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Literature summary extracted from

  • Ng, S.S.; Kavanagh, K.L.; McDonough, M.A.; Butler, D.; Pilka, E.S.; Lienard, B.M.; Bray, J.E.; Savitsky, P.; Gileadi, O.; von Delft, F.; Rose, N.R.; Offer, J.; Scheinost, J.C.; Borowski, T.; Sundstrom, M.; Schofield, C.J.; Oppermann, U.
    Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity (2007), Nature, 448, 87-91 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.14.11.66 gene KDM4A, recombinant expression of N-terminally His-tagged enzyme in Escherichia coli Homo sapiens
1.14.11.69 gene KDM4A, recombinant expression of N-terminally His-tagged enzyme in Escherichia coli Homo sapiens

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.14.11.66 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 Homo sapiens
1.14.11.69 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 at 2.1 A resolution Homo sapiens

Protein Variants

EC Number Protein Variants Comment Organism
1.14.11.69 additional information transposition of the Ala-Pro motif of H3K27 to AARK(me3)SPAAT, to mimic the proline position in H3K36, resulted in no detectable activity Homo sapiens

Inhibitors

EC Number Inhibitors Comment Organism Structure
1.14.11.66 additional information structures of JMJD2A-Ni(II)-Zn(II) inhibitor complexes bound to tri-, di- and monomethyl forms of H3K9 and the trimethyl form of H3K36, overview Homo sapiens
1.14.11.66 Ni2+
-
 Homo sapiens
1.14.11.66 Zn2+
-
 Homo sapiens
1.14.11.69 additional information structures of JMJD2A-Ni(II)-Zn(II) inhibitor complexes bound to tri-, di- and monomethyl forms of H3K9 and the trimethyl form of H3K36, overview Homo sapiens
1.14.11.69 Ni2+
-
 Homo sapiens
1.14.11.69 Zn2+
-
 Homo sapiens

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
1.14.11.69 nucleus
-
 Homo sapiens 5634
-

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
1.14.11.66 Fe2+ the mechanism for achieving methylation state selectivity involves the orientation of the substrate methyl groups towards a ferryl intermediate Homo sapiens
1.14.11.66 additional information structures reveal a lysyl-binding pocket in which substrates are bound in distinct bent conformations involving the Zn-binding site Homo sapiens
1.14.11.69 Fe2+ the mechanism for achieving methylation state selectivity involves the orientation of the substrate methyl groups towards a ferryl intermediate Homo sapiens
1.14.11.69 additional information structures reveal a lysyl-binding pocket in which substrates are bound in distinct bent conformations involving the Zn-binding site Homo sapiens

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.14.11.66 [histone H3]-N6,N6,N6-trimethyl-L-lysine 9 + 2-oxoglutarate + O2 Homo sapiens
-
 [histone H3]-N6,N6-dimethyl-L-lysine 9 + succinate + formaldehyde + CO2
-
 ?
1.14.11.66 [histone H3]-N6,N6-dimethyl-L-lysine 9 + 2-oxoglutarate + O2 Homo sapiens
-
 [histone H3]-N6-methyl-L-lysine 9 + succinate + formaldehyde + CO2
-
 ?
1.14.11.69 [histone H3]-N6,N6,N6-trimethyl-L-lysine 36 + 2-oxoglutarate + O2 Homo sapiens
-
 [histone H3]-N6,N6-dimethyl-L-lysine 36 + succinate + formaldehyde + CO2
-
 ?
1.14.11.69 [histone H3]-N6,N6-dimethyl-L-lysine 36 + 2-oxoglutarate + O2 Homo sapiens
-
 [histone H3]-N6-methyl-L-lysine 36 + succinate + formaldehyde + CO2
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
1.14.11.66 Homo sapiens O75164
-
-
1.14.11.69 Homo sapiens O75164
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.14.11.66 recombinant N-terminally His-tagged enzyme from Escherichia coli by nickel affinity chromatography, gel filtration, and anion exchange chromatography Homo sapiens
1.14.11.69 recombinant N-terminally His-tagged enzyme from Escherichia coli by nickel affinity chromatography, gel filtration, and anion exchange chromatography Homo sapiens

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.14.11.66 additional information human enzyme JMJD2A (jumonji domain containing 2A) is selective towards tri- and dimethylated histone H3 lysyl residues 9 and 36 (H3K9me3/me2 and H3K36me3/me2), it discriminates between methylation states and achieves sequence selectivity for H3K9. Structures reveal a lysyl-binding pocket in which substrates are bound in distinct bent conformations involving the Zn2+-binding site Homo sapiens ?
-
 ?
1.14.11.66 [histone H3]-N6,N6,N6-trimethyl-L-lysine 9 + 2-oxoglutarate + O2
-
 Homo sapiens [histone H3]-N6,N6-dimethyl-L-lysine 9 + succinate + formaldehyde + CO2
-
 ?
1.14.11.66 [histone H3]-N6,N6-dimethyl-L-lysine 9 + 2-oxoglutarate + O2
-
 Homo sapiens [histone H3]-N6-methyl-L-lysine 9 + succinate + formaldehyde + CO2
-
 ?
1.14.11.69 additional information human enzyme JMJD2A (jumonji domain containing 2A) is selective towards tri- and dimethylated histone H3 lysyl residues 9 and 36 (H3K9me3/me2 and H3K36me3/me2), it discriminates between methylation states and achieves sequence selectivity for H3K9. Structures reveal a lysyl-binding pocket in which substrates are bound in distinct bent conformations involving the Zn2+-binding site Homo sapiens ?
-
 ?
1.14.11.69 [histone H3]-N6,N6,N6-trimethyl-L-lysine 36 + 2-oxoglutarate + O2
-
 Homo sapiens [histone H3]-N6,N6-dimethyl-L-lysine 36 + succinate + formaldehyde + CO2
-
 ?
1.14.11.69 [histone H3]-N6,N6-dimethyl-L-lysine 36 + 2-oxoglutarate + O2
-
 Homo sapiens [histone H3]-N6-methyl-L-lysine 36 + succinate + formaldehyde + CO2
-
 ?

Synonyms

EC Number Synonyms Comment Organism
1.14.11.66 histone demethylase JmjD2A
-
 Homo sapiens
1.14.11.66 JMJD2A
-
 Homo sapiens
1.14.11.66 jumonji domain containing 2A
-
 Homo sapiens
1.14.11.66 KDM4A
-
 Homo sapiens
1.14.11.66 More see also EC 1.14.11.69 Homo sapiens
1.14.11.69 histone demethylase JmjD2A
-
 Homo sapiens
1.14.11.69 JMJD2A
-
 Homo sapiens
1.14.11.69 jumonji domain containing 2A
-
 Homo sapiens
1.14.11.69 KDM4A
-
 Homo sapiens
1.14.11.69 More see also EC 1.14.11.66 Homo sapiens

General Information

EC Number General Information Comment Organism
1.14.11.66 additional information the mechanism for achieving methylation state selectivity involves the orientation of the substrate methyl groups towards a ferryl intermediate. Active site structure and mechanism of JMJD2A, overview Homo sapiens
1.14.11.69 additional information the mechanism for achieving methylation state selectivity involves the orientation of the substrate methyl groups towards a ferryl intermediate. Active site structure and mechanism of JMJD2A, overview Homo sapiens