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P0ABP8

- DEOD_ECOLI

UniProt

P0ABP8 - DEOD_ECOLI

Protein

Purine nucleoside phosphorylase DeoD-type

Gene

deoD

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 86 (01 Oct 2014)
      Sequence version 2 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules.

    Catalytic activityi

    Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate.
    Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate.

    GO - Molecular functioni

    1. identical protein binding Source: IntAct
    2. purine-nucleoside phosphorylase activity Source: EcoCyc

    GO - Biological processi

    1. cellular response to DNA damage stimulus Source: EcoliWiki
    2. purine nucleoside catabolic process Source: EcoCyc
    3. purine nucleoside interconversion Source: EcoCyc

    Keywords - Molecular functioni

    Glycosyltransferase, Transferase

    Enzyme and pathway databases

    BioCyciEcoCyc:DEOD-MONOMER.
    ECOL316407:JW4347-MONOMER.
    MetaCyc:DEOD-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Purine nucleoside phosphorylase DeoD-type (EC:2.4.2.1)
    Short name:
    PNP
    Alternative name(s):
    Inosine phosphorylase
    Gene namesi
    Name:deoD
    Synonyms:pup
    Ordered Locus Names:b4384, JW4347
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10222. deoD.

    Subcellular locationi

    GO - Cellular componenti

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

    Pathology & Biotechi

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 239238Purine nucleoside phosphorylase DeoD-typePRO_0000063130Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei27 – 271N6-acetyllysine1 Publication

    Keywords - PTMi

    Acetylation

    Proteomic databases

    PaxDbiP0ABP8.
    PRIDEiP0ABP8.

    2D gel databases

    SWISS-2DPAGEP0ABP8.

    Expressioni

    Gene expression databases

    GenevestigatoriP0ABP8.

    Interactioni

    Subunit structurei

    Homohexamer.

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself7EBI-907568,EBI-907568

    Protein-protein interaction databases

    DIPiDIP-36195N.
    IntActiP0ABP8. 2 interactions.
    MINTiMINT-8328110.
    STRINGi511145.b4384.

    Structurei

    Secondary structure

    1
    239
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi15 – 195
    Helixi23 – 3311
    Beta strandi35 – 417
    Helixi43 – 453
    Beta strandi48 – 536
    Beta strandi56 – 616
    Helixi67 – 8014
    Beta strandi85 – 9410
    Beta strandi96 – 994
    Beta strandi104 – 11310
    Helixi116 – 1205
    Turni121 – 1233
    Helixi132 – 14413
    Beta strandi150 – 1567
    Helixi167 – 1737
    Beta strandi178 – 1825
    Helixi183 – 19311
    Beta strandi196 – 20611
    Turni207 – 2093
    Helixi215 – 23723

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1A69X-ray2.10A/B/C2-239[»]
    1ECPX-ray2.00A/B/C/D/E/F2-239[»]
    1K9SX-ray2.00A/B/C/D/E/F2-238[»]
    1OTXX-ray2.70A/B/C2-239[»]
    1OTYX-ray2.50A/B/C2-239[»]
    1OU4X-ray2.50A/B/C2-239[»]
    1OUMX-ray2.40A/B/C2-239[»]
    1OV6X-ray2.40A/B/C2-239[»]
    1OVGX-ray2.20A/B/C2-239[»]
    3ONVX-ray1.89A/B/C2-238[»]
    3OOEX-ray2.00A/B/C/D/E/F2-238[»]
    3OOHX-ray2.90A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R2-238[»]
    3OPVX-ray2.40A/B/C/D/E/F/G/H/I/J/K/L2-238[»]
    3UT6X-ray1.90A/B/C2-238[»]
    ProteinModelPortaliP0ABP8.
    SMRiP0ABP8. Positions 2-238.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0ABP8.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the PNP/UDP phosphorylase family.Curated

    Phylogenomic databases

    eggNOGiCOG0813.
    HOGENOMiHOG000274896.
    KOiK03784.
    OMAiRQTTFSE.
    OrthoDBiEOG6BKJC5.
    PhylomeDBiP0ABP8.

    Family and domain databases

    Gene3Di3.40.50.1580. 1 hit.
    HAMAPiMF_01627. Pur_nucleosid_phosp.
    InterProiIPR004402. DeoD-type.
    IPR018017. Nucleoside_phosphorylase.
    IPR018016. Nucleoside_phosphorylase_CS.
    IPR000845. Nucleoside_phosphorylase_d.
    [Graphical view]
    PANTHERiPTHR21234. PTHR21234. 1 hit.
    PfamiPF01048. PNP_UDP_1. 1 hit.
    [Graphical view]
    SUPFAMiSSF53167. SSF53167. 1 hit.
    TIGRFAMsiTIGR00107. deoD. 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.

    P0ABP8-1 [UniParc]FASTAAdd to Basket

    « Hide

    MATPHINAEM GDFADVVLMP GDPLRAKYIA ETFLEDAREV NNVRGMLGFT    50
    GTYKGRKISV MGHGMGIPSC SIYTKELITD FGVKKIIRVG SCGAVLPHVK 100
    LRDVVIGMGA CTDSKVNRIR FKDHDFAAIA DFDMVRNAVD AAKALGIDAR 150
    VGNLFSADLF YSPDGEMFDV MEKYGILGVE MEAAGIYGVA AEFGAKALTI 200
    CTVSDHIRTH EQTTAAERQT TFNDMIKIAL ESVLLGDKE 239
    Length:239
    Mass (Da):25,950
    Last modified:January 23, 2007 - v2
    Checksum:i71D3DFAA5A176970
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M60917 Genomic DNA. Translation: AAA24401.1.
    U14003 Genomic DNA. Translation: AAA97280.1.
    U00096 Genomic DNA. Translation: AAC77337.1.
    AP009048 Genomic DNA. Translation: BAE78373.1.
    X05629 Genomic DNA. Translation: CAA29114.1.
    PIRiA41143. A27854.
    RefSeqiNP_418801.1. NC_000913.3.
    YP_492514.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC77337; AAC77337; b4384.
    BAE78373; BAE78373; BAE78373.
    GeneIDi12934012.
    945654.
    KEGGiecj:Y75_p4268.
    eco:b4384.
    PATRICi32124384. VBIEscCol129921_4532.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M60917 Genomic DNA. Translation: AAA24401.1 .
    U14003 Genomic DNA. Translation: AAA97280.1 .
    U00096 Genomic DNA. Translation: AAC77337.1 .
    AP009048 Genomic DNA. Translation: BAE78373.1 .
    X05629 Genomic DNA. Translation: CAA29114.1 .
    PIRi A41143. A27854.
    RefSeqi NP_418801.1. NC_000913.3.
    YP_492514.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1A69 X-ray 2.10 A/B/C 2-239 [» ]
    1ECP X-ray 2.00 A/B/C/D/E/F 2-239 [» ]
    1K9S X-ray 2.00 A/B/C/D/E/F 2-238 [» ]
    1OTX X-ray 2.70 A/B/C 2-239 [» ]
    1OTY X-ray 2.50 A/B/C 2-239 [» ]
    1OU4 X-ray 2.50 A/B/C 2-239 [» ]
    1OUM X-ray 2.40 A/B/C 2-239 [» ]
    1OV6 X-ray 2.40 A/B/C 2-239 [» ]
    1OVG X-ray 2.20 A/B/C 2-239 [» ]
    3ONV X-ray 1.89 A/B/C 2-238 [» ]
    3OOE X-ray 2.00 A/B/C/D/E/F 2-238 [» ]
    3OOH X-ray 2.90 A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R 2-238 [» ]
    3OPV X-ray 2.40 A/B/C/D/E/F/G/H/I/J/K/L 2-238 [» ]
    3UT6 X-ray 1.90 A/B/C 2-238 [» ]
    ProteinModelPortali P0ABP8.
    SMRi P0ABP8. Positions 2-238.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-36195N.
    IntActi P0ABP8. 2 interactions.
    MINTi MINT-8328110.
    STRINGi 511145.b4384.

    Chemistry

    DrugBanki DB00194. Vidarabine.

    2D gel databases

    SWISS-2DPAGE P0ABP8.

    Proteomic databases

    PaxDbi P0ABP8.
    PRIDEi P0ABP8.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC77337 ; AAC77337 ; b4384 .
    BAE78373 ; BAE78373 ; BAE78373 .
    GeneIDi 12934012.
    945654.
    KEGGi ecj:Y75_p4268.
    eco:b4384.
    PATRICi 32124384. VBIEscCol129921_4532.

    Organism-specific databases

    EchoBASEi EB0218.
    EcoGenei EG10222. deoD.

    Phylogenomic databases

    eggNOGi COG0813.
    HOGENOMi HOG000274896.
    KOi K03784.
    OMAi RQTTFSE.
    OrthoDBi EOG6BKJC5.
    PhylomeDBi P0ABP8.

    Enzyme and pathway databases

    BioCyci EcoCyc:DEOD-MONOMER.
    ECOL316407:JW4347-MONOMER.
    MetaCyc:DEOD-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P0ABP8.
    PROi P0ABP8.

    Gene expression databases

    Genevestigatori P0ABP8.

    Family and domain databases

    Gene3Di 3.40.50.1580. 1 hit.
    HAMAPi MF_01627. Pur_nucleosid_phosp.
    InterProi IPR004402. DeoD-type.
    IPR018017. Nucleoside_phosphorylase.
    IPR018016. Nucleoside_phosphorylase_CS.
    IPR000845. Nucleoside_phosphorylase_d.
    [Graphical view ]
    PANTHERi PTHR21234. PTHR21234. 1 hit.
    Pfami PF01048. PNP_UDP_1. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53167. SSF53167. 1 hit.
    TIGRFAMsi TIGR00107. deoD. 1 hit.
    PROSITEi PS01232. PNP_UDP_1. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Use of site-directed mutagenesis to enhance the epitope-shielding effect of covalent modification of proteins with polyethylene glycol."
      Hershfield M.S., Chaffee S., Koro-Johnson L., Mary A., Smith A.A., Short S.A.
      Proc. Natl. Acad. Sci. U.S.A. 88:7185-7189(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
      Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
      Nucleic Acids Res. 23:2105-2119(1995) [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 2-21.
    6. "Analysis of the terminator region after the deoCABD operon of Escherichia coli K-12 using a new class of single copy number operon-fusion vectors."
      Larsen J.E.L., Albrechtsen B., Valentin-Hansen P.
      Nucleic Acids Res. 15:5125-5140(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 225-239.
      Strain: K12.
    7. "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli."
      Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y.
      Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-27, IDENTIFICATION BY MASS SPECTROMETRY.
      Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
    8. "The crystal structure of Escherichia coli purine nucleoside phosphorylase: a comparison with the human enzyme reveals a conserved topology."
      Mao C., Cook W.J., Zhou M., Koszalka G.W., Krenitsky T.A., Ealick S.E.
      Structure 5:1373-1383(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
    9. "Crystal structure of the ternary complex of E. coli purine nucleoside phosphorylase with formycin B, a structural analogue of the substrate inosine, and phosphate (sulphate) at 2.1-A resolution."
      Koellner G., Luic M., Shugar D., Saenger W., Bzowska A.
      J. Mol. Biol. 280:153-166(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).

    Entry informationi

    Entry nameiDEOD_ECOLI
    AccessioniPrimary (citable) accession number: P0ABP8
    Secondary accession number(s): P09743, Q2M5T3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 8, 2005
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 86 of the entry and version 2 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. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3