3.1.1. Overall structure of sirtuin
The alignment of sirtuin´s primary sequence shows that they have a highly conserved catalytic core. At the same time, the regions corresponding to the N- and C-terminal are variable in length and sequence (Yuan & Marmorstein, 2012).
The catalytic core adopts an elongated shape containing a conserved large Rossmann-fold domain, and a smaller and more structurally diverse domain for acyl peptide and NAD+ binding, respectively, connected by a series of loops that contribute to the formation of a cleft between the large and small domains (North & Verdin, 2004; Sanders & Marmorstein, 2010; Zhao, et al., 2004).
The large domain comprises an inverted prototypical open α/β Rossmann fold structure, widely distributed in proteins that bind oxidized or reduced NAD or NADP. This domain comprises six parallel β strands forming a central β sheet packed between several α helices. The exact number of α helices depends on the protein. For example,Escherichia coli sirtuin CoB contains eight α helices. Also, a conserved Gly-X-Gly sequence important for phosphate binding, a pocket to accommodate an NAD+ molecule, and charged residues responsible for ribose group binding are found (Figure 2A) (Sanders & Marmorstein, 2010).
The structural Zn2+-binding domain is composed of three antiparallel β-strands and a variable α helical region. A zinc ion is generally bound to four conserved lysine residues in the β-sheet module in a tetrahedral conformation, except for CobB, which is linked to two cysteine residues and contains three of the four expected zinc-coordinating cysteine residues according to sequence alignment (Sanders & Marmorstein, 2010; Yuan & Marmorstein, 2012). The zinc ion does not participate directly in the deacetylation, and it has been observed that it has an essential structural role in the integrity of the catalytic core domain (Figure 2A) (Blander & Guarente, 2004; Yuan & Marmorstein, 2012).
A binding site located between the sirtuin large and small domain, linked to each other by two flexible loops (L1 and L2), forms a cleft that acts as the enzyme’s active site. NAD+ and acetyl-lysine substrate bind at this cleft (Yuan & Marmorstein, 2012). The binding region is divided into three spatially distinct sites: site A, for an adenine-ribose moiety of NAD binding. Site B for the nicotinamide-ribose moiety binding. And site C site, located deep in the NAD-binding pocket for nicotinamide moiety binding (Figure 2A) (Sanders & Marmorstein, 2010).