1M73

CRYSTAL STRUCTURE OF HUMAN PNP AT 2.3A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of human purine nucleoside phosphorylase at 2.3A resolution.

de Azevedo, W.F.Canduri, F.dos Santos, D.M.Silva, R.G.de Oliveira, J.S.de Carvalho, L.P.Basso, L.A.Mendes, M.A.Palma, M.S.Santos, D.S.

(2003) Biochem.Biophys.Res.Commun. 308: 545-552

  • Also Cited By: 3D1V, 1YRY, 1V3Q, 1V2H, 1PF7

  • PubMed Abstract: 
  • 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 p ...

    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.


    Related Citations: 
    • Application of Crystallographic and Modeling Methods in the Design of Purine Nucleoside Phosphorylase Inhibitors
      Ealick, S.E.,Babu, Y.S.,Bugg, C.E.,Erion, M.D.,Guida, W.C.,Montgomery, J.A.,Secrist, J.A.3rd.
      (1991) Proc.Natl.Acad.Sci.USA 88: 11540


    Organizational Affiliation

    Departamento de Física, UNESP, São José do Rio Preto, SP, Brazil. walterfa@df.ibilce.unesp.br




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PURINE NUCLEOSIDE PHOSPHORYLASE
E
288Homo sapiensMutation(s): 0 
Gene Names: PNP (NP)
EC: 2.4.2.1
Find proteins for P00491 (Homo sapiens)
Go to Gene View: PNP
Go to UniProtKB:  P00491
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.205 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 141.630α = 90.00
b = 141.630β = 90.00
c = 163.160γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-16
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance