Preorganized Internal Electric Field Powers Catalysis in the Active Site of Uracil-DNA Glycosylase

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Abstract

Uracil-DNA glycosylase (UDG) is a monofunctional DNA glycosylase, which is involved in the base excision repair (BER) pathway and responsible for the excision of uracil from DNA. UDG is well known for its high catalytic efficiency and substrate autocatalysis character. Here, using quantum-mechanical/molecular-mechanical (QM/MM) and QM calculations as well as molecular dynamics (MD) simulations, we propose a revised catalytic mechanism of UDG and elucidate the nature of its strong catalytic efficiency. In the initial stage of the reaction, a heterolytic C–N bond cleavage is catalyzed by a strong internal electric field which stabilizes the charge distribution of the transition state more than that of the ground state, yielding an oxocarbenium-ion–uracil-anion species. The catalytic effect of substrate phosphate groups can be included in the effect of the internal electric field, which is counterbalanced by sodium ions, explaining the longstanding discrepancy between theory and experiment. Subsequently, Asp145 acts as the general base to activate the water nucleophile to attack the oxocarbenium ion, forming an abasic site. Interestingly, the proton further transfers from Asp145 to the neutral and more solvent-exposed residue His148 to facilitate its release, which is demonstrated to be driven by the internal electric field. This work deepens our understanding of the catalytic mechanism of UDG and more generally the catalytic effect of internal electric fields in enzymes.

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