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PDBsum entry 1rct

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protein ligands links
Transferase PDB id
1rct
Jmol
Contents
Protein chain
288 a.a. *
Ligands
SO4 ×3
NOS
Waters ×45
* Residue conservation analysis
PDB id:
1rct
Name: Transferase
Title: Crystal structure of human purine nucleoside phosphorylasE C with inosine
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)
Resolution:
2.80Å     R-factor:   0.208     R-free:   0.290
Authors: F.Canduri,D.M.Dos Santos,R.G.Silva,M.A.Mendes,M.S.Palma,W.F. Azevedo Jr.,L.A.Basso,D.S.Santos
Key ref: F.Canduri et al. (2004). Structures of human purine nucleoside phosphorylase complexed with inosine and ddI. Biochem Biophys Res Commun, 313, 907-914. PubMed id: 14706628 DOI: 10.1016/j.bbrc.2003.11.179
Date:
04-Nov-03     Release date:   20-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
Bound ligand (Het Group name = NOS)
matches with 94.74% 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  

 

 
    reference    
 
 
DOI no: 10.1016/j.bbrc.2003.11.179 Biochem Biophys Res Commun 313:907-914 (2004)
PubMed id: 14706628  
 
 
Structures of human purine nucleoside phosphorylase complexed with inosine and ddI.
F.Canduri, D.M.dos Santos, R.G.Silva, M.A.Mendes, L.A.Basso, M.S.Palma, W.F.de Azevedo, D.S.Santos.
 
  ABSTRACT  
 
Human purine nucleoside phosphorylase (PNP) is a ubiquitous enzyme which plays a key role in the purine salvage pathway, and PNP deficiency in humans leads to an impairment of T-cell function, usually with no apparent effect on B-cell function. PNP is highly specific for 6-oxopurine nucleosides and exhibits negligible activity for 6-aminopurine nucleosides. The catalytic efficiency for inosine is 350,000-fold greater than for adenosine. Adenine nucleosides and nucleotides are deaminated by adenosine deaminase and AMP deaminase to their corresponding inosine derivatives which, in turn, may be further degraded. Here we report the crystal structures of human PNP in complex with inosine and 2('),3(')-dideoxyinosine, refined to 2.8A resolution using synchrotron radiation. The present structures provide explanation for ligand binding, refine 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
21169694 H.D'Muniz Pereira, G.Oliva, and R.C.Garratt (2011).
Purine nucleoside phosphorylase from Schistosoma mansoni in complex with ribose-1-phosphate.
  J Synchrotron Radiat, 18, 62-65.
PDB code: 3fb1
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.  
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.  
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.  
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.  
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.  
17407325 A.S.Murkin, M.R.Birck, A.Rinaldo-Matthis, W.Shi, E.A.Taylor, S.C.Almo, and V.L.Schramm (2007).
Neighboring group participation in the transition state of human purine nucleoside phosphorylase.
  Biochemistry, 46, 5038-5049.
PDB codes: 2a0w 2a0x 2a0y 2oc4 2oc9 2on6
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 code is shown on the right.