ID XAPA_ECOLI Reviewed; 277 AA. AC P45563; P77325; DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot. DT 01-NOV-1997, sequence version 2. DT 02-SEP-2026, entry version 176. DE RecName: Full=Purine nucleoside phosphorylase 2; DE EC=2.4.2.1 {ECO:0000269|PubMed:10400599, ECO:0000269|PubMed:15808857, ECO:0000269|PubMed:17151449, ECO:0000269|PubMed:3042752, ECO:0000269|PubMed:7007809, ECO:0000269|PubMed:7559336}; DE AltName: Full=Inosine-guanosine phosphorylase; DE AltName: Full=Purine nucleoside phosphorylase II; DE Short=PNP II; DE AltName: Full=Xanthosine phosphorylase; GN Name=xapA; Synonyms=pndA; OrderedLocusNames=b2407, JW2398; OS Escherichia coli (strain K12). OC Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; OC Enterobacterales; Enterobacteriaceae; Escherichia. OX NCBI_TaxID=83333; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], CATALYTIC ACTIVITY, INDUCTION, AND RP DISRUPTION PHENOTYPE. RC STRAIN=K12; RX PubMed=7559336; DOI=10.1128/jb.177.19.5506-5516.1995; RA Seeger C., Poulsen C., Dandanell G.; RT "Identification and characterization of genes (xapA, xapB, and xapR) RT involved in xanthosine catabolism in Escherichia coli."; RL J. Bacteriol. 177:5506-5516(1995). RN [2] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911; RX PubMed=9205837; DOI=10.1093/dnares/4.2.91; RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S., RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.; RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of RT its sequence features."; RL DNA Res. 4:91-113(1997). RN [3] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / MG1655 / ATCC 47076; RX PubMed=9278503; DOI=10.1126/science.277.5331.1453; RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., RA Shao Y.; RT "The complete genome sequence of Escherichia coli K-12."; RL Science 277:1453-1462(1997). RN [4] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911; RX PubMed=16738553; DOI=10.1038/msb4100049; RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.; RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 RT and W3110."; RL Mol. Syst. Biol. 2:E1-E5(2006). RN [5] RP FUNCTION. RC STRAIN=K12; RX PubMed=7007808; DOI=10.1007/bf00425461; RA Buxton R.S., Hammer-Jespersen K., Valentin-Hansen P.; RT "A second purine nucleoside phosphorylase in Escherichia coli K-12. I. RT Xanthosine phosphorylase regulatory mutants isolated as secondary-site RT revertants of a deoD mutant."; RL Mol. Gen. Genet. 179:331-340(1980). RN [6] RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, SUBUNIT, AND RP INDUCTION. RC STRAIN=K12; RX PubMed=7007809; DOI=10.1007/bf00425462; RA Hammer-Jespersen K., Buxton R.S., Hansen T.D.; RT "A second purine nucleoside phosphorylase in Escherichia coli K-12. II. RT Properties of xanthosine phosphorylase and its induction by xanthosine."; RL Mol. Gen. Genet. 179:341-348(1980). RN [7] RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, ACTIVITY REGULATION, RP AND BIOPHYSICOCHEMICAL PROPERTIES. RC STRAIN=K12; RX PubMed=3042752; DOI=10.1128/jb.170.8.3493-3498.1988; RA Koszalka G.W., Vanhooke J., Short S.A., Hall W.W.; RT "Purification and properties of inosine-guanosine phosphorylase from RT Escherichia coli K-12."; RL J. Bacteriol. 170:3493-3498(1988). RN [8] RP CATALYTIC ACTIVITY, AND INDUCTION. RX PubMed=10400599; DOI=10.1128/jb.181.14.4397-4403.1999; RA Jorgensen C., Dandanell G.; RT "Isolation and characterization of mutations in the Escherichia coli RT regulatory protein XapR."; RL J. Bacteriol. 181:4397-4403(1999). RN [9] RP CATALYTIC ACTIVITY, AND DISRUPTION PHENOTYPE. RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911; RX PubMed=17151449; DOI=10.1271/bbb.60398; RA Shimaoka M., Takenaka Y., Mihara Y., Kurahashi O., Kawasaki H., Matsui H.; RT "Effects of xapA and guaA disruption on inosine accumulation in Escherichia RT coli."; RL Biosci. Biotechnol. Biochem. 70:3069-3072(2006). RN [10] RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) IN COMPLEX WITH GUANINE, XANTHINE RP AND PHOSPHATE, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND MUTAGENESIS OF TYR-191 AND RP ASN-239. RC STRAIN=K12; RX PubMed=15808857; DOI=10.1016/j.jmb.2005.02.019; RA Dandanell G., Szczepanowski R.H., Kierdaszuk B., Shugar D., Bochtler M.; RT "Escherichia coli purine nucleoside phosphorylase II, the product of the RT xapA gene."; RL J. Mol. Biol. 348:113-125(2005). CC -!- FUNCTION: The purine nucleoside phosphorylases catalyze the CC phosphorolytic breakdown of the N-glycosidic bond in the beta- CC (deoxy)ribonucleoside molecules, with the formation of the CC corresponding free purine bases and pentose-1-phosphate. This protein CC can degrade all purine nucleosides including xanthosine, inosine and CC guanosine, but cannot cleave adenosine, deoxyadenosine or hypoxanthine CC arabinoside. Has a preference for the neutral over the monoanionic form CC of xanthosine. {ECO:0000269|PubMed:15808857, CC ECO:0000269|PubMed:3042752, ECO:0000269|PubMed:7007808, CC ECO:0000269|PubMed:7007809}. CC -!- CATALYTIC ACTIVITY: CC Reaction=a purine D-ribonucleoside + phosphate = a purine nucleobase + CC alpha-D-ribose 1-phosphate; Xref=Rhea:RHEA:19805, ChEBI:CHEBI:26386, CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57720, ChEBI:CHEBI:142355; EC=2.4.2.1; CC Evidence={ECO:0000269|PubMed:10400599, ECO:0000269|PubMed:15808857, CC ECO:0000269|PubMed:17151449, ECO:0000269|PubMed:3042752, CC ECO:0000269|PubMed:7007809, ECO:0000269|PubMed:7559336}; CC -!- ACTIVITY REGULATION: Rapidly inactivated by p- CC chloromercuriphenylsulfonic acid (p-CMB). Dithiothreitol incubation CC restores the activity. {ECO:0000269|PubMed:3042752}. CC -!- BIOPHYSICOCHEMICAL PROPERTIES: CC Kinetic parameters: CC KM=51 uM for xanthosine (at pH 7.0) {ECO:0000269|PubMed:3042752}; CC KM=72 uM for xanthosine (at 25 degrees Celsius and pH 7.1) CC {ECO:0000269|PubMed:15808857}; CC KM=110 uM for guanosine (at pH 7.0) {ECO:0000269|PubMed:3042752}; CC KM=155 uM for guanosine (at 25 degrees Celsius and pH 7.1) CC {ECO:0000269|PubMed:15808857}; CC KM=963 uM for inosine (at 25 degrees Celsius and pH 7.1) CC {ECO:0000269|PubMed:15808857}; CC KM=340 uM for inosine (at 25 degrees Celsius and pH 7.0) CC {ECO:0000269|PubMed:3042752}; CC KM=62 uM for 2'-deoxyinosine (at 25 degrees Celsius and pH 7.0) CC {ECO:0000269|PubMed:3042752}; CC KM=600 uM for 5'-deoxyinosine (at 25 degrees Celsius and pH 7.0) CC {ECO:0000269|PubMed:3042752}; CC KM=2600 uM for 2',3'-dideoxyinosine (at 25 degrees Celsius and pH CC 7.0) {ECO:0000269|PubMed:3042752}; CC KM=44 uM for 2'-deoxyguanosine (at 25 degrees Celsius and pH 7.0) CC {ECO:0000269|PubMed:3042752}; CC KM=3.3 uM for hypoxanthine (at 25 degrees Celsius and pH 7.0) CC {ECO:0000269|PubMed:3042752}; CC KM=4.1 uM for guanine (at 25 degrees Celsius and pH 7.0) CC {ECO:0000269|PubMed:3042752}; CC KM=760 uM for phosphate (at 25 degrees Celsius and pH 7.0) CC {ECO:0000269|PubMed:3042752}; CC KM=59 uM for alpha-D-ribose 1-phosphate (at 25 degrees Celsius and pH CC 7.0) {ECO:0000269|PubMed:3042752}; CC KM=58 uM for alpha-D-2'-deoxyribose 1-phosphate (at 25 degrees CC Celsius and pH 7.0) {ECO:0000269|PubMed:3042752}; CC Vmax=8.7 umol/min/mg enzyme with xanthosine as substrate (at 25 CC degrees Celsius and pH 7.1) {ECO:0000269|PubMed:15808857}; CC Vmax=14.2 umol/min/mg enzyme with guanosine as substrate (at 25 CC degrees Celsius and pH 7.1) {ECO:0000269|PubMed:15808857}; CC Vmax=11.9 umol/min/mg enzyme with inosine as substrate (at 25 degrees CC Celsius and pH 7.1) {ECO:0000269|PubMed:15808857}; CC pH dependence: CC Optimum pH is 6.5-7.5 with guanosine as substrate. At pH higher than CC 7.5, there is a marked reduction in reaction rate and a steep drop at CC pH higher than 9. Below pH 6.5, there is a dramatic decrease in CC activity reaching virtually zero at pH 6.0. With xanthosine as CC substrate, the pH optimum is 5.8-7.2. In the reverse reaction with CC guanine or xanthine as substrates, the pH optimum is 6.5-8.0. The pH CC dependence of inosine cleavage does not vary between pH 6 and 8. CC Maximal activity with inosine as substrate is observed at pH 6.6. CC {ECO:0000269|PubMed:15808857, ECO:0000269|PubMed:3042752}; CC Temperature dependence: CC The half-life at 45 degrees Celsius between pH 5 and 8 is 5 to 9 CC minutes. {ECO:0000269|PubMed:15808857, ECO:0000269|PubMed:3042752}; CC -!- PATHWAY: Purine metabolism; xanthosine degradation. CC -!- PATHWAY: Purine metabolism; purine nucleoside salvage. CC -!- SUBUNIT: Hexamer. Dimer of trimers. {ECO:0000269|PubMed:15808857, CC ECO:0000269|PubMed:7007809}. CC -!- INDUCTION: By xanthosine and to a lesser extent by deoxyinosine. Full CC expression requires XapR-xanthosine DNA-binding transcriptional CC activator. {ECO:0000269|PubMed:10400599, ECO:0000269|PubMed:7007809, CC ECO:0000269|PubMed:7559336}. CC -!- DISRUPTION PHENOTYPE: Does not grow on xanthosine. Slightly increases CC inosine productivity compared to wild-type (5.6 g/l of inosine versus CC 4.6 g/l, respectively, from 40 g/l of glucose). CC {ECO:0000269|PubMed:17151449, ECO:0000269|PubMed:7559336}. CC -!- SIMILARITY: Belongs to the PNP/MTAP phosphorylase family. CC {ECO:0000305}. CC -!- SEQUENCE CAUTION: CC Sequence=CAA52049.1; Type=Frameshift; Evidence={ECO:0000305}; CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; X73828; CAA52049.1; ALT_FRAME; Genomic_DNA. DR EMBL; U00096; AAC75460.1; -; Genomic_DNA. DR EMBL; AP009048; BAA16275.1; -; Genomic_DNA. DR PIR; F65014; F65014. DR RefSeq; NP_416902.1; NC_000913.3. DR RefSeq; WP_000084573.1; NZ_CP009789.1. DR PDB; 1YQQ; X-ray; 2.60 A; A/B/C=1-277. DR PDB; 1YQU; X-ray; 3.10 A; A/B/C=1-277. DR PDB; 1YR3; X-ray; 3.20 A; A/B/C/D/E/F=1-277. DR AlphaFoldDB; P45563; -. DR SMR; P45563; -. DR BioGRID; 4260565; 23. DR FunCoup; P45563; 942. DR IntAct; P45563; 4. DR STRING; 511145.b2407; -. DR DrugBank; DB02377; Guanine. DR DrugBank; DB02134; Xanthine. DR PaxDb; 511145-b2407; -. DR EnsemblBacteria; AAC75460; AAC75460; b2407. DR GeneID; 946878; -. DR KEGG; ecj:JW2398; -. DR KEGG; eco:b2407; -. DR KEGG; ecoc:C3026_13380; -. DR PATRIC; fig|1411691.4.peg.4325; -. DR EchoBASE; EB4152; -. DR eggNOG; COG0005; Bacteria. DR HOGENOM; CLU_054456_1_0_6; -. DR InParanoid; P45563; -. DR OMA; EGVYAQF; -. DR OrthoDB; 1523230at2; -. DR PhylomeDB; P45563; -. DR BioCyc; EcoCyc:XANTHOSINEPHOSPHORY-MONOMER; -. DR BioCyc; MetaCyc:XANTHOSINEPHOSPHORY-MONOMER; -. DR BRENDA; 2.4.2.1; 2026. DR UniPathway; UPA00119; -. DR UniPathway; UPA00606; -. DR EvolutionaryTrace; P45563; -. DR PRO; PR:P45563; -. DR Proteomes; UP000000625; Chromosome. DR AbasyAtlas; P45563; -. DR GO; GO:0005737; C:cytoplasm; IDA:EcoliWiki. DR GO; GO:0005829; C:cytosol; IBA:GO_Central. DR GO; GO:0047975; F:guanosine phosphorylase activity; IDA:UniProtKB. DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc. DR GO; GO:0047724; F:inosine nucleosidase activity; IDA:UniProtKB. DR GO; GO:0004731; F:purine-nucleoside phosphorylase activity; IDA:UniProtKB. DR GO; GO:0006161; P:deoxyguanosine catabolic process; IDA:UniProtKB. DR GO; GO:0006149; P:deoxyinosine catabolic process; IDA:UniProtKB. DR GO; GO:0046115; P:guanosine catabolic process; IDA:UniProtKB. DR GO; GO:0006148; P:inosine catabolic process; IDA:UniProtKB. DR GO; GO:0034355; P:NAD+ biosynthetic process via the salvage pathway; EXP:EcoCyc. DR GO; GO:0015949; P:nucleobase-containing small molecule interconversion; IMP:EcoliWiki. DR GO; GO:0055086; P:nucleobase-containing small molecule metabolic process; IMP:EcoliWiki. DR GO; GO:0034214; P:protein hexamerization; IDA:UniProtKB. DR GO; GO:0006152; P:purine nucleoside catabolic process; IDA:UniProtKB. DR GO; GO:1903228; P:xanthosine catabolic process; IMP:EcoCyc. DR CDD; cd09009; PNP-EcPNPII_like; 1. DR FunFam; 3.40.50.1580:FF:000011; Purine nucleoside phosphorylase; 1. DR Gene3D; 3.40.50.1580; Nucleoside phosphorylase domain; 1. DR InterPro; IPR000845; Nucleoside_phosphorylase_d. DR InterPro; IPR035994; Nucleoside_phosphorylase_sf. DR InterPro; IPR011268; Purine_phosphorylase. DR InterPro; IPR018099; Purine_phosphorylase-2_CS. DR InterPro; IPR010943; Xanthosine_phosphorylase. DR NCBIfam; TIGR01697; PNPH-PUNA-XAPA; 1. DR NCBIfam; NF006054; PRK08202.1; 1. DR NCBIfam; TIGR01699; XAPA; 1. DR PANTHER; PTHR11904; METHYLTHIOADENOSINE/PURINE NUCLEOSIDE PHOSPHORYLASE; 1. DR PANTHER; PTHR11904:SF9; PURINE NUCLEOSIDE PHOSPHORYLASE-RELATED; 1. DR Pfam; PF01048; PNP_UDP_1; 1. DR PIRSF; PIRSF000477; PurNPase; 1. DR SUPFAM; SSF53167; Purine and uridine phosphorylases; 1. DR PROSITE; PS01240; PNP_MTAP_2; 1. DR PDBsum; 1YQQ; -. DR PDBsum; 1YQU; -. DR PDBsum; 1YR3; -. PE 1: Evidence at protein level; KW 3D-structure; Glycosyltransferase; Reference proteome; Transferase. FT CHAIN 1..277 FT /note="Purine nucleoside phosphorylase 2" FT /id="PRO_0000184555" FT BINDING 65 FT /ligand="phosphate" FT /ligand_id="ChEBI:CHEBI:43474" FT /evidence="ECO:0000269|PubMed:15808857, FT ECO:0007744|PDB:1YQQ" FT BINDING 85..87 FT /ligand="phosphate" FT /ligand_id="ChEBI:CHEBI:43474" FT /evidence="ECO:0000269|PubMed:15808857, FT ECO:0007744|PDB:1YQQ, ECO:0007744|PDB:1YQU" FT BINDING 117 FT /ligand="phosphate" FT /ligand_id="ChEBI:CHEBI:43474" FT /evidence="ECO:0000269|PubMed:15808857, FT ECO:0007744|PDB:1YQQ, ECO:0007744|PDB:1YQU" FT BINDING 197 FT /ligand="a purine D-ribonucleoside" FT /ligand_id="ChEBI:CHEBI:142355" FT /evidence="ECO:0000269|PubMed:15808857" FT BINDING 216 FT /ligand="phosphate" FT /ligand_id="ChEBI:CHEBI:43474" FT /evidence="ECO:0000269|PubMed:15808857, FT ECO:0007744|PDB:1YQQ, ECO:0007744|PDB:1YQU" FT BINDING 239 FT /ligand="a purine D-ribonucleoside" FT /ligand_id="ChEBI:CHEBI:142355" FT /evidence="ECO:0000269|PubMed:15808857" FT MUTAGEN 191 FT /note="Y->L: No detectable activity with xanthosine as FT substrate, but largely retains its activity against other FT substrates, namely inosine and guanosine, although with FT altered affinities, higher and lower respectively, and FT clearly reduced maximal velocities for both." FT /evidence="ECO:0000269|PubMed:15808857" FT MUTAGEN 239 FT /note="N->D: Catalyzes the phosphorolysis of adenosine with FT moderate efficiency, and essentially has lost all activity FT against the 6-oxo-purine substrates xanthosine, inosine and FT guanosine." FT /evidence="ECO:0000269|PubMed:15808857" FT CONFLICT 144 FT /note="P -> A (in Ref. 1; CAA52049)" FT /evidence="ECO:0000305" FT CONFLICT 261 FT /note="S -> H (in Ref. 1; CAA52049)" FT /evidence="ECO:0000305" FT CONFLICT 265 FT /note="F -> L (in Ref. 1; CAA52049)" FT /evidence="ECO:0000305" FT HELIX 9..20 FT /evidence="ECO:0007829|PDB:1YQQ" FT STRAND 27..32 FT /evidence="ECO:0007829|PDB:1YQQ" FT HELIX 36..42 FT /evidence="ECO:0007829|PDB:1YQQ" FT STRAND 44..50 FT /evidence="ECO:0007829|PDB:1YQQ" FT HELIX 51..53 FT /evidence="ECO:0007829|PDB:1YQQ" FT STRAND 68..74 FT /evidence="ECO:0007829|PDB:1YQQ" FT STRAND 77..84 FT /evidence="ECO:0007829|PDB:1YQQ" FT HELIX 88..90 FT /evidence="ECO:0007829|PDB:1YQQ" FT TURN 94..97 FT /evidence="ECO:0007829|PDB:1YQQ" FT HELIX 98..107 FT /evidence="ECO:0007829|PDB:1YQQ" FT STRAND 110..121 FT /evidence="ECO:0007829|PDB:1YQQ" FT STRAND 130..137 FT /evidence="ECO:0007829|PDB:1YQQ" FT STRAND 140..142 FT /evidence="ECO:0007829|PDB:1YQQ" FT TURN 151..153 FT /evidence="ECO:0007829|PDB:1YQQ" FT STRAND 156..158 FT /evidence="ECO:0007829|PDB:1YQQ" FT HELIX 166..177 FT /evidence="ECO:0007829|PDB:1YQQ" FT TURN 178..180 FT /evidence="ECO:0007829|PDB:1YQQ" FT STRAND 183..190 FT /evidence="ECO:0007829|PDB:1YQQ" FT HELIX 196..198 FT /evidence="ECO:0007829|PDB:1YQQ" FT HELIX 199..207 FT /evidence="ECO:0007829|PDB:1YQQ" FT STRAND 211..217 FT /evidence="ECO:0007829|PDB:1YQQ" FT HELIX 218..226 FT /evidence="ECO:0007829|PDB:1YQQ" FT STRAND 230..240 FT /evidence="ECO:0007829|PDB:1YQQ" FT STRAND 244..246 FT /evidence="ECO:0007829|PDB:1YQQ" FT HELIX 247..249 FT /evidence="ECO:0007829|PDB:1YQQ" FT HELIX 251..256 FT /evidence="ECO:0007829|PDB:1YQQ" FT HELIX 257..259 FT /evidence="ECO:0007829|PDB:1YQQ" FT HELIX 262..276 FT /evidence="ECO:0007829|PDB:1YQQ" SQ SEQUENCE 277 AA; 29835 MW; DD26545755C08F8B CRC64; MSQVQFSHNP LFCIDIIKTY KPDFTPRVAF ILGSGLGALA DQIENAVAIS YEKLPGFPVS TVHGHAGELV LGHLQGVPVV CMKGRGHFYE GRGMTIMTDA IRTFKLLGCE LLFCTNAAGS LRPEVGAGSL VALKDHINTM PGTPMVGLND DRFGERFFSL ANAYDAEYRA LLQKVAKEEG FPLTEGVFVS YPGPNFETAA EIRMMQIIGG DVVGMSVVPE VISARHCDLK VVAVSAITNM AEGLSDVKLS HAQTLAAAEL SKQNFINLIC GFLRKIA //