Preorganized Internal Electric Field Enables Nucleophilic Attack of a Nonactivated Water Molecule in Thymine DNA...

Thymine DNA glycosylase (TDG) is a monofunctional glycosylase, playing an essential role in genome maintenance and in the DNA demethylation pathway. TDG differs from other DNA glycosylases in that it lacks a general base catalyst to activate water nucleophiles, making it appealing to understand its special catalytic mechanism. Through a combination of molecular dynamics (MD) simulations and quantum-mechanical/molecular-mechanical (QM/MM) calculations, we decipher a detailed mechanism of the TDG-catalyzed thymine excision reaction from the G:T mispair, arising mainly from deamination of the 5-methylcytosine (mC), an important epigenetic regulator of gene expression. The catalytic mechanism is shown to be devoid of leaving group protonation and nucleophile deprotonation activations, two common strategies used by other monofunctional DNA glycosylases. Instead, a rearrangement of the flipped nucleotide sugar-phosphate backbone is required before the N-glycosidic bond cleavage, which proceeds via an oxocarbenium-like transition state. Nucleophilic attack on the anomeric carbon by a nonactivated water molecule from the 3' side stabilizes the oxocarbenium ion, which is essentially facilitated by a strong internal electric field (IEF) that points toward the same direction. The IEF mainly comes from the distorted negatively charged DNA backbone phosphodiester groups, an apparent "autocatalysis" character first found in uracil DNA glycosylase (UDG). Finally, the roles of key protein residues, including Asn140, His151, Asn191, Thr197, Asp202, and Arg275, and the substrate itself, are further discussed. These results advance our understanding of the strategy used by TDG to catalyze distinct substrates and inspire further investigation of the effect of IEF on other biological enzymes, especially DNA glycosylases.