PYRF_YEAST
ID PYRF_YEAST Reviewed; 267 AA.
AC P03962; D3DLM7;
DT 23-OCT-1986, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 2.
DT 03-AUG-2022, entry version 201.
DE RecName: Full=Orotidine 5'-phosphate decarboxylase;
DE EC=4.1.1.23;
DE AltName: Full=OMP decarboxylase;
DE Short=OMPDCase;
DE Short=OMPdecase;
DE AltName: Full=Uridine 5'-monophosphate synthase;
DE Short=UMP synthase;
GN Name=URA3; OrderedLocusNames=YEL021W;
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].
RC STRAIN=+D4, and ATCC 28383 / FL100 / VTT C-80102;
RX PubMed=6092217; DOI=10.1016/0378-1119(84)90172-0;
RA Rose M., Grisafi P., Botstein D.;
RT "Structure and function of the yeast URA3 gene: expression in Escherichia
RT coli.";
RL Gene 29:113-124(1984).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169868;
RA Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
RA Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
RA Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S.,
RA Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D.,
RA Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y.,
RA Botstein D., Davis R.W.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";
RL Nature 387:78-81(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 NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Holtz A., Lou Y.;
RL Submitted (JUN-1997) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-73.
RX PubMed=3023868; DOI=10.1128/mcb.6.4.1095-1101.1986;
RA Yarger J.G., Armilei G., Gorman M.C.;
RT "Transcription terminator-like element within a Saccharomyces cerevisiae
RT promoter region.";
RL Mol. Cell. Biol. 6:1095-1101(1986).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-11.
RX PubMed=6315953; DOI=10.1016/s0022-2836(83)80193-4;
RA Rose M., Botstein D.;
RT "Structure and function of the yeast URA3 gene. Differentially regulated
RT expression of hybrid beta-galactosidase from overlapping coding sequences
RT in yeast.";
RL J. Mol. Biol. 170:883-904(1983).
RN [7]
RP MUTAGENESIS OF LYS-59; ASP-91; LYS-93; ASP-96 AND GLN-215.
RX PubMed=11278904; DOI=10.1074/jbc.m011429200;
RA Miller B.G., Snider M.J., Wolfenden R., Short S.A.;
RT "Dissecting a charged network at the active site of orotidine-5'-phosphate
RT decarboxylase.";
RL J. Biol. Chem. 276:15174-15176(2001).
RN [8]
RP UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-93; LYS-209 AND LYS-253, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=SUB592;
RX PubMed=12872131; DOI=10.1038/nbt849;
RA Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G.,
RA Roelofs J., Finley D., Gygi S.P.;
RT "A proteomics approach to understanding protein ubiquitination.";
RL Nat. Biotechnol. 21:921-926(2003).
RN [9]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH
RP TRANSITION STATE ANALOG.
RX PubMed=10681417; DOI=10.1073/pnas.030409797;
RA Miller B.G., Hassell A.M., Wolfenden R., Milburn M.V., Short S.A.;
RT "Anatomy of a proficient enzyme: the structure of orotidine 5'-
RT monophosphate decarboxylase in the presence and absence of a potential
RT transition state analog.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:2011-2016(2000).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + orotidine 5'-phosphate = CO2 + UMP;
CC Xref=Rhea:RHEA:11596, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:57538, ChEBI:CHEBI:57865; EC=4.1.1.23;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU10110};
CC -!- PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway;
CC UMP from orotate: step 2/2.
CC -!- SIMILARITY: Belongs to the OMP decarboxylase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA25010.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; K02206; AAA34824.1; -; Genomic_DNA.
DR EMBL; K02207; AAA34825.1; -; Genomic_DNA.
DR EMBL; U18530; AAB64498.1; -; Genomic_DNA.
DR EMBL; U89671; AAB49978.1; -; Genomic_DNA.
DR EMBL; M12926; AAA35199.1; -; Genomic_DNA.
DR EMBL; X00191; CAA25010.1; ALT_INIT; Genomic_DNA.
DR EMBL; U89927; AAB64383.1; -; Genomic_DNA.
DR EMBL; U63018; AAC53678.1; -; Genomic_DNA.
DR EMBL; BK006939; DAA07631.1; -; Genomic_DNA.
DR PIR; A01082; DEBYOP.
DR PIR; S05735; DCBYOF.
DR RefSeq; NP_010893.3; NM_001178836.3.
DR PDB; 1DQW; X-ray; 2.10 A; A/B/C/D=1-267.
DR PDB; 1DQX; X-ray; 2.40 A; A/B/C/D=1-267.
DR PDB; 3GDK; X-ray; 2.00 A; A/B/C/D=1-267.
DR PDB; 3GDL; X-ray; 1.65 A; A/B=1-267.
DR PDB; 3GDM; X-ray; 1.60 A; A/B=1-267.
DR PDB; 3GDR; X-ray; 1.90 A; A/B/C/D=1-267.
DR PDB; 3GDT; X-ray; 1.60 A; A/B/C/D=1-267.
DR PDBsum; 1DQW; -.
DR PDBsum; 1DQX; -.
DR PDBsum; 3GDK; -.
DR PDBsum; 3GDL; -.
DR PDBsum; 3GDM; -.
DR PDBsum; 3GDR; -.
DR PDBsum; 3GDT; -.
DR AlphaFoldDB; P03962; -.
DR SMR; P03962; -.
DR BioGRID; 36708; 21.
DR DIP; DIP-6576N; -.
DR IntAct; P03962; 3.
DR MINT; P03962; -.
DR STRING; 4932.YEL021W; -.
DR BindingDB; P03962; -.
DR ChEMBL; CHEMBL4858; -.
DR iPTMnet; P03962; -.
DR PaxDb; P03962; -.
DR PRIDE; P03962; -.
DR EnsemblFungi; YEL021W_mRNA; YEL021W; YEL021W.
DR GeneID; 856692; -.
DR KEGG; sce:YEL021W; -.
DR SGD; S000000747; URA3.
DR VEuPathDB; FungiDB:YEL021W; -.
DR eggNOG; KOG1377; Eukaryota.
DR GeneTree; ENSGT00390000001856; -.
DR HOGENOM; CLU_030821_0_0_1; -.
DR OMA; KNFVMGF; -.
DR BioCyc; MetaCyc:YEL021W-MON; -.
DR BioCyc; YEAST:YEL021W-MON; -.
DR BRENDA; 4.1.1.23; 984.
DR SABIO-RK; P03962; -.
DR UniPathway; UPA00070; UER00120.
DR EvolutionaryTrace; P03962; -.
DR PHI-base; PHI:506; -.
DR PRO; PR:P03962; -.
DR Proteomes; UP000002311; Chromosome V.
DR RNAct; P03962; protein.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0004590; F:orotidine-5'-phosphate decarboxylase activity; IDA:SGD.
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:0006222; P:UMP biosynthetic process; IDA:SGD.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR014732; OMPdecase.
DR InterPro; IPR018089; OMPdecase_AS.
DR InterPro; IPR001754; OMPdeCOase_dom.
DR InterPro; IPR011060; RibuloseP-bd_barrel.
DR PANTHER; PTHR32119:SF2; PTHR32119:SF2; 1.
DR Pfam; PF00215; OMPdecase; 1.
DR SMART; SM00934; OMPdecase; 1.
DR SUPFAM; SSF51366; SSF51366; 1.
DR TIGRFAMs; TIGR01740; pyrF; 1.
DR PROSITE; PS00156; OMPDECASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Decarboxylase; Isopeptide bond; Lyase;
KW Pyrimidine biosynthesis; Reference proteome; Ubl conjugation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22814378"
FT CHAIN 2..267
FT /note="Orotidine 5'-phosphate decarboxylase"
FT /id="PRO_0000134692"
FT ACT_SITE 93
FT /note="Proton donor"
FT BINDING 37
FT /ligand="substrate"
FT BINDING 59..61
FT /ligand="substrate"
FT BINDING 91..100
FT /ligand="substrate"
FT BINDING 217
FT /ligand="substrate"
FT BINDING 235
FT /ligand="substrate"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22814378"
FT CROSSLNK 93
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000269|PubMed:12872131"
FT CROSSLNK 209
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000269|PubMed:12872131"
FT CROSSLNK 253
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000269|PubMed:12872131"
FT VARIANT 160
FT /note="A -> S (in strain: +D4)"
FT MUTAGEN 59
FT /note="K->A: Reduces kcat 100-fold. Reduces substrate
FT affinity 900-fold."
FT /evidence="ECO:0000269|PubMed:11278904"
FT MUTAGEN 91
FT /note="D->A: Reduces activity over 100000-fold."
FT /evidence="ECO:0000269|PubMed:11278904"
FT MUTAGEN 93
FT /note="K->A: Reduces activity over 100000-fold."
FT /evidence="ECO:0000269|PubMed:11278904"
FT MUTAGEN 96
FT /note="D->A: Reduces kcat over 100000-fold. Reduces
FT substrate affinity 11-fold."
FT /evidence="ECO:0000269|PubMed:11278904"
FT MUTAGEN 215
FT /note="Q->A: No effect."
FT /evidence="ECO:0000269|PubMed:11278904"
FT CONFLICT 71..73
FT /note="EGT -> RIR (in Ref. 4; AAA35199)"
FT /evidence="ECO:0000305"
FT HELIX 6..12
FT /evidence="ECO:0007829|PDB:3GDM"
FT HELIX 16..28
FT /evidence="ECO:0007829|PDB:3GDM"
FT STRAND 32..35
FT /evidence="ECO:0007829|PDB:3GDM"
FT HELIX 41..51
FT /evidence="ECO:0007829|PDB:3GDM"
FT HELIX 52..54
FT /evidence="ECO:0007829|PDB:3GDM"
FT STRAND 56..60
FT /evidence="ECO:0007829|PDB:3GDM"
FT HELIX 62..64
FT /evidence="ECO:0007829|PDB:3GDM"
FT TURN 70..73
FT /evidence="ECO:0007829|PDB:3GDM"
FT HELIX 74..84
FT /evidence="ECO:0007829|PDB:3GDM"
FT STRAND 87..94
FT /evidence="ECO:0007829|PDB:3GDM"
FT HELIX 98..106
FT /evidence="ECO:0007829|PDB:3GDM"
FT TURN 108..110
FT /evidence="ECO:0007829|PDB:3GDM"
FT HELIX 112..115
FT /evidence="ECO:0007829|PDB:3GDM"
FT STRAND 117..122
FT /evidence="ECO:0007829|PDB:3GDM"
FT HELIX 123..125
FT /evidence="ECO:0007829|PDB:3GDM"
FT HELIX 128..140
FT /evidence="ECO:0007829|PDB:3GDM"
FT STRAND 146..150
FT /evidence="ECO:0007829|PDB:3GDM"
FT HELIX 162..172
FT /evidence="ECO:0007829|PDB:3GDM"
FT TURN 176..178
FT /evidence="ECO:0007829|PDB:3GDM"
FT STRAND 179..183
FT /evidence="ECO:0007829|PDB:3GDM"
FT HELIX 191..193
FT /evidence="ECO:0007829|PDB:3GDM"
FT STRAND 198..201
FT /evidence="ECO:0007829|PDB:3GDM"
FT STRAND 203..205
FT /evidence="ECO:0007829|PDB:3GDM"
FT TURN 208..210
FT /evidence="ECO:0007829|PDB:1DQW"
FT HELIX 214..216
FT /evidence="ECO:0007829|PDB:3GDM"
FT STRAND 217..219
FT /evidence="ECO:0007829|PDB:3GDM"
FT HELIX 220..225
FT /evidence="ECO:0007829|PDB:3GDM"
FT STRAND 229..233
FT /evidence="ECO:0007829|PDB:3GDM"
FT HELIX 235..237
FT /evidence="ECO:0007829|PDB:3GDM"
FT HELIX 244..262
FT /evidence="ECO:0007829|PDB:3GDM"
SQ SEQUENCE 267 AA; 29240 MW; D63EF9877BD0F984 CRC64;
MSKATYKERA ATHPSPVAAK LFNIMHEKQT NLCASLDVRT TKELLELVEA LGPKICLLKT
HVDILTDFSM EGTVKPLKAL SAKYNFLLFE DRKFADIGNT VKLQYSAGVY RIAEWADITN
AHGVVGPGIV SGLKQAAEEV TKEPRGLLML AELSCKGSLA TGEYTKGTVD IAKSDKDFVI
GFIAQRDMGG RDEGYDWLIM TPGVGLDDKG DALGQQYRTV DDVVSTGSDI IIVGRGLFAK
GRDAKVEGER YRKAGWEAYL RRCGQQN
