1YQU

Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene

Dandanell, G.Szczepanowski, R.H.Kierdaszuk, B.Shugar, D.Bochtler, M.

(2005) J.Mol.Biol. 348: 113-125

  • DOI: 10.1016/j.jmb.2005.02.019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Purine nucleoside phosphorylases (PNPs, E. C. 2.4.2.1) use orthophosphate to cleave the N-glycosidic bond of beta-(deoxy)ribonucleosides to yield alpha-(deoxy)ribose 1-phosphate and the free purine base. Escherichia coli PNP-II, the product of the xa ...

    Purine nucleoside phosphorylases (PNPs, E. C. 2.4.2.1) use orthophosphate to cleave the N-glycosidic bond of beta-(deoxy)ribonucleosides to yield alpha-(deoxy)ribose 1-phosphate and the free purine base. Escherichia coli PNP-II, the product of the xapA gene, is similar to trimeric PNPs in sequence, but has been reported to migrate as a hexamer and to accept xanthosine with comparable efficiency to guanosine and inosine, the usual physiological substrates for trimeric PNPs. Here, we present a detailed biochemical characterization and the crystal structure of E.coli PNP-II. In three different crystal forms, PNP-II trimers dimerize, leading to a subunit arrangement that is qualitatively different from the "trimer of dimers" arrangement of conventional high molecular mass PNPs. Crystal structures are compatible with similar binding modes for guanine and xanthine, with a preference for the neutral over the monoanionic form of xanthine. A single amino acid exchange, tyrosine 191 to leucine, is sufficient to convert E.coli PNP-II into an enzyme with the specificity of conventional trimeric PNPs, but the reciprocal mutation in human PNP, valine 195 to tyrosine, does not elicit xanthosine phosphorylase activity in the human enzyme.


    Organizational Affiliation

    Department of Biological Chemistry, Institute of Molecular Biology, Solvgade 83H, 1307 Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xanthosine phosphorylase
A, B, C
277Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: xapA (pndA)
EC: 2.4.2.1
Find proteins for P45563 (Escherichia coli (strain K12))
Go to UniProtKB:  P45563
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GUN
Query on GUN

Download SDF File 
Download CCD File 
A, B, C
GUANINE
C5 H5 N5 O
UYTPUPDQBNUYGX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.245 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.345α = 90.00
b = 71.345β = 90.00
c = 267.537γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
MOLREPphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance