PYRC_SALTY
ID PYRC_SALTY Reviewed; 348 AA.
AC P06204;
DT 01-JAN-1988, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=Dihydroorotase {ECO:0000255|HAMAP-Rule:MF_00219};
DE Short=DHOase {ECO:0000255|HAMAP-Rule:MF_00219};
DE EC=3.5.2.3 {ECO:0000255|HAMAP-Rule:MF_00219};
GN Name=pyrC {ECO:0000255|HAMAP-Rule:MF_00219, ECO:0000303|PubMed:2872051};
GN OrderedLocusNames=STM1163;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=LT2;
RX PubMed=2872051; DOI=10.1111/j.1432-1033.1986.tb09673.x;
RA Neuhrd J., Kelln R.A., Stauning E.;
RT "Cloning and structural characterization of the Salmonella typhimurium pyrC
RT gene encoding dihydroorotase.";
RL Eur. J. Biochem. 157:335-342(1986).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
RN [3] {ECO:0007744|PDB:3JZE}
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH ZINC, AND COFACTOR.
RC STRAIN=LT2;
RA Minasov G., Halavaty A., Shuvalova L., Dubrovska I., Winsor J.,
RA Papazisi L., Anderson W.F.;
RT "1.8 angstrom resolution crystal structure of dihydroorotase (pyrC) from
RT Salmonella enterica subsp. enterica serovar typhimurium str. LT2.";
RL Submitted (SEP-2009) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the reversible cyclization of carbamoyl aspartate
CC to dihydroorotate. {ECO:0000255|HAMAP-Rule:MF_00219}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-dihydroorotate + H2O = H(+) + N-carbamoyl-L-aspartate;
CC Xref=Rhea:RHEA:24296, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30864, ChEBI:CHEBI:32814; EC=3.5.2.3;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00219};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00219, ECO:0000269|Ref.3};
CC Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000255|HAMAP-Rule:MF_00219,
CC ECO:0000269|Ref.3};
CC -!- PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway;
CC (S)-dihydroorotate from bicarbonate: step 3/3. {ECO:0000255|HAMAP-
CC Rule:MF_00219}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00219}.
CC -!- SIMILARITY: Belongs to the metallo-dependent hydrolases superfamily.
CC DHOase family. Class II DHOase subfamily. {ECO:0000255|HAMAP-
CC Rule:MF_00219, ECO:0000305}.
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DR EMBL; X03928; CAA27567.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL20093.1; -; Genomic_DNA.
DR PIR; A27143; DEEBOT.
DR RefSeq; NP_460134.1; NC_003197.2.
DR RefSeq; WP_000126580.1; NC_003197.2.
DR PDB; 3JZE; X-ray; 1.80 A; A/B/C/D=1-348.
DR PDBsum; 3JZE; -.
DR AlphaFoldDB; P06204; -.
DR SMR; P06204; -.
DR STRING; 99287.STM1163; -.
DR PaxDb; P06204; -.
DR EnsemblBacteria; AAL20093; AAL20093; STM1163.
DR GeneID; 1252681; -.
DR KEGG; stm:STM1163; -.
DR PATRIC; fig|99287.12.peg.1231; -.
DR HOGENOM; CLU_041558_1_0_6; -.
DR OMA; TLHHISM; -.
DR PhylomeDB; P06204; -.
DR BioCyc; SENT99287:STM1163-MON; -.
DR UniPathway; UPA00070; UER00117.
DR EvolutionaryTrace; P06204; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0004151; F:dihydroorotase activity; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006207; P:'de novo' pyrimidine nucleobase biosynthetic process; IBA:GO_Central.
DR GO; GO:0044205; P:'de novo' UMP biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0006221; P:pyrimidine nucleotide biosynthetic process; IBA:GO_Central.
DR CDD; cd01294; DHOase; 1.
DR HAMAP; MF_00219; PyrC_classII; 1.
DR InterPro; IPR006680; Amidohydro-rel.
DR InterPro; IPR004721; DHOdimr.
DR InterPro; IPR002195; Dihydroorotase_CS.
DR InterPro; IPR032466; Metal_Hydrolase.
DR PANTHER; PTHR43137; PTHR43137; 1.
DR Pfam; PF01979; Amidohydro_1; 1.
DR PIRSF; PIRSF001237; DHOdimr; 1.
DR SUPFAM; SSF51556; SSF51556; 1.
DR TIGRFAMs; TIGR00856; pyrC_dimer; 1.
DR PROSITE; PS00482; DIHYDROOROTASE_1; 1.
DR PROSITE; PS00483; DIHYDROOROTASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Metal-binding; Pyrimidine biosynthesis;
KW Reference proteome; Zinc.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250"
FT CHAIN 2..348
FT /note="Dihydroorotase"
FT /id="PRO_0000147218"
FT ACT_SITE 251
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT BINDING 17
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219,
FT ECO:0000269|Ref.3, ECO:0007744|PDB:3JZE"
FT BINDING 19..21
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT BINDING 19
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219,
FT ECO:0000269|Ref.3, ECO:0007744|PDB:3JZE"
FT BINDING 45
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT BINDING 103
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /note="via carbamate group"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219,
FT ECO:0000269|Ref.3, ECO:0007744|PDB:3JZE"
FT BINDING 103
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /note="via carbamate group"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219,
FT ECO:0000269|Ref.3, ECO:0007744|PDB:3JZE"
FT BINDING 140
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT BINDING 140
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219,
FT ECO:0000269|Ref.3, ECO:0007744|PDB:3JZE"
FT BINDING 178
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219,
FT ECO:0000269|Ref.3, ECO:0007744|PDB:3JZE"
FT BINDING 223
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT BINDING 251
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219,
FT ECO:0000269|Ref.3, ECO:0007744|PDB:3JZE"
FT BINDING 255
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT BINDING 267
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT MOD_RES 103
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT CONFLICT 67
FT /note="V -> G (in Ref. 1; CAA27567)"
FT /evidence="ECO:0000305"
FT STRAND 7..11
FT /evidence="ECO:0007829|PDB:3JZE"
FT STRAND 15..18
FT /evidence="ECO:0007829|PDB:3JZE"
FT HELIX 23..34
FT /evidence="ECO:0007829|PDB:3JZE"
FT STRAND 38..42
FT /evidence="ECO:0007829|PDB:3JZE"
FT STRAND 46..48
FT /evidence="ECO:0007829|PDB:3JZE"
FT HELIX 53..65
FT /evidence="ECO:0007829|PDB:3JZE"
FT STRAND 74..80
FT /evidence="ECO:0007829|PDB:3JZE"
FT HELIX 87..95
FT /evidence="ECO:0007829|PDB:3JZE"
FT STRAND 99..104
FT /evidence="ECO:0007829|PDB:3JZE"
FT STRAND 116..118
FT /evidence="ECO:0007829|PDB:3JZE"
FT HELIX 121..123
FT /evidence="ECO:0007829|PDB:3JZE"
FT HELIX 124..133
FT /evidence="ECO:0007829|PDB:3JZE"
FT STRAND 137..139
FT /evidence="ECO:0007829|PDB:3JZE"
FT HELIX 150..152
FT /evidence="ECO:0007829|PDB:3JZE"
FT HELIX 153..160
FT /evidence="ECO:0007829|PDB:3JZE"
FT HELIX 162..168
FT /evidence="ECO:0007829|PDB:3JZE"
FT STRAND 174..176
FT /evidence="ECO:0007829|PDB:3JZE"
FT HELIX 182..189
FT /evidence="ECO:0007829|PDB:3JZE"
FT STRAND 195..199
FT /evidence="ECO:0007829|PDB:3JZE"
FT HELIX 201..205
FT /evidence="ECO:0007829|PDB:3JZE"
FT HELIX 208..212
FT /evidence="ECO:0007829|PDB:3JZE"
FT HELIX 218..220
FT /evidence="ECO:0007829|PDB:3JZE"
FT HELIX 229..240
FT /evidence="ECO:0007829|PDB:3JZE"
FT STRAND 246..248
FT /evidence="ECO:0007829|PDB:3JZE"
FT HELIX 257..260
FT /evidence="ECO:0007829|PDB:3JZE"
FT STRAND 261..265
FT /evidence="ECO:0007829|PDB:3JZE"
FT TURN 272..274
FT /evidence="ECO:0007829|PDB:3JZE"
FT HELIX 275..285
FT /evidence="ECO:0007829|PDB:3JZE"
FT HELIX 289..291
FT /evidence="ECO:0007829|PDB:3JZE"
FT HELIX 292..297
FT /evidence="ECO:0007829|PDB:3JZE"
FT HELIX 299..304
FT /evidence="ECO:0007829|PDB:3JZE"
FT STRAND 311..316
FT /evidence="ECO:0007829|PDB:3JZE"
FT STRAND 329..333
FT /evidence="ECO:0007829|PDB:3JZE"
FT TURN 336..339
FT /evidence="ECO:0007829|PDB:3JZE"
FT STRAND 341..343
FT /evidence="ECO:0007829|PDB:3JZE"
SQ SEQUENCE 348 AA; 38605 MW; EBF4CD54B8C04FCE CRC64;
MTAPSQVLKI RRPDDWHVHL RDGDMLKTVV PYTSEIYGRA IVMPNLASPI TTVDAAIAYR
QRILDAVPAG HDFTPLMTCY LTDSLDADEL ERGFHEGVFT AAKLYPANAT TNSSHGVTSV
DAIMPVLERM EKLGIPLLVH GEVTHADVDI FDREARFIDT VMEPLRQRLT ALKVVFEHIT
TKDAAQYVRD GNDYLAATIT PQHLMFNRND MLVGGIRPHL YCLPILKRNI HQQALRELVA
SGFTRAFLGT DSAPHSRHRK ETSCGCAGCF NAPSALGSYA AVFEEMNALA HFEAFCSLNG
PQFYGLPMNT GWVELVRDEQ QIPGNIALAD DSLVPFLAGE TVRWSVKK
