PYRDA_LACLM
ID PYRDA_LACLM Reviewed; 311 AA.
AC A2RJT9; P54321;
DT 01-MAY-2007, integrated into UniProtKB/Swiss-Prot.
DT 06-MAR-2007, sequence version 1.
DT 03-AUG-2022, entry version 88.
DE RecName: Full=Dihydroorotate dehydrogenase A (fumarate);
DE Short=DHOD A;
DE Short=DHODase A;
DE Short=DHOdehase A;
DE EC=1.3.98.1;
GN Name=pyrDA; OrderedLocusNames=llmg_0952;
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 [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 MUTAGENESIS OF LYS-43; CYS-130; ASN-132 AND LYS-164.
RC STRAIN=MG1363;
RX PubMed=9405053; DOI=10.1021/bi971628y;
RA Bjoernberg O., Rowland P., Larsen S., Jensen K.F.;
RT "Active site of dihydroorotate dehydrogenase A from Lactococcus lactis
RT investigated by chemical modification and mutagenesis.";
RL Biochemistry 36:16197-16205(1997).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH FMN, COFACTOR, AND
RP SUBUNIT.
RC STRAIN=MG1363;
RX PubMed=9032071; DOI=10.1016/s0969-2126(97)00182-2;
RA Rowland P., Nielsen F.S., Jensen K.F., Larsen S.;
RT "The crystal structure of the flavin containing enzyme dihydroorotate
RT dehydrogenase A from Lactococcus lactis.";
RL Structure 5:239-252(1997).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH FMN AND OROTATE,
RP COFACTOR, AND REACTION MECHANISM.
RC STRAIN=MG1363;
RX PubMed=9655329; DOI=10.1002/pro.5560070601;
RA Rowland P., Bjoernberg O., Nielsen F.S., Jensen K.F., Larsen S.;
RT "The crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A
RT complexed with the enzyme reaction product throws light on its enzymatic
RT function.";
RL Protein Sci. 7:1269-1279(1998).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF WILD-TYPE AND MUTANTS ALA-56;
RP ARG-56; ALA-67; LYS-136 AND GLU-213 IN COMPLEXES WITH FMN AND SUBSTRATE,
RP MUTAGENESIS OF ARG-50; PRO-56; ARG-57; ASN-67; ASN-127; SER-129; PRO-131;
RP ASN-132; LYS-136; ASN-193 AND LYS-213, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=MG1363;
RX PubMed=12732650; DOI=10.1074/jbc.m303767200;
RA Noerager S., Arent S., Bjoernberg O., Ottosen M., Lo Leggio L.,
RA Jensen K.F., Larsen S.;
RT "Lactococcus lactis dihydroorotate dehydrogenase A mutants reveal important
RT facets of the enzymatic function.";
RL J. Biol. Chem. 278:28812-28822(2003).
CC -!- FUNCTION: Catalyzes the conversion of dihydroorotate to orotate with
CC fumarate as the electron acceptor. Molecular oxygen can replace
CC fumarate in vitro, but cannot use NAD(+) as an electron acceptor.
CC {ECO:0000269|PubMed:8021180}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-dihydroorotate + fumarate = orotate + succinate;
CC Xref=Rhea:RHEA:30059, ChEBI:CHEBI:29806, ChEBI:CHEBI:30031,
CC ChEBI:CHEBI:30839, ChEBI:CHEBI:30864; EC=1.3.98.1;
CC Evidence={ECO:0000269|PubMed:8021180};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000269|PubMed:9032071, ECO:0000269|PubMed:9655329};
CC Note=Binds 1 FMN per subunit. {ECO:0000269|PubMed:9032071,
CC ECO:0000269|PubMed:9655329};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=18 uM for dihydroorotate {ECO:0000269|PubMed:12732650};
CC KM=250 uM for fumarate {ECO:0000269|PubMed:12732650};
CC Vmax=18.6 umol/min/mg enzyme {ECO:0000269|PubMed:12732650};
CC -!- PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:9032071,
CC ECO:0000269|PubMed:9655329}.
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; X74206; CAA52279.1; -; Genomic_DNA.
DR EMBL; AM406671; CAL97544.1; -; Genomic_DNA.
DR RefSeq; WP_011834894.1; NZ_WJVF01000006.1.
DR PDB; 1DOR; X-ray; 2.00 A; A/B=1-311.
DR PDB; 1JQV; X-ray; 2.10 A; A/B=1-311.
DR PDB; 1JQX; X-ray; 1.70 A; A/B=1-311.
DR PDB; 1JRB; X-ray; 1.90 A; A/B=1-311.
DR PDB; 1JRC; X-ray; 1.80 A; A/B=1-311.
DR PDB; 1JUB; X-ray; 1.40 A; A/B=1-311.
DR PDB; 1JUE; X-ray; 1.80 A; A/B=1-311.
DR PDB; 1OVD; X-ray; 2.25 A; A/B=1-311.
DR PDB; 2BSL; X-ray; 2.30 A; A/B=1-311.
DR PDB; 2BX7; X-ray; 2.04 A; A/B=1-311.
DR PDB; 2DOR; X-ray; 2.00 A; A/B=1-311.
DR PDBsum; 1DOR; -.
DR PDBsum; 1JQV; -.
DR PDBsum; 1JQX; -.
DR PDBsum; 1JRB; -.
DR PDBsum; 1JRC; -.
DR PDBsum; 1JUB; -.
DR PDBsum; 1JUE; -.
DR PDBsum; 1OVD; -.
DR PDBsum; 2BSL; -.
DR PDBsum; 2BX7; -.
DR PDBsum; 2DOR; -.
DR AlphaFoldDB; A2RJT9; -.
DR SMR; A2RJT9; -.
DR STRING; 416870.llmg_0952; -.
DR EnsemblBacteria; CAL97544; CAL97544; llmg_0952.
DR KEGG; llm:llmg_0952; -.
DR eggNOG; COG0167; Bacteria.
DR HOGENOM; CLU_042042_3_0_9; -.
DR OMA; CPISFIT; -.
DR PhylomeDB; A2RJT9; -.
DR BioCyc; LLAC416870:LLMG_RS04850-MON; -.
DR BRENDA; 1.3.1.14; 2903.
DR UniPathway; UPA00070; -.
DR EvolutionaryTrace; A2RJT9; -.
DR Proteomes; UP000000364; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:1990663; F:dihydroorotate dehydrogenase (fumarate) 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; cd04741; DHOD_1A_like; 1.
DR Gene3D; 2.30.26.10; -; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_00224; DHO_dh_type1; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR033886; DHOD_1A.
DR InterPro; IPR023359; Dihydro_DH_chainA_dom2.
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; Oxidoreductase;
KW Pyrimidine biosynthesis.
FT CHAIN 1..311
FT /note="Dihydroorotate dehydrogenase A (fumarate)"
FT /id="PRO_0000285239"
FT ACT_SITE 130
FT /note="Nucleophile"
FT BINDING 19
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:9032071,
FT ECO:0000269|PubMed:9655329"
FT BINDING 43..44
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:9032071,
FT ECO:0000269|PubMed:9655329"
FT BINDING 43
FT /ligand="substrate"
FT BINDING 67..71
FT /ligand="substrate"
FT BINDING 127
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:9032071,
FT ECO:0000269|PubMed:9655329"
FT BINDING 127
FT /ligand="substrate"
FT BINDING 164
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:9032071,
FT ECO:0000269|PubMed:9655329"
FT BINDING 192
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:9032071,
FT ECO:0000269|PubMed:9655329"
FT BINDING 193..194
FT /ligand="substrate"
FT BINDING 221
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:9032071,
FT ECO:0000269|PubMed:9655329"
FT BINDING 249..250
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:9032071,
FT ECO:0000269|PubMed:9655329"
FT BINDING 271..272
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:9032071,
FT ECO:0000269|PubMed:9655329"
FT MUTAGEN 43
FT /note="K->A: More than 500-fold reduction of enzymatic
FT activity with oxygen or DCIP as electron acceptor."
FT /evidence="ECO:0000269|PubMed:9405053"
FT MUTAGEN 43
FT /note="K->E: 40-fold reduction of enzymatic activity with
FT oxygen as electron acceptor; more than 120-fold reduction
FT with DCIP as electron acceptor."
FT /evidence="ECO:0000269|PubMed:9405053"
FT MUTAGEN 50
FT /note="R->E: Steady state kinetics comparable to wild-type;
FT 3-fold decrease in flavin bleaching rate."
FT /evidence="ECO:0000269|PubMed:12732650"
FT MUTAGEN 56
FT /note="P->A: More than 500-fold reduction of enzymatic
FT activity."
FT /evidence="ECO:0000269|PubMed:12732650"
FT MUTAGEN 57
FT /note="R->A: More active than wild-type, especially with
FT 2,6-dichloroindophenol as electron acceptor."
FT /evidence="ECO:0000269|PubMed:12732650"
FT MUTAGEN 67
FT /note="N->A: 100-fold lower affinity for dihydroorotate."
FT /evidence="ECO:0000269|PubMed:12732650"
FT MUTAGEN 127
FT /note="N->A: 70-fold lower affinity for dihydroorotate;
FT inhibited by milimolar concentrations of fumarate."
FT /evidence="ECO:0000269|PubMed:12732650"
FT MUTAGEN 129
FT /note="S->A: 6-fold lower enzymatic activity with fumarate
FT as electron acceptor."
FT /evidence="ECO:0000269|PubMed:12732650"
FT MUTAGEN 130
FT /note="C->A,S: Almost total loss of activity with oxygen or
FT 2,6-dichloroindophenol as electron acceptor."
FT /evidence="ECO:0000269|PubMed:9405053"
FT MUTAGEN 131
FT /note="P->A: 4.5-fold lower enzymatic activity with
FT fumarate and 2,6-dichloroindophenol as electron acceptor."
FT /evidence="ECO:0000269|PubMed:12732650"
FT MUTAGEN 132
FT /note="N->A: 54-fold reduction of enzymatic activity with
FT oxygen as electron acceptor; more than 250-fold reduction
FT with 2,6-dichloroindophenol as electron acceptor."
FT /evidence="ECO:0000269|PubMed:12732650,
FT ECO:0000269|PubMed:9405053"
FT MUTAGEN 136
FT /note="K->A: Slightly higher affinity to dihydroorotate; 2-
FT fold decrease in flavin bleaching rate."
FT /evidence="ECO:0000269|PubMed:12732650"
FT MUTAGEN 164
FT /note="K->A: Almost total loss of activity with oxygen or
FT 2,6-dichloroindophenol as electron acceptor."
FT /evidence="ECO:0000269|PubMed:9405053"
FT MUTAGEN 193
FT /note="N->A: 500-fold lower affinity for dihydroorotate;
FT inhibited by milimolar concentrations of fumarate."
FT /evidence="ECO:0000269|PubMed:12732650"
FT MUTAGEN 213
FT /note="K->A: 7-fold decrease in enzymatic activity; 50-fold
FT decrease in flavin bleaching rate."
FT /evidence="ECO:0000269|PubMed:12732650"
FT STRAND 4..6
FT /evidence="ECO:0007829|PDB:1JUB"
FT STRAND 9..17
FT /evidence="ECO:0007829|PDB:1JUB"
FT HELIX 26..34
FT /evidence="ECO:0007829|PDB:1JUB"
FT STRAND 58..61
FT /evidence="ECO:0007829|PDB:1JUB"
FT STRAND 64..67
FT /evidence="ECO:0007829|PDB:1JUB"
FT HELIX 76..89
FT /evidence="ECO:0007829|PDB:1JUB"
FT STRAND 92..94
FT /evidence="ECO:0007829|PDB:1JUB"
FT STRAND 97..100
FT /evidence="ECO:0007829|PDB:1JUB"
FT HELIX 105..117
FT /evidence="ECO:0007829|PDB:1JUB"
FT STRAND 122..128
FT /evidence="ECO:0007829|PDB:1JUB"
FT STRAND 133..135
FT /evidence="ECO:0007829|PDB:1JUB"
FT HELIX 139..141
FT /evidence="ECO:0007829|PDB:1JUB"
FT HELIX 143..153
FT /evidence="ECO:0007829|PDB:1JUB"
FT TURN 154..156
FT /evidence="ECO:0007829|PDB:1JUB"
FT STRAND 161..165
FT /evidence="ECO:0007829|PDB:1JUB"
FT HELIX 171..181
FT /evidence="ECO:0007829|PDB:1JUB"
FT STRAND 188..191
FT /evidence="ECO:0007829|PDB:1JUB"
FT STRAND 195..199
FT /evidence="ECO:0007829|PDB:1JUB"
FT TURN 203..206
FT /evidence="ECO:0007829|PDB:1JUB"
FT STRAND 207..209
FT /evidence="ECO:0007829|PDB:1JUB"
FT HELIX 212..215
FT /evidence="ECO:0007829|PDB:1JUB"
FT STRAND 216..221
FT /evidence="ECO:0007829|PDB:1JUB"
FT HELIX 222..224
FT /evidence="ECO:0007829|PDB:1JUB"
FT HELIX 225..236
FT /evidence="ECO:0007829|PDB:1JUB"
FT STRAND 243..250
FT /evidence="ECO:0007829|PDB:1JUB"
FT HELIX 254..263
FT /evidence="ECO:0007829|PDB:1JUB"
FT STRAND 266..270
FT /evidence="ECO:0007829|PDB:1JUB"
FT HELIX 272..277
FT /evidence="ECO:0007829|PDB:1JUB"
FT HELIX 281..296
FT /evidence="ECO:0007829|PDB:1JUB"
FT HELIX 301..303
FT /evidence="ECO:0007829|PDB:1JUB"
FT TURN 304..306
FT /evidence="ECO:0007829|PDB:1JUB"
SQ SEQUENCE 311 AA; 34210 MW; 30157E3C2791CDD7 CRC64;
MLNTTFANAK FANPFMNASG VHCMTIEDLE ELKASQAGAY ITKSSTLEKR EGNPLPRYVD
LELGSINSMG LPNLGFDYYL DYVLKNQKEN AQEGPIFFSI AGMSAAENIA MLKKIQESDF
SGITELNLSC PNVPGKPQLA YDFEATEKLL KEVFTFFTKP LGVKLPPYFD LVHFDIMAEI
LNQFPLTYVN SVNSIGNGLF IDPEAESVVI KPKDGFGGIG GAYIKPTALA NVRAFYTRLK
PEIQIIGTGG IETGQDAFEH LLCGATMLQI GTALHKEGPA IFDRIIKELE EIMNQKGYQS
IADFHGKLKS L
