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P45563

- XAPA_ECOLI

UniProt

P45563 - XAPA_ECOLI

Protein

Purine nucleoside phosphorylase 2

Gene

xapA

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 114 (01 Oct 2014)
      Sequence version 2 (01 Nov 1997)
      Previous versions | rss
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    Functioni

    The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate. This protein can degrade all purine nucleosides including xanthosine, inosine and guanosine, but cannot cleave adenosine, deoxyadenosine or hypoxanthine arabinoside. Has a preference for the neutral over the monoanionic form of xanthosine.4 Publications

    Catalytic activityi

    Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate.6 Publications

    Enzyme regulationi

    Rapidly inactivated by p-chloromercuriphenylsulfonic acid (p-CMB). Dithiothreitol incubation restores the activity.1 Publication

    Kineticsi

    1. KM=51 µM for xanthosine (at pH 7.0, PubMed:3042752)2 Publications
    2. KM=72 µM for xanthosine (at 25 degrees Celsius and pH 7.1, PubMed:15808857)2 Publications
    3. KM=110 µM for guanosine (at pH 7.0, PubMed:3042752)2 Publications
    4. KM=155 µM for guanosine (at 25 degrees Celsius and pH 7.1, PubMed:15808857)2 Publications
    5. KM=963 µM for inosine (at 25 degrees Celsius and pH 7.1, PubMed:15808857)2 Publications
    6. KM=340 µM for inosine (at 25 degrees Celsius and pH 7.0, PubMed:3042752)2 Publications
    7. KM=62 µM for 2'-deoxyinosine (at 25 degrees Celsius and pH 7.0)2 Publications
    8. KM=600 µM for 5'-deoxyinosine (at 25 degrees Celsius and pH 7.0)2 Publications
    9. KM=2600 µM for 2',3'-dideoxyinosine (at 25 degrees Celsius and pH 7.0)2 Publications
    10. KM=44 µM for 2'-deoxyguanosine (at 25 degrees Celsius and pH 7.0)2 Publications
    11. KM=3.3 µM for hypoxanthine (at 25 degrees Celsius and pH 7.0)2 Publications
    12. KM=4.1 µM for guanine (at 25 degrees Celsius and pH 7.0)2 Publications
    13. KM=760 µM for phosphate (at 25 degrees Celsius and pH 7.0)2 Publications
    14. KM=59 µM for alpha-D-ribose 1-phosphate (at 25 degrees Celsius and pH 7.0)2 Publications
    15. KM=58 µM for alpha-D-2'-deoxyribose 1-phosphate (at 25 degrees Celsius and pH 7.0)2 Publications

    Vmax=8.7 µmol/min/mg enzyme with xanthosine as substrate (at 25 degrees Celsius and pH 7.1, PubMed:15808857)2 Publications

    Vmax=14.2 µmol/min/mg enzyme with guanosine as substrate (at 25 degrees Celsius and pH 7.1, PubMed:15808857)2 Publications

    Vmax=11.9 µmol/min/mg enzyme with inosine as substrate (at 25 degrees Celsius and pH 7.1, PubMed:15808857)2 Publications

    pH dependencei

    Optimum pH is 6.5-7.5 with guanosine as substrate. At pH higher than 7.5, there is a marked reduction in reaction rate and a steep drop at pH higher than 9. Below pH 6.5, there is a dramatic decrease in activity reaching virtually zero at pH 6.0. With xanthosine as substrate, the pH optimum is 5.8-7.2. In the reverse reaction with guanine or xanthine as substrates, the pH optimum is 6.5-8.0. The pH dependence of inosine cleavage does not vary between pH 6 and 8. Maximal activity with inosine as substrate is observed at pH 6.6.2 Publications

    Temperature dependencei

    The half-life at 45 degrees Celsius between pH 5 and 8 is 5 to 9 minutes.2 Publications

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei65 – 651Substrate 2; via tele nitrogen
    Binding sitei117 – 1171Substrate 2; via amide nitrogen
    Binding sitei197 – 1971Substrate 1
    Binding sitei216 – 2161Substrate 2
    Binding sitei239 – 2391Substrate 1

    GO - Molecular functioni

    1. guanosine phosphorylase activity Source: UniProtKB
    2. identical protein binding Source: EcoCyc
    3. inosine nucleosidase activity Source: UniProtKB
    4. purine-nucleoside phosphorylase activity Source: UniProtKB

    GO - Biological processi

    1. deoxyguanosine catabolic process Source: UniProtKB
    2. deoxyinosine catabolic process Source: UniProtKB
    3. guanosine catabolic process Source: UniProtKB
    4. inosine catabolic process Source: UniProtKB
    5. NAD salvage Source: EcoCyc
    6. nucleobase-containing small molecule interconversion Source: EcoliWiki
    7. nucleobase-containing small molecule metabolic process Source: EcoliWiki
    8. protein hexamerization Source: UniProtKB
    9. purine nucleoside catabolic process Source: UniProtKB

    Keywords - Molecular functioni

    Glycosyltransferase, Transferase

    Enzyme and pathway databases

    BioCyciEcoCyc:XANTHOSINEPHOSPHORY-MONOMER.
    ECOL316407:JW2398-MONOMER.
    MetaCyc:XANTHOSINEPHOSPHORY-MONOMER.
    UniPathwayiUPA00119.
    UPA00606.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Purine nucleoside phosphorylase 2 (EC:2.4.2.1)
    Alternative name(s):
    Inosine-guanosine phosphorylase
    Purine nucleoside phosphorylase II
    Short name:
    PNP II
    Xanthosine phosphorylase
    Gene namesi
    Name:xapA
    Synonyms:pndA
    Ordered Locus Names:b2407, JW2398
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG20250. xapA.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: EcoliWiki

    Pathology & Biotechi

    Disruption phenotypei

    Does not grow on xanthosine. Slightly increases inosine productivity compared to wild-type (5.6 g/l of inosine versus 4.6 g/l, respectively, from 40 g/l of glucose).2 Publications

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi191 – 1911Y → L: No detectable activity with xanthosine as substrate, but largely retains its activity against other substrates, namely inosine and guanosine, although with altered affinities, higher and lower respectively, and clearly reduced maximal velocities for both. 1 Publication
    Mutagenesisi239 – 2391N → D: Catalyzes the phosphorolysis of adenosine with moderate efficiency, and essentially has lost all activity against the 6-oxo-purine substrates xanthosine, inosine and guanosine. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 277277Purine nucleoside phosphorylase 2PRO_0000184555Add
    BLAST

    Expressioni

    Inductioni

    By xanthosine and to a lesser extent by deoxyinosine. Full expression requires XapR-xanthosine DNA-binding transcriptional activator.3 Publications

    Gene expression databases

    GenevestigatoriP45563.

    Interactioni

    Subunit structurei

    Hexamer. Dimer of trimers.2 Publications

    Protein-protein interaction databases

    IntActiP45563. 4 interactions.
    STRINGi511145.b2407.

    Structurei

    Secondary structure

    1
    277
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi9 – 2012
    Beta strandi27 – 326
    Helixi36 – 427
    Beta strandi44 – 507
    Helixi51 – 533
    Beta strandi68 – 747
    Beta strandi77 – 848
    Helixi88 – 903
    Turni94 – 974
    Helixi98 – 10710
    Beta strandi110 – 12112
    Beta strandi130 – 1378
    Beta strandi140 – 1423
    Turni151 – 1533
    Beta strandi156 – 1583
    Helixi166 – 17712
    Turni178 – 1803
    Beta strandi183 – 1908
    Helixi199 – 2079
    Beta strandi211 – 2177
    Helixi218 – 2269
    Beta strandi230 – 24011
    Beta strandi244 – 2463
    Helixi251 – 2566
    Helixi257 – 2593
    Helixi262 – 27615

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1YQQX-ray2.60A/B/C1-277[»]
    1YQUX-ray3.10A/B/C1-277[»]
    1YR3X-ray3.20A/B/C/D/E/F1-277[»]
    ProteinModelPortaliP45563.
    SMRiP45563. Positions 5-277.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP45563.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni85 – 873Substrate 2 binding

    Sequence similaritiesi

    Belongs to the PNP/MTAP phosphorylase family.Curated

    Phylogenomic databases

    eggNOGiCOG0005.
    HOGENOMiHOG000045183.
    KOiK03815.
    OMAiDQPLSHD.
    OrthoDBiEOG6423M2.
    PhylomeDBiP45563.

    Family and domain databases

    Gene3Di3.40.50.1580. 1 hit.
    InterProiIPR000845. Nucleoside_phosphorylase_d.
    IPR001369. PNP/MTAP.
    IPR011268. Purine_phosphorylase.
    IPR018099. Purine_phosphorylase-2_CS.
    IPR010943. Xanthosine_phosphorylase.
    [Graphical view]
    PANTHERiPTHR11904. PTHR11904. 1 hit.
    PfamiPF01048. PNP_UDP_1. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000477. PurNPase. 1 hit.
    SUPFAMiSSF53167. SSF53167. 1 hit.
    TIGRFAMsiTIGR01697. PNPH-PUNA-XAPA. 1 hit.
    TIGR01699. XAPA. 1 hit.
    PROSITEiPS01240. PNP_MTAP_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P45563-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSQVQFSHNP LFCIDIIKTY KPDFTPRVAF ILGSGLGALA DQIENAVAIS    50
    YEKLPGFPVS TVHGHAGELV LGHLQGVPVV CMKGRGHFYE GRGMTIMTDA 100
    IRTFKLLGCE LLFCTNAAGS LRPEVGAGSL VALKDHINTM PGTPMVGLND 150
    DRFGERFFSL ANAYDAEYRA LLQKVAKEEG FPLTEGVFVS YPGPNFETAA 200
    EIRMMQIIGG DVVGMSVVPE VISARHCDLK VVAVSAITNM AEGLSDVKLS 250
    HAQTLAAAEL SKQNFINLIC GFLRKIA 277
    Length:277
    Mass (Da):29,835
    Last modified:November 1, 1997 - v2
    Checksum:iDD26545755C08F8B
    GO

    Sequence cautioni

    The sequence CAA52049.1 differs from that shown. Reason: Frameshift at positions 144, 177, 259 and 261.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti144 – 1441P → A in CAA52049. (PubMed:7559336)Curated
    Sequence conflicti261 – 2611S → H in CAA52049. (PubMed:7559336)Curated
    Sequence conflicti265 – 2651F → L in CAA52049. (PubMed:7559336)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X73828 Genomic DNA. Translation: CAA52049.1. Frameshift.
    U00096 Genomic DNA. Translation: AAC75460.1.
    AP009048 Genomic DNA. Translation: BAA16275.1.
    PIRiF65014.
    RefSeqiNP_416902.1. NC_000913.3.
    YP_490642.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75460; AAC75460; b2407.
    BAA16275; BAA16275; BAA16275.
    GeneIDi12931571.
    946878.
    KEGGiecj:Y75_p2367.
    eco:b2407.
    PATRICi32120195. VBIEscCol129921_2500.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X73828 Genomic DNA. Translation: CAA52049.1 . Frameshift.
    U00096 Genomic DNA. Translation: AAC75460.1 .
    AP009048 Genomic DNA. Translation: BAA16275.1 .
    PIRi F65014.
    RefSeqi NP_416902.1. NC_000913.3.
    YP_490642.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1YQQ X-ray 2.60 A/B/C 1-277 [» ]
    1YQU X-ray 3.10 A/B/C 1-277 [» ]
    1YR3 X-ray 3.20 A/B/C/D/E/F 1-277 [» ]
    ProteinModelPortali P45563.
    SMRi P45563. Positions 5-277.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P45563. 4 interactions.
    STRINGi 511145.b2407.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC75460 ; AAC75460 ; b2407 .
    BAA16275 ; BAA16275 ; BAA16275 .
    GeneIDi 12931571.
    946878.
    KEGGi ecj:Y75_p2367.
    eco:b2407.
    PATRICi 32120195. VBIEscCol129921_2500.

    Organism-specific databases

    EchoBASEi EB4152.
    EcoGenei EG20250. xapA.

    Phylogenomic databases

    eggNOGi COG0005.
    HOGENOMi HOG000045183.
    KOi K03815.
    OMAi DQPLSHD.
    OrthoDBi EOG6423M2.
    PhylomeDBi P45563.

    Enzyme and pathway databases

    UniPathwayi UPA00119 .
    UPA00606 .
    BioCyci EcoCyc:XANTHOSINEPHOSPHORY-MONOMER.
    ECOL316407:JW2398-MONOMER.
    MetaCyc:XANTHOSINEPHOSPHORY-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P45563.
    PROi P45563.

    Gene expression databases

    Genevestigatori P45563.

    Family and domain databases

    Gene3Di 3.40.50.1580. 1 hit.
    InterProi IPR000845. Nucleoside_phosphorylase_d.
    IPR001369. PNP/MTAP.
    IPR011268. Purine_phosphorylase.
    IPR018099. Purine_phosphorylase-2_CS.
    IPR010943. Xanthosine_phosphorylase.
    [Graphical view ]
    PANTHERi PTHR11904. PTHR11904. 1 hit.
    Pfami PF01048. PNP_UDP_1. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000477. PurNPase. 1 hit.
    SUPFAMi SSF53167. SSF53167. 1 hit.
    TIGRFAMsi TIGR01697. PNPH-PUNA-XAPA. 1 hit.
    TIGR01699. XAPA. 1 hit.
    PROSITEi PS01240. PNP_MTAP_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Identification and characterization of genes (xapA, xapB, and xapR) involved in xanthosine catabolism in Escherichia coli."
      Seeger C., Poulsen C., Dandanell G.
      J. Bacteriol. 177:5506-5516(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CATALYTIC ACTIVITY, INDUCTION, DISRUPTION PHENOTYPE.
      Strain: K12.
    2. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
      Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
      , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
      DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    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. "A second purine nucleoside phosphorylase in Escherichia coli K-12. I. Xanthosine phosphorylase regulatory mutants isolated as secondary-site revertants of a deoD mutant."
      Buxton R.S., Hammer-Jespersen K., Valentin-Hansen P.
      Mol. Gen. Genet. 179:331-340(1980) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
      Strain: K12.
    6. "A second purine nucleoside phosphorylase in Escherichia coli K-12. II. Properties of xanthosine phosphorylase and its induction by xanthosine."
      Hammer-Jespersen K., Buxton R.S., Hansen T.D.
      Mol. Gen. Genet. 179:341-348(1980) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, SUBUNIT, INDUCTION.
      Strain: K12.
    7. "Purification and properties of inosine-guanosine phosphorylase from Escherichia coli K-12."
      Koszalka G.W., Vanhooke J., Short S.A., Hall W.W.
      J. Bacteriol. 170:3493-3498(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: K12.
    8. "Isolation and characterization of mutations in the Escherichia coli regulatory protein XapR."
      Jorgensen C., Dandanell G.
      J. Bacteriol. 181:4397-4403(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, INDUCTION.
    9. "Effects of xapA and guaA disruption on inosine accumulation in Escherichia coli."
      Shimaoka M., Takenaka Y., Mihara Y., Kurahashi O., Kawasaki H., Matsui H.
      Biosci. Biotechnol. Biochem. 70:3069-3072(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE.
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    10. "Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene."
      Dandanell G., Szczepanowski R.H., Kierdaszuk B., Shugar D., Bochtler M.
      J. Mol. Biol. 348:113-125(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) IN COMPLEX WITH GUANINE, XANTHINE AND PHOSPHATE, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, MUTAGENESIS OF TYR-191 AND ASN-239.
      Strain: K12.

    Entry informationi

    Entry nameiXAPA_ECOLI
    AccessioniPrimary (citable) accession number: P45563
    Secondary accession number(s): P77325
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: November 1, 1997
    Last modified: October 1, 2014
    This is version 114 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, 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