Orchestrated metal ion repositioning defines the dynamic catalytic strategy of the essential DNA repair nuclease APE1

Human AP-endonuclease 1 (APE1) is a vital enzyme in the base excision repair pathway that protects genome stability by eliminating ubiquitous abasic DNA lesions. Despite its importance and therapeutic potential, how APE1 achieves high specificity and single-metalion catalytic efficiency remains unclear. Here, we present a high-resolution structure of the APE1–DNA Michaelis complex coordinated with physiological cofactor Mg ²⁺ . Integrating this snapshot with ab initio molecular dynamics and metadynamics simulations reveals a novel “moving metal ion” mechanism in which Mg ²⁺ undergoes orchestrated repositioning to trigger a concerted catalytic reaction, bypassing the formation of an associative pentavalent intermediate. This distinct catalytic strategy, driven by concerted active-site reorganization, enables APE1 to efficiently process damaged DNA using only one metal ion cofactor. A previously unrecognized hydrogen-bonding network couples catalytic water activation to the metal ion movement – two events that strikingly occur on opposite sides of the active site. These findings provide a blueprint for how enzymes synchronize distal active site rearrangements with transition state formation. Our results further suggest that effective AI-targeted inhibitor design should develop capacities to predict mechanistically critical non-canonical rotamers and transient hydrogen-bonding networks. Our combined findings offer a foundation for the design of inhibitors targeting APE1 overexpression in cancer.