5HGQ

Loa loa Lysyl-tRNA synthetase in complex with Cladosporin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.283 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1371/journal.pntd.0005084

  • 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 negle ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine--tRNA ligase
A, D, B, C
524N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
LYS
Query on LYS

Download SDF File 
Download CCD File 
A, B, C, D
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
KRS
Query on KRS

Download SDF File 
Download CCD File 
A, B, C, D
cladosporin
(3R)-3-[[(2R,6S)-6-methyloxan-2-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one
C16 H20 O5
WOMKDMUZNBFXKG-ZWKOPEQDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.283 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.254 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 120.165α = 90.00
b = 147.355β = 90.00
c = 160.944γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
India--

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2017-08-23
    Type: Database references, Derived calculations