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Protein

Purine nucleoside phosphorylase 2

Gene

xapA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: 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, 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
  1. Vmax=8.7 µmol/min/mg enzyme with xanthosine as substrate (at 25 degrees Celsius and pH 7.1, PubMed:15808857)2 Publications
  2. Vmax=14.2 µmol/min/mg enzyme with guanosine as substrate (at 25 degrees Celsius and pH 7.1, PubMed:15808857)2 Publications
  3. 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: xanthosine degradation

This protein is involved in the pathway xanthosine degradation, which is part of Purine metabolism.
View all proteins of this organism that are known to be involved in the pathway xanthosine degradation and in Purine metabolism.

Pathwayi: purine nucleoside salvage

This protein is involved in the pathway purine nucleoside salvage, which is part of Purine metabolism.
View all proteins of this organism that are known to be involved in the pathway purine nucleoside salvage and in Purine metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei65PhosphateCombined sources1 Publication1
Binding sitei117Phosphate; via amide nitrogenCombined sources1 Publication1
Binding sitei197Purine nucleoside1 Publication1
Binding sitei216PhosphateCombined sources1 Publication1
Binding sitei239Purine nucleoside1 Publication1

GO - Molecular functioni

  • guanosine phosphorylase activity Source: UniProtKB
  • identical protein binding Source: EcoCyc
  • inosine nucleosidase activity Source: UniProtKB
  • purine-nucleoside phosphorylase activity Source: UniProtKB

GO - Biological processi

  • deoxyguanosine catabolic process Source: UniProtKB
  • deoxyinosine catabolic process Source: UniProtKB
  • guanosine catabolic process Source: UniProtKB
  • inosine catabolic process Source: UniProtKB
  • nucleobase-containing small molecule interconversion Source: EcoliWiki
  • nucleobase-containing small molecule metabolic process Source: EcoliWiki
  • protein hexamerization Source: UniProtKB
  • purine-containing compound salvage Source: GO_Central
  • purine nucleoside catabolic process Source: UniProtKB
  • xanthosine catabolic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Glycosyltransferase, Transferase

Enzyme and pathway databases

BioCyciEcoCyc:XANTHOSINEPHOSPHORY-MONOMER.
ECOL316407:JW2398-MONOMER.
MetaCyc:XANTHOSINEPHOSPHORY-MONOMER.
BRENDAi2.4.2.1. 2026.
UniPathwayiUPA00119.
UPA00606.

Names & Taxonomyi

Protein namesi
Recommended name:
Purine nucleoside phosphorylase 2 (EC:2.4.2.16 Publications)
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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG20250. xapA.

Subcellular locationi

GO - Cellular componenti

  • 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)DescriptionActionsGraphical viewLength
Mutagenesisi191Y → 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 Publication1
Mutagenesisi239N → 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 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001845551 – 277Purine nucleoside phosphorylase 2Add BLAST277

Proteomic databases

PaxDbiP45563.
PRIDEiP45563.

Expressioni

Inductioni

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

Interactioni

Subunit structurei

Hexamer. Dimer of trimers.2 Publications

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4260565. 16 interactors.
IntActiP45563. 4 interactors.
STRINGi511145.b2407.

Structurei

Secondary structure

1277
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi9 – 20Combined sources12
Beta strandi27 – 32Combined sources6
Helixi36 – 42Combined sources7
Beta strandi44 – 50Combined sources7
Helixi51 – 53Combined sources3
Beta strandi68 – 74Combined sources7
Beta strandi77 – 84Combined sources8
Helixi88 – 90Combined sources3
Turni94 – 97Combined sources4
Helixi98 – 107Combined sources10
Beta strandi110 – 121Combined sources12
Beta strandi130 – 137Combined sources8
Beta strandi140 – 142Combined sources3
Turni151 – 153Combined sources3
Beta strandi156 – 158Combined sources3
Helixi166 – 177Combined sources12
Turni178 – 180Combined sources3
Beta strandi183 – 190Combined sources8
Helixi199 – 207Combined sources9
Beta strandi211 – 217Combined sources7
Helixi218 – 226Combined sources9
Beta strandi230 – 240Combined sources11
Beta strandi244 – 246Combined sources3
Helixi251 – 256Combined sources6
Helixi257 – 259Combined sources3
Helixi262 – 276Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP45563.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni85 – 87Phosphate bindingCombined sources1 Publication3

Sequence similaritiesi

Belongs to the PNP/MTAP phosphorylase family.Curated

Phylogenomic databases

eggNOGiENOG4107U5R. Bacteria.
COG0005. LUCA.
HOGENOMiHOG000045183.
InParanoidiP45563.
KOiK03815.
OMAiMENGYTY.
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.
PTHR11904:SF9. PTHR11904:SF9. 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

        10         20         30         40         50
MSQVQFSHNP LFCIDIIKTY KPDFTPRVAF ILGSGLGALA DQIENAVAIS
60 70 80 90 100
YEKLPGFPVS TVHGHAGELV LGHLQGVPVV CMKGRGHFYE GRGMTIMTDA
110 120 130 140 150
IRTFKLLGCE LLFCTNAAGS LRPEVGAGSL VALKDHINTM PGTPMVGLND
160 170 180 190 200
DRFGERFFSL ANAYDAEYRA LLQKVAKEEG FPLTEGVFVS YPGPNFETAA
210 220 230 240 250
EIRMMQIIGG DVVGMSVVPE VISARHCDLK VVAVSAITNM AEGLSDVKLS
260 270
HAQTLAAAEL SKQNFINLIC GFLRKIA
Length:277
Mass (Da):29,835
Last modified:November 1, 1997 - v2
Checksum:iDD26545755C08F8B
GO

Sequence cautioni

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

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti144P → A in CAA52049 (PubMed:7559336).Curated1
Sequence conflicti261S → H in CAA52049 (PubMed:7559336).Curated1
Sequence conflicti265F → L in CAA52049 (PubMed:7559336).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
WP_000084573.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75460; AAC75460; b2407.
BAA16275; BAA16275; BAA16275.
GeneIDi946878.
KEGGiecj:JW2398.
eco:b2407.
PATRICi32120195. VBIEscCol129921_2500.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
WP_000084573.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260565. 16 interactors.
IntActiP45563. 4 interactors.
STRINGi511145.b2407.

Proteomic databases

PaxDbiP45563.
PRIDEiP45563.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75460; AAC75460; b2407.
BAA16275; BAA16275; BAA16275.
GeneIDi946878.
KEGGiecj:JW2398.
eco:b2407.
PATRICi32120195. VBIEscCol129921_2500.

Organism-specific databases

EchoBASEiEB4152.
EcoGeneiEG20250. xapA.

Phylogenomic databases

eggNOGiENOG4107U5R. Bacteria.
COG0005. LUCA.
HOGENOMiHOG000045183.
InParanoidiP45563.
KOiK03815.
OMAiMENGYTY.
PhylomeDBiP45563.

Enzyme and pathway databases

UniPathwayiUPA00119.
UPA00606.
BioCyciEcoCyc:XANTHOSINEPHOSPHORY-MONOMER.
ECOL316407:JW2398-MONOMER.
MetaCyc:XANTHOSINEPHOSPHORY-MONOMER.
BRENDAi2.4.2.1. 2026.

Miscellaneous databases

EvolutionaryTraceiP45563.
PROiP45563.

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.
PTHR11904:SF9. PTHR11904:SF9. 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]
ProtoNetiSearch...

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: November 2, 2016
This is version 129 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.