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P28272

- PYRD_YEAST

UniProt

P28272 - PYRD_YEAST

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Protein
Dihydroorotate dehydrogenase (fumarate)
Gene
URA1, YKL216W
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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.UniRule annotation

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. KM=115 µM for 2,6-dichloroindophenol

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

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

pH dependencei

Optimum pH is 8.5. Active from pH 7 to pH 10.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei46 – 461Substrate By similarity
Binding sitei130 – 1301FMN By similarity
Binding sitei130 – 1301Substrate By similarity
Active sitei132 – 1321Nucleophile By similarity
Binding sitei167 – 1671FMN By similarity
Binding sitei195 – 1951FMN; via carbonyl oxygen By similarity
Binding sitei224 – 2241FMN; via amide nitrogen By similarity

Regions

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

GO - Molecular functioni

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

GO - Biological processi

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

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
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 314314Dihydroorotate dehydrogenase (fumarate)UniRule annotation
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.

Family & Domainsi

Region

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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 131 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.

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

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