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

Abstract

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.

Nickel Ligation of the N-Terminal Amine of HypA Is Required for Urease Maturation in Helicobacter pylori

“…S4) similar to the bidentate coordination of α-ketoglutarate Fe-binding in nonheme Fe(II) enzymes used in prior models. 32, 33 This model simulates the formation of five-membered chelate rings that form when the binding of the N-terminal amine is accompanied by backbone amide binding, which lead to the ordering of second coordination sphere C atoms similar to prior models of backbone amidate ligation in the active site of NiSOD. 34, 35 …”

Imposing function down a (cupin)-barrel: secondary structure and metal stereochemistry in the αKG-dependent oxygenases

“…32 XAS studies on ABH2 demonstrate that (Fe + αKG + Substr)ABH2 contains a 5-coordinate Fe(II) center, as suggested by the consensus mechanism. 33 …”

Nonredox Nickel Enzymes

“…2 Indeed, nickel is known to cause cancer by an epigenetic mechanism, 3 which appears to involve substitution of Ni(II) for Fe(II) in non-heme iron dioxygenases that are involved in DNA and histone demethylation. 4 Furthermore, exposure to nickel compounds can also elicit an immune reaction: nickel contact dermatitis is one of the most common allergies in the modern world, 5 and the molecular basis for the immune reaction is now beginning to emerge. 6 Exposure to high levels of nickel has also been shown to impair the normal homeostasis of essential metal ions.…”