7EL8

Crystal structure of Mycobacterium tuberculosis tryptophanyl-tRNA synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Investigate Natural Product Indolmycin and the Synthetically Improved Analogue Toward Antimycobacterial Agents.

Yang, Y.Xu, Y.Yue, Y.Wang, H.Cui, Y.Pan, M.Zhang, X.Zhang, L.Li, H.Xu, M.Tang, Y.Chen, S.

(2022) ACS Chem Biol 17: 39-53

  • DOI: 10.1021/acschembio.1c00394
  • Primary Citation of Related Structures:  
    7EL8, 7ELT, 7ENS, 7ENT, 7EV2, 7EV3

  • PubMed Abstract: 
  • Indolmycin (IND) is a microbial natural product that selectively inhibits bacterial tryptophanyl-tRNA synthetase (TrpRS). The tryptophan biosynthesis pathway was recently shown to be an important target for developing new antibacterial agents against Mycobacterium tuberculosis (Mtb) ...

    Indolmycin (IND) is a microbial natural product that selectively inhibits bacterial tryptophanyl-tRNA synthetase (TrpRS). The tryptophan biosynthesis pathway was recently shown to be an important target for developing new antibacterial agents against Mycobacterium tuberculosis (Mtb). We investigated the antibacterial activity of IND against several mycobacterial model strains. A TrpRS biochemical assay was developed to analyze a library of synthetic IND analogues. The 4″-methylated IND compound, Y-13, showed improved anti-Mtb activity with a minimum inhibitory concentration (MIC) of 1.88 μM (∼0.5 μg/mL). The MIC increased significantly when overexpression of TrpRS was induced in the genetically engineered surrogate M. bovis BCG. The cocrystal structure of Mtb TrpRS complexed with IND and ATP has revealed that the amino acid pocket is in a state between the open form of apo protein and the closed complex with the reaction intermediate. In whole-cell-based experiments, we studied the combination effect of Y-13 paired with different antibacterial agents. We evaluated the killing kinetics, the frequency of resistance to INDs, and the mode of resistance of IND-resistant mycobacteria by genome sequencing. The synergistic interaction of Y-13 with the TrpE allosteric inhibitor, indole propionic acid, suggests that prospective IND analogues could shut down tryptophan biosynthesis and protein biosynthesis in pathogens, leading to a new class of antibiotics. Finally, we discuss a strategy to expand the genome mining of antibiotic-producing microbes specifically for antimycobacterial development.


    Organizational Affiliation

    Global Health Drug Discovery Institute, Haidian, Beijing 100192, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptophan--tRNA ligaseA344Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
EC: 6.1.1.2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.683α = 90
b = 61.683β = 90
c = 334.105γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-16
    Type: Initial release