Structural basis of tRNA recognition by the m³C-RNA-methyltransferase METTL6 in complex with SerRS seryl-tRNA synthetase

Abstract

SummaryMethylation of cytosine 32 in the anticodon loop of tRNAs to 3-methylcytosine (m3C) is crucial for cellular translation fidelity1. Misregulation of the RNA methyltransferases setting this modification can cause aggressive cancers and metabolic disturbances2,3. However, our understanding of the substrate selection and catalysis mode of the m3C RNA methyltransferases is currently still lacking. Here, we report the cryo-electron microscopy structure of the m3C tRNA methyltransferase METTL6 in complex with seryl-tRNA synthetase (SerRS) and their common substrate tRNASer. Through the complex structure, we identify the tRNA binding domain of METTL6. We show that SerRS acts as the tRNASersubstrate selection factor for METTL6. We reveal how METTL6 and SerRS jointly coordinate the long variable arm of tRNASerin their interface. We demonstrate that SerRS augments the methylation activity of METTL6 and that direct contacts between METTL6 and SerRS are necessary for efficient tRNASermethylation. Finally, based on the structure of METTL6 in complex with SerRS and tRNASer, we postulate a universal tRNA binding mode for m3C RNA methyltransferases including METTL2 and METTL8, suggesting that these mammalian paralogues use similar ways to engage their respective tRNA substrates and co-factors.

Nucleotidyltransferase toxin MenT targets and extends the aminoacyl acceptor ends of serine tRNAs in vivo to control Mycobacterium tuberculosis growth

“…This work also revealed the importance of the long variable loop characteristic of tRNA Ser for MenT3 activity (Throll et al , 2023). Noticeably, this region was shown to be important for binding to the Seryl-tRNA synthetase (SerRS) both in E. coli and in humans (Throll et al , 2023; Lenhard et al , 1999), suggesting that it could also contribute to the specific binding of MenT3.…”