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).