Mutational Analysis of Conserved Residues in the GCN5 Family of Histone Acetyltransferases

Abstract

GCN5 is a critical transcriptional co-activator and is the defining member of a large superfamily of N-acetyltransferases. GCN5 catalyzes the transfer of an acetyl group from acetyl-CoA to the ⑀-amino of lysine 14 within the core H3 histone protein. Previous biochemical analyses have indicated a fully ordered kinetic mechanism. Recent structural studies have implicated several conserved residues in catalysis and substrate binding. Here the roles of Glu-173, His-145, and Asp-214 in yeast GCN5 have been evaluated using site-directed mutagenesis, steady state and pre-steady state kinetics, pH analysis, isotope partitioning, and equilibrium binding studies. The results with wild type and E173Q, H145A, and D214A mutants are consistent with chemical catalysis being rate-determining in turnover. All mutants exhibited K d values (3.5-8.5 M) for AcCoA that were similar to wild type enzyme, indicating no functional role for these residues in AcCoA binding. The E173Q mutant demonstrated a ϳ500 -600-fold decreases in k cat and k cat /K m , H3 , consistent with Glu-173 acting as the general base catalyst as proposed previously. No significant effect was observed on substrate binding steps. His-145 was identified as a residue in the peptide binding cleft that must be unprotonated (pK a ‫؍‬ 5.8) for peptide binding and likely hydrogen-bonds to the Ser-10 hydroxyl of histone H3. His-145 also contributes to lowering the pK a value (by 0.8 units) of general base Glu-173 through a water-mediated hydrogen bond to the carboxylate side chain. Analysis of D214A revealed an obligate protein isomerization step that occurs after AcCoA binding and permits efficient peptide binding. Asp-214 is part of a conformationally flexible loop that mediates the isomerization by stabilizing distinct conformers of the protein.Histone acetyltransferases (HATs) 1 are classified as enzymes capable of transferring an acetyl group from acetyl-CoA to an acceptor histone protein substrate. The acceptor site is the ⑀-amino group of lysine side chains within the aminoterminal tails of the core histones, H2A, H2B, H3, and H4. At least four gene families of HATs have been identified in mammals (1, 2). The largest family includes the defining member GCN5 whose catalytic domain is well conserved from yeast to humans. The GCN5 family of HATs are part of a larger superfamily of enzymes capable of acetyl transfer to amine-containing substrates (referred to as GNATs, for GCN5-like N-acetyltransferases). PCAF (p300/CBP-associating factor) (3-6) is also a member of the GCN5 family of HATs, displaying similar substrate specificity within the catalytic domain. In vitro, GCN5 displays a strong preference for Lys-14 of histone H3, although other acetylation sites on H3 and H4 have been observed (7-10). Yeast GCN5 has been known for some time to be essential for full transcriptional activation in a subset of genes (11-13). After the discovery of HAT activity in a related Tetrahymena enzyme (14), the causal link between histone acetylation and gene activation was codifying ...

Investigation of the Roles of Catalytic Residues in Serotonin N-Acetyltransferase

“…In contrast to the relatively modest importance ascribed to general base function in AANAT, another member of the GNAT family, GCN-5 (as well as its close relative PCAF), has been shown to have a critical glutamate serving as a general base (26), predicted to be functionally similar to AANAT His-120 based on sequence (and three-dimensional) alignment between GCN-5 and AANAT (27). Mutation of this GCN-5 Glu residue to Gln results in an ϳ1000-fold acetyltransferase rate drop (28).…”

The Molecular Basis of the Expansive Substrate Specificity of the Antibiotic Resistance Enzyme Aminoglycoside Acetyltransferase-6′-Aminoglycoside Phosphotransferase-2“

“…Shaded text indicates conserved hydrophobic regions, and asterisks indicate positions of residues suggested to play the role of an active site base in different family members. Glu-173 has been suggested to be the active site base in tGCN5 (30,31), and His-122 has been suggested to be the active site base in AANAT (29). The alignment is based on previous structurebased alignments (16,40).…”

“…In members of the GNAT superfamily, there are two amino acid positions that have been suggested to act as the active site base. In the histone acetyltransferase tGCN5, Glu-173 has been suggested to fulfill this role (30,31), whereas in AANAT, the active site base appears to be His-122 (29). The three-dimensional structure of AAC(6Ј)-APH(2Љ) has not been determined, so we used available sequence alignments (16,40) to generate a partial alignment of GNAT family members that could aid in identifying the putative active site base in AAC(6Ј)-Ie (Fig.…”

“…Structural and functional analyses of AANAT (25,26,29) and tGCN5 (24,30,31) have implicated His-122 and Glu-173, respectively, as the catalytic base in these enzymes, and mutation of Glu-173 to Gln results in an ϳ1000-fold decrease in GCN5 acetyltransferase activity (30,31). However, studies with AANAT have been less enlightening, as mutation of His-122 to Gln only results in a 6-fold decrease in activity (29).…”

Snf1p Regulates Gcn5p Transcriptional Activity by Antagonizing Spt3p

“…Kinetic and mutational studies identified residues essential for catalysis, acetyl coenzyme A binding, and histone substrate association Wang et al 1998;Tanner et al 1999;Langer et al 2001;Poux and Marmorstein 2003). The yeast Gcn5p is the catalytic subunit of several chromatographically distinct complexes including SAGA, ADA (Grant et al 1997), SALSA, and SLIK (Pray- Grant et al , 2005Sterner et al 2002a).…”