Lysine‐241 Has a Role in Coupling 2OG Turnover with Substrate Oxidation During KDM4‐Catalysed Histone Demethylation

Abstract

The JmjC histone lysyl demethylases (KDMs) play important roles in modulating histone methylation states and have the potential to be regulated by oxygen availability. Lys241 of the KDM4 subfamily is proposed to be important in oxygen binding by KDM4A. We report evidence that, although Lys241 is unlikely to be directly involved in oxygen binding, it has an important role in coupling 2‐oxoglutarate cosubstrate oxidation with lysine demethylase activity. The results suggest that compounds promoting the uncoupling of substrate oxidation are of interest as JmjC‐KDM inhibitors.

Disruption of the Plasmodium falciparum Life Cycle through Transcriptional Reprogramming by Inhibitors of Jumonji Demethylases

“… 72 , 73 Thus, future work will need to identify the histone, nonhistone protein, and nonprotein substrate(s) of all three P. falciparum Jumonji enzymes and establish their functional significance. 40 At present, our studies provide direct evidence that mammalian Jumonji inhibitors block malaria Jumonji enzyme activity in vitro , increase histone trimethylation in the parasite, alter discrete transcriptional programs, and disrupt parasite development. These findings suggest that the aggregate activities of the P. falciparum Jumonji enzymes are likely essential during the parasite’s life cycle.…”

“…Since the endogenous substrate for PfJmj3 is unknown, we measured the conversion of the 2-OG cosubstrate to succinate, the first step in Jumonji catalysis (Figure B). This step of the reaction is amenable to small molecule inhibition . Increasing concentrations of wild-type recombinant PfJmj3 resulted in increasing concentrations of succinate formation (Figure B).…”

“…This step of the reaction is amenable to small molecule inhibition. 40 Increasing concentrations of wild-type recombinant PfJmj3 resulted in increasing concentrations of succinate formation (Figure 4B). This activity is dependent on the cofactors, ascorbate and Fe(II), as well as the cosubstrate, 2-OG, consistent with the action of the Jumonji family of enzymes (Figures 4C and S4A,B).…”

Structural bioinformatics enhances the interpretation of somatic mutations in KDM6A found in human cancers

“…4 B). However, we also discovered that the variants located immediately distant away from the active site and the substrate binding interface can impact protein function as they are known to serve as the ‘second sphere’, third, and beyond residues for enzymatic activities [29] , [55] . Coordinated functional motions through the physically neighboring residues are critical for this protein since multiple interactions at the active and substrate binding sites appear highly coupled.…”

Human histone demethylase KDM6B can catalyse sequential oxidations

“…Further, 1 H NMR analyses did not indicate reaction or stimulation of 2-oxoglutarate turnover, which can be observed when demethylases are incubated with substrate analogues. 6 , 7 , 10 Further, no reaction was observed in samples containing KDM6B and either N ε -formyl- (Lys(For)), N ε -acetyl- (Lys(Ac)) or N ε -crotonyl-lysine (Lys(Cr)) peptides, implying that the positive charge of the side chain amine is important for KDM6B binding/activity (note: no reaction of these residues was observed with either KDM4E or PHF8). 6 , 7 The lack of oxidation of Lys(For) is interesting given that Lys(Me/Et) and Lys(Me/iPr) residues are likely oxidised to the aldehyde and carboxylic acid derivatives ( Scheme 1 ).…”