Structural basis of ATP-dependent high-fidelity epigenome maintenance

Abstract

SUMMARYEpigenetic evolution occurs over million-year timescales in Cryptococcus neoformans and is mediated by DNMT5, the first maintenance-type cytosine methyltransferase identified in the fungal or protist kingdoms. DNMT5 requires ATP and displays exquisite hemimethyl-DNA specificity. To understand these novel properties, we solved cryo-EM structures of CnDNMT5 in three states. These studies reveal an elaborate allosteric cascade in which hemimethylated DNA first activates the SNF2 ATPase domain by a large rigid body rotation while the target cytosine partially flips out the DNA duplex. ATP binding then triggers a striking structural reconfiguration of the methyltransferase catalytic pocket that enables cofactor binding, completion of base-flipping, and catalysis. Unmethylated DNA binding fails to open cofactor pocket and subsequent ATP binding triggers its ejection to ensure fidelity. This chaperone-like, enzyme-remodeling role of the SNF2 domain illuminates how energy can be used to enable faithful epigenetic memory.HighlightsStructures of DNMT5 reveal mechanism of ATP-dependent DNA methylationHemimethylated CpG recognition triggers partial base flipping of the target cytosineHemimethylated DNA induces rigid body rotation to activate the SNF2 ATPase domainMTase catalytic pocket is remodeled by the SNF2 ATPase to achieve specificity