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crystallization of JMJD2A in complex with histone H3 peptides bearing different methylated forms of K9 and K36, cocrystallization of inactivated substrate with either N-oxalylglycine, a non-reactive 2-OG analog, or with Ni(II), which substitutes for Fe(II) and inhibits the hydroxylation reaction. Structures analysis, overview
in complex with trimethyl-histone 3 L-lysine 9, dimethyl-histone 3 L-lysine 36, and trimethyl-histone 3 L-lysine 36, and N-oxalylglycine, 2-oxoglutarate, and succinate, respectively. Histone substrates are recognized through a network of backbone hydrogen bonds and hydrophobic interactions that deposit the trimethyllysine into the active site. The trimethylated epsilon-ammonium cation is coordinated within a methylammonium-binding pocket through carbonoxygen hydrogen bonds that position one of the methyl groups adjacent to the Fe(II) center for hydroxylation and demethylation
purified recombinant fusion protein, JMJD5 catalytic domain in complex with substrate 2-oxoglutarate and inhibitor N-oxalylglycine, hanging drop vapor diffusion, mixing of 12 mg/ml protein in for the inhibitor complex 15 mM bis-Tris, pH 7.2, 25 mM NaCl, 1.0 mM dithiothreitol, 1.0 mM N--oxalylglycine, and 0.5 mM CoCl2, or for te substrate complex in 15mM Tris, pH 8.5, 25 mM NaCl, 1.5 mM 2-oxoglutarate, 1.5 mM dithiothreitol, and 4 mM H3K36me2-L peptide, ,with an equal volume of mother liquor containing 4.5% w/v PEG 3000, 0.1M bis-Tris, pH 5.5, and 50 mM MgCl2, 20°C, X-ray diffraction structure determination and analysis at 1.05-1.15 A resolution
purified recombinant KDM4C, sitting drop vapor diffusion method, mixing of 7 mg/ml protein with 2 mM N-oxalylglycine with well solution, containing 25% v/v PEG 3350, 0.2 M sodium nitrate, 0.1 M Bis tris propane, pH 6.5, 5% v/v ethylene glycol, 0.01 M NiCl2, in a 2:1 ratio, 4°C, X-ray diffraction structure determination and analysis at 2.55 A resolution
structures of JMJD2A–Ni(II)–Zn(II) inhibitor complexes bound to tri-, di- and monomethyl forms of histone 3 lysine 9 andthe trimethyl form of histone 3 lysine 36. The structures reveal a lysyl-binding pocket in which substrates are bound in distinct bent conformations involving the Zn-binding site. The mechansim for achieving methylation state selectivity involves the orientation of the substrate methyl groups towards a ferryl intermediate
structures of the catalytic core complexed with methylated histone 3 L-lysine36 peptide substrates in the presence of Fe(II) and N-oxalylglycine. The interaction between enzyme and peptides largely involves the main chains of the enzyme and the peptide. The peptide-binding specificity is primarily determined by the primary structure of the peptide