The Functions and Importance of CH···O Bonds in SET Domain Methyltransferases.

Abstract

Methylation is a ubiquitous reaction in biology, particularly with respect to metabolism, signal transduction, and gene regulation. This reaction is most often catalyzed through a convergently evolved SN2 mechanism that utilizes the cofactor S-adenosylmethionine (AdoMet). Despite its importance, little is known of the determinants of this conserved reaction. The following dissertation describes the discovery of one such determinant, unconventional CH•••O hydrogen bonds. A new methodology utilizing NMR spectroscopy is first developed to identify biological CH•••O hydrogen bonds, and applied to the AdoMet methyl group within the active site of model methyltransferase SET7/9. Using a structural survey, the universality of these interactions in the classes of AdoMet-dependent methyltransferases is then demonstrated. The functional importance of CH•••O hydrogen bonds hydrogen within the active site of a model methyltransferase are verified by structural, functional, and dynamic analyses of SET7/9, using a combination of x-ray crystallography, mutagenesis with natural and unnatural amino acids, quantum chemistry calculations, and NMR spin-relaxation experiments. The CH•••O hydrogen bonds are shown to aid in cofactor binding as well as catalysis by stabilizing both the reactant and transition states of methyl transfer, and optimizing the catalytic geometry of the AdoMet methyl group. Together, these studies elucidate a universal mechanism of AdoMet-dependent methyl transfer, providing a molecular framework for this integral biological reaction.