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P28272

- PYRD_YEAST

UniProt

P28272 - PYRD_YEAST

Protein

Dihydroorotate dehydrogenase (fumarate)

Gene

URA1

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 132 (01 Oct 2014)
      Sequence version 1 (01 Dec 1992)
      Previous versions | rss
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    Functioni

    Catalyzes the conversion of dihydroorotate to orotate with fumarate as the electron acceptor. Molecular oxygen can replace fumarate in vitro. Does not use oxaloacetate or NAD or NADP as electron acceptors.6 Publications

    Catalytic activityi

    (S)-dihydroorotate + fumarate = orotate + succinate.1 Publication

    Cofactori

    Binds 1 FMN per subunit.1 Publication

    Enzyme regulationi

    The activity is independent of the presence of oxygen.

    Kineticsi

    1. KM=8.4 µM for (S)-dihydroorotate (at pH 7.5)3 Publications
    2. KM=45 µM for fumarate (at pH 7.5)3 Publications
    3. KM=115 µM for 2,6-dichloroindophenol3 Publications

    Vmax=20.4 µmol/min/mg enzyme (with 2,6-dichloroindophenol as electron acceptor)3 Publications

    Vmax=5.1 µmol/min/mg enzyme (with fumarate as electron acceptor)3 Publications

    pH dependencei

    Optimum pH is 8.5. Active from pH 7 to pH 10.3 Publications

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei46 – 461SubstrateBy similarity
    Binding sitei130 – 1301FMNBy similarity
    Binding sitei130 – 1301SubstrateBy similarity
    Active sitei133 – 1331NucleophileBy similarity
    Binding sitei167 – 1671FMNBy similarity
    Binding sitei195 – 1951FMN; via carbonyl oxygenBy similarity
    Binding sitei224 – 2241FMN; via amide nitrogenBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi46 – 472FMNBy similarity
    Nucleotide bindingi252 – 2532FMNBy similarity
    Nucleotide bindingi274 – 2752FMNBy similarity

    GO - Molecular functioni

    1. dihydroorotate dehydrogenase activity Source: SGD
    2. dihydroorotate oxidase activity Source: InterPro

    GO - Biological processi

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

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Pyrimidine biosynthesis

    Keywords - Ligandi

    Flavoprotein, FMN

    Enzyme and pathway databases

    BioCyciMetaCyc:YKL216W-MONOMER.
    YEAST:YKL216W-MONOMER.
    ReactomeiREACT_209624. Pyrimidine catabolism.
    SABIO-RKP28272.
    UniPathwayiUPA00070.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Dihydroorotate dehydrogenase (fumarate) (EC:1.3.98.1)
    Short name:
    DHOD
    Short name:
    DHODase
    Short name:
    DHOdehase
    Alternative name(s):
    Dihydroorotate oxidase
    Gene namesi
    Name:URA1
    Ordered Locus Names:YKL216W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XI

    Organism-specific databases

    CYGDiYKL216w.
    SGDiS000001699. URA1.

    Subcellular locationi

    Cytoplasm 1 Publication

    GO - Cellular componenti

    1. cytoplasm Source: SGD
    2. extrinsic component of membrane Source: SGD

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 314314Dihydroorotate dehydrogenase (fumarate)PRO_0000148506Add
    BLAST

    Proteomic databases

    MaxQBiP28272.
    PaxDbiP28272.
    PeptideAtlasiP28272.

    Expressioni

    Gene expression databases

    GenevestigatoriP28272.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    BioGridi33949. 50 interactions.
    DIPiDIP-6573N.
    IntActiP28272. 2 interactions.
    MINTiMINT-709357.

    Structurei

    3D structure databases

    ProteinModelPortaliP28272.
    SMRiP28272. Positions 5-314.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni70 – 745Substrate bindingBy similarity
    Regioni196 – 1972Substrate bindingBy similarity

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0167.
    GeneTreeiENSGT00500000044924.
    HOGENOMiHOG000225104.
    KOiK00226.
    OMAiTHIIANI.
    OrthoDBiEOG7Z3FFD.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00224. DHO_dh_type1.
    InterProiIPR013785. Aldolase_TIM.
    IPR005720. Dihydroorotate_DH.
    IPR024920. Dihydroorotate_DH_1.
    IPR012135. Dihydroorotate_DH_1_2.
    IPR001295. Dihydroorotate_DH_CS.
    [Graphical view]
    PfamiPF01180. DHO_dh. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000164. DHO_oxidase. 1 hit.
    TIGRFAMsiTIGR01037. pyrD_sub1_fam. 1 hit.
    PROSITEiPS00911. DHODEHASE_1. 1 hit.
    PS00912. DHODEHASE_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P28272-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTASLTTKFL NNTYENPFMN ASGVHCMTTQ ELDELANSKA GAFITKSATT    50
    LEREGNPEPR YISVPLGSIN SMGLPNEGID YYLSYVLNRQ KNYPDAPAIF 100
    FSVAGMSIDE NLNLLRKIQD SEFNGITELN LSCPNVPGKP QVAYDFDLTK 150
    ETLEKVFAFF KKPLGVKLPP YFDFAHFDIM AKILNEFPLA YVNSINSIGN 200
    GLFIDVEKES VVVKPKNGFG GIGGEYVKPT ALANVRAFYT RLRPEIKVIG 250
    TGGIKSGKDA FEHLLCGASM LQIGTELQKE GVKIFERIEK ELKDIMEAKG 300
    YTSIDQFRGK LNSI 314
    Length:314
    Mass (Da):34,801
    Last modified:December 1, 1992 - v1
    Checksum:i0F1FF9BDA7F8D68E
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti58 – 581E → K in strain: CLIB 95, CLIB 219, CLIB 382, CLIB 388, CLIB 413, CLIB 556, CLIB 630, K1, R12, R13, YIIc12 and YIIc17. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M83295 Genomic DNA. Translation: AAA34566.1.
    X59371 Genomic DNA. Translation: CAA42014.1.
    AJ585637 Genomic DNA. Translation: CAE52157.1.
    AJ585638 Genomic DNA. Translation: CAE52158.1.
    AJ585639 Genomic DNA. Translation: CAE52159.1.
    AJ585640 Genomic DNA. Translation: CAE52160.1.
    AJ585641 Genomic DNA. Translation: CAE52161.1.
    AJ585642 Genomic DNA. Translation: CAE52162.1.
    AJ585643 Genomic DNA. Translation: CAE52163.1.
    AJ585644 Genomic DNA. Translation: CAE52164.1.
    AJ585645 Genomic DNA. Translation: CAE52165.1.
    AJ585646 Genomic DNA. Translation: CAE52166.1.
    AJ585647 Genomic DNA. Translation: CAE52167.1.
    AJ585648 Genomic DNA. Translation: CAE52168.1.
    AJ585649 Genomic DNA. Translation: CAE52169.1.
    AJ585650 Genomic DNA. Translation: CAE52170.1.
    AJ585651 Genomic DNA. Translation: CAE52171.1.
    X75951 Genomic DNA. Translation: CAA53557.1.
    Z28216 Genomic DNA. Translation: CAA82061.1.
    BK006944 Genomic DNA. Translation: DAA08953.1.
    PIRiJC1276.
    RefSeqiNP_012706.1. NM_001179781.1.

    Genome annotation databases

    EnsemblFungiiYKL216W; YKL216W; YKL216W.
    GeneIDi853664.
    KEGGisce:YKL216W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M83295 Genomic DNA. Translation: AAA34566.1 .
    X59371 Genomic DNA. Translation: CAA42014.1 .
    AJ585637 Genomic DNA. Translation: CAE52157.1 .
    AJ585638 Genomic DNA. Translation: CAE52158.1 .
    AJ585639 Genomic DNA. Translation: CAE52159.1 .
    AJ585640 Genomic DNA. Translation: CAE52160.1 .
    AJ585641 Genomic DNA. Translation: CAE52161.1 .
    AJ585642 Genomic DNA. Translation: CAE52162.1 .
    AJ585643 Genomic DNA. Translation: CAE52163.1 .
    AJ585644 Genomic DNA. Translation: CAE52164.1 .
    AJ585645 Genomic DNA. Translation: CAE52165.1 .
    AJ585646 Genomic DNA. Translation: CAE52166.1 .
    AJ585647 Genomic DNA. Translation: CAE52167.1 .
    AJ585648 Genomic DNA. Translation: CAE52168.1 .
    AJ585649 Genomic DNA. Translation: CAE52169.1 .
    AJ585650 Genomic DNA. Translation: CAE52170.1 .
    AJ585651 Genomic DNA. Translation: CAE52171.1 .
    X75951 Genomic DNA. Translation: CAA53557.1 .
    Z28216 Genomic DNA. Translation: CAA82061.1 .
    BK006944 Genomic DNA. Translation: DAA08953.1 .
    PIRi JC1276.
    RefSeqi NP_012706.1. NM_001179781.1.

    3D structure databases

    ProteinModelPortali P28272.
    SMRi P28272. Positions 5-314.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 33949. 50 interactions.
    DIPi DIP-6573N.
    IntActi P28272. 2 interactions.
    MINTi MINT-709357.

    Chemistry

    BindingDBi P28272.
    ChEMBLi CHEMBL5621.

    Proteomic databases

    MaxQBi P28272.
    PaxDbi P28272.
    PeptideAtlasi P28272.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YKL216W ; YKL216W ; YKL216W .
    GeneIDi 853664.
    KEGGi sce:YKL216W.

    Organism-specific databases

    CYGDi YKL216w.
    SGDi S000001699. URA1.

    Phylogenomic databases

    eggNOGi COG0167.
    GeneTreei ENSGT00500000044924.
    HOGENOMi HOG000225104.
    KOi K00226.
    OMAi THIIANI.
    OrthoDBi EOG7Z3FFD.

    Enzyme and pathway databases

    UniPathwayi UPA00070 .
    BioCyci MetaCyc:YKL216W-MONOMER.
    YEAST:YKL216W-MONOMER.
    Reactomei REACT_209624. Pyrimidine catabolism.
    SABIO-RK P28272.

    Miscellaneous databases

    NextBioi 974596.
    PROi P28272.

    Gene expression databases

    Genevestigatori P28272.

    Family and domain databases

    Gene3Di 3.20.20.70. 1 hit.
    HAMAPi MF_00224. DHO_dh_type1.
    InterProi IPR013785. Aldolase_TIM.
    IPR005720. Dihydroorotate_DH.
    IPR024920. Dihydroorotate_DH_1.
    IPR012135. Dihydroorotate_DH_1_2.
    IPR001295. Dihydroorotate_DH_CS.
    [Graphical view ]
    Pfami PF01180. DHO_dh. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000164. DHO_oxidase. 1 hit.
    TIGRFAMsi TIGR01037. pyrD_sub1_fam. 1 hit.
    PROSITEi PS00911. DHODEHASE_1. 1 hit.
    PS00912. DHODEHASE_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Nucleotide sequence of the URA1 gene of Saccharomyces cerevisiae."
      Roy A.
      Gene 118:149-150(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
      Strain: ATCC 28383 / FL100 / VTT C-80102.
    2. "Differential evolution of the Saccharomyces cerevisiae DUP240 paralogs and implication of recombination in phylogeny."
      Leh-Louis V., Wirth B., Despons L., Wain-Hobson S., Potier S., Souciet J.-L.
      Nucleic Acids Res. 32:2069-2078(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANT LYS-58.
      Strain: CLIB 219, CLIB 382, CLIB 388, CLIB 410, CLIB 413, CLIB 556, CLIB 630, CLIB 95, K1, R12, R13, Sigma 1278B, YIIc12 and YIIc17.
    3. "The complete sequencing of a 24.6 kb segment of yeast chromosome XI identified the known loci URA1, SAC1 and TRP3, and revealed 6 new open reading frames including homologues to the threonine dehydratases, membrane transporters, hydantoinases and the phospholipase A2-activating protein."
      Tzermia M., Horaitis O., Alexandraki D.
      Yeast 10:663-679(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    4. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    5. "Complete DNA sequence of yeast chromosome XI."
      Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C.
      , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W.
      Nature 369:371-378(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    6. "Divergent evolution of pyrimidine biosynthesis between anaerobic and aerobic yeasts."
      Nagy M., Lacroute F., Thomas D.
      Proc. Natl. Acad. Sci. U.S.A. 89:8966-8970(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION.
    7. "Catalytic properties of dihydroorotate dehydrogenase from Saccharomyces cerevisiae: studies on pH, alternate substrates, and inhibitors."
      Jordan D.B., Bisaha J.J., Picollelli M.A.
      Arch. Biochem. Biophys. 378:84-92(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBUNIT, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
    8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    9. "Two different dihydroorotate dehydrogenases from yeast Saccharomyces kluyveri."
      Zameitat E., Knecht W., Piskur J., Loeffler M.
      FEBS Lett. 568:129-134(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES.
    10. "Horizontal gene transfer promoted evolution of the ability to propagate under anaerobic conditions in yeasts."
      Gojkovic Z., Knecht W., Zameitat E., Warneboldt J., Coutelis J.-B., Pynyaha Y., Neuveglise C., Moeller K., Loeffler M., Piskur J.
      Mol. Genet. Genomics 271:387-393(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    11. "Dihydroorotate dehydrogenase from Saccharomyces cerevisiae: spectroscopic investigations with the recombinant enzyme throw light on catalytic properties and metabolism of fumarate analogues."
      Zameitat E., Pierik A.J., Zocher K., Loeffler M.
      FEMS Yeast Res. 7:897-904(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
    12. "Sites of ubiquitin attachment in Saccharomyces cerevisiae."
      Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.
      Proteomics 12:236-240(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiPYRD_YEAST
    AccessioniPrimary (citable) accession number: P28272
    Secondary accession number(s): D6VWY7, Q2XN75, Q70DC7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 1, 1992
    Last sequence update: December 1, 1992
    Last modified: October 1, 2014
    This is version 132 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 264000 molecules/cell in log phase SD medium.1 Publication

    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
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome XI
      Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

    External Data

    Dasty 3