PYRK_LACLM
ID PYRK_LACLM Reviewed; 262 AA.
AC P56968; A2RK89;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2000, sequence version 1.
DT 03-AUG-2022, entry version 136.
DE RecName: Full=Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit;
DE AltName: Full=Dihydroorotate oxidase B, electron transfer subunit;
GN Name=pyrK; OrderedLocusNames=llmg_1105;
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].
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 [2]
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 [3]
RP FUNCTION, COFACTOR, AND SUBUNIT.
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 [4]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEXES WITH FAD AND
RP IRON-SULFUR, COFACTOR, AND REACTION MECHANISM.
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: Responsible for channeling the electrons from the oxidation
CC of dihydroorotate from the FMN redox center in the PyrDB subunit to the
CC ultimate electron acceptor NAD(+). {ECO:0000269|PubMed:8910599}.
CC -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC Note=Binds 1 [2Fe-2S] cluster per subunit.;
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Note=Binds 1 FAD per subunit.;
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 P56968; P54322: pyrDB; NbExp=3; IntAct=EBI-1030589, EBI-1030598;
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- SIMILARITY: Belongs to the PyrK family. {ECO:0000305}.
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DR EMBL; X74207; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AM406671; CAL97699.1; -; Genomic_DNA.
DR RefSeq; WP_011835013.1; NZ_WJVF01000012.1.
DR PDB; 1EP1; X-ray; 2.20 A; B=2-262.
DR PDB; 1EP2; X-ray; 2.40 A; B=2-262.
DR PDB; 1EP3; X-ray; 2.10 A; B=1-262.
DR PDBsum; 1EP1; -.
DR PDBsum; 1EP2; -.
DR PDBsum; 1EP3; -.
DR AlphaFoldDB; P56968; -.
DR SMR; P56968; -.
DR IntAct; P56968; 1.
DR MINT; P56968; -.
DR STRING; 416870.llmg_1105; -.
DR EnsemblBacteria; CAL97699; CAL97699; llmg_1105.
DR KEGG; llm:llmg_1105; -.
DR eggNOG; COG0543; Bacteria.
DR HOGENOM; CLU_003827_1_2_9; -.
DR OMA; RYMKCGI; -.
DR PhylomeDB; P56968; -.
DR BioCyc; LLAC416870:LLMG_RS05610-MON; -.
DR UniPathway; UPA00070; UER00945.
DR EvolutionaryTrace; P56968; -.
DR Proteomes; UP000000364; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0009055; F:electron transfer activity; IEA:UniProtKB-UniRule.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0044205; P:'de novo' UMP biosynthetic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 2.10.240.10; -; 1.
DR Gene3D; 3.40.50.80; -; 1.
DR HAMAP; MF_01211; DHODB_Fe_S_bind; 1.
DR InterPro; IPR012165; Cyt_c3_hydrogenase_gsu.
DR InterPro; IPR037117; Dihydroorotate_DH_ele_sf.
DR InterPro; IPR019480; Dihydroorotate_DH_Fe-S-bd.
DR InterPro; IPR023455; Dihydroorotate_DHASE_ETsu.
DR InterPro; IPR017927; FAD-bd_FR_type.
DR InterPro; IPR039261; FNR_nucleotide-bd.
DR InterPro; IPR001433; OxRdtase_FAD/NAD-bd.
DR InterPro; IPR000951; Ph_dOase_redase.
DR InterPro; IPR017938; Riboflavin_synthase-like_b-brl.
DR Pfam; PF10418; DHODB_Fe-S_bind; 1.
DR Pfam; PF00175; NAD_binding_1; 1.
DR PIRSF; PIRSF006816; Cyc3_hyd_g; 1.
DR PRINTS; PR00409; PHDIOXRDTASE.
DR SUPFAM; SSF52343; SSF52343; 1.
DR SUPFAM; SSF63380; SSF63380; 1.
DR PROSITE; PS51384; FAD_FR; 1.
PE 1: Evidence at protein level;
KW 2Fe-2S; 3D-structure; Cytoplasm; Electron transport; FAD; Flavoprotein;
KW Iron; Iron-sulfur; Metal-binding; Pyrimidine biosynthesis; Transport.
FT CHAIN 1..262
FT /note="Dihydroorotate dehydrogenase B (NAD(+)), electron
FT transfer subunit"
FT /id="PRO_0000148363"
FT DOMAIN 3..104
FT /note="FAD-binding FR-type"
FT BINDING 53..56
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT BINDING 70..72
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT BINDING 79..80
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT BINDING 226
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT BINDING 231
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT BINDING 234
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT BINDING 249
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT STRAND 4..17
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 20..27
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 28..32
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 39..42
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 53..56
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 59..61
FT /evidence="ECO:0007829|PDB:1EP3"
FT TURN 62..65
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 66..72
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 79..84
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 91..100
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 111..118
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 119..121
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 123..134
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 138..147
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 148..150
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 154..158
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 163..169
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 173..178
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 180..186
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 192..198
FT /evidence="ECO:0007829|PDB:1EP3"
FT HELIX 200..209
FT /evidence="ECO:0007829|PDB:1EP3"
FT TURN 210..212
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 214..219
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 225..231
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 235..238
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 241..247
FT /evidence="ECO:0007829|PDB:1EP3"
FT TURN 248..251
FT /evidence="ECO:0007829|PDB:1EP3"
FT STRAND 253..256
FT /evidence="ECO:0007829|PDB:1EP3"
FT TURN 257..260
FT /evidence="ECO:0007829|PDB:1EP3"
SQ SEQUENCE 262 AA; 28660 MW; 9373DB3A75200DB3 CRC64;
MSQLQEMMTV VSQREVAYNI FEMVLKGTLV DEMDLPGQFL HLAVPNGAML LRRPISISSW
DKRAKTCTIL YRIGDETTGT YKLSKLESGA KVDVMGPLGN GFPVAEVTST DKILIIGGGI
GVPPLYELAK QLEKTGCQMT ILLGFASENV KILENEFSNL KNVTLKIATD DGSYGTKGHV
GMLMNEIDFE VDALYTCGAP AMLKAVAKKY DQLERLYISM ESRMACGIGA CYACVEHDKE
DESHALKVCE DGPVFLGKQL SL
