Rtt109 is a histone acetyltransferase (HAT) involved in promoting genomic stability, DNA repair, and transcriptional regulation. Rtt109 associates with the NAP1 family histone chaperone Vps75 and stimulates histone acetylation. Here we explore the mechanism of histone acetylation and report a detailed kinetic investigation of the Rtt109-Vps75 complex. Rtt109 and Vps75 form a stable complex with nanomolar binding affinity (K(d) = 10 +/- 2 nM). Steady-state kinetic analysis reveals evidence of a sequential kinetic mechanism whereby the Rtt109-Vps75 complex, AcCoA, and histone H3 substrates form a complex prior to chemical catalysis. Product inhibition studies demonstrate that CoA binds competitively with AcCoA, and equilibrium measurements reveal AcCoA or CoA binding is not stimulated in the presence of H3 substrate. Additionally, the Rtt109-Vps75 complex binds H3 substrates in the absence AcCoA. Pre-steady-state kinetic analysis suggests the chemical attack of substrate lysine on the bound AcCoA is the rate-limiting step of catalysis, while the pH profile of k(cat) reveals a critical ionization with a pK(a) of 8.5 that must be unprotonated for catalysis. Amino acid substitution at D287 and D288 did not substantially change the shape of the k(cat)-pH profile, suggesting these conserved residues do not function as base catalysts for histone acetylation. However, the D288N mutant revealed a dramatic 1000-fold decrease in k(cat)/K(m) for AcCoA, consistent with a role in AcCoA binding. Together, these data support a sequential mechanism in which AcCoA and H3 bind to the Rtt109-Vps75 complex without obligate order, followed by the direct attack of the unprotonated epsilon-amino group on AcCoA, transferring the acetyl group to H3 lysine residues.
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