figure O +supplement O +1B O +/ O +C O +). O + +R B-species +. I-species +rubrum I-species +EncFtn B-protein +forms O +a O +metal O +- O +ion O +stabilized O +decamer B-oligomeric_state +in O +solution O + +Purification B-experimental_method +of I-experimental_method +recombinant I-experimental_method +R B-species +. I-species +rubrum I-species +EncFtnsH B-protein +. O + +( O +A O +) O +Recombinant O +SeMet B-protein_state +- I-protein_state +labeled I-protein_state +EncFtnsH B-protein +produced O +with O +1 O +mM O +Fe B-chemical +( I-chemical +NH4 I-chemical +) I-chemical +2 I-chemical +( I-chemical +SO4 I-chemical +) I-chemical +2 I-chemical +in O +the O +growth O +medium O +was O +purified O +by O +nickel B-experimental_method +affinity I-experimental_method +chromatography I-experimental_method +and O +size B-experimental_method +- I-experimental_method +exclusion I-experimental_method +chromatography I-experimental_method +using O +a O +Superdex O +200 O +16 O +/ O +60 O +column O +( O +GE O +Healthcare O +). O + +Chromatogram B-evidence +traces O +measured O +at O +280 O +nm O +and O +315 O +nm O +are O +shown O +with O +the O +results O +from O +ICP B-experimental_method +- I-experimental_method +MS I-experimental_method +analysis O +of O +the O +iron B-chemical +content O +of O +the O +fractions O +collected O +during O +the O +experiment O +. O + +The O +peak O +around O +73 O +ml O +corresponds O +to O +a O +molecular B-evidence +weight I-evidence +of O +around O +130 O +kDa O +when O +compared O +to O +calibration O +standards O +; O +this O +is O +consistent O +with O +a O +decamer B-oligomeric_state +of O +EncFtnsH B-protein +. O +The O +small O +peak O +at O +85 O +ml O +corresponds O +to O +the O +13 O +kDa O +monomer B-oligomeric_state +compared O +to O +the O +standards O +. O + +Only O +the O +decamer B-oligomeric_state +peak O +contains O +significant O +amounts O +of O +iron B-chemical +as O +indicated O +by O +the O +ICP B-experimental_method +- I-experimental_method +MS I-experimental_method +analysis O +. O + +( O +B O +) O +Peak O +fractions O +from O +the O +gel B-experimental_method +filtration I-experimental_method +run O +were O +resolved O +by O +15 O +% O +acrylamide O +SDS B-experimental_method +- I-experimental_method +PAGE I-experimental_method +and O +stained O +with O +Coomassie O +blue O +stain O +. O + +The O +bands O +around O +13 O +kDa O +and O +26 O +kDa O +correspond O +to O +EncFtnsH B-protein +, O +as O +identified O +by O +MALDI B-experimental_method +peptide I-experimental_method +mass I-experimental_method +fingerprinting I-experimental_method +. O + +The O +band O +at O +13 O +kDa O +is O +consistent O +with O +the O +monomer B-oligomeric_state +mass O +, O +while O +the O +band O +at O +26 O +kDa O +is O +consistent O +with O +a O +dimer B-oligomeric_state +of O +EncFtnsH B-protein +. O +The O +dimer B-oligomeric_state +species O +only O +appears O +in O +the O +decamer B-oligomeric_state +fractions O +. O + +( O +C O +) O +SEC B-experimental_method +- I-experimental_method +MALLS I-experimental_method +analysis O +of O +EncFtnsH B-protein +from O +decamer B-oligomeric_state +fractions O +and O +monomer B-oligomeric_state +fractions O +allows O +assignment O +of O +an O +average O +mass O +of O +132 O +kDa O +to O +decamer B-oligomeric_state +fractions O +and O +13 O +kDa O +to O +monomer B-oligomeric_state +fractions O +, O +consistent O +with O +decamer B-oligomeric_state +and O +monomer B-oligomeric_state +species O +( O +Table O +2 O +). O + +Determination O +of O +the O +Fe B-chemical +/ O +EncFtnsH B-protein +protein O +ratio O +by O +ICP B-experimental_method +- I-experimental_method +MS I-experimental_method +. O + +EncFtnsH B-protein +was O +purified O +as O +a O +SeMet B-chemical +derivative O +from O +E B-species +. I-species +coli I-species +B834 I-species +( I-species +DE3 I-species +) I-species +cells O +grown O +in O +SeMet B-chemical +medium O +with O +1 O +mM O +Fe B-chemical +( I-chemical +NH4 I-chemical +) I-chemical +2 I-chemical +( I-chemical +SO4 I-chemical +) I-chemical +2 I-chemical +. O + +Fractions O +from O +SEC B-experimental_method +were O +collected O +, O +acidified O +and O +analysed O +by O +ICP B-experimental_method +- I-experimental_method +MS I-experimental_method +. O + +EncFtnsH B-protein +concentration O +was O +calculated O +based O +on O +the O +presence B-protein_state +of I-protein_state +two O +SeMet B-chemical +per O +mature B-protein_state +monomer B-oligomeric_state +. O + +These O +data O +were O +collected O +from O +EncFtnsH B-protein +fractions O +from O +a O +single O +gel B-experimental_method +- I-experimental_method +filtration I-experimental_method +run O +. O + +Peak O +EncFtnsHretention B-protein +volume O +( O +ml O +) O +Element O +concentration O +( O +µM O +) O +Derived O +EncFtnsHconcentration B-protein +( O +µM O +) O +Derived O +Fe B-chemical +/ O +EncFtnsH B-protein +monomer B-oligomeric_state +Ca B-chemical +Fe B-chemical +Zn B-chemical +Se B-chemical +Decamer B-oligomeric_state +66 O +. O +5 O +n O +. O +d O +. O + +Estimates O +of O +EncFtnsH B-protein +molecular B-evidence +weight I-evidence +from O +SEC B-experimental_method +- I-experimental_method +MALLS I-experimental_method +analysis O +. O + +EncFtnsH B-protein +was O +purified O +from O +E B-species +. I-species +coli I-species +BL21 I-species +( I-species +DE3 I-species +) I-species +grown O +in O +minimal B-experimental_method +medium I-experimental_method +( O +MM B-experimental_method +) O +by O +nickel B-experimental_method +affinity I-experimental_method +chromatography I-experimental_method +and O +size B-experimental_method +- I-experimental_method +exclusion I-experimental_method +chromatography I-experimental_method +. O + +Fractions O +from O +two O +peaks B-evidence +( O +decamer B-oligomeric_state +and O +monomer B-oligomeric_state +) O +were O +pooled O +separately O +( O +Figure O +1C O +) O +and O +analysed O +by O +SEC B-experimental_method +- I-experimental_method +MALLS I-experimental_method +using O +a O +Superdex O +200 O +10 O +/ O +300 O +GL O +column O +( O +GE O +Healthcare O +) O +and O +Viscotek O +SEC B-experimental_method +- I-experimental_method +MALLS I-experimental_method +instruments O +( O +Malvern O +Instruments O +) O +( O +Figure O +2C O +). O + +The O +decamer B-oligomeric_state +and O +monomer B-oligomeric_state +peaks B-evidence +were O +both O +symmetric O +and O +monodisperse O +, O +allowing O +the O +estimation O +of O +the O +molecular B-evidence +weight I-evidence +of O +the O +species O +in O +these O +fractions O +. O + +The O +proteins O +analyzed O +by O +SEC B-experimental_method +- I-experimental_method +MALLS I-experimental_method +came O +from O +single O +protein O +preparation O +. O + +Molecular B-evidence +Weight I-evidence +( O +kDa O +) O +Decamer B-oligomeric_state +peak O +Monomer B-oligomeric_state +peak O +Theoretical O +133 O +13 O +EncFtnsH B-protein +- O +decamer B-oligomeric_state +fractions O +132 O +15 O +EncFtnsH B-protein +- O +monomer B-oligomeric_state +fractions O +126 O +13 O + +We O +purified O +recombinant O +R B-species +. I-species +rubrum I-species +EncFtn B-protein +as O +both O +the O +full B-protein_state +- I-protein_state +length I-protein_state +sequence O +( O +140 B-residue_range +amino I-residue_range +acids I-residue_range +) O +and O +a O +truncated B-protein_state +C O +- O +terminal O +hexahistidine B-protein_state +- I-protein_state +tagged I-protein_state +variant O +( O +amino O +acids O +1 B-residue_range +– I-residue_range +96 I-residue_range +plus O +the O +tag O +; O +herein O +EncFtnsH B-protein +). O + +In O +both O +cases O +the O +elution B-evidence +profile I-evidence +from O +size B-experimental_method +- I-experimental_method +exclusion I-experimental_method +chromatography I-experimental_method +( O +SEC B-experimental_method +) O +displayed O +two O +peaks B-evidence +( O +Figure O +2A O +). O + +SDS B-experimental_method +- I-experimental_method +PAGE I-experimental_method +analysis O +of O +fractions O +from O +these O +peaks B-evidence +showed O +that O +the O +high O +molecular B-evidence +weight I-evidence +peak O +was O +partially O +resistant O +to O +SDS O +and O +heat O +- O +induced O +denaturation O +; O +in O +contrast O +, O +the O +low O +molecular B-evidence +weight I-evidence +peak O +was O +consistent O +with O +monomeric B-oligomeric_state +mass O +of O +13 O +kDa O +( O +Figure O +2B O +). O + +MALDI B-experimental_method +peptide I-experimental_method +mass I-experimental_method +fingerprinting I-experimental_method +of O +these O +bands O +confirmed O +the O +identity O +of O +both O +as O +EncFtn B-protein +. O + +Inductively B-experimental_method +coupled I-experimental_method +plasma I-experimental_method +mass I-experimental_method +spectrometry I-experimental_method +( O +ICP B-experimental_method +- I-experimental_method +MS I-experimental_method +) O +analysis O +of O +the O +SEC B-experimental_method +fractions O +showed O +100 O +times O +more O +iron B-chemical +in O +the O +oligomeric O +fraction O +than O +the O +monomer B-oligomeric_state +( O +Figure O +2A O +, O +blue O +scatter O +points O +; O +Table O +1 O +), O +suggesting O +that O +EncFtn B-protein +oligomerization O +is O +associated O +with O +iron B-chemical +binding O +. O + +In O +order O +to O +determine O +the O +iron B-chemical +- O +loading O +stoichiometry O +in O +the O +EncFtn B-protein +complex O +, O +further O +ICP B-experimental_method +- I-experimental_method +MS I-experimental_method +experiments O +were O +performed O +using O +selenomethionine B-chemical +( O +SeMet B-chemical +)- O +labelled O +protein O +EncFtn B-protein +( O +Table O +1 O +). O + +In O +these O +experiments O +, O +we O +observed O +sub O +- O +stoichiometric O +metal O +binding O +, O +which O +is O +in O +contrast O +to O +the O +classical B-protein_state +ferritins B-protein_type +. O + +Size B-experimental_method +- I-experimental_method +exclusion I-experimental_method +chromatography I-experimental_method +with O +multi B-experimental_method +- I-experimental_method +angle I-experimental_method +laser I-experimental_method +light I-experimental_method +scattering I-experimental_method +( O +SEC B-experimental_method +- I-experimental_method +MALLS I-experimental_method +) O +analysis O +of O +samples O +taken O +from O +each O +peak O +gave O +calculated O +molecular O +weights O +consistent O +with O +a O +decamer B-oligomeric_state +for O +the O +high O +molecular B-evidence +weight I-evidence +peak O +and O +a O +monomer B-oligomeric_state +for O +the O +low O +molecular B-evidence +weight I-evidence +peak O +( O +Figure O +2C O +, O +Table O +2 O +). O + +Effect O +of O +metal O +ions O +on O +the O +oligomeric O +state O +of O +EncFtnsH B-protein +in O +solution O +. O + +( O +A O +/ O +B O +) O +EncFtnsH B-protein +- O +monomer B-oligomeric_state +was O +incubated B-experimental_method +with O +one O +mole O +equivalent O +of O +various O +metal O +salts O +for O +two O +hours O +prior O +to O +analytical B-experimental_method +gel I-experimental_method +- I-experimental_method +filtration I-experimental_method +using O +a O +Superdex O +200 O +PC O +3 O +. O +2 O +/ O +30 O +column O +. O + +Co2 B-chemical ++ I-chemical +and O +Zn2 B-chemical ++ I-chemical +induced O +the O +formation O +of O +the O +decameric B-oligomeric_state +form O +of O +EncFtnsH B-protein +; O +while O +Mn2 B-chemical ++, I-chemical +Mg2 B-chemical ++ I-chemical +and O +Fe3 B-chemical ++ I-chemical +did O +not O +significantly O +alter O +the O +oligomeric O +state O +of O +EncFtnsH B-protein +. O + +PAGE B-experimental_method +analysis O +of O +the O +effect O +of O +metal O +ions O +on O +the O +oligomeric O +state O +of O +EncFtnsH B-protein +. O + +50 O +µM O +EncFtnsH B-protein +monomer B-oligomeric_state +or O +decamer B-oligomeric_state +samples O +were O +mixed O +with O +equal O +molar O +metal O +ions O +including O +Fe2 B-chemical ++, I-chemical +Co2 B-chemical ++, I-chemical +Zn2 B-chemical ++, I-chemical +Mn2 B-chemical ++, I-chemical +Ca2 B-chemical ++, I-chemical +Mg2 B-chemical ++ I-chemical +and O +Fe3 B-chemical ++, I-chemical +which O +were O +analyzed O +by O +Native B-experimental_method +PAGE I-experimental_method +alongside O +SDS B-experimental_method +- I-experimental_method +PAGE I-experimental_method +. O + +( O +A O +) O +10 O +% O +Native B-experimental_method +PAGE I-experimental_method +analysis O +of O +EncFtnsH B-protein +monomer B-oligomeric_state +fractions O +mixed O +with O +various O +metal O +solutions O +; O +( O +B O +) O +10 O +% O +Native B-experimental_method +PAGE I-experimental_method +analysis O +of O +EncFtnsH B-protein +decamer B-oligomeric_state +fractions O +mixed O +with O +various O +metal O +solutions O +; O +( O +C O +) O +15 O +% O +SDS B-experimental_method +- I-experimental_method +PAGE I-experimental_method +analysis O +on O +the O +mixtures O +of O +EncFtnsH B-protein +monomer B-oligomeric_state +fractions O +and O +metal O +solutions O +; O +( O +D O +) O +15 O +% O +SDS B-experimental_method +- I-experimental_method +PAGE I-experimental_method +analysis O +on O +the O +mixtures O +of O +EncFtnsH B-protein +decamer B-oligomeric_state +fractions O +and O +metal O +solutions O +. O + +Effect O +of O +Fe2 B-chemical ++ I-chemical +and O +protein O +concentration O +on O +the O +oligomeric O +state O +of O +EncFtnsH B-protein +in O +solution O +. O + +( O +A O +) O +Recombinant O +EncFtnsH B-protein +was O +purified O +by O +Gel B-experimental_method +filtration I-experimental_method +Superdex O +200 O +chromatography O +from O +E B-species +. I-species +coli I-species +BL21 I-species +( I-species +DE3 I-species +) I-species +grown O +in O +MM B-experimental_method +or O +in O +MM B-experimental_method +supplemented O +with O +1 O +mM O +Fe B-chemical +( I-chemical +NH4 I-chemical +) I-chemical +2 I-chemical +( I-chemical +SO4 I-chemical +) I-chemical +2 I-chemical +( O +MM B-experimental_method ++ O +Fe2 B-chemical ++). I-chemical + +A O +higher O +proportion O +of O +decamer B-oligomeric_state +( O +peak O +between O +65 O +and O +75 O +ml O +) O +is O +seen O +in O +the O +sample O +purified O +from O +MM B-experimental_method ++ O +Fe2 B-chemical ++ I-chemical +compared O +to O +EncFtnsH B-protein +- O +MM B-experimental_method +, O +indicating O +that O +Fe2 B-chemical ++ I-chemical +facilitates O +the O +multimerization O +of O +EncFtnsH B-protein +in O +vivo O +. O +( O +B O +) O +EncFtnsH B-protein +- O +monomer B-oligomeric_state +was O +incubated O +with O +one O +molar O +equivalent O +of O +Fe2 B-chemical ++ I-chemical +salts O +for O +two O +hours O +prior O +to O +analytical B-experimental_method +gel I-experimental_method +- I-experimental_method +filtration I-experimental_method +using O +a O +Superdex O +200 O +PC O +3 O +. O +2 O +/ O +30 O +column O +( O +GE O +Healthcare O +). O + +Both O +Fe2 B-chemical ++ I-chemical +salts O +tested O +induced O +the O +formation O +of O +decamer B-oligomeric_state +indicated O +by O +the O +peak O +between O +1 O +. O +2 O +and O +1 O +. O +6 O +ml O +. O + +Monomeric B-oligomeric_state +and O +decameric B-oligomeric_state +samples O +of O +EncFtnsH B-protein +are O +shown O +as O +controls O +. O + +Peaks B-evidence +around O +0 O +. O +8 O +ml O +were O +seen O +as O +protein O +aggregation O +. O + +( O +C O +) O +Analytical B-experimental_method +gel I-experimental_method +filtration I-experimental_method +of O +EncFtn B-protein +monomer B-oligomeric_state +at O +different O +concentrations O +to O +illustrate O +the O +effect O +of O +protein O +concentration O +on O +multimerization O +. O + +The O +major O +peak O +shows O +a O +shift O +towards O +a O +dimer B-oligomeric_state +species O +at O +high O +concentration O +of O +protein O +, O +but O +the O +ratio O +of O +this O +peak O +( O +1 O +. O +5 O +– O +1 O +. O +8 O +ml O +) O +to O +the O +decamer B-oligomeric_state +peak O +( O +1 O +. O +2 O +– O +1 O +. O +5 O +ml O +) O +does O +not O +change O +when O +compared O +to O +the O +low O +concentration O +sample O +. O + +Gel B-experimental_method +- I-experimental_method +filtration I-experimental_method +peak B-evidence +area I-evidence +ratios I-evidence +for O +EncFtnsH B-protein +decamer B-oligomeric_state +and O +monomer B-oligomeric_state +on O +addition O +of O +different O +metal O +ions O +. O + +EncFtnsH B-protein +was O +produced O +in O +E B-species +. I-species +coli I-species +BL21 I-species +( I-species +DE3 I-species +) I-species +cultured O +in O +MM B-experimental_method +and O +MM B-experimental_method +with O +1 O +mM O +Fe B-chemical +( I-chemical +NH4 I-chemical +) I-chemical +2 I-chemical +( I-chemical +SO4 I-chemical +) I-chemical +2 I-chemical +( O +MM B-experimental_method ++ O +Fe2 B-chemical ++) I-chemical +and O +purified O +by O +gel B-experimental_method +- I-experimental_method +filtration I-experimental_method +chromatography I-experimental_method +using O +an O +Superdex O +200 O +16 O +/ O +60 O +column O +( O +GE O +Healthcare O +). O + +Monomer B-oligomeric_state +fractions O +of O +EncFtnsH B-protein +purified O +from O +MM B-experimental_method +were O +pooled O +and O +run O +in O +subsequent O +analytical B-experimental_method +gel I-experimental_method +- I-experimental_method +filtration I-experimental_method +runs O +over O +the O +course O +of O +three O +days O +. O + +Samples O +of O +EncFtnsH B-protein +monomer B-oligomeric_state +were O +incubated O +with O +one O +molar O +equivalent O +of O +metal O +ion O +salts O +at O +room O +temperature O +for O +two O +hours O +before O +analysis O +by O +analytical B-experimental_method +gel I-experimental_method +filtration I-experimental_method +chromatography I-experimental_method +( O +AGF B-experimental_method +) O +using O +a O +Superdex O +200 O +10 O +/ O +300 O +GL O +column O +. O + +The O +area O +for O +resulting O +protein O +peaks B-evidence +were O +calculated O +using O +the O +Unicorn O +software O +( O +GE O +Healthcare O +); O +peak B-evidence +ratios I-evidence +were O +calculated O +to O +quantify O +the O +propensity O +of O +EncFtnsH B-protein +to O +multimerize O +in O +the O +presence B-protein_state +of I-protein_state +the O +different O +metal O +ions O +. O + +The O +change O +in O +the O +ratios O +of O +monomer B-oligomeric_state +to O +decamer B-oligomeric_state +over O +the O +three O +days O +of O +experiments O +may O +be O +a O +consequence O +of O +experimental O +variability O +, O +or O +the O +propensity O +of O +this O +protein O +to O +equilibrate O +towards O +decamer B-oligomeric_state +over O +time O +. O + +The O +increased O +decamer B-oligomeric_state +: O +monomer B-oligomeric_state +ratio O +seen O +in O +the O +presence B-protein_state +of I-protein_state +Fe2 B-chemical ++, I-chemical +Co2 B-chemical ++, I-chemical +and O +Zn2 B-chemical ++ I-chemical +indicates O +that O +these O +metal O +ions O +facilitate O +multimerization O +of O +the O +EncFtnsH B-protein +protein O +, O +while O +the O +other O +metal O +ions O +tested O +do O +not O +appear O +to O +induce O +multimerization O +. O + +The O +analytical B-experimental_method +gel I-experimental_method +filtration I-experimental_method +experiment O +was O +repeated O +twice O +using O +two O +independent O +preparations O +of O +protein O +, O +of O +which O +values O +calculated O +from O +one O +sample O +are O +presented O +here O +. O + +Method O +Sample O +Monomer B-oligomeric_state +area O +Decamer B-oligomeric_state +area O +Decamer B-oligomeric_state +/ O +Monomer B-oligomeric_state +Gel B-experimental_method +filtration I-experimental_method +Superdex O +200 O +chromatography O +EncFtnsH B-protein +- O +MM B-experimental_method +64 O +. O +3 O +583 O +. O +6 O +0 O +. O +1 O +EncFtnsH B-protein +- O +MM B-experimental_method ++ O +Fe2 B-chemical ++ I-chemical +1938 O +. O +4 O +426 O +. O +4 O +4 O +. O +5 O +Analytical B-experimental_method +Gel I-experimental_method +filtration I-experimental_method +Day1 O +EncFtnsH B-protein +- O +decamer B-oligomeric_state +fractions O +20 O +. O +2 O +1 O +. O +8 O +11 O +. O +2 O +EncFtnsH B-protein +- O +monomer B-oligomeric_state +fractions O +2 O +. O +9 O +21 O +. O +9 O +0 O +. O +1 O +Fe B-chemical +( I-chemical +NH4 I-chemical +) I-chemical +2 I-chemical +( I-chemical +SO4 I-chemical +) I-chemical +2 I-chemical +/ O +EncFtnsH B-protein +- O +monomer B-oligomeric_state +11 O +. O +0 O +13 O +. O +0 O +0 O +. O +8 O +FeSO4 B-chemical +- I-chemical +HCl I-chemical +/ O +EncFtnsH B-protein +- O +monomer B-oligomeric_state +11 O +. O +3 O +11 O +. O +4 O +1 O +. O +0 O +Analytical B-experimental_method +Gel I-experimental_method +filtration I-experimental_method +Day2 O +EncFtnsH B-protein +- O +monomer B-oligomeric_state +fractions O +8 O +. O +3 O +22 O +. O +8 O +0 O +. O +4 O +CoCl2 B-chemical +/ O +EncFtnsH B-protein +- O +monomer B-oligomeric_state +17 O +. O +7 O +14 O +. O +5 O +1 O +. O +2 O +MnCl2 B-chemical +/ O +EncFtnsH B-protein +- O +monomer B-oligomeric_state +3 O +. O +1 O +30 O +. O +5 O +0 O +. O +1 O +ZnSO4 B-chemical +/ O +EncFtnsH B-protein +- O +monomer B-oligomeric_state +20 O +. O +4 O +9 O +. O +0 O +2 O +. O +3 O +FeCl3 B-chemical +/ O +EncFtnsH B-protein +- O +monomer B-oligomeric_state +3 O +. O +9 O +28 O +. O +6 O +0 O +. O +1 O +Analytical B-experimental_method +Gel I-experimental_method +filtration I-experimental_method +Day3 O +EncFtnsH B-protein +- O +monomer B-oligomeric_state +fractions O +6 O +. O +3 O +23 O +. O +4 O +0 O +. O +3 O +MgSO4 B-chemical +/ O +EncFtnsH B-protein +- O +monomer B-oligomeric_state +5 O +. O +8 O +30 O +. O +2 O +0 O +. O +2 O +Ca B-chemical +acetate I-chemical +/ O +EncFtnsH B-protein +- O +monomer B-oligomeric_state +5 O +. O +6 O +25 O +. O +2 O +0 O +. O +2 O + +We O +purified O +EncFtnsH B-protein +from O +E B-species +. I-species +coli I-species +grown O +in O +MM B-experimental_method +with O +or O +without O +the O +addition O +of O +1 O +mM O +Fe B-chemical +( I-chemical +NH4 I-chemical +) I-chemical +2 I-chemical +( I-chemical +SO4 I-chemical +) I-chemical +2 I-chemical +. O + +The O +decamer B-oligomeric_state +to O +monomer B-oligomeric_state +ratio O +in O +the O +sample O +purified O +from O +cells O +grown O +in O +iron B-chemical +- O +supplemented O +media O +was O +4 O +. O +5 O +, O +while O +that O +from O +the O +iron B-protein_state +- I-protein_state +free I-protein_state +media O +was O +0 O +. O +11 O +, O +suggesting O +that O +iron B-chemical +induces O +the O +oligomerization O +of O +EncFtnsH B-protein +in O +vivo O +( O +Figure O +3A O +, O +Table O +3 O +). O + +To O +test O +the O +metal O +- O +dependent O +oligomerization O +of O +EncFtnsH B-protein +in O +vitro O +, O +we O +incubated B-experimental_method +the O +protein O +with O +various O +metal O +cations O +and O +subjected O +samples O +to O +analytical B-experimental_method +SEC I-experimental_method +and O +non B-experimental_method +- I-experimental_method +denaturing I-experimental_method +PAGE I-experimental_method +. O + +Of O +the O +metals O +tested O +, O +only O +Fe2 B-chemical ++, I-chemical +Zn2 B-chemical ++ I-chemical +and O +Co2 B-chemical ++ I-chemical +induced O +the O +formation O +of O +significant O +amounts O +of O +the O +decamer B-oligomeric_state +( O +Figure O +3B O +, O +Figure O +3 O +— O +figure O +supplement O +1 O +/ O +2 O +). O + +While O +Fe2 B-chemical ++ I-chemical +induces O +the O +multimerization O +of O +EncFtnsH B-protein +, O +Fe3 B-chemical ++ I-chemical +in O +the O +form O +of O +FeCl3 B-chemical +does O +not O +have O +this O +effect O +on O +the O +protein O +, O +highlighting O +the O +apparent O +preference O +this O +protein O +has O +for O +the O +ferrous B-chemical +form I-chemical +of I-chemical +iron I-chemical +. O + +To O +determine O +if O +the O +oligomerization O +of O +EncFtnsH B-protein +was O +concentration O +dependent O +we O +performed O +analytical B-experimental_method +SEC I-experimental_method +at O +90 O +and O +700 O +µM O +protein O +concentration O +( O +Figure O +3C O +). O + +At O +the O +higher O +concentration O +, O +no O +increase O +in O +the O +decameric B-oligomeric_state +form O +of O +EncFtn B-protein +was O +observed O +; O +however O +, O +the O +shift O +in O +the O +major O +peak O +from O +the O +position O +of O +the O +monomer B-oligomeric_state +species O +indicated O +a O +tendency O +to O +dimerize B-oligomeric_state +at O +high O +concentration O +. O + +Crystal B-evidence +structure I-evidence +of O +EncFtnsH B-protein + +Electrostatic O +surface O +of O +EncFtnsH B-protein +. O + +The O +solvent O +accessible O +surface O +of O +EncFtnsH B-protein +is O +shown O +, O +colored O +by O +electrostatic O +potential O +as O +calculated O +using O +the O +APBS O +plugin O +in O +PyMOL O +. O + +Negatively O +charged O +regions O +are O +colored O +red O +and O +positive O +regions O +in O +blue O +, O +neutral O +regions O +in O +grey O +. O +( O +A O +) O +View O +of O +the O +surface O +of O +the O +EncFtnsH B-protein +decamer B-oligomeric_state +looking O +down O +the O +central O +axis O +. O + +( O +B O +) O +Orthogonal O +view O +of O +( O +A O +). O +( O +C O +) O +Cutaway O +view O +of O +( O +B O +) O +showing O +the O +charge O +distribution O +within O +the O +central B-site +cavity I-site +. O + +Crystal B-evidence +structure I-evidence +of O +EncFtnsH B-protein +. O + +( O +A O +) O +Overall O +architecture O +of O +EncFtnsH B-protein +. O +Transparent O +solvent O +accessible O +surface O +view O +with O +α B-structure_element +- I-structure_element +helices I-structure_element +shown O +as O +tubes O +and O +bound O +metal O +ions O +as O +spheres O +. O + +Alternating O +subunits B-structure_element +are O +colored O +blue O +and O +green O +for O +clarity O +. O + +The O +doughnut B-structure_element +- I-structure_element +like I-structure_element +decamer B-oligomeric_state +is O +7 O +nm O +in O +diameter O +and O +4 O +. O +5 O +nm O +thick O +. O +( O +B O +) O +Monomer B-oligomeric_state +of O +EncFtnsH B-protein +shown O +as O +a O +secondary O +structure O +cartoon O +. O +( O +C O +/ O +D O +) O +Dimer B-site +interfaces I-site +formed O +in O +the O +decameric B-oligomeric_state +ring B-structure_element +of O +EncFtnsH B-protein +. O +Subunits B-structure_element +are O +shown O +as O +secondary O +structure O +cartoons O +and O +colored O +blue O +and O +green O +for O +clarity O +. O + +Bound O +metal O +ions O +are O +shown O +as O +orange O +spheres O +for O +Fe3 B-chemical ++ I-chemical +and O +grey O +and O +white O +spheres O +for O +Ca2 B-chemical ++. I-chemical + +We O +determined O +the O +crystal B-evidence +structure I-evidence +of O +EncFtnsH B-protein +by O +molecular B-experimental_method +replacement I-experimental_method +to O +2 O +. O +0 O +Å O +resolution O +( O +see O +Table O +1 O +for O +X B-evidence +- I-evidence +ray I-evidence +data I-evidence +collection I-evidence +and I-evidence +refinement I-evidence +statistics I-evidence +). O + +The O +crystallographic O +asymmetric O +unit O +contained O +thirty O +monomers B-oligomeric_state +of O +EncFtn B-protein +with O +visible O +electron B-evidence +density I-evidence +for O +residues O +7 B-residue_range +– I-residue_range +96 I-residue_range +in O +each O +chain O +. O + +The O +protein O +chains O +were O +arranged O +as O +three O +identical O +annular B-structure_element +decamers B-oligomeric_state +, O +each O +with O +D5 O +symmetry O +. O + +The O +decamer B-oligomeric_state +has O +a O +diameter O +of O +7 O +nm O +and O +thickness O +of O +4 O +nm O +( O +Figure O +4A O +). O + +The O +monomer B-oligomeric_state +of O +EncFtn B-protein +has O +an O +N O +- O +terminal O +310 B-structure_element +- I-structure_element +helix I-structure_element +that O +precedes O +two O +4 O +nm O +long O +antiparallel B-structure_element +α I-structure_element +- I-structure_element +helices I-structure_element +arranged O +with O +their O +long O +axes O +at O +25 O +° O +to O +each O +other O +; O +these O +helices B-structure_element +are O +followed O +by O +a O +shorter O +1 O +. O +4 O +nm O +helix B-structure_element +projecting O +at O +70 O +° O +from O +α2 B-structure_element +( O +Figure O +4B O +). O + +The O +C B-structure_element +- I-structure_element +terminal I-structure_element +region I-structure_element +of O +the O +crystallized O +construct O +extends O +from O +the O +outer O +circumference O +of O +the O +ring B-structure_element +, O +indicating O +that O +the O +encapsulin B-site +localization I-site +sequence I-site +in O +the O +full B-protein_state +- I-protein_state +length I-protein_state +protein O +is O +on O +the O +exterior O +of O +the O +ring B-structure_element +and O +is O +thus O +free O +to O +interact O +with O +its O +binding B-site +site I-site +on O +the O +encapsulin B-protein +shell B-structure_element +protein O +. O + +The O +monomer B-oligomeric_state +of O +EncFtnsH B-protein +forms O +two O +distinct O +dimer B-site +interfaces I-site +within O +the O +decamer B-oligomeric_state +( O +Figure O +4 O +C O +/ O +D O +). O + +The O +first O +dimer B-oligomeric_state +is O +formed O +from O +two O +monomers B-oligomeric_state +arranged O +antiparallel O +to O +each O +other O +, O +with O +α1 B-structure_element +from O +each O +monomer B-oligomeric_state +interacting O +along O +their O +lengths O +and O +α3 B-structure_element +interdigitating O +with O +α2 B-structure_element +and O +α3 B-structure_element +of O +the O +partner O +chain O +. O + +This O +interface B-site +buries O +one O +third O +of O +the O +surface O +area O +from O +each O +partner O +and O +is O +stabilized O +by O +thirty O +hydrogen B-bond_interaction +bonds I-bond_interaction +and O +fourteen O +salt B-bond_interaction +bridges I-bond_interaction +( O +Figure O +4C O +). O + +The O +second O +dimer B-site +interface I-site +forms O +an O +antiparallel B-structure_element +four I-structure_element +- I-structure_element +helix I-structure_element +bundle I-structure_element +between O +helices B-structure_element +1 I-structure_element +and I-structure_element +2 I-structure_element +from O +each O +monomer B-oligomeric_state +( O +Figure O +4D O +). O + +This O +interface B-site +is O +less O +extensive O +than O +the O +first O +and O +is O +stabilized O +by O +twenty O +- O +one O +hydrogen B-bond_interaction +bonds I-bond_interaction +, O +six O +salt B-bond_interaction +bridges I-bond_interaction +, O +and O +a O +number O +of O +metal O +ions O +. O + +The O +arrangement O +of O +ten O +monomers B-oligomeric_state +in O +alternating O +orientation O +forms O +the O +decamer B-oligomeric_state +of O +EncFtn B-protein +, O +which O +assembles O +as O +a O +pentamer B-oligomeric_state +of O +dimers B-oligomeric_state +( O +Figure O +4A O +). O + +Each O +monomer B-oligomeric_state +lies O +at O +45 O +° O +relative O +to O +the O +vertical O +central O +- O +axis O +of O +the O +ring B-structure_element +, O +with O +the O +N O +- O +termini O +of O +alternating O +subunits B-structure_element +capping O +the O +center O +of O +the O +ring B-structure_element +at O +each O +end O +, O +while O +the O +C O +- O +termini O +are O +arranged O +around O +the O +circumference O +. O + +The O +central B-site +hole I-site +in O +the O +ring B-structure_element +is O +2 O +. O +5 O +nm O +at O +its O +widest O +in O +the O +center O +of O +the O +complex O +, O +and O +1 O +. O +5 O +nm O +at O +its O +narrowest O +point O +near O +the O +outer O +surface O +, O +although O +it O +should O +be O +noted O +that O +a O +number O +of O +residues O +at O +the O +N O +- O +terminus O +are O +not O +visible O +in O +the O +crystallographic B-evidence +electron I-evidence +density I-evidence +and O +these O +may O +occupy O +the O +central B-site +channel I-site +. O + +The O +surface O +of O +the O +decamer B-oligomeric_state +has O +distinct O +negatively B-site +charged I-site +patches I-site +, O +both O +within O +the O +central B-site +hole I-site +and O +on O +the O +outer O +circumference O +, O +which O +form O +spokes B-structure_element +through O +the O +radius O +of O +the O +complex O +( O +Figure O +4 O +— O +figure O +supplement O +1 O +). O + +EncFtn B-protein +ferroxidase B-site +center I-site + +Putative O +ligand B-site +- I-site +binding I-site +site I-site +in O +EncFtnsH B-protein +. O + +( O +A O +) O +Wall O +- O +eyed O +stereo O +view O +of O +the O +dimer B-site +interface I-site +of O +EncFtn B-protein +. O + +Protein O +chains O +are O +shown O +as O +sticks O +, O +with O +2mFo B-evidence +- I-evidence +DFc I-evidence +electron I-evidence +density I-evidence +shown O +in O +blue O +mesh O +and O +contoured O +at O +1 O +. O +5 O +σ O +and O +mFo B-evidence +- I-evidence +DFc I-evidence +shown O +in O +green O +mesh O +and O +contoured O +at O +3 O +σ O +. O +( O +B O +) O +Wall O +- O +eyed O +stereo O +view O +of O +putative O +metal B-site +binding I-site +site I-site +at O +the O +external O +surface O +of O +EncFtnsH B-protein +. O +Protein O +chains O +and O +electron B-evidence +density I-evidence +maps I-evidence +are O +shown O +as O +in O +( O +A O +). O + +EncFtnsH B-protein +metal B-site +binding I-site +sites I-site +. O + +( O +A O +) O +Wall O +- O +eyed O +stereo O +view O +of O +the O +metal B-site +- I-site +binding I-site +dimerization I-site +interface I-site +of O +EncFtnsH B-protein +. O +Protein O +residues O +are O +shown O +as O +sticks O +with O +blue O +and O +green O +carbons O +for O +the O +different O +subunits B-structure_element +, O +iron B-chemical +ions O +are O +shown O +as O +orange O +spheres O +and O +calcium B-chemical +as O +grey O +spheres O +, O +and O +the O +glycolic B-chemical +acid I-chemical +ligand O +is O +shown O +with O +yellow O +carbon O +atoms O +coordinated O +above O +the O +di B-site +- I-site +iron I-site +center I-site +. O + +The O +2mFo B-evidence +- I-evidence +DFc I-evidence +electron I-evidence +density I-evidence +map I-evidence +is O +shown O +as O +a O +blue O +mesh O +contoured O +at O +1 O +. O +5 O +σ O +and O +the O +NCS B-evidence +- I-evidence +averaged I-evidence +anomalous I-evidence +difference I-evidence +map I-evidence +is O +shown O +as O +an O +orange O +mesh O +and O +contoured O +at O +10 O +σ O +. O +( O +B O +) O +Iron B-chemical +coordination B-bond_interaction +within O +the O +FOC B-site +including O +residues O +Glu32 B-residue_name_number +, O +Glu62 B-residue_name_number +, O +His65 B-residue_name_number +and O +Tyr39 B-residue_name_number +from O +two O +chains O +. O + +Protein O +and O +metal O +ions O +are O +shown O +as O +in O +A O +. O +Coordination B-bond_interaction +between O +the O +protein O +and O +iron B-chemical +ions O +is O +shown O +as O +yellow O +dashed O +lines O +with O +distances O +indicated O +. O +( O +C O +) O +Coordination B-bond_interaction +of O +calcium B-chemical +within O +the O +dimer B-site +interface I-site +by O +four O +glutamic B-residue_name +acid I-residue_name +residues O +( O +E31 B-residue_name_number +and O +E34 B-residue_name_number +from O +two O +chains O +). O + +The O +calcium B-chemical +ion O +is O +shown O +as O +a O +grey O +sphere O +and O +water B-chemical +molecules O +involved O +in O +the O +coordination B-bond_interaction +of O +the O +calcium B-chemical +ion O +are O +shown O +as O +crosses O +. O +( O +D O +) O +Metal B-site +coordination I-site +site I-site +on O +the O +outer O +surface O +of O +EncFtnsH B-protein +. O +The O +two O +calcium B-chemical +ions O +are O +coordinated B-bond_interaction +by I-bond_interaction +residues O +His57 B-residue_name_number +, O +Glu61 B-residue_name_number +and O +Glu64 B-residue_name_number +from O +the O +two O +chains O +of O +the O +FOC B-site +dimer B-oligomeric_state +, O +and O +are O +located O +at O +the O +outer O +surface O +of O +the O +complex O +, O +positioned O +10 O +Å O +away O +from O +the O +FOC B-site +iron B-chemical +. O + +The O +electron B-evidence +density I-evidence +maps I-evidence +of O +the O +initial O +EncFtnsH B-protein +model O +displayed O +significant O +positive O +peaks O +in O +the O +mFo B-evidence +- I-evidence +DFc I-evidence +map I-evidence +at O +the O +center O +of O +the O +4 B-structure_element +- I-structure_element +helix I-structure_element +bundle I-structure_element +dimer B-oligomeric_state +( O +Figure O +5 O +— O +figure O +supplement O +1 O +). O + +Informed O +by O +the O +ICP B-experimental_method +- I-experimental_method +MS I-experimental_method +data O +indicating O +the O +presence B-protein_state +of I-protein_state +iron B-chemical +in O +the O +protein O +we O +collected O +diffraction B-evidence +data I-evidence +at O +the O +experimentally O +determined O +iron B-chemical +absorption O +edge O +( O +1 O +. O +74 O +Å O +) O +and O +calculated O +an O +anomalous B-evidence +difference I-evidence +Fourier I-evidence +map I-evidence +using O +this O +data O +. O + +Inspection O +of O +this O +map B-evidence +showed O +two O +10 O +- O +sigma O +peaks B-evidence +between O +residues O +Glu32 B-residue_name_number +, O +Glu62 B-residue_name_number +and O +His65 B-residue_name_number +of O +two O +adjacent O +chains O +, O +and O +a O +statistically O +smaller O +5 O +- O +sigma O +peak O +between O +residues O +Glu31 B-residue_name_number +and O +Glu34 B-residue_name_number +of O +the O +two O +chains O +. O + +Modeling O +metal O +ions O +into O +these O +peaks O +and O +refinement B-experimental_method +of O +the O +anomalous B-evidence +scattering I-evidence +parameters I-evidence +allowed O +us O +to O +identify O +these O +as O +two O +iron B-chemical +ions O +and O +a O +calcium B-chemical +ion O +respectively O +( O +Figure O +5A O +). O + +An O +additional O +region O +of O +asymmetric O +electron B-evidence +density I-evidence +near O +the O +di B-site +- I-site +iron I-site +binding I-site +site I-site +in O +the O +mFo B-evidence +- I-evidence +DFc I-evidence +map I-evidence +was O +modeled O +as O +glycolic B-chemical +acid I-chemical +, O +presumably O +a O +breakdown O +product O +of O +the O +PEG B-chemical +3350 I-chemical +used O +for O +crystallization O +. O + +This O +di B-site +- I-site +iron I-site +center I-site +has O +an O +Fe B-evidence +- I-evidence +Fe I-evidence +distance I-evidence +of O +3 O +. O +5 O +Å O +, O +Fe B-evidence +- I-evidence +Glu I-evidence +- I-evidence +O I-evidence +distances I-evidence +between O +2 O +. O +3 O +and O +2 O +. O +5 O +Å O +, O +and O +Fe B-evidence +- I-evidence +His I-evidence +- I-evidence +N I-evidence +distances I-evidence +of O +2 O +. O +5 O +Å O +( O +Figure O +5B O +). O + +This O +coordination B-bond_interaction +geometry O +is O +consistent O +with O +the O +di B-site +- I-site +nuclear I-site +ferroxidase I-site +center I-site +( O +FOC B-site +) O +found O +in O +ferritin B-protein_type +. O + +It O +is O +interesting O +to O +note O +that O +although O +we O +did O +not O +add O +any O +additional O +iron B-chemical +to O +the O +crystallization B-experimental_method +trials I-experimental_method +, O +the O +FOC B-site +was O +fully O +occupied O +with O +iron B-chemical +in O +the O +final O +structure B-evidence +, O +implying O +that O +this O +site O +has O +a O +very O +high O +affinity B-evidence +for O +iron B-chemical +. O + +The O +calcium B-chemical +ion O +coordinated B-bond_interaction +by I-bond_interaction +Glu31 B-residue_name_number +and O +Glu34 B-residue_name_number +adopts O +heptacoordinate B-protein_state +geometry O +, O +with O +coordination B-bond_interaction +distances O +of O +2 O +. O +5 O +Å O +between O +the O +metal O +ion O +and O +carboxylate O +oxygens O +of O +Glu31 B-residue_name_number +and O +Glu34 B-residue_name_number +( O +E31 B-site +/ I-site +34 I-site +- I-site +site I-site +). O + +A O +number O +of O +ordered O +solvent O +molecules O +are O +also O +coordinated B-bond_interaction +to O +this O +metal O +ion O +at O +a O +distance O +of O +2 O +. O +5 O +Å O +. O +This O +heptacoordinate B-protein_state +geometry O +is O +common O +in O +crystal B-evidence +structures I-evidence +with O +calcium B-chemical +ions O +( O +Figure O +5C O +). O + +While O +ICP B-experimental_method +- I-experimental_method +MS I-experimental_method +indicated O +that O +there O +were O +negligible O +amounts O +of O +calcium B-chemical +in O +the O +purified O +protein O +, O +the O +presence B-protein_state +of I-protein_state +140 O +mM O +calcium B-chemical +acetate I-chemical +in O +the O +crystallization O +mother O +liquor O +favors O +the O +coordination B-bond_interaction +of O +calcium B-chemical +at O +this O +site O +. O + +The O +fact O +that O +the O +protein O +does O +not O +multimerize O +in O +solution O +in O +the O +presence B-protein_state +of I-protein_state +Fe3 B-chemical ++ I-chemical +may O +indicate O +that O +these O +metal B-site +binding I-site +sites I-site +have O +a O +lower O +affinity O +for O +the O +ferric O +form O +of O +iron B-chemical +, O +which O +is O +the O +product O +of O +the O +ferroxidase B-protein_type +reaction O +. O + +A O +number O +of O +additional O +metal O +- O +ions O +were O +present O +at O +the O +outer O +circumference O +of O +at O +least O +one O +decamer B-oligomeric_state +in O +the O +asymmetric O +unit O +( O +Figure O +5D O +). O + +These O +ions O +are O +coordinated B-bond_interaction +by I-bond_interaction +His57 B-residue_name_number +, O +Glu61 B-residue_name_number +and O +Glu64 B-residue_name_number +from O +both O +chains O +in O +the O +FOC B-site +dimer B-oligomeric_state +and O +are O +4 O +. O +5 O +Å O +apart O +; O +Fe B-evidence +- I-evidence +Glu I-evidence +- I-evidence +O I-evidence +distances O +are O +between O +2 O +. O +5 O +and O +3 O +. O +5 O +Å O +and O +the O +Fe B-evidence +- I-evidence +His I-evidence +- I-evidence +N I-evidence +distances I-evidence +are O +4 O +and O +4 O +. O +5 O +Å O +. O + +Comparison O +of O +quaternary O +structure O +of O +EncFtnsH B-protein +and O +ferritin B-protein_type +. O + +( O +A O +) O +Aligned B-experimental_method +FOC B-site +of O +EncFtnsH B-protein +and O +Pseudo B-species +- I-species +nitzschia I-species +multiseries I-species +ferritin B-protein +( O +PmFtn B-protein +). O + +The O +metal B-site +binding I-site +site I-site +residues O +from O +two O +EncFtnsH B-protein +chains O +are O +shown O +in O +green O +and O +blue O +, O +while O +the O +PmFtn B-protein +is O +shown O +in O +orange O +. O + +Fe2 B-chemical ++ I-chemical +in O +the O +FOC B-site +is O +shown O +as O +orange O +spheres O +and O +Ca2 B-chemical ++ I-chemical +in O +EncFtnsH B-protein +is O +shown O +as O +a O +grey O +sphere O +. O + +The O +two O +- O +fold O +symmetry O +axis O +of O +the O +EncFtn B-protein +FOC B-site +is O +shown O +with O +a O +grey O +arrow O +( O +B O +) O +Cross O +- O +section O +surface O +view O +of O +quaternary O +structure O +of O +EncFtnsH B-protein +and O +PmFtn B-protein +as O +aligned O +in O +( O +A O +) O +( O +dashed O +black O +box O +). O + +The O +central B-site +channel I-site +of O +EncFtnsH B-protein +is O +spatially O +equivalent O +to O +the O +outer O +surface O +of O +ferritin B-protein_type +and O +its O +outer O +surface O +corresponds O +to O +the O +mineralization B-site +surface I-site +within O +ferritin B-protein_type +. O + +Comparison B-experimental_method +of O +the O +symmetric O +metal B-site +ion I-site +binding I-site +site I-site +of O +EncFtnsH B-protein +and O +the O +ferritin B-protein_type +FOC B-site +. O + +( O +A O +) O +Structural B-experimental_method +alignment I-experimental_method +of O +the O +FOC B-site +residues O +in O +a O +dimer B-oligomeric_state +of O +EncFtnsH B-protein +( O +green O +/ O +blue O +) O +with O +a O +monomer B-oligomeric_state +of O +Pseudo B-species +- I-species +nitzschia I-species +multiseries I-species +ferritin B-protein +( O +PmFtn B-protein +) O +( O +PDBID O +: O +4ITW O +) O +( O +orange O +). O + +Iron B-chemical +ions O +are O +shown O +as O +orange O +spheres O +and O +a O +single O +calcium B-chemical +ion O +as O +a O +grey O +sphere O +. O + +Residues O +within O +the O +FOC B-site +are O +conserved B-protein_state +between O +EncFtn B-protein +and O +ferritin B-protein_type +PmFtn B-protein +, O +with O +the O +exception O +of O +residues O +in O +the O +position O +equivalent O +to O +H65 B-residue_name_number +’ O +in O +the O +second O +subunit B-oligomeric_state +in O +the O +dimer B-oligomeric_state +( O +blue O +). O + +The O +site O +in O +EncFtn B-protein +with O +bound B-protein_state +calcium B-chemical +is O +not O +present O +in O +other O +family O +members O +. O + +( O +B O +) O +Secondary O +structure O +of O +aligned B-experimental_method +dimeric B-oligomeric_state +EncFtnsH B-protein +and O +monomeric B-oligomeric_state +ferritin B-protein_type +highlighting O +the O +conserved B-protein_state +four B-structure_element +- I-structure_element +helix I-structure_element +bundle I-structure_element +. O + +EncFtnsH B-protein +monomers B-oligomeric_state +are O +shown O +in O +green O +and O +blue O +and O +aligned B-experimental_method +PmFtn B-protein +monomer B-oligomeric_state +in O +orange O +as O +in O +A O +. O +( O +C O +) O +Cartoon O +of O +secondary O +structure O +elements O +in O +EncFtn B-protein +dimer B-oligomeric_state +and O +ferritin B-protein_type +. O + +In O +the O +dimer B-oligomeric_state +of O +EncFtn B-protein +that O +forms O +the O +FOC B-site +, O +the O +C O +- O +terminus O +of O +the O +first O +monomer B-oligomeric_state +( O +green O +) O +and O +N O +- O +terminus O +of O +the O +second O +monomer B-oligomeric_state +( O +blue O +) O +correspond O +to O +the O +position O +of O +the O +long B-structure_element +linker I-structure_element +between O +α2 B-structure_element +and O +α3 B-structure_element +in O +ferritin B-protein_type +PmFtn B-protein +. O + +Structural B-experimental_method +alignment I-experimental_method +of O +the O +di B-site +- I-site +iron I-site +binding I-site +site I-site +of O +EncFtnsH B-protein +to O +the O +FOC B-site +of O +Pseudo B-species +- I-species +nitzschia I-species +multiseries I-species +ferritin B-protein_type +( O +PmFtn B-protein +, O +PDB O +ID O +: O +4ITW O +) O +reveals O +a O +striking O +similarity O +between O +the O +metal B-site +binding I-site +sites I-site +of O +EncFtnsH B-protein +and O +the O +classical B-protein_state +ferritins B-protein_type +( O +Figure O +6A O +). O + +The O +di B-site +- I-site +iron I-site +site I-site +of O +EncFtnsH B-protein +is O +by O +necessity O +symmetrical O +, O +as O +it O +is O +formed O +through O +a O +dimer B-site +interface I-site +, O +while O +the O +FOC B-site +of O +ferritin B-protein_type +does O +not O +have O +these O +constraints O +and O +varies O +in O +different O +species O +at O +a O +position O +equivalent O +to O +His65 B-residue_name_number +of O +the O +second O +EncFtn B-protein +monomer B-oligomeric_state +in O +the O +FOC B-site +interface I-site +( O +His65 B-residue_name_number +’) O +( O +Figure O +6A O +). O + +Structural B-experimental_method +superimposition I-experimental_method +of O +the O +FOCs B-site +of O +ferritin B-protein_type +and O +EncFtn B-protein +brings O +the O +four B-structure_element +- I-structure_element +helix I-structure_element +bundle I-structure_element +of O +the O +ferritin B-protein_type +fold O +into O +close O +alignment O +with O +the O +EncFtn B-protein +dimer B-oligomeric_state +, O +showing O +that O +the O +two O +families O +of O +proteins O +have O +essentially O +the O +same O +architecture O +around O +the O +di B-site +- I-site +iron I-site +center I-site +( O +Figure O +6B O +). O + +The O +linker B-structure_element +connecting O +helices B-structure_element +2 I-structure_element +and I-structure_element +3 I-structure_element +of O +ferritin B-protein_type +is O +congruent O +with O +the O +start O +of O +the O +C O +- O +terminal O +helix B-structure_element +of O +one O +EncFtn B-protein +monomer B-oligomeric_state +and O +the O +N O +- O +terminal O +310 B-structure_element +helix I-structure_element +of O +the O +second O +monomer B-oligomeric_state +( O +Figure O +6C O +). O + +Mass B-experimental_method +spectrometry I-experimental_method +of O +the O +EncFtn B-protein +assembly O + +Native B-experimental_method +IM I-experimental_method +- I-experimental_method +MS I-experimental_method +analysis O +of O +the O +apo B-protein_state +- O +EncFtnsH B-protein +monomer B-oligomeric_state +. O + +( O +A O +) O +Mass B-evidence +spectrum I-evidence +of O +apo B-protein_state +- O +EncFtnsH B-protein +acquired O +from O +100 O +mM O +ammonium O +acetate O +pH O +8 O +. O +0 O +under O +native B-experimental_method +MS I-experimental_method +conditions O +. O + +The O +charge B-evidence +state I-evidence +distribution O +observed O +is O +bimodal O +, O +with O +peaks B-evidence +corresponding O +to O +the O +6 O ++ O +to O +15 O ++ O +charge B-evidence +states I-evidence +of O +apo B-protein_state +- O +monomer B-oligomeric_state +EncFtnsH B-protein +( O +neutral O +average O +mass O +13 O +, O +194 O +. O +3 O +Da O +). O +( O +B O +) O +The O +arrival B-evidence +time I-evidence +distributions I-evidence +( O +ion B-evidence +mobility I-evidence +data I-evidence +) O +of O +all O +ions O +in O +the O +apo B-protein_state +- O +EncFtnsH B-protein +charge B-evidence +state I-evidence +distribution O +displayed O +as O +a O +greyscale O +heat O +map O +( O +linear O +intensity O +scale O +). O +( O +B O +) O +Right O +, O +the O +arrival B-evidence +time I-evidence +distribution I-evidence +of O +the O +6 O ++ O +( O +orange O +) O +and O +7 O ++ O +( O +green O +) O +charge B-evidence +state I-evidence +( O +dashed O +colored O +‐ O +box O +) O +has O +been O +extracted O +and O +plotted O +; O +The O +arrival B-evidence +time I-evidence +distributions I-evidence +for O +these O +ion O +is O +shown O +( O +ms O +), O +along O +with O +the O +calibrated O +collision B-evidence +cross I-evidence +section I-evidence +, O +Ω B-evidence +( O +nm2 O +). O +( O +C O +) O +The O +collision B-evidence +cross I-evidence +section I-evidence +of O +a O +single O +monomer B-oligomeric_state +unit O +from O +the O +crystal B-evidence +structure I-evidence +of O +the O +Fe B-protein_state +- I-protein_state +loaded I-protein_state +EncFtnsH B-protein +decamer B-oligomeric_state +was O +calculated O +to O +be O +15 O +. O +8 O +nm2 O +using O +IMPACT O +v O +. O +0 O +. O +9 O +. O +1 O +. O + +The O ++ O +8 O +to O ++ O +15 O +protein O +charge B-evidence +states I-evidence +have O +observed O +CCS B-evidence +between O +20 O +– O +26 O +nm2 O +, O +which O +is O +significantly O +higher O +than O +the O +calculated O +CCS B-evidence +for O +an O +EncFtnsH B-protein +monomer B-oligomeric_state +taken O +from O +the O +decameric B-oligomeric_state +assembly O +crystal B-evidence +structure I-evidence +( O +15 O +. O +8 O +nm2 O +). O + +The O +mobility B-evidence +of O +the O ++ O +7 O +charge B-evidence +state I-evidence +displays O +broad O +drift B-evidence +- I-evidence +time I-evidence +distribution I-evidence +with O +maxima O +consistent O +with O +CCS B-evidence +of O +15 O +. O +9 O +and O +17 O +. O +9 O +nm2 O +. O + +Finally O +, O +the O +6 O ++ O +charge B-evidence +state I-evidence +of O +EncFtnsH B-protein +has O +mobility B-evidence +consistent O +with O +a O +CCS B-evidence +of O +12 O +. O +3 O +nm2 O +, O +indicating O +a O +more O +compact B-protein_state +/ O +collapsed B-protein_state +structure O +. O + +It O +is O +clear O +from O +this O +data O +that O +apo B-protein_state +- O +EncFtnsH B-protein +exists O +in O +several O +gas O +phase O +conformations O +. O + +The O +range O +of O +charge B-evidence +states I-evidence +occupied O +by O +the O +protein O +( O +6 O ++ O +to O +15 O ++) O +and O +the O +range O +of O +CCS B-evidence +in O +which O +the O +protein O +is O +observed O +( O +12 O +. O +3 O +nm2 O +– O +26 O +nm2 O +) O +are O +both O +large O +. O + +In O +addition O +, O +many O +of O +the O +charge B-evidence +states I-evidence +observed O +have O +higher O +charge O +than O +the O +theoretical O +maximal O +charge O +on O +spherical O +globular B-protein_state +protein O +, O +as O +determined O +by O +the O +De B-experimental_method +La I-experimental_method +Mora I-experimental_method +relationship I-experimental_method +( O +ZR B-evidence += O +0 O +. O +0778m O +; O +for O +the O +EncFtnsH B-protein +monomer B-oligomeric_state +ZR B-evidence += O +8 O +. O +9 O +) O +Fernandez O +. O + +As O +described O +by O +Beveridge O +et O +al O +., O +all O +these O +factors O +are O +indicative O +of O +a O +disordered B-protein_state +protein O +. O + +Gas O +- O +phase O +disassembly O +of O +the O +holo B-protein_state +- O +EncFtnsH B-protein +decameric B-oligomeric_state +assembly O +. O + +The O +entire O +charge B-evidence +state I-evidence +distribution O +of O +the O +Fe B-protein_state +- I-protein_state +loaded I-protein_state +holo B-protein_state +- O +EncFtnsH B-protein +assembly O +( O +green O +circles O +) O +was O +subject O +to O +collisional B-experimental_method +- I-experimental_method +induced I-experimental_method +dissociation I-experimental_method +( O +CID B-experimental_method +) O +by O +increasing O +the O +source O +cone O +voltage O +to O +200 O +V O +and O +the O +trap O +voltage O +to O +50 O +V O +. O +The O +resulting O +CID B-experimental_method +mass B-evidence +spectrum I-evidence +( O +A O +) O +revealed O +that O +dissociation O +of O +the O +holo B-protein_state +- O +EncFtnsH B-protein +decamer B-oligomeric_state +primarily O +occurred O +via O +ejection O +of O +a O +highly O +charged O +monomer B-oligomeric_state +( O +blue O +circles O +), O +leaving O +the O +‘ O +stripped B-protein_state +’ O +complex O +( O +a O +9mer B-oligomeric_state +; O +118 O +. O +7 O +kDa O +; O +yellow O +circles O +). O + +The O +mass O +of O +the O +ejected O +- O +monomer B-oligomeric_state +is O +consistent O +with O +apo B-protein_state +- O +EncFtnsH B-protein +( O +13 O +. O +2 O +kDa O +), O +suggesting O +unfolding O +of O +the O +monomer B-oligomeric_state +( O +and O +loss B-protein_state +of I-protein_state +Fe B-chemical +) O +occurs O +during O +ejection O +from O +the O +complex O +. O + +This O +observation O +of O +asymmetric O +charge O +partitioning O +of O +the O +sub O +- O +complexes O +with O +respect O +to O +the O +mass O +of O +the O +complex O +is O +consistent O +with O +the O +' O +typical O +' O +pathway O +of O +dissociation O +of O +protein O +assemblies O +by O +CID B-experimental_method +, O +as O +described O +by O +. O + +In O +addition O +, O +a O +third O +, O +lower O +abundance O +, O +charge B-evidence +state I-evidence +distribution O +is O +observed O +which O +overlaps O +the O +EncFtn B-protein +ejected O +monomer B-oligomeric_state +charge B-evidence +state I-evidence +distribution O +; O +this O +region O +of O +the O +spectrum O +is O +highlighted O +in O +( O +B O +). O + +This O +distribution O +is O +consistent O +with O +an O +ejected O +EncFtnsH B-protein +dimer B-oligomeric_state +( O +orange O +circles O +). O + +Interestingly O +, O +closer O +analysis O +of O +the O +individual O +charge B-evidence +state I-evidence +of O +this O +dimeric B-oligomeric_state +CID B-experimental_method +product O +shows O +that O +this O +sub O +- O +complex O +exists O +in O +three O +forms O +– O +displaying O +mass O +consistent O +with O +an O +EncFtnsH B-protein +dimer B-oligomeric_state +binding O +0 O +, O +1 O +, O +and O +2 O +Fe B-chemical +ions O +. O + +This O +is O +highlighted O +in O +( O +C O +), O +where O +the O +15 O ++ O +charge B-evidence +state I-evidence +of O +the O +EncFtnsH B-protein +dimer B-oligomeric_state +is O +shown O +; O +3 O +peaks B-evidence +are O +observed O +with O +m O +/ O +z O +1760 O +. O +5 O +, O +1763 O +. O +8 O +, O +and O +1767 O +. O +0 O +Th O +– O +the O +lowest O +peak O +corresponds O +to O +neutral O +masses O +of O +26392 O +. O +5 O +Da O +[ O +predicted O +EncFtnsH B-protein +dimer B-oligomeric_state +, O +( O +C572H884N172O185S2 O +) O +2 O +; O +26388 O +. O +6 O +Da O +]. O + +The O +two O +further O +peaks B-evidence +have O +a O +delta O +- O +mass O +of O +~+ O +50 O +Da O +, O +consistent O +with O +Fe B-chemical +binding O +. O + +We O +interpret O +these O +observations O +as O +partial O +‘ O +atypical O +’ O +CID B-experimental_method +fragmentation O +of O +the O +decameric B-oligomeric_state +complex O +– O +i O +. O +e O +. O +fragmentation O +of O +the O +initial O +complex O +with O +retention O +of O +subunit O +and O +ligand O +interactions O +. O + +We O +postulate O +the O +high O +stability O +of O +this O +iron B-protein_state +- I-protein_state +bound I-protein_state +dimer B-oligomeric_state +sub O +- O +complex O +is O +due O +to O +the O +metal B-chemical +coordination B-bond_interaction +at O +the O +dimer B-site +interface I-site +, O +increasing O +the O +strength O +of O +the O +dimer B-site +interface I-site +. O + +Taken O +together O +, O +these O +observations O +support O +our O +findings O +that O +the O +topology O +of O +the O +decameric B-oligomeric_state +EncFtnsH B-protein +assembly O +is O +arranged O +as O +a O +pentamer B-oligomeric_state +of O +dimers B-oligomeric_state +, O +with O +two O +Fe B-chemical +ions O +at O +each O +dimer B-site +interface I-site +. O + +Native B-experimental_method +mass I-experimental_method +spectrometry I-experimental_method +and O +ion B-experimental_method +mobility I-experimental_method +analysis I-experimental_method +of O +iron B-chemical +loading O +in O +EncFtnsH B-protein +. O + +All O +spectra B-evidence +were O +acquired O +in O +100 O +mM O +ammonium O +acetate B-chemical +, O +pH O +8 O +. O +0 O +with O +a O +protein O +concentration O +of O +5 O +µM O +. O +( O +A O +) O +Native B-experimental_method +nanoelectrospray I-experimental_method +ionization I-experimental_method +( O +nESI B-experimental_method +) O +mass B-experimental_method +spectrometry I-experimental_method +of O +EncFtnsH B-protein +at O +varying O +iron B-chemical +concentrations O +. O + +A1 O +, O +nESI B-experimental_method +spectrum B-evidence +of O +iron B-protein_state +- I-protein_state +free I-protein_state +EncFtnsH B-protein +displays O +a O +charge B-evidence +state I-evidence +distribution O +consistent O +with O +EncFtnsH B-protein +monomer B-oligomeric_state +( O +blue O +circles O +, O +13 O +, O +194 O +Da O +). O + +Addition O +of O +100 O +µM O +( O +A2 O +) O +and O +300 O +µM O +( O +A3 O +) O +Fe2 B-chemical ++ I-chemical +results O +in O +the O +appearance O +of O +a O +second O +higher O +molecular B-evidence +weight I-evidence +charge B-evidence +state I-evidence +distribution O +consistent O +with O +a O +decameric B-oligomeric_state +assembly O +of O +EncFtnsH B-protein +( O +green O +circles O +, O +132 O +. O +6 O +kDa O +). O + +( O +B O +) O +Ion B-experimental_method +mobility I-experimental_method +( I-experimental_method +IM I-experimental_method +)- I-experimental_method +MS I-experimental_method +of O +the O +iron B-protein_state +- I-protein_state +bound I-protein_state +holo B-protein_state +- O +EncFtnsH B-protein +decamer B-oligomeric_state +. O + +Top O +, O +Peaks B-evidence +corresponding O +to O +the O +22 O ++ O +to O +26 O ++ O +charge B-evidence +states I-evidence +of O +a O +homo B-oligomeric_state +- I-oligomeric_state +decameric I-oligomeric_state +assembly O +of O +EncFtnsH B-protein +are O +observed O +( O +132 O +. O +6 O +kDa O +). O + +Top O +Insert O +, O +Analysis O +of O +the O +24 O ++ O +charge B-evidence +state I-evidence +of O +the O +assembly O +at O +m O +/ O +z O +5528 O +. O +2 O +Th O +. O + +The O +theoretical O +average O +m O +/ O +z O +of O +the O +24 O ++ O +charge B-evidence +state I-evidence +with O +no O +additional O +metals O +bound O +is O +marked O +by O +a O +red O +line O +( O +5498 O +. O +7 O +Th O +); O +the O +observed O +m O +/ O +z O +of O +the O +24 O ++ O +charge B-evidence +state I-evidence +indicates O +that O +the O +EncFtnsH B-protein +assembly O +binds O +between O +10 O +( O +green O +line O +, O +5521 O +. O +1 O +Th O +) O +and O +15 O +Fe B-chemical +ions O +( O +blue O +line O +, O +5532 O +. O +4 O +Th O +) O +per O +decamer B-oligomeric_state +. O + +Bottom O +, O +The O +arrival B-evidence +time I-evidence +distributions I-evidence +( O +ion B-evidence +mobility I-evidence +data I-evidence +) O +of O +all O +ions O +in O +the O +EncFtnsH B-protein +charge B-evidence +state I-evidence +distribution O +displayed O +as O +a O +greyscale O +heat O +map O +( O +linear O +intensity O +scale O +). O + +Bottom O +right O +, O +The O +arrival B-evidence +time I-evidence +distribution I-evidence +of O +the O +24 O ++ O +charge B-evidence +state I-evidence +( O +dashed O +blue O +box O +) O +has O +been O +extracted O +and O +plotted O +. O + +The O +drift B-evidence +time I-evidence +for O +this O +ion O +is O +shown O +( O +ms O +), O +along O +with O +the O +calibrated O +collision B-evidence +cross I-evidence +section I-evidence +( O +CCS B-evidence +), O +Ω B-evidence +( O +nm2 O +). O + +In O +order O +to O +confirm O +the O +assignment O +of O +the O +oligomeric O +state O +of O +EncFtnsH B-protein +and O +investigate O +further O +the O +Fe2 B-chemical ++- I-chemical +dependent O +assembly O +, O +we O +used O +native B-experimental_method +nano I-experimental_method +- I-experimental_method +electrospray I-experimental_method +ionization I-experimental_method +( O +nESI B-experimental_method +) O +and O +ion B-experimental_method +- I-experimental_method +mobility I-experimental_method +mass I-experimental_method +spectrometry I-experimental_method +( O +IM B-experimental_method +- I-experimental_method +MS I-experimental_method +). O + +As O +described O +above O +, O +by O +recombinant B-experimental_method +production I-experimental_method +of O +EncFtnsH B-protein +in O +minimal O +media O +we O +were O +able O +to O +limit O +the O +bioavailability O +of O +iron B-chemical +. O + +Native B-experimental_method +MS I-experimental_method +analysis O +of O +EncFtnsH B-protein +produced O +in O +this O +way O +displayed O +a O +charge B-evidence +state I-evidence +distribution O +consistent O +with O +an O +EncFtnsH B-protein +monomer B-oligomeric_state +( O +blue O +circles O +, O +Figure O +7A1 O +) O +with O +an O +average O +neutral O +mass O +of O +13 O +, O +194 O +Da O +, O +in O +agreement O +with O +the O +predicted O +mass O +of O +the O +EncFtnsH B-protein +protein O +( O +13 O +, O +194 O +. O +53 O +Da O +). O + +Titration B-experimental_method +with O +Fe2 B-chemical ++ I-chemical +directly O +before O +native B-experimental_method +MS I-experimental_method +analysis O +resulted O +in O +the O +appearance O +of O +a O +new O +charge B-evidence +state I-evidence +distribution O +, O +consistent O +with O +an O +EncFtnsH B-protein +decameric B-oligomeric_state +assembly O +(+ O +22 O +to O ++ O +26 O +; O +132 O +. O +65 O +kDa O +) O +( O +Figure O +7A2 O +/ O +3 O +). O + +After O +instrument O +optimization O +, O +the O +mass O +resolving O +power O +achieved O +was O +sufficient O +to O +assign O +iron B-chemical +- O +loading O +in O +the O +complex O +to O +between O +10 O +and O +15 O +Fe B-chemical +ions O +per O +decamer B-oligomeric_state +( O +Figure O +7B O +, O +inset O +top O +right O +), O +consistent O +with O +the O +presence B-protein_state +of I-protein_state +10 O +irons B-chemical +in O +the O +FOC B-site +and O +the O +coordination B-bond_interaction +of O +iron B-chemical +in O +the O +Glu31 B-site +/ I-site +34 I-site +- I-site +site I-site +occupied O +by O +calcium B-chemical +in O +the O +crystal B-evidence +structure I-evidence +( O +Δmass B-evidence +observed O +~ O +0 O +. O +67 O +kDa O +). O + +MS B-experimental_method +analysis O +of O +EncFtnsH B-protein +after O +addition O +of O +further O +Fe2 B-chemical ++ I-chemical +did O +not O +result O +in O +iron B-chemical +loading O +above O +this O +stoichiometry O +. O + +Therefore O +, O +the O +extent O +of O +iron B-chemical +binding O +seen O +is O +limited O +to O +the O +FOC B-site +and O +Glu31 B-site +/ I-site +34 I-site +secondary I-site +metal I-site +binding I-site +site I-site +. O + +These O +data O +suggest O +that O +the O +decameric B-oligomeric_state +assembly O +of O +EncFtnsH B-protein +does O +not O +accrue O +iron B-chemical +in O +the O +same O +manner O +as O +classical B-protein_state +ferritin B-protein_type +, O +which O +is O +able O +to O +sequester O +around O +4500 O +iron B-chemical +ions O +within O +its O +nanocage B-complex_assembly +. O + +Ion B-experimental_method +mobility I-experimental_method +analysis I-experimental_method +of O +the O +EncFtnsH B-protein +decameric B-oligomeric_state +assembly O +, O +collected O +with O +minimal O +collisional O +activation O +, O +suggested O +that O +it O +consists O +of O +a O +single O +conformation O +with O +a O +collision B-evidence +cross I-evidence +section I-evidence +( O +CCS B-evidence +) O +of O +58 O +. O +2 O +nm2 O +( O +Figure O +7B O +). O + +This O +observation O +is O +in O +agreement O +with O +the O +calculated O +CCS B-evidence +of O +58 O +. O +7 O +nm2derived O +from O +our O +crystal B-evidence +structure I-evidence +of O +the O +EncFtnsH B-protein +decamer B-oligomeric_state +. O + +By O +contrast O +, O +IM B-experimental_method +- I-experimental_method +MS I-experimental_method +measurements O +of O +the O +monomeric B-oligomeric_state +EncFtnsH B-protein +at O +pH B-protein_state +8 I-protein_state +. I-protein_state +0 I-protein_state +under O +the O +same O +instrumental O +conditions O +revealed O +that O +the O +metal B-protein_state +- I-protein_state +free I-protein_state +protein B-protein +monomer B-oligomeric_state +exists O +in O +a O +wide O +range O +of O +charge B-evidence +states I-evidence +(+ O +6 O +to O ++ O +16 O +) O +and O +adopts O +many O +conformations O +in O +the O +gas O +phase O +with O +collision O +cross O +sections O +ranging O +from O +12 O +nm2 O +to O +26 O +nm2 O +( O +Figure O +7 O +— O +figure O +supplement O +1 O +). O + +Thus O +, O +IM B-experimental_method +- I-experimental_method +MS I-experimental_method +studies O +highlight O +that O +higher O +order O +structure O +in O +EncFtnsH B-protein +is O +mediated O +/ O +stabilized O +by O +metal O +binding O +, O +an O +observation O +that O +is O +in O +agreement O +with O +our O +solution O +studies O +. O + +Taken O +together O +, O +these O +results O +suggest O +that O +di O +- O +iron B-chemical +binding O +, O +forming O +the O +FOC B-site +in O +EncFtnsH B-protein +, O +is O +required O +to O +stabilize O +the O +4 B-structure_element +- I-structure_element +helix I-structure_element +bundle I-structure_element +dimer B-site +interface I-site +, O +essentially O +reconstructing O +the O +classical B-protein_state +ferritin B-protein_type +- O +like O +fold O +; O +once O +stabilized O +, O +these O +dimers B-oligomeric_state +readily O +associate O +as O +pentamers O +, O +and O +the O +overall O +assembly O +adopts O +the O +decameric B-oligomeric_state +ring O +arrangement O +observed O +in O +the O +crystal B-evidence +structure I-evidence +. O + +We O +subsequently O +performed O +gas O +phase O +disassembly O +of O +the O +decameric B-oligomeric_state +EncFtnsH B-protein +using O +collision B-experimental_method +- I-experimental_method +induced I-experimental_method +dissociation I-experimental_method +( O +CID B-experimental_method +) O +tandem B-experimental_method +mass I-experimental_method +spectrometry I-experimental_method +. O + +Under O +the O +correct O +CID B-experimental_method +conditions O +, O +protein O +assemblies O +can O +dissociate O +with O +retention O +of O +subunit O +and O +ligand O +interactions O +, O +and O +thus O +provide O +structurally O +- O +informative O +evidence O +as O +to O +the O +topology O +of O +the O +original O +assembly O +; O +this O +has O +been O +termed O +‘ O +atypical O +’ O +dissociation O +. O + +For O +EncFtnsH B-protein +, O +this O +atypical O +dissociation O +pathway O +was O +clearly O +evident O +; O +CID B-experimental_method +of O +the O +EncFtnsH B-protein +decamer B-oligomeric_state +resulted O +in O +the O +appearance O +of O +a O +dimeric B-oligomeric_state +EncFtnsH B-protein +subcomplex O +containing O +0 O +, O +1 O +, O +or O +2 O +iron B-chemical +ions O +( O +Figure O +7 O +— O +figure O +supplement O +2 O +). O + +In O +light O +of O +the O +crystal B-evidence +structure I-evidence +, O +this O +observation O +can O +be O +rationalized O +as O +dissociation O +of O +the O +EncFtnsH B-protein +decamer B-oligomeric_state +by O +disruption O +of O +the O +non B-site +- I-site +FOC I-site +interface I-site +with O +at O +least O +partial O +retention O +of O +the O +FOC B-site +interface I-site +and O +the O +FOC B-site +- O +Fe B-chemical +. O + +Thus O +, O +this O +observation O +supports O +our O +crystallographic O +assignment O +of O +the O +overall O +topology O +of O +the O +EncFtnsH B-protein +assembly O +as O +a O +pentameric B-oligomeric_state +assembly O +of O +dimers B-oligomeric_state +with O +two O +iron B-chemical +ions O +located O +at O +the O +FOC B-site +dimer I-site +interface I-site +. O + +In O +addition O +, O +this O +analysis O +provides O +evidence O +that O +the O +overall O +architecture O +of O +the O +complex O +is O +consistent O +in O +the O +crystal B-evidence +, O +solution O +and O +gas O +phases O +. O + +Ferroxidase B-protein_type +activity O + +TEM B-experimental_method +visualization O +of O +iron B-protein_state +- I-protein_state +loaded I-protein_state +bacterial B-taxonomy_domain +nanocompartments B-complex_assembly +and O +ferritin B-protein_type +. O + +Decameric B-oligomeric_state +EncFtnsH B-protein +, O +encapsulin B-protein +, O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +and O +apoferritin B-protein_state +, O +at O +8 O +. O +5 O +µM O +, O +were O +mixed O +with O +147 O +µM O +, O +1 O +mM O +, O +1 O +mM O +and O +215 O +µM O +acidic O +Fe B-chemical +( I-chemical +NH4 I-chemical +) I-chemical +2 I-chemical +( I-chemical +SO4 I-chemical +) I-chemical +2 I-chemical +, O +respectively O +. O + +Protein O +mixtures O +were O +incubated O +at O +room O +temperature O +for O +1 O +hr O +prior O +to O +TEM B-experimental_method +analysis O +with O +or O +without O +uranyl B-chemical +acetate I-chemical +stain O +. O + +( O +A O +– O +D O +) O +Unstained O +EncFtnsH B-protein +, O +encapsulin B-protein +, O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +, O +apoferritin B-protein_state +loaded B-protein_state +with I-protein_state +Fe2 B-chemical ++, I-chemical +respectively O +, O +with O +35 O +, O +000 O +x O +magnification O +and O +scale O +bars O +indicate O +100 O +nm O +. O +( O +E O +) O +Protein O +- O +free O +sample O +as O +a O +control O +. O +( O +F O +– O +I O +) O +Stained B-experimental_method +EncFtnsH B-protein +, O +encapsulin B-protein +, O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +, O +apoferritin B-protein_state +loaded B-protein_state +with I-protein_state +Fe2 B-chemical ++, I-chemical +respectively O +, O +with O +140 O +, O +000 O +x O +magnification O +and O +scale O +bars O +indicate O +25 O +nm O +. O + +Spectroscopic O +evidence O +for O +the O +ferroxidase B-protein_type +activity O +and O +comparison O +of O +iron B-chemical +loading O +capacity O +of O +apoferritin B-protein_state +, O +EncFtnsH B-protein +, O +encapsulin B-protein +, O +and O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +. O + +( O +A O +) O +Apoferritin B-protein_state +( O +10 O +μM O +monomer B-oligomeric_state +concentration O +) O +and O +EncFtnsH B-protein +decamer B-oligomeric_state +fractions O +( O +20 O +μM O +monomer B-oligomeric_state +concentration O +, O +10 O +μM O +FOC B-site +concentration O +) O +were O +incubated O +with O +20 O +and O +100 O +μM O +iron B-chemical +( O +2 O +and O +10 O +times O +molar O +equivalent O +Fe2 B-chemical ++ I-chemical +per O +FOC B-site +) O +and O +progress B-evidence +curves I-evidence +of O +the O +oxidation O +of O +Fe2 B-chemical ++ I-chemical +to O +Fe3 B-chemical ++ I-chemical +at O +315 O +nm O +were O +recorded O +in O +a O +spectrophotometer O +. O + +The O +background O +oxidation O +of O +iron B-chemical +at O +20 O +and O +100 O +μM O +in O +enzyme O +- O +free O +controls O +are O +shown O +for O +reference O +. O +( O +B O +) O +Encapsulin B-protein +and O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +complexes O +at O +10 O +μM O +asymmetric O +unit O +concentration O +were O +incubated B-experimental_method +with O +Fe2 B-chemical ++ I-chemical +at O +20 O +and O +100 O +μM O +and O +progress B-evidence +curves I-evidence +for O +iron B-chemical +oxidation O +at O +A315 O +were O +measured O +in O +a O +UV B-experimental_method +/ I-experimental_method +visible I-experimental_method +spectrophotometer I-experimental_method +. O + +Enzyme O +free O +controls O +for O +background O +oxidation O +of O +Fe2 B-chemical ++ I-chemical +are O +shown O +for O +reference O +. O +( O +C O +) O +Histogram O +of O +the O +iron B-chemical +loading O +capacity O +per O +biological O +assembly O +of O +EncFtnsH B-protein +, O +encapsulin B-protein +, O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +and O +apoferritin B-protein_state +. O + +The O +results O +shown O +are O +for O +three O +technical O +replicates O +and O +represent O +the O +optimal O +iron B-chemical +loading O +by O +the O +complexes O +after O +three O +hours O +when O +incubated O +with O +Fe2 B-chemical ++. I-chemical + +In O +light O +of O +the O +identification O +of O +an O +iron B-protein_state +- I-protein_state +loaded I-protein_state +FOC B-site +in O +the O +crystal B-evidence +structure I-evidence +of O +EncFtn B-protein +and O +our O +native B-experimental_method +mass I-experimental_method +spectrometry I-experimental_method +data O +, O +we O +performed O +ferroxidase B-experimental_method +and I-experimental_method +peroxidase I-experimental_method +assays I-experimental_method +to O +demonstrate O +the O +catalytic O +activity O +of O +this O +protein O +. O + +In O +addition O +, O +we O +also O +assayed O +equine B-taxonomy_domain +apoferritin B-protein_state +, O +an O +example O +of O +a O +classical B-protein_state +ferritin B-protein_type +enzyme O +, O +as O +a O +positive O +control O +. O + +Unlike O +the O +Dps B-protein_type +family I-protein_type +of O +ferritin B-protein_type +- I-protein_type +like I-protein_type +proteins I-protein_type +, O +EncFtn B-protein +showed O +no O +peroxidase O +activity O +when O +assayed O +with O +the O +substrate O +ortho B-chemical +- I-chemical +phenylenediamine I-chemical +. O + +The O +ferroxidase B-protein_type +activity O +of O +EncFtnsH B-protein +was O +measured O +by O +recording O +the O +progress B-evidence +curve I-evidence +of O +Fe2 B-chemical ++ I-chemical +oxidation O +to O +Fe3 B-chemical ++ I-chemical +at O +315 O +nm O +after O +addition O +of O +20 O +and O +100 O +µM O +Fe2 B-chemical ++ I-chemical +( O +2 O +and O +10 O +times O +molar O +ratio O +Fe2 B-chemical ++/ I-chemical +FOC B-site +). O + +In O +both O +experiments O +the O +rate O +of O +oxidation O +was O +faster O +than O +background O +oxidation O +of O +Fe2 B-chemical ++ I-chemical +by O +molecular O +oxygen B-chemical +, O +and O +was O +highest O +for O +100 O +µM O +Fe2 B-chemical ++ I-chemical +( O +Figure O +8A O +). O + +These O +data O +show O +that O +recombinant O +EncFtnsH B-protein +acts O +as O +an O +active B-protein_state +ferroxidase B-protein_type +enzyme O +. O + +When O +compared O +to O +apoferritin B-protein_state +, O +EncFtnsH B-protein +oxidized O +Fe2 B-chemical ++ I-chemical +at O +a O +slower O +rate O +and O +the O +reaction O +did O +not O +run O +to O +completion O +over O +the O +1800 O +s O +of O +the O +experiment O +. O + +Addition O +of O +higher O +quantities O +of O +iron B-chemical +resulted O +in O +the O +formation O +of O +a O +yellow O +/ O +red O +precipitate O +at O +the O +end O +of O +the O +reaction O +. O + +We O +also O +performed O +these O +assays O +on O +purified O +recombinant O +encapsulin B-protein +; O +which O +, O +when O +assayed O +alone O +, O +did O +not O +display O +ferroxidase B-protein_type +activity O +above O +background O +Fe2 B-chemical ++ I-chemical +oxidation O +( O +Figure O +8B O +). O + +In O +contrast O +, O +complexes O +of O +the O +full B-protein_state +EncFtn B-protein +encapsulin B-protein +nanocompartment B-complex_assembly +( O +i O +. O +e O +. O +the O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +protein O +complex O +) O +displayed O +ferroxidase B-protein_type +activity O +comparable O +to O +apoferritin B-protein_state +without O +the O +formation O +of O +precipitates O +( O +Figure O +8B O +). O + +We O +attributed O +the O +precipitates O +observed O +in O +the O +EncFtnsH B-protein +ferroxidase B-experimental_method +assay I-experimental_method +to O +the O +production O +of O +insoluble O +Fe3 B-chemical ++ I-chemical +complexes O +, O +which O +led O +us O +to O +propose O +that O +EncFtn B-protein +does O +not O +directly O +store O +Fe3 B-chemical ++ I-chemical +in O +a O +mineral O +form O +. O + +This O +observation O +agrees O +with O +native B-experimental_method +MS I-experimental_method +results O +, O +which O +indicates O +a O +maximum O +iron B-chemical +loading O +of O +10 O +– O +15 O +iron B-chemical +ions O +per O +decameric B-oligomeric_state +EncFtn B-protein +; O +and O +the O +structure B-evidence +, O +which O +does O +not O +possess O +the O +enclosed O +iron B-site +- I-site +storage I-site +cavity I-site +characteristic O +of O +classical B-protein_state +ferritins B-protein_type +and O +Dps B-protein_type +family I-protein_type +proteins I-protein_type +that O +can O +directly O +accrue O +mineralized O +Fe3 B-chemical ++ I-chemical +within O +their O +nanocompartment B-complex_assembly +structures B-evidence +. O + +To O +analyze O +the O +products O +of O +these O +reactions O +and O +determine O +whether O +the O +EncFtn B-protein +and O +encapsulin B-protein +were O +able O +to O +store O +iron B-chemical +in O +a O +mineral O +form O +, O +we O +performed O +TEM B-experimental_method +on O +the O +reaction O +mixtures O +from O +the O +ferroxidase B-experimental_method +assay I-experimental_method +. O + +The O +EncFtnsH B-protein +reaction O +mixture O +showed O +the O +formation O +of O +large O +, O +irregular O +electron O +- O +dense O +precipitates O +( O +Figure O +8 O +— O +figure O +supplement O +1A O +). O + +A O +similar O +distribution O +of O +particles O +was O +observed O +after O +addition O +of O +Fe2 B-chemical ++ I-chemical +to O +the O +encapsulin B-protein +protein O +( O +Figure O +8 O +— O +figure O +supplement O +1B O +). O + +In O +contrast O +, O +addition O +of O +Fe2 B-chemical ++ I-chemical +to O +the O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +nanocompartment B-complex_assembly +resulted O +in O +small O +, O +highly O +regular O +, O +electron O +dense O +particles O +of O +approximately O +5 O +nm O +in O +diameter O +( O +Figure O +8 O +— O +figure O +supplement O +1C O +); O +we O +interpret O +these O +observations O +as O +controlled O +mineralization O +of O +iron B-chemical +within O +the O +nanocompartment B-complex_assembly +. O + +Addition O +of O +Fe2 B-chemical ++ I-chemical +to O +apoferritin B-protein_state +resulted O +in O +a O +mixture O +of O +large O +particles O +and O +small O +(~ O +2 O +nm O +) O +particles O +consistent O +with O +partial O +mineralization O +by O +the O +ferritin B-protein_type +and O +some O +background O +oxidation O +of O +the O +iron B-chemical +( O +Figure O +8 O +— O +figure O +supplement O +1D O +). O + +Negative B-experimental_method +stain I-experimental_method +TEM I-experimental_method +of O +these O +samples O +revealed O +that O +upon O +addition O +of O +iron B-chemical +, O +the O +EncFtnsH B-protein +protein O +showed O +significant O +aggregation O +( O +Figure O +8 O +— O +figure O +supplement O +1F O +); O +while O +the O +encapsulin B-protein +, O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +system O +, O +and O +apoferritin B-protein_state +are O +present O +as O +distinct O +nanocompartments B-complex_assembly +without O +significant O +protein O +aggregation O +( O +Figure O +8 O +— O +figure O +supplement O +1G O +– O +I O +). O + +Iron B-chemical +storage O +in O +encapsulin B-protein +nanocompartments B-complex_assembly + +The O +results O +of O +the O +ferroxidase B-experimental_method +assay I-experimental_method +and O +micrographs B-evidence +of O +the O +reaction O +products O +suggest O +that O +the O +oxidation O +and O +mineralization O +function O +of O +the O +classical B-protein_state +ferritins B-protein_type +are O +split O +between O +the O +EncFtn B-protein +and O +encapsulin B-protein +proteins O +, O +with O +the O +EncFtn B-protein +acting O +as O +a O +ferroxidase B-protein_type +and O +the O +encapsulin B-protein +shell B-structure_element +providing O +an O +environment O +and O +template O +for O +iron B-chemical +mineralization O +and O +storage O +. O + +To O +investigate O +this O +further O +, O +we O +added O +Fe2 B-chemical ++ I-chemical +at O +various O +concentrations O +to O +samples O +of O +apo B-protein_state +- O +ferritin B-protein_type +, O +EncFtn B-protein +, O +isolated O +encapsulin B-protein +, O +and O +the O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +protein O +complex O +, O +and O +subjected O +these O +samples O +to O +a O +ferrozine B-experimental_method +assay I-experimental_method +to O +quantify O +the O +amount O +of O +iron B-chemical +associated O +with O +the O +proteins O +after O +three O +hours O +of O +incubation O +. O + +The O +maximum O +iron B-chemical +loading O +capacity O +of O +these O +systems O +was O +calculated O +as O +the O +quantity O +of O +iron B-chemical +per O +biological O +assembly O +( O +Figure O +8C O +). O + +In O +this O +assay O +, O +the O +EncFtnsH B-protein +decamer B-oligomeric_state +binds O +a O +maximum O +of O +around O +48 O +iron B-chemical +ions O +before O +excess O +iron B-chemical +induces O +protein O +precipitation O +. O + +The O +encapsulin B-protein +shell B-structure_element +protein O +can O +sequester O +about O +2200 O +iron B-chemical +ions O +before O +significant O +protein O +loss O +occurs O +, O +and O +the O +reconstituted O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +nanocompartment B-complex_assembly +sequestered O +about O +4150 O +iron B-chemical +ions O +. O + +This O +latter O +result O +is O +significantly O +more O +than O +the O +apoferritin B-protein_state +used O +in O +our O +assay O +, O +which O +sequesters O +approximately O +570 O +iron B-chemical +ions O +in O +this O +assay O +( O +Figure O +8C O +, O +Table O +5 O +). O + +Consideration O +of O +the O +functional O +oligomeric O +states O +of O +these O +proteins O +, O +where O +EncFtn B-protein +is O +a O +decamer B-oligomeric_state +and O +encapsulin B-protein +forms O +an O +icosahedral B-protein_state +cage B-complex_assembly +, O +and O +estimation O +of O +the O +iron B-chemical +loading O +capacity O +of O +these O +complexes O +gives O +insight O +into O +the O +role O +of O +the O +two O +proteins O +in O +iron B-chemical +storage O +and O +mineralization O +. O + +EncFtn B-protein +decamers B-oligomeric_state +bind O +up O +to O +48 O +iron B-chemical +ions O +( O +Figure O +8C O +), O +which O +is O +significantly O +higher O +than O +the O +stoichiometry O +of O +fifteen O +metal O +ions O +visible O +in O +the O +FOC B-site +and O +E31 B-site +/ I-site +34 I-site +- I-site +site I-site +of O +the O +crystal B-evidence +structure I-evidence +of O +the O +EncFtnsH B-protein +decamer B-oligomeric_state +and O +our O +MS B-experimental_method +analysis O +. O + +The O +discrepancy O +between O +these O +solution B-experimental_method +measurements I-experimental_method +and O +our O +MS B-experimental_method +analysis O +may O +indicate O +that O +there O +are O +additional O +metal B-site +- I-site +binding I-site +sites I-site +on O +the O +interior O +channel B-site +and O +exterior O +faces O +of O +the O +protein O +; O +this O +is O +consistent O +with O +our O +identification O +of O +a O +number O +of O +weak O +metal B-site +- I-site +binding I-site +sites I-site +at O +the O +surface O +of O +the O +protein O +in O +the O +crystal B-evidence +structure I-evidence +( O +Figure O +5D O +). O + +These O +observations O +are O +consistent O +with O +hydrated O +Fe2 B-chemical ++ I-chemical +ions O +being O +channeled O +to O +the O +active B-site +site I-site +from O +the O +E31 B-site +/ I-site +34 I-site +- I-site +site I-site +and O +the O +subsequent O +exit O +of O +Fe3 B-chemical ++ I-chemical +products O +on O +the O +outer O +surface O +, O +as O +is O +seen O +in O +other O +ferritin B-protein_type +family O +proteins O +. O + +While O +the O +isolated O +encapsulin B-protein +shell B-structure_element +does O +not O +display O +any O +ferroxidase B-protein_type +activity O +, O +it O +binds O +around O +2200 O +iron B-chemical +ions O +in O +our O +assay O +( O +Table O +5 O +). O + +This O +implies O +that O +the O +shell B-structure_element +can O +bind O +a O +significant O +amount O +of O +iron B-chemical +on O +its O +outer O +and O +inner O +surfaces O +. O + +While O +the O +maximum O +reported O +loading O +capacity O +of O +classical B-protein_state +ferritins B-protein_type +is O +approximately O +4500 O +iron B-chemical +ions O +, O +in O +our O +assay O +system O +we O +were O +only O +able O +to O +load O +apoferritin B-protein_state +with O +around O +570 O +iron B-chemical +ions O +. O + +However O +, O +the O +recombinant O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +nanocompartment B-complex_assembly +was O +able O +to O +bind O +over O +4100 O +iron B-chemical +ions O +in O +the O +same O +time O +period O +, O +over O +seven O +times O +the O +amount O +seen O +for O +the O +apoferritin B-protein_state +. O + +We O +note O +we O +do O +not O +reach O +the O +experimental O +maximum O +iron B-chemical +loading O +for O +apoferritin B-protein_state +and O +therefore O +the O +total O +iron B-chemical +- O +loading O +capacity O +of O +our O +system O +may O +be O +significantly O +higher O +than O +in O +this O +experimental O +system O +. O + +Taken O +together O +, O +our O +data O +show O +that O +EncFtn B-protein +can O +catalytically O +oxidize O +Fe2 B-chemical ++ I-chemical +to O +Fe3 B-chemical ++; I-chemical +however O +, O +iron B-chemical +binding O +in O +EncFtn B-protein +is O +limited O +to O +the O +FOC B-site +and O +several O +surface O +metal B-site +binding I-site +sites I-site +. O + +In O +contrast O +, O +the O +encapsulin B-protein +protein O +displays O +no O +catalytic O +activity O +, O +but O +has O +the O +ability O +to O +bind O +a O +considerable O +amount O +of O +iron B-chemical +. O + +Finally O +, O +the O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +nanocompartment B-complex_assembly +complex O +retains O +the O +catalytic O +activity O +of O +EncFtn B-protein +, O +and O +sequesters O +iron B-chemical +within O +the O +encapsulin B-protein +shell B-structure_element +at O +a O +higher O +level O +than O +the O +isolated O +components O +of O +the O +system O +, O +and O +at O +a O +significantly O +higher O +level O +than O +the O +classical B-protein_state +ferritins B-protein_type +. O + +Furthermore O +, O +our O +recombinant O +nanocompartments B-complex_assembly +may O +not O +have O +the O +physiological O +subunit O +stoichiometry O +, O +and O +the O +iron B-chemical +- O +loading O +capacity O +of O +native B-protein_state +nanocompartments B-complex_assembly +is O +potentially O +much O +higher O +than O +the O +level O +we O +have O +observed O +. O + +Mutagenesis B-experimental_method +of O +the O +EncFtnsHferroxidase B-protein +center B-site + +Purification O +of O +recombinant O +R B-species +. I-species +rubrum I-species +EncFtnsH B-protein +FOC B-site +mutants B-protein_state +. O + +Single O +mutants B-protein_state +E32A B-mutant +, O +E62A B-mutant +, O +and O +H65A B-mutant +of O +EncFtnsH B-protein +produced O +from O +E B-species +. I-species +coli I-species +BL21 I-species +( I-species +DE3 I-species +) I-species +cells O +grown O +in O +MM B-experimental_method +and O +MM B-experimental_method +supplemented O +with O +iron B-chemical +were O +subjected O +to O +Superdex O +200 O +size B-experimental_method +- I-experimental_method +exclusion I-experimental_method +chromatography I-experimental_method +. O + +( O +A O +) O +Gel B-evidence +- I-evidence +filtration I-evidence +chromatogram I-evidence +of O +the O +E32A B-mutant +mutant B-protein_state +form O +of O +EncFtnsH B-protein +resulted O +in O +an O +elution B-evidence +profile I-evidence +with O +a O +majority O +of O +the O +protein O +eluting O +as O +the O +decameric B-oligomeric_state +form O +of O +the O +protein O +and O +a O +small O +proportion O +of O +monomer B-oligomeric_state +. O +( O +B O +) O +Gel B-experimental_method +- I-experimental_method +filtration I-experimental_method +chromatograhy I-experimental_method +of O +the O +E62A B-mutant +mutant B-protein_state +form O +of O +EncFtnsH B-protein +resulted O +in O +an O +elution B-evidence +profile I-evidence +with O +a O +single O +major O +decameric B-oligomeric_state +peak O +. O +( O +C O +) O +Gel B-experimental_method +- I-experimental_method +filtration I-experimental_method +chromatography I-experimental_method +of O +the O +H65A B-mutant +mutant B-protein_state +form O +of O +EncFtnsH B-protein +resulted O +in O +a O +single O +peak O +corresponding O +to O +the O +protein O +monomer B-oligomeric_state +. O + +To O +investigate O +the O +structural O +and O +biochemical O +role O +played O +by O +the O +metal B-site +binding I-site +residues I-site +in O +the O +di B-site +- I-site +iron I-site +FOC I-site +of O +EncFtnsH B-protein +we O +produced O +alanine B-experimental_method +mutations I-experimental_method +in O +each O +of O +these O +residues O +: O +Glu32 B-residue_name_number +, O +Glu62 B-residue_name_number +, O +and O +His65 B-residue_name_number +. O + +These O +EncFtnsH B-protein +mutants B-protein_state +were O +produced O +in O +E B-species +. I-species +coli I-species +cells O +grown O +in O +MM B-experimental_method +, O +both O +in O +the O +absence B-protein_state +and O +presence B-protein_state +of I-protein_state +additional O +iron B-chemical +. O + +The O +E32A B-mutant +and O +E62A B-mutant +mutants B-protein_state +eluted O +from O +SEC B-experimental_method +at O +a O +volume O +consistent O +with O +the O +decameric B-oligomeric_state +form O +of O +EncFtnsH B-protein +, O +with O +a O +small O +proportion O +of O +monomer B-oligomeric_state +; O +the O +H65A B-mutant +mutant B-protein_state +eluted O +at O +a O +volume O +consistent O +with O +the O +monomeric B-oligomeric_state +form O +of O +EncFtnsH B-protein +( O +Figure O +9 O +). O + +For O +all O +of O +the O +mutants B-protein_state +studied O +, O +no O +change O +in O +oligomerization O +state O +was O +apparent O +upon O +addition O +of O +Fe2 B-chemical ++ I-chemical +in O +vitro O +. O + +Native B-experimental_method +mass I-experimental_method +spectrometry I-experimental_method +of O +EncFtnsH B-protein +mutants B-protein_state +. O + +All O +spectra B-evidence +were O +acquired O +in O +100 O +mM O +ammonium O +acetate B-chemical +, O +pH O +8 O +. O +0 O +with O +a O +protein O +concentration O +of O +5 O +µM O +. O +( O +A O +) O +Wild B-protein_state +- I-protein_state +type I-protein_state +EncFtnsH B-protein +in O +the O +absence B-protein_state +of I-protein_state +iron B-chemical +displays O +a O +charge B-evidence +state I-evidence +distribution I-evidence +consistent O +with O +a O +monomer B-oligomeric_state +( O +see O +also O +Figure O +8 O +). O +( O +B O +) O +E32A B-mutant +EncFtnsH B-protein +displays O +a O +charge B-evidence +states I-evidence +consistent O +with O +a O +decamer B-oligomeric_state +( O +green O +circles O +); O +a O +minor O +species O +, O +consistent O +with O +the O +monomer B-oligomeric_state +of O +E32A B-mutant +mutant B-protein_state +is O +also O +observed O +( O +blue O +circles O +). O + +( O +C O +) O +E62A B-mutant +EncFtnsH B-protein +displays O +charge B-evidence +states I-evidence +consistent O +with O +a O +decamer B-oligomeric_state +( O +green O +circles O +). O +( O +D O +) O +H65A B-mutant +EncFtnsH B-protein +displays O +charge B-evidence +states I-evidence +consistent O +with O +both O +monomer B-oligomeric_state +( O +blue O +circles O +) O +and O +dimer B-oligomeric_state +( O +purple O +circles O +). O + +In O +addition O +to O +SEC B-experimental_method +studies O +, O +native B-experimental_method +mass I-experimental_method +spectrometry I-experimental_method +of O +the O +apo B-protein_state +- O +EncFtnsH B-protein +mutants B-protein_state +was O +performed O +and O +compared O +with O +the O +wild B-protein_state +- I-protein_state +type I-protein_state +apo B-protein_state +- O +EncFtnsH B-protein +protein O +( O +Figure O +10 O +). O + +As O +described O +above O +, O +the O +apo B-protein_state +- O +EncFtnsH B-protein +has O +a O +charge B-evidence +state I-evidence +distribution O +consistent O +with O +an O +unstructured B-protein_state +monomer B-oligomeric_state +, O +and O +decamer B-oligomeric_state +formation O +is O +only O +initiated O +upon O +addition O +of O +ferrous O +iron B-chemical +. O + +Both O +the O +E32A B-mutant +mutant B-protein_state +and O +E62A B-mutant +mutant B-protein_state +displayed O +charge B-evidence +state I-evidence +distributions O +consistent O +with O +decamers B-oligomeric_state +, O +even O +in O +the O +absence B-protein_state +of I-protein_state +Fe2 B-chemical ++. I-chemical + +This O +gas O +- O +phase O +observation O +is O +consistent O +with O +SEC B-experimental_method +measurements O +, O +which O +indicate O +both O +of O +these O +variants O +were O +also O +decamers B-oligomeric_state +in O +solution O +. O + +Thus O +it O +seems O +that O +these O +mutations O +allow O +the O +decamer B-oligomeric_state +to O +form O +in O +the O +absence B-protein_state +of I-protein_state +iron B-chemical +in O +the O +FOC B-site +. O + +In O +contrast O +to O +the O +glutamic B-residue_name +acid I-residue_name +mutants B-protein_state +, O +MS B-experimental_method +analysis O +of O +the O +H65A B-mutant +mutant B-protein_state +is O +similar O +to O +wild B-protein_state +- I-protein_state +type I-protein_state +apo B-protein_state +- O +EncFtnsH B-protein +and O +is O +present O +as O +a O +monomer B-oligomeric_state +; O +interestingly O +a O +minor O +population O +of O +dimeric B-oligomeric_state +H65A B-mutant +was O +also O +observed O +. O + +We O +propose O +that O +the O +observed O +differences O +in O +the O +oligomerization O +state O +of O +the O +E32A B-mutant +and O +E62A B-mutant +mutants B-protein_state +compared O +to O +wild B-protein_state +- I-protein_state +type I-protein_state +are O +due O +to O +the O +changes O +in O +the O +electrostatic O +environment O +within O +the O +FOC B-site +. O + +At O +neutral B-protein_state +pH I-protein_state +the O +glutamic B-residue_name +acid I-residue_name +residues O +are O +negatively O +charged O +, O +while O +the O +histidine B-residue_name +residues O +are O +predominantly O +in O +their O +uncharged O +state O +. O + +In O +the O +wild B-protein_state +- I-protein_state +type I-protein_state +( O +WT B-protein_state +) O +EncFtnsH B-protein +this O +leads O +to O +electrostatic O +repulsion O +between O +subunits B-structure_element +in O +the O +absence B-protein_state +of I-protein_state +iron B-chemical +. O + +Coordination B-bond_interaction +of O +Fe2 B-chemical ++ I-chemical +in O +this O +site O +stabilizes O +the O +dimer B-oligomeric_state +and O +reconstitutes O +the O +active B-protein_state +FOC B-site +. O + +The O +geometric O +arrangement O +of O +Glu32 B-residue_name_number +and O +Glu62 B-residue_name_number +in O +the O +FOC B-site +explains O +their O +behavior O +in O +solution O +and O +the O +gas O +phase O +, O +where O +they O +both O +favor O +the O +formation O +of O +decamers B-oligomeric_state +due O +to O +the O +loss O +of O +a O +repulsive O +negative O +charge O +. O + +The O +FOC B-site +in O +the O +H65A B-mutant +mutant B-protein_state +is O +destabilized O +through O +the O +loss B-protein_state +of I-protein_state +this O +metal B-site +coordinating I-site +residue I-site +and O +potential O +positive O +charge O +carrier O +, O +thus O +favoring O +the O +monomer B-oligomeric_state +in O +solution O +and O +the O +gas O +phase O +. O + +Data B-evidence +collection I-evidence +and I-evidence +refinement I-evidence +statistics I-evidence +. O + +WT B-protein_state +E32A B-mutant +E62A B-mutant +H65A B-mutant +Data O +collection O +Wavelength O +( O +Å O +) O +1 O +. O +74 O +1 O +. O +73 O +1 O +. O +73 O +1 O +. O +74 O +Resolution O +range O +( O +Å O +) O +49 O +. O +63 O +- O +2 O +. O +06 O +( O +2 O +. O +10 O +- O +2 O +. O +06 O +) O +48 O +. O +84 O +- O +2 O +. O +59 O +( O +2 O +. O +683 O +- O +2 O +. O +59 O +) O +48 O +. O +87 O +- O +2 O +. O +21 O +( O +2 O +. O +29 O +- O +2 O +. O +21 O +) O +48 O +. O +86 O +- O +2 O +. O +97 O +( O +3 O +. O +08 O +- O +2 O +. O +97 O +) O +Space O +group O +P O +1 O +21 O +1 O +P O +1 O +21 O +1 O +P O +1 O +21 O +1 O +P O +1 O +21 O +1 O +Unit O +cell O +( O +Å O +) O +a O +b O +c O +β O +(°) O +98 O +. O +18 O +120 O +. O +53 O +140 O +. O +30 O +95 O +. O +36 O +97 O +. O +78 O +120 O +. O +28 O +140 O +. O +53 O +95 O +. O +41 O +98 O +. O +09 O +120 O +. O +23 O +140 O +. O +36 O +95 O +. O +50 O +98 O +. O +03 O +120 O +. O +29 O +140 O +. O +43 O +95 O +. O +39 O +Total O +reflections O +1 O +, O +264 O +, O +922 O +( O +41 O +, O +360 O +) O +405 O +, O +488 O +( O +36 O +, O +186 O +) O +1 O +, O +069 O +, O +345 O +( O +95 O +, O +716 O +) O +323 O +, O +853 O +( O +32 O +, O +120 O +) O +Unique O +reflections O +197 O +, O +873 O +( O +8 O +, O +766 O +) O +100 O +, O +067 O +( O +9 O +, O +735 O +) O +162 O +, O +379 O +( O +15 O +, O +817 O +) O +66 O +, O +658 O +( O +6 O +, O +553 O +) O +Multiplicity O +6 O +. O +4 O +( O +4 O +. O +7 O +) O +4 O +. O +1 O +( O +3 O +. O +7 O +) O +6 O +. O +6 O +( O +6 O +. O +1 O +) O +4 O +. O +9 O +( O +4 O +. O +9 O +) O +Anomalous O +multiplicity O +3 O +. O +2 O +( O +2 O +. O +6 O +) O +N O +/ O +A O +N O +/ O +A O +N O +/ O +A O +Completeness O +(%) O +99 O +. O +2 O +( O +88 O +. O +6 O +) O +99 O +. O +0 O +( O +97 O +. O +0 O +) O +100 O +( O +97 O +. O +0 O +) O +100 O +( O +99 O +. O +0 O +) O +Anomalous O +completeness O +(%) O +96 O +. O +7 O +( O +77 O +. 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O + +The O +FOC B-site +residues O +of O +the O +mutants B-protein_state +and O +native B-protein_state +EncFtnsH B-protein +structures B-evidence +are O +shown O +as O +sticks O +with O +coordinated B-bond_interaction +Fe2 B-chemical ++ I-chemical +as O +orange O +and O +Ca2 B-chemical ++ I-chemical +as O +grey O +spheres O +and O +are O +colored O +as O +follows O +: O +wild B-protein_state +type I-protein_state +, O +grey O +; O +E32A B-mutant +, O +pink O +; O +E62A B-mutant +, O +green O +; O +H65A B-mutant +, O +blue O +. O + +Of O +the O +mutants B-protein_state +, O +only O +H65A B-mutant +has O +any O +coordinated B-bond_interaction +metal O +ions O +, O +which O +appear O +to O +be O +calcium B-chemical +ions O +from O +the O +crystallization O +condition O +. O + +The O +overall O +organization O +of O +FOC B-site +residues O +is O +retained O +in O +the O +mutants B-protein_state +, O +with O +almost O +no O +backbone O +movements O +. O + +Significant O +differences O +center O +around O +Tyr39 B-residue_name_number +, O +which O +moves O +to O +coordinate B-bond_interaction +the O +bound B-protein_state +calcium B-chemical +ions O +in O +the O +H65A B-mutant +mutant B-protein_state +; O +and O +Glu32 B-residue_name_number +, O +which O +moves O +away O +from O +the O +metal O +ions O +in O +this O +structure B-evidence +. O + +Close O +inspection O +of O +the O +region O +of O +the O +protein O +around O +the O +FOC B-site +in O +each O +of O +the O +mutants B-protein_state +highlights O +their O +effect O +on O +metal O +binding O +( O +Figure O +11 O +and O +Figure O +11 O +— O +figure O +supplement O +1 O +– O +3 O +). O + +In O +the O +E32A B-mutant +mutant B-protein_state +the O +position O +of O +the O +side O +chains O +of O +the O +remaining O +iron B-site +coordinating I-site +residues I-site +in O +the O +FOC B-site +is O +essentially O +unchanged O +, O +but O +the O +absence B-protein_state +of I-protein_state +the O +axial O +- O +metal O +coordinating B-bond_interaction +ligand O +provided O +by O +the O +Glu32 B-residue_name_number +side O +chain O +abrogates B-protein_state +metal I-protein_state +binding I-protein_state +in O +this O +site O +. O + +The O +Glu31 B-site +/ I-site +34 I-site +- I-site +site I-site +also O +lacks B-protein_state +metal B-chemical +, O +with O +the O +side O +chain O +of O +Glu31 B-residue_name_number +rotated O +by O +180 O +° O +at O +the O +Cβ O +in O +the O +absence B-protein_state +of I-protein_state +metal B-chemical +( O +Figure O +11 O +— O +figure O +supplement O +1 O +). O + +The O +E62A B-mutant +mutant B-protein_state +has O +a O +similar O +effect O +on O +the O +FOC B-site +to O +the O +E32A B-mutant +mutant B-protein_state +, O +however O +the O +entry B-site +site I-site +still O +has O +a O +calcium B-chemical +ion O +coordinated B-bond_interaction +between O +residues O +Glu31 B-residue_name_number +and O +Glu34 B-residue_name_number +( O +Figure O +11 O +— O +figure O +supplement O +2 O +). O + +The O +H65A B-mutant +mutant B-protein_state +diverges O +significantly O +from O +the O +wild B-protein_state +type I-protein_state +in O +the O +position O +of O +the O +residues O +Glu32 B-residue_name_number +and O +Tyr39 B-residue_name_number +in O +the O +FOC B-site +. O + +E32 B-residue_name_number +appears O +in O +either O +the O +original O +orientation O +as O +the O +wild B-protein_state +type I-protein_state +and O +coordinates B-bond_interaction +Ca2 B-chemical ++ I-chemical +in O +this O +position O +, O +or O +it O +is O +flipped O +by O +180 O +° O +at O +the O +Cβ O +, O +moving O +away O +from O +the O +coordinated B-bond_interaction +calcium B-chemical +ion O +in O +the O +FOC B-site +. O + +Tyr39 B-residue_name_number +moves O +closer O +to O +Ca2 B-chemical ++ I-chemical +compared O +to O +the O +wild B-protein_state +- I-protein_state +type I-protein_state +and O +coordinates B-bond_interaction +the O +calcium B-chemical +ion O +( O +Figure O +11 O +— O +figure O +supplement O +3 O +). O + +A O +single O +calcium B-chemical +ion O +is O +present O +in O +the O +entry B-site +site I-site +of O +this O +mutant B-protein_state +; O +however O +, O +Glu31 B-residue_name_number +of O +one O +chain O +is O +rotated O +away O +from O +the O +metal O +ion O +and O +is O +not O +involved O +in O +coordination B-bond_interaction +. O + +Taken O +together O +the O +results O +of O +our O +data O +show O +that O +these O +changes O +to O +the O +FOC B-site +of O +EncFtn B-protein +still O +permit O +the O +formation O +of O +the O +decameric B-oligomeric_state +form O +of O +the O +protein O +. O + +While O +the O +proteins O +all O +appear O +decameric B-oligomeric_state +in O +crystals B-evidence +, O +their O +solution O +and O +gas O +- O +phase O +behavior O +differs O +considerably O +and O +the O +mutants B-protein_state +no O +longer O +show O +metal O +- O +dependent O +oligomerization O +. O + +These O +results O +highlight O +the O +importance O +of O +metal B-chemical +coordination B-bond_interaction +in O +the O +FOC B-site +for O +the O +stability O +and O +assembly O +of O +the O +EncFtn B-protein +protein O +. O + +Progress B-evidence +curves I-evidence +recording O +ferroxidase B-protein_type +activity O +of O +EncFtnsH B-protein +mutants B-protein_state +. O + +20 O +µM O +wild B-protein_state +- I-protein_state +type I-protein_state +EncFtnsH B-protein +, O +E32A B-mutant +, O +E62A B-mutant +and O +H65A B-mutant +mutants B-protein_state +were O +mixed O +with O +20 O +µM O +or O +100 O +µM O +acidic O +Fe B-chemical +( I-chemical +NH4 I-chemical +) I-chemical +2 I-chemical +( I-chemical +SO4 I-chemical +) I-chemical +2 I-chemical +, O +respectively O +. O + +Absorbance O +at O +315 O +nm O +was O +recorded O +for O +1800 O +s O +at O +25 O +° O +C O +as O +an O +indication O +of O +Fe3 B-chemical ++ I-chemical +formation O +. O + +Protein O +free O +samples O +( O +dashed O +and O +dotted O +lines O +) O +were O +measured O +for O +Fe2 B-chemical ++ I-chemical +background O +oxidation O +as O +controls O +. O + +Relative O +ferroxidase B-protein_type +activity O +of O +EncFtnsH B-protein +mutants B-protein_state +. O + +EncFtnsH B-protein +, O +and O +the O +mutant B-protein_state +forms O +E32A B-mutant +, O +E62A B-mutant +and O +H65A B-mutant +, O +each O +at O +20 O +µM O +, O +were O +mixed O +with O +100 O +µM O +acidic O +Fe B-chemical +( I-chemical +NH4 I-chemical +) I-chemical +2 I-chemical +( I-chemical +SO4 I-chemical +) I-chemical +2 I-chemical +. O + +Ferroxidase B-protein_type +activity O +of O +the O +mutant B-protein_state +forms O +is O +determined O +by O +measuring B-experimental_method +the I-experimental_method +absorbance I-experimental_method +at I-experimental_method +315 I-experimental_method +nm I-experimental_method +for O +1800 O +s O +at O +25 O +° O +C O +as O +an O +indication O +of O +Fe3 B-chemical ++ I-chemical +formation O +. O + +The O +relative O +ferroxidase B-protein_type +activity O +of O +mutants B-protein_state +is O +plotted O +as O +a O +proportion O +of O +the O +activity O +of O +the O +wild B-protein_state +- I-protein_state +type I-protein_state +protein O +using O +the O +endpoint O +measurement B-experimental_method +of I-experimental_method +A315 I-experimental_method +. O + +The O +FOC B-site +mutants B-protein_state +showed O +reduced O +ferroxidase B-protein_type +activity O +to O +varied O +extents O +, O +among O +which O +E62A B-mutant +significantly O +abrogated O +the O +ferroxidase B-protein_type +activity O +. O + +To O +address O +the O +question O +of O +how O +mutagenesis B-experimental_method +of O +the O +iron B-site +coordinating I-site +residues I-site +affects O +the O +enzymatic O +activity O +of O +the O +EncFtnsH B-protein +protein O +we O +recorded O +progress B-evidence +curves I-evidence +for O +the O +oxidation O +of O +Fe2 B-chemical ++ I-chemical +to O +Fe3 B-chemical ++ I-chemical +by O +the O +different O +mutants B-protein_state +as O +before O +. O + +Mutagenesis B-experimental_method +of O +E32A B-mutant +and O +H65A B-mutant +reduces O +the O +activity O +of O +EncFtnsH B-protein +by O +about O +40 O +%- O +55 O +%; O +the O +E62A B-mutant +mutant B-protein_state +completely O +abrogates O +activity O +, O +presumably O +through O +the O +loss B-protein_state +of I-protein_state +the O +bridging O +coordination B-bond_interaction +for O +the O +formation O +of O +the O +di B-site +- I-site +nuclear I-site +iron I-site +center I-site +of O +the O +FOC B-site +( O +Figure O +12 O +). O + +Collectively O +, O +the O +effect O +of O +mutating B-experimental_method +these O +residues O +in O +the O +FOC B-site +confirms O +the O +importance O +of O +the O +iron B-site +coordinating I-site +residues I-site +for O +the O +ferroxidase B-protein_type +activity O +of O +the O +EncFtnsH B-protein +protein O +. O + +Phylogenetic B-evidence +tree I-evidence +of O +ferritin B-protein_type +family O +proteins O +. O + +The O +tree O +was O +built O +using O +the O +Neighbor B-experimental_method +- I-experimental_method +Joining I-experimental_method +method I-experimental_method +based O +on O +step B-experimental_method +- I-experimental_method +wise I-experimental_method +amino I-experimental_method +acid I-experimental_method +sequence I-experimental_method +alignment I-experimental_method +of O +the O +four B-structure_element +- I-structure_element +helical I-structure_element +bundle I-structure_element +portions O +of O +ferritin B-protein_type +family O +proteins O +( O +Supplementary O +file O +1 O +). O + +The O +evolutionary B-evidence +distances I-evidence +were O +computed O +using O +the O +p B-experimental_method +- I-experimental_method +distance I-experimental_method +method I-experimental_method +and O +are O +in O +the O +units O +of O +the O +number O +of O +amino O +acid O +differences O +per O +site O +. O + +Our O +study O +reports O +on O +a O +new O +class O +of O +ferritin B-protein_type +- O +like O +proteins O +( O +EncFtn B-protein +), O +which O +are O +associated O +with O +bacterial B-taxonomy_domain +encapsulin B-protein +nanocompartments B-complex_assembly +( O +Enc B-protein +). O + +By O +studying O +the O +EncFtn B-protein +from O +R B-species +. I-species +rubrum I-species +we O +demonstrate O +that O +iron B-chemical +binding O +results O +in O +assembly O +of O +EncFtn B-protein +decamers B-oligomeric_state +, O +which O +display O +a O +unique O +annular O +architecture O +. O + +Despite O +a O +radically O +different O +quaternary O +structure O +to O +the O +classical B-protein_state +ferritins B-protein_type +, O +the O +four B-structure_element +- I-structure_element +helical I-structure_element +bundle I-structure_element +scaffold I-structure_element +and O +FOC B-site +of O +EncFtnsH B-protein +are O +strikingly O +similar O +to O +ferritin B-protein_type +( O +Figure O +6A O +). O + +A O +sequence B-experimental_method +- I-experimental_method +based I-experimental_method +phylogenetic I-experimental_method +tree I-experimental_method +for O +proteins O +in O +the O +ferritin B-protein_type +family O +was O +constructed O +; O +in O +addition O +to O +the O +classical B-protein_state +ferritins B-protein_type +, O +bacterioferritins B-protein_type +and O +Dps B-protein_type +proteins O +, O +our O +analysis O +included O +the O +encapsulin B-protein_type +- I-protein_type +associated I-protein_type +ferritin I-protein_type +- I-protein_type +like I-protein_type +proteins I-protein_type +( O +EncFtns B-protein_type +) O +and O +a O +group O +related O +to O +these O +, O +but O +lacking O +the O +encapsulin B-protein +sequence O +( O +Non B-protein_type +- I-protein_type +EncFtn I-protein_type +). O + +The O +analysis O +revealed O +that O +the O +EncFtn B-protein +and O +Non B-protein_type +- I-protein_type +EncFtn I-protein_type +proteins O +form O +groups O +distinct O +from O +the O +other O +clearly O +delineated O +groups O +of O +ferritins B-protein_type +, O +and O +represent O +outliers O +in O +the O +tree O +( O +Figure O +13 O +). O + +While O +it O +is O +difficult O +to O +infer O +ancestral O +lineages O +in O +protein O +families O +, O +the O +similarity O +seen O +in O +the O +active B-site +site I-site +scaffold I-site +of O +these O +proteins O +highlights O +a O +shared O +evolutionary O +relationship O +between O +EncFtn B-protein_type +proteins O +and O +other O +members O +of O +the O +ferritin B-protein_type +superfamily O +that O +has O +been O +noted O +in O +previous O +studies O +(; O +). O + +From O +this O +analysis O +, O +we O +propose O +that O +the O +four B-structure_element +- I-structure_element +helical I-structure_element +fold I-structure_element +of O +the O +classical B-protein_state +ferritins B-protein_type +may O +have O +arisen O +through O +gene O +duplication O +of O +an O +ancestor O +of O +EncFtn B-protein +. O + +This O +gene O +duplication O +would O +result O +in O +the O +C B-structure_element +- I-structure_element +terminal I-structure_element +region I-structure_element +of O +one O +EncFtn B-protein +monomer B-oligomeric_state +being O +linked O +to O +the O +N O +- O +terminus O +of O +another O +and O +thus O +stabilizing O +the O +four B-structure_element +- I-structure_element +helix I-structure_element +bundle I-structure_element +fold I-structure_element +within O +a O +single O +polypeptide O +chain O +( O +Figure O +6B O +). O + +Linking O +the O +protein O +together O +in O +this O +way O +relaxes O +the O +requirement O +for O +the O +maintenance O +of O +a O +symmetrical O +FOC B-site +and O +thus O +provides O +a O +path O +to O +the O +diversity O +in O +active B-site +- I-site +site I-site +residues I-site +seen O +across O +the O +ferritin B-protein_type +family O +( O +Figure O +6A O +, O +residues O +Glu95 B-residue_name_number +, O +Gln128 B-residue_name_number +and O +Glu131 B-residue_name_number +in O +PmFtn B-protein +, O +Supplementary O +file O +1 O +). O + +Relationship O +between O +ferritin B-protein_type +structure B-evidence +and O +activity O + +The O +quaternary O +arrangement O +of O +classical B-protein_state +ferritins B-protein_type +into O +an O +octahedral B-protein_state +nanocage B-complex_assembly +and O +Dps B-protein +into O +a O +dodecamer B-oligomeric_state +is O +absolutely O +required O +for O +their O +function O +as O +iron B-chemical +storage O +compartments O +. O + +The O +oxidation O +and O +mineralization O +of O +iron B-chemical +must O +be O +spatially O +separated O +from O +the O +host O +cytosol O +to O +prevent O +the O +formation O +of O +damaging O +hydroxyl O +radicals O +in O +the O +Fenton O +and O +Haber O +- O +Weiss O +reactions O +. O + +This O +is O +achieved O +in O +all O +ferritins B-protein_type +by O +confining O +the O +oxidation O +of O +iron B-chemical +to O +the O +interior O +of O +the O +protein O +complex O +, O +thus O +achieving O +sequestration O +of O +the O +Fe3 B-chemical ++ I-chemical +mineralization O +product O +. O + +A O +structural B-experimental_method +alignment I-experimental_method +of O +the O +FOC B-site +of O +EncFtn B-protein +with O +the O +classical B-protein_state +ferritin B-protein_type +PmFtn B-protein +shows O +that O +the O +central B-structure_element +ring I-structure_element +of O +EncFtn B-protein +corresponds O +to O +the O +external O +surface O +of O +ferritin B-protein_type +, O +while O +the O +outer O +circumference O +of O +EncFtn B-protein +is O +congruent O +with O +the O +inner O +mineralization B-site +surface I-site +of O +ferritin B-protein_type +( O +Figure O +6 O +— O +figure O +supplement O +1A O +). O + +This O +overlay B-experimental_method +highlights O +the O +fact O +that O +the O +ferroxidase B-site +center I-site +of O +EncFtn B-protein +faces O +in O +the O +opposite O +direction O +relative O +to O +the O +classical B-protein_state +ferritins B-protein_type +and O +is O +essentially O +inside O +out O +regarding O +iron B-chemical +storage O +space O +( O +Figure O +6 O +— O +figure O +supplement O +1B O +, O +boxed O +region O +). O + +Analysis O +of O +each O +of O +the O +single O +mutations B-experimental_method +( O +E32A B-mutant +, O +E62A B-mutant +and O +H65A B-mutant +) O +made O +in O +the O +FOC B-site +highlights O +the O +importance O +of O +the O +iron B-site +- I-site +coordinating I-site +residues I-site +in O +the O +catalytic O +activity O +of O +EncFtn B-protein +. O + +Furthermore O +, O +the O +position O +of O +the O +calcium B-chemical +ion O +coordinated B-bond_interaction +by I-bond_interaction +Glu31 B-residue_name_number +and O +Glu34 B-residue_name_number +seen O +in O +the O +EncFtnsH B-protein +structure B-evidence +suggests O +an O +entry B-site +site I-site +to O +channel O +metal O +ions O +into O +the O +FOC B-site +; O +we O +propose O +that O +this O +site O +binds O +hydrated O +iron B-chemical +ions O +in O +vivo O +and O +acts O +as O +a O +selectivity O +filter O +and O +gate O +for O +the O +FOC B-site +. O + +The O +constellation O +of O +charged O +residues O +on O +the O +outer O +circumference O +of O +EncFtn B-protein +( O +His57 B-residue_name_number +, O +Glu61 B-residue_name_number +and O +Glu64 B-residue_name_number +) O +could O +function O +in O +the O +same O +way O +as O +the O +residues O +lining O +the O +mineralization B-site +surface I-site +within O +the O +classical B-protein_state +ferritin B-protein_type +nanocage B-complex_assembly +, O +and O +given O +their O +proximity O +to O +the O +FOC B-site +these O +sites O +may O +be O +the O +exit B-site +portal I-site +and O +mineralization B-site +site I-site +. O + +The O +absolute O +requirement O +for O +the O +spatial O +separation O +of O +oxidation O +and O +mineralization O +in O +ferritins B-protein_type +suggests O +that O +the O +EncFtn B-protein_type +family O +proteins O +are O +not O +capable O +of O +storing O +iron B-chemical +minerals O +due O +to O +the O +absence B-protein_state +of I-protein_state +an O +enclosed O +compartment O +in O +their O +structure O +( O +Figure O +6 O +— O +figure O +supplement O +1B O +). O + +Our O +biochemical B-experimental_method +characterization I-experimental_method +of O +EncFtn B-protein +supports O +this O +hypothesis O +, O +indicating O +that O +while O +this O +protein O +is O +capable O +of O +oxidizing O +iron B-chemical +, O +it O +does O +not O +accrue O +mineralized O +iron B-chemical +in O +an O +analogous O +manner O +to O +classical B-protein_state +ferritins B-protein_type +. O + +While O +EncFtn B-protein +does O +not O +store O +iron B-chemical +itself O +, O +its O +association O +with O +the O +encapsulin B-protein +nanocage B-complex_assembly +suggests O +that O +mineralization O +occurs O +within O +the O +cavity B-site +of O +the O +encapsulin B-protein +shell B-structure_element +. O + +Our O +ferroxidase B-experimental_method +assay I-experimental_method +data O +on O +the O +recombinant O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +nanocompartments B-complex_assembly +, O +which O +accrue O +over O +4100 O +iron B-chemical +ions O +per O +complex O +and O +form O +regular O +nanoparticles B-complex_assembly +, O +are O +consistent O +with O +the O +encapsulin B-protein +protein O +acting O +as O +the O +store O +for O +iron B-chemical +oxidized O +by O +the O +EncFtn B-protein +enzyme O +. O + +TEM B-experimental_method +analysis O +of O +the O +reaction O +products O +shows O +the O +production O +of O +homogeneous O +iron B-chemical +nanoparticles O +only O +in O +the O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +nanocompartment B-complex_assembly +( O +Figure O +8 O +— O +figure O +supplement O +1 O +). O + +Model O +of O +iron B-chemical +oxidation O +in O +encapsulin B-protein +nanocompartments B-complex_assembly +. O + +( O +A O +) O +Model O +of O +EncFtnsH B-protein +docking B-experimental_method +to O +the O +encapsulin B-protein +shell B-structure_element +. O + +A O +single O +pentamer B-oligomeric_state +of O +the O +icosahedral B-protein_state +T B-species +. I-species +maritima I-species +encapsulin B-protein +structure B-evidence +( O +PDBID O +: O +3DKT O +) O +is O +shown O +as O +a O +blue O +surface O +with O +the O +encapsulin B-protein +localization B-structure_element +sequence I-structure_element +of O +EncFtn B-protein +shown O +as O +a O +purple O +surface O +. O + +The O +C O +- O +terminal O +regions O +of O +the O +EncFtn B-protein +subunits B-structure_element +correspond O +to O +the O +position O +of O +the O +localization B-structure_element +sequences I-structure_element +seen O +in O +3DKT O +. O + +Alignment B-experimental_method +of O +EncFtnsH B-protein +with O +3DKT O +positions O +the O +central B-site +channel I-site +directly O +above O +the O +pore B-site +in O +the O +3DKT O +pentamer B-oligomeric_state +axis O +( O +shown O +as O +a O +grey O +pentagon O +). O +( O +B O +) O +Surface O +view O +of O +EncFtn B-protein +within O +the O +encapsulin B-protein +nanocompartment B-complex_assembly +( O +grey O +and O +blue O +respectively O +). O + +The O +lumen O +of O +the O +encapsulin B-protein +nanocompartment B-complex_assembly +is O +considerably O +larger O +than O +the O +interior O +of O +ferritin B-protein_type +( O +shown O +in O +orange O +behind O +the O +encapsulin B-protein +for O +reference O +) O +and O +thus O +allows O +the O +storage O +of O +significantly O +more O +iron B-chemical +. O + +The O +proposed O +pathway O +for O +iron B-chemical +movement O +through O +the O +encapsulin B-protein +shell B-structure_element +and O +EncFtn B-protein +FOC B-site +is O +shown O +with O +arrows O +. O +( O +C O +) O +Model O +ofiron O +oxidation O +within O +an O +encapsulin B-protein +nanocompartment B-complex_assembly +. O + +As O +EncFtn B-protein +is O +unable O +to O +mineralize O +iron B-chemical +on O +its O +surface O +directly O +, O +Fe2 B-chemical ++ I-chemical +must O +pass O +through O +the O +encapsulin B-protein +shell B-structure_element +to O +access O +the O +first O +metal B-site +binding I-site +site I-site +within O +the O +central B-site +channel I-site +of O +EncFtnsH B-protein +( O +entry B-site +site I-site +) O +prior O +to O +oxidation O +within O +the O +FOC B-site +and O +release O +as O +Fe3 B-chemical ++ I-chemical +to O +the O +outer O +surface O +of O +the O +protein O +where O +it O +can O +be O +mineralized O +within O +the O +lumen O +of O +the O +encapsulin B-protein +cage O +. O + +Docking B-experimental_method +the O +decamer B-oligomeric_state +structure B-evidence +of O +EncFtnsH B-protein +into O +the O +pentamer B-oligomeric_state +of O +the O +T B-species +. I-species +maritima I-species +encapsulin B-protein +Tmari_0786 B-gene +( O +PDB O +ID O +: O +3DKT O +) O +shows O +that O +the O +position O +of O +the O +C B-structure_element +- I-structure_element +terminal I-structure_element +extensions I-structure_element +of O +our O +EncFtnsH B-protein +structure B-evidence +are O +consistent O +with O +the O +localization B-structure_element +sequences I-structure_element +seen O +bound B-protein_state +to I-protein_state +the O +encapsulin B-protein +protein O +( O +Figure O +14A O +). O + +Thus O +, O +it O +appears O +that O +the O +EncFtn B-protein +decamer B-oligomeric_state +is O +the O +physiological O +state O +of O +this O +protein O +. O + +This O +arrangement O +positions O +the O +central B-structure_element +ring I-structure_element +of O +EncFtn B-protein +directly O +above O +the O +pore B-site +at O +the O +five O +- O +fold O +symmetry O +axis O +of O +the O +encapsulin B-protein +shell B-structure_element +and O +highlights O +a O +potential O +route O +for O +the O +entry O +of O +iron B-chemical +into O +the O +encapsulin B-protein +and O +towards O +the O +active B-site +site I-site +of O +EncFtn B-protein +. O + +A O +comparison O +of O +the O +encapsulin B-protein +nanocompartment B-complex_assembly +and O +the O +ferritin B-protein_type +nanocage B-complex_assembly +highlights O +the O +size O +differential O +between O +the O +two O +complexes O +( O +Figure O +14B O +) O +that O +allows O +the O +encapsulin B-protein +to O +store O +significantly O +more O +iron B-chemical +. O + +The O +presence B-protein_state +of I-protein_state +five O +FOCs B-site +per O +EncFtnsH B-protein +decamer B-oligomeric_state +and O +the O +fact O +that O +the O +icosahedral B-protein_state +encapsulin B-protein +nanocage B-complex_assembly +can O +hold O +up O +to O +twelve O +of O +decameric B-oligomeric_state +EncFtn B-protein +between O +each O +of O +the O +internal O +five O +- O +fold O +vertices O +means O +that O +they O +can O +achieve O +a O +high O +rate O +of O +iron B-chemical +mineralization O +across O +the O +entire O +nanocompartment B-complex_assembly +. O + +This O +arrangement O +of O +multiple O +reaction O +centers O +in O +a O +single O +protein O +assembly O +is O +reminiscent O +of O +classical B-protein_state +ferritins B-protein_type +, O +which O +has O +24 O +FOCs B-site +distributed O +around O +the O +nanocage B-complex_assembly +. O + +Our O +structural B-evidence +data I-evidence +, O +coupled O +with O +biochemical B-experimental_method +and I-experimental_method +ICP I-experimental_method +- I-experimental_method +MS I-experimental_method +analysis O +, O +suggest O +a O +model O +for O +the O +activity O +of O +the O +encapsulin B-protein +iron B-complex_assembly +- I-complex_assembly +megastore I-complex_assembly +( O +Figure O +14C O +). O + +The O +crystal B-evidence +structure I-evidence +of O +the O +T B-species +. I-species +maritima I-species +encapsulin B-protein +shell B-structure_element +protein O +has O +a O +negatively B-site +charged I-site +pore I-site +positioned O +to O +allow O +the O +passage O +of O +Fe2 B-chemical ++ I-chemical +into O +the O +encapsulin B-protein +and O +directs O +the O +metal O +towards O +the O +central O +, O +negatively B-site +charged I-site +hole I-site +of O +the O +EncFtn B-protein +ring B-structure_element +( O +Figure O +4 O +— O +figure O +supplement O +1 O +). O + +The O +five O +metal B-site +- I-site +binding I-site +sites I-site +on O +the O +interior O +of O +the O +ring B-structure_element +( O +Glu31 B-site +/ I-site +34 I-site +- I-site +sites I-site +) O +may O +select O +for O +the O +Fe2 B-chemical ++ I-chemical +ion O +and O +direct O +it O +towards O +their O +cognate O +FOCs B-site +. O + +We O +propose O +that O +the O +oxidation O +of O +Fe2 B-chemical ++ I-chemical +to O +Fe3 B-chemical ++ I-chemical +occurs O +within O +the O +FOC B-site +according O +to O +the O +model O +postulated O +by O +in O +which O +the O +FOC B-site +acts O +as O +a O +substrate B-site +site I-site +through O +which O +iron B-chemical +passes O +and O +is O +released O +on O +to O +weakly B-site +coordinating I-site +sites I-site +at O +the O +outer O +circumference O +of O +the O +protein O +( O +His57 B-residue_name_number +, O +Glu61 B-residue_name_number +and O +Glu64 B-residue_name_number +), O +where O +it O +is O +able O +to O +form O +ferrihydrite B-chemical +minerals O +which O +can O +be O +safely O +deposited O +within O +the O +lumen O +of O +the O +encapsulin B-protein +nanocompartment B-complex_assembly +( O +Figure O +14 O +). O + +Here O +we O +describe O +for O +the O +first O +time O +the O +structure B-evidence +and O +biochemistry O +of O +a O +new O +class O +of O +encapsulin B-protein_type +- I-protein_type +associated I-protein_type +ferritin I-protein_type +- I-protein_type +like I-protein_type +protein I-protein_type +and O +demonstrate O +that O +it O +has O +an O +absolute O +requirement O +for O +compartmentalization O +within O +an O +encapsulin B-protein +nanocage B-complex_assembly +to O +act O +as O +an O +iron B-chemical +store O +. O + +Further O +work O +on O +the O +EncFtn B-complex_assembly +- I-complex_assembly +Enc I-complex_assembly +nanocompartment B-complex_assembly +will O +establish O +the O +structural O +basis O +for O +the O +movement O +of O +iron B-chemical +through O +the O +encapsulin B-protein +shell B-structure_element +, O +the O +mechanism O +of O +iron B-chemical +oxidation O +by O +the O +EncFtn B-protein +FOC B-site +and O +its O +subsequent O +storage O +in O +the O +lumen O +of O +the O +encapsulin B-protein +nanocompartment B-complex_assembly +. O +