Abstact

Sirtuins are an evolutionarily conserved family of NAD+-dependent deacylases whose catalytic mechanism remains under active investigation. While previous studies have captured sirtuin reaction intermediates using thioacetyl-lysine analogs, here we report six crystal structures of human SIRT2 in complex with native myristoylated peptides and NAD+, revealing the sequence of changes from initial NAD+ binding to the formation of intermediate I. Our structures provide direct structural evidence for: (1) zinc-binding domain shift during NAD+ entry, (2) water-mediated hydrogen-bond formation that disrupts nicotinamide aromaticity preceding cleavage, and (3) the formation of intermediate I. Additionally, we determined the structures of two functionally critical mutants (SIRT2F96A and SIRT2H187A), demonstrating their roles in stabilizing NAD+ in a productive conformation. These findings complete the comprehensive structural framework for the sirtuin deacylation mechanism and highlight key residues governing catalytic efficiency.