PYRC_YERPE
ID PYRC_YERPE Reviewed; 348 AA.
AC Q8ZFU4; Q0WGJ0;
DT 20-JUN-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 143.
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};
GN OrderedLocusNames=YPO1587, y1746, YP_2265;
OS Yersinia pestis.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Yersinia.
OX NCBI_TaxID=632;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CO-92 / Biovar Orientalis;
RX PubMed=11586360; DOI=10.1038/35097083;
RA Parkhill J., Wren B.W., Thomson N.R., Titball R.W., Holden M.T.G.,
RA Prentice M.B., Sebaihia M., James K.D., Churcher C.M., Mungall K.L.,
RA Baker S., Basham D., Bentley S.D., Brooks K., Cerdeno-Tarraga A.-M.,
RA Chillingworth T., Cronin A., Davies R.M., Davis P., Dougan G., Feltwell T.,
RA Hamlin N., Holroyd S., Jagels K., Karlyshev A.V., Leather S., Moule S.,
RA Oyston P.C.F., Quail M.A., Rutherford K.M., Simmonds M., Skelton J.,
RA Stevens K., Whitehead S., Barrell B.G.;
RT "Genome sequence of Yersinia pestis, the causative agent of plague.";
RL Nature 413:523-527(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=KIM10+ / Biovar Mediaevalis;
RX PubMed=12142430; DOI=10.1128/jb.184.16.4601-4611.2002;
RA Deng W., Burland V., Plunkett G. III, Boutin A., Mayhew G.F., Liss P.,
RA Perna N.T., Rose D.J., Mau B., Zhou S., Schwartz D.C., Fetherston J.D.,
RA Lindler L.E., Brubaker R.R., Plano G.V., Straley S.C., McDonough K.A.,
RA Nilles M.L., Matson J.S., Blattner F.R., Perry R.D.;
RT "Genome sequence of Yersinia pestis KIM.";
RL J. Bacteriol. 184:4601-4611(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=91001 / Biovar Mediaevalis;
RX PubMed=15368893; DOI=10.1093/dnares/11.3.179;
RA Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D.,
RA Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L.,
RA Dai R., Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H.,
RA Wang J., Huang P., Yang R.;
RT "Complete genome sequence of Yersinia pestis strain 91001, an isolate
RT avirulent to humans.";
RL DNA Res. 11:179-197(2004).
RN [4] {ECO:0007744|PDB:6CTY}
RP X-RAY CRYSTALLOGRAPHY (2.41 ANGSTROMS) IN COMPLEX WITH ZINC, AND COFACTOR.
RA Lipowska J., Shabalin I.G., Anderson W.F., Minor W.;
RT "Crystal structure of dihydroorotase pyrC from Yersinia pestis in complex
RT with zinc and unknown ligand at 2.4 A resolution.";
RL Submitted (FEB-2017) 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.4};
CC Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000255|HAMAP-Rule:MF_00219,
CC ECO:0000269|Ref.4};
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; AL590842; CAL20232.1; -; Genomic_DNA.
DR EMBL; AE009952; AAM85314.1; -; Genomic_DNA.
DR EMBL; AE017042; AAS62471.1; -; Genomic_DNA.
DR PIR; AF0193; AF0193.
DR RefSeq; WP_002213109.1; NZ_WUCM01000147.1.
DR RefSeq; YP_002346598.1; NC_003143.1.
DR PDB; 6CTY; X-ray; 2.41 A; A/B/C/D/E/F=1-348.
DR PDBsum; 6CTY; -.
DR AlphaFoldDB; Q8ZFU4; -.
DR SMR; Q8ZFU4; -.
DR IntAct; Q8ZFU4; 4.
DR STRING; 214092.YPO1587; -.
DR MEROPS; M38.A02; -.
DR PaxDb; Q8ZFU4; -.
DR DNASU; 1146693; -.
DR EnsemblBacteria; AAM85314; AAM85314; y1746.
DR EnsemblBacteria; AAS62471; AAS62471; YP_2265.
DR GeneID; 57976984; -.
DR KEGG; ype:YPO1587; -.
DR KEGG; ypk:y1746; -.
DR KEGG; ypm:YP_2265; -.
DR PATRIC; fig|214092.21.peg.1929; -.
DR eggNOG; COG0418; Bacteria.
DR HOGENOM; CLU_041558_1_0_6; -.
DR OMA; TLHHISM; -.
DR BRENDA; 3.5.2.3; 4559.
DR UniPathway; UPA00070; UER00117.
DR Proteomes; UP000000815; Chromosome.
DR Proteomes; UP000001019; Chromosome.
DR Proteomes; UP000002490; 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; PS00483; DIHYDROOROTASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Metal-binding; Pyrimidine biosynthesis;
KW Reference proteome; Zinc.
FT CHAIN 1..348
FT /note="Dihydroorotase"
FT /id="PRO_0000147225"
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.4"
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.4"
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.4"
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.4"
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.4"
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.4"
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.4"
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 STRAND 7..11
FT /evidence="ECO:0007829|PDB:6CTY"
FT STRAND 15..18
FT /evidence="ECO:0007829|PDB:6CTY"
FT HELIX 23..34
FT /evidence="ECO:0007829|PDB:6CTY"
FT STRAND 38..42
FT /evidence="ECO:0007829|PDB:6CTY"
FT STRAND 46..48
FT /evidence="ECO:0007829|PDB:6CTY"
FT HELIX 53..66
FT /evidence="ECO:0007829|PDB:6CTY"
FT STRAND 74..80
FT /evidence="ECO:0007829|PDB:6CTY"
FT HELIX 87..95
FT /evidence="ECO:0007829|PDB:6CTY"
FT STRAND 98..104
FT /evidence="ECO:0007829|PDB:6CTY"
FT STRAND 116..119
FT /evidence="ECO:0007829|PDB:6CTY"
FT HELIX 120..123
FT /evidence="ECO:0007829|PDB:6CTY"
FT HELIX 124..133
FT /evidence="ECO:0007829|PDB:6CTY"
FT STRAND 137..139
FT /evidence="ECO:0007829|PDB:6CTY"
FT HELIX 150..152
FT /evidence="ECO:0007829|PDB:6CTY"
FT HELIX 153..160
FT /evidence="ECO:0007829|PDB:6CTY"
FT HELIX 162..168
FT /evidence="ECO:0007829|PDB:6CTY"
FT STRAND 174..176
FT /evidence="ECO:0007829|PDB:6CTY"
FT HELIX 182..189
FT /evidence="ECO:0007829|PDB:6CTY"
FT STRAND 195..199
FT /evidence="ECO:0007829|PDB:6CTY"
FT HELIX 201..205
FT /evidence="ECO:0007829|PDB:6CTY"
FT HELIX 208..212
FT /evidence="ECO:0007829|PDB:6CTY"
FT HELIX 218..220
FT /evidence="ECO:0007829|PDB:6CTY"
FT HELIX 229..240
FT /evidence="ECO:0007829|PDB:6CTY"
FT STRAND 246..248
FT /evidence="ECO:0007829|PDB:6CTY"
FT HELIX 257..260
FT /evidence="ECO:0007829|PDB:6CTY"
FT STRAND 261..265
FT /evidence="ECO:0007829|PDB:6CTY"
FT HELIX 275..285
FT /evidence="ECO:0007829|PDB:6CTY"
FT HELIX 289..291
FT /evidence="ECO:0007829|PDB:6CTY"
FT HELIX 292..297
FT /evidence="ECO:0007829|PDB:6CTY"
FT HELIX 299..304
FT /evidence="ECO:0007829|PDB:6CTY"
FT STRAND 312..316
FT /evidence="ECO:0007829|PDB:6CTY"
FT STRAND 326..328
FT /evidence="ECO:0007829|PDB:6CTY"
FT STRAND 331..333
FT /evidence="ECO:0007829|PDB:6CTY"
FT TURN 336..339
FT /evidence="ECO:0007829|PDB:6CTY"
FT STRAND 341..343
FT /evidence="ECO:0007829|PDB:6CTY"
SQ SEQUENCE 348 AA; 38542 MW; B9215D6E02697221 CRC64;
MTAQPQTLKI RRPDDWHIHL RDDEMLSTVL PYTSEVFARA IVMPNLAQPI TTVASAIAYR
ERILAAVPAG HKFTPLMTCY LTNSLDAKEL TTGFEQGVFT AAKLYPANAT TNSTHGVSDI
PAIYPLFEQM QKIGMPLLIH GEVTDAAVDI FDREARFIDQ ILEPIRQKFP ELKIVFEHIT
TKDAADYVLA GNRFLGATVT PQHLMFNRNH MLVGGIRPHL FCLPILKRST HQQALRAAVA
SGSDRFFLGT DSAPHAKHRK ESSCGCAGVF NAPAALPAYA SVFEELNALQ HLEAFCALNG
PRFYGLPVND DVVELVRTPF LQPEEIPLGN ESVIPFLAGQ TLNWSVKR
