A "moving metal mechanism" for substrate cleavage by the DNA repair endonuclease APE-1

Apurinic/apyrimidinic endonuclease (APE-1) is essential for base excision repair (BER) of damaged DNA. Here molecular dynamics (MD) simulations of APE1 complexed with cleaved and uncleaved damaged DNA were used to determine the role and position of the metal ion(s) in the active site before and after DNA cleavage. The simulations started from an energy minimized wild-type structure of the metal-free APE1/damaged-DNA complex (1DE8). A grid search with one Mg²⁺ ion located two low energy clusters of Mg²⁺ consistent with the experimentally determined metal ion positions. At the start of the longer MD simulations, Mg²⁺ ions were placed at different positions as seen in the crystal structures and the movement of the ion was followed over the course of the trajectory. Our analysis suggests a "moving metal mechanism" in which one Mg²⁺ ion moves from the B- (more buried) to the A-site during substrate cleavage. The anticipated inversion of the phosphate oxygens occurs during the in-line cleavage reaction. Experimental results, which show competition between Ca²⁺ and Mg²⁺ for catalyzing the reaction, and high concentrations of Mg²⁺ are inihibitory, indicate that both sites cannot be simultaneously occupied for maximal activity.