Studies on the catalytic domains of multiple JmjC oxygenases using peptide substrates

Abstract

These authors contributed equally to this work.Keywords: demethylation, Epigenetics, histone, methyllysine, JmjC histone demethylase, 2OG oxygenases The JmjC-domain-containing 2-oxoglutarate-dependent oxygenases catalyze protein hydroxylation and N emethyllysine demethylation via hydroxylation. A subgroup of this family, the JmjC lysine demethylases (JmjC KDMs) are involved in histone modifications at multiple sites. There are conflicting reports as to the substrate selectivity of some JmjC oxygenases with respect to KDM activities. In this study, a panel of modified histone H3 peptides was tested for demethylation against 15 human JmjC-domain-containing proteins. The results largely confirmed known N emethyllysine substrates. However, the purified KDM4 catalytic domains showed greater substrate promiscuity than previously reported (i.e., KDM4A was observed to catalyze demethylation at H3K27 as well as H3K9/K36). Crystallographic analyses revealed that the N e -methyllysine of an H3K27me3 peptide binds similarly to N e -methyllysines of H3K9me3/H3K36me3 with KDM4A. A subgroup of JmjC proteins known to catalyze hydroxylation did not display demethylation activity. Overall, the results reveal that the catalytic domains of the KDM4 enzymes may be less selective than previously identified. They also draw a distinction between the N e -methyllysine demethylation and hydroxylation activities within the JmjC subfamily. These results will be of use to those working on functional studies of the JmjC enzymes.

Hole hopping through tyrosine/tryptophan chains protects proteins from oxidative damage

“…The structure of the catalytic domain of the human 2-oxoglutarate dependent nonheme iron oxygenase N e -methyllysine demethylase (KDM4A) is characterized by an eight-residue linear Tyr/Trp chain [5-Å ET cutoff, PDB ID 4W2V (45)]. The enzyme is believed to catalyze lysine demethylation in a hydroxylation/demthylation sequence involving an Fe IV (O) intermediate (45). The central portion of the Tyr/Trp chain (Tyr275 and Trp187) passes ∼9 Å from the active site Fe center and terminates near surface exposed residues (Tyr273 and Trp181; Fig.…”

Pleiotropic Functions of H3K27Me3 Demethylases in Immune Cell Differentiation

“…In contrast with the strict specificity of Jmjd3 and Utx, some members of other JmjC sub-families have a broader substrate range. However, they have little if any demethylase activity on H3K27Me3, with the possible exception of Kdm4 family members [36]. While the JmjC protein Jhdm1d (encoded by Kdm7) also demethylates H3K27Me2, and has been reported to associate with Jmjd3 [18], it has not been shown to act on its own on H3K27Me3.…”

“…It was recently reported that additional JmjC-family demethylases, including members of the Kdm4 family, exhibit H3K27Me3 demethylase activity [36], and future studies will examine their impact of H3K27Me3 in vivo . Of note, such functional redundancy would be gene specific, as H3K27Me3 removal at specific promoters (e.g.…”

Mitochondrial metabolites extend lifespan

“…Relevant targets of JmjC histone demethylases (Loenarz & Schofield, 2008) were measured in whole‐worm extracts across multiple stages of development, and included H3K4me3, H3K27me3, H3K9me3, and H3K36me3. The latter three sites are demethylated by JMJD‐2/JMJD2A (Williams et al ., 2014). Analysis at this gross level, however, revealed no significant disruption in the methylation patterns of these four targets (Fig.…”