1M73

CRYSTAL STRUCTURE OF HUMAN PNP AT 2.3A RESOLUTION

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.239 

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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

  • DOI: 10.1016/s0006-291x(03)01431-1
  • Primary Citation of Related Structures:  
    1M73

  • 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 profound T-cell mediated immunosuppression ...

    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 U S A 88: 11540
    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PURINE NUCLEOSIDE PHOSPHORYLASEA [auth E]288Homo sapiensMutation(s): 0 
Gene Names: PNP, NP
EC: 2.4.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00491 (Homo sapiens)
Explore P00491 
Go to UniProtKB:  P00491
PHAROS:  P00491
GTEx:  ENSG00000198805 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00491
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B [auth E],
C [auth E],
D [auth E]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.239 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.63α = 90
b = 141.63β = 90
c = 163.16γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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