P45563 (XAPA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Purine nucleoside phosphorylase 2
EC=2.4.2.1

Alternative name(s):
Inosine-guanosine phosphorylase
Purine nucleoside phosphorylase II
Short name=PNP II
Xanthosine phosphorylase

Gene names

Name:	xapA
Synonyms:	pndA
Ordered Locus Names:	b2407, JW2398

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	277 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

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. Ref.5 Ref.6 Ref.7 Ref.10
Catalytic activity	Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate. Ref.1 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10
Enzyme regulation	Rapidly inactivated by p-chloromercuriphenylsulfonic acid (p-CMB). Dithiothreitol incubation restores the activity. Ref.7
Pathway	Purine metabolism; xanthosine degradation. Purine metabolism; purine nucleoside salvage.
Subunit structure	Hexamer. Dimer of trimers. Ref.6 Ref.10
Induction	By xanthosine and to a lesser extent by deoxyinosine. Full expression requires XapR-xanthosine DNA-binding transcriptional activator. Ref.1 Ref.6 Ref.7 Ref.8
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). Ref.1 Ref.9
Sequence similarities	Belongs to the PNP/MTAP phosphorylase family.
Biophysicochemical properties	Kinetic parameters: KM=51 µM for xanthosine (at pH 7.0, Ref.7) Ref.7 Ref.10 KM=72 µM for xanthosine (at 25 degrees Celsius and pH 7.1, Ref.10) KM=110 µM for guanosine (at pH 7.0, Ref.7) KM=155 µM for guanosine (at 25 degrees Celsius and pH 7.1, Ref.10) KM=963 µM for inosine (at 25 degrees Celsius and pH 7.1, Ref.10) KM=340 µM for inosine (at 25 degrees Celsius and pH 7.0, Ref.7) KM=62 µM for 2'-deoxyinosine (at 25 degrees Celsius and pH 7.0) KM=600 µM for 5'-deoxyinosine (at 25 degrees Celsius and pH 7.0) KM=2600 µM for 2',3'-dideoxyinosine (at 25 degrees Celsius and pH 7.0) KM=44 µM for 2'-deoxyguanosine (at 25 degrees Celsius and pH 7.0) KM=3.3 µM for hypoxanthine (at 25 degrees Celsius and pH 7.0) KM=4.1 µM for guanine (at 25 degrees Celsius and pH 7.0) KM=760 µM for phosphate (at 25 degrees Celsius and pH 7.0) KM=59 µM for alpha-D-ribose 1-phosphate (at 25 degrees Celsius and pH 7.0) KM=58 µM for alpha-D-2'-deoxyribose 1-phosphate (at 25 degrees Celsius and pH 7.0) Vmax=8.7 µmol/min/mg enzyme with xanthosine as substrate (at 25 degrees Celsius and pH 7.1, Ref.10) Vmax=14.2 µmol/min/mg enzyme with guanosine as substrate (at 25 degrees Celsius and pH 7.1, Ref.10) Vmax=11.9 µmol/min/mg enzyme with inosine as substrate (at 25 degrees Celsius and pH 7.1, Ref.10) 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. Temperature dependence: The half-life at 45 degrees Celsius between pH 5 and 8 is 5 to 9 minutes.
Sequence caution	The sequence CAA52049.1 differs from that shown. Reason: Frameshift at positions 144, 177, 259 and 261.

Ontologies

Keywords
Molecular function	Glycosyltransferase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	deoxyguanosine catabolic process Inferred from direct assay Ref.7. Source: UniProtKB deoxyinosine catabolic process Inferred from direct assay Ref.7. Source: UniProtKB guanosine catabolic process Inferred from direct assay Ref.10Ref.7. Source: UniProtKB inosine catabolic process Inferred from direct assay Ref.10Ref.9Ref.7. Source: UniProtKB nucleobase-containing small molecule interconversion Inferred from mutant phenotype Ref.1. Source: EcoliWiki protein hexamerization Inferred from direct assay Ref.10. Source: UniProtKB
Cellular_component	cytoplasm Inferred from direct assay Ref.10. Source: EcoliWiki
Molecular_function	guanosine phosphorylase activity Inferred from direct assay Ref.10Ref.7. Source: UniProtKB inosine nucleosidase activity Inferred from direct assay Ref.10Ref.9Ref.7. Source: UniProtKB purine-nucleoside phosphorylase activity Inferred from direct assay Ref.8Ref.9Ref.7Ref.1. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 277

277

Purine nucleoside phosphorylase 2

PRO_0000184555

Regions

Region

85 – 87

3

Substrate 2 binding

Sites

Binding site

65

1

Substrate 2; via tele nitrogen

Binding site

117

1

Substrate 2; via amide nitrogen

Binding site

197

1

Substrate 1

Binding site

216

1

Substrate 2

Binding site

239

1

Substrate 1

Experimental info

Mutagenesis

191

1

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. Ref.10

Mutagenesis

239

1

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. Ref.10

Sequence conflict

144

1

P → A in CAA52049. Ref.1

Sequence conflict

261

1

S → H in CAA52049. Ref.1

Sequence conflict

265

1

F → L in CAA52049. Ref.1

Secondary structure

1

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277

Helix Strand Turn

Details...

Helix

9 – 20

12

Beta strand

27 – 32

6

Helix

36 – 42

7

Beta strand

44 – 50

7

Helix

51 – 53

3

Beta strand

68 – 74

7

Beta strand

77 – 84

8

Helix

88 – 90

3

Turn

94 – 97

4

Helix

98 – 107

10

Beta strand

110 – 121

12

Beta strand

130 – 137

8

Beta strand

140 – 142

3

Turn

151 – 153

3

Beta strand

156 – 158

3

Helix

166 – 177

12

Turn

178 – 180

3

Beta strand

183 – 190

8

Helix

199 – 207

9

Beta strand

211 – 217

7

Helix

218 – 226

9

Beta strand

230 – 240

11

Beta strand

244 – 246

3

Helix

251 – 256

6

Helix

257 – 259

3

Helix

262 – 276

15

Sequences

	Sequence		Length	Mass (Da)
	P45563 [UniParc]. Last modified November 1, 1997. Version 2. Checksum: DD26545755C08F8B	FASTA	277	29,835
	10 20 30 40 50 60 MSQVQFSHNP LFCIDIIKTY KPDFTPRVAF ILGSGLGALA DQIENAVAIS YEKLPGFPVS 70 80 90 100 110 120 TVHGHAGELV LGHLQGVPVV CMKGRGHFYE GRGMTIMTDA IRTFKLLGCE LLFCTNAAGS 130 140 150 160 170 180 LRPEVGAGSL VALKDHINTM PGTPMVGLND DRFGERFFSL ANAYDAEYRA LLQKVAKEEG 190 200 210 220 230 240 FPLTEGVFVS YPGPNFETAA EIRMMQIIGG DVVGMSVVPE VISARHCDLK VVAVSAITNM 250 260 270 AEGLSDVKLS HAQTLAAAEL SKQNFINLIC GFLRKIA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification and characterization of genes (xapA, xapB, and xapR) involved in xanthosine catabolism in Escherichia coli." Seeger C., Poulsen C., Dandanell G. J. Bacteriol. 177:5506-5516(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CATALYTIC ACTIVITY, INDUCTION, DISRUPTION PHENOTYPE. Strain: K12.
[2]	"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." 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. DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." 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. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"A second purine nucleoside phosphorylase in Escherichia coli K-12. I. Xanthosine phosphorylase regulatory mutants isolated as secondary-site revertants of a deoD mutant." Buxton R.S., Hammer-Jespersen K., Valentin-Hansen P. Mol. Gen. Genet. 179:331-340(1980) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION. Strain: K12.
[6]	"A second purine nucleoside phosphorylase in Escherichia coli K-12. II. Properties of xanthosine phosphorylase and its induction by xanthosine." Hammer-Jespersen K., Buxton R.S., Hansen T.D. Mol. Gen. Genet. 179:341-348(1980) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, SUBUNIT, INDUCTION. Strain: K12.
[7]	"Purification and properties of inosine-guanosine phosphorylase from Escherichia coli K-12." Koszalka G.W., Vanhooke J., Short S.A., Hall W.W. J. Bacteriol. 170:3493-3498(1988) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES. Strain: K12.
[8]	"Isolation and characterization of mutations in the Escherichia coli regulatory protein XapR." Jorgensen C., Dandanell G. J. Bacteriol. 181:4397-4403(1999) [PubMed] [Europe PMC] [Abstract] Cited for: CATALYTIC ACTIVITY, INDUCTION.
[9]	"Effects of xapA and guaA disruption on inosine accumulation in Escherichia coli." Shimaoka M., Takenaka Y., Mihara Y., Kurahashi O., Kawasaki H., Matsui H. Biosci. Biotechnol. Biochem. 70:3069-3072(2006) [PubMed] [Europe PMC] [Abstract] Cited for: CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[10]	"Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene." Dandanell G., Szczepanowski R.H., Kierdaszuk B., Shugar D., Bochtler M. J. Mol. Biol. 348:113-125(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) IN COMPLEX WITH GUANINE, XANTHINE AND PHOSPHATE, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, MUTAGENESIS OF TYR-191 AND ASN-239. Strain: K12.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X73828 Genomic DNA. Translation: CAA52049.1. Frameshift.
U00096 Genomic DNA. Translation: AAC75460.1.
AP009048 Genomic DNA. Translation: BAA16275.1.

PIR

F65014.

RefSeq

NP_416902.1. NC_000913.2.
YP_490642.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P45563.

SMR

P45563. Positions 5-277.

ModBase

Search...

Protein-protein interaction databases

IntAct

P45563. 4 interactions.

STRING

511145.b2407.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75460; AAC75460; b2407.
BAA16275; BAA16275; BAA16275.

GeneID

12931571.
946878.

KEGG

ecj:Y75_p2367.
eco:b2407.

PATRIC

32120195. VBIEscCol129921_2500.

Organism-specific databases

EchoBASE

EB4152.

EcoGene

EG20250. xapA.

Phylogenomic databases

eggNOG

COG0005.

HOGENOM

HOG000045183.

KO

K03815.

OMA

MKVMTTP.

ProtClustDB

PRK08202.

Enzyme and pathway databases

BioCyc

EcoCyc:XANTHOSINEPHOSPHORY-MONOMER.
ECOL316407:JW2398-MONOMER.
MetaCyc:XANTHOSINEPHOSPHORY-MONOMER.

UniPathway

UPA00119.
UPA00606.

Gene expression databases

Genevestigator

P45563.

Family and domain databases

Gene3D

3.40.50.1580. 1 hit.

InterPro

IPR000845. Nucleoside_phosphorylase_d.
IPR001369. PNP/MTAP.
IPR011268. Purine_phosphorylase.
IPR018099. Purine_phosphorylase-2_CS.
IPR010943. Xanthosine_phosphorylase.
[Graphical view]

PANTHER

PTHR11904. PTHR11904. 1 hit.
PTHR11904:SF9. PTHR11904:SF9. 1 hit.

Pfam

PF01048. PNP_UDP_1. 1 hit.
[Graphical view]

PIRSF

PIRSF000477. PurNPase. 1 hit.

TIGRFAMs

TIGR01697. PNPH-PUNA-XAPA. 1 hit.
TIGR01699. XAPA. 1 hit.

PROSITE

PS01240. PNP_MTAP_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P45563.

Entry information

Entry name

XAPA_ECOLI

Accession

Primary (citable) accession number: P45563
Secondary accession number(s): P77325

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1995
Last sequence update:	November 1, 1997
Last modified:	May 29, 2013
This is version 106 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program