Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 78.26 kDa 
• Atom Count: 5805 
• Residue Count: 706 
• Unique protein chains: 1

1PKE

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

• DOI: 10.2210/pdb1PKE/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli O157:H7
• Mutation(s): No 


• Deposited: 2003-06-05 Released: 2003-11-25 
• Deposition Author(s): Bennett, E.M., Li, C., Allan, P.W., Parker, W.B., Ealick, S.E.

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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 

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

• PubMed: 12937174 
• DOI: 10.1074/jbc.M304622200
• Structures With Same Primary Citation


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Purine nucleoside phosphorylase DeoD-type	A, B, C	237	Escherichia coli O157:H7	Mutation(s): 0  Gene Names: deoD, Z5986, ECs5343 EC: 2.4.2.1
Find proteins for P0ABP9 (Escherichia coli O157:H7) Go to UniProtKB:  P0ABP9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2FD	A, B, C	5-(6-AMINO-2-FLUORO-PURIN-9-YL)-2-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-OL C10 H12 F N5 O3 ZWPYUXAXLRFWQC-KVQBGUIXSA-N
PO4	A, B, C	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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 = 122.7	α = 90
b = 122.7	β = 90
c = 243.7	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
CNS	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-06-05 
• Released Date: 2003-11-25 
Deposition Author(s): Bennett, E.M., Li, C., Allan, P.W., Parker, W.B., Ealick, S.E.

Revision History 

• 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