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 

wwPDB Validation   3D Report Full Report


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
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Purine nucleoside phosphorylaseA, B279Toxoplasma gondiiMutation(s): 0 
Gene Names: PNP
EC: 2.4.2.1
Find proteins for Q2HXR2 (Toxoplasma gondii)
Explore Q2HXR2 
Go to UniProtKB:  Q2HXR2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMH
Query on IMH
Download Ideal Coordinates CCD File 
 C [auth A], G [auth B]1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL
C11 H14 N4 O4
IWKXDMQDITUYRK-KUBHLMPHSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
 D [auth A], H [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
 E [auth A], F [auth A], I [auth B], J [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
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

View Full Validation Report


View more in-depth experimental data

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