3MB8

Crystal structure of purine nucleoside phosphorylase from toxoplasma gondii in complex with immucillin-H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

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This is version 1.4 of the entry. See complete history


Literature

Inhibition and Structure of Toxoplasma gondii Purine Nucleoside Phosphorylase.

Donaldson, T.M.Cassera, M.B.Ho, M.C.Zhan, C.Merino, E.F.Evans, G.B.Tyler, P.C.Almo, S.C.Schramm, V.L.Kim, K.

(2014) Eukaryot Cell 13: 572-579

  • DOI: 10.1128/EC.00308-13
  • Primary Citation of Related Structures:  
    3MB8

  • PubMed Abstract: 
  • The intracellular pathogen Toxoplasma gondii is a purine auxotroph that relies on purine salvage for proliferation. We have optimized T. gondii purine nucleoside phosphorylase (TgPNP) stability and crystallized TgPNP with phosphate and immucillin-H, a transition-state analogue that has high affinity for the enzyme ...

    The intracellular pathogen Toxoplasma gondii is a purine auxotroph that relies on purine salvage for proliferation. We have optimized T. gondii purine nucleoside phosphorylase (TgPNP) stability and crystallized TgPNP with phosphate and immucillin-H, a transition-state analogue that has high affinity for the enzyme. Immucillin-H bound to TgPNP with a dissociation constant of 370 pM, the highest affinity of 11 immucillins selected to probe the catalytic site. The specificity for transition-state analogues indicated an early dissociative transition state for TgPNP. Compared to Plasmodium falciparum PNP, large substituents surrounding the 5'-hydroxyl group of inhibitors demonstrate reduced capacity for TgPNP inhibition. Catalytic discrimination against large 5' groups is consistent with the inability of TgPNP to catalyze the phosphorolysis of 5'-methylthioinosine to hypoxanthine. In contrast to mammalian PNP, the 2'-hydroxyl group is crucial for inhibitor binding in the catalytic site of TgPNP. This first crystal structure of TgPNP describes the basis for discrimination against 5'-methylthioinosine and similarly 5'-hydroxy-substituted immucillins; structural differences reflect the unique adaptations of purine salvage pathways of Apicomplexa.


    Organizational Affiliation

    Department of Microbiology and Immunology, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Purine nucleoside phosphorylaseA, B279Toxoplasma gondiiMutation(s): 0 
Gene Names: PNP
EC: 2.4.2.1
UniProt
Find proteins for Q2HXR2 (Toxoplasma gondii)
Explore Q2HXR2 
Go to UniProtKB:  Q2HXR2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2HXR2
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.622α = 90
b = 159.622β = 90
c = 53.606γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-04-02
    Changes: Database references
  • Version 1.3: 2014-05-14
    Changes: Database references
  • Version 1.4: 2017-11-08
    Changes: Refinement description