5HGQ

Loa loa Lysyl-tRNA synthetase in complex with Cladosporin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Protein Translation Enzyme lysyl-tRNA Synthetase Presents a New Target for Drug Development against Causative Agents of Loiasis and Schistosomiasis

Sharma, A.Sharma, M.Yogavel, M.Sharma, A.

(2016) PLoS Negl Trop Dis 10: e0005084-e0005084

  • DOI: https://doi.org/10.1371/journal.pntd.0005084
  • Primary Citation of Related Structures:  
    5HGQ

  • PubMed Abstract: 

    Helminth parasites are an assemblage of two major phyla of nematodes (also known as roundworms) and platyhelminths (also called flatworms). These parasites are a major human health burden, and infections caused by helminths are considered under neglected tropical diseases (NTDs). These infections are typified by limited clinical treatment options and threat of drug resistance. Aminoacyl-tRNA synthetases (aaRSs) are vital enzymes that decode genetic information and enable protein translation. The specific inhibition of pathogen aaRSs bores well for development of next generation anti-parasitics. Here, we have identified and annotated aaRSs and accessory proteins from Loa loa (nematode) and Schistosoma mansoni (flatworm) to provide a glimpse of these protein translation enzymes within these parasites. Using purified parasitic lysyl-tRNA synthetases (KRSs), we developed series of assays that address KRS enzymatic activity, oligomeric states, crystal structure and inhibition profiles. We show that L. loa and S. mansoni KRSs are potently inhibited by the fungal metabolite cladosporin. Our co-crystal structure of Loa loa KRS-cladosporin complex reveals key interacting residues and provides a platform for structure-based drug development. This work hence provides a new direction for both novel target discovery and inhibitor development against eukaryotic pathogens that include L. loa and S. mansoni.


  • Organizational Affiliation

    Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine--tRNA ligaseA,
B [auth D],
C [auth B],
D [auth C]
524Loa loaMutation(s): 0 
Gene Names: LOAG_03217
EC: 6.1.1.6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KRS
Query on KRS

Download Ideal Coordinates CCD File 
F [auth A],
I [auth D],
K [auth B],
M [auth C]
cladosporin
C16 H20 O5
WOMKDMUZNBFXKG-ZWKOPEQDSA-N
LYS
Query on LYS

Download Ideal Coordinates CCD File 
E [auth A],
H [auth D],
J [auth B],
L [auth C]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.165α = 90
b = 147.355β = 90
c = 160.944γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
India--

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description