UDP_ECOLI
ID UDP_ECOLI Reviewed; 253 AA.
AC P12758; Q2M8D6;
DT 01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 191.
DE RecName: Full=Uridine phosphorylase;
DE Short=UPase;
DE Short=UrdPase;
DE EC=2.4.2.3;
GN Name=udp; OrderedLocusNames=b3831, JW3808;
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=2674901; DOI=10.1093/nar/17.16.6741;
RA Walton L., Richards C.A., Elwell L.P.;
RT "Nucleotide sequence of the Escherichia coli uridine phosphorylase (udp)
RT gene.";
RL Nucleic Acids Res. 17:6741-6741(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=1379743; DOI=10.1126/science.1379743;
RA Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R.;
RT "Analysis of the Escherichia coli genome: DNA sequence of the region from
RT 84.5 to 86.5 minutes.";
RL Science 257:771-778(1992).
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 PROTEIN SEQUENCE OF 2-18.
RX PubMed=8506346; DOI=10.1073/pnas.90.11.5011;
RA Henzel W.J., Billeci T.M., Stults J.T., Wong S.C., Grimley C., Watanabe C.;
RT "Identifying proteins from two-dimensional gels by molecular mass searching
RT of peptide fragments in protein sequence databases.";
RL Proc. Natl. Acad. Sci. U.S.A. 90:5011-5015(1993).
RN [6]
RP PROTEIN SEQUENCE OF 2-12.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RA Frutiger S., Hughes G.J., Pasquali C., Hochstrasser D.F.;
RL Submitted (FEB-1996) to UniProtKB.
RN [7]
RP PROTEIN SEQUENCE OF 2-16.
RC STRAIN=K12;
RX PubMed=8899705; DOI=10.1111/j.1365-2958.1996.tb02652.x;
RA Gonzalez-Gil G., Bringmann P., Kahmann R.;
RT "FIS is a regulator of metabolism in Escherichia coli.";
RL Mol. Microbiol. 22:21-29(1996).
RN [8]
RP MUTAGENESIS OF ASP-5.
RX PubMed=9661793;
RA Veiko V.P., Chebotaev D.V., Ovcharova I.V., Gul'Ko L.B.;
RT "Protein engineering of uridine phosphorylase from Escherichia coli K-12.
RT I. Cloning and expression of uridine phosphorylase genes from Klebsiella
RT aerogenes and Salmonella typhimurium in E. coli.";
RL Bioorg. Khim. 24:381-387(1998).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
RX PubMed=7796917; DOI=10.1016/0014-5793(95)00489-v;
RA Morgunova E.Y., Mikhailov A.M., Popov A.N., Blagova E.V., Smirnova E.A.,
RA Vainshtein B.K., Mao C., Armstrong S.H.R., Ealick S.E., Komissarov A.A.,
RA Linkova E.V., Burlakova A.A., Mironov A.S., Debabov V.G.;
RT "Atomic structure at 2.5-A resolution of uridine phosphorylase from E. coli
RT as refined in the monoclinic crystal lattice.";
RL FEBS Lett. 367:183-187(1995).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
RX PubMed=12499542; DOI=10.1107/s0907444902018929;
RA Burling F.T., Kniewel R., Buglino J.A., Chadha T., Beckwith A., Lima C.D.;
RT "Structure of Escherichia coli uridine phosphorylase at 2.0 A.";
RL Acta Crystallogr. D 59:73-76(2003).
CC -!- FUNCTION: Catalyzes the reversible phosphorylytic cleavage of uridine
CC and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The
CC produced molecules are then utilized as carbon and energy sources or in
CC the rescue of pyrimidine bases for nucleotide synthesis.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=phosphate + uridine = alpha-D-ribose 1-phosphate + uracil;
CC Xref=Rhea:RHEA:24388, ChEBI:CHEBI:16704, ChEBI:CHEBI:17568,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57720; EC=2.4.2.3;
CC -!- PATHWAY: Pyrimidine metabolism; UMP biosynthesis via salvage pathway;
CC uracil from uridine (phosphorylase route): step 1/1.
CC -!- SUBUNIT: Homohexamer. The homohexamer shows 4-fold, 6-fold or 8-fold
CC symmetry.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- SIMILARITY: Belongs to the PNP/UDP phosphorylase family. {ECO:0000305}.
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DR EMBL; X15689; CAA33724.1; -; Genomic_DNA.
DR EMBL; M87049; AAA67626.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76834.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77470.1; -; Genomic_DNA.
DR PIR; S05491; S05491.
DR RefSeq; NP_418275.1; NC_000913.3.
DR RefSeq; WP_000045177.1; NZ_LN832404.1.
DR PDB; 1K3F; X-ray; 2.50 A; A/B/C/D/E/F=1-253.
DR PDB; 1LX7; X-ray; 2.00 A; A/B=1-253.
DR PDB; 1RXC; X-ray; 2.35 A; A/B/C/D/E/F/G/H/I/J/K/L=1-253.
DR PDB; 1RXS; X-ray; 2.80 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/a/b/c/d/e/h/i/j/k/l/m/o=1-253.
DR PDB; 1RXU; X-ray; 3.10 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R=1-253.
DR PDB; 1RXY; X-ray; 1.70 A; A/B=1-253.
DR PDB; 1T0U; X-ray; 2.20 A; A/B=1-253.
DR PDB; 1TGV; X-ray; 2.20 A; A/B=1-253.
DR PDB; 1TGY; X-ray; 2.20 A; A/B=1-253.
DR PDB; 1U1C; X-ray; 2.20 A; A/B/C/D/E/F=2-253.
DR PDB; 1U1D; X-ray; 2.00 A; A/B/C/D/E/F=2-253.
DR PDB; 1U1E; X-ray; 2.00 A; A/B/C/D/E/F=2-253.
DR PDB; 1U1F; X-ray; 2.30 A; A/B/C/D/E/F=2-253.
DR PDB; 1U1G; X-ray; 1.95 A; A/B/C/D/E/F=2-253.
DR PDB; 3KVV; X-ray; 1.80 A; A/B/C/D/E/F=1-253.
DR PDB; 7Q31; X-ray; 1.75 A; AAA/BBB=4-253.
DR PDBsum; 1K3F; -.
DR PDBsum; 1LX7; -.
DR PDBsum; 1RXC; -.
DR PDBsum; 1RXS; -.
DR PDBsum; 1RXU; -.
DR PDBsum; 1RXY; -.
DR PDBsum; 1T0U; -.
DR PDBsum; 1TGV; -.
DR PDBsum; 1TGY; -.
DR PDBsum; 1U1C; -.
DR PDBsum; 1U1D; -.
DR PDBsum; 1U1E; -.
DR PDBsum; 1U1F; -.
DR PDBsum; 1U1G; -.
DR PDBsum; 3KVV; -.
DR PDBsum; 7Q31; -.
DR AlphaFoldDB; P12758; -.
DR SMR; P12758; -.
DR BioGRID; 4263299; 11.
DR DIP; DIP-11075N; -.
DR IntAct; P12758; 4.
DR MINT; P12758; -.
DR STRING; 511145.b3831; -.
DR DrugBank; DB07439; 1-((2-HYDROXYETHOXY)METHYL)-5-(3-(BENZYLOXY)BENZYL)-6-HYDROXYPYRIMIDINE-2,4(1H,3H)-DIONE.
DR DrugBank; DB06873; 1-((2-HYDROXYETHOXY)METHYL)-5-(3-(BENZYLOXY)BENZYL)PYRIMIDINE-2,4(1H,3H)-DIONE.
DR DrugBank; DB06872; 1-((2-HYDROXYETHOXY)METHYL)-5-(PHENYLTHIO)PYRIMIDINE-2,4(1H,3H)-DIONE.
DR DrugBank; DB02256; 2'-Deoxyuridine.
DR DrugBank; DB02681; 2,8-bis[oxido(oxo)vanadio]-1,1,1,3,5,5,7,7,9,9,9-undecaoxopentavanadoxane-2,8-diium.
DR DrugBank; DB07437; 5-Benzylacyclouridine.
DR DrugBank; DB01629; 5-fluorouridine.
DR DrugBank; DB03101; Ribose-1-Phosphate.
DR DrugBank; DB04485; Thymidine.
DR SWISS-2DPAGE; P12758; -.
DR jPOST; P12758; -.
DR PaxDb; P12758; -.
DR PRIDE; P12758; -.
DR EnsemblBacteria; AAC76834; AAC76834; b3831.
DR EnsemblBacteria; BAE77470; BAE77470; BAE77470.
DR GeneID; 60670502; -.
DR GeneID; 948987; -.
DR KEGG; ecj:JW3808; -.
DR KEGG; eco:b3831; -.
DR PATRIC; fig|511145.12.peg.3947; -.
DR EchoBASE; EB1038; -.
DR eggNOG; COG2820; Bacteria.
DR HOGENOM; CLU_068457_0_0_6; -.
DR InParanoid; P12758; -.
DR OMA; MSDVFHL; -.
DR PhylomeDB; P12758; -.
DR BioCyc; EcoCyc:URPHOS-MON; -.
DR BioCyc; MetaCyc:URPHOS-MON; -.
DR BRENDA; 2.4.2.3; 2026.
DR UniPathway; UPA00574; UER00633.
DR EvolutionaryTrace; P12758; -.
DR PRO; PR:P12758; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0032991; C:protein-containing complex; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0030955; F:potassium ion binding; IDA:EcoCyc.
DR GO; GO:0004850; F:uridine phosphorylase activity; IDA:EcoCyc.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IEP:EcoliWiki.
DR GO; GO:0009166; P:nucleotide catabolic process; IEA:InterPro.
DR GO; GO:0044206; P:UMP salvage; IEA:UniProtKB-UniPathway.
DR GO; GO:0006218; P:uridine catabolic process; IMP:EcoCyc.
DR Gene3D; 3.40.50.1580; -; 1.
DR InterPro; IPR018016; Nucleoside_phosphorylase_CS.
DR InterPro; IPR000845; Nucleoside_phosphorylase_d.
DR InterPro; IPR035994; Nucleoside_phosphorylase_sf.
DR InterPro; IPR010058; Uridine_phosphorylase.
DR Pfam; PF01048; PNP_UDP_1; 1.
DR SUPFAM; SSF53167; SSF53167; 1.
DR TIGRFAMs; TIGR01718; Uridine-psphlse; 1.
DR PROSITE; PS01232; PNP_UDP_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; Glycosyltransferase;
KW Reference proteome; Transferase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:8506346,
FT ECO:0000269|PubMed:8899705, ECO:0000269|Ref.6"
FT CHAIN 2..253
FT /note="Uridine phosphorylase"
FT /id="PRO_0000063183"
FT MUTAGEN 5
FT /note="D->A,E,N: No change in activity."
FT /evidence="ECO:0000269|PubMed:9661793"
FT CONFLICT 11
FT /note="L -> Y (in Ref. 7; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 15
FT /note="D -> Y (in Ref. 7; AA sequence)"
FT /evidence="ECO:0000305"
FT STRAND 6..9
FT /evidence="ECO:0007829|PDB:1RXY"
FT HELIX 13..16
FT /evidence="ECO:0007829|PDB:1RXY"
FT STRAND 21..23
FT /evidence="ECO:0007829|PDB:1RXY"
FT HELIX 28..30
FT /evidence="ECO:0007829|PDB:1RXY"
FT HELIX 31..35
FT /evidence="ECO:0007829|PDB:1RXY"
FT STRAND 38..47
FT /evidence="ECO:0007829|PDB:1RXY"
FT STRAND 50..57
FT /evidence="ECO:0007829|PDB:1RXY"
FT STRAND 60..65
FT /evidence="ECO:0007829|PDB:1RXY"
FT HELIX 71..83
FT /evidence="ECO:0007829|PDB:1RXY"
FT STRAND 88..97
FT /evidence="ECO:0007829|PDB:1RXY"
FT STRAND 107..116
FT /evidence="ECO:0007829|PDB:1RXY"
FT HELIX 119..122
FT /evidence="ECO:0007829|PDB:1RXY"
FT HELIX 134..146
FT /evidence="ECO:0007829|PDB:1RXY"
FT STRAND 151..160
FT /evidence="ECO:0007829|PDB:1RXY"
FT HELIX 164..166
FT /evidence="ECO:0007829|PDB:1RXY"
FT STRAND 171..173
FT /evidence="ECO:0007829|PDB:1RXY"
FT HELIX 178..180
FT /evidence="ECO:0007829|PDB:1RXY"
FT HELIX 183..189
FT /evidence="ECO:0007829|PDB:1RXY"
FT STRAND 194..198
FT /evidence="ECO:0007829|PDB:1RXY"
FT HELIX 199..207
FT /evidence="ECO:0007829|PDB:1RXY"
FT TURN 208..210
FT /evidence="ECO:0007829|PDB:1RXY"
FT STRAND 212..222
FT /evidence="ECO:0007829|PDB:1RXY"
FT TURN 223..225
FT /evidence="ECO:0007829|PDB:1U1D"
FT HELIX 231..251
FT /evidence="ECO:0007829|PDB:1RXY"
SQ SEQUENCE 253 AA; 27159 MW; 7446DE45BA04D88D CRC64;
MSKSDVFHLG LTKNDLQGAT LAIVPGDPDR VEKIAALMDK PVKLASHREF TTWRAELDGK
PVIVCSTGIG GPSTSIAVEE LAQLGIRTFL RIGTTGAIQP HINVGDVLVT TASVRLDGAS
LHFAPLEFPA VADFECTTAL VEAAKSIGAT THVGVTASSD TFYPGQERYD TYSGRVVRHF
KGSMEEWQAM GVMNYEMESA TLLTMCASQG LRAGMVAGVI VNRTQQEIPN AETMKQTESH
AVKIVVEAAR RLL
