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Purine nucleoside phosphorylase 2 (EC 2.4.2.1) (Inosine-guanosine phosphorylase) (Purine nucleoside phosphorylase II) (PNP II) (Xanthosine phosphorylase)

 XAPA_ECOLI              Reviewed;         277 AA.
P45563; P77325;
01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
01-NOV-1997, sequence version 2.
25-OCT-2017, entry version 135.
RecName: Full=Purine nucleoside phosphorylase 2;
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};
AltName: Full=Inosine-guanosine phosphorylase;
AltName: Full=Purine nucleoside phosphorylase II;
Short=PNP II;
AltName: Full=Xanthosine phosphorylase;
Name=xapA; Synonyms=pndA; OrderedLocusNames=b2407, JW2398;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], CATALYTIC ACTIVITY, INDUCTION, AND
DISRUPTION PHENOTYPE.
STRAIN=K12;
PubMed=7559336; DOI=10.1128/jb.177.19.5506-5516.1995;
Seeger C., Poulsen C., Dandanell G.;
"Identification and characterization of genes (xapA, xapB, and xapR)
involved in xanthosine catabolism in Escherichia coli.";
J. Bacteriol. 177:5506-5516(1995).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=9205837; DOI=10.1093/dnares/4.2.91;
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., 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.;
"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.";
DNA Res. 4:91-113(1997).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
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.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[5]
FUNCTION.
STRAIN=K12;
PubMed=7007808; DOI=10.1007/BF00425461;
Buxton R.S., Hammer-Jespersen K., Valentin-Hansen P.;
"A second purine nucleoside phosphorylase in Escherichia coli K-12. I.
Xanthosine phosphorylase regulatory mutants isolated as secondary-site
revertants of a deoD mutant.";
Mol. Gen. Genet. 179:331-340(1980).
[6]
FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, SUBUNIT, AND
INDUCTION.
STRAIN=K12;
PubMed=7007809; DOI=10.1007/BF00425462;
Hammer-Jespersen K., Buxton R.S., Hansen T.D.;
"A second purine nucleoside phosphorylase in Escherichia coli K-12.
II. Properties of xanthosine phosphorylase and its induction by
xanthosine.";
Mol. Gen. Genet. 179:341-348(1980).
[7]
FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, ENZYME
REGULATION, AND BIOPHYSICOCHEMICAL PROPERTIES.
STRAIN=K12;
PubMed=3042752; DOI=10.1128/jb.170.8.3493-3498.1988;
Koszalka G.W., Vanhooke J., Short S.A., Hall W.W.;
"Purification and properties of inosine-guanosine phosphorylase from
Escherichia coli K-12.";
J. Bacteriol. 170:3493-3498(1988).
[8]
CATALYTIC ACTIVITY, AND INDUCTION.
PubMed=10400599;
Jorgensen C., Dandanell G.;
"Isolation and characterization of mutations in the Escherichia coli
regulatory protein XapR.";
J. Bacteriol. 181:4397-4403(1999).
[9]
CATALYTIC ACTIVITY, AND DISRUPTION PHENOTYPE.
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=17151449; DOI=10.1271/bbb.60398;
Shimaoka M., Takenaka Y., Mihara Y., Kurahashi O., Kawasaki H.,
Matsui H.;
"Effects of xapA and guaA disruption on inosine accumulation in
Escherichia coli.";
Biosci. Biotechnol. Biochem. 70:3069-3072(2006).
[10]
X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) IN COMPLEX WITH GUANINE,
XANTHINE AND PHOSPHATE, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE
SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND MUTAGENESIS
OF TYR-191 AND ASN-239.
STRAIN=K12;
PubMed=15808857; DOI=10.1016/j.jmb.2005.02.019;
Dandanell G., Szczepanowski R.H., Kierdaszuk B., Shugar D.,
Bochtler M.;
"Escherichia coli purine nucleoside phosphorylase II, the product of
the xapA gene.";
J. Mol. Biol. 348:113-125(2005).
-!- 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. {ECO:0000269|PubMed:15808857,
ECO:0000269|PubMed:3042752, ECO:0000269|PubMed:7007808,
ECO:0000269|PubMed:7007809}.
-!- CATALYTIC ACTIVITY: Purine nucleoside + phosphate = purine +
alpha-D-ribose 1-phosphate. {ECO:0000269|PubMed:10400599,
ECO:0000269|PubMed:15808857, ECO:0000269|PubMed:17151449,
ECO:0000269|PubMed:3042752, ECO:0000269|PubMed:7007809,
ECO:0000269|PubMed:7559336}.
-!- ENZYME REGULATION: Rapidly inactivated by p-
chloromercuriphenylsulfonic acid (p-CMB). Dithiothreitol
incubation restores the activity. {ECO:0000269|PubMed:3042752}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=51 uM for xanthosine (at pH 7.0, PubMed:3042752)
{ECO:0000269|PubMed:15808857, ECO:0000269|PubMed:3042752};
KM=72 uM for xanthosine (at 25 degrees Celsius and pH 7.1,
PubMed:15808857) {ECO:0000269|PubMed:15808857,
ECO:0000269|PubMed:3042752};
KM=110 uM for guanosine (at pH 7.0, PubMed:3042752)
{ECO:0000269|PubMed:15808857, ECO:0000269|PubMed:3042752};
KM=155 uM for guanosine (at 25 degrees Celsius and pH 7.1,
PubMed:15808857) {ECO:0000269|PubMed:15808857,
ECO:0000269|PubMed:3042752};
KM=963 uM for inosine (at 25 degrees Celsius and pH 7.1,
PubMed:15808857) {ECO:0000269|PubMed:15808857,
ECO:0000269|PubMed:3042752};
KM=340 uM for inosine (at 25 degrees Celsius and pH 7.0,
PubMed:3042752) {ECO:0000269|PubMed:15808857,
ECO:0000269|PubMed:3042752};
KM=62 uM for 2'-deoxyinosine (at 25 degrees Celsius and pH 7.0)
{ECO:0000269|PubMed:15808857, ECO:0000269|PubMed:3042752};
KM=600 uM for 5'-deoxyinosine (at 25 degrees Celsius and pH 7.0)
{ECO:0000269|PubMed:15808857, ECO:0000269|PubMed:3042752};
KM=2600 uM for 2',3'-dideoxyinosine (at 25 degrees Celsius and
pH 7.0) {ECO:0000269|PubMed:15808857,
ECO:0000269|PubMed:3042752};
KM=44 uM for 2'-deoxyguanosine (at 25 degrees Celsius and pH
7.0) {ECO:0000269|PubMed:15808857, ECO:0000269|PubMed:3042752};
KM=3.3 uM for hypoxanthine (at 25 degrees Celsius and pH 7.0)
{ECO:0000269|PubMed:15808857, ECO:0000269|PubMed:3042752};
KM=4.1 uM for guanine (at 25 degrees Celsius and pH 7.0)
{ECO:0000269|PubMed:15808857, ECO:0000269|PubMed:3042752};
KM=760 uM for phosphate (at 25 degrees Celsius and pH 7.0)
{ECO:0000269|PubMed:15808857, ECO:0000269|PubMed:3042752};
KM=59 uM for alpha-D-ribose 1-phosphate (at 25 degrees Celsius
and pH 7.0) {ECO:0000269|PubMed:15808857,
ECO:0000269|PubMed:3042752};
KM=58 uM for alpha-D-2'-deoxyribose 1-phosphate (at 25 degrees
Celsius and pH 7.0) {ECO:0000269|PubMed:15808857,
ECO:0000269|PubMed:3042752};
Vmax=8.7 umol/min/mg enzyme with xanthosine as substrate (at 25
degrees Celsius and pH 7.1, PubMed:15808857)
{ECO:0000269|PubMed:15808857, ECO:0000269|PubMed:3042752};
Vmax=14.2 umol/min/mg enzyme with guanosine as substrate (at 25
degrees Celsius and pH 7.1, PubMed:15808857)
{ECO:0000269|PubMed:15808857, ECO:0000269|PubMed:3042752};
Vmax=11.9 umol/min/mg enzyme with inosine as substrate (at 25
degrees Celsius and pH 7.1, PubMed:15808857)
{ECO:0000269|PubMed:15808857, ECO:0000269|PubMed:3042752};
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. {ECO:0000269|PubMed:15808857,
ECO:0000269|PubMed:3042752};
Temperature dependence:
The half-life at 45 degrees Celsius between pH 5 and 8 is 5 to 9
minutes. {ECO:0000269|PubMed:15808857,
ECO:0000269|PubMed:3042752};
-!- PATHWAY: Purine metabolism; xanthosine degradation.
-!- PATHWAY: Purine metabolism; purine nucleoside salvage.
-!- SUBUNIT: Hexamer. Dimer of trimers. {ECO:0000269|PubMed:15808857,
ECO:0000269|PubMed:7007809}.
-!- INDUCTION: By xanthosine and to a lesser extent by deoxyinosine.
Full expression requires XapR-xanthosine DNA-binding
transcriptional activator. {ECO:0000269|PubMed:10400599,
ECO:0000269|PubMed:7007809, ECO:0000269|PubMed:7559336}.
-!- 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).
{ECO:0000269|PubMed:17151449, ECO:0000269|PubMed:7559336}.
-!- SIMILARITY: Belongs to the PNP/MTAP phosphorylase family.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=CAA52049.1; Type=Frameshift; Positions=144, 177, 259, 261; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; X73828; CAA52049.1; ALT_FRAME; Genomic_DNA.
EMBL; U00096; AAC75460.1; -; Genomic_DNA.
EMBL; AP009048; BAA16275.1; -; Genomic_DNA.
PIR; F65014; F65014.
RefSeq; NP_416902.1; NC_000913.3.
RefSeq; WP_000084573.1; NZ_LN832404.1.
PDB; 1YQQ; X-ray; 2.60 A; A/B/C=1-277.
PDB; 1YQU; X-ray; 3.10 A; A/B/C=1-277.
PDB; 1YR3; X-ray; 3.20 A; A/B/C/D/E/F=1-277.
PDBsum; 1YQQ; -.
PDBsum; 1YQU; -.
PDBsum; 1YR3; -.
ProteinModelPortal; P45563; -.
SMR; P45563; -.
BioGrid; 4260565; 16.
IntAct; P45563; 4.
STRING; 316385.ECDH10B_2571; -.
DrugBank; DB02377; Guanine.
DrugBank; DB02134; Xanthine.
PaxDb; P45563; -.
PRIDE; P45563; -.
EnsemblBacteria; AAC75460; AAC75460; b2407.
EnsemblBacteria; BAA16275; BAA16275; BAA16275.
GeneID; 946878; -.
KEGG; ecj:JW2398; -.
KEGG; eco:b2407; -.
PATRIC; fig|1411691.4.peg.4325; -.
EchoBASE; EB4152; -.
EcoGene; EG20250; xapA.
eggNOG; ENOG4107U5R; Bacteria.
eggNOG; COG0005; LUCA.
HOGENOM; HOG000045183; -.
InParanoid; P45563; -.
KO; K03815; -.
PhylomeDB; P45563; -.
BioCyc; EcoCyc:XANTHOSINEPHOSPHORY-MONOMER; -.
BioCyc; MetaCyc:XANTHOSINEPHOSPHORY-MONOMER; -.
BRENDA; 2.4.2.1; 2026.
UniPathway; UPA00119; -.
UniPathway; UPA00606; -.
EvolutionaryTrace; P45563; -.
PRO; PR:P45563; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005737; C:cytoplasm; IDA:EcoliWiki.
GO; GO:0047975; F:guanosine phosphorylase activity; IDA:UniProtKB.
GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
GO; GO:0047724; F:inosine nucleosidase activity; IDA:UniProtKB.
GO; GO:0004731; F:purine-nucleoside phosphorylase activity; IDA:UniProtKB.
GO; GO:0006161; P:deoxyguanosine catabolic process; IDA:UniProtKB.
GO; GO:0006149; P:deoxyinosine catabolic process; IDA:UniProtKB.
GO; GO:0046115; P:guanosine catabolic process; IDA:UniProtKB.
GO; GO:0006148; P:inosine catabolic process; IDA:UniProtKB.
GO; GO:0015949; P:nucleobase-containing small molecule interconversion; IMP:EcoliWiki.
GO; GO:0055086; P:nucleobase-containing small molecule metabolic process; IMP:EcoliWiki.
GO; GO:0034214; P:protein hexamerization; IDA:UniProtKB.
GO; GO:0006152; P:purine nucleoside catabolic process; IDA:UniProtKB.
GO; GO:1903228; P:xanthosine catabolic process; IMP:EcoCyc.
InterPro; IPR000845; Nucleoside_phosphorylase_d.
InterPro; IPR035994; Nucleoside_phosphorylase_sf.
InterPro; IPR011268; Purine_phosphorylase.
InterPro; IPR018099; Purine_phosphorylase-2_CS.
InterPro; IPR010943; Xanthosine_phosphorylase.
PANTHER; PTHR11904; PTHR11904; 1.
Pfam; PF01048; PNP_UDP_1; 1.
PIRSF; PIRSF000477; PurNPase; 1.
SUPFAM; SSF53167; SSF53167; 1.
TIGRFAMs; TIGR01697; PNPH-PUNA-XAPA; 1.
TIGRFAMs; TIGR01699; XAPA; 1.
PROSITE; PS01240; PNP_MTAP_2; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Glycosyltransferase;
Reference proteome; Transferase.
CHAIN 1 277 Purine nucleoside phosphorylase 2.
/FTId=PRO_0000184555.
REGION 85 87 Phosphate binding. {ECO:0000244|PDB:1YQQ,
ECO:0000244|PDB:1YQU,
ECO:0000269|PubMed:15808857}.
BINDING 65 65 Phosphate. {ECO:0000244|PDB:1YQQ,
ECO:0000269|PubMed:15808857}.
BINDING 117 117 Phosphate; via amide nitrogen.
{ECO:0000244|PDB:1YQQ,
ECO:0000244|PDB:1YQU,
ECO:0000269|PubMed:15808857}.
BINDING 197 197 Purine nucleoside.
{ECO:0000269|PubMed:15808857}.
BINDING 216 216 Phosphate. {ECO:0000244|PDB:1YQQ,
ECO:0000244|PDB:1YQU,
ECO:0000269|PubMed:15808857}.
BINDING 239 239 Purine nucleoside.
{ECO:0000269|PubMed:15808857}.
MUTAGEN 191 191 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.
{ECO:0000269|PubMed:15808857}.
MUTAGEN 239 239 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.
{ECO:0000269|PubMed:15808857}.
CONFLICT 144 144 P -> A (in Ref. 1; CAA52049).
{ECO:0000305}.
CONFLICT 261 261 S -> H (in Ref. 1; CAA52049).
{ECO:0000305}.
CONFLICT 265 265 F -> L (in Ref. 1; CAA52049).
{ECO:0000305}.
HELIX 9 20 {ECO:0000244|PDB:1YQQ}.
STRAND 27 32 {ECO:0000244|PDB:1YQQ}.
HELIX 36 42 {ECO:0000244|PDB:1YQQ}.
STRAND 44 50 {ECO:0000244|PDB:1YQQ}.
HELIX 51 53 {ECO:0000244|PDB:1YQQ}.
STRAND 68 74 {ECO:0000244|PDB:1YQQ}.
STRAND 77 84 {ECO:0000244|PDB:1YQQ}.
HELIX 88 90 {ECO:0000244|PDB:1YQQ}.
TURN 94 97 {ECO:0000244|PDB:1YQQ}.
HELIX 98 107 {ECO:0000244|PDB:1YQQ}.
STRAND 110 121 {ECO:0000244|PDB:1YQQ}.
STRAND 130 137 {ECO:0000244|PDB:1YQQ}.
STRAND 140 142 {ECO:0000244|PDB:1YQQ}.
TURN 151 153 {ECO:0000244|PDB:1YQQ}.
STRAND 156 158 {ECO:0000244|PDB:1YQQ}.
HELIX 166 177 {ECO:0000244|PDB:1YQQ}.
TURN 178 180 {ECO:0000244|PDB:1YQQ}.
STRAND 183 190 {ECO:0000244|PDB:1YQQ}.
HELIX 199 207 {ECO:0000244|PDB:1YQQ}.
STRAND 211 217 {ECO:0000244|PDB:1YQQ}.
HELIX 218 226 {ECO:0000244|PDB:1YQQ}.
STRAND 230 240 {ECO:0000244|PDB:1YQQ}.
STRAND 244 246 {ECO:0000244|PDB:1YQQ}.
HELIX 251 256 {ECO:0000244|PDB:1YQQ}.
HELIX 257 259 {ECO:0000244|PDB:1YQQ}.
HELIX 262 276 {ECO:0000244|PDB:1YQQ}.
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


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