Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with DADMe-ImmG and phosphate

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

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Catalytic Site Conformations in Human PNP by (19)F-NMR and Crystallography.

Suarez, J.Haapalainen, A.M.Cahill, S.M.Ho, M.C.Yan, F.Almo, S.C.Schramm, V.L.

(2013) Chem Biol 20: 212-222

  • DOI: https://doi.org/10.1016/j.chembiol.2013.01.009
  • Primary Citation of Related Structures:  
    4EAR, 4EB8, 4ECE, 4GKA

  • PubMed Abstract: 

    Purine nucleoside phosphorylase (PNP) is a target for leukemia, gout, and autoimmune disorders. Dynamic motion of catalytic site loops has been implicated in catalysis, but experimental evidence was lacking. We replaced catalytic site groups His257 or His64 with 6-fluoro-tryptophan (6FW) as site-specific NMR probes. Conformational adjustments in the 6FW-His257-helical and His64-6FW-loop regions were characterized in PNP phosphate-bound enzyme and in complexes with catalytic site ligands, including transition state analogs. Chemical shift and line-shape changes associated with these complexes revealed dynamic coexistence of several conformational states in these regions in phosphate-bound enzyme and altered or single conformations in other complexes. These conformations were also characterized by X-ray crystallography. Specific (19)F-Trp labels and X-ray crystallography provide multidimensional characterization of conformational states for free, catalytic, and inhibited complexes of human PNP.

  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Purine nucleoside phosphorylase
A, B, C
324Homo sapiensMutation(s): 5 
Gene Names: NPPNPX00737.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00491 (Homo sapiens)
Explore P00491 
Go to UniProtKB:  P00491
PHAROS:  P00491
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00491
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on FT6
A, B, C
Binding Affinity Annotations 
IDSourceBinding Affinity
IM5 BindingDB:  4EAR Ki: min: 0.16, max: 7 (nM) from 2 assay(s)
PDBBind:  4EAR Kd: 0.15 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.916α = 90
b = 131.1β = 90
c = 137.68γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-06
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Database references
  • Version 1.2: 2013-03-13
    Changes: Database references