PYRC_VIBCH
ID PYRC_VIBCH Reviewed; 342 AA.
AC Q9KL24;
DT 20-JUN-2002, integrated into UniProtKB/Swiss-Prot.
DT 20-JUN-2002, sequence version 2.
DT 03-AUG-2022, entry version 123.
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}; OrderedLocusNames=VC_A0925;
OS Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=243277;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 39315 / El Tor Inaba N16961;
RX PubMed=10952301; DOI=10.1038/35020000;
RA Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L.,
RA Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R.,
RA Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D.,
RA Vamathevan J.J., Bass S., Qin H., Dragoi I., Sellers P., McDonald L.A.,
RA Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L.,
RA Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M.;
RT "DNA sequence of both chromosomes of the cholera pathogen Vibrio
RT cholerae.";
RL Nature 406:477-483(2000).
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};
CC Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_00219};
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF96822.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AE003853; AAF96822.1; ALT_INIT; Genomic_DNA.
DR PIR; E82398; E82398.
DR RefSeq; NP_233310.1; NC_002506.1.
DR RefSeq; WP_000210005.1; NZ_LT906615.1.
DR PDB; 5VGM; X-ray; 1.95 A; A/B=1-342.
DR PDBsum; 5VGM; -.
DR AlphaFoldDB; Q9KL24; -.
DR SMR; Q9KL24; -.
DR STRING; 243277.VC_A0925; -.
DR MEROPS; M38.A02; -.
DR DNASU; 2612885; -.
DR EnsemblBacteria; AAF96822; AAF96822; VC_A0925.
DR KEGG; vch:VC_A0925; -.
DR PATRIC; fig|243277.26.peg.3538; -.
DR eggNOG; COG0418; Bacteria.
DR HOGENOM; CLU_041558_1_0_6; -.
DR OMA; TLHHISM; -.
DR BRENDA; 3.5.2.3; 15862.
DR UniPathway; UPA00070; UER00117.
DR Proteomes; UP000000584; Chromosome 2.
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 CHAIN 1..342
FT /note="Dihydroorotase"
FT /id="PRO_0000147221"
FT ACT_SITE 246
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT BINDING 13
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT BINDING 15..17
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT BINDING 15
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT BINDING 41
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT BINDING 98
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 BINDING 98
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 BINDING 135
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT BINDING 135
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT BINDING 173
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT BINDING 218
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT BINDING 246
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT BINDING 250
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT BINDING 262
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT MOD_RES 98
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00219"
FT STRAND 3..7
FT /evidence="ECO:0007829|PDB:5VGM"
FT STRAND 11..14
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 19..21
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 22..29
FT /evidence="ECO:0007829|PDB:5VGM"
FT TURN 30..32
FT /evidence="ECO:0007829|PDB:5VGM"
FT STRAND 34..38
FT /evidence="ECO:0007829|PDB:5VGM"
FT STRAND 42..44
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 49..61
FT /evidence="ECO:0007829|PDB:5VGM"
FT STRAND 69..75
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 82..90
FT /evidence="ECO:0007829|PDB:5VGM"
FT STRAND 92..99
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 115..118
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 119..128
FT /evidence="ECO:0007829|PDB:5VGM"
FT STRAND 131..134
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 145..147
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 148..155
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 157..163
FT /evidence="ECO:0007829|PDB:5VGM"
FT STRAND 169..171
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 177..185
FT /evidence="ECO:0007829|PDB:5VGM"
FT STRAND 190..194
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 197..200
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 203..207
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 213..215
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 224..236
FT /evidence="ECO:0007829|PDB:5VGM"
FT STRAND 241..243
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 252..255
FT /evidence="ECO:0007829|PDB:5VGM"
FT STRAND 256..260
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 270..280
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 284..286
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 287..292
FT /evidence="ECO:0007829|PDB:5VGM"
FT HELIX 294..299
FT /evidence="ECO:0007829|PDB:5VGM"
FT STRAND 305..316
FT /evidence="ECO:0007829|PDB:5VGM"
FT STRAND 321..323
FT /evidence="ECO:0007829|PDB:5VGM"
FT STRAND 326..328
FT /evidence="ECO:0007829|PDB:5VGM"
FT TURN 331..334
FT /evidence="ECO:0007829|PDB:5VGM"
FT STRAND 335..342
FT /evidence="ECO:0007829|PDB:5VGM"
SQ SEQUENCE 342 AA; 37462 MW; 9FAD2DE66E1818DA CRC64;
MTTLTITRPD DWHVHLRDGD VLADTVRDIS RYNGRALIMP NTVPPVTTTE MALAYRERIM
AAQPQAHFEP LMALYLTDNT SPEEIRKAKA SGKVVAAKLY PAGATTNSDS GVTSAKNIYP
VLQAMQEVGM LLLVHGEVTT HEVDIFDREK TFLDTVLAPI VNDFPQLKIV LEHITTADAV
TFVQQAGDNV AATITAHHLL FNRNHMLVGG IRPHFYCLPI LKRATHQHAL VAAATSGSKK
FFLGTDSAPH AKGRKEAACG CAGSYTAHAA LELYAEVFEK EGKLENLEAF ASFNGPDFYG
LPRNQETVTL TKQAWPVAES MPFGSDIVVP IRAGENIEWT VK
