N ⁶ -methyladenosine binding induces a metal-centered rearrangement that activates the human RNA demethylase Alkbh5

Abstract

Alkbh5 catalyzes demethylation of the N6-methyladenosine (m6A), an epigenetic mark that controls several physiological processes including carcinogenesis and stem cell differentiation. The activity of Alkbh5 comprises two coupled reactions. The first reaction involves decarboxylation of α-ketoglutarate (αKG) and formation of a Fe4+═O species. This oxyferryl intermediate oxidizes the m6A to reestablish the canonical base. Despite coupling between the two reactions being required for the correct Alkbh5 functioning, the mechanisms linking dioxygen activation to m6A binding are not fully understood. Here, we use solution NMR to investigate the structure and dynamics of apo and holo Alkbh5. We show that binding of m6A to Alkbh5 induces a metal-centered rearrangement of αKG that increases the exposed area of the metal, making it available for binding O2. Our study reveals the molecular mechanisms underlying activation of Alkbh5, therefore opening new perspectives for the design of novel strategies to control gene expression and cancer progression.

Molecular Simulations Matching Denaturation Experiments for N6-Methyladenosine

“…Molecular dynamics (MD) simulations give access to structural dynamics at the atomistic resolution and are thus an ideal tool to complement NMR studies. The capability of classical force fields to predict the dynamics of difficult structural motifs is steadily increasing. − However, the number of applications of MD simulations to N6-methylated RNAs reported to date is still limited. ,− Force fields parameters for m 6 A developed by Aduri et al . were determined in a bottom-up fashion and are compatible with the AMBER force field, which is widely adopted for RNA simulations .…”

Solution NMR methods for structural and thermodynamic investigation of nanoparticle adsorption equilibria

“…Although CPMG RD has been one of the most popular methods to characterize protein conformational equilibria, [210][211][212][213][214][215][216] its standalone application to the characterization of ligand-NP systems has been quite limited. Recently, CPMG RD has been combined with DEST, DR 2 , and R 1 data to investigate sorption equilibria involving both protein and small molecule ligands.…”

Current Advances in N6-Methyladenosine Methylation Modification During Bladder Cancer

“…FTO catalyzes m6A demethylation and displays strict substrate selectivity near alternatively spliced exons and poly-A sites ( Lan et al, 2020 ; Jiang et al, 2021b ; He and He 2021 ). ALKBH5 functions with FTO to ensure balanced m6A modifications in the transcriptome ( Chen et al, 2021a ; Purslow et al, 2021 ; Wu et al, 2021 ). ALKBH3 was identified as another m6A demethylase with easier binding to tRNA m6A sites than mRNA or rRNA sites ( Esteve-Puig et al, 2021 ; Wollen et al, 2021 ).…”