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).