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Dihydroorotate dehydrogenase (fumarate) (DHOD) (DHODase) (DHOdehase) (EC 1.3.98.1) (Dihydroorotate oxidase)

 PYRD_YEAST              Reviewed;         314 AA.
P28272; D6VWY7; Q2XN75; Q70DC7;
01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
01-DEC-1992, sequence version 1.
18-JUL-2018, entry version 168.
RecName: Full=Dihydroorotate dehydrogenase (fumarate);
Short=DHOD;
Short=DHODase;
Short=DHOdehase;
EC=1.3.98.1;
AltName: Full=Dihydroorotate oxidase;
Name=URA1; OrderedLocusNames=YKL216W;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
STRAIN=ATCC 28383 / FL100 / VTT C-80102;
PubMed=1511880; DOI=10.1016/0378-1119(92)90265-Q;
Roy A.;
"Nucleotide sequence of the URA1 gene of Saccharomyces cerevisiae.";
Gene 118:149-150(1992).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND 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;
PubMed=15087486; DOI=10.1093/nar/gkh529;
Leh-Louis V., Wirth B., Despons L., Wain-Hobson S., Potier S.,
Souciet J.-L.;
"Differential evolution of the Saccharomyces cerevisiae DUP240
paralogs and implication of recombination in phylogeny.";
Nucleic Acids Res. 32:2069-2078(2004).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=7941750; DOI=10.1002/yea.320100511;
Tzermia M., Horaitis O., Alexandraki D.;
"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.";
Yeast 10:663-679(1994).
[4]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=8196765; DOI=10.1038/369371a0;
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.;
"Complete DNA sequence of yeast chromosome XI.";
Nature 369:371-378(1994).
[6]
FUNCTION, AND SUBCELLULAR LOCATION.
PubMed=1409592; DOI=10.1073/pnas.89.19.8966;
Nagy M., Lacroute F., Thomas D.;
"Divergent evolution of pyrimidine biosynthesis between anaerobic and
aerobic yeasts.";
Proc. Natl. Acad. Sci. U.S.A. 89:8966-8970(1992).
[7]
FUNCTION, SUBUNIT, COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=10871048; DOI=10.1006/abbi.2000.1823;
Jordan D.B., Bisaha J.J., Picollelli M.A.;
"Catalytic properties of dihydroorotate dehydrogenase from
Saccharomyces cerevisiae: studies on pH, alternate substrates, and
inhibitors.";
Arch. Biochem. Biophys. 378:84-92(2000).
[8]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[9]
FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND
BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=15196933; DOI=10.1016/j.febslet.2004.05.017;
Zameitat E., Knecht W., Piskur J., Loeffler M.;
"Two different dihydroorotate dehydrogenases from yeast Saccharomyces
kluyveri.";
FEBS Lett. 568:129-134(2004).
[10]
FUNCTION.
PubMed=15014982; DOI=10.1007/s00438-004-0995-7;
Gojkovic Z., Knecht W., Zameitat E., Warneboldt J., Coutelis J.-B.,
Pynyaha Y., Neuveglise C., Moeller K., Loeffler M., Piskur J.;
"Horizontal gene transfer promoted evolution of the ability to
propagate under anaerobic conditions in yeasts.";
Mol. Genet. Genomics 271:387-393(2004).
[11]
FUNCTION, AND BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=17617217; DOI=10.1111/j.1567-1364.2007.00275.x;
Zameitat E., Pierik A.J., Zocher K., Loeffler M.;
"Dihydroorotate dehydrogenase from Saccharomyces cerevisiae:
spectroscopic investigations with the recombinant enzyme throw light
on catalytic properties and metabolism of fumarate analogues.";
FEMS Yeast Res. 7:897-904(2007).
[12]
UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-46, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22106047; DOI=10.1002/pmic.201100166;
Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.;
"Sites of ubiquitin attachment in Saccharomyces cerevisiae.";
Proteomics 12:236-240(2012).
-!- 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. {ECO:0000269|PubMed:10871048,
ECO:0000269|PubMed:1409592, ECO:0000269|PubMed:15014982,
ECO:0000269|PubMed:1511880, ECO:0000269|PubMed:15196933,
ECO:0000269|PubMed:17617217}.
-!- CATALYTIC ACTIVITY: (S)-dihydroorotate + fumarate = orotate +
succinate. {ECO:0000269|PubMed:15196933}.
-!- COFACTOR:
Name=FMN; Xref=ChEBI:CHEBI:58210;
Evidence={ECO:0000269|PubMed:10871048};
Note=Binds 1 FMN per subunit. {ECO:0000269|PubMed:10871048};
-!- ENZYME REGULATION: The activity is independent of the presence of
oxygen.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=8.4 uM for (S)-dihydroorotate (at pH 7.5)
{ECO:0000269|PubMed:10871048, ECO:0000269|PubMed:15196933,
ECO:0000269|PubMed:17617217};
KM=45 uM for fumarate (at pH 7.5) {ECO:0000269|PubMed:10871048,
ECO:0000269|PubMed:15196933, ECO:0000269|PubMed:17617217};
KM=115 uM for 2,6-dichloroindophenol
{ECO:0000269|PubMed:10871048, ECO:0000269|PubMed:15196933,
ECO:0000269|PubMed:17617217};
Vmax=20.4 umol/min/mg enzyme (with 2,6-dichloroindophenol as
electron acceptor) {ECO:0000269|PubMed:10871048,
ECO:0000269|PubMed:15196933, ECO:0000269|PubMed:17617217};
Vmax=5.1 umol/min/mg enzyme (with fumarate as electron acceptor)
{ECO:0000269|PubMed:10871048, ECO:0000269|PubMed:15196933,
ECO:0000269|PubMed:17617217};
pH dependence:
Optimum pH is 8.5. Active from pH 7 to pH 10.
{ECO:0000269|PubMed:10871048, ECO:0000269|PubMed:15196933,
ECO:0000269|PubMed:17617217};
-!- PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo
pathway.
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10871048}.
-!- INTERACTION:
P14136:GFAP (xeno); NbExp=3; IntAct=EBI-14386, EBI-744302;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:1409592}.
-!- MISCELLANEOUS: Present with 264000 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the dihydroorotate dehydrogenase family.
Type 1 subfamily. {ECO:0000305}.
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution (CC BY 4.0) License
-----------------------------------------------------------------------
EMBL; M83295; AAA34566.1; -; Genomic_DNA.
EMBL; X59371; CAA42014.1; -; Genomic_DNA.
EMBL; AJ585637; CAE52157.1; -; Genomic_DNA.
EMBL; AJ585638; CAE52158.1; -; Genomic_DNA.
EMBL; AJ585639; CAE52159.1; -; Genomic_DNA.
EMBL; AJ585640; CAE52160.1; -; Genomic_DNA.
EMBL; AJ585641; CAE52161.1; -; Genomic_DNA.
EMBL; AJ585642; CAE52162.1; -; Genomic_DNA.
EMBL; AJ585643; CAE52163.1; -; Genomic_DNA.
EMBL; AJ585644; CAE52164.1; -; Genomic_DNA.
EMBL; AJ585645; CAE52165.1; -; Genomic_DNA.
EMBL; AJ585646; CAE52166.1; -; Genomic_DNA.
EMBL; AJ585647; CAE52167.1; -; Genomic_DNA.
EMBL; AJ585648; CAE52168.1; -; Genomic_DNA.
EMBL; AJ585649; CAE52169.1; -; Genomic_DNA.
EMBL; AJ585650; CAE52170.1; -; Genomic_DNA.
EMBL; AJ585651; CAE52171.1; -; Genomic_DNA.
EMBL; X75951; CAA53557.1; -; Genomic_DNA.
EMBL; Z28216; CAA82061.1; -; Genomic_DNA.
EMBL; BK006944; DAA08953.1; -; Genomic_DNA.
PIR; JC1276; JC1276.
RefSeq; NP_012706.1; NM_001179781.1.
ProteinModelPortal; P28272; -.
SMR; P28272; -.
BioGrid; 33949; 104.
DIP; DIP-6573N; -.
IntAct; P28272; 11.
MINT; P28272; -.
STRING; 4932.YKL216W; -.
BindingDB; P28272; -.
ChEMBL; CHEMBL5621; -.
iPTMnet; P28272; -.
MaxQB; P28272; -.
PaxDb; P28272; -.
PRIDE; P28272; -.
EnsemblFungi; YKL216W; YKL216W; YKL216W.
GeneID; 853664; -.
KEGG; sce:YKL216W; -.
EuPathDB; FungiDB:YKL216W; -.
SGD; S000001699; URA1.
GeneTree; ENSGT00500000044924; -.
HOGENOM; HOG000225104; -.
InParanoid; P28272; -.
KO; K00226; -.
OMA; SCPHAKG; -.
OrthoDB; EOG092C37TJ; -.
BioCyc; MetaCyc:YKL216W-MONOMER; -.
BioCyc; YEAST:YKL216W-MONOMER; -.
Reactome; R-SCE-500753; Pyrimidine biosynthesis.
SABIO-RK; P28272; -.
UniPathway; UPA00070; -.
PRO; PR:P28272; -.
Proteomes; UP000002311; Chromosome XI.
GO; GO:0005737; C:cytoplasm; IDA:SGD.
GO; GO:0019898; C:extrinsic component of membrane; IDA:SGD.
GO; GO:1990663; F:dihydroorotate dehydrogenase (fumarate) activity; IEA:UniProtKB-EC.
GO; GO:0004152; F:dihydroorotate dehydrogenase activity; IDA:SGD.
GO; GO:0006207; P:'de novo' pyrimidine nucleobase biosynthetic process; IDA:SGD.
GO; GO:0044205; P:'de novo' UMP biosynthetic process; IEA:UniProtKB-UniPathway.
CDD; cd04741; DHOD_1A_like; 1.
Gene3D; 2.30.26.10; -; 2.
Gene3D; 3.20.20.70; -; 3.
HAMAP; MF_00224; DHO_dh_type1; 1.
InterPro; IPR013785; Aldolase_TIM.
InterPro; IPR033886; DHOD_1A.
InterPro; IPR023359; Dihydro_DH_chainA_dom2.
InterPro; IPR005720; Dihydroorotate_DH.
InterPro; IPR024920; Dihydroorotate_DH_1.
InterPro; IPR012135; Dihydroorotate_DH_1_2.
InterPro; IPR001295; Dihydroorotate_DH_CS.
Pfam; PF01180; DHO_dh; 1.
PIRSF; PIRSF000164; DHO_oxidase; 1.
TIGRFAMs; TIGR01037; pyrD_sub1_fam; 1.
PROSITE; PS00911; DHODEHASE_1; 1.
PROSITE; PS00912; DHODEHASE_2; 1.
1: Evidence at protein level;
Complete proteome; Cytoplasm; Flavoprotein; FMN; Isopeptide bond;
Oxidoreductase; Pyrimidine biosynthesis; Reference proteome;
Ubl conjugation.
CHAIN 1 314 Dihydroorotate dehydrogenase (fumarate).
/FTId=PRO_0000148506.
NP_BIND 46 47 FMN. {ECO:0000250}.
NP_BIND 252 253 FMN. {ECO:0000250}.
NP_BIND 274 275 FMN. {ECO:0000250}.
REGION 70 74 Substrate binding. {ECO:0000250}.
REGION 196 197 Substrate binding. {ECO:0000250}.
ACT_SITE 133 133 Nucleophile. {ECO:0000250}.
BINDING 46 46 Substrate. {ECO:0000250}.
BINDING 130 130 FMN. {ECO:0000250}.
BINDING 130 130 Substrate. {ECO:0000250}.
BINDING 167 167 FMN. {ECO:0000250}.
BINDING 195 195 FMN; via carbonyl oxygen. {ECO:0000250}.
BINDING 224 224 FMN; via amide nitrogen. {ECO:0000250}.
CROSSLNK 46 46 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in ubiquitin).
{ECO:0000244|PubMed:22106047}.
VARIANT 58 58 E -> K (in strain: CLIB 95, CLIB 219,
CLIB 382, CLIB 388, CLIB 413, CLIB 556,
CLIB 630, K1, R12, R13, YIIc12 and
YIIc17). {ECO:0000269|PubMed:15087486}.
SEQUENCE 314 AA; 34801 MW; 0F1FF9BDA7F8D68E CRC64;
MTASLTTKFL NNTYENPFMN ASGVHCMTTQ ELDELANSKA GAFITKSATT LEREGNPEPR
YISVPLGSIN SMGLPNEGID YYLSYVLNRQ KNYPDAPAIF FSVAGMSIDE NLNLLRKIQD
SEFNGITELN LSCPNVPGKP QVAYDFDLTK ETLEKVFAFF KKPLGVKLPP YFDFAHFDIM
AKILNEFPLA YVNSINSIGN GLFIDVEKES VVVKPKNGFG GIGGEYVKPT ALANVRAFYT
RLRPEIKVIG TGGIKSGKDA FEHLLCGASM LQIGTELQKE GVKIFERIEK ELKDIMEAKG
YTSIDQFRGK LNSI


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