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Q87L95

- METH_VIBPA

UniProt

Q87L95 - METH_VIBPA

Protein

Methionine synthase

Gene

metH

Organism
Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 79 (01 Oct 2014)
      Sequence version 1 (01 Jun 2003)
      Previous versions | rss
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    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

    Methylcobalamin (MeCBL).By similarity
    Binds 1 zinc ion per subunit.By similarity

    Pathwayi

    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

    1. cobalamin binding Source: UniProtKB-KW
    2. methionine synthase activity Source: UniProtKB-EC
    3. S-adenosylmethionine-homocysteine S-methyltransferase activity Source: InterPro
    4. zinc ion binding Source: InterPro

    GO - Biological processi

    1. pteridine-containing compound metabolic process Source: InterPro

    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

    BioCyciVPAR223926:GHK4-2806-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:VP2717
    OrganismiVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
    Taxonomic identifieri223926 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
    ProteomesiUP000002493: Chromosome 1

    Subcellular locationi

    GO - Cellular componenti

    1. intracellular Source: InterPro

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 12261226Methionine synthasePRO_0000204541Add
    BLAST

    Proteomic databases

    PRIDEiQ87L95.

    Interactioni

    Protein-protein interaction databases

    STRINGi223926.VP2717.

    Structurei

    3D structure databases

    ProteinModelPortaliQ87L95.
    SMRiQ87L95. 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.
    OMAiLTEHYAM.
    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.

    Q87L95-1 [UniParc]FASTAAdd to Basket

    « Hide

    MGSKVRQQIE AQLKQRILLI DGGMGTMIQG YKLEEQDYRG ERFANWHCDL     50
    KGNNDLLVLS QPQLIKEIHS AYLEAGADIL ETNTFNATTI AMADYEMESL 100
    SEEINFAAAK LAREVADEWT AKTPDKPRYV AGVLGPTNRT CSISPDVNDP 150
    GYRNVSFDEL VEAYSESTRA LIRGGADLIL IETIFDTLNA KACAFAVDSV 200
    FEELGVALPV MISGTITDAS GRTLSGQTTE AFYNSLRHVR PLSFGLNCAL 250
    GPDELRPYVE ELSRISESFV SAHPNAGLPN AFGEYDLSPE DMAEHVKEWA 300
    SSGFLNLIGG CCGTTPEHIR QMAQAVEGVT PRALPDLPVA CRLSGLEPLT 350
    IEKETLFINV GERTNVTGSA RFKRLIKEEQ YDEALEVARQ QVENGAQIID 400
    INMDEGMLDA QACMVRFLNL CASEPEISKV PIMVDSSKWE VIEAGLKCIQ 450
    GKGIVNSISL KEGKEKFVEQ AKLIRRYGAA VIVMAFDEVG QAETRTRKLE 500
    ICTNAYRILV DEVGFPPEDI IFDPNIFAVA TGIDEHNNYA VDFIEAVADI 550
    KRDLPHAMIS GGVSNVSFSF RGNNYVREAI HAVFLYHCFK NGMDMGIVNA 600
    GQLEIYDNVP EKLREAVEDV VLNRRDDATE RLLDIAAEYA DKGVGKEEDA 650
    SALEWRTWPV AKRLEHALVK GITEFIVADT EEARVNAVKP LEVIEGPLMD 700
    GMNVVGDLFG EGKMFLPQVV KSARVMKQAV AHLEPFINAE KQSGSSNGKI 750
    LLATVKGDVH DIGKNIVGVV LQCNNYEIID LGVMVPCEKI LKVAIEENVD 800
    IIGLSGLITP SLDEMVHVAK EMERLNFDLP LLIGGATTSK AHTAVKIEQN 850
    YKNPVVYVNN ASRAVGVCSS LLSDERRPAF IEKLDADYER VRDQHNRKKP 900
    RTKPVTLEQA RANKVAIDWD AYTPPVPAKP GLHIFDDFDV ATLRKYIDWT 950
    PFFMTWSLVG KYPTIFKHEE VGEEAQRLFH DANELLDRVE REGLLKARGI 1000
    CGLFPAASVG DDIEVYTDES RTEVAKVLRN LRQQTEKPKG FNYCLSDYIA 1050
    PKESGKQDWV GAFAVTGGIG ERELADEYKA QGDDYNAIMI QAVADRLAEA 1100
    FAEYLHERVR KEIWGYAADE NLSNDELIRE KYQGIRPAPG YPACPEHTEK 1150
    GPLWELLNVE ENIGMSLTTS YAMYPGASVS GWYFSHPDSR YFAIAQIQDD 1200
    QLESYADRKG WDRIEAEKWL GPNING 1226
    Length:1,226
    Mass (Da):136,218
    Last modified:June 1, 2003 - v1
    Checksum:i2F7A3269FB7C20A9
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000031 Genomic DNA. Translation: BAC60980.1.
    RefSeqiNP_799096.1. NC_004603.1.

    Genome annotation databases

    EnsemblBacteriaiBAC60980; BAC60980; BAC60980.
    GeneIDi1190262.
    KEGGivpa:VP2717.
    PATRICi20143630. VBIVibPar50997_2612.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000031 Genomic DNA. Translation: BAC60980.1 .
    RefSeqi NP_799096.1. NC_004603.1.

    3D structure databases

    ProteinModelPortali Q87L95.
    SMRi Q87L95. Positions 654-1224.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 223926.VP2717.

    Proteomic databases

    PRIDEi Q87L95.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAC60980 ; BAC60980 ; BAC60980 .
    GeneIDi 1190262.
    KEGGi vpa:VP2717.
    PATRICi 20143630. VBIVibPar50997_2612.

    Phylogenomic databases

    eggNOGi COG1410.
    HOGENOMi HOG000251409.
    KOi K00548.
    OMAi LTEHYAM.
    OrthoDBi EOG6091CH.

    Enzyme and pathway databases

    UniPathwayi UPA00051 ; UER00081 .
    BioCyci VPAR223926:GHK4-2806-MONOMER.

    Family and domain databases

    Gene3Di 1.10.1240.10. 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.
    InterProi IPR003759. 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 ]
    Pfami PF02310. 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 ]
    PIRSFi PIRSF000381. MetH. 1 hit.
    SMARTi SM01018. B12-binding_2. 1 hit.
    [Graphical view ]
    SUPFAMi SSF47644. SSF47644. 1 hit.
    SSF51717. SSF51717. 1 hit.
    SSF52242. SSF52242. 1 hit.
    SSF56507. SSF56507. 1 hit.
    SSF82282. SSF82282. 1 hit.
    TIGRFAMsi TIGR02082. metH. 1 hit.
    PROSITEi PS50974. 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 ]
    ProtoNeti Search...

    Publicationsi

    1. "Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae."
      Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K., Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S., Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T.
      Lancet 361:743-749(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: RIMD 2210633.

    Entry informationi

    Entry nameiMETH_VIBPA
    AccessioniPrimary (citable) accession number: Q87L95
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 22, 2005
    Last sequence update: June 1, 2003
    Last modified: October 1, 2014
    This is version 79 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, Reference proteome

    Documents

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

    External Data

    Dasty 3