PYRD_VIBPA
ID PYRD_VIBPA Reviewed; 336 AA.
AC Q87PB7;
DT 30-MAY-2003, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2003, sequence version 1.
DT 03-AUG-2022, entry version 116.
DE RecName: Full=Dihydroorotate dehydrogenase (quinone) {ECO:0000255|HAMAP-Rule:MF_00225};
DE EC=1.3.5.2 {ECO:0000255|HAMAP-Rule:MF_00225};
DE AltName: Full=DHOdehase {ECO:0000255|HAMAP-Rule:MF_00225};
DE Short=DHOD {ECO:0000255|HAMAP-Rule:MF_00225};
DE Short=DHODase {ECO:0000255|HAMAP-Rule:MF_00225};
DE AltName: Full=Dihydroorotate oxidase {ECO:0000255|HAMAP-Rule:MF_00225};
GN Name=pyrD {ECO:0000255|HAMAP-Rule:MF_00225}; OrderedLocusNames=VP1601;
OS Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=223926;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=RIMD 2210633;
RX PubMed=12620739; DOI=10.1016/s0140-6736(03)12659-1;
RA Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K.,
RA Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S.,
RA Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T.;
RT "Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism
RT distinct from that of V. cholerae.";
RL Lancet 361:743-749(2003).
CC -!- FUNCTION: Catalyzes the conversion of dihydroorotate to orotate with
CC quinone as electron acceptor. {ECO:0000255|HAMAP-Rule:MF_00225}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-dihydroorotate + a quinone = a quinol + orotate;
CC Xref=Rhea:RHEA:30187, ChEBI:CHEBI:24646, ChEBI:CHEBI:30839,
CC ChEBI:CHEBI:30864, ChEBI:CHEBI:132124; EC=1.3.5.2;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00225};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00225};
CC Note=Binds 1 FMN per subunit. {ECO:0000255|HAMAP-Rule:MF_00225};
CC -!- PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway;
CC orotate from (S)-dihydroorotate (quinone route): step 1/1.
CC {ECO:0000255|HAMAP-Rule:MF_00225}.
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_00225}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000255|HAMAP-Rule:MF_00225};
CC Peripheral membrane protein {ECO:0000255|HAMAP-Rule:MF_00225}.
CC -!- SIMILARITY: Belongs to the dihydroorotate dehydrogenase family. Type 2
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_00225}.
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DR EMBL; BA000031; BAC59863.1; -; Genomic_DNA.
DR RefSeq; NP_797979.1; NC_004603.1.
DR RefSeq; WP_005458264.1; NC_004603.1.
DR AlphaFoldDB; Q87PB7; -.
DR SMR; Q87PB7; -.
DR STRING; 223926.28806591; -.
DR EnsemblBacteria; BAC59863; BAC59863; BAC59863.
DR GeneID; 1189107; -.
DR KEGG; vpa:VP1601; -.
DR PATRIC; fig|223926.6.peg.1524; -.
DR eggNOG; COG0167; Bacteria.
DR HOGENOM; CLU_013640_2_0_6; -.
DR OMA; ERIKMGA; -.
DR UniPathway; UPA00070; UER00946.
DR Proteomes; UP000002493; Chromosome 1.
DR GO; GO:0005737; C:cytoplasm; IEA:InterPro.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0004152; F:dihydroorotate dehydrogenase activity; IEA:UniProtKB-UniRule.
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; cd04738; DHOD_2_like; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_00225; DHO_dh_type2; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR005720; Dihydroorotate_DH.
DR InterPro; IPR012135; Dihydroorotate_DH_1_2.
DR InterPro; IPR005719; Dihydroorotate_DH_2.
DR InterPro; IPR001295; Dihydroorotate_DH_CS.
DR Pfam; PF01180; DHO_dh; 1.
DR PIRSF; PIRSF000164; DHO_oxidase; 1.
DR TIGRFAMs; TIGR01036; pyrD_sub2; 1.
DR PROSITE; PS00911; DHODEHASE_1; 1.
DR PROSITE; PS00912; DHODEHASE_2; 1.
PE 3: Inferred from homology;
KW Cell membrane; Flavoprotein; FMN; Membrane; Oxidoreductase;
KW Pyrimidine biosynthesis; Reference proteome.
FT CHAIN 1..336
FT /note="Dihydroorotate dehydrogenase (quinone)"
FT /id="PRO_0000148486"
FT ACT_SITE 175
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 62..66
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 66
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 86
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 111..115
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 139
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 172
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 172
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 177
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 217
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 245
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 246..247
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 268
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 297
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 318..319
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
SQ SEQUENCE 336 AA; 36882 MW; FFFF6C4D5F8F33D3 CRC64;
MLYRLARTGF FQLDAEKAHD LAIKNFQRFN GTPLDLFYRQ QLPNRPVECM GLTFRNPVGL
AAGLDKNGEC IEAFDAMGFG FVEVGTVTPR PQPGNDKPRL FRLVEAEGII NRMGFNNLGV
DHLVENVKKA KFNCVLGINI GKNKDTPIEN GAEDYLICME KVYEYAGYIA VNISSPNTPG
LRSLQYGEAL DELLSELKAK QSELAEKHGK YVPLALKIAP DLSDDEITQI CESLLKNNID
GVIATNTTLD RTVVEGMKHA NEAGGLSGRP VQSRSTEVVR KLHEALGDKL PIIGVGGIDS
YVAAKEKMMA GAQLVQVYTG FIYHGPGLVR DIVKNL
