PDBsum entry 1pr5

Transferase

PDB id: 1pr5

Contents

Protein chains

231 a.a. *

Ligands

PO4 ×3

TBN ×3

Waters ×106

* Residue conservation analysis

PDB id:

1pr5

Name:

Transferase

Title:

Escherichia coli purine nucleoside phosphorylase complexed with 7- deazaadenosine and phosphate/sulfate

Structure:

Purine nucleoside phosphorylase deod-type. Chain: a, b, c. Synonym: pnp. Ec: 2.4.2.1

Source:

Escherichia coli o157:h7. Organism_taxid: 83334

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.50Å R-factor: 0.207 R-free: 0.259

Authors:

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

Key ref:

E.M.Bennett et al. (2003). Structural basis for substrate specificity of Escherichia coli purine nucleoside phosphorylase. J Biol Chem, 278, 47110-47118. PubMed id: 12937174 DOI: 10.1074/jbc.M304622200

Date:

19-Jun-03 Release date: 25-Nov-03

Protein chains

P0ABP9  (DEOD_ECO57) -  Purine nucleoside phosphorylase DeoD-type from Escherichia coli O157:H7

Seq: 239 a.a.

Struc: 231 a.a.

Enzyme reactions

• Enzyme class: E.C.2.4.2.1 - purine-nucleoside phosphorylase.
• Reaction:
  1. a purine D-ribonucleoside + phosphate = a purine nucleobase + alpha- D-ribose 1-phosphate
  2. a purine 2'-deoxy-D-ribonucleoside + phosphate = a purine nucleobase + 2-deoxy-alpha-D-ribose 1-phosphate

purine D-ribonucleoside + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly) = purine nucleobase + alpha- D-ribose 1-phosphate

purine 2'-deoxy-D-ribonucleoside + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly) = purine nucleobase + 2-deoxy-alpha-D-ribose 1-phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M304622200

J Biol Chem 278:47110-47118 (2003)

PubMed id: 12937174

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

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

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.

Selected figure(s)

Figure 3.
FIG. 3. Schematic diagram showing key active site residues and the contacts that are made with the substrates inosine and phosphate. Dashed lines indicate hydrogen bonds (or partial double bonds in carboxylate groups), and W indicates a water molecule.

Figure 7.
FIG. 7. Schematic diagrams of the two possible hydrogen bonding schemes of the water channel near the purine N-1 position. A, hydrogen bonding scheme in which the first water molecule is a donor to N-1 of 6-aminopurines (distances are from the F-Ado A subunit). B, hydrogen bonding scheme in which the first water molecule is an acceptor from N-1 of 6-oxopurines (distances are from the Ino C subunit).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 47110-47118) copyright 2003.

Figures were selected by an automated process.