PYRC_YEAST
ID PYRC_YEAST Reviewed; 364 AA.
AC P20051; D6VZ56;
DT 01-FEB-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 2.
DT 03-AUG-2022, entry version 180.
DE RecName: Full=Dihydroorotase;
DE Short=DHOase;
DE EC=3.5.2.3 {ECO:0000305|PubMed:2897615};
GN Name=URA4; OrderedLocusNames=YLR420W; ORFNames=L9931.1;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND CATALYTIC ACTIVITY.
RC STRAIN=ATCC 28383 / FL100 / VTT C-80102;
RX PubMed=2897615; DOI=10.1007/bf00322456;
RA Guyonvarch A., Nguyen-Juilleret M., Hubert J.-C., Lacroute F.;
RT "Structure of the Saccharomyces cerevisiae URA4 gene encoding
RT dihydroorotase.";
RL Mol. Gen. Genet. 212:134-141(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
CC -!- FUNCTION: Catalyzes the conversion of ureidosuccinic acid (USA) to
CC dihydroorotate, the third step of the de novo pyrimidine biosynthetic
CC pathway. {ECO:0000305|PubMed:2897615}.
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:0000305|PubMed:2897615};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:24298;
CC Evidence={ECO:0000305|PubMed:2897615};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:P05020};
CC Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000250|UniProtKB:P05020};
CC -!- PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway;
CC (S)-dihydroorotate from bicarbonate: step 3/3.
CC {ECO:0000305|PubMed:2897615}.
CC -!- INDUCTION: By N-carbamoyl-L-aspartate.
CC -!- MISCELLANEOUS: Present with 12700 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the metallo-dependent hydrolases superfamily.
CC DHOase family. Class II DHOase subfamily. {ECO:0000305}.
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DR EMBL; X07561; CAA30444.1; -; Genomic_DNA.
DR EMBL; U20162; AAB67491.1; -; Genomic_DNA.
DR EMBL; U20939; AAB67510.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09722.1; -; Genomic_DNA.
DR PIR; S59385; DEBYO.
DR RefSeq; NP_013524.1; NM_001182308.1.
DR PDB; 6L0A; X-ray; 1.79 A; A/B/C/D=1-364.
DR PDB; 6L0B; X-ray; 2.70 A; A/B/C/D=1-364.
DR PDB; 6L0F; X-ray; 3.26 A; A/B/C/D=1-364.
DR PDB; 6L0G; X-ray; 2.05 A; A/B/C/D=1-364.
DR PDB; 6L0H; X-ray; 2.05 A; A/B/C/D=1-364.
DR PDB; 6L0I; X-ray; 2.20 A; A/B/C/D=1-364.
DR PDB; 6L0J; X-ray; 1.93 A; A/B/C/D=1-364.
DR PDB; 6L0K; X-ray; 3.30 A; A/B/C/D=1-364.
DR PDB; 7CA0; X-ray; 2.50 A; A/B/C/D=1-364.
DR PDB; 7CA1; X-ray; 3.60 A; A/B/C/D=1-364.
DR PDBsum; 6L0A; -.
DR PDBsum; 6L0B; -.
DR PDBsum; 6L0F; -.
DR PDBsum; 6L0G; -.
DR PDBsum; 6L0H; -.
DR PDBsum; 6L0I; -.
DR PDBsum; 6L0J; -.
DR PDBsum; 6L0K; -.
DR PDBsum; 7CA0; -.
DR PDBsum; 7CA1; -.
DR AlphaFoldDB; P20051; -.
DR SMR; P20051; -.
DR BioGRID; 31679; 115.
DR DIP; DIP-5074N; -.
DR IntAct; P20051; 2.
DR MINT; P20051; -.
DR STRING; 4932.YLR420W; -.
DR MaxQB; P20051; -.
DR PaxDb; P20051; -.
DR PRIDE; P20051; -.
DR EnsemblFungi; YLR420W_mRNA; YLR420W; YLR420W.
DR GeneID; 851139; -.
DR KEGG; sce:YLR420W; -.
DR SGD; S000004412; URA4.
DR VEuPathDB; FungiDB:YLR420W; -.
DR eggNOG; KOG2902; Eukaryota.
DR GeneTree; ENSGT01030000234527; -.
DR HOGENOM; CLU_041558_0_0_1; -.
DR InParanoid; P20051; -.
DR OMA; TLHHISM; -.
DR BioCyc; MetaCyc:YLR420W-MON; -.
DR BioCyc; YEAST:YLR420W-MON; -.
DR BRENDA; 3.5.2.3; 984.
DR UniPathway; UPA00070; UER00117.
DR PRO; PR:P20051; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; P20051; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0004151; F:dihydroorotase activity; IMP:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006207; P:'de novo' pyrimidine nucleobase biosynthetic process; IMP:SGD.
DR GO; GO:0044205; P:'de novo' UMP biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0006221; P:pyrimidine nucleotide biosynthetic process; IMP:SGD.
DR CDD; cd01294; DHOase; 1.
DR HAMAP; MF_00219; PyrC_classII; 1.
DR InterPro; IPR004721; DHOdimr.
DR InterPro; IPR002195; Dihydroorotase_CS.
DR InterPro; IPR032466; Metal_Hydrolase.
DR PANTHER; PTHR43137; PTHR43137; 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..364
FT /note="Dihydroorotase"
FT /id="PRO_0000147292"
FT BINDING 14
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P05020"
FT BINDING 16
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P05020"
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:0000250|UniProtKB:P05020"
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:0000250|UniProtKB:P05020"
FT BINDING 137
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P05020"
FT BINDING 180
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P05020"
FT BINDING 258
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P05020"
FT MOD_RES 98
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000250|UniProtKB:P05020"
FT CONFLICT 107..119
FT /note="NSAAGVDPNDFSA -> IRLLGWIQMTSAH (in Ref. 1)"
FT /evidence="ECO:0000305"
FT CONFLICT 156
FT /note="A -> R (in Ref. 1; CAA30444)"
FT /evidence="ECO:0000305"
FT CONFLICT 240
FT /note="K -> R (in Ref. 1; CAA30444)"
FT /evidence="ECO:0000305"
FT CONFLICT 269
FT /note="N -> K (in Ref. 1; CAA30444)"
FT /evidence="ECO:0000305"
FT CONFLICT 319
FT /note="V -> M (in Ref. 1; CAA30444)"
FT /evidence="ECO:0000305"
FT STRAND 4..9
FT /evidence="ECO:0007829|PDB:6L0A"
FT STRAND 11..15
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 20..26
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 29..32
FT /evidence="ECO:0007829|PDB:6L0A"
FT STRAND 36..40
FT /evidence="ECO:0007829|PDB:6L0A"
FT STRAND 44..46
FT /evidence="ECO:0007829|PDB:6L0B"
FT HELIX 51..64
FT /evidence="ECO:0007829|PDB:6L0A"
FT STRAND 68..71
FT /evidence="ECO:0007829|PDB:6L0A"
FT STRAND 73..75
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 82..90
FT /evidence="ECO:0007829|PDB:6L0A"
FT STRAND 95..99
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 117..120
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 121..129
FT /evidence="ECO:0007829|PDB:6L0A"
FT STRAND 133..136
FT /evidence="ECO:0007829|PDB:6L0A"
FT STRAND 146..149
FT /evidence="ECO:0007829|PDB:6L0J"
FT TURN 153..155
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 156..170
FT /evidence="ECO:0007829|PDB:6L0A"
FT STRAND 174..178
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 184..193
FT /evidence="ECO:0007829|PDB:6L0A"
FT TURN 194..196
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 200..202
FT /evidence="ECO:0007829|PDB:6L0A"
FT STRAND 205..209
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 212..214
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 218..221
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 225..227
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 236..246
FT /evidence="ECO:0007829|PDB:6L0A"
FT STRAND 253..255
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 264..266
FT /evidence="ECO:0007829|PDB:6L0A"
FT STRAND 270..272
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 280..282
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 283..293
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 297..299
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 300..304
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 306..312
FT /evidence="ECO:0007829|PDB:6L0A"
FT HELIX 316..318
FT /evidence="ECO:0007829|PDB:6L0A"
FT STRAND 324..328
FT /evidence="ECO:0007829|PDB:6L0A"
FT STRAND 341..343
FT /evidence="ECO:0007829|PDB:6L0A"
FT TURN 349..352
FT /evidence="ECO:0007829|PDB:6L0A"
FT STRAND 354..356
FT /evidence="ECO:0007829|PDB:6L0A"
FT STRAND 358..362
FT /evidence="ECO:0007829|PDB:6L0A"
SQ SEQUENCE 364 AA; 40313 MW; D92FD56E7568FA7C CRC64;
MVQEIDLGLT CDMHVHVREG AMCELVTPKI RDGGVSIAYI MPNLQPPITT LDRVIEYKKT
LQKLAPKTTF LMSFYLSKDL TPDLIHEAAQ QHAIRGVKCY PAGVTTNSAA GVDPNDFSAF
YPIFKAMQEE NLVLNLHGEK PSVHDGDKEP IHVLNAEEAF LPALKKLHND FPNLKIILEH
CTSESAIKTI EDINKNVKKA TDVKVAATLT AHHLFLTIDD WAGNPVNFCK PVAKLPNDKK
ALVKAAVSGK PYFFFGSDSA PHPVQNKANY EGVCAGVYSQ SFAIPYIAQV FEEQNALENL
KGFVSDFGIS FYEVKDSEVA SSDKAILFKK EQVIPQVISD GKDISIIPFK AGDKLSWSVR
WEPR
