Promiscuous DNA alkyladenine glycosylase dramatically favors a bound lesion over undamaged adenine

Abstract

The human DNA alkyladenine glycosylase (AAG) is a DNA repair enzyme catalyzing the initial step of DNA repair via lesion excision. Its binding site has an incredible plasticity, and recognizes a variety of DNA lesions resulting from deamination or alkylation of adenine. Based on this plasticity, it is natural to wonder how, and if AAG can discriminate against undamaged adenine. It has even been proposed that it cannot. If, however, AAG is specific, the specificity can be expressed at the stage of the base binding, or base excision. There is also a possibility that the propensity of the base to flip out of the DNA double helix governs its selective subsequent removal. Here, we show that binding to AAG is, in fact, dramatically more thermodynamically favorable for hypoxanthine, at least, a specific lesion, produced by oxidative deamination of adenine, than for undamaged adenine. This preference originates from the more constructive interactions of the lesion with the binding site. Of these, a shorter hydrogen bond between the lesion and the backbone of His136 that does not cause a structural distortion of the base in a major player, in agreement with an earlier kinetic study (P.J. O'Brien and T. J. Ellenberger, J. Biol. Chem. 279 (2004), 9750–9757). Mutating His136 to Pro almost completely eliminates the selectivity. Otherwise, bound adenine and the lesion are positioned very similarly at the binding site, suggesting no predisposition to selective removal. The base flip out of the double helix that precedes the binding has approximately equal thermodynamic facility for the lesion and undamaged adenine. This study employs the Monte Carlo simulations in conjunction with Free Energy Perturbation, and Density Functional Theory (DFT) calculations.