1VFN

PURINE NUCLEOSIDE PHOSPHORYLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Work: 0.180 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of calf spleen purine nucleoside phosphorylase in a complex with hypoxanthine at 2.15 A resolution.

Koellner, G.Luic, M.Shugar, D.Saenger, W.Bzowska, A.

(1997) J Mol Biol 265: 202-216

  • DOI: https://doi.org/10.1006/jmbi.1996.0730
  • Primary Citation of Related Structures:  
    1VFN

  • PubMed Abstract: 

    Trimeric calf spleen purine nucleoside phosphorylase has been complexed with hypoxanthine via phosphorolysis of inosine in the presence of phosphate. The resulting, "Michaelis" complex (three hypoxanthine molecules per trimer), presumed to be formed under these conditions, crystallized in the cubic space group P2(1)3, with unit cell dimension a = 94.11 A and one monomer in the asymmetric crystal unit; the biologically active trimer is located on the crystallographic 3-fold axis. High-resolution X-ray diffraction data were collected using synchrotron radiation (EMBL outstation, Hamburg, c/o DESY). The crystal structure has been determined by molecular replacement and refined at 2.15 A resolution to an R-value of 0.18. In the hypoxanthine binding site, a cis-peptide bond between Asn243 and Lys244 is observed. Side-chains of GIu201 and Asn243, as well as one integral water molecule located in the base binding site, form hydrogen bonds with the hypoxanthine N-1 H, N-7 H and O-6. A second water molecule links the base positions N-3 and N-9 with an adjacent pocket, which presumably is the phosphate-binding site. This pocket is filled completely by a cluster of six water molecules. Hence all possible donor/acceptor-positions of hypoxanthine are saturated by hydrogen-bonding to protein side-chains or integral water molecules. Purine nucleoside phosphorylase isolated form human tissues is a primary target for chemotherapeutic intervention, and the more stable calf enzyme has similar physico-chemical and kinetic properties, as well as response to inhibitors. Hence the high-resolution structure presented here may serve for design of inhibitors with potential pharmacological applications.


  • Organizational Affiliation

    Institut für Kristallographie Freie Universität Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PURINE-NUCLEOSIDE PHOSPHORYLASE281Bos taurusMutation(s): 0 
EC: 2.4.2.1
UniProt
Find proteins for P55859 (Bos taurus)
Explore P55859 
Go to UniProtKB:  P55859
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55859
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
HPA PDBBind:  1VFN Ki: 2500 (nM) from 1 assay(s)
BindingDB:  1VFN Kd: 680 (nM) from 1 assay(s)
ΔH: -1.28e+2 (kJ/mol) from 1 assay(s)
ΔG: -3.10e+1 (kJ/mol) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Work: 0.180 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.11α = 90
b = 94.11β = 90
c = 94.11γ = 90
Software Package:
Software NamePurpose
AMoREphasing
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-11-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-05-22
    Changes: Data collection