1PR2

Escherichia coli Purine Nucleoside Phosphorylase Complexed with 9-beta-D-[2-deoxyribofuranosyl]-6-methylpurine and Phosphate/Sulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for substrate specificity of Escherichia coli purine nucleoside phosphorylase.

Bennett, E.M.Li, C.Allan, P.W.Parker, W.B.Ealick, S.E.

(2003) J.Biol.Chem. 278: 47110-47118

  • DOI: 10.1074/jbc.M304622200
  • Primary Citation of Related Structures:  1PK7, 1PK9, 1PKE, 1PR0, 1PR1, 1PR4, 1PR5, 1PR6, 1PW7

  • PubMed Abstract: 
  • Purine nucleoside phosphorylase catalyzes reversible phosphorolysis of purine nucleosides and 2'-deoxypurine nucleosides to the free base and ribose (or 2'-deoxyribose) 1-phosphate. Whereas the human enzyme is specific for 6-oxopurine ribonucleosides ...

    Purine nucleoside phosphorylase catalyzes reversible phosphorolysis of purine nucleosides and 2'-deoxypurine nucleosides to the free base and ribose (or 2'-deoxyribose) 1-phosphate. Whereas the human enzyme is specific for 6-oxopurine ribonucleosides, the Escherichia coli enzyme accepts additional substrates including 6-oxopurine ribonucleosides, 6-aminopurine ribonucleosides, and to a lesser extent purine arabinosides. These differences have been exploited in a potential suicide gene therapy treatment for solid tumors. In an effort to optimize this suicide gene therapy approach, we have determined the three-dimensional structure of the E. coli enzyme in complex with 10 nucleoside analogs and correlated the structures with kinetic measurements and computer modeling. These studies explain the preference of the enzyme for ribose sugars, show increased flexibility for active site residues Asp204 and Arg24, and suggest that interactions involving the 1- and 6-positions of the purine and the 4'- and 5'-positions of the ribose provide the best opportunities to increase prodrug specificity and enzyme efficiency.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase
A, B, C
239Escherichia coli O157:H7Gene Names: deoD
EC: 2.4.2.1
Find proteins for P0ABP9 (Escherichia coli O157:H7)
Go to UniProtKB:  P0ABP9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MDR
Query on MDR

Download SDF File 
Download CCD File 
A, B, C
9-(2-DEOXY-BETA-D-RIBOFURANOSYL)-6-METHYLPURINE
C11 H14 N4 O3
SJXRKKYXNZWKDB-DJLDLDEBSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.173 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 121.200α = 90.00
b = 121.200β = 90.00
c = 240.800γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
CNSrefinement
DENZOdata reduction
X-PLORphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-25
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance