Chemistry of gene silencing: The mechanism of NAD⁺-dependent deacetylation reactions

The Sir2 enzyme family is responsible for a newly classified chemical reaction, NAD⁺-dependent protein deacetylation. New peptide substrates, the reaction mechanism, and the products of the acetyl transfer to NAD⁺ are described for SIR2. The final products of SIR2 reactions are the deacetylated peptide and the 2′ and 3′ regioisomers of O-acetyl ADP ribose (AADPR), formed through an α-1′-acetyl ADP ribose intermediate and intramolecular transesterification reactions (2′ → 3′). The regioisomers, their anomeric forms, the interconversion rates, and the reaction equilibria were characterized by NMR, HPLC, ¹⁸O exchange, and MS methods. The mechanism of acetyl transfer to NAD⁺ includes (1) ADP ribosylation of the peptide acyl oxygen to form a high-energy O-alkyl amidate intermediate, (2) attack of the 2′-OH group on the amidate to form a 1′,2′ -acyloxonium species, (3) hydrolysis to 2′-AADPR by the attack of water on the carbonyl carbon, and (4) an SIR2-independent transesterification equilibrating the 2′- and 3′-AADPRs. This mechanism is unprecedented in ADP-ribosyl transferase enzymology. The 2′-and 3′-AADPR products are candidate molecules for SIR2-initiated signaling pathways.