Sirtuin structure

The class III deacetylases, named sirtuins, are structurally and functionally different from other HDACs. In contrast to the zinc-dependent deacetylation of classic HDACs, sirtuins depend on NAD" to carry out catalytic reactions. A variety of sirtuin crystal structures have been published over the past few years. The structures of human Sirt2 and SirtS as well as several bacterial Sir2 proteins could be derived, whereas no 3D structure is available for Sirtl and the other subtypes [69]. All solved sirtuin structures contain a conserved 270-amino-acid catalytic domain with variable N- and C-termini. The structure of the catalytic domain consists of a large classic Rossmann fold and a small zinc binding domain. The interface between the large and the small subdomain is commonly subdivided into A, B and C pockets. This division is based on the interaction of adenine (A), ribose (B) and nicotinamide (C) which are parts of the NAD" cofactor. (Figure 3.5) Whereas the interaction of adenine and... 

The sirtuins (silent information regulator 2-related proteins class III HDACs) form a specific class of histone deacetylases. First, they do not share any sequence or structural homology with the other HDACs. Second, they do not require zinc for activity, but rather use the oxidized form of nicotinamide adenine dinucleotide (NAD ) as cofactor. The reaction catalyzed by these enzymes is the conversion of histones acetylated at specific lysine residues into deacetylated histones, the other products of the reaction being nicotinamide and the metabolite 2 -0-acetyl-adenosine diphosphate ribose (OAADPR) [51, 52]. As HATs and other HDACs, sirtuins not only use acetylated histones as substrates but can also deacetylate other proteins. Intriguingly, some sirtuins do not display any deacetylase activity but act as ADP-ribosyl transferases. 

Sirtuins have been conserved from bacteria to eukaryotes. Notably, they all possess a conserved catalytic core domain flanked by sequence-divergent N- and C-terminal regions. If bacteria and archaebacteria generally possess one or two sirtuins, this number is higher in eukaryotes, with five sirtuins in Saccharomyces cerevisiae and seven in human. The presence of sirtuins in all phyla of life led to a wealth of structural data, not only on eukaryotic enzymes but also on bacterial and archaebacteria enzymes. 

Figure 2.4 Structures of histone deacetylases from the sirtuin family. Ribbon representation of the structures of the conserved catalytic domain of histone deacetylases (a) Homo sapiens SirT2 (PDB code IjSf) and (b) Thermotoga maritima Sir2 bound to NAD and an acetylated p53 peptide (PDB code 2h4f).

Despite the large amount of biochemical and structural studies of sirtuins in complex with various substrates, cofactors and reaction products, the catalytic mechanism of this class of enzymes is still a matter of debate. SN -like [56] and SN -like [60] mechanisms have been inferred from structural studies but further biochemical and possibly structural studies will be required to clarify which mechanism is used by sirtuins. It should also be noted that another matter of debate concerns the mode of noncompetitive inhibition of sirtuins by the reaction product nicotinamide [62], various structural studies having highlighted different binding pockets for this molecule [63, 64]. 

Hoff, K.G., Avalos, J.L., Sens, K. and Wolberger, C. (2006) Insights into the sirtuin mechanism from ternary complexes containing NAD + and acetylated peptide. Structure (London, England 1993), 14 (8), 1231-1240. 

So far 18 different members of HDACs have been discovered in humans and classified into four classes based on their homology to yeast histone deacetylases [33]. Class I includes four different subtypes (HDACl, 2, 3, 8), class II contains six subtypes tvhich are divided into two subclasses class Ila with subtypes HDAC4, 5, 7, 9 and class Ilb with HDAC6, 10. Class I and class II HDAC share significant structural homology, especially within the highly conserved catalytic domains. HDACs 6 and 10 are unique as they have two catalytic domains. HDACll is referred to as class IV. While the activity of class I, II and IV HDACs depends on a zinc based catalysis mechanism, the class III enzymes, also called sirtuins, require nicotinamide adenine dinucleotide as a cofactor for their catalysis. 

Figure 3.7 Molecular structures of sirtuin inhibitors mentioned in the text.

Figure 3.10 Molecular structure of the sirtuin inhibitors suramin and NF675.

Structure-activity studies on suramin analogues as inhibitors of NAD( + )-dependent histone deacetylases (sirtuins). ChemMedChem, 2, 1419-1431. 

Tervo, A.J., Suuronen, T, Kyrylenko, S., Kuusisto, E., Kiviranta, P.H., Salmirmen, A. et al. (2006) Discovering inhibitors of human sirtuin type 2 novel structural scaffolds./oumoi of Medicinal Chemistry, 49, 7239-7241. 

E., Sippl, W. and Jung, M. (2008) Structure-activity studies on splitomicin derivatives as sirtuin inhibitors and computational prediction of binding mode. Journal of Medicinal Chemistry, 51, 1203-1213. 

Trapp, J., Meier, R., Hongwiset, D., Kassack, M. U., Sippl, W., Jung, M. Structure-activity studies on suramin analogues as inhibitors of NAD(-H)-dependent histone deacetylases (sirtuins). Chem. Med. Chem. 2007, 2(10), 1419-1431. 

Compared to the zinc-dependent HDACs, the sirtuins act by a very different mechanism and require NAD+ as a cofactor. Unsurprisingly, they show no sequence similarity with the other HDACs and are structurally very distinct [97]. The size of most sirtuins (Sirt2 to Sirt7) varies from 310 to 400 amino acid residues, while Sirtl is larger (747 residues). Multiple crystal structures of eukaryotic and prokaryotic sirtuin proteins have been reported, which either are apo-forms or include ligands such as NAD+ derivatives, W-acetylated lysine substrates, and/or other small molecules [98-110]. These data have shed much light on the mode of action of this enzyme class. 

All sirtuins share a catalytic NAD+ binding domain, which is fairly well conserved across the family [115] and a substrate-binding pocket. Structural data also provided insights to the substrate selectivity of sirtuins [108]. 

Several structurally diverse sirtuin inhibitors have been reported, some of which are illustrated in Fig. 10. Nicotinamide is a product of NAD+ degradation that occurs during sirtuin-mediated catalytic process. Its inhibitory function at high concentrations is a result of a reaction with the ribosyl oxycarbenium intermediate formed as part of the mechanism, thus reversing the catalytic process and preventing deacetylation. Sirtinol 26 and salermide 27 [116], cambinol 28 [117], the tenovins 29 [118], and splitomycin 30 all show moderate inhibitory activity in the micromolar range. 

Fig. 11 Structure of resveratrol and other polyphenolic natural products with reported sirtuin-activating properties...

Fig. 13 Structures of sirtuin activators (a) pyrroloquinoxaline 48 (b) Structure and Sirtl activation data for dihydropyridines 49-51...

Cosgrove MS et al (2006) The structural basis of sirtuin substrate affinity. Biochemistry 45(24) 7511-7521... 

Tervo AJ et al (2006) Discovering inhibitors of human sirtuin type 2 novel structural scaffolds. J Med Chem 49(24) 7239-7241... 

Mai A et al (2009) Study of 1, 4-dihydropyridine structural scaffold discovery of novel sirtuin activators and inhibitors. J Med Chem 52(17) 5496-5504... 

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