1.14.11.27: [histone-H3]-lysine-36 demethylase

This is an abbreviated version, for detailed information about [histone-H3]-lysine-36 demethylase, go to the full flat file.

Reaction

protein N6,N6-dimethyl-L-lysine
+
2-oxoglutarate
+
O2
=
protein N6-methyl-L-lysine
+
succinate
+
formaldehyde
+
CO2

Synonyms

CG33182, CG33185, dJMJD2(1), dJMJD2(1)/CG15835, dJMJD2(2), dJMJD2(2)/CG33182, dKDM2, dKDM4A, dRAF, H3-K36 demethylase, H3-K36-specific demethylase, H3K36 demethylase, H3K36 histone demethylase, H3K36me2 demethylase, H3K36me2 histone demethylase, H3K36me2-specific demethylase, H3K9/36me3 lysine demethylase, histone demethylase JmjD2A, histone H3 lysine 36 demethylase, histone H3 lysine 36 dimethyl–specific demethylase, histone H3K36 demethylase, histone H3K9/H3K36 trimethyldemethylase, histone-lysine(H3-K36) demethylase, Jhd1, JHDM1A, Jhdm1b/Kdm2b, JmjC domain histone demethylase, JmjC domain-containing histone demethylase 1, JmjC domain-containing histone demethylase 1A, JmjC domain-containing histone demethylation protein 3A, JmjC domain-containing histone demethylation protein 3b, JmjC protein, JmjC+N, JmjC+N histone demethylase, JMJD2, JMJD2A, JMJD2B, JMJD2D, JMJD5, KDM2B, KDM2b/JHDM1b, KDM4, KDM4A, KDM4A demethylase, KDM4A/JMJD2A, KDM8, More, Ndy1, PfJmjC1, Rph1, Rph1/KDM4, scJHDM1, [histone-H3]-lysine-36 demethylase 1

ECTree

     1 Oxidoreductases
         1.14 Acting on paired donors, with incorporation or reduction of molecular oxygen
             1.14.11 With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
                1.14.11.27 [histone-H3]-lysine-36 demethylase

Crystallization

Crystallization on EC 1.14.11.27 - [histone-H3]-lysine-36 demethylase

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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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
catalytic core of Rph1, hanging drop vapour diffusion method, X-ray diffraction structure determination and analysis at 2.5 A resolution