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Q87KS8

- PUR2_VIBPA

UniProt

Q87KS8 - PUR2_VIBPA

Protein

Phosphoribosylamine--glycine ligase

Gene

purD

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 77 (01 Oct 2014)
      Sequence version 1 (23 May 2003)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N(1)-(5-phospho-D-ribosyl)glycinamide.UniRule annotation

    Cofactori

    Binds 1 magnesium or manganese ion per subunit.By similarity

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi286 – 2861Magnesium or manganeseUniRule annotation
    Metal bindingi288 – 2881Magnesium or manganeseUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi135 – 19662ATPUniRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-HAMAP
    2. magnesium ion binding Source: UniProtKB-HAMAP
    3. manganese ion binding Source: UniProtKB-HAMAP
    4. phosphoribosylamine-glycine ligase activity Source: UniProtKB-HAMAP

    GO - Biological processi

    1. 'de novo' IMP biosynthetic process Source: UniProtKB-UniPathway
    2. purine nucleobase biosynthetic process Source: InterPro

    Keywords - Molecular functioni

    Ligase

    Keywords - Biological processi

    Purine biosynthesis

    Keywords - Ligandi

    ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciVPAR223926:GHK4-3017-MONOMER.
    UniPathwayiUPA00074; UER00125.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Phosphoribosylamine--glycine ligaseUniRule annotation (EC:6.3.4.13UniRule annotation)
    Alternative name(s):
    GARSUniRule annotation
    Glycinamide ribonucleotide synthetaseUniRule annotation
    Phosphoribosylglycinamide synthetaseUniRule annotation
    Gene namesi
    Name:purDUniRule annotation
    Ordered Locus Names:VP2898
    OrganismiVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
    Taxonomic identifieri223926 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
    ProteomesiUP000002493: Chromosome 1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 429429Phosphoribosylamine--glycine ligasePRO_0000151498Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi223926.VP2898.

    Structurei

    3D structure databases

    ProteinModelPortaliQ87KS8.
    SMRiQ87KS8. Positions 1-425.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini109 – 316208ATP-graspUniRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the GARS family.UniRule annotation
    Contains 1 ATP-grasp domain.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0151.
    HOGENOMiHOG000033463.
    KOiK01945.
    OMAiYKGFLYA.
    OrthoDBiEOG69SKD1.

    Family and domain databases

    Gene3Di3.30.1490.20. 1 hit.
    3.30.470.20. 1 hit.
    3.40.50.20. 1 hit.
    3.90.600.10. 1 hit.
    HAMAPiMF_00138. GARS.
    InterProiIPR011761. ATP-grasp.
    IPR013815. ATP_grasp_subdomain_1.
    IPR013816. ATP_grasp_subdomain_2.
    IPR016185. PreATP-grasp_dom.
    IPR020561. PRibGlycinamid_synth_ATP-grasp.
    IPR000115. PRibGlycinamide_synth.
    IPR020560. PRibGlycinamide_synth_C-dom.
    IPR020559. PRibGlycinamide_synth_CS.
    IPR020562. PRibGlycinamide_synth_N.
    IPR011054. Rudment_hybrid_motif.
    [Graphical view]
    PfamiPF01071. GARS_A. 1 hit.
    PF02843. GARS_C. 1 hit.
    PF02844. GARS_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF51246. SSF51246. 1 hit.
    SSF52440. SSF52440. 1 hit.
    TIGRFAMsiTIGR00877. purD. 1 hit.
    PROSITEiPS50975. ATP_GRASP. 1 hit.
    PS00184. GARS. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q87KS8-1 [UniParc]FASTAAdd to Basket

    « Hide

    MRVLIIGSGG REHALGWKAA QNPNVETIFI APGNAGTALE PKLENVNIDV    50
    EDIAGLVAFA KEKAIELTIV GPEAPLVIGV VDAFREAGLP IFGPTQAAAQ 100
    LEGSKAFTKD FLARHQIPTG AYANFTEIEP ALAYVREQGA PIVVKADGLA 150
    AGKGVIVAMT LEEAEDAIKD MLAGNAFGDA GSRVVIEEFL DGEEASFIVM 200
    VDGENVLPMA TSQDHKRVGD KDTGPNTGGM GAYSPAPVVT PEIHNRIMEE 250
    VIYPTVRGMA SEGNPYTGFL YAGLMIDKDG TPKVIEYNCR FGDPETQPIM 300
    MRMESDLVDL CLAAIDEKLD QVESKWDPRA SIGIVLAAGG YPAAYNKGDV 350
    ISGLPQVEIE GEKVFHAGTD NQDGDIVTNG GRVLCATALG NSVSEAQQRA 400
    YELAKQISWD GMFHRNDIGY RAIAREQEK 429
    Length:429
    Mass (Da):45,791
    Last modified:May 23, 2003 - v1
    Checksum:i03124D4773881E5E
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000031 Genomic DNA. Translation: BAC61161.1.
    RefSeqiNP_799277.1. NC_004603.1.

    Genome annotation databases

    EnsemblBacteriaiBAC61161; BAC61161; BAC61161.
    GeneIDi1190473.
    KEGGivpa:VP2898.
    PATRICi20144042. VBIVibPar50997_2788.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000031 Genomic DNA. Translation: BAC61161.1 .
    RefSeqi NP_799277.1. NC_004603.1.

    3D structure databases

    ProteinModelPortali Q87KS8.
    SMRi Q87KS8. Positions 1-425.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 223926.VP2898.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAC61161 ; BAC61161 ; BAC61161 .
    GeneIDi 1190473.
    KEGGi vpa:VP2898.
    PATRICi 20144042. VBIVibPar50997_2788.

    Phylogenomic databases

    eggNOGi COG0151.
    HOGENOMi HOG000033463.
    KOi K01945.
    OMAi YKGFLYA.
    OrthoDBi EOG69SKD1.

    Enzyme and pathway databases

    UniPathwayi UPA00074 ; UER00125 .
    BioCyci VPAR223926:GHK4-3017-MONOMER.

    Family and domain databases

    Gene3Di 3.30.1490.20. 1 hit.
    3.30.470.20. 1 hit.
    3.40.50.20. 1 hit.
    3.90.600.10. 1 hit.
    HAMAPi MF_00138. GARS.
    InterProi IPR011761. ATP-grasp.
    IPR013815. ATP_grasp_subdomain_1.
    IPR013816. ATP_grasp_subdomain_2.
    IPR016185. PreATP-grasp_dom.
    IPR020561. PRibGlycinamid_synth_ATP-grasp.
    IPR000115. PRibGlycinamide_synth.
    IPR020560. PRibGlycinamide_synth_C-dom.
    IPR020559. PRibGlycinamide_synth_CS.
    IPR020562. PRibGlycinamide_synth_N.
    IPR011054. Rudment_hybrid_motif.
    [Graphical view ]
    Pfami PF01071. GARS_A. 1 hit.
    PF02843. GARS_C. 1 hit.
    PF02844. GARS_N. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51246. SSF51246. 1 hit.
    SSF52440. SSF52440. 1 hit.
    TIGRFAMsi TIGR00877. purD. 1 hit.
    PROSITEi PS50975. ATP_GRASP. 1 hit.
    PS00184. GARS. 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 nameiPUR2_VIBPA
    AccessioniPrimary (citable) accession number: Q87KS8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 23, 2003
    Last sequence update: May 23, 2003
    Last modified: October 1, 2014
    This is version 77 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. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3