PDBsum entry 1pr1

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protein ligands Protein-protein interface(s) links
Transferase PDB id
Jmol PyMol
Protein chains
226 a.a. *
PO4 ×3
FMB ×3
Waters ×125
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Escherichia coli purine nucleoside phosphorylase complexed w formycin b and phosphate/sulfate
Structure: Purine nucleoside phosphorylase. Chain: a, b, c. Synonym: inosine phosphorylase, pnp. Ec:
Source: Escherichia coli, escherichia coli o15 ,. Organism_taxid: 562,83334. Strain: , o157:h7
Biol. unit: Hexamer (from PDB file)
2.30Å     R-factor:   0.215     R-free:   0.271
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
19-Jun-03     Release date:   25-Nov-03    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0ABP9  (DEOD_ECO57) -  Purine nucleoside phosphorylase DeoD-type
239 a.a.
226 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Purine-nucleoside phosphorylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
1. Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate
2. Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
Purine nucleoside
Bound ligand (Het Group name = FMB)
matches with 48.00% similarity
Bound ligand (Het Group name = PO4)
corresponds exactly
= purine
+ alpha-D-ribose 1-phosphate
Purine deoxynucleoside
+ phosphate
= purine
+ 2'-deoxy-alpha-D-ribose 1-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleobase-containing compound metabolic process   2 terms 
  Biochemical function     catalytic activity     4 terms  


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.
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20525731 D.P.Nannemann, K.W.Kaufmann, J.Meiler, and B.O.Bachmann (2010).
Design and directed evolution of a dideoxy purine nucleoside phosphorylase.
  Protein Eng Des Sel, 23, 607-616.  
20048065 J.Fernández-Lucas, C.Acebal, J.V.Sinisterra, M.Arroyo, and la Mata (2010).
Lactobacillus reuteri 2'-deoxyribosyltransferase, a novel biocatalyst for tailoring of nucleosides.
  Appl Environ Microbiol, 76, 1462-1470.  
20124695 Y.N.Kang, Y.Zhang, P.W.Allan, W.B.Parker, J.W.Ting, C.Y.Chang, and S.E.Ealick (2010).
Structure of grouper iridovirus purine nucleoside phosphorylase.
  Acta Crystallogr D Biol Crystallogr, 66, 155-162.
PDB code: 3khs
19575810 A.Chaikuad, and R.L.Brady (2009).
Conservation of structure and activity in Plasmodium purine nucleoside phosphorylases.
  BMC Struct Biol, 9, 42.
PDB codes: 3emv 3enz
19388075 S.Afshar, M.R.Sawaya, and S.L.Morrison (2009).
Structure of a mutant human purine nucleoside phosphorylase with the prodrug, 2-fluoro-2'-deoxyadenosine and the cytotoxic drug, 2-fluoroadenine.
  Protein Sci, 18, 1107-1114.
PDB codes: 3gb9 3ggs
19139128 S.Afshar, T.Asai, and S.L.Morrison (2009).
Humanized ADEPT comprised of an engineered human purine nucleoside phosphorylase and a tumor targeting peptide for treatment of cancer.
  Mol Cancer Ther, 8, 185-193.  
17639373 A.Modrak-Wójcik, A.Kirilenko, D.Shugar, and B.Kierdaszuk (2008).
Role of ionization of the phosphate cosubstrate on phosphorolysis by purine nucleoside phosphorylase (PNP) of bacterial (E. coli) and mammalian (human) origin.
  Eur Biophys J, 37, 153-164.  
18299797 X.Li, X.Jiang, H.Li, and D.Ren (2008).
Purine nucleoside phosphorylase from Pseudoalteromonas sp. Bsi590: molecular cloning, gene expression and characterization of the recombinant protein.
  Extremophiles, 12, 325-333.  
17223688 A.Rinaldo-Matthis, C.Wing, M.Ghanem, H.Deng, P.Wu, A.Gupta, P.C.Tyler, G.B.Evans, R.H.Furneaux, S.C.Almo, C.C.Wang, and V.L.Schramm (2007).
Inhibition and structure of Trichomonas vaginalis purine nucleoside phosphorylase with picomolar transition state analogues.
  Biochemistry, 46, 659-668.
PDB codes: 2i4t 2isc
16964310 A.Toro, and E.Grunebaum (2006).
TAT-mediated intracellular delivery of purine nucleoside phosphorylase corrects its deficiency in mice.
  J Clin Invest, 116, 2717-2726.  
16132363 C.P.Landowski, X.Song, P.L.Lorenzi, J.M.Hilfinger, and G.L.Amidon (2005).
Floxuridine amino acid ester prodrugs: enhancing Caco-2 permeability and resistance to glycosidic bond metabolism.
  Pharm Res, 22, 1510-1518.  
16131758 C.Schnick, M.A.Robien, A.M.Brzozowski, E.J.Dodson, G.N.Murshudov, L.Anderson, J.R.Luft, C.Mehlin, W.G.Hol, J.A.Brannigan, and A.J.Wilkinson (2005).
Structures of Plasmodium falciparum purine nucleoside phosphorylase complexed with sulfate and its natural substrate inosine.
  Acta Crystallogr D Biol Crystallogr, 61, 1245-1254.
PDB codes: 1sq6 2bsx
15296732 Y.Zhang, S.E.Cottet, and S.E.Ealick (2004).
Structure of Escherichia coli AMP nucleosidase reveals similarity to nucleoside phosphorylases.
  Structure, 12, 1383-1394.
PDB codes: 1t8r 1t8s 1t8w 1t8y
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.