Crystal structure of the P.falciparum cytosolic leucyl-tRNA synthetase editing domain (space group P1)

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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This is version 1.2 of the entry. See complete history


Anti-Malarial Benzoxaboroles Target P. Falciparum Leucyl-tRNA Synthetase.

Sonoiki, E.Palencia, A.Guo, D.Ahyong, V.Dong, C.Li, X.Hernandez, V.S.Zhang, Y.K.Choi, W.Gut, J.Legac, J.Cooper, R.Alley, M.R.Freund, Y.R.Derisi, J.Cusack, S.Rosenthal, P.J.

(2016) Antimicrob Agents Chemother 60: 4886

  • DOI: https://doi.org/10.1128/AAC.00820-16
  • Primary Citation of Related Structures:  
    5FO4, 5FOC, 5FOD, 5FOF

  • PubMed Abstract: 

    There is a need for new antimalarials, ideally with novel mechanisms of action. Benzoxaboroles have been shown to be active against bacteria, fungi, and trypanosomes. Therefore, we investigated the antimalarial activity and mechanism of action of 3-aminomethyl benzoxaboroles against Plasmodium falciparum Two 3-aminomethyl compounds, AN6426 and AN8432, demonstrated good potency against cultured multidrug-resistant (W2 strain) P. falciparum (50% inhibitory concentration [IC50] of 310 nM and 490 nM, respectively) and efficacy against murine Plasmodium berghei infection when administered orally once daily for 4 days (90% effective dose [ED90], 7.4 and 16.2 mg/kg of body weight, respectively). To characterize mechanisms of action, we selected parasites with decreased drug sensitivity by culturing with stepwise increases in concentration of AN6426. Resistant clones were characterized by whole-genome sequencing. Three generations of resistant parasites had polymorphisms in the predicted editing domain of the gene encoding a P. falciparum leucyl-tRNA synthetase (LeuRS; PF3D7_0622800) and in another gene (PF3D7_1218100), which encodes a protein of unknown function. Solution of the structure of the P. falciparum LeuRS editing domain suggested key roles for mutated residues in LeuRS editing. Short incubations with AN6426 and AN8432, unlike artemisinin, caused dose-dependent inhibition of [(14)C]leucine incorporation by cultured wild-type, but not resistant, parasites. The growth of resistant, but not wild-type, parasites was impaired in the presence of the unnatural amino acid norvaline, consistent with a loss of LeuRS editing activity in resistant parasites. In summary, the benzoxaboroles AN6426 and AN8432 offer effective antimalarial activity and act, at least in part, against a novel target, the editing domain of P. falciparum LeuRS.

  • Organizational Affiliation

    Department of Medicine, University of California, San Francisco, California, USA Division of Infectious Diseases and Immunology, School of Public Health, University of California, Berkeley, California, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
374Plasmodium falciparumMutation(s): 2 
Gene Names: PFF1095W
Find proteins for C6KT64 (Plasmodium falciparum (isolate 3D7))
Explore C6KT64 
Go to UniProtKB:  C6KT64
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6KT64
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.7α = 88.9
b = 53.4β = 74.3
c = 63γ = 89.7
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Other, Refinement description