Information on EC 1.14.11.27 - [histone-H3]-lysine-36 demethylase

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The expected taxonomic range for this enzyme is: Eukaryota

EC NUMBER
COMMENTARY hide
1.14.11.27
-
RECOMMENDED NAME
GeneOntology No.
[histone-H3]-lysine-36 demethylase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
protein N6,N6-dimethyl-L-lysine + 2-oxoglutarate + O2 = protein N6-methyl-L-lysine + succinate + formaldehyde + CO2
show the reaction diagram
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-
-
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protein N6-methyl-L-lysine + 2-oxoglutarate + O2 = protein L-lysine + succinate + formaldehyde + CO2
show the reaction diagram
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-
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SYSTEMATIC NAME
IUBMB Comments
protein-N6,N6-dimethyl-L-lysine,2-oxoglutarate:oxygen oxidoreductase
Requires iron(II). Of the seven potential methylation sites in histones H3 (K4, K9, K27, K36, K79) and H4 (K20, R3) from HeLa cells, the enzyme is specific for Lys-36. Lysine residues exist in three methylation states (mono-, di- and trimethylated). The enzyme preferentially demethylates the dimethyl form of Lys-36 (K36me2), which is its natural substrate, to form the monomethyl and unmethylated forms of Lys-36. It can also demethylate the monomethyl- but not the trimethyl form of Lys-36.
CAS REGISTRY NUMBER
COMMENTARY hide
55071-98-2
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
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Manually annotated by BRENDA team
Mus musculus C57BL/6
C57BL/6 mice
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-
Manually annotated by BRENDA team
Mus musculus C57BL/6J
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-
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Manually annotated by BRENDA team
gene MAL8P1.111
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Manually annotated by BRENDA team
histone demethylases Ndy1
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-
Manually annotated by BRENDA team
gene rph1
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Manually annotated by BRENDA team
gene JHDM1A
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
metabolism
dKDM2 couples histone H2A ubiquitylation to histone H3 demethylation during Polycomb group gene silencing as a mode of histone crosstalk, the enzyme acts as part of the dRING-associated factor, dRAF, a Polycomb group silencing complex harboring also the histone H2A ubiquitin ligase dRING, Posterior sex combs and the F-box protein, overview. dRAF and PCR1 are separtate Polycomb group complexes, dKDM2 and PRC1 control overlapping transcriptomes, mechanisms, overview
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
dimethyl-histone 3 L-lysine 36 + 2-oxoglutarate + O2
methyl-histone 3 L-lysine 36 + succinate + formaldehyde + CO2
show the reaction diagram
histone H3 N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2
histone H3 N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
show the reaction diagram
histone H3 N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
show the reaction diagram
histone H3 N6-methyl-L-lysine36 + 2-oxoglutarate + O2
histone H3 L-lysine36 + succinate + formaldehyde + CO2
show the reaction diagram
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2
histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
show the reaction diagram
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
show the reaction diagram
protein 6-N,6-N-dimethyl-L-lysine + 2-oxoglutarate + O2
protein 6-N-methyl-L-lysine + succinate + formaldehyde + CO2
show the reaction diagram
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specifically demethylates Lys36 of histone H3
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-
?
protein 6-N-methyl-L-lysine + 2-oxoglutarate + O2
protein L-lysine + succinate + formaldehyde + CO2
show the reaction diagram
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specifically demethylates Lys36 of histone H3
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-
?
protein C/EBPalpha-N6,N6-dimethyl-L-lysine + 2-oxoglutarate + O2
protein C/EBPalpha-N6-methyl-L-lysine + succinate + formaldehyde + CO2
show the reaction diagram
protein N6,N6-dimethyl-L-lysine + 2-oxoglutarate + O2
protein N6-methyl-L-lysine + succinate + formaldehyde + CO2
show the reaction diagram
-
specifically demethylates Lys36 of histone H3
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-
?
protein N6-methyl-L-lysine + 2-oxoglutarate + O2
protein L-lysine + succinate + formaldehyde + CO2
show the reaction diagram
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specifically demethylates Lys36 of histone H3
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-
?
trimethyl-histone 3 L-lysine 36 + 2-oxoglutarate + O2
dimethyl-histone 3 L-lysine 36 + ?
show the reaction diagram
-
-
-
?
trimethyl-histone 3 L-lysine 36 + 2-oxoglutarate + O2
dimethyl-histone 3 L-lysine 36 + succinate + formaldehyde + CO2
show the reaction diagram
-
enzyme Rph1 is specific for di- and trimethyl-histone 3 L-lysine36
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-
?
trimethyl-histone 3 L-lysine 36 + alpha-ketoglutarate + O2
dimethyl-histone 3 L-lysine 36 + ?
show the reaction diagram
-
-
-
?
[histone H3]-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2
[histone H3]-L-lysine36 + succinate + formaldehyde + CO2
show the reaction diagram
[histone H3]-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
[histone H3]-L-lysine36 + succinate + formaldehyde + CO2
show the reaction diagram
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
show the reaction diagram
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
dimethyl-histone 3 L-lysine 36 + 2-oxoglutarate + O2
methyl-histone 3 L-lysine 36 + succinate + formaldehyde + CO2
show the reaction diagram
-
enzyme Rph1 is specific for di- and trimethyl-histone 3 L-lysine36
-
-
?
histone H3 N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2
histone H3 N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
show the reaction diagram
histone H3 N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
show the reaction diagram
P39956
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-
-
?
histone H3 N6-methyl-L-lysine36 + 2-oxoglutarate + O2
histone H3 L-lysine36 + succinate + formaldehyde + CO2
show the reaction diagram
P39956
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-
-
?
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2
histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
show the reaction diagram
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
show the reaction diagram
protein C/EBPalpha-N6,N6-dimethyl-L-lysine + 2-oxoglutarate + O2
protein C/EBPalpha-N6-methyl-L-lysine + succinate + formaldehyde + CO2
show the reaction diagram
trimethyl-histone 3 L-lysine 36 + 2-oxoglutarate + O2
dimethyl-histone 3 L-lysine 36 + succinate + formaldehyde + CO2
show the reaction diagram
-
enzyme Rph1 is specific for di- and trimethyl-histone 3 L-lysine36
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-
?
[histone H3]-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2
[histone H3]-L-lysine36 + succinate + formaldehyde + CO2
show the reaction diagram
O75164
JMJD2A is a trimethyllysine-specific JmjC HDM
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-
?
[histone H3]-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
[histone H3]-L-lysine36 + succinate + formaldehyde + CO2
show the reaction diagram
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
show the reaction diagram
Q9V333, Q9V6L0
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-
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?
additional information
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ni2+
the Ni2+ ion at the active site is chelated by conserved residues and the cofactor 2-oxoglutarate
Zn2+
structure of Zn2+ binding sites of the isozymes, overview; structure of Zn2+ binding sites of the isozymes, overview; structure of Zn2+ binding sites of the isozymes, overview
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Co2+
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cobalt ions increase H3K9me3 and H3K36me3 by inhibiting histone demethylation process. Cobalt ions do not affect JMJD2A protein level but directly inhibit its demethylase activity. Exposure of both lung carcinoma A-549 cells and bronchial epithelial Beas-2B cells, to CoCl2 at 0.2 mM for 24 h increases methylation of histone H3 lysine residues 4, 9, 27 and 36, i.e. H3K4me3, H3K9me2, H3K9me3, H3K27me3, H3K36me3, as well as ubiquitination of histone H2A and H2B, while it decreases acetylation at histone H4, overview
N-oxalylglycine
i.e. NOG, a non-reactive 2-oxoglutarate analogue
Ni2+
substitutes Fe2+ and inhibits the hydroxylation reaction
additional information
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expression of GTT1, UGX2, CTT1, and HSP26 is highly induced by H2O2 treatment and causes the dissociation of Rph1 from the promoters of these genes
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ascorbate
heterochromatin protein 1
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predominant localization to centric heterochromatin. HP1a, when resident near centromeres, plays a role in the gene silencing associated with heterochromatin packaging. HP1a binding, two molecules HP1a per enzyme molecule, stimulates demethylation of H3K36me2 and H3K36me3 by dKDM4a, mechanism, overview. HP1a mutant V26M is inactive
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HP1 a protein
HP1a, encoded by the Su(var)2-5 gene and involved in the establishment and maintenance of higher-order structure of heterochromatin, stimulates the histone H3K36 demethylation activity of dKDM4A, and this stimulation depends on the H3K9me-binding motif of HP1a. HP1a and dKDM4A interact with each other, and loss of HP1a leads to an increased level of histone H3K36me3. The CSD of HP1a and a consensus HP1-interacting PxVxL motif in dKDM4A are responsible for the HP1a-dKDM4A interaction
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.32
trimethyl-histone 3 L-lysine 36
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pH 7.3, 37°C
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additional information
additional information
binding affinities of c-Rph1 with H3K36 and H3K9 peptides, overview
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00022
trimethyl-histone 3 L-lysine 36
Homo sapiens
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pH 7.3, 37°C
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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Manually annotated by BRENDA team
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quantitative RT-PCRof dKDM4A expression analysis of wild-type and mutant enzymes in larvae
Manually annotated by BRENDA team
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high expression level of KDM2b/JHDM1b
Manually annotated by BRENDA team
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Manually annotated by BRENDA team
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
250000
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oligomer
x * 56500, calculated
additional information
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phosphoprotein
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystallization of JMJD2A in complex with histone H3 peptides bearing different methylated forms of K9 and K36, cocrystallization of inactivated substrate with either N-oxalylglycine, a non-reactive 2-OG analog, or with Ni(II), which substitutes for Fe(II) and inhibits the hydroxylation reaction. Structures analysis, overview
in complex with trimethyl-histone 3 L-lysine 9, dimethyl-histone 3 L-lysine 36, and trimethyl-histone 3 L-lysine 36, and N-oxalylglycine, 2-oxoglutarate, and succinate, respectively. Histone substrates are recognized through a network of backbone hydrogen bonds and hydrophobic interactions that deposit the trimethyllysine into the active site. The trimethylated epsilon-ammonium cation is coordinated within a methylammonium-binding pocket through carbonoxygen hydrogen bonds that position one of the methyl groups adjacent to the Fe(II) center for hydroxylation and demethylation
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purified recombinant fusion protein, JMJD5 catalytic domain in complex with substrate 2-oxoglutarate and inhibitor N-oxalylglycine, hanging drop vapor diffusion, mixing of 12 mg/ml protein in for the inhibitor complex 15 mM bis-Tris, pH 7.2, 25 mM NaCl, 1.0 mM dithiothreitol, 1.0 mM N--oxalylglycine, and 0.5 mM CoCl2, or for te substrate complex in 15mM Tris, pH 8.5, 25 mM NaCl, 1.5 mM 2-oxoglutarate, 1.5 mM dithiothreitol, and 4 mM H3K36me2-L peptide, ,with an equal volume of mother liquor containing 4.5% w/v PEG 3000, 0.1M bis-Tris, pH 5.5, and 50 mM MgCl2, 20°C, X-ray diffraction structure determination and analysis at 1.05-1.15 A resolution
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
structures of JMJD2A–Ni(II)–Zn(II) inhibitor complexes bound to tri-, di- and monomethyl forms of histone 3 lysine 9 andthe trimethyl form of histone 3 lysine 36. The structures reveal a lysyl-binding pocket in which substrates are bound in distinct bent conformations involving the Zn-binding site. The mechansim for achieving methylation state selectivity involves the orientation of the substrate methyl groups towards a ferryl intermediate
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structures of the catalytic core complexed with methylated histone 3 L-lysine36 peptide substrates in the presence of Fe(II) and N-oxalylglycine. The interaction between enzyme and peptides largely involves the main chains of the enzyme and the peptide. The peptide-binding specificity is primarily determined by the primary structure of the peptide
catalytic core of Rph1, hanging drop vapour diffusion method, X-ray diffraction structure determination and analysis at 2.5 A resolution
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
the JmjN domain is important in maintaining protein stability and the repressive effect of Rph1
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme purified from baculovirus-infected Sf9 cells
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recombinant fusion proteins His6-Smt3-JMJD5183–416 and His6-Smt3-JMJD52–416 from Escherichia coli strain BL21 Rosetta2 DE3 by nickel affinity chromatography and gel filtration
recombinant N-terminally His-tagged KDM4A from Escherichia coli by nickel affinity chromatography; recombinant N-terminally His-tagged KDM4B from Escherichia coli by nickel affinity chromatography; recombinant N-terminally His-tagged KDM4C from Escherichia coli by nickel affinity chromatography
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
characterization of dKDM4A alleles, and the dKDM4A genomic locus, the dKDM4A locus contains four exons, overview. Quantitative RT-PCR of dKDM4A expression analysis of wild-type and mutant enzymes in larvae
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DNA and amino acid sequence determination and analysis, chromosomal location and association analysis , the porcine JHDM1A gene encodes 1,162 amino acids and contains JmjC, F-box, and CXXC zinc-finger domains, which coding sequence and deduced protein shares 91 and 99% similarity with human JHDM1A, respectively
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ectopic expression of either wild-type Jhdm1a or H212A point mutant in the liver of diabetic ob/ob mice
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ectopic expression of Jhdm1a in HeLa and wild-type and enzyme-deficient Hep-G2 cells via lentivirus transfection
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enzyme overexpression in HEK-293T cells, phenotype,, overview
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expression analysis by quantitative reverse transcriptase PCR, overexpression of wild-type Jhdm1b in HeLa and HEK293 cells
expression in Escherichia coli, His-tagged
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expression in mouse embryo fibroblast
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expression of FLAG-tagged JMJD2A in Spodoptera frugiperda Sf9 cells
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expression of Flag-tagged protein
expression of fusion proteins His6-Smt3-JMJD5183–416 and His6-Smt3-JMJD52–416 in Escherichia coli strain BL21 Rosetta2 DE3
expression of GFP-tagged JmjD2A under the control beta-actin promoter in chicken fibroblasts
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expression of N-terminally His-tagged KDM4A in Escherichia coli; expression of N-terminally His-tagged KDM4B in Escherichia coli; expression of N-terminally His-tagged KDM4C in Escherichia coli
expression of wild-type and mutant dKDM4A in Spodoptera frugiperda Sf21 cells using baculovirus transfection
gene dkdm4a, expression of FLAG-tagged wild-type and V423A mutant enzymes
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gene Jmjd5, FLAG-His6 tagged mutant H319A is cloned into the pDON-5 Neo plasmid to produce retroviruses, shRNA-expressing retroviruses are used for silencing of the enzyme, expression of C-terminally His-tagged JMJD5 in Escherichia coli, quantitative reverse transcription PCR expression analysis
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gene MAL8P1.111, located on chromosome 8, DNA and amino acid sequence determination and analysis, detailed phylogenetic analysis, overview
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Ndy1 overexpression in mouse embryonic fibroblasts, quantitative real-time reverse transcriptase PCR expression analysis
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overexpression of FLAG-tagged CG15835 in S2 cells
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
CG15835 overexpression induces spreading of HP1, out of heterochromatin, into euchromatin, without affecting the actual pattern of histone modifications of heterochromatin. Overexpression of dJMJD2(1)/CG15835 results in a strong decrease on the levels of H3K9me3 and H3K36me3, but it does not show any significant effect on the extent of H3K9me3 and H3K9me2 at the chromocentre
checkpoint kinase Rad53 negatively modulates Rph1 protein level; the crucial checkpoint protein Rad53 acts as an upstream regulator of Rph1 and dominates the phosphorylation of Rph1 that is required for efficient PHR1 expression and the dissociation of Rph1
knockdown of Jhdm1b in primary mouse embryonic fibroblasts inhibits cell proliferation and induces cellular senescence in a pRb and p53 pathway-dependent manner. The effect of Jhdm1b on cell proliferation and cellular senescence is mediated through de-repression of p15Ink4b as loss of p15Ink4b function rescues cell proliferation defects in Jhdm1b knockdown cells
Rph1 is phosphorylated under oxidative stress, which leads to Rph1 dissociation and transcriptional activation. Rad53 may be the key kinase essential for Rph1 phosphorylation on oxidative stress with H2O2 treatment
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
V423A
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site-directed mutagenesis, the point mutation at the central valine of PxVxL motif disrupts the interaction between dKDM4A and HP1a in vitro
H188A
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inactive mutant
H212A
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mutation completely abolishes the enzymatic activity
H211A
inactive mutant
H212A
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inactive mutant
H319A
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a catalytically inactive mutant
H212A
Mus musculus C57BL/6J
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inactive mutant
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H235A
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catalytically deficient mutant
T302A
more than 90% loss of activity
Y315A
more than 90% loss of activity
H235A
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catalytically deficient mutant
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additional information