Structures and mechanisms of tRNA methylation by METTL1–WDR4

Victor M. Ruiz-Arroyo, Rishi Raj, Kesavan Babu, Otgonbileg Onolbaatar, Paul H. Roberts and Yunsun Nam ()
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Victor M. Ruiz-Arroyo: University of Texas Southwestern Medical Center
Rishi Raj: University of Texas Southwestern Medical Center
Kesavan Babu: University of Texas Southwestern Medical Center
Otgonbileg Onolbaatar: University of Texas Southwestern Medical Center
Paul H. Roberts: University of Texas Southwestern Medical Center
Yunsun Nam: University of Texas Southwestern Medical Center

Nature, 2023, vol. 613, issue 7943, 383-390

Abstract: Abstract Specific, regulated modification of RNAs is important for proper gene expression1,2. tRNAs are rich with various chemical modifications that affect their stability and function3,4. 7-Methylguanosine (m7G) at tRNA position 46 is a conserved modification that modulates steady-state tRNA levels to affect cell growth5,6. The METTL1–WDR4 complex generates m7G46 in humans, and dysregulation of METTL1–WDR4 has been linked to brain malformation and multiple cancers7–22. Here we show how METTL1 and WDR4 cooperate to recognize RNA substrates and catalyse methylation. A crystal structure of METTL1–WDR4 and cryo-electron microscopy structures of METTL1–WDR4–tRNA show that the composite protein surface recognizes the tRNA elbow through shape complementarity. The cryo-electron microscopy structures of METTL1–WDR4–tRNA with S-adenosylmethionine or S-adenosylhomocysteine along with METTL1 crystal structures provide additional insights into the catalytic mechanism by revealing the active site in multiple states. The METTL1 N terminus couples cofactor binding with conformational changes in the tRNA, the catalytic loop and the WDR4 C terminus, acting as the switch to activate m7G methylation. Thus, our structural models explain how post-translational modifications of the METTL1 N terminus can regulate methylation. Together, our work elucidates the core and regulatory mechanisms underlying m7G modification by METTL1, providing the framework to understand its contribution to biology and disease.

Date: 2023
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DOI: 10.1038/s41586-022-05565-5

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