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Q3J8N5

- PYRF_NITOC

UniProt

Q3J8N5 - PYRF_NITOC

Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Nitrosococcus oceani (strain ATCC 19707 / NCIMB 11848)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 60 (01 Oct 2014)
      Sequence version 2 (27 Jun 2006)
      Previous versions | rss
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    Functioni

    Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).UniRule annotation

    Catalytic activityi

    Orotidine 5'-phosphate = UMP + CO2.UniRule annotation

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei11 – 111SubstrateUniRule annotation
    Binding sitei33 – 331SubstrateUniRule annotation
    Active sitei62 – 621Proton donorUniRule annotation
    Binding sitei119 – 1191SubstrateUniRule annotation
    Binding sitei180 – 1801SubstrateUniRule annotation
    Binding sitei189 – 1891SubstrateUniRule annotation
    Binding sitei209 – 2091Substrate; via amide nitrogenUniRule annotation
    Binding sitei210 – 2101SubstrateUniRule annotation

    GO - Molecular functioni

    1. orotidine-5'-phosphate decarboxylase activity Source: UniProtKB-HAMAP

    GO - Biological processi

    1. 'de novo' pyrimidine nucleobase biosynthetic process Source: InterPro
    2. 'de novo' UMP biosynthetic process Source: UniProtKB-UniPathway

    Keywords - Molecular functioni

    Decarboxylase, Lyase

    Keywords - Biological processi

    Pyrimidine biosynthesis

    Enzyme and pathway databases

    BioCyciNOCE323261:GCI3-2396-MONOMER.
    UniPathwayiUPA00070; UER00120.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Orotidine 5'-phosphate decarboxylaseUniRule annotation (EC:4.1.1.23UniRule annotation)
    Alternative name(s):
    OMP decarboxylaseUniRule annotation
    Short name:
    OMPDCaseUniRule annotation
    Short name:
    OMPdecaseUniRule annotation
    Gene namesi
    Name:pyrFUniRule annotation
    Ordered Locus Names:Noc_2353
    OrganismiNitrosococcus oceani (strain ATCC 19707 / NCIMB 11848)
    Taxonomic identifieri323261 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaChromatialesChromatiaceaeNitrosococcus
    ProteomesiUP000006838: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 232232Orotidine 5'-phosphate decarboxylasePRO_0000241880Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation

    Protein-protein interaction databases

    STRINGi323261.Noc_2353.

    Structurei

    3D structure databases

    ProteinModelPortaliQ3J8N5.
    SMRiQ3J8N5. Positions 1-229.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni60 – 6910Substrate bindingUniRule annotation

    Sequence similaritiesi

    Belongs to the OMP decarboxylase family. Type 1 subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0284.
    HOGENOMiHOG000226070.
    KOiK01591.
    OrthoDBiEOG6N6815.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_01200_B. OMPdecase_type1_B.
    InterProiIPR013785. Aldolase_TIM.
    IPR014732. OMPdecase.
    IPR018089. OMPdecase_AS.
    IPR001754. OMPdeCOase_dom.
    IPR011060. RibuloseP-bd_barrel.
    [Graphical view]
    PfamiPF00215. OMPdecase. 1 hit.
    [Graphical view]
    SMARTiSM00934. OMPdecase. 1 hit.
    [Graphical view]
    SUPFAMiSSF51366. SSF51366. 1 hit.
    TIGRFAMsiTIGR01740. pyrF. 1 hit.
    PROSITEiPS00156. OMPDECASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q3J8N5-1 [UniParc]FASTAAdd to Basket

    « Hide

    MEKSRIIIAL DYPNEEQALS LVRQLDPAQC RLKVGKELFT RAGPSLVKRL    50
    AAQGFPIFLD LKFHDIPHTV ARACLAAADL GVWMLNIHAL GGLSMMKAAQ 100
    EALANHPSHP QLIAVTVLTS MDQAALSQIG LAGTPEDNVL QLALLTQEAG 150
    LDGIVCSGQE APALRQTLGK EFLLVTPGIR PAGAAPKDQQ RVLTPREALA 200
    KGANYLVIGR PITAAPDPMM ALRAIEAEIS NV 232
    Length:232
    Mass (Da):24,743
    Last modified:June 27, 2006 - v2
    Checksum:iB07F22D45EB25394
    GO

    Sequence cautioni

    The sequence ABA58811.1 differs from that shown. Reason: Erroneous initiation.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000127 Genomic DNA. Translation: ABA58811.1. Different initiation.
    RefSeqiYP_344341.1. NC_007484.1.

    Genome annotation databases

    EnsemblBacteriaiABA58811; ABA58811; Noc_2353.
    GeneIDi3704793.
    KEGGinoc:Noc_2353.
    PATRICi22709118. VBINitOce57959_2764.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000127 Genomic DNA. Translation: ABA58811.1 . Different initiation.
    RefSeqi YP_344341.1. NC_007484.1.

    3D structure databases

    ProteinModelPortali Q3J8N5.
    SMRi Q3J8N5. Positions 1-229.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 323261.Noc_2353.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABA58811 ; ABA58811 ; Noc_2353 .
    GeneIDi 3704793.
    KEGGi noc:Noc_2353.
    PATRICi 22709118. VBINitOce57959_2764.

    Phylogenomic databases

    eggNOGi COG0284.
    HOGENOMi HOG000226070.
    KOi K01591.
    OrthoDBi EOG6N6815.

    Enzyme and pathway databases

    UniPathwayi UPA00070 ; UER00120 .
    BioCyci NOCE323261:GCI3-2396-MONOMER.

    Family and domain databases

    Gene3Di 3.20.20.70. 1 hit.
    HAMAPi MF_01200_B. OMPdecase_type1_B.
    InterProi IPR013785. Aldolase_TIM.
    IPR014732. OMPdecase.
    IPR018089. OMPdecase_AS.
    IPR001754. OMPdeCOase_dom.
    IPR011060. RibuloseP-bd_barrel.
    [Graphical view ]
    Pfami PF00215. OMPdecase. 1 hit.
    [Graphical view ]
    SMARTi SM00934. OMPdecase. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51366. SSF51366. 1 hit.
    TIGRFAMsi TIGR01740. pyrF. 1 hit.
    PROSITEi PS00156. OMPDECASE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707."
      Klotz M.G., Arp D.J., Chain P.S.G., El-Sheikh A.F., Hauser L.J., Hommes N.G., Larimer F.W., Malfatti S.A., Norton J.M., Poret-Peterson A.T., Vergez L.M., Ward B.B.
      Appl. Environ. Microbiol. 72:6299-6315(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 19707 / NCIMB 11848.

    Entry informationi

    Entry nameiPYRF_NITOC
    AccessioniPrimary (citable) accession number: Q3J8N5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 27, 2006
    Last sequence update: June 27, 2006
    Last modified: October 1, 2014
    This is version 60 of the entry and version 2 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