PDBsum entry 1yry

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protein ligands links
Transferase PDB id
Protein chain
288 a.a. *
SO4 ×3
Waters ×119
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of human pnp complexed with mesg
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 PQS)
2.80Å     R-factor:   0.207     R-free:   0.290
Authors: R.G.Silva,J.H.Pereira,F.Canduri,L.A.Basso,W.F.De Azevedo Jr. D.S.Santos
Key ref: R.G.Silva et al. (2005). Kinetics and crystal structure of human purine nucleoside phosphorylase in complex with 7-methyl-6-thio-guanosine. Arch Biochem Biophys, 442, 49-58. PubMed id: 16154528 DOI: 10.1016/
05-Feb-05     Release date:   17-Jan-06    
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
Bound ligand (Het Group name = MSG)
matches with 85.71% similarity
+ 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/ Arch Biochem Biophys 442:49-58 (2005)
PubMed id: 16154528  
Kinetics and crystal structure of human purine nucleoside phosphorylase in complex with 7-methyl-6-thio-guanosine.
R.G.Silva, J.H.Pereira, F.Canduri, Azevedo, L.A.Basso, D.S.Santos.
Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of nucleosides and deoxynucleosides, generating ribose 1-phosphate and the purine base, which is an important step of purine catabolism pathway. The lack of such an activity in humans, owing to a genetic disorder, causes T-cell impairment, and drugs that inhibit this enzyme may have the potential of being utilized as modulators of the immunological system to treat leukemia, autoimmune diseases, and rejection in organ transplantation. Here, we describe kinetics and crystal structure of human PNP in complex with 7-methyl-6-thio-guanosine, a synthetic substrate, which is largely used in activity assays. Analysis of the structure identifies different protein conformational changes upon ligand binding, and comparison of kinetic and structural data permits an understanding of the effects of atomic substitution on key positions of the synthetic substrate and their consequences to enzyme binding and catalysis. Such knowledge may be helpful in designing new 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.  
20210752 M.L.Bellows, and C.A.Floudas (2010).
Computational methods for de novo protein design and its applications to the human immunodeficiency virus 1, purine nucleoside phosphorylase, ubiquitin specific protease 7, and histone demethylases.
  Curr Drug Targets, 11, 264-278.  
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
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.  
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.  
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