Homologs of the chromatin-bound yeast silent information regulator 2 (SIR2) protein are found in organisms from all biological kingdoms. SIR2 itself was originally discovered to influence mating-type control in haploid cells by locus-specific transcriptional silencing. Since then, SIR2 and its homologs have been suggested to play additional roles in suppression of recombination, chromosomal stability, metabolic regulation, meiosis, and aging. Considering the far-ranging nature of these functions, a major experimental goal has been to understand the molecular mechanism(s) by which this family of proteins acts. We report here that members of the SIR2 family catalyze an NAD-nicotinamide exchange reaction that requires the presence of acetylated lysines such as those found in the N termini of histones. Significantly, these enzymes also catalyze histone deacetylation in a reaction that absolutely requires NAD, thereby distinguishing them from previously characterized deacetylases. The enzymes are active on histone substrates that have been acetylated by both chromatin assemblylinked and transcription-related acetyltransferases. Contrary to a recent report, we find no evidence that these proteins ADPribosylate histones. Discovery of an intrinsic deacetylation activity for the conserved SIR2 family provides a mechanism for modifying histones and other proteins to regulate transcription and diverse biological processes.Y east silent information regulator 2 (SIR2) protein functions in transcriptional silencing of the silent mating loci, telomeres, and rDNA (1-3). It is found in a chromatin-bound complex with SIR3 and SIR4 at the silent mating loci and telomeres, and in a different complex at rDNA (4-6). Four additional SIR2 homologs exist in yeast (HST1-4), and related proteins are found from archaeabacteria to eubacteria to mammals (7). Until recently, very little was known about the in vivo activity of this family of proteins. An important breakthrough came with the identification of the Salmonella typhimurium CobB protein as a SIR2 homolog (8). CobB can partially fulfill the requirement for CobT in vitamin B 12 synthesis. Because CobT protein was known to transfer ribose 5Ј-phosphate from nicotinic acid mononucleotide to a precursor of vitamin B 12 , it prompted tests of Sir2-like proteins for phosphoribosyltransferase activity. Indeed, Frye (9) found that Escherichia coli CobB had NAD-dependent ADP-ribosyltransferase activity. He also reported that both CobB and a human SIR2-like protein could transfer radioactivity from [ 32 P]NAD to albumin. Very recently, another group (10) reported that yeast SIR2 can ADP-ribosylate itself as well as histones and albumin.Here we show that members of the SIR2 family of enzymes catalyze an NAD-nicotinamide exchange reaction that requires the presence of acetylated lysines such as are found in the N termini of histones. Furthermore, these enzymes also catalyze histone deacetylation in a reaction that absolutely depends on NAD, thereby distinguishing them from previously known deacet...

The SIR2 protein family comprises a novel class of nicotinamide-adenine dinucleotide (NAD)-dependent protein deacetylases that function in transcriptional silencing, DNA repair, and life-span extension in Saccharomyces cerevisiae. Two crystal structures of a SIR2 homolog from Archaeoglobus fulgidus complexed with NAD have been determined at 2.1 A and 2.4 A resolutions. The structures reveal that the protein consists of a large domain having a Rossmann fold and a small domain containing a three-stranded zinc ribbon motif. NAD is bound in a pocket between the two domains. A distinct mode of NAD binding and an unusual configuration of the zinc ribbon motif are observed. The structures also provide important insights into the catalytic mechanism of NAD-dependent protein deacetylation by this family of enzymes.

Uncovering the true enzymatic function of SIR2 is critical to the basic understanding of its cellular function. Therefore, we set out to authenticate the reaction products and to determine the intrinsic catalytic mechanism. We provide direct evidence that the efficient histone͞protein deacetylase reaction is tightly coupled to the formation of a previously unidentified acetyl-ADP-ribose product (1-O-acetyl-ADP ribose). One molecule of NAD ؉ and one molecule of acetyl-lysine are readily catalyzed to one molecule of deacetylated lysine, nicotinamide, and 1-O-acetyl-ADP-ribose. A unique reaction mechanism involving the attack of enzyme-bound acetate or the direct attack of acetyl-lysine on an oxocarbenium ADP-ribose intermediate is proposed. We suggest that the reported histone͞protein ADPribosyltransferase activity is a low-efficiency side reaction that can be explained through the partial uncoupling of the intrinsic deacetylation and acetate transfer to ADP-ribose.