Structure of the p300 Histone Acetyltransferase Bound to Acetyl-Coenzyme A and Its Analogues

Abstract

The p300 and CBP transcriptional coactivator paralogs (p300/CBP) regulate a variety of different cellular pathways, in part, by acetylating histones and more than 70 non-histone protein substrates. Mutation, chromosomal translocation, or other aberrant activities of p300/CBP are linked to many different diseases, including cancer. Because of its pleiotropic biological roles and connection to disease, it is important to understand the mechanism of acetyl transfer by p300/CBP, in part so that inhibitors can be more rationally developed. Toward this goal, a structure of p300 bound to a Lys-CoA bisubstrate HAT inhibitor has been previously elucidated, and the enzyme’s catalytic mechanism has been investigated. Nonetheless, many questions underlying p300/CBP structure and mechanism remain. Here, we report a structural characterization of different reaction states in the p300 activity cycle. We present the structures of p300 in complex with an acetyl-CoA substrate, a CoA product, and an acetonyl-CoA inhibitor. A comparison of these structures with the previously reported p300/Lys-CoA complex demonstrates that the conformation of the enzyme active site depends on the interaction of the enzyme with the cofactor, and is not apparently influenced by protein substrate lysine binding. The p300/CoA crystals also contain two poly(ethylene glycol) moieties bound proximal to the cofactor binding site, implicating the path of protein substrate association. The structure of the p300/acetonyl-CoA complex explains the inhibitory and tight binding properties of the acetonyl-CoA toward p300. Together, these studies provide new insights into the molecular basis of acetylation by p300 and have implications for the rational development of new small molecule p300 inhibitors.

Tissue-specific sequence and structural environments of lysine acetylation sites

“…2A), as reported before (Choudhary et al, 2009;Hou et al, 2014;Lundby et al, 2012b;Suo et al, 2013Suo et al, , 2012. In accordance with the previous studies (Maksimoska et al, 2014) we also find that glycine is strongly enriched at position À1, while non-polar and hydrophobic isoleucine (I), valine (V) and leucine (L) residues are preferred at positions +1 and +2. Negatively charged residues frequently occur at positions from À3 to +3, while the wider sequence context of LASs exhibits a strong preference to positively charged residues.…”

Structure of p300 in complex with acyl-CoA variants

“…2c–e) and of lysyl-CoA and acetyl-CoA reported previously (Fig. 2f,g)38–40. Previous structures containing the lysyl-CoA bisubstrate inhibitor show that the substrate lysine invades the active site through a hydrophobic tunnel comprised of Tyr1397, Trp1436, Tyr1446 and Cys1438 that interact with the aliphatic portion of the lysine side chain (Fig.…”

“…The structures obtained with the lysyl-CoA bisubstrate inhibitor mimic a post-reaction CoA-lysine intermediate, while the structures of the isolated HAT domain in complex with acetyl-CoA and CoA represent pre- and post-reaction conformations, respectively38–40. We were able to crystallize p300_coreΔ in the absence of extraneously added acyl-CoA ligand.…”

Nutrigenomics, the Microbiome, and Gene-Environment Interactions: New Directions in Cardiovascular Disease Research, Prevention, and Treatment

“…[132][133][134] In addition, acetylCoA, a byproduct of fatty acid metabolism, acts as a cofactor for histone acetylation carried out by members of the histone acetyltransferase gene family. 135,136 High-fat diet-induced obesity in mice leads to distinct changes in promoter methylation, potentially linked to the downstream health consequences associated with obesity. 137 Similarly, research in nonhuman primates has highlighted a link between diet-induced obesity and epigenetic changes.…”