Catalysis and substrate selection by histone/protein lysine acetyltransferases

Abstract

Reversible protein acetylation is controlled by the opposing actions of protein lysine acetyltransferases and deacetylations. Recent developments on the structure and biochemical mechanisms of histone acetyltransferases (HATs) have provided new insight into catalysis and substrate selection. Diverse families of HATs appear to perform a conserved mechanism of acetyl transfer, where the lysine-containing substrate directly attacks enzyme-bound acetyl-CoA. The ability of HATs to form distinct multi-subunit complexes provides a means to regulate HAT activity by altering substrate specificity, targeting to specific loci, enhancing acetyltransferase activity, restricting access of non-target proteins, and coordinating the multiple enzyme activities of the complex. In the case of newly discovered Rtt109 HAT, association with distinct histone chaperones directs substrate selection between N-terminal lysines (H3K9, H3K23) and those (H3K56) within the histone fold domain. Moreover, the ability of some HATs to utilize longer chain acyl-CoA (i.e. propionyl-CoA) as alternative substrates suggests a potential direct link between the metabolic state of the cell and transcriptional regulation.

Figure 1. Representative structures of protein/histone lysine acetyltransferases from S. cerevisiae

X-ray crystal structures of Rtt109 bound to acetyl-CoA (purple, 3D35), Esa1 bound to CoA (green, 1FY7) and Gcn5 (yellow, 1YGH) [15,19,27•].

Figure 2. Propose kinetic and catalytic mechanism of acetyl transfer

Proposed sequential mechanism of acetylation for histone/protein acetyltransferases. After binding acetyl-CoA and peptide substrate to form a ternary complex, an active site glutamate (e.g. Glu338 from Esa1) deprotonates the ɛ-amine of substrate lysine. Lysine attacks the carbonyl carbon of the acetyl moiety of acetyl-CoA forming a tetrahedral intermediate, which then collapses to form CoA and acetylated product. The recent p300 structure did not reveal a putative base, although a backbone amide may assist in removing a proton from the ɛ-amine [26•].

Figure 3. Conceptual model for the interaction of histone acetyltransferase Rtt109 with histone chaperone Vps75

The structures of Vps75 and Rtt109 have been solved separately. The basic patches of Vps75 (shown in light blue) were manually aligned with the acidic patches of Rtt109 (shown in red) in MacPyMOL (DeLano Scientific LLC, San Francisco) [27•,29].