PDBsum entry 1m73

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protein ligands links
Transferase PDB id
Protein chain
288 a.a. *
SO4 ×3
Waters ×68
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of human pnp at 2.3a resolution
Structure: Purine nucleoside phosphorylase. Chain: e. Synonym: inosine phosphorylase, pnp. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PDB file)
2.30Å     R-factor:   0.205     R-free:   0.222
Authors: W.F.De Azevedo Jr.,D.Marangoni Dos Santos,F.Canduri,G.C.Sant J.R.Olivieri,R.G.Silva,L.A.Basso,M.S.Palma,D.S.Santos
Key ref: Azevedo et al. (2003). Crystal structure of human purine nucleoside phosphorylase at 2.3A resolution. Biochem Biophys Res Commun, 308, 545-552. PubMed id: 12914785 DOI: 10.1016/S0006-291X(03)01431-1
18-Jul-02     Release date:   16-Sep-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00491  (PNPH_HUMAN) -  Purine nucleoside phosphorylase
289 a.a.
288 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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
= 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!
  Cellular component     intracellular   5 terms 
  Biological process     small molecule metabolic process   16 terms 
  Biochemical function     catalytic activity     9 terms  


DOI no: 10.1016/S0006-291X(03)01431-1 Biochem Biophys Res Commun 308:545-552 (2003)
PubMed id: 12914785  
Crystal structure of human purine nucleoside phosphorylase at 2.3A resolution. Azevedo, F.Canduri, D.M.dos Santos, R.G.Silva, Oliveira, Carvalho, L.A.Basso, M.A.Mendes, M.S.Palma, D.S.Santos.
Purine nucleoside phosphorylase (PNP) catalyzes the phosphorolysis of the N-ribosidic bonds of purine nucleosides and deoxynucleosides. In human, PNP is the only route for degradation of deoxyguanosine and genetic deficiency of this enzyme leads to profound T-cell mediated immunosuppression. PNP is therefore a target for inhibitor development aiming at T-cell immune response modulation and its low resolution structure has been used for drug design. Here we report the structure of human PNP solved to 2.3A resolution using synchrotron radiation and cryocrystallographic techniques. This structure allowed a more precise analysis of the active site, generating a more reliable model for substrate binding. The higher resolution data allowed the identification of water molecules in the active site, which suggests binding partners for potential ligands. Furthermore, the present structure may be used in the new structure-based design of PNP inhibitors.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19669809 F.B.Zanchi, R.A.Caceres, R.G.Stabeli, and Azevedo (2010).
Molecular dynamics studies of a hexameric purine nucleoside phosphorylase.
  J Mol Model, 16, 543-550.  
19425594 A.A.Edwards, J.M.Mason, K.Clinch, P.C.Tyler, G.B.Evans, and V.L.Schramm (2009).
Altered enthalpy-entropy compensation in picomolar transition state analogues of human purine nucleoside phosphorylase.
  Biochemistry, 48, 5226-5238.  
19172318 I.Pauli, L.F.Timmers, R.A.Caceres, L.A.Basso, D.S.Santos, and Azevedo (2009).
Molecular modeling and dynamics studies of purine nucleoside phosphorylase from Bacteroides fragilis.
  J Mol Model, 15, 913-922.  
19778725 M.Ghanem, A.S.Murkin, and V.L.Schramm (2009).
Ribocation transition state capture and rebound in human purine nucleoside phosphorylase.
  Chem Biol, 16, 971-979.  
19191546 M.Ghanem, N.Zhadin, R.Callender, and V.L.Schramm (2009).
Loop-tryptophan human purine nucleoside phosphorylase reveals submillisecond protein dynamics.
  Biochemistry, 48, 3658-3668.  
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
15983407 F.Canduri, R.G.Silva, D.M.dos Santos, M.S.Palma, L.A.Basso, D.S.Santos, and Azevedo (2005).
Structure of human PNP complexed with ligands.
  Acta Crystallogr D Biol Crystallogr, 61, 856-862.
PDB codes: 1rfg 1v41 1v45
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