Crystallographic and kinetic study of the catalytic mechanism of yeast Esa1, a MYST family histone acetyltransferase

Histone acetyltransferases (HATs) catalyze the transfer of an acetyl moiety from the acetyl-CoA cofactor to the ϵ-amino group of the target histone lysine residue to promote gene activation. Yeast Esa1 is a member of the MYST family of histone acetyltransferase proteins that includes the human MOZ oncoprotein and the HIV-1 Tat interacting protein Tip60. It is also the catalytic subunit of the NuA4 HAT complex that acetylates histone H4. Extensive deletion studies on Esa1 resulted in a minimal HAT domain containing residues 160–435. A high-resolution crystal structure of the Esa1 HAT domain bound to coenzyme-A substrate revealed a central core domain with structural similarity to the catalytic and substrate binding region of the GCN5/PCAF subfamily of HAT enzymes. Further structural and functional studies on Esa1 HAT domain demonstrated that histone lysine acetylation proceeds through an acetyl-cysteine-304 enzyme intermediate. Furthermore, we demonstrate that formation of this catalytic intermediate is mediated by glutamate-338. Both cysteine-304 and glutmate-338 are strictly conserved within the MYST members, suggesting a common mode of catalysis by members of this HAT subfamily. Surprisingly, this mode of catalysis differs dramatically from the GCN5/PCAF subfamily of HAT enzymes, which mediate direct nucleophilic attack of the acetyl-CoA cofactor by the enzyme-deprotonated histone lysine substrate. These results demonstrate that functionally and structurally similar HAT subfamilies can employ distinct catalytic mechanisms, and have implications for the distinct biological roles played by different HAT subfamilies and for the development of HAT-specific small molecule inhibitors