Catalytic Mechanism of a MYST Family Histone Acetyltransferase

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Abstract
Distinct catalytic mechanisms have been proposed for the Gcn5 and MYST histone acetyltransferase (HAT) families. Gcn5-like HATs utilize an ordered sequential mechanism involving direct nucleophilic attack of the N-ε-lysine on the enzyme-bound acetyl-CoA. Recently, MYST enzymes were reported to employ a ping-pong route of catalysis via an acetyl−cysteine intermediate. Here, using the prototypical MYST family member Esa1, and its physiological complex (piccolo NuA4), steady-state kinetic analyses revealed a kinetic mechanism that requires the formation of a ternary complex prior to catalysis, where acetyl-CoA binds first and CoA is the last product released. In the absence of histone acceptor, slow rates of enzyme auto-acetylation (7 × 10-4 s-1, or ∼2500-fold slower than histone acetylation; kcat = 1.6 s-1) and of CoA formation (0.0021 s-1) were inconsistent with a kinetically competent acetyl−enzyme intermediate. Previously, Cys-304 of Esa1 was the proposed nucleophile that forms an acetyl−cysteine intermediate. Here, mutation of this cysteine (C304A) in Esa1 or within the piccolo NuA4 complex yielded an enzyme that was catalytically indistinguishable from the wild type. Similarly, a pH rate (kcat) analysis of the wild type and C304A revealed an ionization (pKa = 7.6−7.8) that must be unprotonated. Mutation of a conserved active-site glutamate (E338Q) reduced kcat ∼200-fold at pH 7.5; however, at higher pH, E338Q exhibited nearly wild-type activity. These data are consistent with Glu-338 (general base) activating the N-ε-lysine by deprotonation. Together, the results suggest that MYST family HATs utilize a direct-attack mechanism within an Esa1·acetyl-CoA·histone ternary complex.