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P45563 (XAPA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 113. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:xapA
Synonyms:pndA
Ordered Locus Names:b2407, JW2398
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length277 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.5 Ref.6 Ref.7 Ref.10

Catalytic activity

Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate. Ref.1 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10

Enzyme regulation

Rapidly inactivated by p-chloromercuriphenylsulfonic acid (p-CMB). Dithiothreitol incubation restores the activity. Ref.7

Pathway

Purine metabolism; xanthosine degradation.

Purine metabolism; purine nucleoside salvage.

Subunit structure

Hexamer. Dimer of trimers. Ref.6 Ref.10

Induction

By xanthosine and to a lesser extent by deoxyinosine. Full expression requires XapR-xanthosine DNA-binding transcriptional activator. Ref.1 Ref.6 Ref.7 Ref.8

Disruption phenotype

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). Ref.1 Ref.9

Sequence similarities

Belongs to the PNP/MTAP phosphorylase family.

Biophysicochemical properties

Kinetic parameters:

KM=51 µM for xanthosine (at pH 7.0, Ref.7) Ref.7 Ref.10

KM=72 µM for xanthosine (at 25 degrees Celsius and pH 7.1, Ref.10)

KM=110 µM for guanosine (at pH 7.0, Ref.7)

KM=155 µM for guanosine (at 25 degrees Celsius and pH 7.1, Ref.10)

KM=963 µM for inosine (at 25 degrees Celsius and pH 7.1, Ref.10)

KM=340 µM for inosine (at 25 degrees Celsius and pH 7.0, Ref.7)

KM=62 µM for 2'-deoxyinosine (at 25 degrees Celsius and pH 7.0)

KM=600 µM for 5'-deoxyinosine (at 25 degrees Celsius and pH 7.0)

KM=2600 µM for 2',3'-dideoxyinosine (at 25 degrees Celsius and pH 7.0)

KM=44 µM for 2'-deoxyguanosine (at 25 degrees Celsius and pH 7.0)

KM=3.3 µM for hypoxanthine (at 25 degrees Celsius and pH 7.0)

KM=4.1 µM for guanine (at 25 degrees Celsius and pH 7.0)

KM=760 µM for phosphate (at 25 degrees Celsius and pH 7.0)

KM=59 µM for alpha-D-ribose 1-phosphate (at 25 degrees Celsius and pH 7.0)

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, Ref.10)

Vmax=14.2 µmol/min/mg enzyme with guanosine as substrate (at 25 degrees Celsius and pH 7.1, Ref.10)

Vmax=11.9 µmol/min/mg enzyme with inosine as substrate (at 25 degrees Celsius and pH 7.1, Ref.10)

pH dependence:

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 dependence:

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

Sequence caution

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 277277Purine nucleoside phosphorylase 2
PRO_0000184555

Regions

Region85 – 873Substrate 2 binding

Sites

Binding site651Substrate 2; via tele nitrogen
Binding site1171Substrate 2; via amide nitrogen
Binding site1971Substrate 1
Binding site2161Substrate 2
Binding site2391Substrate 1

Experimental info

Mutagenesis1911Y → 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. Ref.10
Mutagenesis2391N → 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. Ref.10
Sequence conflict1441P → A in CAA52049. Ref.1
Sequence conflict2611S → H in CAA52049. Ref.1
Sequence conflict2651F → L in CAA52049. Ref.1

Secondary structure

................................................ 277
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P45563 [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: DD26545755C08F8B

FASTA27729,835
        10         20         30         40         50         60 
MSQVQFSHNP LFCIDIIKTY KPDFTPRVAF ILGSGLGALA DQIENAVAIS YEKLPGFPVS 

        70         80         90        100        110        120 
TVHGHAGELV LGHLQGVPVV CMKGRGHFYE GRGMTIMTDA IRTFKLLGCE LLFCTNAAGS 

       130        140        150        160        170        180 
LRPEVGAGSL VALKDHINTM PGTPMVGLND DRFGERFFSL ANAYDAEYRA LLQKVAKEEG 

       190        200        210        220        230        240 
FPLTEGVFVS YPGPNFETAA EIRMMQIIGG DVVGMSVVPE VISARHCDLK VVAVSAITNM 

       250        260        270 
AEGLSDVKLS HAQTLAAAEL SKQNFINLIC GFLRKIA 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X73828 Genomic DNA. Translation: CAA52049.1. Frameshift.
U00096 Genomic DNA. Translation: AAC75460.1.
AP009048 Genomic DNA. Translation: BAA16275.1.
PIRF65014.
RefSeqNP_416902.1. NC_000913.3.
YP_490642.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1YQQX-ray2.60A/B/C1-277[»]
1YQUX-ray3.10A/B/C1-277[»]
1YR3X-ray3.20A/B/C/D/E/F1-277[»]
ProteinModelPortalP45563.
SMRP45563. Positions 5-277.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActP45563. 4 interactions.
STRING511145.b2407.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75460; AAC75460; b2407.
BAA16275; BAA16275; BAA16275.
GeneID12931571.
946878.
KEGGecj:Y75_p2367.
eco:b2407.
PATRIC32120195. VBIEscCol129921_2500.

Organism-specific databases

EchoBASEEB4152.
EcoGeneEG20250. xapA.

Phylogenomic databases

eggNOGCOG0005.
HOGENOMHOG000045183.
KOK03815.
OMADQPLSHD.
OrthoDBEOG6423M2.
PhylomeDBP45563.

Enzyme and pathway databases

BioCycEcoCyc:XANTHOSINEPHOSPHORY-MONOMER.
ECOL316407:JW2398-MONOMER.
MetaCyc:XANTHOSINEPHOSPHORY-MONOMER.
UniPathwayUPA00119.
UPA00606.

Gene expression databases

GenevestigatorP45563.

Family and domain databases

Gene3D3.40.50.1580. 1 hit.
InterProIPR000845. Nucleoside_phosphorylase_d.
IPR001369. PNP/MTAP.
IPR011268. Purine_phosphorylase.
IPR018099. Purine_phosphorylase-2_CS.
IPR010943. Xanthosine_phosphorylase.
[Graphical view]
PANTHERPTHR11904. PTHR11904. 1 hit.
PfamPF01048. PNP_UDP_1. 1 hit.
[Graphical view]
PIRSFPIRSF000477. PurNPase. 1 hit.
SUPFAMSSF53167. SSF53167. 1 hit.
TIGRFAMsTIGR01697. PNPH-PUNA-XAPA. 1 hit.
TIGR01699. XAPA. 1 hit.
PROSITEPS01240. PNP_MTAP_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP45563.
PROP45563.

Entry information

Entry nameXAPA_ECOLI
AccessionPrimary (citable) accession number: P45563
Secondary accession number(s): P77325
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene