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Literature summary for 1.14.11.27 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)

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 (Commentary)

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

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

Metals/Ions

Metals/Ions Comment Organism Structure
Zn2+ structure of Zn2+ binding sites of the isozymes, overview 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-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

Organism UniProt Comment Textmining
Homo sapiens
-
KDM4B
-
Homo sapiens O75164 KDM4A; KDM4A
-
Homo sapiens Q9H3R0 KDM4C; KDM4C
-

Purification (Commentary)

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 and Products (Substrate)

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

Synonyms Comment Organism
H3K36 demethylase
-
Homo sapiens
JMJD2
-
Homo sapiens
KDM4
-
Homo sapiens

General Information

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