Molecular basis for the autoregulation of the protein acetyl transferase Rtt109

Abstract

Rtt109 is a protein acetyltransferase (PAT) that is responsible for the acetylation of lysine-56 of histone 3 (H3K56) in yeast. H3K56 acetylation has been implicated in the weakening of the interaction between the histone core and the surrounding DNA in the nucleosomal particle. Rtt109, in cooperation with various histone chaperones, promotes genomic stability and is required for resistance to DNA damaging agents. Here, we present the crystal structure of Rtt109 in complex with acetyl-CoA at a 2.0-Å resolution. Rtt109 consists of a core PAT domain, which binds the acetyl-CoA cofactor. A second domain, the activation domain, is tightly associated with the PAT domain. Autoacetylation of lysine-290 within the activation domain is required for stabilizing the interaction between the two domains and is essential for catalysis. Biochemical analysis demonstrates the requirement of a loop within the PAT domain for the binding of the histone chaperone Vps75, and mutational analysis identifies key residues for catalysis. We propose a model in which the autoacetylation of Rtt109 is crucial for the regulation of its catalytic activity.DNA repair ͉ histone ͉ structure E ukaryotic genomic DNA is organized into a compact structure called chromatin. Chromatin formation is mainly established by a set of proteins termed histones. Histones are small globular proteins that are positively charged with flexible, N-terminal tails Ϸ40 residues in length. An octamer of histones, namely a H3/H4 tetramer that assembles with two H2A/H2B dimers, interacts with 147 bp of helical DNA to form the fundamental unit of chromatin, the nucleosomal particle (1). Histones undergo a variety of posttranslational modifications that are either attached or removed by enzyme families of counteracting activity (2, 3). The majority of the modifications are concentrated on the flexible N-terminal tails, although residues within the histone fold have also been found to be modified (4).Recently, the functionally important acetylation of lysine-56 of histone H3 (Ac-H3K56), located within the folded histone core, has been described (5-9). Structural studies have revealed that H3K56 contributes to the formation of the stable quaternary structure of the nucleosome. The acetylation of H3K56 neutralizes the positive charge of lysine-56, disrupting the electrostatic interaction between the helical DNA of the nucleosomal complex, potentially resulting in a more flexible wrapping of DNA around the proteinaceous histone core (1). Acetylation of H3K56 is predominately seen on newly synthesized histones during the S phase of the meiotic or mitotic cell cycle (6, 9, 10). Yeast mutants that cannot acetylate H3K56 because of the expression of an unmodifiable histone H3 variant in which arginine replaces lysine-56 (H3-K56R) are sensitive to genotoxic compounds during the S phase of the cell cycle and display an accumulation of stalled replication forks (6, 9-11). Moreover, the acetylation of H3K56 has been associated with the repair of DNA lesions that occur during replication...

Catalytic activation of histone acetyltransferase Rtt109 by a histone chaperone

“…S2B). Though not observed in any solved structures to date, previous studies have implicated important binding regions within residues 130-179 of Rtt109 (16,36) and the α8 helix (residues 209-222) of Vps75 (28). Consistent with this idea, the Rtt109-Vps75 complex is stable to high salt and requires the use of strong hydrophobic chromatography to disrupt the native complex (29).…”

Autoacetylation regulates differentially the roles of ARD1 variants in tumorigenesis

“…A number of acetyltransferases are known to be self-activated by autoacetylation (17)(18)(19)(20). The present study provides data demonstrating that there is a conserved autoregulatory mechanism in ARD1 variants and shows how autoacetylation differentially regulates the enzymatic activities and biological functions of ARD1 variants, depending on the specific isoforms and physiological conditions.…”

“…Autoacetylation is an important mechanism to regulate the enzymatic activity and the biological functions of acetyltransferase (17)(18)(19)(20). Based on previous reports suggesting that ARD1 variants might have different biological functions , and GST-hARD1 235 were subjected to the in vitro acetylation assay for 30 and 60 min.…”

Histone acetyltransferase Rtt109 is required for Candida albicans pathogenesis

“…We identified C. albicans ORF19.7491 as the likely Rtt109 functional homolog through primary sequence homology. Also, the recent high-resolution structures of S. cerevisiae Rtt109 (25,35) highlight several catalytic domains that are well conserved between the two species (Fig. S1A).…”