spacer
spacer

PDBsum entry 1v2h

Go to PDB code: 
protein ligands links
Transferase PDB id
1v2h
Jmol
Contents
Protein chain
288 a.a. *
Ligands
SO4 ×4
GUN
Waters ×38
* Residue conservation analysis
PDB id:
1v2h
Name: Transferase
Title: Crystal structure of human pnp complexed with guanine
Structure: Purine nucleoside phosphorylase. Chain: e. Synonym: inosine phosphorylase, pnp. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: pnp. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PDB file)
Resolution:
2.70Å     R-factor:   0.218     R-free:   0.293
Authors: W.F.De Azevedo Jr.,F.Canduri,J.H.Pereira,D.M.Dos Santos,M.V. Dias,R.G.Silva,M.S.Palma,L.A.Basso,D.S.Santos
Key ref: W.F.de Azevedo et al. (2003). Crystal structure of human PNP complexed with guanine. Biochem Biophys Res Commun, 312, 767-772. PubMed id: 14680831 DOI: 10.1016/j.bbrc.2003.10.190
Date:
16-Oct-03     Release date:   13-Jan-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00491  (PNPH_HUMAN) -  Purine nucleoside phosphorylase
Seq:
Struc:
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.2.4.2.1  - Purine-nucleoside phosphorylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
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
Bound ligand (Het Group name = GUN)
matches with 81.82% similarity
+ 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  

 

 
    reference    
 
 
DOI no: 10.1016/j.bbrc.2003.10.190 Biochem Biophys Res Commun 312:767-772 (2003)
PubMed id: 14680831  
 
 
Crystal structure of human PNP complexed with guanine.
W.F.de Azevedo, F.Canduri, D.M.dos Santos, J.H.Pereira, M.V.Bertacine Dias, R.G.Silva, M.A.Mendes, L.A.Basso, M.S.Palma, D.S.Santos.
 
  ABSTRACT  
 
Purine nucleoside phosphorylase (PNP) catalyzes the phosphorolysis of the N-ribosidic bonds of purine nucleosides and deoxynucleosides. PNP is a target for inhibitor development aiming at T-cell immune response modulation and has been submitted to extensive structure-based drug design. More recently, the 3-D structure of human PNP has been refined to 2.3A resolution, which allowed a redefinition of the residues involved in the substrate-binding sites and provided a more reliable model for structure-based design of inhibitors. This work reports crystallographic study of the complex of Human PNP:guanine (HsPNP:Gua) solved at 2.7A resolution using synchrotron radiation. Analysis of the structural differences among the HsPNP:Gua complex, PNP apoenzyme, and HsPNP:immucillin-H provides explanation for inhibitor binding, refines the purine-binding site, and can be used for future inhibitor design.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19669809 F.B.Zanchi, R.A.Caceres, R.G.Stabeli, and W.F.de Azevedo (2010).
Molecular dynamics studies of a hexameric purine nucleoside phosphorylase.
  J Mol Model, 16, 543-550.  
19172318 I.Pauli, L.F.Timmers, R.A.Caceres, L.A.Basso, D.S.Santos, and W.F.de Azevedo (2009).
Molecular modeling and dynamics studies of purine nucleoside phosphorylase from Bacteroides fragilis.
  J Mol Model, 15, 913-922.  
15983407 F.Canduri, R.G.Silva, D.M.dos Santos, M.S.Palma, L.A.Basso, D.S.Santos, and W.F.de Azevedo (2005).
Structure of human PNP complexed with ligands.
  Acta Crystallogr D Biol Crystallogr, 61, 856-862.
PDB codes: 1rfg 1v41 1v45
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 codes are shown on the right.