UniProtKB - P45563 (XAPA_ECOLI)
Protein
Purine nucleoside phosphorylase 2
Gene
xapA
Organism
Escherichia coli (strain K12)
Status
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
- EC:2.4.2.16 Publications
Activity regulationi
Rapidly inactivated by p-chloromercuriphenylsulfonic acid (p-CMB). Dithiothreitol incubation restores the activity.1 Publication
Kineticsi
- KM=51 µM for xanthosine (at pH 7.0)1 Publication
- KM=72 µM for xanthosine (at 25 degrees Celsius and pH 7.1)1 Publication
- KM=110 µM for guanosine (at pH 7.0)1 Publication
- KM=155 µM for guanosine (at 25 degrees Celsius and pH 7.1)1 Publication
- KM=963 µM for inosine (at 25 degrees Celsius and pH 7.1)1 Publication
- KM=340 µM for inosine (at 25 degrees Celsius and pH 7.0)1 Publication
- KM=62 µM for 2'-deoxyinosine (at 25 degrees Celsius and pH 7.0)1 Publication
- KM=600 µM for 5'-deoxyinosine (at 25 degrees Celsius and pH 7.0)1 Publication
- KM=2600 µM for 2',3'-dideoxyinosine (at 25 degrees Celsius and pH 7.0)1 Publication
- KM=44 µM for 2'-deoxyguanosine (at 25 degrees Celsius and pH 7.0)1 Publication
- KM=3.3 µM for hypoxanthine (at 25 degrees Celsius and pH 7.0)1 Publication
- KM=4.1 µM for guanine (at 25 degrees Celsius and pH 7.0)1 Publication
- KM=760 µM for phosphate (at 25 degrees Celsius and pH 7.0)1 Publication
- KM=59 µM for alpha-D-ribose 1-phosphate (at 25 degrees Celsius and pH 7.0)1 Publication
- KM=58 µM for alpha-D-2'-deoxyribose 1-phosphate (at 25 degrees Celsius and pH 7.0)1 Publication
- 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 6.6.2 Publications
Temperature dependencei
The half-life at 45 degrees Celsius between pH 5 and 8 is 5 to 9 minutes.2 Publications
: xanthosine degradation Pathwayi
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 key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Binding sitei | 65 | PhosphateCombined sources1 Publication | 1 | |
Binding sitei | 117 | Phosphate; via amide nitrogenCombined sources1 Publication | 1 | |
Binding sitei | 197 | Purine nucleoside1 Publication | 1 | |
Binding sitei | 216 | PhosphateCombined sources1 Publication | 1 | |
Binding sitei | 239 | Purine nucleoside1 Publication | 1 |
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 nucleoside catabolic process Source: UniProtKB
- xanthosine catabolic process Source: EcoCyc
Keywordsi
Molecular function | Glycosyltransferase, Transferase |
Enzyme and pathway databases
BioCyci | EcoCyc:XANTHOSINEPHOSPHORY-MONOMER MetaCyc:XANTHOSINEPHOSPHORY-MONOMER |
BRENDAi | 2.4.2.1, 2026 |
UniPathwayi | UPA00119 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 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
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 key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 191 | Y → 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 | 1 | |
Mutagenesisi | 239 | N → 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 | 1 |
Chemistry databases
DrugBanki | DB02377, Guanine DB02134, Xanthine |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000184555 | 1 – 277 | Purine nucleoside phosphorylase 2Add BLAST | 277 |
Proteomic databases
PaxDbi | P45563 |
PRIDEi | P45563 |
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 PublicationsGO - Molecular functioni
- identical protein binding Source: EcoCyc
Protein-protein interaction databases
BioGRIDi | 4260565, 18 interactors |
IntActi | P45563, 4 interactors |
STRINGi | 511145.b2407 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | P45563 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P45563 |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 85 – 87 | Phosphate bindingCombined sources1 Publication | 3 |
Sequence similaritiesi
Belongs to the PNP/MTAP phosphorylase family.Curated
Phylogenomic databases
eggNOGi | COG0005, Bacteria |
HOGENOMi | CLU_054456_1_0_6 |
InParanoidi | P45563 |
PhylomeDBi | P45563 |
Family and domain databases
Gene3Di | 3.40.50.1580, 1 hit |
InterProi | View protein in InterPro IPR000845, Nucleoside_phosphorylase_d IPR035994, Nucleoside_phosphorylase_sf IPR011268, Purine_phosphorylase IPR018099, Purine_phosphorylase-2_CS IPR010943, Xanthosine_phosphorylase |
PANTHERi | PTHR11904, PTHR11904, 1 hit |
Pfami | View protein in Pfam PF01048, PNP_UDP_1, 1 hit |
PIRSFi | PIRSF000477, PurNPase, 1 hit |
SUPFAMi | SSF53167, SSF53167, 1 hit |
TIGRFAMsi | TIGR01697, PNPH-PUNA-XAPA, 1 hit TIGR01699, XAPA, 1 hit |
PROSITEi | View protein in PROSITE PS01240, PNP_MTAP_2, 1 hit |
i Sequence
Sequence statusi: Complete.
P45563-1 [UniParc]FASTAAdd to basket
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
Sequence cautioni
The sequence CAA52049 differs from that shown. Reason: Frameshift.Curated
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 144 | P → A in CAA52049 (PubMed:7559336).Curated | 1 | |
Sequence conflicti | 261 | S → H in CAA52049 (PubMed:7559336).Curated | 1 | |
Sequence conflicti | 265 | F → L in CAA52049 (PubMed:7559336).Curated | 1 |
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 |
PIRi | F65014 |
RefSeqi | NP_416902.1, NC_000913.3 WP_000084573.1, NZ_STEB01000039.1 |
Genome annotation databases
EnsemblBacteriai | AAC75460; AAC75460; b2407 BAA16275; BAA16275; BAA16275 |
GeneIDi | 946878 |
KEGGi | ecj:JW2398 eco:b2407 |
PATRICi | fig|1411691.4.peg.4325 |
Similar proteinsi
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 |
PIRi | F65014 |
RefSeqi | NP_416902.1, NC_000913.3 WP_000084573.1, NZ_STEB01000039.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB 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 | [»] | |
SMRi | P45563 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 4260565, 18 interactors |
IntActi | P45563, 4 interactors |
STRINGi | 511145.b2407 |
Chemistry databases
DrugBanki | DB02377, Guanine DB02134, Xanthine |
Proteomic databases
PaxDbi | P45563 |
PRIDEi | P45563 |
Genome annotation databases
EnsemblBacteriai | AAC75460; AAC75460; b2407 BAA16275; BAA16275; BAA16275 |
GeneIDi | 946878 |
KEGGi | ecj:JW2398 eco:b2407 |
PATRICi | fig|1411691.4.peg.4325 |
Organism-specific databases
EchoBASEi | EB4152 |
Phylogenomic databases
eggNOGi | COG0005, Bacteria |
HOGENOMi | CLU_054456_1_0_6 |
InParanoidi | P45563 |
PhylomeDBi | P45563 |
Enzyme and pathway databases
UniPathwayi | UPA00119 UPA00606 |
BioCyci | EcoCyc:XANTHOSINEPHOSPHORY-MONOMER MetaCyc:XANTHOSINEPHOSPHORY-MONOMER |
BRENDAi | 2.4.2.1, 2026 |
Miscellaneous databases
EvolutionaryTracei | P45563 |
PROi | PR:P45563 |
Family and domain databases
Gene3Di | 3.40.50.1580, 1 hit |
InterProi | View protein in InterPro IPR000845, Nucleoside_phosphorylase_d IPR035994, Nucleoside_phosphorylase_sf IPR011268, Purine_phosphorylase IPR018099, Purine_phosphorylase-2_CS IPR010943, Xanthosine_phosphorylase |
PANTHERi | PTHR11904, PTHR11904, 1 hit |
Pfami | View protein in Pfam PF01048, PNP_UDP_1, 1 hit |
PIRSFi | PIRSF000477, PurNPase, 1 hit |
SUPFAMi | SSF53167, SSF53167, 1 hit |
TIGRFAMsi | TIGR01697, PNPH-PUNA-XAPA, 1 hit TIGR01699, XAPA, 1 hit |
PROSITEi | View protein in PROSITE PS01240, PNP_MTAP_2, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | XAPA_ECOLI | |
Accessioni | P45563Primary (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: | December 2, 2020 | |
This is version 153 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- PATHWAY comments
Index of metabolic and biosynthesis pathways - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families