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Protein

Methionine synthase

Gene

metH

Organism
Vibrio vulnificus (strain YJ016)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

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).By similarity

Catalytic activityi

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

Cofactori

Protein has several cofactor binding sites:

Pathway: L-methionine biosynthesis via de novo pathway

This protein is involved in step 1 of the subpathway that synthesizes L-methionine from L-homocysteine (MetH route).
Proteins known to be involved in this subpathway in this organism are:
  1. Methionine synthase (metH)
This subpathway is part of the pathway L-methionine biosynthesis via de novo pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-methionine from L-homocysteine (MetH route), the pathway L-methionine biosynthesis via de novo pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi248 – 2481ZincPROSITE-ProRule annotation
Metal bindingi311 – 3111ZincPROSITE-ProRule annotation
Metal bindingi312 – 3121ZincPROSITE-ProRule annotation
Metal bindingi760 – 7601Cobalt (cobalamin axial ligand)By similarity
Binding sitei805 – 8051CobalaminBy similarity
Binding sitei948 – 9481S-adenosyl-L-methionineBy similarity
Binding sitei1136 – 11361S-adenosyl-L-methionine; via carbonyl oxygenBy similarity
Binding sitei1140 – 11401Cobalamin; via carbonyl oxygenBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

Amino-acid biosynthesis, Methionine biosynthesis

Keywords - Ligandi

Cobalamin, Cobalt, Metal-binding, S-adenosyl-L-methionine, Zinc

Enzyme and pathway databases

BioCyciVVUL196600:GJ9W-3052-MONOMER.
UniPathwayiUPA00051; UER00081.

Names & Taxonomyi

Protein namesi
Recommended name:
Methionine synthase (EC:2.1.1.13)
Alternative name(s):
5-methyltetrahydrofolate--homocysteine methyltransferase
Methionine synthase, vitamin-B12 dependent
Short name:
MS
Gene namesi
Name:metH
Ordered Locus Names:VV2960
OrganismiVibrio vulnificus (strain YJ016)
Taxonomic identifieri196600 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000002675 Componenti: Chromosome I

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12261226Methionine synthasePRO_0000204543Add
BLAST

Proteomic databases

PRIDEiQ7MHB1.

Structurei

3D structure databases

ProteinModelPortaliQ7MHB1.
SMRiQ7MHB1. Positions 654-1224.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini6 – 326321Hcy-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini357 – 618262Pterin-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini651 – 74595B12-binding N-terminalPROSITE-ProRule annotationAdd
BLAST
Domaini747 – 882136B12-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini898 – 1226329AdoMet activationPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni835 – 8362Cobalamin-bindingBy similarity
Regioni1191 – 11922S-adenosyl-L-methionine bindingBy similarity

Domaini

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).By similarity

Sequence similaritiesi

Contains 1 AdoMet activation domain.PROSITE-ProRule annotation
Contains 1 B12-binding domain.PROSITE-ProRule annotation
Contains 1 Hcy-binding domain.PROSITE-ProRule annotation
Contains 1 pterin-binding domain.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG1410.
HOGENOMiHOG000251409.
KOiK00548.
OMAiDYNSIMV.
OrthoDBiEOG6091CH.

Family and domain databases

Gene3Di1.10.1240.10. 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.
InterProiIPR003759. 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]
PfamiPF02310. 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]
PIRSFiPIRSF000381. MetH. 1 hit.
SMARTiSM01018. B12-binding_2. 1 hit.
[Graphical view]
SUPFAMiSSF47644. SSF47644. 1 hit.
SSF51717. SSF51717. 1 hit.
SSF52242. SSF52242. 1 hit.
SSF56507. SSF56507. 1 hit.
SSF82282. SSF82282. 1 hit.
TIGRFAMsiTIGR02082. metH. 1 hit.
PROSITEiPS50974. 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]

Sequencei

Sequence statusi: Complete.

Q7MHB1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGSNIRAQIE AQLKQRILLI DGGMGTMIQG YKLQEQDYRG ERFADWHSDL
60 70 80 90 100
KGNNDLLVLT QPQLIKEIHH AYLEAGADIL ETNTFNATTI AMADYDMESL
110 120 130 140 150
SEEINFAAAK LAREAADEWT AKNPAKPRYV AGVLGPTNRT CSISPDVNDP
160 170 180 190 200
GYRNVSFDEL VEAYSESTRA LIRGGSDLIL IETIFDTLNA KACAFAVESV
210 220 230 240 250
FEELGFALPV MISGTITDAS GRTLSGQTTE AFYNSLRHVR PISFGLNCAL
260 270 280 290 300
GPDELRPYVE ELSRISETFV STHPNAGLPN AFGEYDLSPE EMAEHVKEWA
310 320 330 340 350
QSGFLNLIGG CCGTTPEHIR HMAMAVEGES PRVLPEIPVA CRLSGLEPLT
360 370 380 390 400
IAKDTLFVNV GERTNVTGSA RFKRLIKEEL YDEALDVARE QVENGAQIID
410 420 430 440 450
INMDEGMLDA EACMVRFLNL CASEPEISKV PIMVDSSKWE VIEAGLKCIQ
460 470 480 490 500
GKGIVNSISL KEGKEKFVEQ AKLIRRYGAA VIVMAFDEVG QADTRERKLE
510 520 530 540 550
ICTKAYRILV DEVGFPPEDV IFDPNIFAVA TGIDEHNNYA VDFIEAVADI
560 570 580 590 600
KRDLPHAMIS GGVSNVSFSF RGNNYVREAI HAVFLYHCFK NGMDMGIVNA
610 620 630 640 650
GQLEIYDNVP EKLREAVEDV VLNRRDDATE RLLEIAEEYR ENAVGKQEDA
660 670 680 690 700
SALEWRTWSV EKRLEHALVK GITEFIVEDT EEARLNASKP LEVIEGPLMD
710 720 730 740 750
GMNVVGDLFG EGKMFLPQVV KSARVMKQAV AHLEPFINAS KQVGSSNGKI
760 770 780 790 800
LLATVKGDVH DIGKNIVGVV LQCNNYEIID LGVMVPCEQI LKVAKEQQVD
810 820 830 840 850
IIGLSGLITP SLDEMVHVAK EMERLGFDLP LLIGGATTSK AHTAVKIEQN
860 870 880 890 900
YSHPVVYVNN ASRAVGVCTS LLSDELRPAF VERLQADYEL VRDQHNRKKP
910 920 930 940 950
RTKPVTLEAA RANKVAIDWQ SYTPPAPSQP GVHVFDDFDV ATLRQYIDWT
960 970 980 990 1000
PFFLTWSLVG KYPTIFEHEE VGEEAKRLFE DANEWLDRIE QEGLLKARGM
1010 1020 1030 1040 1050
CGLFPAASVG DDIEVYTDES RTQVAKVLHN LRQQTEKPKG ANYCLSDYVA
1060 1070 1080 1090 1100
PKESGKKDWI GAFAVTGGVN ERELADQFKA QGDDYNAIMI QAVADRLAEA
1110 1120 1130 1140 1150
FAEYLHERVR KEIWGYAADE NLSNEELIRE KYQGIRPAPG YPACPEHTEK
1160 1170 1180 1190 1200
GPLWELLNVE ETIGMSLTSS YAMWPGASVS GWYFSHPDSR YFAIAQIQQD
1210 1220
QVESYAKRKG WDLLEAEKWL GPNING
Length:1,226
Mass (Da):136,333
Last modified:December 15, 2003 - v1
Checksum:i299B647CC6D24028
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000037 Genomic DNA. Translation: BAC95724.1.
RefSeqiNP_935753.1. NC_005139.1.
WP_011151258.1. NC_005139.1.

Genome annotation databases

EnsemblBacteriaiBAC95724; BAC95724; BAC95724.
GeneIDi2625802.
KEGGivvy:VV2960.
PATRICi20172780. VBIVibVul40472_2940.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000037 Genomic DNA. Translation: BAC95724.1.
RefSeqiNP_935753.1. NC_005139.1.
WP_011151258.1. NC_005139.1.

3D structure databases

ProteinModelPortaliQ7MHB1.
SMRiQ7MHB1. Positions 654-1224.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiQ7MHB1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC95724; BAC95724; BAC95724.
GeneIDi2625802.
KEGGivvy:VV2960.
PATRICi20172780. VBIVibVul40472_2940.

Phylogenomic databases

eggNOGiCOG1410.
HOGENOMiHOG000251409.
KOiK00548.
OMAiDYNSIMV.
OrthoDBiEOG6091CH.

Enzyme and pathway databases

UniPathwayiUPA00051; UER00081.
BioCyciVVUL196600:GJ9W-3052-MONOMER.

Family and domain databases

Gene3Di1.10.1240.10. 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.
InterProiIPR003759. 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]
PfamiPF02310. 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]
PIRSFiPIRSF000381. MetH. 1 hit.
SMARTiSM01018. B12-binding_2. 1 hit.
[Graphical view]
SUPFAMiSSF47644. SSF47644. 1 hit.
SSF51717. SSF51717. 1 hit.
SSF52242. SSF52242. 1 hit.
SSF56507. SSF56507. 1 hit.
SSF82282. SSF82282. 1 hit.
TIGRFAMsiTIGR02082. metH. 1 hit.
PROSITEiPS50974. 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]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: YJ016.

Entry informationi

Entry nameiMETH_VIBVY
AccessioniPrimary (citable) accession number: Q7MHB1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: December 15, 2003
Last modified: June 24, 2015
This is version 87 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.