PYRD_SHELP
ID PYRD_SHELP Reviewed; 341 AA.
AC A3QDX8;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 17-APR-2007, sequence version 1.
DT 03-AUG-2022, entry version 102.
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=Shew_1810;
OS Shewanella loihica (strain ATCC BAA-1088 / PV-4).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC Shewanellaceae; Shewanella.
OX NCBI_TaxID=323850;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-1088 / PV-4;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M.,
RA Hauser L., Kyrpides N., Mikhailova N., Romine M.F., Serres G.,
RA Fredrickson J., Tiedje J., Richardson P.;
RT "Complete sequence of Shewanella loihica PV-4.";
RL Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases.
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; CP000606; ABO23676.1; -; Genomic_DNA.
DR RefSeq; WP_011865608.1; NC_009092.1.
DR AlphaFoldDB; A3QDX8; -.
DR SMR; A3QDX8; -.
DR STRING; 323850.Shew_1810; -.
DR EnsemblBacteria; ABO23676; ABO23676; Shew_1810.
DR KEGG; slo:Shew_1810; -.
DR eggNOG; COG0167; Bacteria.
DR HOGENOM; CLU_013640_2_0_6; -.
DR OMA; ERIKMGA; -.
DR OrthoDB; 1109542at2; -.
DR UniPathway; UPA00070; UER00946.
DR Proteomes; UP000001558; Chromosome.
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..341
FT /note="Dihydroorotate dehydrogenase (quinone)"
FT /id="PRO_1000024224"
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 341 AA; 36640 MW; 3EB755EE4ACD4FC9 CRC64;
MFYKIAQKVM FQMDPEKAHN LAIGSLKSTA NSPLNCFYAQ KLQAAPVEFM GLTFPNPVGL
AAGMDKDGEC IDAFHAMGFG HVEVGTVTPR PQPGNDQPRL FRLKPAKAII NRMGFNNKGV
DNLVANLKAA KSGAMVGVNI GKNKDTPVEQ GKEDYLICME KVYPYAAYIA VNISSPNTPG
LRSLQYGDLL DDLLGSLKAK QKDLAERHGK YVPIALKIAP DLEPDEIEKI AESLIRNEFD
GAIATNTTLT RDGVSGLVNS NEAGGLSGKP LNSLSTKVIK QLADCLKGQV PIIGVGGINS
AADALDKLDA GATMVQIYSG FIYRGPELIK EIVDAYRVKS K
