5XIL

Crystal Structure of Leishmania major Prolyl-tRNA Synthetase (LmPRS)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Targeting Prolyl-tRNA Synthetase to Accelerate Drug Discovery against Malaria, Leishmaniasis, Toxoplasmosis, Cryptosporidiosis, and Coccidiosis

Jain, V.Yogavel, M.Kikuchi, H.Oshima, Y.Hariguchi, N.Matsumoto, M.Goel, P.Touquet, B.Jumani, R.S.Tacchini-Cottier, F.Harlos, K.Huston, C.D.Hakimi, M.A.Sharma, A.

(2017) Structure 25: 1495-1505.e6

  • DOI: https://doi.org/10.1016/j.str.2017.07.015
  • Primary Citation of Related Structures:  
    5XIF, 5XIG, 5XIH, 5XII, 5XIJ, 5XIK, 5XIL, 5XIO, 5XIP, 5XIQ

  • PubMed Abstract: 

    Developing anti-parasitic lead compounds that act on key vulnerabilities are necessary for new anti-infectives. Malaria, leishmaniasis, toxoplasmosis, cryptosporidiosis and coccidiosis together kill >500,000 humans annually. Their causative parasites Plasmodium, Leishmania, Toxoplasma, Cryptosporidium and Eimeria display high conservation in many housekeeping genes, suggesting that these parasites can be attacked by targeting invariant essential proteins. Here, we describe selective and potent inhibition of prolyl-tRNA synthetases (PRSs) from the above parasites using a series of quinazolinone-scaffold compounds. Our PRS-drug co-crystal structures reveal remarkable active site plasticity that accommodates diversely substituted compounds, an enzymatic feature that can be leveraged for refining drug-like properties of quinazolinones on a per parasite basis. A compound we termed In-5 exhibited a unique double conformation, enhanced drug-like properties, and cleared malaria in mice. It thus represents a new lead for optimization. Collectively, our data offer insights into the structure-guided optimization of quinazolinone-based compounds for drug development against multiple human eukaryotic pathogens.


  • Organizational Affiliation

    Molecular Medicine - Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative prolyl-tRNA synthetase512Leishmania majorMutation(s): 0 
Gene Names: LMJF_18_1220
EC: 6.1.1.5 (PDB Primary Data), 6.1.1.7 (PDB Primary Data)
UniProt
Find proteins for Q4QDS0 (Leishmania major)
Explore Q4QDS0 
Go to UniProtKB:  Q4QDS0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4QDS0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.294α = 90
b = 98.861β = 90
c = 146.327γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata reduction
HKLdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description