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C5CRW8

- GCSP_VARPS

UniProt

C5CRW8 - GCSP_VARPS

Protein

Glycine dehydrogenase (decarboxylating)

Gene

gcvP

Organism
Variovorax paradoxus (strain S110)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 37 (01 Oct 2014)
      Sequence version 1 (28 Jul 2009)
      Previous versions | rss
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    Functioni

    The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO2 is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein.UniRule annotation

    Catalytic activityi

    Glycine + [glycine-cleavage complex H protein]-N(6)-lipoyl-L-lysine = [glycine-cleavage complex H protein]-S-aminomethyl-N(6)-dihydrolipoyl-L-lysine + CO2.UniRule annotation

    Cofactori

    Pyridoxal phosphate.UniRule annotation

    GO - Molecular functioni

    1. glycine dehydrogenase (decarboxylating) activity Source: UniProtKB-EC
    2. pyridoxal phosphate binding Source: InterPro

    GO - Biological processi

    1. glycine decarboxylation via glycine cleavage system Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciVPAR543728:GHLL-3332-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glycine dehydrogenase (decarboxylating)UniRule annotation (EC:1.4.4.2UniRule annotation)
    Alternative name(s):
    Glycine cleavage system P-proteinUniRule annotation
    Glycine decarboxylaseUniRule annotation
    Glycine dehydrogenase (aminomethyl-transferring)UniRule annotation
    Gene namesi
    Name:gcvPUniRule annotation
    Ordered Locus Names:Vapar_3301
    OrganismiVariovorax paradoxus (strain S110)
    Taxonomic identifieri543728 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaeVariovorax
    ProteomesiUP000000453: Chromosome 1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 968968Glycine dehydrogenase (decarboxylating)PRO_1000212658Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei713 – 7131N6-(pyridoxal phosphate)lysineUniRule annotation

    Interactioni

    Subunit structurei

    The glycine cleavage system is composed of four proteins: P, T, L and H.UniRule annotation

    Protein-protein interaction databases

    STRINGi543728.Vapar_3301.

    Structurei

    3D structure databases

    ProteinModelPortaliC5CRW8.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the GcvP family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG1003.
    HOGENOMiHOG000239369.
    KOiK00281.
    OMAiFDSRPYS.
    OrthoDBiEOG6HMXDX.

    Family and domain databases

    Gene3Di3.40.640.10. 2 hits.
    HAMAPiMF_00711. GcvP.
    InterProiIPR020580. GDC-P_N.
    IPR020581. GDC_P.
    IPR003437. GDC_P_homo.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    [Graphical view]
    PANTHERiPTHR11773. PTHR11773. 1 hit.
    PfamiPF02347. GDC-P. 2 hits.
    [Graphical view]
    SUPFAMiSSF53383. SSF53383. 3 hits.
    TIGRFAMsiTIGR00461. gcvP. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    C5CRW8-1 [UniParc]FASTAAdd to Basket

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    MPIPALPSLQ QLENAEEFLA RHIGIDAADE ARMLPVIGSE TRAELIDGIV    50
    PAAIRRAKPM RLPAPATEAD ALAELKAIAA KNKVFRSFIG QGYYGTHTPG 100
    VILRNVLENP AWYTAYTPYQ AEISQGRMEA LLNFQTMVCD LTGMAIANAS 150
    MLDEATAAAE AMTLAKRSVK SKSNVFLVSG DCHPQTIEVI KTRAAPLGIE 200
    VKVSTVSETL PHLMVSGEFF GVLAQYPATT GHVHDLRPLA GHAHQCDAAF 250
    CVAADLLALT LLAPPGEWDA DIVCGTTQRF GMPMCNGGPH AAYLACRDEF 300
    KRSLPGRLVG VSVDTHGQPA YRLALQTREQ HIRREKATSN ICTAQVLPAV 350
    VASMYAVYHG PDGLTRIAQR VAALTAILAQ GLAQMGREPV NGTAFDSLTI 400
    RTGDDTPKII ERAQAAGVNL RQRLQQHLGI SLDETTTRAD IETLWALFVP 450
    AGTPMPRFDD LANAVPRLPE DLRRTSAFLT HPVFNTHKSE TAMLRYIRSL 500
    SDKDLALDRS MIPLGSCTMK LNATSEMIPI TWPEFANIHP FAPAEQLVGY 550
    AQLDAQLRAW LCEATGYAGI SLQPNAGSQG EYAGLLAIRS FHEANGQGHR 600
    NICLIPSSAH GTNPASAQMV GLQVVVTACD AQGNVDMDDL RRACEKHSDK 650
    LAAVMITYPS THGVFETRVK ELCELVHEHG GRVYVDGANM NALVGVAAPG 700
    EFGGDVSHLN LHKTFCIPHG GGGPGVGPVC VVEDLVPYLP GHATAGVASN 750
    GVGAVSAAPL GNAAVLPISW MYCRMMGAKG LQAATEIAIL SANYISARLK 800
    DHYPTLYASP NGHVAHECIL DLRPLKDSSG VTAEDVAKRL IDYGFHAPTL 850
    SFPVPGTLMV EPTESEPLAE LDRFIDAMIA IRGEIRRVEE GVWPKDDNPL 900
    KHAPHTAASL MAAEWPHPYS RELGAFPLAE LKLAKYWPPI GRVDNVYGDR 950
    NLFCSCVPVG DYKETEEA 968
    Length:968
    Mass (Da):104,204
    Last modified:July 28, 2009 - v1
    Checksum:i8DFF68ABC656715D
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001635 Genomic DNA. Translation: ACS19919.1.
    RefSeqiYP_002945185.1. NC_012791.1.

    Genome annotation databases

    EnsemblBacteriaiACS19919; ACS19919; Vapar_3301.
    GeneIDi7973697.
    KEGGivap:Vapar_3301.
    PATRICi24007035. VBIVarPar36677_3304.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001635 Genomic DNA. Translation: ACS19919.1 .
    RefSeqi YP_002945185.1. NC_012791.1.

    3D structure databases

    ProteinModelPortali C5CRW8.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 543728.Vapar_3301.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACS19919 ; ACS19919 ; Vapar_3301 .
    GeneIDi 7973697.
    KEGGi vap:Vapar_3301.
    PATRICi 24007035. VBIVarPar36677_3304.

    Phylogenomic databases

    eggNOGi COG1003.
    HOGENOMi HOG000239369.
    KOi K00281.
    OMAi FDSRPYS.
    OrthoDBi EOG6HMXDX.

    Enzyme and pathway databases

    BioCyci VPAR543728:GHLL-3332-MONOMER.

    Family and domain databases

    Gene3Di 3.40.640.10. 2 hits.
    HAMAPi MF_00711. GcvP.
    InterProi IPR020580. GDC-P_N.
    IPR020581. GDC_P.
    IPR003437. GDC_P_homo.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    [Graphical view ]
    PANTHERi PTHR11773. PTHR11773. 1 hit.
    Pfami PF02347. GDC-P. 2 hits.
    [Graphical view ]
    SUPFAMi SSF53383. SSF53383. 3 hits.
    TIGRFAMsi TIGR00461. gcvP. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Complete genome sequence of the metabolically versatile plant growth-promoting endophyte, Variovorax paradoxus S110."
      Han J.I., Choi H.K., Lee S.W., Orwin P.M., Kim J., Laroe S.L., Kim T.G., O'Neil J., Leadbetter J.R., Lee S.Y., Hur C.G., Spain J.C., Ovchinnikova G., Goodwin L., Han C.
      J. Bacteriol. 193:1183-1190(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: S110.

    Entry informationi

    Entry nameiGCSP_VARPS
    AccessioniPrimary (citable) accession number: C5CRW8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 22, 2009
    Last sequence update: July 28, 2009
    Last modified: October 1, 2014
    This is version 37 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3