Leucine-sensing mechanism of leucyl-tRNA synthetase 1 for mTORC1 activation

Highlights

• Leucine binding induces conformational change of LARS1 for RagD binding

• ATP increases leucine binding to LARS1 for enhanced RagD binding

• Leucine-controlled R-lever triggers long-range conformational change of LARS1

• LARS1 cycles between “sensing on (leucine+)” and “sensing off (leucine−)” states.

Summary

Leucyl-tRNA synthetase 1 (LARS1) mediates activation of leucine-dependent mechanistic target of rapamycin complex 1 (mTORC1) as well as ligation of leucine to its cognate tRNAs, yet its mechanism of leucine sensing is poorly understood. Here we describe leucine binding-induced conformational changes of LARS1. We determine different crystal structures of LARS1 complexed with leucine, ATP, and a reaction intermediate analog, leucyl-sulfamoyl-adenylate (Leu-AMS), and find two distinct functional states of LARS1 for mTORC1 activation. Upon leucine binding to the synthetic site, H251 and R517 in the connective polypeptide and ⁵⁰FPYPY⁵⁴ in the catalytic domain change the hydrogen bond network, leading to conformational change in the C-terminal domain, correlating with RagD association. Leucine binding to LARS1 is increased in the presence of ATP, further augmenting leucine-dependent interaction of LARS1 and RagD. Thus, this work unveils the structural basis for leucine-dependent long-range communication between the catalytic and RagD-binding domains of LARS1 for mTORC1 activation.