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PDBsum entry 2ai2

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protein ligands metals links
Transferase PDB id
2ai2
Jmol
Contents
Protein chain
274 a.a. *
Ligands
144
P1D
Metals
_MG
_ZN
Waters ×258
* Residue conservation analysis
PDB id:
2ai2
Name: Transferase
Title: Purine nucleoside phosphorylase from calf spleen
Structure: Purine nucleoside phosphorylase. Chain: a. Synonym: inosine phosphorylase, pnp. Ec: 2.4.2.1
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: spleen. Other_details: calf spleen purine nucleoside phosphorylase from sigma co.
Biol. unit: Trimer (from PDB file)
Resolution:
1.70Å     R-factor:   0.196     R-free:   0.231
Authors: A.V.Toms,W.Wang,Y.Li,B.Ganem,S.E.Ealick
Key ref:
A.V.Toms et al. (2005). Novel multisubstrate inhibitors of mammalian purine nucleoside phosphorylase. Acta Crystallogr D Biol Crystallogr, 61, 1449-1458. PubMed id: 16239721 DOI: 10.1107/S0907444905025503
Date:
28-Jul-05     Release date:   25-Oct-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P55859  (PNPH_BOVIN) -  Purine nucleoside phosphorylase
Seq:
Struc:
289 a.a.
274 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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 = P1D)
matches with 53.57% 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     cytoplasm   2 terms 
  Biological process     nucleobase-containing compound metabolic process   2 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444905025503 Acta Crystallogr D Biol Crystallogr 61:1449-1458 (2005)
PubMed id: 16239721  
 
 
Novel multisubstrate inhibitors of mammalian purine nucleoside phosphorylase.
A.V.Toms, W.Wang, Y.Li, B.Ganem, S.E.Ealick.
 
  ABSTRACT  
 
In an effort to develop potent multisubstrate-analog inhibitors of purine nucleoside phosphorylase (PNP), three nucleoside phosphonates were designed utilizing structural information from the previously reported structures of complexes of bovine PNP with substrates and products. The nucleoside phosphonates contain an acetal linkage at the O2' and O3' positions and a two-C-atom spacer between the ribose and phosphate moieties. The linkage enables the compounds to simultaneously occupy the purine-, ribose- and phosphate-binding sites. The chemical syntheses, inhibition profiles and structural characterization of these novel multisubstrate analog inhibitors with bovine PNP are described.
 
  Selected figure(s)  
 
Figure 5.
Figure 5 Stereo diagrams of the PNP active site with (a) compound (1), (b) compound (2) and (c) compound (3). The PNP residues are shown in ball-and stick representation with O atoms in red, C atoms in gray, N atoms in blue and P atoms in purple. The C atoms of the inhibitor are colored yellow. Phe159 from the neighboring subunit is shown in dark gray. Hydrogen bonds are indicated by dashed lines.
Figure 9.
Figure 9 Comparison with the binding of inosine and sulfate. (a) Schematic view of the binding of inosine and sulfate in the active site of bovine PNP (PDB code 1a9s ). (b) Stereoview of the active-site superposition of compound (2) with inosine and sulfate. Compound (2) is shown in red and the surrounding protein in pink. Inosine and sulfate are shown in blue and the surrounding protein residues in gray.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 1449-1458) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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