6AQS

Crystal structure of Plasmodium falciparum purine nucleoside phosphorylase (V181D) mutant complexed with DADMe-ImmG and phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Genetic resistance to purine nucleoside phosphorylase inhibition in

Ducati, R.G.Namanja-Magliano, H.A.Harijan, R.K.Fajardo, J.E.Fiser, A.Daily, J.P.Schramm, V.L.

(2018) Proc Natl Acad Sci U S A 115: 2114-2119

  • DOI: https://doi.org/10.1073/pnas.1525670115
  • Primary Citation of Related Structures:  
    6AQS, 6AQU

  • PubMed Abstract: 

    Plasmodium falciparum causes the most lethal form of human malaria and is a global health concern. The parasite responds to antimalarial therapies by developing drug resistance. The continuous development of new antimalarials with novel mechanisms of action is a priority for drug combination therapies. The use of transition-state analog inhibitors to block essential steps in purine salvage has been proposed as a new antimalarial approach. Mutations that reduce transition-state analog binding are also expected to reduce the essential catalytic function of the target. We have previously reported that inhibition of host and P. falciparum purine nucleoside phosphorylase ( Pf PNP) by DADMe-Immucillin-G (DADMe-ImmG) causes purine starvation and parasite death in vitro and in primate infection models. P. falciparum cultured under incremental DADMe-ImmG drug pressure initially exhibited increased Pf PNP gene copy number and protein expression. At increased drug pressure, additional Pf PNP gene copies appeared with point mutations at catalytic site residues involved in drug binding. Mutant Pf PNPs from resistant clones demonstrated reduced affinity for DADMe-ImmG, but also reduced catalytic efficiency. The catalytic defects were partially overcome by gene amplification in the region expressing Pf PNP. Crystal structures of native and mutated Pf PNPs demonstrate altered catalytic site contacts to DADMe-ImmG. Both point mutations and gene amplification are required to overcome purine starvation induced by DADMe-ImmG. Resistance developed slowly, over 136 generations (2 136 clonal selection). Transition-state analog inhibitors against Pf PNP are slow to induce resistance and may have promise in malaria therapy.


  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Purine nucleoside phosphorylase246Plasmodium falciparumMutation(s): 1 
Gene Names: PNP
EC: 2.4.2.1
UniProt
Find proteins for Q8I3X4 (Plasmodium falciparum (isolate 3D7))
Explore Q8I3X4 
Go to UniProtKB:  Q8I3X4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I3X4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
IM5 Binding MOAD:  6AQS Ki: 28 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.11α = 90
b = 95.11β = 90
c = 135.561γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-02-28
    Changes: Database references
  • Version 1.2: 2018-03-14
    Changes: Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description