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P28272 (PYRD_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 129. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Dihydroorotate dehydrogenase (fumarate)

Short name=DHOD
Short name=DHODase
Short name=DHOdehase
EC=1.3.98.1
Alternative name(s):
Dihydroorotate oxidase
Gene names
Name:URA1
Ordered Locus Names:YKL216W
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length314 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1 Ref.6 Ref.7 Ref.9 Ref.10 Ref.11

Catalytic activity

(S)-dihydroorotate + fumarate = orotate + succinate. Ref.9

Cofactor

Binds 1 FMN per subunit. Ref.7

Enzyme regulation

The activity is independent of the presence of oxygen. HAMAP-Rule MF_00224

Pathway

Pyrimidine metabolism; UMP biosynthesis via de novo pathway. HAMAP-Rule MF_00224

Subunit structure

Homodimer. Ref.7

Subcellular location

Cytoplasm Ref.6.

Miscellaneous

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

Sequence similarities

Belongs to the dihydroorotate dehydrogenase family. Type 1 subfamily.

Biophysicochemical properties

Kinetic parameters:

KM=8.4 µM for (S)-dihydroorotate (at pH 7.5) Ref.7 Ref.9 Ref.11

KM=45 µM for fumarate (at pH 7.5)

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 dependence:

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 314314Dihydroorotate dehydrogenase (fumarate) HAMAP-Rule MF_00224
PRO_0000148506

Regions

Nucleotide binding46 – 472FMN By similarity
Nucleotide binding252 – 2532FMN By similarity
Nucleotide binding274 – 2752FMN By similarity
Region70 – 745Substrate binding By similarity
Region196 – 1972Substrate binding By similarity

Sites

Active site1321Nucleophile By similarity
Binding site461Substrate By similarity
Binding site1301FMN By similarity
Binding site1301Substrate By similarity
Binding site1671FMN By similarity
Binding site1951FMN; via carbonyl oxygen By similarity
Binding site2241FMN; via amide nitrogen By similarity

Natural variations

Natural variant581E → K in strain: CLIB 95, CLIB 219, CLIB 382, CLIB 388, CLIB 413, CLIB 556, CLIB 630, K1, R12, R13, YIIc12 and YIIc17. Ref.2

Sequences

Sequence LengthMass (Da)Tools
P28272 [UniParc].

Last modified December 1, 1992. Version 1.
Checksum: 0F1FF9BDA7F8D68E

FASTA31434,801
        10         20         30         40         50         60 
MTASLTTKFL NNTYENPFMN ASGVHCMTTQ ELDELANSKA GAFITKSATT LEREGNPEPR 

        70         80         90        100        110        120 
YISVPLGSIN SMGLPNEGID YYLSYVLNRQ KNYPDAPAIF FSVAGMSIDE NLNLLRKIQD 

       130        140        150        160        170        180 
SEFNGITELN LSCPNVPGKP QVAYDFDLTK ETLEKVFAFF KKPLGVKLPP YFDFAHFDIM 

       190        200        210        220        230        240 
AKILNEFPLA YVNSINSIGN GLFIDVEKES VVVKPKNGFG GIGGEYVKPT ALANVRAFYT 

       250        260        270        280        290        300 
RLRPEIKVIG TGGIKSGKDA FEHLLCGASM LQIGTELQKE GVKIFERIEK ELKDIMEAKG 

       310 
YTSIDQFRGK LNSI 

« Hide

References

« Hide 'large scale' references
[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]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
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. expand/collapse author list , 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]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
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].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRJC1276.
RefSeqNP_012706.1. NM_001179781.1.

3D structure databases

ProteinModelPortalP28272.
SMRP28272. Positions 5-314.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid33949. 50 interactions.
DIPDIP-6573N.
IntActP28272. 2 interactions.
MINTMINT-709357.

Chemistry

BindingDBP28272.
ChEMBLCHEMBL5621.

Proteomic databases

PaxDbP28272.
PeptideAtlasP28272.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYKL216W; YKL216W; YKL216W.
GeneID853664.
KEGGsce:YKL216W.

Organism-specific databases

CYGDYKL216w.
SGDS000001699. URA1.

Phylogenomic databases

eggNOGCOG0167.
GeneTreeENSGT00500000044924.
HOGENOMHOG000225104.
KOK00226.
OMAGISGKCI.
OrthoDBEOG7Z3FFD.

Enzyme and pathway databases

BioCycMetaCyc:YKL216W-MONOMER.
YEAST:YKL216W-MONOMER.
SABIO-RKP28272.
UniPathwayUPA00070.

Gene expression databases

GenevestigatorP28272.

Family and domain databases

Gene3D3.20.20.70. 1 hit.
HAMAPMF_00224. DHO_dh_type1.
InterProIPR013785. Aldolase_TIM.
IPR005720. Dihydroorotate_DH.
IPR024920. Dihydroorotate_DH_1.
IPR012135. Dihydroorotate_DH_1_2.
IPR001295. Dihydroorotate_DH_CS.
[Graphical view]
PfamPF01180. DHO_dh. 1 hit.
[Graphical view]
PIRSFPIRSF000164. DHO_oxidase. 1 hit.
TIGRFAMsTIGR01037. pyrD_sub1_fam. 1 hit.
PROSITEPS00911. DHODEHASE_1. 1 hit.
PS00912. DHODEHASE_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio974596.
PROP28272.

Entry information

Entry namePYRD_YEAST
AccessionPrimary (citable) accession number: P28272
Secondary accession number(s): D6VWY7, Q2XN75, Q70DC7
Entry history
Integrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: December 1, 1992
Last modified: March 19, 2014
This is version 129 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XI

Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways