PYRD_ECOLI
ID PYRD_ECOLI Reviewed; 336 AA.
AC P0A7E1; P05021;
DT 13-AUG-1987, integrated into UniProtKB/Swiss-Prot.
DT 13-AUG-1987, sequence version 1.
DT 03-AUG-2022, entry version 136.
DE RecName: Full=Dihydroorotate dehydrogenase (quinone);
DE EC=1.3.5.2;
DE AltName: Full=DHOdehase;
DE Short=DHOD;
DE Short=DHODase;
DE AltName: Full=Dihydroorotate oxidase;
GN Name=pyrD; OrderedLocusNames=b0945, JW0928;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 1-7.
RX PubMed=2992959; DOI=10.1111/j.1432-1033.1985.tb09068.x;
RA Larsen N.J., Jensen K.F.;
RT "Nucleotide sequence of the pyrD gene of Escherichia coli and
RT characterization of the flavoprotein dihydroorotate dehydrogenase.";
RL Eur. J. Biochem. 151:59-65(1985).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP PROTEIN SEQUENCE OF 1-10 AND 183-192, FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF SER-175, AND ENZYME KINETICS.
RX PubMed=10074342; DOI=10.1021/bi982352c;
RA Bjoernberg O., Gruener A.-C., Roepstorff P., Jensen K.F.;
RT "The activity of Escherichia coli dihydroorotate dehydrogenase is dependent
RT on a conserved loop identified by sequence homology, mutagenesis, and
RT limited proteolysis.";
RL Biochemistry 38:2899-2908(1999).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH FMN AND OROTATE,
RP COFACTOR, SUBUNIT, AND REACTION MECHANISM.
RX PubMed=12220493; DOI=10.1016/s0969-2126(02)00831-6;
RA Noerager S., Jensen K.F., Bjoernberg O., Larsen S.;
RT "E. coli dihydroorotate dehydrogenase reveals structural and functional
RT distinctions between different classes of dihydroorotate dehydrogenases.";
RL Structure 10:1211-1223(2002).
CC -!- FUNCTION: Catalyzes the conversion of dihydroorotate to orotate with
CC quinone as electron acceptor. {ECO:0000269|PubMed:10074342}.
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:0000269|PubMed:10074342};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000269|PubMed:12220493};
CC Note=Binds 1 FMN per subunit. {ECO:0000269|PubMed:12220493};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=28.8 uM for dihydroorotate {ECO:0000269|PubMed:10074342};
CC Vmax=180 umol/min/mg enzyme {ECO:0000269|PubMed:10074342};
CC -!- PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway;
CC orotate from (S)-dihydroorotate (quinone route): step 1/1.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:12220493}.
CC -!- SUBCELLULAR LOCATION: Cell membrane; Peripheral membrane protein.
CC -!- SIMILARITY: Belongs to the dihydroorotate dehydrogenase family. Type 2
CC subfamily. {ECO:0000305}.
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DR EMBL; X02826; CAA26594.1; -; Genomic_DNA.
DR EMBL; U00096; AAC74031.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35700.1; -; Genomic_DNA.
DR PIR; A23109; DEECDO.
DR RefSeq; NP_415465.1; NC_000913.3.
DR RefSeq; WP_001295352.1; NZ_STEB01000006.1.
DR PDB; 1F76; X-ray; 2.50 A; A/B/D/E=1-336.
DR PDB; 7T5K; X-ray; 2.25 A; A/B=1-336.
DR PDB; 7T5Y; X-ray; 2.62 A; A/B=1-336.
DR PDB; 7T6C; X-ray; 2.53 A; A/B=1-336.
DR PDB; 7T6H; X-ray; 2.42 A; A/B=1-336.
DR PDBsum; 1F76; -.
DR PDBsum; 7T5K; -.
DR PDBsum; 7T5Y; -.
DR PDBsum; 7T6C; -.
DR PDBsum; 7T6H; -.
DR AlphaFoldDB; P0A7E1; -.
DR SMR; P0A7E1; -.
DR BioGRID; 4259440; 30.
DR BioGRID; 849930; 1.
DR DIP; DIP-35945N; -.
DR IntAct; P0A7E1; 6.
DR STRING; 511145.b0945; -.
DR DrugBank; DB03247; Flavin mononucleotide.
DR DrugBank; DB01942; Formic acid.
DR DrugBank; DB02262; Orotic acid.
DR SWISS-2DPAGE; P0A7E1; -.
DR jPOST; P0A7E1; -.
DR PaxDb; P0A7E1; -.
DR PRIDE; P0A7E1; -.
DR EnsemblBacteria; AAC74031; AAC74031; b0945.
DR EnsemblBacteria; BAA35700; BAA35700; BAA35700.
DR GeneID; 945556; -.
DR KEGG; ecj:JW0928; -.
DR KEGG; eco:b0945; -.
DR PATRIC; fig|1411691.4.peg.1329; -.
DR EchoBASE; EB0800; -.
DR eggNOG; COG0167; Bacteria.
DR HOGENOM; CLU_013640_2_0_6; -.
DR InParanoid; P0A7E1; -.
DR OMA; ERIKMGA; -.
DR PhylomeDB; P0A7E1; -.
DR BioCyc; EcoCyc:DIHYDROOROTOX-MON; -.
DR BioCyc; MetaCyc:DIHYDROOROTOX-MON; -.
DR BRENDA; 1.3.5.2; 2026.
DR SABIO-RK; P0A7E1; -.
DR UniPathway; UPA00070; UER00946.
DR EvolutionaryTrace; P0A7E1; -.
DR PRO; PR:P0A7E1; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0016020; C:membrane; IDA:EcoCyc.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0004152; F:dihydroorotate dehydrogenase activity; IDA:EcoCyc.
DR GO; GO:0010181; F:FMN binding; IDA:EcoCyc.
DR GO; GO:0006207; P:'de novo' pyrimidine nucleobase biosynthetic process; IMP:EcoCyc.
DR GO; GO:0044205; P:'de novo' UMP biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0009220; P:pyrimidine ribonucleotide biosynthetic process; IBA:GO_Central.
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 1: Evidence at protein level;
KW 3D-structure; Cell membrane; Direct protein sequencing; Flavoprotein; FMN;
KW Membrane; Oxidoreductase; Pyrimidine biosynthesis; Reference proteome.
FT CHAIN 1..336
FT /note="Dihydroorotate dehydrogenase (quinone)"
FT /id="PRO_0000148437"
FT ACT_SITE 175
FT /note="Nucleophile"
FT BINDING 62..66
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:12220493"
FT BINDING 66
FT /ligand="substrate"
FT BINDING 86
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:12220493"
FT BINDING 111..115
FT /ligand="substrate"
FT BINDING 139
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:12220493"
FT BINDING 172
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:12220493"
FT BINDING 172
FT /ligand="substrate"
FT BINDING 177
FT /ligand="substrate"
FT BINDING 217
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:12220493"
FT BINDING 245
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:12220493"
FT BINDING 246..247
FT /ligand="substrate"
FT BINDING 268
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:12220493"
FT BINDING 297
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:12220493"
FT BINDING 318..319
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:12220493"
FT MUTAGEN 175
FT /note="S->A: Almost no activity."
FT /evidence="ECO:0000269|PubMed:10074342"
FT MUTAGEN 175
FT /note="S->C: 500-fold reduction in activity."
FT /evidence="ECO:0000269|PubMed:10074342"
FT HELIX 3..10
FT /evidence="ECO:0007829|PDB:1F76"
FT HELIX 15..29
FT /evidence="ECO:0007829|PDB:1F76"
FT HELIX 33..37
FT /evidence="ECO:0007829|PDB:1F76"
FT STRAND 47..49
FT /evidence="ECO:0007829|PDB:1F76"
FT STRAND 52..60
FT /evidence="ECO:0007829|PDB:1F76"
FT HELIX 71..76
FT /evidence="ECO:0007829|PDB:1F76"
FT STRAND 80..87
FT /evidence="ECO:0007829|PDB:1F76"
FT STRAND 100..103
FT /evidence="ECO:0007829|PDB:1F76"
FT TURN 104..107
FT /evidence="ECO:0007829|PDB:1F76"
FT STRAND 108..111
FT /evidence="ECO:0007829|PDB:1F76"
FT HELIX 120..129
FT /evidence="ECO:0007829|PDB:1F76"
FT STRAND 134..140
FT /evidence="ECO:0007829|PDB:1F76"
FT HELIX 148..151
FT /evidence="ECO:0007829|PDB:1F76"
FT HELIX 152..162
FT /evidence="ECO:0007829|PDB:1F76"
FT HELIX 163..165
FT /evidence="ECO:0007829|PDB:1F76"
FT STRAND 167..172
FT /evidence="ECO:0007829|PDB:1F76"
FT STRAND 176..178
FT /evidence="ECO:0007829|PDB:1F76"
FT HELIX 181..185
FT /evidence="ECO:0007829|PDB:1F76"
FT HELIX 187..208
FT /evidence="ECO:0007829|PDB:1F76"
FT STRAND 214..217
FT /evidence="ECO:0007829|PDB:1F76"
FT HELIX 224..236
FT /evidence="ECO:0007829|PDB:1F76"
FT STRAND 240..244
FT /evidence="ECO:0007829|PDB:1F76"
FT TURN 258..261
FT /evidence="ECO:0007829|PDB:1F76"
FT STRAND 263..268
FT /evidence="ECO:0007829|PDB:1F76"
FT HELIX 269..271
FT /evidence="ECO:0007829|PDB:1F76"
FT HELIX 272..286
FT /evidence="ECO:0007829|PDB:1F76"
FT STRAND 292..297
FT /evidence="ECO:0007829|PDB:1F76"
FT HELIX 301..310
FT /evidence="ECO:0007829|PDB:1F76"
FT STRAND 313..318
FT /evidence="ECO:0007829|PDB:1F76"
FT HELIX 319..324
FT /evidence="ECO:0007829|PDB:1F76"
FT HELIX 326..335
FT /evidence="ECO:0007829|PDB:1F76"
SQ SEQUENCE 336 AA; 36775 MW; 973227EAE6B83622 CRC64;
MYYPFVRKAL FQLDPERAHE FTFQQLRRIT GTPFEALVRQ KVPAKPVNCM GLTFKNPLGL
AAGLDKDGEC IDALGAMGFG SIEIGTVTPR PQPGNDKPRL FRLVDAEGLI NRMGFNNLGV
DNLVENVKKA HYDGVLGINI GKNKDTPVEQ GKDDYLICME KIYAYAGYIA INISSPNTPG
LRTLQYGEAL DDLLTAIKNK QNDLQAMHHK YVPIAVKIAP DLSEEELIQV ADSLVRHNID
GVIATNTTLD RSLVQGMKNC DQTGGLSGRP LQLKSTEIIR RLSLELNGRL PIIGVGGIDS
VIAAREKIAA GASLVQIYSG FIFKGPPLIK EIVTHI
