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P45563

- XAPA_ECOLI

UniProt

P45563 - XAPA_ECOLI

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Protein

Purine nucleoside phosphorylase 2

Gene
xapA, pndA, b2407, JW2398
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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

Vmax=8.7 µmol/min/mg enzyme with xanthosine as substrate (at 25 degrees Celsius and pH 7.1, 1 Publication

)

Vmax=14.2 µmol/min/mg enzyme with guanosine as substrate (at 25 degrees Celsius and pH 7.1, 1 Publication

)

Vmax=11.9 µmol/min/mg enzyme with inosine as substrate (at 25 degrees Celsius and pH 7.1, 1 Publication

)

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.

Temperature dependencei

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

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. inosine nucleosidase activity Source: UniProtKB
  3. 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. nucleobase-containing small molecule interconversion Source: EcoliWiki
  6. nucleobase-containing small molecule metabolic process Source: EcoliWiki
  7. protein hexamerization Source: UniProtKB
  8. purine nucleoside catabolic process Source: UniProtKB
Complete GO annotation...

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
Complete GO annotation...

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.4 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.

Miscellaneous databases

EvolutionaryTraceiP45563.

Family & Domainsi

Region

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

Sequence similaritiesi

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.

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti144 – 1441P → A in CAA52049. 1 Publication
Sequence conflicti261 – 2611S → H in CAA52049. 1 Publication
Sequence conflicti265 – 2651F → L in CAA52049. 1 Publication

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

« Hide 'large scale' publications
  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: June 11, 2014
This is version 113 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

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