X-ray Absorption Spectroscopy Structural Investigation of Early Intermediates in the Mechanism of DNA Repair by Human ABH2

Human ABH2 repairs DNA lesions by using an Fe(II)- and αKG-dependent oxidative demethylation mechanism. The structure of the active site features the facial triad of protein ligands consisting of the side chains of two histidine and one aspartate residues that is common to many nonheme Fe(II) oxygenases. X-ray absorption spectroscopy (XAS) of metallated (Fe and Ni) samples of ABH2 were used to investigate the mechanism of ABH2 and its inhibition by Ni(II) ions. The data are consistent with a sequential mechanism that features a five coordinate metal center in both the presence and absence of the α-ketoglutarate cofactor. This aspect is not altered in the Ni(II)-substituted enzyme, and both metals are shown to bind the cofactor. When substrate is bound to the native Fe(II) complex with α-ketoglutarate bound, a five-coordinate Fe(II) center is retained that features an open coordination position for O2 binding. However, in the case of the Ni(II)-substituted enzyme, the complex that forms in the presence of cofactor and substrate is six-coordinate, and therefore features no open coordination site for oxygen activation at the metal.