Dihydroorotate dehydrogenase (fumarate) - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P28272 (PYRD_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 112. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended 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

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	314 AA.
Sequence status	Complete.
Protein existence	Evidence 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.
Pathway	Pyrimidine metabolism; UMP biosynthesis via de novo pathway.
Subunit structure	Homodimer. Ref.7
Subcellular location	Cytoplasm Ref.6.
Miscellaneous	Present with 264000 molecules/cell in log phase SD medium. Ref.8
Sequence similarities	Belongs to the dihydroorotate dehydrogenase family. Type 1 subfamily.
Biophysicochemical properties	Kinetic parameters: K_M=8.4 µM for (S)-dihydroorotate (at pH 7.5) Ref.7 Ref.9 Ref.11 K_M=45 µM for fumarate (at pH 7.5) K_M=115 µM for 2,6-dichloroindophenol V_max=20.4 µmol/min/mg enzyme (with 2,6-dichloroindophenol as electron acceptor) V_max=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.

Ontologies

Keywords
Biological process	Pyrimidine biosynthesis
Cellular component	Cytoplasm
Ligand	FMN Flavoprotein
Molecular function	Oxidoreductase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	'de novo' pyrimidine base biosynthetic process Inferred from mutant phenotype. Source: SGD UMP biosynthetic process Inferred from electronic annotation. Source: InterPro
Cellular component	cytoplasm Inferred from direct assay Ref.6. Source: SGD extrinsic to membrane Inferred from direct assay. Source: SGD
Molecular function	dihydroorotate oxidase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 314

314

Dihydroorotate dehydrogenase (fumarate)

PRO_0000148506

Regions

Nucleotide binding

46 – 47

FMN By similarity

Nucleotide binding

252 – 253

FMN By similarity

Nucleotide binding

274 – 275

FMN By similarity

Region

70 – 74

Substrate binding By similarity

Region

196 – 197

Substrate binding By similarity

Sites

Active site

132

Nucleophile By similarity

Binding site

Substrate By similarity

Binding site

130

FMN By similarity

Binding site

130

Substrate By similarity

Binding site

167

FMN By similarity

Binding site

195

FMN; via carbonyl oxygen By similarity

Binding site

224

FMN; via amide nitrogen By similarity

Natural variations

Natural variant

E → 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

Length

Mass (Da)

Tools

P28272 [UniParc].

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

314

34,801

        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' referencesShow 'large scale' references »
[1]	"Nucleotide sequence of the URA1 gene of Saccharomyces cerevisiae." Roy A. Gene 118:149-150(1992) [PubMed: 1511880] [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: 15087486] [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: 7941750] [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. Mewes H.-W. Nature 369:371-378(1994) [PubMed: 8196765] [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: 1409592] [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: 10871048] [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: 14562106] [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: 15196933] [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: 15014982] [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: 17617217] [Abstract] Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
+	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.
PIR	JC1276.
RefSeq	NP_012706.1. NM_001179781.1.
3D structure databases
ProteinModelPortal	P28272.
SMR	P28272. Positions 5-314.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-6573N.
IntAct	P28272. 2 interactions.
MINT	MINT-709357.
STRING	P28272.
Proteomic databases
PeptideAtlas	P28272.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YKL216W; YKL216W; YKL216W.
GeneID	853664.
KEGG	sce:YKL216W.
NMPDR	fig\|4932.3.peg.3684.
Organism-specific databases
CYGD	YKL216w.
SGD	S000001699. URA1.
Phylogenomic databases
eggNOG	fuNOG12166.
HOGENOM	HBG472415.
OMA	YQRLNPS.
OrthoDB	EOG43XZCD.
Enzyme and pathway databases
BioCyc	MetaCyc:YKL216W-MONOMER.
Gene expression databases
ArrayExpress	P28272.
Genevestigator	P28272.
GermOnline	YKL216W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR013785. Aldolase_TIM. IPR005720. Dihydroorotate_DH. IPR024920. Dihydroorotate_DH_1. IPR012135. Dihydroorotate_DH_1_2. IPR001295. Dihydroorotate_DH_CS. [Graphical view]
Gene3D	G3DSA:3.20.20.70. Aldolase_TIM. 1 hit.
KO	K00226.
Pfam	PF01180. DHO_dh. 1 hit. [Graphical view]
PIRSF	PIRSF000164. DHO_oxidase. 1 hit.
TIGRFAMs	TIGR01037. PyrD_sub1_fam. 1 hit.
PROSITE	PS00911. DHODEHASE_1. 1 hit. PS00912. DHODEHASE_2. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	974596.

Entry information

Entry name

PYRD_YEAST

Accession

Primary (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:	January 25, 2012
This is version 112 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

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

Yeast chromosome XI

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

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Natural variations

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents