1. Enzymatic acetylation
Nɛ-acetylation (K-acetylation) refers to an addition of an acetyl group from a donor molecule, like acetyl coenzyme A, to an epsilon amino group of lysine side chains, the reaction produces an increase in the size of the side chain and neutralizes the positive charge. K-acetylation is a reversible process where the acetate is enzymatically added and removed by lysine acetyltransferases and lysine deacetylases (KDACs), respectively (Alonso & Serra 2012; Christensen et al., 2019).
KATs are grouped into three major families based on amino acid sequence homology and biochemical characteristics of catalysis: (i) Gcn5- related N-acetyltransferases (GNATs); (ii) the p300/CBP family; and (iii) MYST family. The MYST and p300/CBP families are presented only in eukaryotic cells, while the Gcn5-related N-acetyltransferase (GNAT) family, contains orthologous proteins among bacteria, eukaryotes, and archaea (Favrot et al., 2016; Finkel et al., 2009; Gu & Roeder, 1997; Lee & Workman, 2007; Vetting et al., 2005).
KATs families differ in sequence similarity, domain organization, substrate specificity, and catalytic mechanism. The GNAT family uses a sequential mechanism where the acetyl-CoA and the protein substrate bind to form a ternary complex in which active site glutamate acts as a general base to deprotonate the amino group of the lysine, allowing it a nucleophilic attack on the carbonyl carbon of the acetyl moiety of CoA (Liu et al., 2008) (Figure 1B). Members of the MYST family can either use this ternary complex mechanism or a ping-pong mechanism, where the acetyl group is covalently attached to the enzyme to form an acyl-enzyme intermediate before being transferred to the substrate (Yan et al., 2002). In contrast, the p300/CBP family does not use a catalytic base to initiate the transfers of the acyl moiety, the mechanism for this family is categorized as “hit and run” (Theorell–Chance), a sequential mechanism where the ternary complex formed is kinetically irrelevant for the catalysis. In this catalytic mechanism, a tyrosine in the active site residue acts as a catalytic acid to increase the nucleophilicity of the lysine side chain (Liu et al., 2008). The protein substrate-AcCoA association binds transiently to the enzyme surface, allowing the lysine residue to receive the acetyl group, followed by rapid protein dissociation (Zhang et al., 2014).