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1.14.11.66: [histone H3]-trimethyl-L-lysine9 demethylase

This is an abbreviated version!
For detailed information about [histone H3]-trimethyl-L-lysine9 demethylase, go to the full flat file.

Word Map on EC 1.14.11.66

Reaction

a [histone H3]-N6,N6,N6-trimethyl-L-lysine9
+ 2 2-oxoglutarate + 2 O2 =
a [histone H3]-N6-methyl-L-lysine9
 + 2 succinate + 2 formaldehyde + 2 CO2

Synonyms

5qNCA, AN1060, BHC110, CG15835, CG33182, Dmel\Kdm4A, GASC1, H3K9 demethylase, H3K9 trimethyl demethylase, H3K9-specific demethylase, H3K9/36me3 lysine demethylase, H3K9me2/3 demethylase, H3K9Me3 demethylase, H3K9me3 histone demethylase, H3K9me3-specific demethylase, histone demethylase, histone demethylase JmjD2A, histone demethylase JMJD2A/KDM4A, histone demethylase JMJD2B, histone H3 demethylase, histone H3 Lys 9 demethylase, histone H3K9 demethylase, histone H3K9/H3K36 trimethyldemethylase, histone lysine demethylase, histone-3 lysine-9 di-/tri-methyl demethylase, JDHM3A, JHDM2A, JHDM2B, JHDM3A, JmjC histone lysine demethylase, JmjC-domain-containing histone demethylase 3A, JMJD1A, JMJD1B, JMJD2, JMJD2(1), JMJD2(2), JMJD2A, JMJD2A demethylase, JMJD2A/KDM4A, JMJD2B, JMJD2b histone demethylase, JMJD2C, JMJD2D, jumonji C-domaincontaining histone demethylase 3A, jumonji domain containing 2A, Jumonji domaincontaining demethylase, JumonjiC-domain-containing histone demethylase, JumonjiD2A, KDM1, KDM2B, Kdm3a, Kdm3b, KDM4, KDM4A, KDM4A lysine demethylase, KDM4A/JMJD2A, KDM4B, KDM4B/JMJD2B histone demethylase, Kdm4c, KDM4D, KDM4E, KdmA, KIAA0601, LD33386, LSD1, LSD1 demethylase, LSD1 H3 demethylase, lysine-specific demethylase 1, lysine-specific demethylase 4A, lysine-specific demethylase 4B, lysine-specific demethylase 4C, lysine-specific demethylase 4D, More, testis-enriched histone demethylase, tridemethylase of H3K9, trimethylated histone H3-lysine 9-specific demethylase, trimethyllysine-specific histone demethylase, trimethyllysine-specific JmjC HDM, [histone H3]-lysine-9 demethylase

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
                1.14.11.66 [histone H3]-trimethyl-L-lysine9 demethylase

Crystallization

Crystallization on EC 1.14.11.66 - [histone H3]-trimethyl-L-lysine9 demethylase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure determinations of JMJD2A in complex with histone H3 peptides bearing different methylated forms of K9 and K36
crystal structures of LSD1/Co-REST complexes bound to histone H3 peptides. LSD1/Co-REST-C complex co-crystallized with a 20-residue histone H3 peptide inhibitor in which Lys4 is mutated to a methionine. Cocrystallization of the enzyme with a suicide inhibitor consisting of a 21-residue histone H3 peptide in which K4 is modified by an N-methylpropargylgroup. Complex structure analysis, overview
purified JMJD2A catalytic domain in complex with H3K9me3, H3K36me2 and H3K36me3 peptides, vapor diffusion method, from 0.2 M sodium/potassium phosphate, pH 6.5, and 20% w/v PEG 3350, at 4°C, and by microseeding from 12% w/v PEG monomethyl ether 5000 and 0.1 M HEPES, pH 7.0, X-ray diffraction structure determination and analysis at 2.05-2.30 A resolution
purified recombinant detagged enzyme in apo form and in complex with several inhibitors, hanging drop vapor diffusion method, mixing of 0.0015 ml of 7 mg/ml protein solution with 0.0015 ml of reservoir solution containing 2-16% w/v PEG 4000 and 0.1 M BTP, pH 7.5, and equilibration against 0.8 ml, 18°C, 1 week, the crystals are then soaked by addition of 750 nL of ligand solution at 10-200 mM in DMSO directly to the crystallizatin drops, followed by 4-48 h incubation at 18°C, X-ray diffraction structure determination and analysis
purified recombinant enzyme in complex with inhibitor, sitting drop vapor diffusion method, mixing of 10 mg/ml protein and 2.5 mM 2,4-pyridinedicarboxylic acid with well solution, containing 20% v/v PEG 3350, 0.1 M sodium citrate, pH 5.5, and 2 mM NiCl2, in a 2:1 ratio, 4°C, X-ray diffraction structure determination and analysis at 2.1 A resolution. The zinc-binding site in KDM4E is disordered possibly due to loss of zinc in the crystallization process
purified recombinant enzyme in complex with inhibitor, sitting drop vapor diffusion method, mixing of 7 mg/ml protein and 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
purified recombinant enzyme in complex with substrate peptides, by vapour diffusion at 4°C from 0.1 M citrate, pH 5.5, 20% PEG 3350 and 4 mM NiCl2, X-ray diffraction structure determination and analysis
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 and the 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