N6-methyladenosine binding induces a metal-centered rearrangement that activates the human RNA demethylase Alkbh5

Alkbh5 catalyzes demethylation of the N-6-methyladenosine (m(6)A), 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 alpha-ketoglutarate (alpha KG) and formation of a Fe4+= O species. This oxyferryl intermediate oxidizes the m(6)A 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 m(6)A to Alkbh5 induces a metal-centered rearrangement of alpha KG that increases the exposed area of the metal, making it available for binding O-2. 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.

Automated summary

Alkbh5 catalyzes demethylation of m(6)A, an epigenetic mark controlling physiological processes. Study shows m(6)A binding induces metal center rearrangement in Alkbh5, increasing oxygen binding capacity.