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P03962

- PYRF_YEAST

UniProt

P03962 - PYRF_YEAST

Protein

Orotidine 5'-phosphate decarboxylase

Gene

URA3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 152 (01 Oct 2014)
      Sequence version 2 (01 Feb 1995)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    Orotidine 5'-phosphate = UMP + CO2.PROSITE-ProRule annotation

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei37 – 371Substrate
    Active sitei93 – 931Proton donor
    Binding sitei217 – 2171Substrate
    Binding sitei235 – 2351Substrate

    GO - Molecular functioni

    1. orotidine-5'-phosphate decarboxylase activity Source: SGD

    GO - Biological processi

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

    Keywords - Molecular functioni

    Decarboxylase, Lyase

    Keywords - Biological processi

    Pyrimidine biosynthesis

    Enzyme and pathway databases

    BioCyciYEAST:YEL021W-MONOMER.
    SABIO-RKP03962.
    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
    Uridine 5'-monophosphate synthase
    Short name:
    UMP synthase
    Gene namesi
    Name:URA3
    Ordered Locus Names:YEL021W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome V

    Organism-specific databases

    CYGDiYEL021w.
    SGDiS000000747. URA3.

    Subcellular locationi

    GO - Cellular componenti

    1. cytosol Source: SGD

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi59 – 591K → A: Reduces Kcat 100-fold. Reduces substrate affinity 900-fold. 1 Publication
    Mutagenesisi91 – 911D → A: Reduces activity over 100000-fold. 1 Publication
    Mutagenesisi93 – 931K → A: Reduces activity over 100000-fold. 1 Publication
    Mutagenesisi96 – 961D → A: Reduces Kcat over 100000-fold. Reduces substrate affinity 11-fold. 1 Publication
    Mutagenesisi215 – 2151Q → A: No effect. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 267266Orotidine 5'-phosphate decarboxylasePRO_0000134692Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylserine1 Publication
    Cross-linki93 – 93Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
    Cross-linki209 – 209Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
    Cross-linki253 – 253Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication

    Keywords - PTMi

    Acetylation, Isopeptide bond, Ubl conjugation

    Proteomic databases

    PaxDbiP03962.
    PeptideAtlasiP03962.
    PRIDEiP03962.

    Expressioni

    Gene expression databases

    GenevestigatoriP03962.

    Interactioni

    Protein-protein interaction databases

    BioGridi36708. 11 interactions.
    DIPiDIP-6576N.
    MINTiMINT-410591.
    STRINGi4932.YEL021W.

    Structurei

    Secondary structure

    1
    267
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 127
    Helixi16 – 2813
    Beta strandi32 – 354
    Helixi41 – 5111
    Helixi52 – 543
    Beta strandi56 – 605
    Helixi62 – 643
    Turni70 – 734
    Helixi74 – 8411
    Beta strandi87 – 948
    Helixi98 – 1069
    Turni108 – 1103
    Helixi112 – 1154
    Beta strandi117 – 1226
    Helixi123 – 1253
    Helixi128 – 14013
    Beta strandi146 – 1505
    Helixi162 – 17211
    Turni176 – 1783
    Beta strandi179 – 1835
    Helixi191 – 1933
    Beta strandi198 – 2014
    Beta strandi203 – 2053
    Turni208 – 2103
    Helixi214 – 2163
    Beta strandi217 – 2193
    Helixi220 – 2256
    Beta strandi229 – 2335
    Helixi235 – 2373
    Helixi244 – 26219

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1DQWX-ray2.10A/B/C/D1-267[»]
    1DQXX-ray2.40A/B/C/D1-267[»]
    3GDKX-ray2.00A/B/C/D1-267[»]
    3GDLX-ray1.65A/B1-267[»]
    3GDMX-ray1.60A/B1-267[»]
    3GDRX-ray1.90A/B/C/D1-267[»]
    3GDTX-ray1.60A/B/C/D1-267[»]
    ProteinModelPortaliP03962.
    SMRiP03962. Positions 3-263.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP03962.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni59 – 613Substrate binding
    Regioni91 – 10010Substrate binding

    Sequence similaritiesi

    Belongs to the OMP decarboxylase family.Curated

    Phylogenomic databases

    eggNOGiCOG0284.
    GeneTreeiENSGT00390000001856.
    HOGENOMiHOG000213905.
    KOiK01591.
    OMAiMGQQYRT.
    OrthoDBiEOG7CVQ76.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    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.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P03962-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSKATYKERA ATHPSPVAAK LFNIMHEKQT NLCASLDVRT TKELLELVEA    50
    LGPKICLLKT HVDILTDFSM EGTVKPLKAL SAKYNFLLFE DRKFADIGNT 100
    VKLQYSAGVY RIAEWADITN AHGVVGPGIV SGLKQAAEEV TKEPRGLLML 150
    AELSCKGSLA TGEYTKGTVD IAKSDKDFVI GFIAQRDMGG RDEGYDWLIM 200
    TPGVGLDDKG DALGQQYRTV DDVVSTGSDI IIVGRGLFAK GRDAKVEGER 250
    YRKAGWEAYL RRCGQQN 267
    Length:267
    Mass (Da):29,240
    Last modified:February 1, 1995 - v2
    Checksum:iD63EF9877BD0F984
    GO

    Sequence cautioni

    The sequence CAA25010.1 differs from that shown. Reason: Erroneous initiation.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti71 – 733EGT → RIR in AAA35199. 1 PublicationCurated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti160 – 1601A → S in strain: +D4.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    K02206 Genomic DNA. Translation: AAA34824.1.
    K02207 Genomic DNA. Translation: AAA34825.1.
    U18530 Genomic DNA. Translation: AAB64498.1.
    U89671 Genomic DNA. Translation: AAB49978.1.
    M12926 Genomic DNA. Translation: AAA35199.1.
    X00191 Genomic DNA. Translation: CAA25010.1. Different initiation.
    U89927 Genomic DNA. Translation: AAB64383.1.
    U63018 Genomic DNA. Translation: AAC53678.1.
    BK006939 Genomic DNA. Translation: DAA07631.1.
    PIRiA01082. DEBYOP.
    S05735. DCBYOF.
    RefSeqiNP_010893.3. NM_001178836.3.

    Genome annotation databases

    EnsemblFungiiYEL021W; YEL021W; YEL021W.
    GeneIDi856692.
    KEGGisce:YEL021W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    K02206 Genomic DNA. Translation: AAA34824.1 .
    K02207 Genomic DNA. Translation: AAA34825.1 .
    U18530 Genomic DNA. Translation: AAB64498.1 .
    U89671 Genomic DNA. Translation: AAB49978.1 .
    M12926 Genomic DNA. Translation: AAA35199.1 .
    X00191 Genomic DNA. Translation: CAA25010.1 . Different initiation.
    U89927 Genomic DNA. Translation: AAB64383.1 .
    U63018 Genomic DNA. Translation: AAC53678.1 .
    BK006939 Genomic DNA. Translation: DAA07631.1 .
    PIRi A01082. DEBYOP.
    S05735. DCBYOF.
    RefSeqi NP_010893.3. NM_001178836.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1DQW X-ray 2.10 A/B/C/D 1-267 [» ]
    1DQX X-ray 2.40 A/B/C/D 1-267 [» ]
    3GDK X-ray 2.00 A/B/C/D 1-267 [» ]
    3GDL X-ray 1.65 A/B 1-267 [» ]
    3GDM X-ray 1.60 A/B 1-267 [» ]
    3GDR X-ray 1.90 A/B/C/D 1-267 [» ]
    3GDT X-ray 1.60 A/B/C/D 1-267 [» ]
    ProteinModelPortali P03962.
    SMRi P03962. Positions 3-263.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 36708. 11 interactions.
    DIPi DIP-6576N.
    MINTi MINT-410591.
    STRINGi 4932.YEL021W.

    Chemistry

    BindingDBi P03962.
    ChEMBLi CHEMBL4858.

    Proteomic databases

    PaxDbi P03962.
    PeptideAtlasi P03962.
    PRIDEi P03962.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YEL021W ; YEL021W ; YEL021W .
    GeneIDi 856692.
    KEGGi sce:YEL021W.

    Organism-specific databases

    CYGDi YEL021w.
    SGDi S000000747. URA3.

    Phylogenomic databases

    eggNOGi COG0284.
    GeneTreei ENSGT00390000001856.
    HOGENOMi HOG000213905.
    KOi K01591.
    OMAi MGQQYRT.
    OrthoDBi EOG7CVQ76.

    Enzyme and pathway databases

    UniPathwayi UPA00070 ; UER00120 .
    BioCyci YEAST:YEL021W-MONOMER.
    SABIO-RK P03962.

    Miscellaneous databases

    EvolutionaryTracei P03962.
    NextBioi 982739.

    Gene expression databases

    Genevestigatori P03962.

    Family and domain databases

    Gene3Di 3.20.20.70. 1 hit.
    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. "Structure and function of the yeast URA3 gene: expression in Escherichia coli."
      Rose M., Grisafi P., Botstein D.
      Gene 29:113-124(1984) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: +D4 and ATCC 28383 / FL100 / VTT C-80102.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. Holtz A., Lou Y.
      Submitted (JUN-1997) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    5. "Transcription terminator-like element within a Saccharomyces cerevisiae promoter region."
      Yarger J.G., Armilei G., Gorman M.C.
      Mol. Cell. Biol. 6:1095-1101(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-73.
    6. "Structure and function of the yeast URA3 gene. Differentially regulated expression of hybrid beta-galactosidase from overlapping coding sequences in yeast."
      Rose M., Botstein D.
      J. Mol. Biol. 170:883-904(1983) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-11.
    7. "Dissecting a charged network at the active site of orotidine-5'-phosphate decarboxylase."
      Miller B.G., Snider M.J., Wolfenden R., Short S.A.
      J. Biol. Chem. 276:15174-15176(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF LYS-59; ASP-91; LYS-93; ASP-96 AND GLN-215.
    8. Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-93; LYS-209 AND LYS-253.
      Strain: SUB592.
    9. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
    10. "Anatomy of a proficient enzyme: the structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog."
      Miller B.G., Hassell A.M., Wolfenden R., Milburn M.V., Short S.A.
      Proc. Natl. Acad. Sci. U.S.A. 97:2011-2016(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH TRANSITION STATE ANALOG.

    Entry informationi

    Entry nameiPYRF_YEAST
    AccessioniPrimary (citable) accession number: P03962
    Secondary accession number(s): D3DLM7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 23, 1986
    Last sequence update: February 1, 1995
    Last modified: October 1, 2014
    This is version 152 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference 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
    4. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    5. Yeast chromosome V
      Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

    External Data

    Dasty 3