Structural basis of N6-adenosine methylation by the METTL3–METTL14 complex

Abstract

Chemical modifications of RNA have essential roles in a vast range of cellular processes. N(6)-methyladenosine (m(6)A) is an abundant internal modification in messenger RNA and long non-coding RNA that can be dynamically added and removed by RNA methyltransferases (MTases) and demethylases, respectively. An MTase complex comprising methyltransferase-like 3 (METTL3) and methyltransferase-like 14 (METTL14) efficiently catalyses methyl group transfer. In contrast to the well-studied DNA MTase, the exact roles of these two RNA MTases in the complex remain to be elucidated. Here we report the crystal structures of the METTL3-METTL14 heterodimer with MTase domains in the ligand-free, S-adenosyl methionine (AdoMet)-bound and S-adenosyl homocysteine (AdoHcy)-bound states, with resolutions of 1.9, 1.71 and 1.61 Å, respectively. Both METTL3 and METTL14 adopt a class I MTase fold and they interact with each other via an extensive hydrogen bonding network, generating a positively charged groove. Notably, AdoMet was observed in only the METTL3 pocket and not in METTL14. Combined with biochemical analysis, these results suggest that in the m(6)A MTase complex, METTL3 primarily functions as the catalytic core, while METTL14 serves as an RNA-binding platform, reminiscent of the target recognition domain of DNA N(6)-adenine MTase. This structural information provides an important framework for the functional investigation of m(6)A.

m6A Facilitates eIF4F-Independent mRNA Translation

“…Given the inherent AdoMet binding pocket of METTL3 (Wang et al, 2016a; Wang et al, 2016b), we next examined whether METTL3 directly interacts with methylated mRNA. Using a synthesized 30 nt mRNA with or without a single m 6 A site at the consensus sequence, we conducted a gel-shifting assay.…”

The Major Protein Arginine Methyltransferase in Trypanosoma brucei Functions as an Enzyme-Prozyme Complex

“…The most striking parallel with the prozyme paradigm emerged from the work on the human RNA methyltransferase complex METTL3-METTL14. In this complex, METTL3 constitutes the catalytic core and binds AdoMet but requires allosteric activation and stabilization by METTL14 (48,49). Although METTL14 has been reported to exhibit weak in vitro methylation activity (50), the phylogenetic analysis suggests that the METTL14 catalytic core has lost its function (51).…”

RNA m6A modification and its function in diseases

“…In addition, purified METTL14 manifested methyltransferase activities [10,20], suggesting that METTL14 is a distinct m 6 A writer. However, recent independent crystallization studies [22][23][24] demonstrated that METTL3, not METT14, bound to SAM and catalyzed m 6 A formation. Based on crystal structure analysis of METTL3-METTL14 complex, METTL14 possessed a degenerated SAM-binding domain, which was not functional.…”