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Literature summary for 1.14.11.66 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
Search for more literature for 1.14.11.66

Cloned(Commentary)

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

Crystallization (Commentary)

Crystallization (Comment) Organism
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

Inhibitors

Inhibitors Comment Organism Structure
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
Ni2+
-
 Homo sapiens
Zn2+
-
 Homo sapiens

Metals/Ions

Metals/Ions Comment Organism Structure
Fe2+ the mechanism for achieving methylation state selectivity involves the orientation of the substrate methyl groups towards a ferryl intermediate Homo sapiens
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)

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

Organism

Organism UniProt Comment Textmining
Homo sapiens O75164
-
-

Purification (Commentary)

Purification (Comment) Organism
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)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
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 ?
-
 ?
[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
-
 ?
[histone H3]-N6,N6-dimethyl-L-lysine 9 + 2-oxoglutarate + O2
-
 Homo sapiens [histone H3]-N6-methyl-L-lysine 9 + succinate + formaldehyde + CO2
-
 ?

Synonyms

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

General Information

General Information Comment Organism
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