Chemistry of Gene Silencing: The Mechanism of NAD+-Dependent Deacetylation Reactions

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Abstract
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.