Evidence for Carbon-Oxygen Hydrogen Bonding in Lysine Methyltransferase Set7/9 by NMR Chemical Shift

Abstract

SET domain methyltransferases are S-Adenosylmethionine (AdoMet)-dependent enzymes that catalyze the site-specific methylation of lysyl residues in histone and non-histone proteins in eukaryotes. Based on crystallographic and ligand binding studies, an unusual type of hydrogen bond, known as a carbon-oxygen (CH...O) hydrogen bond, has been proposed to coordinate the AdoMet methyl group in the active site of SET domain methyltransferases, aligning and activating it for transfer to the lysine e-amine group during catalysis. The fundamental question we address here: Is there spectroscopic evidence for CH...O hydrogen bonding between the AdoMet methyl group and the SET domain active site? To address this question, we used Nuclear Magnetic Resonance (NMR) spectroscopy and quantum mechanics calculations to examine whether the AdoMet methyl group is bound through CH...O hydrogen bonding in the human lysine methyltransferase SET7/9 via 1H chemical shift studies. Our results indicate that at least two of the three protons in the AdoMet methyl group engage in CH...O hydrogen bonding, suggesting a role for these interactions in the SN2 methyl transfer reaction. The methods described here are applicable to characterizing CH...O hydrogen bonding in other proteins as well as nucleic acids.