The ZN domain acts as a dynamic switch coordinating multiple-step aminoacylation in bacterial leucyl-tRNA synthetase

Abstract

Abstract Aminoacyl-tRNA synthetases (AARSs) safeguard translational fidelity by coordinating amino acid activation and tRNA charging within distinct catalytic and editing domains. In leucyl-tRNA synthetase (LeuRS), the small, centrally located zinc-binding domain (ZN domain) sits at the crossroads of these functional centres, yet its role has remained enigmatic. Here, we present crystal structures of the Escherichia coli LeuRS–tRNALeu complex that capture the ZN domain in a previously unobserved conformation, revealing the pre-activation state. By integrating structural data with kinetic analysis, we propose a model for the aminoacylation reaction in which the ZN domain functions as a dynamic molecular switch that coordinates the different catalytic steps of the reaction cycle. We show that the ZN domain first acts as a wedge to prime the synthetic active site while locking the 3′-end tRNALeu in the editing domain. It subsequently reorients to stabilize the tRNA acceptor stem for aminoacyl transfer, before releasing it for proofreading. These findings resolve the mechanism of long-range domain communication in LeuRS and identify a discrete, druggable intermediate for the design of next-generation antimicrobials.