9KY3

Crystal structure of E. coli tryptophanyl-tRNA synthetase complexed with 3-demethylchuangxinmycin and tryptophanyl-5'-AMP

This is a non-PDB format compatible entry.

Summary for 9KY3

• Entry DOI: 10.2210/pdb9ky3/pdb
• Related: 9KWW 9KXR
• Descriptor: Tryptophan--tRNA ligase, (6~{R})-7-thia-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(11),3,8(12),9-tetraene-6-carboxylic acid, SULFATE ION, ... (5 entities in total)
• Functional Keywords: tryptophanyl-trna synthetase, aminoacyl-trna synthetase, antibiotic, ligase
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 77572.13

Authors

Ren, Y.,Wang, S.,Liu, W.,Fang, P. (deposition date: 2024-12-07, release date: 2025-07-23)

Primary citation

Ren, Y.,Wang, S.,Liu, W.,Wang, J.,Fang, P.
Mechanistic insights into the ATP-mediated and species-dependent inhibition of TrpRS by chuangxinmycin.
Rsc Chem Biol, 6:1079-1088, 2025

PubMed Abstract: Chuangxinmycin (CXM) is a promising antimicrobial compound targeting bacterial tryptophanyl-tRNA synthetase (TrpRS), an essential enzyme in protein synthesis. The detailed inhibitory mechanism of CXM, particularly in clinically relevant pathogenic bacteria, is poorly understood. In this study, based on the determination of 10 crystal structures, including TrpRS (TrpRS) and TrpRS (TrpRS) in complex with CXM, ATP, tryptophan, or CXM derivatives, either individually or in combination, as well as the structure of apo-TrpRS, we provide key insights into the binding mode of CXM and its species-specific inhibitory mechanisms. Combined with molecular dynamics simulations and binding energy analysis, we demonstrate that CXM binds to TrpRS in a manner highly similar to the natural substrate tryptophan. Key residues, including D135 and Y128, play critical roles in CXM recognition and fixation, while conserved hydrophobic residues contribute significantly to binding free energy. This binding pattern is consistent with that observed in TrpRS (TrpRS). However, TrpRS exhibits distinct behavior due to structural differences, particularly the orientation of Y126 (corresponding to Y128 in TrpRS). This difference results in the selectivity of 3-methylchuangxinmycin (mCXM), a CXM derivative, against TrpRS. Furthermore, modeling CXM into the tryptophan-binding site of human cytoplasmic TrpRS (TrpRS) reveals the lack of key hydrogen bonds and a salt bridge interaction, which likely underlies CXM's significantly weaker inhibition of TrpRS. These findings deepen our understanding of the inhibitory mechanism of CXM and its selectivity toward bacterial TrpRSs, and thus can facilitate the design of next-generation antibiotics targeting bacterial TrpRSs.

PubMed: 40406164
DOI: 10.1039/d5cb00060b

Experimental method

X-RAY DIFFRACTION (2.25 Å)