PYRDB_ENTFA
ID PYRDB_ENTFA Reviewed; 312 AA.
AC P0DH74; Q47741;
DT 27-JUL-2011, integrated into UniProtKB/Swiss-Prot.
DT 27-JUL-2011, sequence version 1.
DT 03-AUG-2022, entry version 48.
DE RecName: Full=Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit;
DE Short=DHOD B;
DE Short=DHODase B;
DE Short=DHOdehase B;
DE EC=1.3.1.14;
DE AltName: Full=Dihydroorotate oxidase B;
DE AltName: Full=Orotate reductase (NADH);
GN Name=pyrDB; Synonyms=pyrD, pyrD-2; OrderedLocusNames=EF_1714;
OS Enterococcus faecalis (strain ATCC 700802 / V583).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae;
OC Enterococcus.
OX NCBI_TaxID=226185;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700802 / V583;
RX PubMed=12663927; DOI=10.1126/science.1080613;
RA Paulsen I.T., Banerjei L., Myers G.S.A., Nelson K.E., Seshadri R.,
RA Read T.D., Fouts D.E., Eisen J.A., Gill S.R., Heidelberg J.F., Tettelin H.,
RA Dodson R.J., Umayam L.A., Brinkac L.M., Beanan M.J., Daugherty S.C.,
RA DeBoy R.T., Durkin S.A., Kolonay J.F., Madupu R., Nelson W.C.,
RA Vamathevan J.J., Tran B., Upton J., Hansen T., Shetty J., Khouri H.M.,
RA Utterback T.R., Radune D., Ketchum K.A., Dougherty B.A., Fraser C.M.;
RT "Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus
RT faecalis.";
RL Science 299:2071-2074(2003).
RN [2]
RP CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES,
RP ENZYME KINETICS, AND REACTION MECHANISM.
RC STRAIN=ATCC 29212 / DSM 2570;
RX PubMed=10529184; DOI=10.1021/bi990674q;
RA Marcinkeviciene J., Tinney L.M., Wang K.H., Rogers M.J., Copeland R.A.;
RT "Dihydroorotate dehydrogenase B of Enterococcus faecalis. Characterization
RT and insights into chemical mechanism.";
RL Biochemistry 38:13129-13137(1999).
CC -!- FUNCTION: Catalyzes the conversion of dihydroorotate to orotate with
CC NAD(+) as electron acceptor.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-dihydroorotate + NAD(+) = H(+) + NADH + orotate;
CC Xref=Rhea:RHEA:13513, ChEBI:CHEBI:15378, ChEBI:CHEBI:30839,
CC ChEBI:CHEBI:30864, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=1.3.1.14;
CC Evidence={ECO:0000269|PubMed:10529184};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000269|PubMed:10529184};
CC Note=Binds 1 FMN per subunit. {ECO:0000269|PubMed:10529184};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=36.4 uM for orotate {ECO:0000269|PubMed:10529184};
CC KM=33.2 uM for dihydroorotate {ECO:0000269|PubMed:10529184};
CC KM=135 uM for NAD(+) {ECO:0000269|PubMed:10529184};
CC KM=27 uM for NADH {ECO:0000269|PubMed:10529184};
CC pH dependence:
CC Optimum pH is 6-8. {ECO:0000269|PubMed:10529184};
CC -!- PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway;
CC orotate from (S)-dihydroorotate (NAD(+) route): step 1/1.
CC -!- SUBUNIT: Heterotetramer of 2 PyrK and 2 PyrD type B subunits.
CC {ECO:0000269|PubMed:10529184}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the dihydroorotate dehydrogenase family. Type 1
CC subfamily. {ECO:0000305}.
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DR EMBL; AE016830; AAO81490.1; -; Genomic_DNA.
DR RefSeq; NP_815420.1; NC_004668.1.
DR RefSeq; WP_002369312.1; NZ_KE136528.1.
DR AlphaFoldDB; P0DH74; -.
DR SMR; P0DH74; -.
DR STRING; 226185.EF_1714; -.
DR EnsemblBacteria; AAO81490; AAO81490; EF_1714.
DR KEGG; efa:EF1714; -.
DR PATRIC; fig|226185.45.peg.1798; -.
DR eggNOG; COG0167; Bacteria.
DR HOGENOM; CLU_042042_0_0_9; -.
DR OMA; SCPHAKG; -.
DR UniPathway; UPA00070; UER00945.
DR Proteomes; UP000001415; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004152; F:dihydroorotate dehydrogenase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0004589; F:orotate reductase (NADH) activity; IEA:UniProtKB-EC.
DR GO; GO:0006207; P:'de novo' pyrimidine nucleobase biosynthetic process; IEA:InterPro.
DR GO; GO:0044205; P:'de novo' UMP biosynthetic process; IEA:UniProtKB-UniPathway.
DR CDD; cd04740; DHOD_1B_like; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_00224; DHO_dh_type1; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR033888; DHOD_1B.
DR InterPro; IPR005720; Dihydroorotate_DH.
DR InterPro; IPR024920; Dihydroorotate_DH_1.
DR InterPro; IPR012135; Dihydroorotate_DH_1_2.
DR InterPro; IPR001295; Dihydroorotate_DH_CS.
DR Pfam; PF01180; DHO_dh; 1.
DR PIRSF; PIRSF000164; DHO_oxidase; 1.
DR TIGRFAMs; TIGR01037; pyrD_sub1_fam; 1.
DR PROSITE; PS00911; DHODEHASE_1; 1.
DR PROSITE; PS00912; DHODEHASE_2; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Flavoprotein; FMN; NAD; Oxidoreductase; Pyrimidine biosynthesis;
KW Reference proteome.
FT CHAIN 1..312
FT /note="Dihydroorotate dehydrogenase B (NAD(+)), catalytic
FT subunit"
FT /id="PRO_0000148391"
FT ACT_SITE 133
FT /note="Nucleophile"
FT BINDING 23
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 47..48
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 47
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 71..75
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 102
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 130
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 130
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 168
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 194
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 195..196
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 220
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 246..247
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 268..269
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
SQ SEQUENCE 312 AA; 33093 MW; B97956521B85541F CRC64;
MMKNPLAVSI PGLTLKNPII PASGCFGFGE EYANYYDLDQ LGSIMIKATT PQARYGNPTP
RVAETPSGML NAIGLQNPGL EVVMQEKLPK LEKYPNLPII ANVAGACEED YVAVCAKIGQ
APNVKAIELN ISCPNVKHGG IAFGTDPEVA FQLTQAVKKV ASVPIYVKLS PNVTDIVPIA
QAIEAGGADG FSMINTLLGM RIDLKTRKPI LANQTGGLSG PAIKPVAIRL IRQVASVSQL
PIIGMGGVQT VDDVLEMFMA GASAVGVGTA NFTDPYICPK LIDGLPKRME ELGIESLEQL
IKEVREGQQN AR
