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Q5E814 (METH_VIBF1) Reviewed, UniProtKB/Swiss-Prot

Last modified November 13, 2013. Version 68. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Methionine synthase

EC=2.1.1.13
Alternative name(s):
5-methyltetrahydrofolate--homocysteine methyltransferase
Methionine synthase, vitamin-B12 dependent
Short name=MS
Gene names
Name:metH
Ordered Locus Names:VF_0337
OrganismVibrio fischeri (strain ATCC 700601 / ES114) [Reference proteome] [HAMAP]
Taxonomic identifier312309 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeAliivibrio

Protein attributes

Sequence length1226 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

Catalyzes the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Subsequently, remethylates the cofactor using methyltetrahydrofolate By similarity.

Catalytic activity

5-methyltetrahydrofolate + L-homocysteine = tetrahydrofolate + L-methionine.

Cofactor

Methylcobalamin (MeCBL) By similarity.

Binds 1 zinc ion per subunit By similarity.

Pathway

Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; L-methionine from L-homocysteine (MetH route): step 1/1.

Domain

Modular enzyme with four functionally distinct domains. The isolated Hcy-binding domain catalyzes methyl transfer from free methylcobalamin to homocysteine. The Hcy-binding domain in association with the pterin-binding domain catalyzes the methylation of cob(I)alamin by methyltetrahydrofolate and the methylation of homocysteine. The B12-binding domain binds the cofactor. The AdoMet activation domain binds S-adenosyl-L-methionine. Under aerobic conditions cob(I)alamin can be converted to inactive cob(II)alamin. Reductive methylation by S-adenosyl-L-methionine and flavodoxin regenerates methylcobalamin By similarity.

Miscellaneous

L-homocysteine is bound via the zinc atom By similarity.

Sequence similarities

Belongs to the vitamin-B12 dependent methionine synthase family.

Contains 1 AdoMet activation domain.

Contains 1 B12-binding domain.

Contains 1 B12-binding N-terminal domain.

Contains 1 Hcy-binding domain.

Contains 1 pterin-binding domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 12261226Methionine synthase
PRO_0000204539

Regions

Domain7 – 327321Hcy-binding
Domain358 – 619262Pterin-binding
Domain652 – 74695B12-binding N-terminal
Domain748 – 883136B12-binding
Domain899 – 1226328AdoMet activation
Region836 – 8372Cobalamin-binding By similarity
Region1192 – 11932S-adenosyl-L-methionine binding By similarity

Sites

Metal binding2491Zinc By similarity
Metal binding3121Zinc By similarity
Metal binding3131Zinc By similarity
Metal binding7611Cobalt (cobalamin axial ligand) By similarity
Binding site8061Cobalamin By similarity
Binding site9491S-adenosyl-L-methionine By similarity
Binding site11371S-adenosyl-L-methionine; via carbonyl oxygen By similarity
Binding site11411Cobalamin; via carbonyl oxygen By similarity

Sequences

Sequence LengthMass (Da)Tools
Q5E814 [UniParc].

Last modified March 15, 2005. Version 1.
Checksum: A1464CA5E141F3BD

FASTA1,226136,369
        10         20         30         40         50         60 
MAGSNIKVQI EKQLSERILL IDGGMGTMIQ GYKFEEEDYR GERFNKWHCD LKGNNDLLVL 

        70         80         90        100        110        120 
SQPQIIRDIH EAYLEAGADI LETNTFNATT IAMADYDMES LSEEINFEAA KLAREVADKW 

       130        140        150        160        170        180 
TEKTPNKPRY VAGVLGPTNR TCSISPDVND PGFRNVSFDE LVEAYSESTR ALIRGGSDLI 

       190        200        210        220        230        240 
LIETIFDTLN AKACSFAVES VFEELDITLP VMISGTITDA SGRTLSGQTT EAFYNALRHV 

       250        260        270        280        290        300 
KPISFGLNCA LGPDELREYV SDLSRISECY VSAHPNAGLP NAFGEYDLSP EDMAEHVAEW 

       310        320        330        340        350        360 
ASSGFLNLIG GCCGTTPEHI RQMALVVEGV KPRQLPELPV ACRLSGLEPL TIEKDSLFIN 

       370        380        390        400        410        420 
VGERTNVTGS ARFKRLIKEE LYDEALSVAQ EQVENGAQII DINMDEGMLD AEACMVRFLN 

       430        440        450        460        470        480 
LCASEPEISK VPVMVDSSKW EVIEAGLKCI QGKGIVNSIS LKEGKEKFVH QAKLIRRYGA 

       490        500        510        520        530        540 
AVIVMAFDEV GQADTRERKI EICTNAYNIL VDEVGFPPED IIFDPNIFAV ATGIDEHNNY 

       550        560        570        580        590        600 
AVDFIEAVGD IKRTLPHAMI SGGVSNVSFS FRGNNYVREA IHAVFLYHCF KNGMDMGIVN 

       610        620        630        640        650        660 
AGQLEIYDNV PEDLREAVED VVLNRRDDST ERLLDIATEY LERAVGKVED KSALEWRDWP 

       670        680        690        700        710        720 
VEKRLEHSLV KGITEFIVED TEEARINAEK PIEVIEGPLM DGMNVVGDLF GEGKMFLPQV 

       730        740        750        760        770        780 
VKSARVMKQA VAHLEPFINA SKEVGATNGK ILLATVKGDV HDIGKNIVGV VLQCNNYEII 

       790        800        810        820        830        840 
DLGVMVSCET ILKVAKEENV DIIGLSGLIT PSLDEMVHVA KEMERQGFDL PLLIGGATTS 

       850        860        870        880        890        900 
KAHTAVKIEQ NYSQPVVYVN NASRAVGVCT SLLSDELKPS FVEKLDIDYE RVREQHSRKQ 

       910        920        930        940        950        960 
PRTKPVTLEV ARANKVAIDW ASYTPPVPLK PGVHIFDNFD VSTLRNYIDW TPFFMTWSLV 

       970        980        990       1000       1010       1020 
GKYPKILDHE EVGEEAKRLF KDANDLLDRV EKEGLLKARG MCALFPASSV GDDIEVYTDE 

      1030       1040       1050       1060       1070       1080 
SRTKVAKVLH NLRQQTEKPK GFNYCLSDYI APKESGKNDW IGGFAVTGGI GERELADEYK 

      1090       1100       1110       1120       1130       1140 
ANGDDYNAIM IQAVADRLAE AFAEYLHEKV RKEIWGYSPN ETLSNDDLIR EKYQGIRPAP 

      1150       1160       1170       1180       1190       1200 
GYPACPEHTE KGALWELMNV EESIGMSLTS SYAMWPGASV SGMYFSHPDS RYFAIAQIQQ 

      1210       1220 
DQAESYADRK GWNMLEAEKW LGPNLN 

« Hide

References

[1]"Complete genome sequence of Vibrio fischeri: a symbiotic bacterium with pathogenic congeners."
Ruby E.G., Urbanowski M., Campbell J., Dunn A., Faini M., Gunsalus R., Lostroh P., Lupp C., McCann J., Millikan D., Schaefer A., Stabb E., Stevens A., Visick K., Whistler C., Greenberg E.P.
Proc. Natl. Acad. Sci. U.S.A. 102:3004-3009(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 700601 / ES114.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000020 Genomic DNA. Translation: AAW84832.1.
RefSeqYP_203720.1. NC_006840.2.

3D structure databases

ProteinModelPortalQ5E814.
SMRQ5E814. Positions 655-1225.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING312309.VF_0337.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAW84832; AAW84832; VF_0337.
GeneID3277291.
KEGGvfi:VF_0337.
PATRIC20111162. VBIVibFis127983_0328.

Phylogenomic databases

eggNOGCOG1410.
HOGENOMHOG000251409.
KOK00548.
OMASMKEGEA.
OrthoDBEOG6091CH.
ProtClustDBPRK09490.

Enzyme and pathway databases

BioCycAFIS312309:GIWP-343-MONOMER.
UniPathwayUPA00051; UER00081.

Family and domain databases

Gene3D1.10.1240.10. 1 hit.
3.10.196.10. 1 hit.
3.20.20.20. 1 hit.
3.20.20.330. 1 hit.
3.40.50.280. 1 hit.
InterProIPR003759. Cbl-bd_cap.
IPR006158. Cobalamin-bd.
IPR011005. Dihydropteroate_synth-like.
IPR011822. MetH.
IPR000489. Pterin-binding.
IPR003726. S_MeTrfase.
IPR004223. VitB12-dep_Met_synth_activ_dom.
[Graphical view]
PfamPF02310. B12-binding. 1 hit.
PF02607. B12-binding_2. 1 hit.
PF02965. Met_synt_B12. 1 hit.
PF00809. Pterin_bind. 1 hit.
PF02574. S-methyl_trans. 1 hit.
[Graphical view]
PIRSFPIRSF000381. MetH. 1 hit.
SMARTSM01018. B12-binding_2. 1 hit.
[Graphical view]
SUPFAMSSF47644. SSF47644. 1 hit.
SSF51717. SSF51717. 1 hit.
SSF52242. SSF52242. 1 hit.
SSF56507. SSF56507. 1 hit.
SSF82282. SSF82282. 1 hit.
TIGRFAMsTIGR02082. metH. 1 hit.
PROSITEPS50974. ADOMET_ACTIVATION. 1 hit.
PS51332. B12_BINDING. 1 hit.
PS51337. B12_BINDING_NTER. 1 hit.
PS50970. HCY. 1 hit.
PS50972. PTERIN_BINDING. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameMETH_VIBF1
AccessionPrimary (citable) accession number: Q5E814
Entry history
Integrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: March 15, 2005
Last modified: November 13, 2013
This is version 68 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways