Structural basis of regulated m7G tRNA modification by METTL1-WDR4

Chemical modifications of RNA have key roles in many biological processes(1-3). N-7-methylguanosine (m(7)G) is required for integrity and stability of a large subset of tRNAs(4-7). The methyltransferase 1-WD repeat-containing protein 4 (METTL1-WDR4) complex is the methyltransferase that modifies G46 in the variable loop of certain tRNAs, and its dysregulation drives tumorigenesis in numerous cancer types(8-14). Mutations in WDR4 cause human developmental phenotypes including microcephaly(15-17). How METTL1-WDR4 modifies tRNA substrates and is regulated remains elusive(18). Here we show, through structural, biochemical and cellular studies of human METTL1-WDR4, that WDR4 serves as a scaffold for METTL1 and the tRNA T-arm. Upon tRNA binding, the alpha C region of METTL1 transforms into a helix, which together with the alpha 6 helix secures both ends of the tRNA variable loop. Unexpectedly, we find that the predicted disordered N-terminal region of METTL1 is part of the catalytic pocket and essential for methyltransferase activity. Furthermore, we reveal that S27 phosphorylation in the METTL1 N-terminal region inhibits methyltransferase activity by locally disrupting the catalytic centre. Our results provide a molecular understanding of tRNA substrate recognition and phosphorylation-mediated regulation of METTL1-WDR4, and reveal the presumed disordered N-terminal region of METTL1 as a nexus of methyltransferase activity.