Sirtuins: Sir2-related NAD-dependent protein deacetylases

Abstract

Silent information regulator 2 (Sir2) proteins, or sirtuins, are protein deacetylases dependent on nicotine adenine dinucleotide (NAD) and are found in organisms ranging from bacteria to humans. In eukaryotes, sirtuins regulate transcriptional repression, recombination, the cell-division cycle, microtubule organization, and cellular responses to DNA-damaging agents. Sirtuins have also been implicated in regulating the molecular mechanisms of aging. The Sir2 catalytic domain, which is shared among all sirtuins, consists of two distinct domains that bind NAD and the acetyl-lysine substrate, respectively. In addition to the catalytic domain, eukaryotic sirtuins contain variable amino- and carboxy-terminal extensions that regulate their subcellular localizations and catalytic activity.

Figure 1

An unrooted tree diagram derived from phylogenetic analysis of the conserved domains of 60 sirtuin sequences from all sirtuin classes. Classes I, II, III, IV, and U and subdivisions of classes I and IV are indicated. Organism abbreviations: A. act, Actinobacillus actinomycetemcomitans; A. aeo, Aquifex aeolicus; A. ful, Archaeoglobus fulgidus; A. per, Aeropyrum pernix; A. tha, Arabidopsis thaliana; B. per, Bordetella pertussis; B. sub, Bacillus subtilis; C. ace, Clostridium acetabutylicum; C. alb, Candida albicans; C. dif, Clostridium difficile; C. ele, Caenorhabditis elegans; C. jej, Campylobacter jejuni; D. mel, Drosophila melanogaster; D. rad, Deinococcus radiodurans; E. col, Escherichia coli; E. fae, Enterococcus faecalis; H. sap, Homo sapiens; H. pyl, Helicobacter pylori; L. maj, Leishmania major; M. avi, Mycobacterium avium; M. tub, Mycobacterium tuberculosis; O. sat, Oryza sativa; P. aby, Pyrococcus abyssi; P. fal, Plasmodium falciparum; P. hor, Pyrococcus horikoshii; S. aur, Staphylococcus aureus; S. coe, Streptomyces coelicolor; S. pom, Schizosaccharomyces pombe, S. typ, Salmonella typhimurium; S. cer, Saccharomyces cerevisiae; T. bru, Trypanosoma brucei; T. mar, Thermotoga maritima; Y. pes, Yersinia pestis. Modified from [17].

Figure 2

Three-dimensional high-resolution crystal structures of four sirtuin proteins. The zinc-binding module is shown at the top left in each panel, the helical modules of the small domain are lighter and at the top right, and the large Rossmann-fold domain is in the lower half. Each α helix and β strand is labeled to facilitate comparisons. (a) Sir2-Af1 complexed with NAD (in stick representation; PDB accession number: 1ICI) [20]. (b) Sir2-Af2 complexed with acetylated p53 peptide (in stick notation, with acetyl-lysine darker). Two β strands (β10 and β11) are shown that might mediate the binding of the substrate peptide (PDB accession number: IMA3) [21]. An acetylated peptide, such as p53, may be bound through the formation of an enzyme-substrate β sheet, in which the substrate β strand is sandwiched between the β11 strand within the Rossmann fold and a β10 strand within the FGE loop, named for its highly conserved FGExL motif [21]. (c) Human Sirt2 (catalytic core; PDB accession number: 1J8F) [18]. (d) Full-length yeast Hst2p with the carboxy-terminal α14 helix interacting with the NAD-binding pocket (PDB accession number: 1Q14) [19]. Structural coordinates were taken from the Protein Data Bank and models were drawn with PYMOL [77].

Figure 3

The enzymatic activity of sirtuins. (a) The components necessary for sirtuin-mediated deacetylase activity are the sirtuin, β-NAD, and the N-acetylated substrate. (b) The components form a tertiary complex and, during the enzymatic reaction, the nicotinamide is expelled from bound NAD to generate an oxocarbonium-like transition state in which the carbonyl oxygen of the acetyl group attacks the C1 carbon of ADP. After alkylamidate and cyclic intermediates and possibly protonation of the amine leaving group (not shown), the products (c) are formed: the deacetylated protein, 2'-O-acetyl-ADP-ribose, and nicotinamide. The 2'-O-acetyl-ADP-ribose is released into solution, where it equilibrates with 3'-O-acetyl-ADP-ribose. Adapted with modifications from [78].

Figure 4

Localization and functions of the human sirtuins Sirt1, Sirt2 and Sirt3. Sirt1 is found in the nucleus; it associates with several partners and targets for deacetylation, as discussed in the text. Sirt2 is found in the cytoplasm bound to the microtubule network, where it forms a complex with the histone deacetylase HDAC6. Both proteins can deacetylate α-tubulin. Sirt3 is imported into the mitochondrial matrix and proteolytically processed by the peptidase MPP, leading to its enzymatic activation (asterisk). Ac, acetyl moiety; ProteinX, an unknown protein substrate.