1PKE

Crystal Structure of E. coli purine nucleoside phosphorylase complexed with 2-fluoro-2'-deoxyadenosine and sulfate/phosphate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    1PR2, 1PR1, 1PR0, 1PR6, 1PR5, 1PR4, 1PW7, 1PKE, 1PK9, 1PK7

  • 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, the Escherichia coli enzyme accepts additional substrates including 6-oxopurine ribonucleosides, 6-aminopurine ribonucleosides, and to a lesser extent purine arabinosides ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Purine nucleoside phosphorylase DeoD-typeA, B, C237Escherichia coli O157:H7Mutation(s): 0 
Gene Names: deoD, Z5986, ECs5343
EC: 2.4.2.1
Find proteins for P0ABP9 (Escherichia coli O157:H7)
Explore P0ABP9 
Go to UniProtKB:  P0ABP9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2FD
Query on 2FD
Download Ideal Coordinates CCD File 
 E [auth A], G [auth B], I [auth C]5-(6-AMINO-2-FLUORO-PURIN-9-YL)-2-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-OL
C10 H12 F N5 O3
ZWPYUXAXLRFWQC-KVQBGUIXSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
 D [auth A], F [auth B], H [auth C]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.7α = 90
b = 122.7β = 90
c = 243.7γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-25
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2019-12-11
    Changes: Database references, Source and taxonomy, Structure summary