PYRDB_LACLA
ID PYRDB_LACLA Reviewed; 311 AA.
AC Q9CFW8;
DT 26-SEP-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 131.
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=pydB; OrderedLocusNames=LL1346; ORFNames=L182555;
OS Lactococcus lactis subsp. lactis (strain IL1403) (Streptococcus lactis).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC Lactococcus.
OX NCBI_TaxID=272623;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=IL1403;
RX PubMed=11337471; DOI=10.1101/gr.gr-1697r;
RA Bolotin A., Wincker P., Mauger S., Jaillon O., Malarme K., Weissenbach J.,
RA Ehrlich S.D., Sorokin A.;
RT "The complete genome sequence of the lactic acid bacterium Lactococcus
RT lactis ssp. lactis IL1403.";
RL Genome Res. 11:731-753(2001).
CC -!- FUNCTION: Catalyzes the conversion of dihydroorotate to orotate with
CC NAD(+) as electron acceptor. {ECO:0000250}.
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 -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210; Evidence={ECO:0000250};
CC Note=Binds 1 FMN per subunit. {ECO:0000250};
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:0000250}.
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; AE005176; AAK05444.1; -; Genomic_DNA.
DR PIR; B86793; B86793.
DR RefSeq; NP_267502.1; NC_002662.1.
DR RefSeq; WP_010905897.1; NC_002662.1.
DR PDB; 5KSW; X-ray; 2.47 A; A/C=5-310.
DR PDB; 5UE9; X-ray; 2.72 A; A/C=5-310.
DR PDBsum; 5KSW; -.
DR PDBsum; 5UE9; -.
DR AlphaFoldDB; Q9CFW8; -.
DR SMR; Q9CFW8; -.
DR STRING; 272623.L182555; -.
DR PaxDb; Q9CFW8; -.
DR EnsemblBacteria; AAK05444; AAK05444; L182555.
DR KEGG; lla:L182555; -.
DR PATRIC; fig|272623.7.peg.1452; -.
DR eggNOG; COG0167; Bacteria.
DR HOGENOM; CLU_042042_0_0_9; -.
DR OMA; SCPHAKG; -.
DR BioCyc; MetaCyc:MON-14471; -.
DR SABIO-RK; Q9CFW8; -.
DR UniPathway; UPA00070; UER00945.
DR Proteomes; UP000002196; 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 3D-structure; Cytoplasm; Flavoprotein; FMN; NAD; Oxidoreductase;
KW Pyrimidine biosynthesis; Reference proteome.
FT CHAIN 1..311
FT /note="Dihydroorotate dehydrogenase B (NAD(+)), catalytic
FT subunit"
FT /id="PRO_0000148395"
FT ACT_SITE 135
FT /note="Nucleophile"
FT BINDING 24
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 48..49
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 48
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 72..76
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 104
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 132
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 132
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 170
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 196
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 197..198
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 222
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 248..249
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 270..271
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT STRAND 9..11
FT /evidence="ECO:0007829|PDB:5KSW"
FT STRAND 14..22
FT /evidence="ECO:0007829|PDB:5KSW"
FT HELIX 33..35
FT /evidence="ECO:0007829|PDB:5KSW"
FT HELIX 39..41
FT /evidence="ECO:0007829|PDB:5KSW"
FT STRAND 45..50
FT /evidence="ECO:0007829|PDB:5KSW"
FT STRAND 63..66
FT /evidence="ECO:0007829|PDB:5KSW"
FT STRAND 69..72
FT /evidence="ECO:0007829|PDB:5KSW"
FT HELIX 81..86
FT /evidence="ECO:0007829|PDB:5KSW"
FT HELIX 88..95
FT /evidence="ECO:0007829|PDB:5KSW"
FT STRAND 101..105
FT /evidence="ECO:0007829|PDB:5KSW"
FT HELIX 110..120
FT /evidence="ECO:0007829|PDB:5KSW"
FT STRAND 126..132
FT /evidence="ECO:0007829|PDB:5KSW"
FT TURN 138..141
FT /evidence="ECO:0007829|PDB:5KSW"
FT HELIX 145..147
FT /evidence="ECO:0007829|PDB:5UE9"
FT HELIX 149..160
FT /evidence="ECO:0007829|PDB:5KSW"
FT STRAND 167..170
FT /evidence="ECO:0007829|PDB:5KSW"
FT HELIX 178..187
FT /evidence="ECO:0007829|PDB:5KSW"
FT STRAND 191..195
FT /evidence="ECO:0007829|PDB:5KSW"
FT STRAND 199..201
FT /evidence="ECO:0007829|PDB:5KSW"
FT TURN 206..208
FT /evidence="ECO:0007829|PDB:5KSW"
FT STRAND 210..213
FT /evidence="ECO:0007829|PDB:5KSW"
FT STRAND 216..222
FT /evidence="ECO:0007829|PDB:5KSW"
FT HELIX 223..225
FT /evidence="ECO:0007829|PDB:5KSW"
FT HELIX 226..237
FT /evidence="ECO:0007829|PDB:5KSW"
FT STRAND 244..246
FT /evidence="ECO:0007829|PDB:5KSW"
FT HELIX 253..262
FT /evidence="ECO:0007829|PDB:5KSW"
FT STRAND 265..269
FT /evidence="ECO:0007829|PDB:5KSW"
FT HELIX 272..275
FT /evidence="ECO:0007829|PDB:5KSW"
FT HELIX 279..293
FT /evidence="ECO:0007829|PDB:5KSW"
FT HELIX 299..307
FT /evidence="ECO:0007829|PDB:5KSW"
SQ SEQUENCE 311 AA; 32916 MW; 6FF419606B2E733C CRC64;
MTENNRLSVK LPGLDLKNPI IPASGCFGFG EEYAKYYDLN KLGSIMVKAT TLHPRFGNPT
PRVAETASGM LNAIGLQNPG LEVIMAEKLP WLNENFPDLP IIANVAGSEE DDYVAVCAKI
GDAPNVKVIE LNISCPNVKH GGQAFGTDPD VAAALVKACK AVSKVPLYVK LSPNVTDIVP
IAKAVEAAGA DGLTMINTLM GVRFDLKTRK PVLANITGGL SGPAIKPVAL KLIHQVAQVV
DIPIIGMGGV ESAQDVLEMY MAGASAVAVG TANFADPFVC PKIIEKLPEV MDQYGIDSLE
NLIQEVKNSK K
