PYRDB_LACLM
ID PYRDB_LACLM Reviewed; 311 AA.
AC P54322; A2RK90;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2007, sequence version 2.
DT 03-AUG-2022, entry version 142.
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; OrderedLocusNames=llmg_1106;
OS Lactococcus lactis subsp. cremoris (strain MG1363).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC Lactococcus; Lactococcus cremoris subsp. cremoris.
OX NCBI_TaxID=416870;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, AND
RP SUBSTRATE SPECIFICITY.
RC STRAIN=MG1363;
RX PubMed=8021180; DOI=10.1128/jb.176.13.3975-3982.1994;
RA Andersen P.S., Jansen P.J.G., Hammer K.;
RT "Two different dihydroorotate dehydrogenases in Lactococcus lactis.";
RL J. Bacteriol. 176:3975-3982(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=MG1363;
RX PubMed=8759867; DOI=10.1128/jb.178.16.5005-5012.1996;
RA Andersen P.S., Martinussen J., Hammer K.;
RT "Sequence analysis and identification of the pyrKDbF operon from
RT Lactococcus lactis including a novel gene, pyrK, involved in pyrimidine
RT biosynthesis.";
RL J. Bacteriol. 178:5005-5012(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MG1363;
RX PubMed=17307855; DOI=10.1128/jb.01768-06;
RA Wegmann U., O'Connell-Motherway M., Zomer A., Buist G., Shearman C.,
RA Canchaya C., Ventura M., Goesmann A., Gasson M.J., Kuipers O.P.,
RA van Sinderen D., Kok J.;
RT "The complete genome sequence of the lactic acid bacterial paradigm
RT Lactococcus lactis subsp. cremoris MG1363.";
RL J. Bacteriol. 189:3256-3270(2007).
RN [4]
RP CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=MG1363;
RX PubMed=8910599; DOI=10.1074/jbc.271.46.29359;
RA Nielsen F.S., Andersen P.S., Jensen K.F.;
RT "The B form of dihydroorotate dehydrogenase from Lactococcus lactis
RT consists of two different subunits, encoded by the pyrDb and pyrK genes,
RT and contains FMN, FAD, and [FeS] redox centers.";
RL J. Biol. Chem. 271:29359-29365(1996).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEXES WITH FMN AND OROTATE,
RP COFACTOR, AND REACTION MECHANISM.
RC STRAIN=MG1363;
RX PubMed=11188687; DOI=10.1016/s0969-2126(00)00530-x;
RA Rowland P., Noerager S., Jensen K.F., Larsen S.;
RT "Structure of dihydroorotate dehydrogenase B: electron transfer between two
RT flavin groups bridged by an iron-sulphur cluster.";
RL Structure 8:1227-1238(2000).
CC -!- FUNCTION: Catalyzes the conversion of dihydroorotate to orotate with
CC NAD(+) as electron acceptor. Cannot use fumarate as an electron
CC acceptor. {ECO:0000269|PubMed:8021180}.
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:8021180, ECO:0000269|PubMed:8910599};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000269|PubMed:11188687, ECO:0000269|PubMed:8910599};
CC Note=Binds 1 FMN per subunit. {ECO:0000269|PubMed:11188687,
CC ECO:0000269|PubMed:8910599};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=28 uM for orotate {ECO:0000269|PubMed:8910599};
CC KM=111 uM for NAD(+) {ECO:0000269|PubMed:8910599};
CC pH dependence:
CC Optimum pH is 8. {ECO:0000269|PubMed:8910599};
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:8910599}.
CC -!- INTERACTION:
CC P54322; P56968: pyrK; NbExp=3; IntAct=EBI-1030598, EBI-1030589;
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- SIMILARITY: Belongs to the dihydroorotate dehydrogenase family. Type 1
CC subfamily. {ECO:0000305}.
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DR EMBL; X74207; CAA52280.1; -; Genomic_DNA.
DR EMBL; AM406671; CAL97700.1; -; Genomic_DNA.
DR RefSeq; WP_011835014.1; NZ_WJVF01000012.1.
DR PDB; 1EP1; X-ray; 2.20 A; A=1-311.
DR PDB; 1EP2; X-ray; 2.40 A; A=1-311.
DR PDB; 1EP3; X-ray; 2.10 A; A=1-311.
DR PDBsum; 1EP1; -.
DR PDBsum; 1EP2; -.
DR PDBsum; 1EP3; -.
DR AlphaFoldDB; P54322; -.
DR SMR; P54322; -.
DR IntAct; P54322; 1.
DR MINT; P54322; -.
DR STRING; 416870.llmg_1106; -.
DR EnsemblBacteria; CAL97700; CAL97700; llmg_1106.
DR KEGG; llm:llmg_1106; -.
DR eggNOG; COG0167; Bacteria.
DR HOGENOM; CLU_042042_0_0_9; -.
DR OMA; SCPHAKG; -.
DR PhylomeDB; P54322; -.
DR BioCyc; LLAC416870:LLMG_RS05615-MON; -.
DR UniPathway; UPA00070; UER00945.
DR EvolutionaryTrace; P54322; -.
DR Proteomes; UP000000364; 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.
FT CHAIN 1..311
FT /note="Dihydroorotate dehydrogenase B (NAD(+)), catalytic
FT subunit"
FT /id="PRO_0000148396"
FT ACT_SITE 135
FT /note="Nucleophile"
FT BINDING 24
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT BINDING 48..49
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT BINDING 48
FT /ligand="substrate"
FT BINDING 72..76
FT /ligand="substrate"
FT BINDING 104
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT BINDING 132
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT BINDING 132
FT /ligand="substrate"
FT BINDING 170
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT BINDING 196
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT BINDING 197..198
FT /ligand="substrate"
FT BINDING 222
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT BINDING 248..249
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT BINDING 270..271
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT CONFLICT 123
FT /note="A -> R (in Ref. 1; CAA52280 and 2)"
FT /evidence="ECO:0000305"
FT CONFLICT 239
FT /note="V -> D (in Ref. 1; CAA52280 and 2)"
FT /evidence="ECO:0000305"
FT CONFLICT 255
FT /note="D -> V (in Ref. 1; CAA52280 and 2)"
FT /evidence="ECO:0000305"
FT CONFLICT 266
FT /note="A -> R (in Ref. 1; CAA52280 and 2)"
FT /evidence="ECO:0000305"
FT TURN 5..7
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 9..11
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 14..22
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 33..35
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 39..41
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 45..50
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 63..66
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 69..72
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 81..86
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 88..95
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 101..105
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 110..120
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 126..132
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 135..137
FT /evidence="ECO:0007829|PDB:1EP1"
FT HELIX 138..140
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 145..147
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 149..162
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 167..171
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 179..187
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 191..195
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 199..201
FT /evidence="ECO:0007829|PDB:1EP3"
FT TURN 206..208
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 210..213
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 218..222
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 223..225
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 226..237
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 244..246
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 253..262
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 265..269
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 272..275
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 279..293
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 299..308
FT /evidence="ECO:0007829|PDB:1EP3"
SQ SEQUENCE 311 AA; 32930 MW; 1854517E5B585BB9 CRC64;
MTENNRLSVK LPGLDLKNPI IPASGCFGFG EEYAKYYDLN KLGSIMVKAT TLHPRFGNPT
PRVAETASGM LNAIGLQNPG LEVIMTEKLP WLNENFPELP IIANVAGSEE ADYVAVCAKI
GDAANVKAIE LNISCPNVKH GGQAFGTDPE VAAALVKACK AVSKVPLYVK LSPNVTDIVP
IAKAVEAAGA DGLTMINTLM GVRFDLKTRQ PILANITGGL SGPAIKPVAL KLIHQVAQVV
DIPIIGMGGV ANAQDVLEMY MAGASAVAVG TANFADPFVC PKIIDKLPEL MDQYRIESLE
SLIQEVKEGK K
