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Literature summary extracted from

  • Hillringhaus, L.; Yue, W.W.; Rose, N.R.; Ng, S.S.; Gileadi, C.; Loenarz, C.; Bello, S.H.; Bray, J.E.; Schofield, C.J.; Oppermann, U.
    Structural and evolutionary basis for the dual substrate selectivity of human KDM4 histone demethylase family (2011), J. Biol. Chem., 286, 41616-41625 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.14.11.66 gene KDM4A, phylogenetic analysis, recombinant expression of N-terminally His-tagged KDM4A catalytic domain in Escherichia coli Homo sapiens
1.14.11.66 gene KDM4B, phylogenetic analysis, recombinant expression of N-terminally His-tagged KDM4B catalytic domain in Escherichia coli Homo sapiens
1.14.11.66 gene KDM4C, phylogenetic analysis, recombinant expression of N-terminally His-tagged KDM4C catalytic domain in Escherichia coli Homo sapiens
1.14.11.66 gene KDM4D, phylogenetic analysis, recombinant expression of N-terminally His-tagged KDM4D catalytic domain in Escherichia coli Homo sapiens
1.14.11.66 gene KDM4E, phylogenetic analysis, recombinant expression of N-terminally His-tagged KDM4E catalytic domain in Escherichia coli Homo sapiens
1.14.11.69 gene KDM4A, phylogenetic analysis, recombinant expression of N-terminally His-tagged KDM4A catalytic domain in Escherichia coli Homo sapiens
1.14.11.69 gene KDM4B, phylogenetic analysis, recombinant expression of N-terminally His-tagged KDM4B catalytic domain in Escherichia coli Homo sapiens
1.14.11.69 gene KDM4C, phylogenetic analysis, recombinant expression of N-terminally His-tagged KDM4C catalytic domain in Escherichia coli Homo sapiens

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.14.11.66 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 Homo sapiens
1.14.11.66 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 Homo sapiens
1.14.11.69 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 Homo sapiens

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.14.11.66 0.023
-
 [histone H3]-N6,N6,N6-trimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4E Homo sapiens
1.14.11.66 0.025
-
 [histone H3]-N6,N6-dimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4E Homo sapiens
1.14.11.66 0.031
-
 [histone H3]-N6,N6,N6-trimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4B Homo sapiens
1.14.11.66 0.037
-
 [histone H3]-N6,N6,N6-trimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4D Homo sapiens
1.14.11.66 0.045
-
 [histone H3]-N6,N6,N6-trimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4A Homo sapiens
1.14.11.66 0.048
-
 [histone H3]-N6,N6,N6-trimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4C Homo sapiens
1.14.11.66 0.05
-
 [histone H3]-N6,N6-dimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4B Homo sapiens
1.14.11.66 0.066
-
 [histone H3]-N6,N6-dimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4C Homo sapiens
1.14.11.66 0.073
-
 [histone H3]-N6,N6-dimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4A Homo sapiens
1.14.11.66 0.074
-
 [histone H3]-N6,N6-dimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4D 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+ required Homo sapiens
1.14.11.66 Zn2+ comparison of the Zn(II)-binding site Homo sapiens
1.14.11.69 Fe2+ required Homo sapiens
1.14.11.69 Zn2+ comparison of the Zn(II)-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 additional information Homo sapiens the enzyme acts on H3K9me3/me2, but not on H3K36 substrates ?
-
 ?
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 B2RXH2
-
-
1.14.11.66 Homo sapiens O75164
-
-
1.14.11.66 Homo sapiens O94953
-
-
1.14.11.66 Homo sapiens Q6B0I6
-
-
1.14.11.66 Homo sapiens Q9H3R0
-
-
1.14.11.69 Homo sapiens O75164
-
-
1.14.11.69 Homo sapiens O94953
-
-
1.14.11.69 Homo sapiens Q9H3R0
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.14.11.66 recombinant N-terminally His-tagged KDM4A catalytic domain from Escherichia coli Homo sapiens
1.14.11.69 recombinant N-terminally His-tagged KDM4A catalytic domain from Escherichia coli Homo sapiens

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.14.11.66 additional information the enzyme acts on H3K9me3/me2, but not on H3K36 substrates Homo sapiens ?
-
 ?
1.14.11.66 additional information bifunctional KDM4A catalyzes demethylation of tri- and di-methylated forms of both histone H3 lysine 9 (H3K9me3/me2) and lysine 36 (H3K36me3/me2). Enzyme KDM4A preferentially catalyzes demethylation at Lys9 rather than Lys36 under identical conditions. Demethylation of H3K9me3 to H3K9me0 is observed on prolonged incubation of 15-residue H3K9me3 peptides Homo sapiens ?
-
 ?
1.14.11.66 additional information bifunctional KDM4A catalyzes demethylation of tri- and di-methylated forms of both histone H3 lysine 9 (H3K9me3/me2) and lysine 36 (H3K36me3/me2). Enzyme KDM4B preferentially catalyzes demethylation at Lys9 rather than Lys36 under identical conditions. Demethylation of H3K9me3 to H3K9me0 is observed on prolonged incubation of 15-residue H3K9me3 peptides Homo sapiens ?
-
 ?
1.14.11.66 additional information bifunctional KDM4A catalyzes demethylation of tri- and di-methylated forms of both histone H3 lysine 9 (H3K9me3/me2) and lysine 36 (H3K36me3/me2). Enzyme KDM4C preferentially catalyzes demethylation at Lys9 rather than Lys36 under identical conditions. Demethylation of H3K9me3 to H3K9me0 is observed on prolonged incubation of 15-residue H3K9me3 peptides Homo sapiens ?
-
 ?
1.14.11.66 additional information the enzyme acts on tri- and di-methylated forms of H3K9, but not on H3K36 substrates. Demethylation of H3K9me3 to H3K9me0 is observed on prolonged incubation of 15-residue H3K9me3 peptides 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 bifunctional KDM4A catalyzes demethylation of tri- and di-methylated forms of both histone H3 lysine 9 (H3K9me3/me2) and lysine 36 (H3K36me3/me2). Enzyme KDM4A preferentially catalyzes demethylation at Lys9 rather than Lys36 under identical conditions. Demethylation of H3K9me3 to H3K9me0 is observed on prolonged incubation of 15-residue H3K9me3 peptides Homo sapiens ?
-
 ?
1.14.11.69 additional information bifunctional KDM4A catalyzes demethylation of tri- and di-methylated forms of both histone H3 lysine 9 (H3K9me3/me2) and lysine 36 (H3K36me3/me2). Enzyme KDM4B preferentially catalyzes demethylation at Lys9 rather than Lys36 under identical conditions. Demethylation of H3K9me3 to H3K9me0 is observed on prolonged incubation of 15-residue H3K9me3 peptides Homo sapiens ?
-
 ?
1.14.11.69 additional information bifunctional KDM4A catalyzes demethylation of tri- and di-methylated forms of both histone H3 lysine 9 (H3K9me3/me2) and lysine 36 (H3K36me3/me2). Enzyme KDM4C preferentially catalyzes demethylation at Lys9 rather than Lys36 under identical conditions. Demethylation of H3K9me3 to H3K9me0 is observed on prolonged incubation of 15-residue H3K9me3 peptides 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 JMJD2A
-
 Homo sapiens
1.14.11.66 JMJD2B
-
 Homo sapiens
1.14.11.66 JMJD2C
-
 Homo sapiens
1.14.11.66 KDM4A
-
 Homo sapiens
1.14.11.66 KDM4B
-
 Homo sapiens
1.14.11.66 Kdm4c
-
 Homo sapiens
1.14.11.66 KDM4D
-
 Homo sapiens
1.14.11.66 KDM4E
-
 Homo sapiens
1.14.11.66 More see also EC 1.14.11.69 Homo sapiens
1.14.11.69 JMJD2A
-
 Homo sapiens
1.14.11.69 JMJD2B
-
 Homo sapiens
1.14.11.69 JMJD2C
-
 Homo sapiens
1.14.11.69 KDM4A
-
 Homo sapiens
1.14.11.69 KDM4B
-
 Homo sapiens
1.14.11.69 Kdm4c
-
 Homo sapiens
1.14.11.69 More see also EC 1.14.11.66 Homo sapiens

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.14.11.66 0.0029
-
 [histone H3]-N6,N6-dimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4A Homo sapiens
1.14.11.66 0.01
-
 [histone H3]-N6,N6,N6-trimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4A Homo sapiens
1.14.11.66 0.012
-
 [histone H3]-N6,N6-dimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4D Homo sapiens
1.14.11.66 0.015
-
 [histone H3]-N6,N6,N6-trimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4D Homo sapiens
1.14.11.66 0.028
-
 [histone H3]-N6,N6,N6-trimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4B Homo sapiens
1.14.11.66 0.029
-
 [histone H3]-N6,N6,N6-trimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4C Homo sapiens
1.14.11.66 0.05
-
 [histone H3]-N6,N6-dimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4B Homo sapiens
1.14.11.66 0.065
-
 [histone H3]-N6,N6-dimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4E Homo sapiens
1.14.11.66 0.072
-
 [histone H3]-N6,N6-dimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4C Homo sapiens
1.14.11.66 0.076
-
 [histone H3]-N6,N6,N6-trimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4E Homo sapiens

General Information

EC Number General Information Comment Organism
1.14.11.66 evolution the enzyme belongs to the KDM4/JmjC demethylase histone demethylase family. KDM4F is very similar to KDM4E sharing 94% identity over 369 residues. The selectivity of KDM4 enzymes is determined by multiple interactions within the catalytic domain but outside the active site. Evolutionary analysis of the KDM4 demethylase subfamily Homo sapiens
1.14.11.66 evolution the enzyme belongs to the KDM4/JmjC demethylase histone demethylase family. The selectivity of KDM4 enzymes is determined by multiple interactions within the catalytic domain but outside the active site. All KDM4 subfamily members have highly conserved residues lining the methylammonium-binding pocket. The exceptions are Ser288A/Ser-289B/Ser290C and Thr289A/Thr290B/Thr291C in KDM4A, B, and C, which are substituted by Ala287D/Ala289E/Ala286F and Ile288D/Ile290E/Ile287F in KDM4D-F, respectively. Evolutionary analysis of the KDM4 demethylase subfamily Homo sapiens
1.14.11.66 evolution the enzyme belongs to the KDM4/JmjC demethylase histone demethylase family. The selectivity of KDM4 enzymes is determined by multiple interactions within the catalytic domain but outside the active site. Evolutionary analysis of the KDM4 demethylase subfamily Homo sapiens
1.14.11.66 evolution the enzyme belongs to the KDM4/JmjC demethylase histone demethylase family. The selectivity of KDM4 enzymes is determined by multiple interactions within the catalytic domain but outside the active site. Evolutionary analysis of the KDM4 demethylase subfamily, a KDM4D type activity is important in eutherian biology Homo sapiens
1.14.11.66 additional information enzyme structure-function relationships and substrate selectivity, comparisons of KDM4 enzymes, overview Homo sapiens
1.14.11.69 evolution the enzyme belongs to the KDM4/JmjC demethylase histone demethylase family. The selectivity of KDM4 enzymes is determined by multiple interactions within the catalytic domain but outside the active site. All KDM4 subfamily members have highly conserved residues lining the methylammonium-binding pocket. The exceptions are Ser288A/Ser-289B/Ser290C and Thr289A/Thr290B/Thr291C in KDM4A, B, and C, which are substituted by Ala287D/Ala289E/Ala286F and Ile288D/Ile290E/Ile287F in KDM4D-F, respectively. Evolutionary analysis of the KDM4 demethylase subfamily Homo sapiens
1.14.11.69 evolution the enzyme belongs to the KDM4/JmjC demethylase histone demethylase family. The selectivity of KDM4 enzymes is determined by multiple interactions within the catalytic domain but outside the active site. Evolutionary analysis of the KDM4 demethylase subfamily Homo sapiens
1.14.11.69 additional information enzyme structure-function relationships and substrate selectivity, comparisons of KDM4 enzymes, overview Homo sapiens

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
1.14.11.66 0.0397
-
 [histone H3]-N6,N6-dimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4A Homo sapiens
1.14.11.66 0.162
-
 [histone H3]-N6,N6-dimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4D Homo sapiens
1.14.11.66 0.222
-
 [histone H3]-N6,N6,N6-trimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4A Homo sapiens
1.14.11.66 0.405
-
 [histone H3]-N6,N6,N6-trimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4D Homo sapiens
1.14.11.66 0.604
-
 [histone H3]-N6,N6,N6-trimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4C Homo sapiens
1.14.11.66 0.903
-
 [histone H3]-N6,N6,N6-trimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4B Homo sapiens
1.14.11.66 1
-
 [histone H3]-N6,N6-dimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4B Homo sapiens
1.14.11.66 1.09
-
 [histone H3]-N6,N6-dimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4C Homo sapiens
1.14.11.66 2.6
-
 [histone H3]-N6,N6-dimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4E Homo sapiens
1.14.11.66 3.304
-
 [histone H3]-N6,N6,N6-trimethyl-L-lysine 9 pH and temperature not specified in the publication, recombinant isozyme KDM4E Homo sapiens