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

Abstract

N, cations in the presence of [(AcO) 2 (imidazole) 2 (H 2 O)Fe=O] complexh ave been studied by density functional theory.These transformations are suitable modelsfor the N-demethylation of tri-, di-, and monomethylatedl ysine residues of histones in the presence of Jumonji-Cc ontaining histoned emethylases. It has been found that the N-demethylation reactioni ss tepwise and occurs on triplet and quintet potential energy hypersurfaces. Both spin states are nearly degenerated and the quantum jump from one state to another has at ransitionp robability close to one. The preferred intrinsic mechanism depends upon the methylation degree. For trimethylated residues the mechanism consists of ap roton abstraction from am ethyl group followed by af ormation of ah ydroxymethylaminium intermediate. This mechanism also occurs when dimethylated residues are ablet oo rientate one methyl group towards the Fe=Og roup of the catalytic site. In contrast, when aN ÀH groupo ft he substrate is close enough to the Fe=Og roup, the intrinsically preferred N-demethylation reaction leads to the formation of an iminium intermediate that can be hydrolyzed to form the correspondingN-demethylated product.Scheme1.Catalytic methylation and demethylation of lysine residues (Km) of histones (Hn).Scheme2.Generalcatalytic cycle for Jumonji-C domain-containing histone demethylases.The details of the demethylation process (highlighted in grey) are gathered in Scheme 3.Scheme3.Demethylation steps associatedwith the reaction mechanism of Jumonji-C domain-containing histone demethylases.

Reaction Mechanism of Histone Demethylation in αKG-dependent Non-Heme Iron Enzymes

“…The transition state TS4 is characterized by C-H and O-H bond distance of 1.45Å and 1.16Å, respectively ( Figure 5B, Figure 6A). These results are in agreement with the DFT-optimized saddle point associated with the H-abstraction in the conversion of dimethylated substrates by a JHDM enzyme, JMJD2A 9 and with the QM/MM calculations of the AlkB enzyme 8 . It is worth noting that in TS4 the NH of dimehtylated lysine approaches the non-coordinating oxygen of succinate to form a hydrogen bond with distance of 2.35Å ( Figure 6A).…”

What Is the Catalytic Mechanism of Enzymatic Histone N‐Methyl Arginine Demethylation and Can It Be Influenced by an External Electric Field?

“…We explored the possibility for HAT of the NH hydrogen as this has been proposed in model studies of KDMs [25b] . The barrier for NH hydrogen abstraction is higher than for CH abstraction, being 26.5 kcal/mol at the QM(B2+ZPE)/MM level of theory and 31.8 kcal/mol at the QM(B2)/MM level of theory [Figure 4c].…”

Density Functional Theory Study on the Demethylation Reaction between Methylamine, Dimethylamine, Trimethylamine, and Tamoxifen Catalyzed by a Fe(IV)–Oxo Porphyrin Complex

“…In our previous paper 40 on N-demethylation reactions catalyzed by Jumonji-C-containing histone demethylases, we observed subtle electronic and steric effects to selectively demethylate tri-, di-, and monomethylated lysine residues, as one would expect for epigenetic enzymes. In contrast, the reactions studied in this paper show low-barrier N-demethylation processes via two almost isoenergetic mechanisms that lead to the same products after hydrolysis of the imine or aminocarbinol intermediates.…”

“…In a recent work, 40 we performed a computational study on the demethylation of lysine residues catalyzed by histone demethylases containing Jumonji-C sites. The obtained results concluded that the intrinsically preferred mechanism is different depending upon the N-methylation degree of the lysine residue.…”