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O58462

- PYRF_PYRHO

UniProt

O58462 - PYRF_PYRHO

Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 94 (01 Oct 2014)
      Sequence version 2 (23 Jan 2002)
      Previous versions | rss
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    Functioni

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

    Catalytic activityi

    Orotidine 5'-phosphate = UMP + CO2.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei7 – 71Substrate
    Binding sitei29 – 291Substrate
    Active sitei59 – 591Proton donor
    Binding sitei109 – 1091Substrate
    Binding sitei185 – 1851Substrate; via amide nitrogen
    Binding sitei186 – 1861Substrate

    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

    BioCyciPHOR70601:GJWR-730-MONOMER.
    UniPathwayiUPA00070; UER00120.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Orotidine 5'-phosphate decarboxylase (EC:4.1.1.23)
    Alternative name(s):
    OMP decarboxylase
    Short name:
    OMPDCase
    Short name:
    OMPdecase
    Gene namesi
    Name:pyrF
    Ordered Locus Names:PH0731
    OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
    Taxonomic identifieri70601 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
    ProteomesiUP000000752: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 208208Orotidine 5'-phosphate decarboxylasePRO_0000134616Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRINGi70601.PH0731.

    Structurei

    Secondary structure

    1
    208
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 54
    Helixi11 – 2111
    Helixi22 – 243
    Beta strandi26 – 316
    Helixi32 – 387
    Helixi42 – 509
    Beta strandi53 – 608
    Helixi64 – 7613
    Beta strandi80 – 867
    Helixi90 – 978
    Beta strandi100 – 1056
    Helixi111 – 1144
    Turni115 – 1173
    Helixi118 – 1203
    Helixi121 – 13111
    Beta strandi134 – 1374
    Helixi144 – 1529
    Beta strandi158 – 1614
    Beta strandi166 – 1694
    Helixi170 – 1778
    Beta strandi180 – 1845
    Helixi186 – 1894
    Beta strandi191 – 1933
    Helixi194 – 20512

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2CZ5X-ray1.85A/B1-208[»]
    2CZDX-ray1.60A/B1-208[»]
    2CZEX-ray1.85A/B1-208[»]
    2CZFX-ray1.85A/B1-208[»]
    ProteinModelPortaliO58462.
    SMRiO58462. Positions 1-208.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO58462.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni57 – 6610Substrate binding
    Regioni162 – 17211Substrate bindingAdd
    BLAST

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0284.
    HOGENOMiHOG000226069.
    KOiK01591.
    OMAiTEMSHPG.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_01200_A. OMPdecase_type1_A.
    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.

    O58462-1 [UniParc]FASTAAdd to Basket

    « Hide

    MIVLALDVYE GERAIKIAKS VKDYISMIKV NWPLILGSGV DIIRRLKEET    50
    GVEIIADLKL ADIPNTNRLI ARKVFGAGAD YVIVHTFVGR DSVMAVKELG 100
    EIIMVVEMSH PGALEFINPL TDRFIEVANE IEPFGVIAPG TRPERIGYIR 150
    DRLKEGIKIL APGIGAQGGK AKDAVKAGAD YIIVGRAIYN APNPREAAKA 200
    IYDEIRGV 208
    Length:208
    Mass (Da):22,692
    Last modified:January 23, 2002 - v2
    Checksum:iF0D3124758EB4C43
    GO

    Sequence cautioni

    The sequence BAA29822.1 differs from that shown. Reason: Erroneous initiation.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000001 Genomic DNA. Translation: BAA29822.1. Different initiation.
    PIRiD71120.
    RefSeqiNP_142676.1. NC_000961.1.

    Genome annotation databases

    EnsemblBacteriaiBAA29822; BAA29822; BAA29822.
    GeneIDi1443064.
    KEGGipho:PH0731.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000001 Genomic DNA. Translation: BAA29822.1 . Different initiation.
    PIRi D71120.
    RefSeqi NP_142676.1. NC_000961.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2CZ5 X-ray 1.85 A/B 1-208 [» ]
    2CZD X-ray 1.60 A/B 1-208 [» ]
    2CZE X-ray 1.85 A/B 1-208 [» ]
    2CZF X-ray 1.85 A/B 1-208 [» ]
    ProteinModelPortali O58462.
    SMRi O58462. Positions 1-208.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 70601.PH0731.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAA29822 ; BAA29822 ; BAA29822 .
    GeneIDi 1443064.
    KEGGi pho:PH0731.

    Phylogenomic databases

    eggNOGi COG0284.
    HOGENOMi HOG000226069.
    KOi K01591.
    OMAi TEMSHPG.

    Enzyme and pathway databases

    UniPathwayi UPA00070 ; UER00120 .
    BioCyci PHOR70601:GJWR-730-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei O58462.

    Family and domain databases

    Gene3Di 3.20.20.70. 1 hit.
    HAMAPi MF_01200_A. OMPdecase_type1_A.
    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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.
    2. "Crystal structure of orotidine 5'-phosphate decarboxylase from Pyrococcus horikoshii OT3."
      RIKEN structural genomics initiative (RSGI)
      Submitted (JAN-2006) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF NATIVE PROTEIN AND COMPLEXES WITH UMP AND XMP, SUBUNIT.
      Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.

    Entry informationi

    Entry nameiPYRF_PYRHO
    AccessioniPrimary (citable) accession number: O58462
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: January 23, 2002
    Last modified: October 1, 2014
    This is version 94 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

    3D-structure, Complete proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3