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Structural Investigations of the Nickel-Induced Inhibition of Truncated Constructs of the JMJD2 Family of Histone Demethylases Using X‑ray Absorption Spectroscopy

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journal contribution
posted on 18.06.2013, 00:00 by Nitai Charan Giri, Lisa Passantino, Hong Sun, Maria Antonietta Zoroddu, Max Costa, Michael J. Maroney
Occupational and/or environmental exposure to nickel has been implicated in various types of cancer, and in vitro exposure to nickel compounds results in the accumulation of Ni­(II) ions in cells. One group of major targets of Ni­(II) ions inside the cell consists of Fe­(II)- and αKG-dependent dioxygenases. Using JMJD2A and JMJD2C as examples, we show that the JMJD2 family of histone demethylases, which are products of putative oncogenes as well as Fe­(II)- and αKG-dependent dioxygenases, are highly sensitive to inhibition by Ni­(II) ions. In this work, X-ray absorption spectroscopy (XAS) has been used to investigate the Fe­(II) active site of truncated JMJD2A and JMJD2C (1–350 amino acids) in the presence and absence of αKG and/or substrate to obtain mechanistic details of the early steps in catalysis that precede O2 binding in histone demethylation by the JMJD2 family of histone demethylases. Zinc K-edge XAS has been performed on the resting JMJD2A (with iron in the active site) to confirm the presence of the expected structural zinc site. XAS of the Ni­(II)-substituted enzymes has also been performed to investigate the inhibition of these enzymes by Ni­(II) ions. Our XAS results indicate that the five-coordinate Fe­(II) center in the resting enzyme is retained in the binary and ternary complexes. In contrast, the Ni­(II) center is six-coordinate in the resting enzyme and binary and ternary complexes. XAS results indicate that both Fe­(II) and Ni­(II) bind αKG in the binary and ternary complexes. The electron density buildup that is observed at the Fe­(II) center in the presence of αKG and substrate is not observed at the Ni­(II) center. Thus, both electronic and steric factors are responsible for Ni-induced inhibition of the JMJD2 family of histone demethylases. Ni-induced inhibition of these enzymes may explain the alteration of the epigenetic mechanism of gene expression that is responsible for Ni-induced carcinogenesis.

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