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Enzyme Nomenclature
Information on EC 1.14.11.B2 - [histone-H3]-lysine-4-demethylase
for references in articles please use BRENDA:EC1.14.11.B2
Word Map on EC 1.14.11.B2
- 1.14.11.B2
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lysine-specific
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h3k4me2
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jhdm1b
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k-specific
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x-inactivation
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histone-modifying
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tri-methylation
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The enzyme appears in viruses and cellular organisms
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EC NUMBER 
COMMENTARY 
1.14.11.B2
preliminary BRENDA-supplied EC number
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RECOMMENDED NAME
GeneOntology No.
[histone-H3]-lysine-4-demethylase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
protein N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2 = protein N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
metabolism
physiological function
additional information
evolution
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KDM5C is a member of the evolutionarily conserved KDM5 family of four proteins, KDM5A/B/C and D. KDM5A/C/D demethylate tri- and di-methylated forms of H3K4, whereas KDM5B is capable of demethylating all three forms (tri-, di-, and mono) of H3K4 methylation
evolution
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Fbxl10 (Jhdm1b/Kdm2b) is a conserved and ubiquitously expressed member of the JHDM (JmjC domain-containing histone demethylase) family
malfunction
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LSD1 deficiency in embryonic stem cells results in growth and differentiation defects
malfunction
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mutations in the X-linked KDM5C gene, encoding a histone H3 lysine 4 demethylase, lading to significant loss of DNA methylation in blood of males with intellectual disability, especially loss of DNA methylation at the promoters of the three top candidate genes FBXL5, SCMH1, CACYBP. Mutant clinical features most consistently reported in males with mutations include mild to severe intellectual disability, epilepsy, short stature, hyperreflexia, aggressive behavior and microcephaly, phenotypes, overview. Significant loss of DNA methylation at specific genomic loci in blood samples of male patients carrying KDM5C mutations, suggesting these genes are epigenetic targets of KDM5C
malfunction
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reduction of Fbxl10 levels results in increased Xist, Ccl2, Ccl5, Ccl7, and Cxcl10 RNA expression. Other genes differentially expressed in D5 cells are not affected by the knockdown of Fbxl10
malfunction
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Cre-induced deletion of SALL4 in gene-targeted BM progenitors results in a remarkable decrease of SALL4-bound and LSD1-bound EBF1, accompanied by a 750fold increase of Lys4-dimethylated histon H3. Knockdown of LSD1 in bone marrow hematopoietic stem and progenitor cells leads to altered SALL4 downstream gene expression and increased cellular activity
malfunction
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loss of LSD1 causes gamma-irradiation hypersensitivity and increased homologous recombination
malfunction
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LSD1 knockdown by RNA interference or its displacement from the chromatin by antineoplastic agents caused an increase in the levels of a subset of LSD1 target genes
malfunction
loss of the enzyme reduces cell division rate of the stem and the size of plant stature
malfunction
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impaired JMJ703 activity leads to elevated levels of H3K4me3, the misregulation of numerous endogenous genes, and the transpositional reactivation of two families of non-LTR retrotransposons. But loss of JMJ703 did not affect transposable elements (such as Tos17) previously found to be silenced by other epigenetic pathways
malfunction
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Cre-induced deletion of SALL4 in gene-targeted BM progenitors results in a remarkable decrease of SALL4-bound and LSD1-bound EBF1, accompanied by a 750fold increase of Lys4-dimethylated histon H3. Knockdown of LSD1 in bone marrow hematopoietic stem and progenitor cells leads to altered SALL4 downstream gene expression and increased cellular activity
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metabolism
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histone methylation is a dynamic process regulated by the addition of methyl groups by histone methyltransferases and removal of methyl groups from mono- and dimethyllysines by lysine specific demethylase 1, LSD1, and from mono-, di, and trimethyllysines by specific JumonjiC, JmjC, domain-containing demethylases
metabolism
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hyperglycemia/hyperinsulinemia induced changes in expression of chromatin modifying genes and their regulation by histone modifications, overview. Crosstalk between these histone modifications under hyperinsulinemic/hyperglycemic conditions: no change in H3K9me1 levels at the coding regions of histone H3K9 demethylase (Jmjd2b) and H3K4 demethylase (Aof1), and decreased H3K4me1 levels at Myst4 and Jmjd2b and increased H3K4me1 levels on Set and Aof1. Levels of H3K9me1 are only changed at histone acetylase (Myst4) and deacetylase (Set), highlighting the role of this modification in regulating histone acetylation only. The chromatin remodelling genes Myst4, Jmjd2b, Set, and Aof1 show similar pattern of change for H3Ac and H3K4me1 on Myst4, Jmjd2b, Aof1 and Set gene promoter regions under both low glucose and high glucose condition after insulin stimulation
physiological function
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dJMJD2(1)/CG15835 is excluded from heterochromatin and localizes to multiple euchromatic sites, where it regulates H3K36 methylation and heterochromatin organization. CG15835 contributes to delimit hetero- and euchromatic territories through the regulation of H3K36 methylation in euchromatin
physiological function
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LSD1 allows transcription factors or corepressor complexes to selectively initiate or repress transcription via demethylation of lysine residues 4 or 9 of histone 3, thereby controlling gene expression programs. LSD1 modulates tumor cell biology by demethylating monomethyl and dimethyl lysines 4 or 9 in histone H3
physiological function
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LSD1 is associated with co-repressor complexes and promotes suppression or activation of gene expression, e.g. LSD1 might be associated to cooperative recruitment to the NFkappaB p65 site for activation in hyperglycemia
physiological function
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LSD1 is associated with co-repressor complexes and promotes suppression or activation of gene expression, e.g. LSD1 might be associated to cooperative recruitment to the NFkappaB p65 site for activation in hyperglycemia
physiological function
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LSD1 is essential for mammalian development and likely involved in many biological processes
physiological function
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histone methyl-L-lysine marks display dynamic changes during the parasite asexual erythrocytic cycle, suggesting that they constitute an important epigenetic mechanism of gene regulation in malaria parasites
physiological function
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LSD1 is required for gastrulation during mouse embryogenesis, and LSD1 is essential for maintaining global DNA methylation in embryonic stem cells
physiological function
rice JMJ706 encodes a heterochromatin-associated H3K9 demethylase involved in the regulation of flower development in rice. JMJ706 regulates a subset of flower development regulatory genes
physiological function
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H3 histone methylation and demethylation controls expression of estrogen-responsive genes, and DNA-bound estrogen receptor directs transcription by participating in bending chromatin to contact the RNA polymerase II recruited to the promoter driven by receptor-targeted demethylation of H3 lysine 9 through LSD1 at both enhancer and promoter sites, molecular mechanism, overview. The produced hydrogen peroxide, which modifies the surrounding DNA and recruits 8-oxoguanine�DNA glycosylase 1 and topoisomerase IIb, triggering chromatin and DNA conformational changes that are essential for estrogen-induced transcription
physiological function
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histone lysine demethylase 5 specifically demethylates H3K4me3/me2 and therefore plays a transcriptional repressor role. PLU-1 is able to promote breast cancer cell proliferation by facilitating G1/S phase transition. PLU-1 is involved in cancer growth amd proliferation, and PLU-1 is associated with androgen receptor and regulates its transcriptional activity
physiological function
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JARID1B act as transcriptional repressor, with hPc2 acting as a transcriptional co-repressor, overview
physiological function
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the histone demethylase KDM5A is an integral, conserved component of Notch/RBP-J gene silencing. KDM5A regulates gene expression at Notch target genes. Methylation of histone H3 Lys 4 is dynamically erased and re-established at RBP-J sites upon inhibition and reactivation of Notch signaling. KDM5A interacts physically with the core transcription factor RBP-J, this interaction is crucial for Notch-induced growth and tumorigenesis responses. Interaction analysis by ChIP-sequencing. KDM5A but not KDM5C binds strongly to GST-RBP-J
physiological function
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LSD1 plays an important role in the epigenetic control of gene expression, and aberrant gene silencing secondary to LSD1 overexpression is thought to contribute to the development of cancer
physiological function
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The lysine-specific histone demethylase 1 is a chromatin modifying enzyme that specifically removes methyl groups from lysine 4 of histone 3 and induces transcriptional repression. Tightly regulated distribution for LSD1 in the brain of rats under ischemic insult, suggesting a critical role in neuron function, overview
physiological function
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the catalytic activity of lysine-specific demethylase 1 is required for regulation of inflammatory cytokines. Lysine-specific demethylase 1 functions as a transcriptional coregulator by demethylating histone H3 on lysine 4 and lysine 9. Repressive role of LSD1 in proinflammatory cytokine expression such as IL1alpha, IL1beta, IL6 and IL8 and classical complement components, LSD1 occupies and regulates the promoter of these genes. LSD1 regulates several genes of the complement system in Hep-G2 cells
physiological function
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methylation on the N-terminal tails of histone lysines serves as an epigenetic control mechanism, which is regulated by demethylases
physiological function
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The KDM5C protein is likely to play a role not only in intellectual disability but also in sex-specific differences in brain function, parallel sex-specific DNA methylation profiles in brain samples from control males and females were observed at FBXL5 and CACYBP
physiological function
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Fbxl10 is described as a nucleolar protein to repress rRNA transcription, to be involved in apoptosis, and inhibition of cellular senescence. Fbxl10 is implicated in the demethylation of H3K4me3 or H3K36me2 thereby removing active chromatin marks and inhibiting gene transcription, but Fbxl10 is rather a H3K4me3 than a H3K36me2 histone demethylase. The PHD domain exerts a dual function in binding H3K4me3 and H3K36me2 and exhibiting E3 ubiquitin ligase activity. Fbxl10 regulates genes involved in the cellular metabolome and anatomical structures
physiological function
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histone demethylase LSD1 is involved in SALL4 mediated transcriptional repression in hematopoietic stem cells, SALL4 and LSD1 co-occupy the same regions of GATA1, CEBPA, and TNF promoters, and SALL4 does dynamically recruit LSD1 to its target genes. LSD1 also appears to act as a central regulator for hematopoietic stem and progenitor cell proliferation and differentiation
physiological function
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H3K4me2 demethylation marks sites of DNA damage and is cell cycle and LSD1 dependent. LSD1 recruitment to sites of DNA damage is dependent on E3 ligase RNF168, overview. LSD1 is recruited to sites of DNA damage but its retention is relatively transient. LSD1 promotes 53BP1 foci formation primarily in late S/G2 cells, and LSD1 promotes H2A/H2A.X ubiquitylation upon DNA damage
physiological function
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LSD1 is regulated in a cell cycle-dependent manner, overview. Histone demethylase LSD1, a component of the CoREST (corepressor for element 1-silencing transcription factor) corepressor complex, plays an important role in the downregulation of gene expression during development, correlation between the genomic levels of LSD1/H3K4me2 and gene expression, including many highly expressed ES cell genes, mechanisms underlying these two distinct functions of LSD1, overview. Cell cycle-dependent association and dissociation of LSD1 with chromatin mediates short-time-scale gene expression changes during embryonic stem cell cycle progression
physiological function
the JmjC domain-containing protein, JMJ703, is a histone lysine demethylase that specifically reverses all three forms of H3K4me, mono-, di-, or trimethylated state histone 3, in rice. Histone H3 lysine 4 demethylase is required for stem elongation in rice, importance of the protein in plant growth
physiological function
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JMJ703 is an active H3K4-specific demethylase required for transposable elements silencing, overview. The removal of active histone modifications is involved in transposable elements silencing and different subsets of transposable elements may be regulated by distinct epigenetic pathways
physiological function
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histone demethylase LSD1 is involved in SALL4 mediated transcriptional repression in hematopoietic stem cells, SALL4 and LSD1 co-occupy the same regions of GATA1, CEBPA, and TNF promoters, and SALL4 does dynamically recruit LSD1 to its target genes. LSD1 also appears to act as a central regulator for hematopoietic stem and progenitor cell proliferation and differentiation
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physiological function
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The lysine-specific histone demethylase 1 is a chromatin modifying enzyme that specifically removes methyl groups from lysine 4 of histone 3 and induces transcriptional repression. Tightly regulated distribution for LSD1 in the brain of rats under ischemic insult, suggesting a critical role in neuron function, overview
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additional information
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expression of the chromatin-modifying enzyme lysine-specific demethylase 1 in neuroblastoma is correlated with adverse outcome and inversely correlated with differentiation in neuroblastic tumors. Differentiation of neuroblastoma cells results in down-regulation of LSD1. Small interfering RNA-mediated knockdown of LSD1 decreases cellular growth, induces expression of differentiation-associated genes, and increases target gene-specific H3K4 methylation. LSD1 inhibition using monoamine oxidase inhibitors results in an increase of global H3K4 methylation and growth inhibition of neuroblastoma cells in vitro
additional information
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inhibition of LSD1 by oligoamines increases activating H3K4me2 and H3K4me1 marks and decreases repressive H3K9me2 marks at the promoters of reexpressed genes
additional information
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active mark H3K4me3 disappear upon gamma-secretase inhibitor N-[N-(3,5-difluorophenylacetyl-L-alanyl)]-S-phenylglycine t-butyl ester treatment at the RBP-J-binding site of the genes Deltex-1, Hes-1, and CD25 enhancer, as well as at the promoter of preTa. The Notch target genes are down-regulated. After removal of GSI, the peak of H3K4me3 at the RBP-J-binding site reappears. H3K4 trimethylation at Notch target gene Deltex-1 is dynamic only at the RBP-J-binding sites
additional information
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mechanism of histone H3 demethylation by demethylase LSD1, overview
additional information
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stable overexpression of N-terminally HA-tagged Fbxl10 in murine embryonic fibroblasts leads to an increase in cell and nuclear size and changes the transcriptome, but with no effect on proliferation, mitosis, and apoptosis or global histone marks, quantitative real-time PCR expression analysis
additional information
five solvent-exposed regions in c-JMJ703 structure, including P195-K199, S224-R261, R288-S295, T329-Y349, and Q363-V377. Three key residues, H394, E396, and H482, are perfectly conserved in JMJD2 proteins. They chelated Fe(II) in them active site through their hydrophilic side chains. The methyl group binding pocket of JmjC domain is unique among methylated peptide binding proteins due to the polar rather than hydrophobic environment
additional information
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overexpression of JMJ703-YFP-HA reduces the levels of H3K4me3/2/1 in vivo. Karma, a non-LTR LINE-type retrotransposon (LOC_Os11g44750), shows up-regulated gene expression and significantly increased association with H3K4me3 in jmj703. In T-DNA insertion disruption mutants of JMJ703, four of the validated target genes show the decreased CpG methylation at their 5' regions with the increased H3K4me3 in the mutant compared with wild-type
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
dimethyl-histone 3-Lys4 peptide + H2O
histone 3-Lys4 peptide + ?
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amino acids 1-21 of histone 3
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-
?
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
histone H3 N6-methyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 L-lysine4 + succinate + formaldehyde + CO2
protein 6-N,6-N-dimethyl-L-lysine + 2-oxoglutarate + O2
protein 6-N-methyl-L-lysine + succinate + formaldehyde + CO2
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LSD1 relieves repressive histone marks by demethylation of histone H3 at lysine 9, thereby leading to derepression of androgen receptor target genes
-
-
?
protein 6-N-methyl-L-lysine + 2-oxoglutarate + O2
protein L-lysine + succinate + formaldehyde + CO2
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LSD1 relieves repressive histone marks by demethylation of histone H3 at lysine 9, thereby leading to derepression of androgen receptor target genes
-
-
?
[chromodomain Y-like protein]-N6,N6,N6-trimethyl-L-lysine135 + 2-oxoglutarate + O2
?
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-
-
?
[Cockayne syndrome group B protein]-N6,N6,N6-trimethyl-L-lysine1054 + 2-oxoglutarate + O2
?
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-
-
-
?
[Cockayne syndrome group B protein]-N6,N6,N6-trimethyl-L-lysine170 + 2-oxoglutarate + O2
?
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-
-
-
?
[Cockayne syndrome group B protein]-N6,N6,N6-trimethyl-L-lysine297 + 2-oxoglutarate + O2
?
-
-
-
-
?
[Cockayne syndrome group B protein]-N6,N6,N6-trimethyl-L-lysine448 + 2-oxoglutarate + O2
?
-
-
-
-
?
[Dnmt1]-methyl-L-lysine + 2-oxoglutarate + O2
[Dnmt1]-L-lysine + succinate + formaldehyde + CO2
[Dnmt1]-methyl-L-lysine-1096 + 2-oxoglutarate + O2
[Dnmt1]-L-lysine-1096 + succinate + formaldehyde + CO2
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human substrate protein, demethylation of the non-histone substrate at the Set7/9 methylation site Lys1096. Dnmt1, which contains over 120 lysine residues, seems to be methylated at multiple sites, as metabolic labeling experiments reveal that mutating K1096 in mouse Dnmt1 slightly reduces, but does not abolish, Dnmt1 methylation. Probably methylation at other sites is also involved in the regulation of Dnmt1 stability
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-
?
[Dnmt1]-methyl-L-lysine1096 + 2-oxoglutarate + O2
[Dnmt1]-L-lysine1096 + succinate + formaldehyde + CO2
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mechanistic link between the histone and DNA methylation systems
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?
[G9a protein]-N6,N6,N6-trimethyl-L-lysine185 + 2-oxoglutarate + O2
?
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a customer synthesized protein
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-
?
[histone H3]-N6,N6,N6-trimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
[histone H3]-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
[histone H3]-L-lysine36 + succinate + formaldehyde + CO2
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
[histone H3]-N6-methyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
-
-
-
?
[histone-H3]-tridimethyllysine4 + 2-oxoglutarate + O2
?
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RBP2 is a demethylase that specifically catalyzes demethylation. RBP2 displayes robust H3K4 demethylase activity against H3K4me3 and me2, resulting in 80%-90% demethylation of the modified substrate, but fails to catalyze removal of the me1 modification state. The enzyme is capable of processively demethylating the H3K4me3 and me2 modifications to the unmodified state
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-
?
[p53]-methyl-L-lysine + 2-oxoglutarate + O2
[p53]-L-lysine + succinate + formaldehyde + CO2
[widely interspaced zinc finger motifs protein]-N6,N6,N6-trimethyl-L-lysine305 + 2-oxoglutarate + O2
?
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-
-
-
?
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
?
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
Aof1 is a histone demethylase specifically demethylating H3K4
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6-methyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6-methyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 L-lysine4 + succinate + formaldehyde + CO2
-
-
-
?
histone H3 N6-methyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6-methyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
[Dnmt1]-methyl-L-lysine + 2-oxoglutarate + O2
[Dnmt1]-L-lysine + succinate + formaldehyde + CO2
-
-
-
-
?
[Dnmt1]-methyl-L-lysine + 2-oxoglutarate + O2
[Dnmt1]-L-lysine + succinate + formaldehyde + CO2
-
LSD1 demethylates the protein and regulates its function
-
-
?
[histone H3]-N6,N6,N6-trimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
-
-
?
[histone H3]-N6,N6,N6-trimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
JMJD2A is a trimethyllysine-specific JmjC HDM
-
-
?
[histone H3]-N6,N6,N6-trimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
[histone H3]-L-lysine36 + succinate + formaldehyde + CO2
-
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
[histone H3]-L-lysine36 + succinate + formaldehyde + CO2
-
dJMJD2(1)/CG15835 and dJMJD2(2)/CG33182 demethylate both H3K9me3 and H3K36me3
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
the lysine methylase complexes recognize its own reaction products. The H3K9me2 methylases G9A/KMT1C and GLP/KMT1D, can also bind to their reaction product H3K9me2 via their ankyrin repeat domains
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
dJMJD2(1)/CG15835 and dJMJD2(2)/CG33182 demethylate both H3K9me3 and H3K36me3
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
isozyme JMJD2A substrate binding structure, overview
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
Jmjd2c is recruited to the P2 promoter region of Mdm2 gene resulting in demethylation of histone H3 lysine 9, as typically found in actively transcribed genes
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
predicted site-specificity from phylogenetic analysis
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
propagation of the silencing mark, H3K9me3, at the centromeric and Mating type regions requires the RNAi machinery and DNA recognition factors
-
-
?
[histone-H3]-dimethyllysine4 + 2-oxoglutarate + O2
?
-
the JARID1 family of demethylases specifically remove both the di- and trimethylated H3K4 epigenetic mark
-
-
?
[histone-H3]-dimethyllysine4 + 2-oxoglutarate + O2
?
-
recombinant PLU-1 can only demethylate H3K4me3 and H3K4me2 when analyzed in vitro
-
-
?
[histone-H3]-dimethyllysine4 + 2-oxoglutarate + O2
?
-
RBP2 is a demethylase that specifically catalyzes demethylation. RBP2 displayes robust H3K4 demethylase activity against H3K4me3 and me2, resulting in 80%-90% demethylation of the modified substrate, but fails to catalyze removal of the me1 modification state. The enzyme is capable of processively demethylating the H3K4me3 and me2 modifications to the unmodified state
-
-
?
[histone-H3]-dimethyllysine4 + 2-oxoglutarate + O2
?
-
RBP2 is a demethylase that specifically catalyzes demethylation. The enzyme is capable of erasing trimethylated H3K4. The enzyme is capable of processively demethylating the H3K4me3 and me2 modifications to the unmodified state
-
-
?
[histone-H3]-trimethyllysine4 + 2-oxoglutarate + O2
?
Lid knockdown using RNA interference results in a specific genome-wide increase in H3K4me3 levels without affecting other patterns of H3 methylation
-
-
?
[histone-H3]-trimethyllysine4 + 2-oxoglutarate + O2
?
-
the JARID1 family of demethylases specifically remove both the di- and trimethylated H3K4 epigenetic mark
-
-
?
[histone-H3]-trimethyllysine4 + 2-oxoglutarate + O2
?
RNA-interference-mediated depletion of SMCX increases H3K4 trimethylation at the sodium channel type 2A (SCN2A) and synapsin I (SYN1) promoters. SMCX activity impairs REST-mediated neuronal gene regulation, thereby contributing to SMCX-associated X-linked mental retardation
-
-
?
[histone-H3]-trimethyllysine4 + 2-oxoglutarate + O2
?
-
recombinant PLU-1 can only demethylate H3K4me3 and H3K4me2 when analyzed in vitro
-
-
?
[histone-H3]-trimethyllysine4 + 2-oxoglutarate + O2
?
-
RBP2 is a demethylase that specifically catalyzes demethylation. RBP2 displayes robust H3K4 demethylase activity against H3K4me3 and me2, resulting in 80%-90% demethylation of the modified substrate, but fails to catalyze removal of the me1 modification state. The enzyme is capable of processively demethylating the H3K4me3 and me2 modifications to the unmodified state
-
-
?
[p53]-methyl-L-lysine + 2-oxoglutarate + O2
[p53]-L-lysine + succinate + formaldehyde + CO2
-
-
-
-
?
[p53]-methyl-L-lysine + 2-oxoglutarate + O2
[p53]-L-lysine + succinate + formaldehyde + CO2
-
LSD1 demethylates the protein and regulates its function
-
-
?
additional information
?
-
histone H3K4 demethylases are essential in development and differentiation
-
-
-
additional information
?
-
-
dynamic nature of histone methylation regulation on four of the main lysine sites of methylation on histone H3 and H4 tails, i.e. H3K4, H3K9, H3K27 and H3K36, overview. Methylation of non-histone proteins may be a general means to regulate epigenetic information
-
-
-
additional information
?
-
-
demethylase activity of dJMJD2(1)/CG15835 depends on the JmjC domain. No activity with H3K4me3 and H3K27me3 by dJMJD2(1)/CG15835 and dJMJD2(2)/CG33182
-
-
-
additional information
?
-
-
histone H3K4 demethylases are essential in development and differentiation
-
-
-
additional information
?
-
-
Lid is required for Myc-induced cell growth
-
-
-
additional information
?
-
-
lysine-specific demethylase 1 represses telomerase reverse transcriptase transcription via demethylating histone 3 lysine 4 in normal and cancerous cells, and together with histone deacetylases, participates in the establishment of a stable repression state of the telomerase reverse transcriptase gene in normal and differentiated malignant cells
-
-
-
additional information
?
-
JMJD2A associates with the androgen receptor to upregulate the expression of androgen receptor-dependent genes. Human JMJD2A exhibits dual specificity for the trimethylated and, to a lesser extent, the dimethylated forms of H3K9 and H3K36, while other JMJD2 paralogs, such as JMJD2B and JMJD2D, are specific for H3K9me2/3, analysis of the molecular basis of JMJD2A substrate specificity, overview
-
-
-
additional information
?
-
-
LSD1 is a nuclear amine oxidase that utilizes oxygen as an electron acceptor to reduce methylated lysine to form lysine. It demethylates H3K4m1 and H3K4m2, as well as H3K9m1 and H3K9m2 as a removal of the active nethylation mark
-
-
-
additional information
?
-
-
JMJD2A also catalyzes the reaction of the [histone H3]-lysine-36 demethylase, EC 1.14.11.27. JMJD2A exclusively catalyzes the demethylation of H3K9me3 and H3K36me3, converting H3K9/36me3 to H3K9/36me2 but it cannot convert H3K9/36me1 or unmethylated H3K9/K36, overview
-
-
-
additional information
?
-
JMJD2A is unable to demethylate other sites, notably H3K4 or H4K20, and JMJD2 enzymes are unable to recognize H3K36me3. Analysis of the substrate binding structure at the active site
-
-
-
additional information
?
-
-
LSD1 is also responsible for demethylation of H3K4me2
-
-
-
additional information
?
-
-
substrate specificity of recombinant isozymes, overview
-
-
-
additional information
?
-
-
LSD1 specificity and mechanism of action are complex-dependent
-
-
-
additional information
?
-
-
the enzyme interacts with the C-terminus of hPc2, a Polycomb group PcG protein, via its N-terminus in vitro and in vivo, role for hPc2 acting as a transcriptional co-repressor, interaction analysis, overview
-
-
-
additional information
?
-
-
LSD1 removes the methyl groups from lysines 4 and 9 of histone 3 with the generation of formaldehyde from the methyl group
-
-
-
additional information
?
-
-
LSD1 demethylate histone and non-histone proteins. It associates with several protein complexes
-
-
-
additional information
?
-
-
LSD1 also catalyzes the reaction of the [histone H3]-lysine-4 demethylase
-
-
-
additional information
?
-
histone H3K4 demethylases are essential in development and differentiation
-
-
-
additional information
?
-
-
LSD1 is a nuclear amine oxidase that utilizes oxygen as an electron acceptor to reduce methylated lysine to form lysine. It demethylates H3K4m1 and H3K4m2, as well as H3K9m1 and H3K9m2 as a removal of the active nethylation mark
-
-
-
additional information
?
-
-
H3K4me3 marks are found at regulatory elements as well as transcriptional start sites. In the Deltex-1 promoter region two major peaks are observed: one at the transcriptional start site, and one at the RBP-J-binding site, 1.2 kb upstream of the transcriptional start site, mechanism by which RBP-J bound to promoters of Notch target genes recruits KDM5A to facilitate histone demethylation, overview
-
-
-
additional information
?
-
the enzyme from rice is specific for Lys9 of histone H3
-
-
-
additional information
?
-
-
JMJ703 specifically reverses all three forms of H3K4me, mono-, di-, or trimethylated state histone 3, in rice
-
-
-
additional information
?
-
JMJ703 specifically reverses all three forms of H3K4me, mono-, di-, or trimethylated state histone 3, in rice
-
-
-
additional information
?
-
-
the recombinant enzyme is specific for H3K4me1/2/3 in vitro, no activity of FLAG:HA-tagged JmjN-JmjC-zinc finger region to demethylate H3K9me1/2/3, or H3K36me1/2/3. Binding affinities of c-JMJ703 to H3K4 peptides with mono-, di-, or trimethylation, overview
-
-
-
additional information
?
-
the recombinant enzyme is specific for H3K4me1/2/3 in vitro, no activity of FLAG:HA-tagged JmjN-JmjC-zinc finger region to demethylate H3K9me1/2/3, or H3K36me1/2/3. Binding affinities of c-JMJ703 to H3K4 peptides with mono-, di-, or trimethylation, overview
-
-
-
additional information
?
-
-
histone methyl-lysine marks display dynamic changes during the parasite asexual erythrocytic cycle, suggesting that they constitute an important epigenetic mechanism of gene regulation in malaria parasites
-
-
-
additional information
?
-
-
the enzyme also demethylates [histone H3]-N6,N6-dimethyl-L-lysine36
-
-
-
additional information
?
-
-
dynamic nature of histone methylation regulation on four of the main lysine sites of methylation on histone H3 and H4 tails, i.e. H3K4, H3K9, H3K27 and H3K36, overview. Methylation of non-histone proteins may be a general means to regulate epigenetic information
-
-
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
histone H3 N6-methyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 L-lysine4 + succinate + formaldehyde + CO2
protein 6-N,6-N-dimethyl-L-lysine + 2-oxoglutarate + O2
protein 6-N-methyl-L-lysine + succinate + formaldehyde + CO2
-
LSD1 relieves repressive histone marks by demethylation of histone H3 at lysine 9, thereby leading to derepression of androgen receptor target genes
-
-
?
protein 6-N-methyl-L-lysine + 2-oxoglutarate + O2
protein L-lysine + succinate + formaldehyde + CO2
-
LSD1 relieves repressive histone marks by demethylation of histone H3 at lysine 9, thereby leading to derepression of androgen receptor target genes
-
-
?
[Dnmt1]-methyl-L-lysine + 2-oxoglutarate + O2
[Dnmt1]-L-lysine + succinate + formaldehyde + CO2
-
LSD1 demethylates the protein and regulates its function
-
-
?
[Dnmt1]-methyl-L-lysine1096 + 2-oxoglutarate + O2
[Dnmt1]-L-lysine1096 + succinate + formaldehyde + CO2
-
mechanistic link between the histone and DNA methylation systems
-
-
?
[histone H3]-N6,N6,N6-trimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
[histone H3]-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
[histone H3]-L-lysine36 + succinate + formaldehyde + CO2
-
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
[histone H3]-N6-methyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
-
-
-
?
[histone-H3]-tridimethyllysine4 + 2-oxoglutarate + O2
?
-
RBP2 is a demethylase that specifically catalyzes demethylation. RBP2 displayes robust H3K4 demethylase activity against H3K4me3 and me2, resulting in 80%-90% demethylation of the modified substrate, but fails to catalyze removal of the me1 modification state. The enzyme is capable of processively demethylating the H3K4me3 and me2 modifications to the unmodified state
-
-
?
[p53]-methyl-L-lysine + 2-oxoglutarate + O2
[p53]-L-lysine + succinate + formaldehyde + CO2
-
LSD1 demethylates the protein and regulates its function
-
-
?
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
Q53WJ1
-
-
-
?
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
Aof1 is a histone demethylase specifically demethylating H3K4
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
Q53WJ1
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6-methyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6-methyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 L-lysine4 + succinate + formaldehyde + CO2
Q53WJ1
-
-
-
?
histone H3 N6-methyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6-methyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
[histone H3]-N6,N6,N6-trimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
O75164
JMJD2A is a trimethyllysine-specific JmjC HDM
-
-
?
[histone H3]-N6,N6,N6-trimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
Q336N8
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
the lysine methylase complexes recognize its own reaction products. The H3K9me2 methylases G9A/KMT1C and GLP/KMT1D, can also bind to their reaction product H3K9me2 via their ankyrin repeat domains
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
O75164
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
Jmjd2c is recruited to the P2 promoter region of Mdm2 gene resulting in demethylation of histone H3 lysine 9, as typically found in actively transcribed genes
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
Q336N8
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
predicted site-specificity from phylogenetic analysis
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3]-L-lysine9 + succinate + formaldehyde + CO2
-
propagation of the silencing mark, H3K9me3, at the centromeric and Mating type regions requires the RNAi machinery and DNA recognition factors
-
-
?
[histone-H3]-dimethyllysine4 + 2-oxoglutarate + O2
?
-
the JARID1 family of demethylases specifically remove both the di- and trimethylated H3K4 epigenetic mark
-
-
?
[histone-H3]-dimethyllysine4 + 2-oxoglutarate + O2
?
-
RBP2 is a demethylase that specifically catalyzes demethylation. The enzyme is capable of erasing trimethylated H3K4. The enzyme is capable of processively demethylating the H3K4me3 and me2 modifications to the unmodified state
-
-
?
[histone-H3]-trimethyllysine4 + 2-oxoglutarate + O2
?
Q9VMJ7
Lid knockdown using RNA interference results in a specific genome-wide increase in H3K4me3 levels without affecting other patterns of H3 methylation
-
-
?
[histone-H3]-trimethyllysine4 + 2-oxoglutarate + O2
?
-
the JARID1 family of demethylases specifically remove both the di- and trimethylated H3K4 epigenetic mark
-
-
?
[histone-H3]-trimethyllysine4 + 2-oxoglutarate + O2
?
P41229
RNA-interference-mediated depletion of SMCX increases H3K4 trimethylation at the sodium channel type 2A (SCN2A) and synapsin I (SYN1) promoters. SMCX activity impairs REST-mediated neuronal gene regulation, thereby contributing to SMCX-associated X-linked mental retardation
-
-
?
additional information
?
-
Q6IQX0
histone H3K4 demethylases are essential in development and differentiation
-
-
-
additional information
?
-
-
dynamic nature of histone methylation regulation on four of the main lysine sites of methylation on histone H3 and H4 tails, i.e. H3K4, H3K9, H3K27 and H3K36, overview. Methylation of non-histone proteins may be a general means to regulate epigenetic information
-
-
-
additional information
?
-
-
histone H3K4 demethylases are essential in development and differentiation
-
-
-
additional information
?
-
-
Lid is required for Myc-induced cell growth
-
-
-
additional information
?
-
-
lysine-specific demethylase 1 represses telomerase reverse transcriptase transcription via demethylating histone 3 lysine 4 in normal and cancerous cells, and together with histone deacetylases, participates in the establishment of a stable repression state of the telomerase reverse transcriptase gene in normal and differentiated malignant cells
-
-
-
additional information
?
-
O75164
JMJD2A associates with the androgen receptor to upregulate the expression of androgen receptor-dependent genes. Human JMJD2A exhibits dual specificity for the trimethylated and, to a lesser extent, the dimethylated forms of H3K9 and H3K36, while other JMJD2 paralogs, such as JMJD2B and JMJD2D, are specific for H3K9me2/3, analysis of the molecular basis of JMJD2A substrate specificity, overview
-
-
-
additional information
?
-
-
LSD1 is a nuclear amine oxidase that utilizes oxygen as an electron acceptor to reduce methylated lysine to form lysine. It demethylates H3K4m1 and H3K4m2, as well as H3K9m1 and H3K9m2 as a removal of the active nethylation mark
-
-
-
additional information
?
-
-
LSD1 specificity and mechanism of action are complex-dependent
-
-
-
additional information
?
-
-
the enzyme interacts with the C-terminus of hPc2, a Polycomb group PcG protein, via its N-terminus in vitro and in vivo, role for hPc2 acting as a transcriptional co-repressor, interaction analysis, overview
-
-
-
additional information
?
-
-
LSD1 removes the methyl groups from lysines 4 and 9 of histone 3 with the generation of formaldehyde from the methyl group
-
-
-
additional information
?
-
-
LSD1 demethylate histone and non-histone proteins. It associates with several protein complexes
-
-
-
additional information
?
-
Q3UXZ9
histone H3K4 demethylases are essential in development and differentiation
-
-
-
additional information
?
-
-
LSD1 is a nuclear amine oxidase that utilizes oxygen as an electron acceptor to reduce methylated lysine to form lysine. It demethylates H3K4m1 and H3K4m2, as well as H3K9m1 and H3K9m2 as a removal of the active nethylation mark
-
-
-
additional information
?
-
-
H3K4me3 marks are found at regulatory elements as well as transcriptional start sites. In the Deltex-1 promoter region two major peaks are observed: one at the transcriptional start site, and one at the RBP-J-binding site, 1.2 kb upstream of the transcriptional start site, mechanism by which RBP-J bound to promoters of Notch target genes recruits KDM5A to facilitate histone demethylation, overview
-
-
-
additional information
?
-
-
JMJ703 specifically reverses all three forms of H3K4me, mono-, di-, or trimethylated state histone 3, in rice
-
-
-
additional information
?
-
Q53WJ1
JMJ703 specifically reverses all three forms of H3K4me, mono-, di-, or trimethylated state histone 3, in rice
-
-
-
additional information
?
-
-
histone methyl-lysine marks display dynamic changes during the parasite asexual erythrocytic cycle, suggesting that they constitute an important epigenetic mechanism of gene regulation in malaria parasites
-
-
-
additional information
?
-
-
dynamic nature of histone methylation regulation on four of the main lysine sites of methylation on histone H3 and H4 tails, i.e. H3K4, H3K9, H3K27 and H3K36, overview. Methylation of non-histone proteins may be a general means to regulate epigenetic information
-
-
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
LSD1 recruitment to sites of DNA damage is dependent on E3 ligase RNF168, RNF168 interacts with LSD1, overview. Rapid, transient recruitment of RNF168 to damage sites is H2A.X independent
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe2+
Fe2+
required essential for the demethylase activity in vivo. Conserved key residues, H394, E396, and H482, chelate Fe(II) in the active site through their hydrophilic side chains
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(25E)-N,N'-diethyl-5,11,17,23,28,33,39,45-octaazapentacont-25-ene-1,50-diamine
-
-
(25Z)-N,N'-diethyl-6,12,18,23,28,33,39,45-octaazapentacont-25-ene-1,50-diamine
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-
(2Z)-N-ethyl-N'-[4-[(4-[[(2Z)-4-(ethylamino)but-2-en-1-yl]amino]butyl)amino]butyl]but-2-ene-1,4-diamine
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-
(2Z)-N-[4-(ethylamino)butyl]-N'-(4-[[4-(ethylamino)butyl]amino]butyl)but-2-ene-1,4-diamine
-
-
1,11-bis-[3-[1-(1,1-diphenylmethyl)thioureado]]-4,8-diazaundecane
-
48.9% inhibition at 0.01 mM
1,11-bis-[3-[1-(2,2-diphenylethyl)thioureado]]-4,8-diazaundecane
-
75.2% inhibition at 0.01 mM
1,11-bis-[3-[1-(3,3-diphenylpropyl)thioureado]]-4,8-diazaundecane
-
7.8% inhibition at 0.01 mM
1,11-bis-[3-[1-(3,3-diphenylpropyl)ureado]]-4,8-diazaundecane
-
7.1% inhibition at 0.01 mM
1,11-bis-[3-[1-(benzyl)thioureado]]-4,8-diazaundecane
-
47.9% inhibition at 0.01 mM
1,11-bis-[3-[1-(ethyl)thioureado]]-4,8-diazaundecane
-
63.8% inhibition at 0.01 mM
1,11-bis-[3-[1-(n-propyl)ureado]]-4,8-diazaundecane
-
; 48.7% inhibition at 0.01 mM
1,11-bis-[5-[1-(N,N-diphenyl)carbamyl]ureado]-4,8-diazaundecane
-
8.5% inhibition at 0.01 mM
1,12-bis-[3-[1-(1,1-diphenylmethyl)thioureado]]-4,9-diazadodecane
-
65.6% inhibition at 0.01 mM
1,12-bis-[3-[1-(2,2-diphenylethyl)thioureado]]-4,9-diazadodecane
-
82.9% inhibition at 0.01 mM
1,12-bis-[3-[1-(3,3-diphenylpropyl)thioureado]]-4,9-diazadodecane
-
21.4% inhibition at 0.01 mM
1,12-bis-[3-[1-(3,3-diphenylpropyl)ureado]]-4,9-diazadodecane
-
25.4% inhibition at 0.01 mM
1,12-bis-[3-[1-(ethyl)thioureado]]-4,9-diazadodecane
-
60% inhibition at 0.01 mM
1,12-bis-[3-[1-(n-propyl)thioureado]]-4,9-diazadodecane
-
10.4% inhibition at 0.01 mM
1,12-bis-[5-[1-(N,N-diphenyl)carbamyl]ureado]-4,9-diazadodecane
-
73.9% inhibition at 0.01 mM
1,15-bis-[3-[1-(1,1-diphenylmethyl)thioureado]]-4,12-diazapentadecane
-
71.1% inhibition at 0.01 mM
1,15-bis-[3-[1-(2,2-diphenylethyl)thioureado]]-4,12-diazapentadecane
-
80.5% inhibition at 0.01 mM
1,15-bis-[3-[1-(3,3-diphenylpropyl)thioureado]]-4,12-diazapentadecane
-
22.7% inhibition at 0.01 mM
1,15-bis-[3-[1-(3,3-diphenylpropyl)ureado]]-4,12-diazapentadecane
-
48.5% inhibition at 0.01 mM
1,15-bis-[3-[1-(benzyl)thioureado]]-4,12-diazapentadecane
-
64.1% inhibition at 0.01 mM
1,15-bis-[3-[1-(n-propyl)ureado]]-4,12-diazapentadecane
-
8.5% inhibition at 0.01 mM
1,15-bis-[5-[1-(N,N-diphenyl)carbamyl]ureado]-4,12-diazapentadecane
-
30.0% inhibition at 0.01 mM
1,2-dimethyl-3-[(13E)-13-(methylamino)-4,8,12,14-tetraazapentadec-13-en-1-yl]guanidine
-
1 mM, about 80% inhibition. Inhibition affects a reexpression of multiple, aberrantly silenced genes important in the develoment of colon cancer. Reexpression is concurrent with increased dimethylated histone 3 lysine 4 and acetyl-histone 3 lysine 4 marks
1-(2,2-diphenylethyl)-3-(14-imino-17,17-diphenyl-4,9,13,15-tetraazaheptadec-1-yl)guanidine
-
1 mM, about 55% inhibition. Inhibition affects a reexpression of multiple, aberrantly silenced genes important in the develoment of colon cancer. Reexpression is concurrent with increased dimethylated histone 3 lysine 4 and acetyl-histone 3 lysine 4 marks
1-(3,3-diphenylpropyl)-3-(14-imino-18,18-diphenyl-4,9,13,15-tetraazaoctadec-1-yl)guanidine
-
1 mM, about 60% inhibition. Inhibition affects a reexpression of multiple, aberrantly silenced genes important in the develoment of colon cancer. Reexpression is concurrent with increased dimethylated histone 3 lysine 4 and acetyl-histone 3 lysine 4 marks
Co2+
-
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 A549 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'-(13,15-diimino-18,18-diphenyl-4,8,12,14,16-pentaazaoctadec-1-yl)-N-(2,2-diphenylethyl)imidodicarbonimidic diamide
-
1 mM, about 65% inhibition. Inhibition affects a reexpression of multiple, aberrantly silenced genes important in the develoment of colon cancer. Reexpression is concurrent with increased dimethylated histone 3 lysine 4 and acetyl-histone 3 lysine 4 marks
N'-(14,16-diimino-20,20-diphenyl-4,9,13,15,17-pentaazaicos-1-yl)-N-(3,3-diphenylpropyl)imidodicarbonimidic diamide
-
1 mM, about 70% inhibition. Inhibition affects a reexpression of multiple, aberrantly silenced genes important in the develoment of colon cancer. Reexpression is concurrent with increased dimethylated histone 3 lysine 4 and acetyl-histone 3 lysine 4 marks
N'-(17,19-diimino-23,23-diphenyl-4,12,16,18,20-pentaazatricos-1-yl)-N-(3,3-diphenylpropyl)imidodicarbonimidic diamide
-
1 mM, about 90% inhibition. Inhibition affects a reexpression of multiple, aberrantly silenced genes important in the develoment of colon cancer. Reexpression is concurrent with increased dimethylated histone 3 lysine 4 and acetyl-histone 3 lysine 4 marks
N-ethyl-N'-[[2-([[4-([[2-([[4-(ethylamino)butyl]amino]methyl)cyclopropyl]methyl]amino)butyl]amino]methyl)cyclopropyl]methyl]butane-1,4-diamine
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Pargyline
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i.e. N-methyl-N-propargylbenzylamine, the LSD1 inhibitor prevents demethylation of Dnmt1-C by LSD1
Tranylcypromine
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inhibition of lysine-specific demethylase 1 results in decreased expression of telomerase reverse transcriptase
additional information
-
LSD1 inhibition using monoamine oxidase inhibitors results in an increase of global H3K4 methylation and growth inhibition of neuroblastoma cells in vitro
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additional information
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oligoamine analogues inhibit lysine-specific demethylase 1 and induce reexpression of epigenetically silenced genes, overview. Treatment of HCT-116 colon adenocarcinoma cells in vitro results in increased H3K4 methylation and reexpression of silenced SFRP genes. This reexpression is also accompanied by a decrease in H3K9me2 repressive mark
-
additional information
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(bis)urea and (bis)thiourea inhibitors of lysine-specific demethylase 1 as epigenetic modulators with the potential for use as antitumor agents, overview. No inhibition by 7 and 17, poor inhibition by 11
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
HP1a
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Suv(Var)3-9/KMT1 interacts with HP1 that binds [histone H3]-N6,N6-trimethyl-L-lysine9
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additional information
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transient hyperglycemia induces recruitment of LSD1 to gene regulation sites/promoters
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additional information
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local demethylation of H3K9me2 is triggered by recruitment of liganded estrogen receptor ERalpha to chromatin
-
additional information
-
binding kinetic analysis of folate derivatives, e.g. folates bound to glutamates, the (6R,S) form of the natural pentaglutamate form of tetrahydrofolate bound with the highest affinity to full-length LSD1, overview
-
additional information
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transient hyperglycemia induces recruitment of LSD1 to gene regulation sites/promoters
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
specific isozyme activities with non-histone substrates, overview
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8.5
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LSD1 is strongly expressed in poorly differentiated neuroblastomas, real-time reverse transcription-PCR expression analysis
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histone H3 lysine 4 demethylase JARID1B is up-regulated in prostate cancer. JARID1B associates with androgen receptor and regulates its transcriptional activity
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lysine-specific demethylase 1 colocalizes with androgen receptor
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lysine-specific demethylase 1 colocalizes with androgen receptor
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JMJ703 is expressed at relatively high levels in leaves of 7 d-after-germination in seedlings compared with all of the other tissues tested
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Beko cell, spontaneous T-cell lymphoma cell line derived from T-cell receptor beta knockout mice, only KDM5A and KDM5C are expressed
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the distributions of H3-K4 mono-, di-, and tri-methylated histones exhibit exactly the same pattern as the LSD1 protein, immunofluoresecence histochemic analysis, overview
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the distributions of H3-K4 mono-, di-, and tri-methylated histones exhibit exactly the same pattern as the LSD1 protein, immunofluoresecence histochemic analysis, overview
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BALB c nu/nu athymic nude mice are implanted with the human colorectal cancer HCT-116 cells
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PLU-1-mediated H3K4 demethylase activity plays an important role in the proliferative capacity of breast cancer cells through repression of tumor suppressor genes, including BRCA1
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
LSD1 is present on chromatin in both the presence and the absence of estrogens
additional information
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association of LSD1 with sites of DNA damage, immunohistochemic localization, overview
additional information
-
H3K4me2 demethylation marks sites of DNA damage and occurs primarily in late S/G2
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additional information
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genome-wide mapping and cellular localization studies of LSD1, transcriptional corepressor LSD1 is enriched at the promoter regions of highly expressed genes in ES cells
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
domain organization and sequence homology analysis of JmjC+N proteins, overview
additional information
-
the enzyme consists of DNA binding domain, catalytic domain, and plant homeodomain
additional information
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Fbxl10 consists of the catalytic JmjC domain, a CxxC domain, a PHD domain, and an Fbox domain
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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 inhibitor tranylcypromine, diffraction to 2.25 A. In the inhibitor-free structure, a water molecule forms a hydrogen bond with the flavin N(5) atom and Lys661. The LSD1-tranylcypromine complex is not completely composed of the five-membered adduct, but partially contains an intermediate
purified recombinant enzyme, free or in complex with N-oxalylglycine, X-ray diffraction structure determination and analysis at 2.35 A resolution
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant FLAG:HA-tagged JmjN-JmjC-zinc finger region from Nicotiana tabacum leaf nuclei byy affinity chromatography
recombinant GST-tagged isozymes JMJD2A, JMJD2B, and JMJD2C from Escherichia coli strain BL21(DE3) by glutathione affinity chromatography
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recombinant His-tagged N-terminal fragment of JARID1B from Sf9 insect cells by nickel affinity chromatography
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recombinant N-terminally His-tagged enzyme by nickel affinity chromatography from Escherichia coli BL21(DE3), or by ammonium sulfate fractionation and anion exchange chromatography, recombinant N-terminally truncated GST-tagged LSD1 by glutathione affinity chromatography
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cDNA encoding for Myc-tagged JARID1B is transfected into HeLa cells, and the effect on histone lysine methylation is examined
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co-expression of FLAG-CMV-tagged hPc2 and the HA-tagged N-terminal fragment of JARDI1B in HEK-293T cells. Expression the His-tagged N-terminal fragment of JARID1B in Spodoptera frugiperda Sf9 cells using the baculovirus transfection system
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coexpression of HA-tagged SALL4 and FLAG-tagged LSD1 in HEK-293 cells, coexpression of LSD1 and SALL4 proteins in mouse bone marrow hematopoietic stem and progenitor cells
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expression of FLAG-tagged wild-type and H190A mutant Jmjd2c in mouse embryonic fibroblasts
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fragment consisting of residues 172-833, expression as glutathione S-transferase fusion protein in Escherichia coli
full-length Flag-tagged human PLU-1 is expressed in SF9 cells. PLU-1 is overexpressed in U2OS cells
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gene JMJ703, functional overexpression of YFP-HA-tagged JMJ703 in Nicotiana tabacum cells
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gene JMJ703, functional transient overexpression of the FLAG:HA-tagged JmjN-JmjC-zinc finger region in Nicotiana tabacum leaf nuclei
gene JMJ706, DNA and amino acid sequence determination and analysis, phylogenetic analysis, expression as GST-fusion protein
gene Kdm5c, encoded on the X-chromosome, genotyping, quantitative real-time RT-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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JMJD2A-C genes, DNA and amino acid sequence determination and analysis, expression of the GST-tagged isozymes JMJD2A, JMJD2B, and JMJD2C in Escherichia coli strain BL21(DE3)
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LSD1 genome-wide mapping and expression analysis, LSD1 genomic regions overlap H3K4me2 regions, transcriptional corepressor LSD1 is enriched at the promoter regions of highly expressed genes in ES cells
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stable overexpression of N-terminally HA-tagged Fbxl10 in murine embryonic fibroblasts leading to an increase in cell and nuclear size and changes the transcriptome, but with no effect on proliferation, mitosis, and apoptosis or global histone marks, quantitative real-time PCR expression analysis
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
LSD1 expression in the brain is induced both region and cell specifically after ischemic/perfusion
LSD1 expression in the brain is induced both region and cell specifically after ischemic/perfusion
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LSD1 expression in the brain is induced both region and cell specifically after ischemic/perfusion
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
S288A
the mutant displays enhanced specificity for H3K9me2 and H3K36me2 without altering activity toward trimethyllysines, consistent with the H3K9me2/3 specificity of JMJD2D which possesses an alanine, Ala29, in this position. Kinetic analysis of S288A mutant shows a 12fold increase in H3K9me2 specificity versus the native enzyme, whereas the converse A291S mutant in JMJD2D reduces H3K9me2 specificity approximately fivefold
K1096R
-
the mutant Dnmt1 shows highly reduced Dnmt1 methylation activity compared to the wild-type enzyme, and is more stable than wild-type Dnmt1 when expressed in Dnmt1-/- embryonic stem cells
E396A
site directed mutagenesis of a Fe2+ binding active site residue, inactive mutant, the mutation impairs the H3K4 demethylase activity of JMJ703 in tobacco cells
G376A
site directed mutagenesis, inactive mutant, the mutation impairs the H3K4 demethylase activity of JMJ703 in tobacco cells, the mutation impairs the H3K4 demethylase activity of JMJ703 in tobacco cells
H394A
site directed mutagenesis of a Fe2+ binding active site residue, inactive mutant
H482A
site directed mutagenesis of a Fe2+ binding active site residue, inactive mutant
K412A
site directed mutagenesis, the mutation abolishes the demethylation activity of H3K4 in all three methylation states
N496A
site directed mutagenesis, the mutant retains a residual activity to demethylate H3K4me2/3, the mutation impairs the H3K4 demethylase activity of JMJ703 in tobacco cells
Y321A
site directed mutagenesis decreases H3K4me1 demethylase activity but does not affect H3K4me2 and H3K4me3 demethylase activity
Y383A
site directed mutagenesis, the mutant retains a residual activity to demethylate H3K4me2, the mutation impairs the H3K4 demethylase activity of JMJ703 in tobacco cells
additional information
additional information
-
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
additional information
-
depletion of both lysine-specific demethylase 1 and corepressor in histone deacetylase containing complexes, CoREST, by siRNA, synergistically activate transcription of telomerase reverse transcriptase. Lysine-specific demethylase 1 occupies the telomerase reverse transcriptase proximal promoter
additional information
-
LSD1 knockdown by siRNA inhibits 8-oxo-guanine production
additional information
-
MDA-MB231 cells are transiently transfected with three different siRNA directed against LSD1 causing significant knockdown of LSD1 in all samples on both mRNA and protein level, LSD1 knockdown leads to significant induction of the steady state transcript levels of interleukins 1alpha, 1beta, 6 and 8 genes. Interleukin1beta protein levels are significantly enhanced in the supernatant of the cells after LSD1 knockdown
additional information
-
overexpression of wild-type Jmjd2c, but not of mutant H190A, increases the expression of Mdm2 oncogene dependent on its demethylase activity, which leads to the reduction of p53 tumor suppressor gene product in the cells
additional information
-
construction of Aof2 knockout mutant mice, phenotypes of hetero and homozygous mice, overview. Targeted deletion of the gene Aof2 encoding LSD1 in embryonic stem cells induces progressive loss of DNA methylation. This loss correlates with a decrease in DNA methyltransferase 1, Dnmt1, protein, as a result of reduced Dnmt1 stability. Dnmt1 protein is methylated in vivo, and its methylation is enhanced in the absence of LSD1
additional information
-
hairpin RNA enzyme LSD1 knockdown, RNAi rescue experiments by expressing the human LSD1 cDNA
additional information
-
hairpin RNA enzyme LSD1 knockdown, RNAi rescue experiments by expressing the human LSD1 cDNA
-
additional information
a JMJ706 loss-of-function mutation affects floral organogenesis, construction of knockout mutants that show altered content and ratios of methylated histone H3K9, overview
additional information
T-DNA insertion and RNAi mutation sof gene JMJ703, phenotypes, overview
additional information
-
overexpression of JMJ703-YFP-HA reduces the levels of H3K4me3/2/1 in vivo. T-DNA insertion disruption of JMJ703 transcription, four of the validated target genes show the decreased CpG methylation at their 5' regions with the increased H3K4me3 in the mutant compared with wild-type
additional information
-
histone methyl-lysine marks display dynamic changes during the parasite asexual erythrocytic cycle, suggesting that they constitute an important epigenetic mechanism of gene regulation in malaria parasites
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