Sirtuins are NAD(+)-dependent protein deacetylases and are emerging as molecular targets for the development of pharmaceuticals to treat human metabolic and neurological diseases and cancer. To date, several sirtuin inhibitors and activators have been identified, but the structural mechanisms of how these compounds modulate sirtuin activity have not yet been determined. We identified suramin as a compound that binds to human SIRT5 and showed that it inhibits SIRT5 NAD(+)-dependent deacetylase activity with an IC(50) value of 22 microM. To provide insights into how sirtuin function is altered by inhibitors, we determined two crystal structures of SIRT5, one in complex with ADP-ribose, the other bound to suramin. Our structural studies provide a view of a synthetic inhibitory compound in a sirtuin active site revealing that suramin binds into the NAD(+), the product, and the substrate-binding site. Finally, our structures may enable the rational design of more potent inhibitors.

In Saccharomyces cerevisiae, the two cryptic mating type loci, HML and HMR, are transcriptionally silent. Previous studies on the establishment of silencing at HMR identified a requirement for passage through S phase. However, the underlying mechanism for this requirement is still unknown. In contrast to HMR, we found that substantial silencing of HML could be established without passage through S phase. To understand this difference, we analyzed several chimeric HM loci and found that promoter strength determined the S phase requirement. To silence a locus with a strong promoter such as the a1/a2 promoter required passage through S phase while HM loci with weaker promoters such as the a1/a2 or TRP1 promoter did not show this requirement. Thus, transcriptional activity counteracts the establishment of silencing but can be overcome by passage through S phase. E PIGENETIC silencing refers to a transcriptionally inactive state and its heritable transmission. It involves the formation, maintenance, and inheritance of a specialized, constitutively compact chromatin structure, termed heterochromatin. This kind of transcriptional silencing plays an important role in establishing and maintaining distinct patterns of gene expression in genetically identical cells during growth and differentiation. Examples of transcriptional silencing include the inactive mammalian X chromosome, position effect variegation in Drosophila melanogaster, and the cryptic mating-type loci in fission and budding yeasts (Rusche et al. 2003;Probst et al. 2009).In the budding yeast Saccharomyces cerevisiae, the MAT locus encodes transcriptional regulatory proteins that are responsible for the differences between the two mating types. HML and HMR harbor cryptic copies of the mating type information genes, a and a, respectively. Transcriptional silencing at these loci relies on cisregulatory DNA elements called silencers and on a number of trans -acting gene products. Previous studies revealed that establishment of silencing involves a series of protein-DNA and protein-protein interactions (reviewed in Gasser and Cockell 2001;Rusche et al. 2003;Fox and Mcconnell 2005). The silencer elements flanking the HM loci recruit the DNA binding proteins Rap1, Abf1, and ORC, which in turn recruit the silent information regulator (Sir) proteins, Sir1, Sir2, Sir3, and Sir4. A Sir2-Sir3-Sir4 complex spreads from the silencers into nearby nucleosomes (Hoppe et al. 2002;Rusche et al. 2002;Liou et al. 2005;Rudner et al. 2005). This spreading requires Sir2, which deacetylates histone H4 K16, thereby creating a binding site for Sir3 and Sir4 and hence the Sir2/3/4 complex (Carmen et al. 2002;Liou et al. 2005). Multiple rounds of deacetylation by Sir2 allow the Sir complex to spread to adjacent nucleosomes, thus creating a stretch of silent chromatin.To investigate the establishment of silencing and its relationship to the cell cycle, previous studies utilized conditional or inducible alleles of the Sir proteins to create a transition from Sir À to Sir 1 and th...

A screen for Saccharomyces cerevisiae temperature-sensitive silencing mutants identified a strain with a point mutation in the SIR2 gene. The mutation changed Ser276 to Cys. This amino acid is in the highly conserved NAD 1 binding pocket of the Sir2 family of proteins. Haploid strains of either mating type carrying the mutation were severely defective at mating at 37°but normal at 25°. Measurements of RNA from the HMR locus demonstrated that silencing was lost rapidly upon shifting the mutant from the low to the high temperature, but it took .8 hours to reestablish silencing after a shift back to 25°. Silencing at the rDNA locus was also temperature sensitive. On the other hand, telomeric silencing was totally defective at both temperatures. Enzymatic activity of the recombinant wild-type and mutant Sir2 protein was compared by three different assays. The mutant exhibited less deacetylase activity than the wild-type protein at both 37°and 25°. Interestingly, the mutant had much more NAD 1 -nicotinamide exchange activity than wild type, as did a mutation in the same region of the protein in the Sir2 homolog, Hst2. Thus, mutations in this region of the NAD 1 binding pocket of the protein are able to carry out cleavage of NAD 1 to nicotinamide but are defective at the subsequent deacetylation step of the reaction.