Abstract
The nuclear METTL3-METTL14 transfers a methyl group from SAM to convert the N6 of adenosine (A) in RNA to m6A and in ssDNA to 6mA. m6A marks are prevalent in eukaryotic mRNAs and lncRNAs and modulate their stability and fate in a context-dependent manner. The cytoplasmic METTL3 can act as a m6A reader. However, the precise mechanism during m6A writing, reading, or sensing is unclear. Here, we present a ~2.5 Å structure of the methyltransferase core of human METTL3-METTL14 in complex with the reaction product mimic, N6-methyladenosine monophosphate (m6A), representing a state post-catalysis but before the release of m6A. m6A occupies an evolutionarily conserved RNA-binding pocket ~16 Å away from the SAM pocket that also frequently mutates in cancer. We propose a two-step model of swiveling of target A upon conversion to m6A and sensing its methylation status by this pocket, enabling it to actuate enzymes’ switch from writer to an m6A-sensor. Cancer-associated mutations show impaired RNA binding dynamics, de-stacking, and defective m6A writing and sensing.