7EV2

Crystal structure of Mycobacterium tuberculosis tryptophanyl-tRNA synthetase complexed with Y-11 and ATP

7EV2 の概要

• エントリーDOI: 10.2210/pdb7ev2/pdb
• 関連するPDBエントリー: 7EL8 7ELT 7ENS 7ENT
• 分子名称: Tryptophan--tRNA ligase, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... (5 entities in total)
• 機能のキーワード: trprs, aminoacylation, trna-binding, aminoacyl-trna synthetase, atp-binding, ligase
• 由来する生物種: Mycobacterium tuberculosis
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 38204.21

構造登録者

Xu, M.,Chen, S. (登録日: 2021-05-20, 公開日: 2022-02-16, 最終更新日: 2023-11-29)

主引用文献

Yang, Y.,Xu, Y.,Yue, Y.,Wang, H.,Cui, Y.,Pan, M.,Zhang, X.,Zhang, L.,Li, H.,Xu, M.,Tang, Y.,Chen, S.
Investigate Natural Product Indolmycin and the Synthetically Improved Analogue Toward Antimycobacterial Agents.
Acs Chem.Biol., 17:39-53, 2022

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 (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 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.

PubMed: 34908399
DOI: 10.1021/acschembio.1c00394

実験手法

X-RAY DIFFRACTION (2.1 Å)