XAPA_ECOLI
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 03-AUG-2022, entry version 159.
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; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC 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};
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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_STEB01000039.1.
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 PDBsum; 1YQQ; -.
DR PDBsum; 1YQU; -.
DR PDBsum; 1YR3; -.
DR AlphaFoldDB; P45563; -.
DR SMR; P45563; -.
DR BioGRID; 4260565; 18.
DR IntAct; P45563; 4.
DR STRING; 511145.b2407; -.
DR DrugBank; DB02377; Guanine.
DR DrugBank; DB02134; Xanthine.
DR PaxDb; P45563; -.
DR PRIDE; P45563; -.
DR EnsemblBacteria; AAC75460; AAC75460; b2407.
DR EnsemblBacteria; BAA16275; BAA16275; BAA16275.
DR GeneID; 66673723; -.
DR GeneID; 946878; -.
DR KEGG; ecj:JW2398; -.
DR KEGG; eco:b2407; -.
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 PhylomeDB; P45563; -.
DR BioCyc; EcoCyc:XANTHOSINEPHOSPHORY-MON; -.
DR BioCyc; MetaCyc:XANTHOSINEPHOSPHORY-MON; -.
DR BRENDA; 2.4.2.1; 2026.
DR UniPathway; UPA00119; -.
DR UniPathway; UPA00606; -.
DR EvolutionaryTrace; P45563; -.
DR PRO; PR:P45563; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IDA:EcoliWiki.
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: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 Gene3D; 3.40.50.1580; -; 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 PANTHER; PTHR11904; PTHR11904; 1.
DR Pfam; PF01048; PNP_UDP_1; 1.
DR PIRSF; PIRSF000477; PurNPase; 1.
DR SUPFAM; SSF53167; SSF53167; 1.
DR TIGRFAMs; TIGR01697; PNPH-PUNA-XAPA; 1.
DR TIGRFAMs; TIGR01699; XAPA; 1.
DR PROSITE; PS01240; PNP_MTAP_2; 1.
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 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 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
