Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 32.34 kDa 
• Atom Count: 2334 
• Residue Count: 288 
• Unique protein chains: 1

1M73

CRYSTAL STRUCTURE OF HUMAN PNP AT 2.3A RESOLUTION

• DOI: 10.2210/pdb1M73/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-07-18 Released: 2003-09-16 
• Deposition Author(s): De Azevedo Jr., W.F., Marangoni Dos Santos, D., Canduri, F., Santos, G.C., Olivieri, J.R., Silva, R.G., Basso, L.A., Palma, M.S., Santos, D.S.

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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 

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

• PubMed: 12914785 
• DOI: 10.1016/s0006-291x(03)01431-1
• Structures With Same Primary Citation


• 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. 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.

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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

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Organizational Affiliation: 

Departamento de Física, UNESP, São José do Rio Preto, SP, Brazil. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PURINE NUCLEOSIDE PHOSPHORYLASE	E	288	Homo sapiens	Mutation(s): 0  Gene Names: PNP, NP EC: 2.4.2.1
Find proteins for P00491 (Homo sapiens) Go to UniProtKB:  P00491
NIH Common Fund Data Resources
PHAROS  P00491 GTEx  ENSG00000198805

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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 = 141.63	α = 90
b = 141.63	β = 90
c = 163.16	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-07-18 
• Released Date: 2003-09-16 
Deposition Author(s): De Azevedo Jr., W.F., Marangoni Dos Santos, D., Canduri, F., Santos, G.C., Olivieri, J.R., Silva, R.G., Basso, L.A., Palma, M.S., Santos, D.S.

Revision History 

• 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