1PBN

PURINE NUCLEOSIDE PHOSPHORYLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Calf spleen purine nucleoside phosphorylase complexed with substrates and substrate analogues.

Mao, C.Cook, W.J.Zhou, M.Federov, A.A.Almo, S.C.Ealick, S.E.

(1998) Biochemistry 37: 7135-7146

  • DOI: 10.1021/bi9723919
  • Primary Citation of Related Structures:  1A9O, 1A9P, 1A9Q, 1A9R, 1A9S, 1A9T
  • Also Cited By: 2AI1, 2AI2, 2AI3

  • PubMed Abstract: 
  • Purine nucleoside phosphorylase (PNP) is a key enzyme in the purine salvage pathway, which provides an alternative to the de novo pathway for the biosynthesis of purine nucleotides. PNP catalyzes the reversible phosphorolysis of 2'-deoxypurine ribonu ...

    Purine nucleoside phosphorylase (PNP) is a key enzyme in the purine salvage pathway, which provides an alternative to the de novo pathway for the biosynthesis of purine nucleotides. PNP catalyzes the reversible phosphorolysis of 2'-deoxypurine ribonucleosides to the free bases and 2-deoxyribose 1-phosphate. Absence of PNP activity in humans is associated with specific T-cell immune suppression. Its key role in these two processes has made PNP an important drug design target. We have investigated the structural details of the PNP-catalyzed reaction by determining the structures of bovine PNP complexes with various substrates and substrate analogues. The preparation of phosphate-free crystals of PNP has allowed us to analyze several novel complexes, including the ternary complex of PNP, purine base, and ribose 1-phosphate and of the completely unbound PNP. These results provide an atomic view for the catalytic mechanism for PNP proposed by M. D. Erion et al. [(1997) Biochemistry 36, 11735-11748], in which an oxocarbenium intermediate is stabilized by phosphate and the negative charge on the purine base is stabilized by active site residues. The bovine PNP structure reveals several new details of substrate and inhibitor binding, including two phosphate-induced conformational changes involving residues 33-36 and 56-69 and a previously undetected role for His64 in phosphate binding. In addition, a well-ordered water molecule is found in the PNP active site when purine base or nucleoside is also present. In contrast to human PNP, only one phosphate binding site was observed. Although binary complexes were observed for nucleoside, purine base, or phosphate, ribose 1-phosphate binding occurs only in the presence of purine base.


    Organizational Affiliation

    Section of Biochemistry, Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PURINE NUCLEOSIDE PHOSPHORYLASE
A
289Bos taurusGene Names: PNP (NP)
EC: 2.4.2.1
Find proteins for P55859 (Bos taurus)
Go to Gene View: PNP
Go to UniProtKB:  P55859
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.200 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 94.200α = 90.00
b = 94.200β = 90.00
c = 94.200γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
SDMSdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1995-07-10 
  • Released Date: 1995-11-14 
  • Deposition Author(s): Mao, C., Ealick, S.E.

Revision History 

  • Version 1.0: 1995-11-14
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance