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 |
expression of N-terminally His-tagged KDM4D in Escherichia coli | Homo sapiens |
expression of N-terminally His-tagged KDM4E 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 |
Protein Variants | Comment | Organism |
---|---|---|
I71L | KDM4E mutant, no demethylation of H3K9me2, but the mutant demethylates H3K9me3 to H3K9me2 and H3K9me1 in a similar manner to wild-type KDM4A | Homo sapiens |
I87K | KDM4E mutant, no demethylation of H3K9me2, but the mutant demethylates H3K9me3 to H3K9me2 and H3K9me1 in a similar manner to wild-type KDM4A | Homo sapiens |
N86H | KDM4E mutant, no demethylation of H3K9me2, but the mutant demethylates H3K9me3 to H3K9me2 and H3K9me1 in a similar manner to wild-type KDM4A | Homo sapiens |
Q88K | KDM4E mutant, the mutant shows demethylation of H3K9me2, and the mutant demethylates H3K9me3 to H3K9me2 and H3K9me1 in a similar manner to wild-type KDM4A | Homo sapiens |
R309G | KDM4E mutant, poor demethylation of H3K9me2, but the mutant demethylates H3K9me3 to H3K9me2 and H3K9me1 in a similar manner to wild-type KDM4A | Homo sapiens |
KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
---|---|---|---|---|---|
0.023 | - |
histone H3 N6,N6,N6-trimethyl-L-lysine9 | KDM4E, pH and temperature not specified in the publication | Homo sapiens | |
0.025 | - |
histone H3 N6,N6-dimethyl-L-lysine9 | KDM4E, pH and temperature not specified in the publication | Homo sapiens | |
0.031 | - |
histone H3 N6,N6,N6-trimethyl-L-lysine9 | KDM4B, pH and temperature not specified in the publication | Homo sapiens | |
0.037 | - |
histone H3 N6,N6,N6-trimethyl-L-lysine9 | KDM4D, pH and temperature not specified in the publication | Homo sapiens | |
0.045 | - |
histone H3 N6,N6,N6-trimethyl-L-lysine9 | KDM4A, pH and temperature not specified in the publication | Homo sapiens | |
0.048 | - |
histone H3 N6,N6,N6-trimethyl-L-lysine9 | KDM4C, pH and temperature not specified in the publication | Homo sapiens | |
0.05 | - |
histone H3 N6,N6-dimethyl-L-lysine9 | KDM4B, pH and temperature not specified in the publication | Homo sapiens | |
0.066 | - |
histone H3 N6,N6-dimethyl-L-lysine9 | KDM4C, pH and temperature not specified in the publication | Homo sapiens | |
0.073 | - |
histone H3 N6,N6-dimethyl-L-lysine9 | KDM4A, pH and temperature not specified in the publication | Homo sapiens | |
0.074 | - |
histone H3 N6,N6-dimethyl-L-lysine9 | KDM4D, pH and temperature not specified in the publication | 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-lysine9 + 2-oxoglutarate + O2 | Homo sapiens | - |
histone H3 N6,N6-dimethyl-L-lysine9 + succinate + formaldehyde + CO2 | - |
? | |
histone H3 N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2 | Homo sapiens | - |
histone H3 N6-methyl-L-lysine9 + succinate + formaldehyde + CO2 | - |
? | |
additional information | Homo sapiens | 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 | ? | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Homo sapiens | B2RXH2 | KDM4E | - |
Homo sapiens | O75164 | KDM4A; KDM4A | - |
Homo sapiens | O94953 | KDM4B | - |
Homo sapiens | Q6B0I6 | KDM4D | - |
Homo sapiens | Q9H3R0 | 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 |
recombinant N-terminally His-tagged KDM4D from Escherichia coli by nickel affinity chromatography | Homo sapiens |
recombinant N-terminally His-tagged KDM4E 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-lysine9 + 2-oxoglutarate + O2 | - |
Homo sapiens | histone H3 N6,N6-dimethyl-L-lysine9 + succinate + formaldehyde + CO2 | - |
? | |
histone H3 N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2 | - |
Homo sapiens | histone H3 N6-methyl-L-lysine9 + 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 |
---|---|---|
H3K9 demethylase | - |
Homo sapiens |
JMJD2 | - |
Homo sapiens |
KDM4 | - |
Homo sapiens |
Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
---|---|---|---|---|---|
0.0029 | - |
histone H3 N6,N6-dimethyl-L-lysine9 | KDM4A, pH and temperature not specified in the publication | Homo sapiens | |
0.005 | - |
histone H3 N6,N6-dimethyl-L-lysine9 | KDM4B, pH and temperature not specified in the publication | Homo sapiens | |
0.0072 | - |
histone H3 N6,N6-dimethyl-L-lysine9 | KDM4C, pH and temperature not specified in the publication | Homo sapiens | |
0.01 | - |
histone H3 N6,N6,N6-trimethyl-L-lysine9 | KDM4A, pH and temperature not specified in the publication | Homo sapiens | |
0.012 | - |
histone H3 N6,N6-dimethyl-L-lysine9 | KDM4D, pH and temperature not specified in the publication | Homo sapiens | |
0.015 | - |
histone H3 N6,N6,N6-trimethyl-L-lysine9 | KDM4D, pH and temperature not specified in the publication | Homo sapiens | |
0.028 | - |
histone H3 N6,N6,N6-trimethyl-L-lysine9 | KDM4B, pH and temperature not specified in the publication | Homo sapiens | |
0.029 | - |
histone H3 N6,N6,N6-trimethyl-L-lysine9 | KDM4C, pH and temperature not specified in the publication | Homo sapiens | |
0.065 | - |
histone H3 N6,N6-dimethyl-L-lysine9 | KDM4E, pH and temperature not specified in the publication | Homo sapiens | |
0.076 | - |
histone H3 N6,N6,N6-trimethyl-L-lysine9 | KDM4E, pH and temperature not specified in the publication | 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. 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, 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. Ile71A, Asn86A, Ile87A, Gln88A, and Arg309A may not be required for binding of H3K9 substrate | Homo sapiens |
kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
---|---|---|---|---|---|
4 | - |
histone H3 N6,N6-dimethyl-L-lysine9 | KDM4A, pH and temperature not specified in the publication | Homo sapiens | |
10 | - |
histone H3 N6,N6-dimethyl-L-lysine9 | KDM4B, pH and temperature not specified in the publication | Homo sapiens | |
11 | - |
histone H3 N6,N6-dimethyl-L-lysine9 | KDM4C, pH and temperature not specified in the publication | Homo sapiens | |
16 | - |
histone H3 N6,N6-dimethyl-L-lysine9 | KDM4D, pH and temperature not specified in the publication | Homo sapiens | |
22 | - |
histone H3 N6,N6,N6-trimethyl-L-lysine9 | KDM4A, pH and temperature not specified in the publication | Homo sapiens | |
41 | - |
histone H3 N6,N6,N6-trimethyl-L-lysine9 | KDM4D, pH and temperature not specified in the publication | Homo sapiens | |
60 | - |
histone H3 N6,N6,N6-trimethyl-L-lysine9 | KDM4C, pH and temperature not specified in the publication | Homo sapiens | |
90 | - |
histone H3 N6,N6,N6-trimethyl-L-lysine9 | KDM4B, pH and temperature not specified in the publication | Homo sapiens | |
260 | - |
histone H3 N6,N6-dimethyl-L-lysine9 | KDM4E, pH and temperature not specified in the publication | Homo sapiens | |
330 | - |
histone H3 N6,N6,N6-trimethyl-L-lysine9 | KDM4E, pH and temperature not specified in the publication | Homo sapiens |