PDBsum entry 3gb9

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Transferase PDB id
Protein chain
283 a.a. *
A2F ×3
SO4 ×33
Waters ×211
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Human purine nucleoside phosphorylase double mutant e201q,n2 complexed with 2-fluoroadenine
Structure: Purine nucleoside phosphorylase. Chain: a, b, c. Synonym: pnp, inosine phosphorylase. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: np, pnp. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.30Å     R-factor:   0.186     R-free:   0.227
Authors: M.R.Sawaya,S.Afshar
Key ref: S.Afshar et al. (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. PubMed id: 19388075
19-Feb-09     Release date:   14-Apr-09    
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Protein chains
Pfam   ArchSchema ?
P00491  (PNPH_HUMAN) -  Purine nucleoside phosphorylase
289 a.a.
283 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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
+ phosphate
Bound ligand (Het Group name = A2F)
matches with 81.82% similarity
alpha-D-ribose 1-phosphate
Bound ligand (Het Group name = GOL)
matches with 42.86% similarity
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!
  Cellular component     intracellular   5 terms 
  Biological process     small molecule metabolic process   16 terms 
  Biochemical function     catalytic activity     9 terms  


Protein Sci 18:1107-1114 (2009)
PubMed id: 19388075  
Structure of a mutant human purine nucleoside phosphorylase with the prodrug, 2-fluoro-2'-deoxyadenosine and the cytotoxic drug, 2-fluoroadenine.
S.Afshar, M.R.Sawaya, S.L.Morrison.
A double mutant of human purine nucleoside phosphorylase (hDM) with the amino acid mutations Glu201Gln:Asn243Asp cleaves adenosine-based prodrugs to their corresponding cytotoxic drugs. When fused to an anti-tumor targeting component, hDM is targeted to tumor cells, where it effectively catalyzes phosphorolysis of the prodrug, 2-fluoro-2'-deoxyadenosine (F-dAdo) to the cytotoxic drug, 2-fluoroadenine (F-Ade). This cytotoxicity should be restricted only to the tumor microenvironment, because the endogenously expressed wild type enzyme cannot use adenosine-based prodrugs as substrates. To gain insight into the interaction of hDM with F-dAdo, we have determined the crystal structures of hDM with F-dAdo and F-Ade. The structures reveal that despite the two mutations, the overall fold of hDM is nearly identical to the wild type enzyme. Importantly, the residues Gln201 and Asp243 introduced by the mutation form hydrogen bond contacts with F-dAdo that result in its binding and catalysis. Comparison of substrate and product complexes suggest that the side chains of Gln201 and Asp243 as well as the purine base rotate during catalysis possibly facilitating cleavage of the glycosidic bond. The two structures suggest why hDM, unlike the wild-type enzyme, can utilize F-dAdo as substrate. More importantly, they provide a critical foundation for further optimization of cleavage of adenosine-based prodrugs, such as F-dAdo by mutants of human purine nucleoside phosphorylase.

Literature references that cite this PDB file's key reference

  PubMed id Reference
  19958550 S.Afshar, T.Olafsen, A.M.Wu, and S.L.Morrison (2009).
Characterization of an engineered human purine nucleoside phosphorylase fused to an anti-her2/neu single chain Fv for use in ADEPT.
  J Exp Clin Cancer Res, 28, 147.  
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