Structure of human apurinic/apyrimidinic endonuclease 1 with the essential Mg(2+) cofactor

Apurinic/apyrimidinic endonuclease 1 (APE1) mediates the repair of abasic sites and other DNA lesions and is essential for base-excision repair and strand-break repair pathways. APE1 hydrolyzes the phosphodiester bond at abasic sites, producing 5′-deoxyribose phosphate and the 3′-OH primer needed for repair synthesis. It also has additional repair activities, including the removal of 3′-blocking groups. APE1 is a powerful enzyme that absolutely requires Mg(2+), but the stoichiometry and catalytic function of the divalent cation remain unresolved for APE1 and for other enzymes in the DNase I superfamily. Previously reported structures of DNA-free APE1 contained either Sm(3+) or Pb(2+) in the active site. However, these are poor surrogates for Mg(2+) because Sm(3+) is not a cofactor and Pb(2+) inhibits APE1, and their coordination geometry is expected to differ from that of Mg(2+). A crystal structure of human APE1 was solved at 1.92 Å resolution with a single Mg(2+) ion in the active site. The structure reveals ideal octahedral coordination of Mg(2+) via two carboxylate groups and four water molecules. One residue that coordinates Mg(2+) directly and two that bind inner-sphere water molecules are strictly conserved in the DNase I superfamily. This structure, together with a recent structure of the enzyme–product complex, inform on the stoichiometry and the role of Mg(2+) in APE1-catalyzed reactions.