PYRF_ECOLI
ID PYRF_ECOLI Reviewed; 245 AA.
AC P08244;
DT 01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1988, sequence version 1.
DT 03-AUG-2022, entry version 174.
DE RecName: Full=Orotidine 5'-phosphate decarboxylase;
DE EC=4.1.1.23;
DE AltName: Full=OMP decarboxylase;
DE Short=OMPDCase;
DE Short=OMPdecase;
GN Name=pyrF; OrderedLocusNames=b1281, JW1273;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=2956254; DOI=10.1016/s0021-9258(18)61103-2;
RA Turnbough C.L. Jr., Kerr K.H., Funderburg W.R., Donahue J.P., Powell F.E.;
RT "Nucleotide sequence and characterization of the pyrF operon of Escherichia
RT coli K12.";
RL J. Biol. Chem. 262:10239-10245(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 28.0-40.1 min region on the linkage map.";
RL DNA Res. 3:363-377(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-14.
RX PubMed=3052852; DOI=10.1016/0092-8674(88)90033-5;
RA Hidaka M., Akiyama M., Horiuchi T.;
RT "A consensus sequence of three DNA replication terminus sites on the E.
RT coli chromosome is highly homologous to the terR sites of the R6K
RT plasmid.";
RL Cell 55:467-475(1988).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG, AND
RP SUBUNIT.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=10757968; DOI=10.1021/bi992952r;
RA Harris P., Poulsen J.-C.N., Jensen K.F., Larsen S.;
RT "Structural basis for the catalytic mechanism of a proficient enzyme:
RT orotidine 5'-monophosphate decarboxylase.";
RL Biochemistry 39:4217-4224(2000).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG, AND
RP SUBUNIT.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=11526316; DOI=10.1107/s0907444901010393;
RA Poulsen J.-C.N., Harris P., Jensen K.F., Larsen S.;
RT "Selenomethionine substitution of orotidine-5'-monophosphate decarboxylase
RT causes a change in crystal contacts and space group.";
RL Acta Crystallogr. D 57:1251-1259(2001).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF THE NATIVE PROTEIN, AND SUBUNIT.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=12054799; DOI=10.1016/s0022-2836(02)00200-0;
RA Harris P., Poulsen J.-C.N., Jensen K.F., Larsen S.;
RT "Substrate binding induces domain movements in orotidine 5'-monophosphate
RT decarboxylase.";
RL J. Mol. Biol. 318:1019-1029(2002).
CC -!- FUNCTION: Catalyzes the decarboxylation of orotidine 5'-monophosphate
CC (OMP) to uridine 5'-monophosphate (UMP).
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 -!- PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway;
CC UMP from orotate: step 2/2.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10757968,
CC ECO:0000269|PubMed:11526316, ECO:0000269|PubMed:12054799}.
CC -!- INTERACTION:
CC P08244; P0A7I7: ribA; NbExp=2; IntAct=EBI-1123202, EBI-1123314;
CC -!- SIMILARITY: Belongs to the OMP decarboxylase family. Type 1 subfamily.
CC {ECO:0000305}.
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DR EMBL; J02768; AAA24483.1; -; Genomic_DNA.
DR EMBL; U00096; AAC74363.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA14835.1; -; Genomic_DNA.
DR EMBL; M23250; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; A28440; DCECOP.
DR RefSeq; NP_415797.1; NC_000913.3.
DR RefSeq; WP_000176270.1; NZ_SSZK01000012.1.
DR PDB; 1EIX; X-ray; 2.50 A; A/B/C/D=1-245.
DR PDB; 1JJK; X-ray; 3.00 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P=1-245.
DR PDB; 1L2U; X-ray; 2.50 A; A/B=1-245.
DR PDBsum; 1EIX; -.
DR PDBsum; 1JJK; -.
DR PDBsum; 1L2U; -.
DR AlphaFoldDB; P08244; -.
DR SMR; P08244; -.
DR IntAct; P08244; 4.
DR STRING; 511145.b1281; -.
DR DrugBank; DB02890; 6-hydroxyuridine-5'-phosphate.
DR DrugBank; DB03668; 6-oxouridine 5'-phosphate.
DR SWISS-2DPAGE; P08244; -.
DR jPOST; P08244; -.
DR PaxDb; P08244; -.
DR PRIDE; P08244; -.
DR EnsemblBacteria; AAC74363; AAC74363; b1281.
DR EnsemblBacteria; BAA14835; BAA14835; BAA14835.
DR GeneID; 947121; -.
DR KEGG; ecj:JW1273; -.
DR KEGG; eco:b1281; -.
DR PATRIC; fig|511145.12.peg.1333; -.
DR EchoBASE; EB0802; -.
DR eggNOG; COG0284; Bacteria.
DR HOGENOM; CLU_067069_0_0_6; -.
DR InParanoid; P08244; -.
DR OMA; NFKIFLD; -.
DR PhylomeDB; P08244; -.
DR BioCyc; EcoCyc:OROTPDECARB-MON; -.
DR BioCyc; MetaCyc:OROTPDECARB-MON; -.
DR SABIO-RK; P08244; -.
DR UniPathway; UPA00070; UER00120.
DR EvolutionaryTrace; P08244; -.
DR PRO; PR:P08244; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IDA:EcoliWiki.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0016831; F:carboxy-lyase activity; IDA:EcoliWiki.
DR GO; GO:0004590; F:orotidine-5'-phosphate decarboxylase activity; IDA:EcoCyc.
DR GO; GO:0006207; P:'de novo' pyrimidine nucleobase biosynthetic process; IMP:EcoCyc.
DR GO; GO:0044205; P:'de novo' UMP biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0015949; P:nucleobase-containing small molecule interconversion; IDA:EcoliWiki.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_01200_B; OMPdecase_type1_B; 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; Decarboxylase; Lyase; Pyrimidine biosynthesis;
KW Reference proteome.
FT CHAIN 1..245
FT /note="Orotidine 5'-phosphate decarboxylase"
FT /id="PRO_0000134539"
FT ACT_SITE 73
FT /note="Proton donor"
FT BINDING 22
FT /ligand="substrate"
FT BINDING 44
FT /ligand="substrate"
FT BINDING 71..80
FT /ligand="substrate"
FT BINDING 131
FT /ligand="substrate"
FT BINDING 192
FT /ligand="substrate"
FT BINDING 201
FT /ligand="substrate"
FT BINDING 221
FT /ligand="substrate"
FT BINDING 222
FT /ligand="substrate"
FT STRAND 17..21
FT /evidence="ECO:0007829|PDB:1EIX"
FT HELIX 26..33
FT /evidence="ECO:0007829|PDB:1EIX"
FT TURN 38..40
FT /evidence="ECO:0007829|PDB:1EIX"
FT STRAND 42..46
FT /evidence="ECO:0007829|PDB:1EIX"
FT HELIX 47..63
FT /evidence="ECO:0007829|PDB:1EIX"
FT STRAND 68..74
FT /evidence="ECO:0007829|PDB:1EIX"
FT HELIX 78..91
FT /evidence="ECO:0007829|PDB:1EIX"
FT STRAND 94..99
FT /evidence="ECO:0007829|PDB:1EIX"
FT HELIX 100..102
FT /evidence="ECO:0007829|PDB:1EIX"
FT HELIX 104..112
FT /evidence="ECO:0007829|PDB:1EIX"
FT HELIX 113..120
FT /evidence="ECO:0007829|PDB:1EIX"
FT STRAND 123..127
FT /evidence="ECO:0007829|PDB:1EIX"
FT HELIX 135..139
FT /evidence="ECO:0007829|PDB:1EIX"
FT TURN 140..142
FT /evidence="ECO:0007829|PDB:1EIX"
FT HELIX 147..160
FT /evidence="ECO:0007829|PDB:1EIX"
FT STRAND 164..167
FT /evidence="ECO:0007829|PDB:1EIX"
FT HELIX 170..172
FT /evidence="ECO:0007829|PDB:1EIX"
FT HELIX 173..180
FT /evidence="ECO:0007829|PDB:1EIX"
FT STRAND 182..188
FT /evidence="ECO:0007829|PDB:1EIX"
FT HELIX 207..212
FT /evidence="ECO:0007829|PDB:1EIX"
FT STRAND 216..220
FT /evidence="ECO:0007829|PDB:1EIX"
FT HELIX 222..225
FT /evidence="ECO:0007829|PDB:1EIX"
FT STRAND 227..229
FT /evidence="ECO:0007829|PDB:1EIX"
FT HELIX 230..240
FT /evidence="ECO:0007829|PDB:1EIX"
SQ SEQUENCE 245 AA; 26350 MW; 556877A222F0F501 CRC64;
MTLTASSSSR AVTNSPVVVA LDYHNRDDAL AFVDKIDPRD CRLKVGKEMF TLFGPQFVRE
LQQRGFDIFL DLKFHDIPNT AAHAVAAAAD LGVWMVNVHA SGGARMMTAA REALVPFGKD
APLLIAVTVL TSMEASDLVD LGMTLSPADY AERLAALTQK CGLDGVVCSA QEAVRFKQVF
GQEFKLVTPG IRPQGSEAGD QRRIMTPEQA LSAGVDYMVI GRPVTQSVDP AQTLKAINAS
LQRSA
