SNAP output for PDB entry 8d9l [SNAP web server]

PDB-id

8d9l; SNAP-derived features in text and JSON formats; DNAproDB

Class

transferase-RNA

Method

cryo-EM (4.04 Å)

Summary

Cryoem structure of human mettl1-wdr4 in complex with lys-trna and sam

Reference

Ruiz-Arroyo VM, Raj R, Babu K, Onolbaatar O, Roberts PH, Nam Y (2023): "Structures and mechanisms of tRNA methylation by METTL1-WDR4." Nature, 613, 383-390. doi: 10.1038/s41586-022-05565-5.

Abstract

Specific, regulated modification of RNAs is important for proper gene expression_1,2. tRNAs are rich with various chemical modifications that affect their stability and function_3,4. 7-Methylguanosine (m₇G) at tRNA position 46 is a conserved modification that modulates steady-state tRNA levels to affect cell growth_5,6. The METTL1-WDR4 complex generates m₇G46 in humans, and dysregulation of METTL1-WDR4 has been linked to brain malformation and multiple cancers_7-22. 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.