Dioxygen Binding in the Active Site of Histone Demethylase JMJD2A and the Role of the Protein Environment

Abstract

JMJD2A catalyses the demethylation of di- and trimethylated lysine residues in histone tails and is a target for the development of new anticancer medicines. Mechanistic details of demethylation are yet to be elucidated and are important for the understanding of epigenetic processes. We have evaluated the initial step of histone demethylation by JMJD2A and demonstrate the dramatic effect of the protein environment upon oxygen binding using quantum mechanics/molecular mechanics (QM/MM) calculations. The changes in electronic structure have been studied for possible spin states and different conformations of O2 , using a combination of quantum and classical simulations. O2 binding to this histone demethylase is computed to occur preferentially as an end-on superoxo radical bound to a high-spin ferric centre, yielding an overall quintet ground state. The favourability of binding is strongly influenced by the surrounding protein: we have quantified this effect using an energy decomposition scheme into electrostatic and dispersion contributions. His182 and the methylated lysine assist while Glu184 and the oxoglutarate cofactor are deleterious for O2 binding. Charge separation in the superoxo-intermediate benefits from the electrostatic stabilization provided by the surrounding residues, stabilizing the binding process significantly. This work demonstrates the importance of the extended protein environment in oxygen binding, and the role of energy decomposition in understanding the physical origin of binding/recognition.

Production of ROS by Gallic Acid Activates KDM2A to Reduce rRNA Transcription

“…This dioxygen binding plays a critical role and shows a strong dependence on the protein environment [ 10 ]. According to the model presented [ 10 , 34 , 35 ], ROS could directly affect this process. Another possibility is modifications of proteins that affect the activity of KDMs.…”

“…The JmjC-type KDMs are one group of α-ketoglutarate-dependent oxygenases that catalyze a remarkably diverse range of oxidative reactions [ 9 ]. The JmjC-type KDMs remove methyl groups on lysine in the specific amino acid stretches of histones, and the selectivity of substrates is determined by the structure of the JmjC domain and also the dynamics of the amino acid sequence near the JmjC domain [ 10 , 11 ]. KDMs also distinguish the number of methyl groups attached to lysine [ 7 ].…”

Two‐State Reactivity of Histone Demethylases Containing Jumonji‐C Active Sites: Different Mechanisms for Different Methylation Degrees

“…[8b, 9] The LSD family of enzymes comprises two enzymes named LSD1 andL SD2, which contain FADa sacofactor and only accept di-and monomethylated lysinesa ss uitable substrates. The a-ketoglutarate cofactor 4 is incorporatedt ot he active site to give rise to intermediate 5.T his preparation step is followed by activation of the metallic site by binding to one molecule of oxygen to yield af erric superoxo adduct 6,i nw hich only one oxygen atom is bound to the metallicc enter.P aton et al [17] have shown that in JMJD2A the O 2 -Fe interaction accountsf or half the total interaction energy at the mosts table quintet state. These enzymesc an be classified in different subfamilies JMJDn,i nw hich n = 1-8.…”

Protein effects in non-heme iron enzyme catalysis: insights from multiscale models

“…[53] Later the protein contributions to binding have been quantified also for IPNS, MIOX, and JMJD2A. [74][75][76] These results show a consistent stabilization, see Figure 9. There are two major contributions: 1) the van der Waals interactions between the bound dioxygen and the protein atoms and (2) electrostatic effects on a charge transfer from iron(II) to oxygen to form iron(III)-superoxide.…”