Cloned (Comment) | Organism |
---|---|
expression of N-terminally His-tagged KDM4A in Escherichia coli | Homo sapiens |
expression of N-terminally His-tagged KDM4B in Escherichia coli | Homo sapiens |
expression of N-terminally His-tagged KDM4C in Escherichia coli | Homo sapiens |
Crystallization (Comment) | Organism |
---|---|
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 | Homo sapiens |
Localization | Comment | Organism | GeneOntology No. | Textmining |
---|---|---|---|---|
nucleus | - |
Homo sapiens | 5634 | - |
Metals/Ions | Comment | Organism | Structure |
---|---|---|---|
Zn2+ | structure of Zn2+ binding sites of the isozymes, overview | Homo sapiens |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2 | Homo sapiens | - |
histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2 | - |
? | |
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2 | Homo sapiens | - |
histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2 | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Homo sapiens | - |
KDM4B | - |
Homo sapiens | O75164 | KDM4A; KDM4A | - |
Homo sapiens | Q9H3R0 | KDM4C; KDM4C | - |
Purification (Comment) | Organism |
---|---|
recombinant N-terminally His-tagged KDM4A from Escherichia coli by nickel affinity chromatography | Homo sapiens |
recombinant N-terminally His-tagged KDM4B from Escherichia coli by nickel affinity chromatography | Homo sapiens |
recombinant N-terminally His-tagged KDM4C from Escherichia coli by nickel affinity chromatography | Homo sapiens |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2 | - |
Homo sapiens | histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2 | - |
? | |
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2 | substrate is preferred compared to histone H3-N6,N6-dimethyl-L-lysine36 | Homo sapiens | histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2 | - |
? | |
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2 | - |
Homo sapiens | histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2 | - |
? | |
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2 | low activity | Homo sapiens | histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2 | - |
? | |
additional information | KDM4D and -E only act on H3K9, with no evidence for demethylation of H3K36, while KDM4A/B/C act on both H3K9 and, less efficiently, on H3K36-methylated substrates. No activity by all isozymes with H3K4me3, H3K9me1, and H3K27me3 | Homo sapiens | ? | - |
? |
Synonyms | Comment | Organism |
---|---|---|
H3K36 demethylase | - |
Homo sapiens |
JMJD2 | - |
Homo sapiens |
KDM4 | - |
Homo sapiens |
General Information | Comment | Organism |
---|---|---|
evolution | human JMJD2 (KDM4) H3K9 and H3K36 demethylases can be divided into members that act on both H3K9 and H3K36 and H3K9 alone, structural and phylogenetic analysis, overview. KDM4A/B/C act on both H3K9 and, less efficiently, on H3K36-methylated substrates, substrate selectivity of the human KDM4 histone demethylase subfamily, overview | Homo sapiens |
additional information | substrate selectivity is determined by multiple interactions within the catalytic domain but outside the active site, structural basis of sequence celectivity between KDM4 members, overview | Homo sapiens |