Preorganized Internal Electric Field Promotes a Double-displacement Mechanism for the Adenine Excision Reaction by Adenine DNA Glycosylase

Adenine DNA glycosylase (MutY) is a monofunctional glycosylase, removing adenines (A) misinserted opposite 8-oxo-7,8-dihydroguanine (OG), a common product of oxidative damage to DNA. Through multiscale calculations, we decipher a de-tailed adenine excision mechanism of MutY that is consistent with all available experimental data, involving an initial proto-nation step and two nucleophilic displacement steps. During the first displacement step, N-glycosidic bond cleavage is ac-companied by the attack of residue Asp144 at the anomeric carbon (C1′), forming a covalent glycosyl-enzyme intermediate to stabilize the fleeting oxocarbenium ion. After departure of the excised base, water nucleophiles can be recruited to displace Asp144, completing the catalytic cycle with retention of stereochemistry at the C1′ position. Unsurprisingly, in the absence of the protein environment, the first displacement reaction, where Asp144 acts as the nucleophile, is highly exothermic with a negative barrier, yet the second, where an un-activated water molecule acts as the nucleophile, is prohibitive both kinetically and thermodynamically. Intriguingly, we find that the enzyme modulates these two reactions by coupling them together through an internal electric field at its active site, which reduces the barrier of the difficult one at the expense of raising that of the easy one, thereby allowing both reactions to occur. These findings not only increase our understanding of the strate-gies used by DNA glycosylases to repair DNA lesions, but also have important implications for how internal/external electric field can be applied to modulate multi-step reactions.