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P12758

- UDP_ECOLI

UniProt

P12758 - UDP_ECOLI

Protein

Uridine phosphorylase

Gene

udp

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 147 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.

    Catalytic activityi

    Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate.

    Pathwayi

    GO - Molecular functioni

    1. identical protein binding Source: EcoCyc
    2. uridine phosphorylase activity Source: EcoCyc

    GO - Biological processi

    1. cellular response to DNA damage stimulus Source: EcoliWiki
    2. nucleotide catabolic process Source: InterPro
    3. UMP salvage Source: UniProtKB-UniPathway

    Keywords - Molecular functioni

    Glycosyltransferase, Transferase

    Enzyme and pathway databases

    BioCyciEcoCyc:URPHOS-MONOMER.
    ECOL316407:JW3808-MONOMER.
    MetaCyc:URPHOS-MONOMER.
    UniPathwayiUPA00574; UER00633.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Uridine phosphorylase (EC:2.4.2.3)
    Short name:
    UPase
    Short name:
    UrdPase
    Gene namesi
    Name:udp
    Ordered Locus Names:b3831, JW3808
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG11045. udp.

    Subcellular locationi

    GO - Cellular componenti

    1. cytosol Source: UniProtKB
    2. membrane Source: UniProtKB

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi5 – 51D → A, E or N: No change in activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed3 Publications
    Chaini2 – 253252Uridine phosphorylasePRO_0000063183Add
    BLAST

    Proteomic databases

    PaxDbiP12758.
    PRIDEiP12758.

    2D gel databases

    SWISS-2DPAGEP12758.

    Expressioni

    Gene expression databases

    GenevestigatoriP12758.

    Interactioni

    Subunit structurei

    Homohexamer. The homohexamer shows 4-fold, 6-fold or 8-fold symmetry.

    Protein-protein interaction databases

    DIPiDIP-11075N.
    IntActiP12758. 4 interactions.
    MINTiMINT-6478293.
    STRINGi511145.b3831.

    Structurei

    Secondary structure

    1
    253
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi6 – 94
    Helixi13 – 164
    Beta strandi21 – 233
    Helixi28 – 303
    Helixi31 – 355
    Beta strandi38 – 4710
    Beta strandi50 – 578
    Beta strandi60 – 656
    Helixi71 – 8313
    Beta strandi88 – 9710
    Beta strandi107 – 11610
    Helixi119 – 1224
    Helixi134 – 14613
    Beta strandi151 – 16010
    Helixi164 – 1663
    Beta strandi171 – 1733
    Helixi178 – 1803
    Helixi183 – 1897
    Beta strandi194 – 1985
    Helixi199 – 2079
    Turni208 – 2103
    Beta strandi212 – 22211
    Turni223 – 2253
    Helixi231 – 25121

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1K3FX-ray2.50A/B/C/D/E/F1-253[»]
    1LX7X-ray2.00A/B1-253[»]
    1RXCX-ray2.35A/B/C/D/E/F/G/H/I/J/K/L1-253[»]
    1RXSX-ray2.80A/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/o1-253[»]
    1RXUX-ray3.10A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R1-253[»]
    1RXYX-ray1.70A/B1-253[»]
    1T0UX-ray2.20A/B1-253[»]
    1TGVX-ray2.20A/B1-253[»]
    1TGYX-ray2.20A/B1-253[»]
    1U1CX-ray2.20A/B/C/D/E/F2-253[»]
    1U1DX-ray2.00A/B/C/D/E/F2-253[»]
    1U1EX-ray2.00A/B/C/D/E/F2-253[»]
    1U1FX-ray2.30A/B/C/D/E/F2-253[»]
    1U1GX-ray1.95A/B/C/D/E/F2-253[»]
    3KVVX-ray1.80A/B/C/D/E/F1-253[»]
    ProteinModelPortaliP12758.
    SMRiP12758. Positions 4-253.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP12758.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the PNP/UDP phosphorylase family.Curated

    Phylogenomic databases

    eggNOGiCOG2820.
    HOGENOMiHOG000274897.
    KOiK00757.
    OMAiNVMNFEM.
    OrthoDBiEOG676Z3T.
    PhylomeDBiP12758.

    Family and domain databases

    Gene3Di3.40.50.1580. 1 hit.
    InterProiIPR018017. Nucleoside_phosphorylase.
    IPR018016. Nucleoside_phosphorylase_CS.
    IPR000845. Nucleoside_phosphorylase_d.
    IPR010058. Uridine_phosphorylase.
    [Graphical view]
    PANTHERiPTHR21234. PTHR21234. 1 hit.
    PfamiPF01048. PNP_UDP_1. 1 hit.
    [Graphical view]
    SUPFAMiSSF53167. SSF53167. 1 hit.
    TIGRFAMsiTIGR01718. Uridine-psphlse. 1 hit.
    PROSITEiPS01232. PNP_UDP_1. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P12758-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSKSDVFHLG LTKNDLQGAT LAIVPGDPDR VEKIAALMDK PVKLASHREF    50
    TTWRAELDGK PVIVCSTGIG GPSTSIAVEE LAQLGIRTFL RIGTTGAIQP 100
    HINVGDVLVT TASVRLDGAS LHFAPLEFPA VADFECTTAL VEAAKSIGAT 150
    THVGVTASSD TFYPGQERYD TYSGRVVRHF KGSMEEWQAM GVMNYEMESA 200
    TLLTMCASQG LRAGMVAGVI VNRTQQEIPN AETMKQTESH AVKIVVEAAR 250
    RLL 253
    Length:253
    Mass (Da):27,159
    Last modified:January 23, 2007 - v3
    Checksum:i7446DE45BA04D88D
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti11 – 111L → Y AA sequence (PubMed:8899705)Curated
    Sequence conflicti15 – 151D → Y AA sequence (PubMed:8899705)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X15689 Genomic DNA. Translation: CAA33724.1.
    M87049 Genomic DNA. Translation: AAA67626.1.
    U00096 Genomic DNA. Translation: AAC76834.1.
    AP009048 Genomic DNA. Translation: BAE77470.1.
    PIRiS05491.
    RefSeqiNP_418275.1. NC_000913.3.
    YP_491611.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76834; AAC76834; b3831.
    BAE77470; BAE77470; BAE77470.
    GeneIDi12934305.
    948987.
    KEGGiecj:Y75_p3347.
    eco:b3831.
    PATRICi32123163. VBIEscCol129921_3947.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X15689 Genomic DNA. Translation: CAA33724.1 .
    M87049 Genomic DNA. Translation: AAA67626.1 .
    U00096 Genomic DNA. Translation: AAC76834.1 .
    AP009048 Genomic DNA. Translation: BAE77470.1 .
    PIRi S05491.
    RefSeqi NP_418275.1. NC_000913.3.
    YP_491611.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1K3F X-ray 2.50 A/B/C/D/E/F 1-253 [» ]
    1LX7 X-ray 2.00 A/B 1-253 [» ]
    1RXC X-ray 2.35 A/B/C/D/E/F/G/H/I/J/K/L 1-253 [» ]
    1RXS X-ray 2.80 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 [» ]
    1RXU X-ray 3.10 A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R 1-253 [» ]
    1RXY X-ray 1.70 A/B 1-253 [» ]
    1T0U X-ray 2.20 A/B 1-253 [» ]
    1TGV X-ray 2.20 A/B 1-253 [» ]
    1TGY X-ray 2.20 A/B 1-253 [» ]
    1U1C X-ray 2.20 A/B/C/D/E/F 2-253 [» ]
    1U1D X-ray 2.00 A/B/C/D/E/F 2-253 [» ]
    1U1E X-ray 2.00 A/B/C/D/E/F 2-253 [» ]
    1U1F X-ray 2.30 A/B/C/D/E/F 2-253 [» ]
    1U1G X-ray 1.95 A/B/C/D/E/F 2-253 [» ]
    3KVV X-ray 1.80 A/B/C/D/E/F 1-253 [» ]
    ProteinModelPortali P12758.
    SMRi P12758. Positions 4-253.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-11075N.
    IntActi P12758. 4 interactions.
    MINTi MINT-6478293.
    STRINGi 511145.b3831.

    Chemistry

    DrugBanki DB00544. Fluorouracil.

    2D gel databases

    SWISS-2DPAGE P12758.

    Proteomic databases

    PaxDbi P12758.
    PRIDEi P12758.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC76834 ; AAC76834 ; b3831 .
    BAE77470 ; BAE77470 ; BAE77470 .
    GeneIDi 12934305.
    948987.
    KEGGi ecj:Y75_p3347.
    eco:b3831.
    PATRICi 32123163. VBIEscCol129921_3947.

    Organism-specific databases

    EchoBASEi EB1038.
    EcoGenei EG11045. udp.

    Phylogenomic databases

    eggNOGi COG2820.
    HOGENOMi HOG000274897.
    KOi K00757.
    OMAi NVMNFEM.
    OrthoDBi EOG676Z3T.
    PhylomeDBi P12758.

    Enzyme and pathway databases

    UniPathwayi UPA00574 ; UER00633 .
    BioCyci EcoCyc:URPHOS-MONOMER.
    ECOL316407:JW3808-MONOMER.
    MetaCyc:URPHOS-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P12758.
    PROi P12758.

    Gene expression databases

    Genevestigatori P12758.

    Family and domain databases

    Gene3Di 3.40.50.1580. 1 hit.
    InterProi IPR018017. Nucleoside_phosphorylase.
    IPR018016. Nucleoside_phosphorylase_CS.
    IPR000845. Nucleoside_phosphorylase_d.
    IPR010058. Uridine_phosphorylase.
    [Graphical view ]
    PANTHERi PTHR21234. PTHR21234. 1 hit.
    Pfami PF01048. PNP_UDP_1. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53167. SSF53167. 1 hit.
    TIGRFAMsi TIGR01718. Uridine-psphlse. 1 hit.
    PROSITEi PS01232. PNP_UDP_1. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Nucleotide sequence of the Escherichia coli uridine phosphorylase (udp) gene."
      Walton L., Richards C.A., Elwell L.P.
      Nucleic Acids Res. 17:6741-6741(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. "Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes."
      Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R.
      Science 257:771-778(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. "Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases."
      Henzel W.J., Billeci T.M., Stults J.T., Wong S.C., Grimley C., Watanabe C.
      Proc. Natl. Acad. Sci. U.S.A. 90:5011-5015(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-18.
    6. Frutiger S., Hughes G.J., Pasquali C., Hochstrasser D.F.
      Submitted (FEB-1996) to UniProtKB
      Cited for: PROTEIN SEQUENCE OF 2-12.
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    7. "FIS is a regulator of metabolism in Escherichia coli."
      Gonzalez-Gil G., Bringmann P., Kahmann R.
      Mol. Microbiol. 22:21-29(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-16.
      Strain: K12.
    8. "Protein engineering of uridine phosphorylase from Escherichia coli K-12. I. Cloning and expression of uridine phosphorylase genes from Klebsiella aerogenes and Salmonella typhimurium in E. coli."
      Veiko V.P., Chebotaev D.V., Ovcharova I.V., Gul'Ko L.B.
      Bioorg. Khim. 24:381-387(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF ASP-5.
    9. "Atomic structure at 2.5-A resolution of uridine phosphorylase from E. coli as refined in the monoclinic crystal lattice."
      Morgunova E.Y., Mikhailov A.M., Popov A.N., Blagova E.V., Smirnova E.A., Vainshtein B.K., Mao C., Armstrong S.H.R., Ealick S.E., Komissarov A.A., Linkova E.V., Burlakova A.A., Mironov A.S., Debabov V.G.
      FEBS Lett. 367:183-187(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
    10. "Structure of Escherichia coli uridine phosphorylase at 2.0 A."
      Burling F.T., Kniewel R., Buglino J.A., Chadha T., Beckwith A., Lima C.D.
      Acta Crystallogr. D 59:73-76(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).

    Entry informationi

    Entry nameiUDP_ECOLI
    AccessioniPrimary (citable) accession number: P12758
    Secondary accession number(s): Q2M8D6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1989
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 147 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3