8I2J

E. coli tryptophanyl-tRNA synthetase bound with a chemical fragment at the dimerization interface

Summary for 8I2J

• Entry DOI: 10.2210/pdb8i2j/pdb
• Descriptor: Tryptophan--tRNA ligase, 1-(4-methoxyphenyl)ethanone, TRYPTOPHANYL-5'AMP, ... (5 entities in total)
• Functional Keywords: tryptophanyl-trna synthetase, dimer interface, fragment screening, antibacterials, ligase
• Biological source: Escherichia coli K-12
• Total number of polymer chains: 2
• Total formula weight: 77527.14

Authors

Xiang, M.,Zhou, H. (deposition date: 2023-01-14, release date: 2023-04-12, Last modification date: 2024-05-29)

Primary citation

Xiang, M.,Xia, K.,Chen, B.,Luo, Z.,Yu, Y.,Jiang, L.,Zhou, H.
An asymmetric structure of bacterial TrpRS supports the half-of-the-sites catalytic mechanism and facilitates antimicrobial screening.
Nucleic Acids Res., 51:4637-4649, 2023

PubMed Abstract: Tryptophanyl-tRNA synthetase (TrpRS) links tryptophan to tRNATrp, thereby playing an indispensable role in protein translation. Unlike most class I aminoacyl-tRNA synthetases (AARSs), TrpRS functions as a homodimer. Herein, we captured an 'open-closed' asymmetric structure of Escherichia coli TrpRS (EcTrpRS) with one active site occupied by a copurified intermediate product and the other remaining empty, providing structural evidence for the long-discussed half-of-the-sites reactivity of bacterial TrpRS. In contrast to its human counterpart, bacterial TrpRS may rely on this asymmetric conformation to functionally bind with substrate tRNA. As this asymmetric conformation is probably a dominant form of TrpRS purified from bacterial cells, we performed fragment screening against asymmetric EcTrpRS to support antibacterial discovery. Nineteen fragment hits were identified, and 8 of them were successfully cocrystallized with EcTrpRS. While a fragment named niraparib bound to the L-Trp binding site of the 'open' subunit, the other 7 fragments all bound to an unprecedented pocket at the interface between two TrpRS subunits. Binding of these fragments relies on residues specific to bacterial TrpRS, avoiding undesired interactions with human TrpRS. These findings improve our understanding of the catalytic mechanism of this important enzyme and will also facilitate the discovery of bacterial TrpRS inhibitors with therapeutic potential.

PubMed: 37070195
DOI: 10.1093/nar/gkad278

Experimental method

X-RAY DIFFRACTION (2.65 Å)