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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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demethylation
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trimethylation
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polycomb
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ccrcc
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k-specific
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histone-modifying
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jarid1
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tri-methylated
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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
evolution
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the enzyme belongs to the superfamily of flavin adenine dinucleotide (FAD)-dependent amine oxidases
evolution
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Jhd2 is an evolutionarily conserved JARID1 family H3 Lys4 demethylase and a Jumonji C (JmjC) domain-containing histone demethylase (JHDM). Jhd2/Kdm5 is an evolutionarily conserved JARID1 family protein that has demethylase activity toward H3K4me3 in vitro or in vivo
evolution
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RBR-2 is the sole homolog of the KDM5 family of H3K4me3/2 demethylases in Caenorhabditis elegans
evolution
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the enzyme blongs to the KDM5/JARID1 subfamily of histone H3 lysine 4 demethylases of the Fe(II)- and 2-oxoglutarate-dependent demethylases family. The KDM5 family is unique among the Jumonji domain-containing histone demethylases in that there is an atypical insertion of a DNA-binding ARID domain and a histone-binding PHD domain into the Jumonji domain, which separates the catalytic domain into two fragments (JmjN and JmjC); the enzyme blongs to the KDM5/JARID1 subfamily of histone H3 lysine 4 demethylases of the Fe(II)- and 2-oxoglutarate-dependent demethylases family. The KDM5 family is unique among the Jumonji domain-containing histone demethylases in that there is an atypical insertion of a DNA-binding ARID domain and a histone-binding PHD domain into the Jumonji domain, which separates the catalytic domain into two fragments (JmjN and JmjC); the enzyme blongs to the KDM5/JARID1 subfamily of histone H3 lysine 4 demethylases of the Fe(II)- and 2-oxoglutarate-dependent demethylases family. The KDM5 family is unique among the Jumonji domain-containing histone demethylases in that there is an atypical insertion of a DNA-binding ARID domain and a histone-binding PHD domain into the Jumonji domain, which separates the catalytic domain into two fragments (JmjN and JmjC)
evolution
the SE14 enzyme is Jumonji C (JmjC) domain-containing protein, overview
evolution
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Jhd2 belongs to an expansive protein family distinguished by the presence of a JmjC domain. The JmjC domain, initially identified in the C-terminal region of the mouse Jumonji protein, mediates the demethylation of histone lysine residues
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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both pharmacological inhibition of LSD1 and small interfering RNA (siRNA) knockdown prevents interleukin 1beta-induced H3K9 demethylation at the mPGES-1 promoter as well as concomitant mPGES-1 protein expression. The level of LSD1 expression is elevated in osteoarthritis cartilage
malfunction
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changes in RENT component recruitment at NTS regions due to loss of H3 methylases or demethylases. JHD2-deficient cells contain the mostly hypercondensed rDNA mislocalized away from the nuclear periphery
malfunction
multiple myeloma MM1S cells treated with inhibitor 2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinamide show increased global H3K4 methylation at transcriptional start sites and impaired proliferation. Inhibitor 2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinamide increases H3K4me3 levels in HeLa cells; multiple myeloma MM1S cells treated with inhibitor 2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinamide show increased global H3K4 methylation at transcriptional start sites and impaired proliferation. Inhibitor 2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinamide increases H3K4me3 levels in HeLa cells; multiple myeloma MM1S cells treated with inhibitor KDOAM-25 show increased global H3K4 methylation at transcriptional start sites and impaired proliferation. Inhibitor KDOAM-25 increases H3K4me3 levels in HeLa cells; multiple myeloma MM1S cells treated with inhibitor KDOAM-25 show increased global H3K4 methylation at transcriptional start sites and impaired proliferation. Inhibitor KDOAM-25 increases H3K4me3 levels in HeLa cells. Increased KDM5B expression is associated with shorter survival in myeloma patients and ex vivo inhibition with KDOAM-25 results in cell-cycle arrest
malfunction
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Kdm5a-/- mice are highly susceptible to Listeria monocytogenes infection. During natural killer (NK) cell activation, loss of Kdm5a profoundly impairs phosphorylation and nuclear localization of STAT4, along with increased expression of suppressor of cytokine signaling 1 (SOCS1). Kdm5a-/- NK cells are hyporesponsive to inflammatory stimulus in vitro. Loss of Kdm5a profoundly impairs interleukin-12-induced phosphorylation and nuclear localization of STAT4
malfunction
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423 genes are upregulated and 333 genes are downregulated in KDM5B knockdown MDA-MB 231 cells, downregulated genes in KDM5B knockdown cells do not cluster. The expression of the KDM5B-dependent genes is validated by quantitative real-time PCR. The PHD1 finger mutants may act as dominant-negative mutants, altering the dynamics and interactions of endogenous KDM5B. In contrast, the W1502A mutant of PHD3 that is defective in H3K4me3 binding shows an inhibitory effect oncell migration similar to the effect of the wild-type protein
malfunction
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the dynamic regulation of histone modifications is important for modulating transcriptional programs during development. Aberrant H3K4 methylation is associated with neurological disorders. Loss of rbr-2 results in increased levels of H3K4me3 at the transcriptional start site of wsp-1, with concomitant higher wsp-1 expression responsible for defective axon guidance, overexpression of WSP-1 mimics rbr-2 loss, and its depletion restores normal axon guidance in rbr-2 mutants, phenotypes in rbr-2(tm3141) mutants, overview. Re-expression of WSP-1 in rbr-2/wsp-1 double mutants results in a significant increase of PVQ defects
malfunction
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overexpression of Rbp2, but not its enzymatically inactive mutant Rbp2H483G/E485Q, retards the transcription activities of IFNI, whereas small interfering RNA-mediated or short hairpin RNA-mediated knockdown of Rbp2 enhances IFNI promoter responses
malfunction
overexpression of the gene in gain-of-function mutants reduces the plant height with accumulation of lignin in stems, while the loss-of-function mutation does not produce any visible phenotype. The gain-of-function mutants show enhanced salt tolerance, whereas the loss-of-function mutant is more sensitive to salt compared to the wild-type. Overexpression of JMJ15 downregulates many genes which are preferentially marked by H3K4me3 and H3K4me2. Many of the downregulated genes encode transcription regulators involved in stress responses
malfunction
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the rbr-2(tm1231) mutant exhibits complex defects in vulval development, the rbr-2(tm1231) mutant displays the Muv or vulvaless phenotype, overview
malfunction
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internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes; internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes; internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes
malfunction
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depletion of LSD1 in an immortalized olfactory-placode-derived cell line (OP6) results in multigenic and multiallelic odorant receptor transcription per cell, while not seemingly disrupting the ability of these cells to activate new odorant receptor genes during clonal expansion. The H3K4me2/me3 levels at odorant receptor loci are near background levels. LSD1 depletion has a gradual and subtle impact on H3K4 methylation in a systematic way across all tested odorant receptor loci, while no a significant or systematic difference in H3K9me3 at odorant receptor loci in LSD1-depleted cells is observed. LSD1-depleted cells show other phenotypic effects, including a significant decrease in global 5-methyl-cytosine DNA methylation, a significant increase in global histone H4 acetylation, a significant downregulation of the LSD1-corepressor protein, CoREST, and a significant upregulation of the matrix-associated lamin-B-receptor
malfunction
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pharmacological inhibition of LSD1 in retinal explants cultured from PN1 to PN8 has three major effects. It prevents the normal decrease in expression of genes associated with progenitor function, it blocks rod photoreceptor development, and it increases expression of genes associated with other retinal cell types, e.g. genes Gnat2, Otop3, Pde6c, and Gnb3. Enzyme inhibition blocks rhodopsin expression in PN1 retinal explants, changes in rhodopsin expression caused by trans-2-phenylcyclopropylamine are not secondary to changes in cell proliferation or cell death. LSD1 enzyme inhibition changes the expression of many genes, but does not change the expression levels of these key regulators of retina development, microarrays, detailed overview
malfunction
Se14-deficient mutant line HS112 is an early flowering time mutant. The expressions of RFT1, a floral initiator known as a florigen-like gene, and Ehd1, a flowering time activator, are upregulated in Se14-deficient mutant line HS112, whereas this upregulation is not observed in the original variety of Gimbozu. The trimethylated H3K4 in the promoter region of the RFT1 chromatin is significantly increased in mutant line HS112
malfunction
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mutant jhd2DELTA causes only limited gene expression defects in fermenting cells. Mutnat jhd2DELTA causes increased accumulation of the ETC components Cox2 and Sdh3, but not of the mitochondrial membrane proteins Por1 and Tim23. SDH3 mRNA is almost 2fold upregulated in jhd2DELTA
malfunction
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overexpression of the gene in gain-of-function mutants reduces the plant height with accumulation of lignin in stems, while the loss-of-function mutation does not produce any visible phenotype. The gain-of-function mutants show enhanced salt tolerance, whereas the loss-of-function mutant is more sensitive to salt compared to the wild-type. Overexpression of JMJ15 downregulates many genes which are preferentially marked by H3K4me3 and H3K4me2. Many of the downregulated genes encode transcription regulators involved in stress responses
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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
metabolism
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different roles of histone H3 methylases in regulating Net1/Sir2 recruitment to rDNA regions and the resultant rDNA silencing. In particular, both H3K4 and H3K79 methylation by Set1 and Dot1 positively regulate rDNA silencing, whereas H3K36 methylation by Set2 has the opposite effect
metabolism
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KDM5B associates with the deacetylase NuRD complex, i.e. with two catalytic subunits of the NuRD complex. One subunit is a chromodomain helicase DNA binding protein 4 (CHD4) ATPase, which hydrolyses ATP necessary for DNA sliding and repositioning of nucleosomes. The second catalytic subunit is histone deacetylase 1 (HDAC1), which deacetylates acetylated lysine residues of histones. KDM5B is recruited to about 140000 genomic regions, and 76268 of these regions overlap with the regions occupied by HDAC1. About 50% of the KDM5B-HDAC1 binding sites overlap with tri-, di-, or monomethylated H3K4 (H3K4me3/2/1), which are substrates for the KDM5B enzymatic activity
metabolism
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NURF-1, an H3K4me3-binding protein and member of the chromatin-remodeling complex NURF, is required for promoting aberrant wsp-1 transcription in rbr-2 mutants and its ablation restores wild-type expression of wsp-1 and axon guidance
metabolism
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yeast possesses solitary H3K4 methyltransferase and demethylase enzymes
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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LSD1 modulates gene expression through demethylation of either H3K4 or H3K9. H3K9 methylation usually suppresses transcription, whereas H3K4 methylation generally activates transcription. H3K4 methylation is a critical epigenetic marker of transcriptional activation. Lysine-specific demethylase 1-mediated demethylation of histone H3 lysine 9, but not lysine 4, contributes to interleukin 1beta-induced microsomal prostaglandin E synthase 1 (mPGES-1) expression in human osteoarthritic chondrocytes. Levels of di- and trimethylated H3K4 are significantly enhanced after 4 h of interleukin-1beta stimulation, reach a maximum at 12 h, persist through 24 h and decrease at 48 h. In contrast, the level of monomethylated H3K4 remain almost unchanged following interleukin-1beta stimulation. The increase in H3K4 di- and trimethylation by interleukin-1beta at the mPGES-1 promoter paralleles the increased transcription of mPGES-1, suggesting that, in addition to H3K9 demethylation, H3K4 methylation also contributes to interleukin-1beta-induced mPGES-1 expression, the induction of mPGES-1 by interleukin-1beta is associated with H3K4 methylation
physiological function
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changes in histone H3 lysine methylation levels distinctly regulate rDNA silencing by recruiting different silencing proteins to rDNA, thereby contributing to rDNA silencing and nucleolar organization in yeast. Jhd2 regulates rDNA recombination through the Tof2/Csm1/Lrs4 pathway and prevents excessive recruitment of Tof2, Csm1/Lrs4 and condensin subunits to the replication fork barrier site within the NTS1 region. The demethylase activity of Jhd2 regulates telomeric silencing and mitotic rDNA condensation and rDNA repeat stability and rDNA silencing in a Sir2-independent manner by maintaining Csm1/Lrs4 and condensin association with rDNA regions during mitosis. Jhd2 is the only JmjC demethylase that contributes to the regulation of rDNA silencing and acts through a pathway that is independent of Net1 and Sir2, but through a Tof2/Csm1/Lrs4 pathway. Jhd2-mediated alleviation of excessive Csm1/Lrs4 or condensin at the NTS1 region of rDNA is required for the integrity of rDNA repeats and proper rDNA silencing during mitosis. The role of yeast JmjC-demethylases in regulating telomeric silencing is not restricted to Jhd2. The effect of Jhd2 on rDNA silencing is independent on the enzymatic activity of Jhd2
physiological function
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the H3K4me3 demethylase Kdm5a is required for natural killer (NK) cell activation by associating with p50 to suppress suppressor of cytokine signaling 1 (SOCS1), repressor of the JAK-STAT pathway. Kdm5a is recruited to the SOCS1 promoter by p50 to maintain a repressive chromatin configuration. Kdm5a-mediated suppression of SOCS1 is required for NK cell activation and initiation of innate immune responses to infection. Kdm5a promotes NK cell activation by regulating interferon-gamma production. Kdm5a inhibits SOCS1 expression and promotes STAT4 activation. Kdm5a is required for clearance of Listeria monocytogenes. Kdm5a associates with p50 and binds to the Socs1 promoter region in resting NK cells, leading to a substantial decrease in H3K4me3 modification and repressive chromatin configuration at the Socs1 promoter. Kdm5a enhances JAK2-STAT4 signaling by suppressing SOCS1 expression
physiological function
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histone lysine demethylase KDM5B regulates gene transcription and cell differentiation and is implicated in carcinogenesis
physiological function
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the H3K4me3/2 histone demethylase RBR-2 is required during embryogenesis in the nervous system to ensure correct axon guidance. RBR-2 controls axon guidance by repressing the actin-remodeling gene wsp-1. RBR-2 is essential for establishing correct axon guidance of the PVQ neurons during embryonic development, but it does not play any role in its maintenance. Role of rbr-2 in neuronal development, role of H3K4me3 readers in axon patterning, and epigenetic regulation of transcription. RBR-2 is required specifically in the nervous system (F25B3.3 promoter), but its presence in hypodermal cells (dpy-7 promoter) and in muscles(myo-3 promoter) is not essential
physiological function
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retinoblastoma binding protein 2 (Rbp2) is a H3K4me3 demethylase that interacts with Piasy, a Pias (protein inhibitor of activated signal transducer and activator of transcription) family member, which possesses the ability to suppress IFNI transcriptions in mouse embryonic fibroblasts (MEFs). The H3K4me3 levels, one activation mark of genes, in MEFsthat are stimulated by poly(I:C), are impaired by Piasy in the IFN-beta gene. Piasy binds to the Jmjc domain (residues 451-503) of Rbp2 via its PINIT domain (residues 101-218), which is consistent with the domain required for their attenuation of transcription and H3K4me3 levels of IFNI genes. Piasy may prevent exaggerated transcription of IFNI by Rbp2-mediated demethylation of H3K4me3 of IFNI, avoiding excessive immune responses. Piasy reduces H3K4me3 levels of IFNI genes upon activation in MEFs, the Jmjc domain of Rbp2 and the PINIT domain of Piasy are prerequisites. Demethylase activity of Rbp2, but not DNA contact by K152, is indispensable
physiological function
histone lysine methylation is an important epigenetic modification for gene expression in eukaryotic cells. Increased JMJ15 levels may regulate the gene expression program that enhances stress tolerance
physiological function
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histone H3K4 methylation is linked to transcriptional activation. KDM5A, a histone H3K4 demethylase, physically interacts with the nucleosome remodeling and deacetylase (NuRD) complex, KDM5A and the NuRD complex cooperatively function to control developmentally regulated genes. Caenorhabditis elegans homologues of KDM5, RBR-2, and CHD4 functions cooperatively with NuRD in vulval development, functional interaction between KDM5 and the NuRD complex during developmental processes
physiological function
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histone H3K4 methylation is linked to transcriptional activation. KDM5A, a histone H3K4 demethylase, physically interacts with the nucleosome remodeling and deacetylase (NuRD) complex, KDM5A and the NuRD complex cooperatively function to control developmentally regulated genes, and KDM5A and the NuRD complex cooperatively regulate H3K4me2/3 levels. CHD4 modulates H3K4 methylation levels at the promoter and coding regions of target genes
physiological function
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role for KDM5A (JARID1A/RBP2) as oncogenic driver; role for KDM5B (JARID1B/PLU1) as oncogenic driver
physiological function
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enzyme LSD1 participates in development and differentiation regulation of chromatin remodeling and histone demethylation, and specifically catalyses the demethylation of mono- and di-methylated histone H3 lysine 4 (H3K4) and H3 lysine 9 (H3K9) through a redox process. LSD1 directly binds to the promoter of P21 where it catalyzes H3K4me2 demethylation. FEZF1-AS1, a 2564 bp RNA overexpressed in gastric cancer, epigenetically represses the expression of P21 via binding with LSD1. Knockdown FEZF1-AS1 significantly inhibits gastric cancer cells proliferation by inducing G1 arrest and apoptosis, whereas endogenous expression FEZF1-AS1 promotes cell growth. FEZF1-AS1 epigenetically silences P21 transcription through LSD1-mediated H3K4me2 demethylation
physiological function
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the lysine-specific demethylase-1 (LSD1) protein removes activating H3K4 or silencing H3K9 methylationmarks in a variety of developmental contexts, and is thought to be important for proper odorant receptor regulation. Function of the mammalian olfactory system depends on specialized olfactory sensory neurons (OSNs) that each express only one allele (monoallelic) of one odorant receptor (OR) gene (monogenic). Enzyme LSD1 has a role in silencing additional odorant receptor alleles, as opposed to being required for the activation of odorant receptor alleles, within the OP6 cellular context. LSD1 seems not to be required for de novo odorant receptor activation events. But LSD1 is normally required to prevent multiple odorant receptor activation events per cell. LSD1 plays a role in suppressing competing odorant receptor genes/alleles
physiological function
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LSD1 is an enzyme active at key stages of development in a number of tissues, including the central nervous system. LSD1-mediated demethylation of H3K4me2 is required for the transition from late progenitor to differentiated mouse rod photoreceptor. LSD1 acts in concert with a series of nuclear receptors to modify chromatin structure and repress progenitor genes as well as to inhibit ectopic patterns of gene expression in the differentiating postmitotic retinal cells
physiological function
Se14 is a photoperiod-sensitivity gene that has a suppressive effect on floral transition (flowering time) under long day-length conditions through the modification of chromatin structure by H3K4me3 demethylation in the promoter region of RFT1
physiological function
-
Saccharomyces cerevisiae Jumonji demethylase Jhd2 opposes the accumulation of H3K4me3 in fermenting cells only when they are nutritionally manipulated to contain an elevated 2-oxoglutarate/succinate ratio. Jhd2 opposes H3K4me3 in respiratory cells that do not exhibit such an elevated 2-oxoglutarate/succinate ratio. JHD2 restrains respiration in nonfermentable growth conditions. Enzyme JHD2 restricts mitochondrial respiratory capacity in cells grown in non-fermentable carbon in an H3K4me-dependent manner. JHD2 limits yeast proliferative capacity under physiologically challenging conditions as measured by both replicative lifespan and colony growth on non-fermentable carbon. JHD2's impact on nutrient response may reflect an ancestral role of its gene family in mediating mitochondrial regulation. The JmjC domain mediates the demethylation of histone lysine residues. Nutritional conditions impact Jhd2 control of H3K4me3 and gene expression. JHD2 controls mitochondrial respiration through H3K4me
physiological function
-
histone lysine methylation is an important epigenetic modification for gene expression in eukaryotic cells. Increased JMJ15 levels may regulate the gene expression program that enhances stress tolerance
-
physiological function
-
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
-
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
-
additional information
-
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
-
inhibition of LSD1 by oligoamines increases activating H3K4me2 and H3K4me1 marks and decreases repressive H3K9me2 marks at the promoters of reexpressed genes
additional information
-
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
-
mechanism of histone H3 demethylation by demethylase LSD1, overview
additional information
-
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
-
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
additional information
-
enzyme KDM5B contains multiple conserved chromatin-associated domains, including three PHD fingers. The first and third, but not the second, PHD finger of KDM5B possess histone binding activities. The PHD1 finger is highly specific for unmodified histone H3 (H3K4me0), whereas the PHD3 finger shows preference for the trimethylated histone mark H3K4me3, but also binds H3K4me0. Mechanism of H3K4me0 recognition by PHD1, the H3K4me0 binding mode is conserved overview. KDM5B inhibits the migration and invasion abilities of MDA-MB 231 breast cancer cells, and binding of the PHD1 finger to H3K4me0 is required to suppress cell migration
additional information
-
enzyme KDM5A uses distinct domains to associate with the SIN3B and NuRD complexes
additional information
-
minimal requirements for enzymatic activity of the KDM5 family is the linked JmjNJmjC domain coupled with the immediate C-terminal helical zinc-binding domain; minimal requirements for enzymatic activity of the KDM5 family is the linked JmjNJmjC domain coupled with the immediate C-terminal helical zinc-binding domain, hypothetical modeling of the N-terminal half of KDM5, overview; minimal requirements for enzymatic activity of the KDM5 family is the linked JmjNJmjC domain coupled with the immediate C-terminal helical zinc-binding domain, hypothetical modeling of the N-terminal half of KDM5, overview
additional information
-
LSD1 has no DNA-binding domain, LSD1 may interact with nuclear receptors NR2E1/ NR2E3 to bind to specific loci around progenitor genes and its promoters and that this binding is developmentally regulated
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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 + ?
-
amino acids 1-21 of histone 3
-
-
?
H3(1-20) K4-dimethylated peptide + 2-oxoglutarate + O2
H3(1-20) K4-monomethylated peptide + 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-lysine9 + succinate + formaldehyde + CO2
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 peptide1-21 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 peptide1-21 + succinate + formaldehyde + CO2
-
minimal peptide substrate, binding of KDM1A to the peptide substrate H3K4me2_1-21 is electrostatic in nature
-
-
?
histone H3 N6-dimethyl-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 peptide1-21 + 2-oxoglutarate + O2
histone H3 L-lysine4 peptide1-21 + succinate + formaldehyde + CO2
-
minimal peptide substrate, binding of KDM1A to the peptide substrate H3K4me1_1-21 is electrostatic in nature
-
-
?
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
-
-
?
[chromodomain Y-like protein]-N6,N6,N6-trimethyl-L-lysine135 + 2-oxoglutarate + O2
?
-
-
-
-
?
[Cockayne syndrome group B protein]-N6,N6,N6-trimethyl-L-lysine1054 + 2-oxoglutarate + O2
?
-
-
-
-
?
[Cockayne syndrome group B protein]-N6,N6,N6-trimethyl-L-lysine170 + 2-oxoglutarate + O2
?
-
-
-
-
?
[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
-
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
-
-
?
[Dnmt1]-methyl-L-lysine1096 + 2-oxoglutarate + O2
[Dnmt1]-L-lysine1096 + succinate + formaldehyde + CO2
-
mechanistic link between the histone and DNA methylation systems
-
-
?
[G9a protein]-N6,N6,N6-trimethyl-L-lysine185 + 2-oxoglutarate + O2
?
-
a customer synthesized protein
-
-
?
[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
[widely interspaced zinc finger motifs protein]-N6,N6,N6-trimethyl-L-lysine305 + 2-oxoglutarate + O2
?
-
-
-
-
?
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
specific for
-
-
?
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
specific for
-
-
?
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,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,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
SE14 catalyzes H3K4me3 demethylation in the promoter region of RFT1
-
-
?
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
yeast Jhd2 demethylates histone H3 Lys4 near the rDNA locus, Jhd2 demethylates H3K4 within the rDNA regions in vivo
-
-
?
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
yeast Jhd2 demethylates histone H3 Lys4 near the rDNA locus
-
-
?
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,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,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
-
-
-
-
?
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
?
-
the enzyme shows no activity with histone H3 N6,N6-dimethyl-L-lysine4 and histone H3 N6-methyl-L-lysine4
-
-
-
additional information
?
-
the enzyme shows no activity with histone H3 N6,N6-dimethyl-L-lysine4 and histone H3 N6-methyl-L-lysine4
-
-
-
additional information
?
-
-
KDM5A, a histone H3K4 demethylase, physically interacts with the nucleosome remodeling and deacetylase (NuRD) complex
-
-
-
additional information
?
-
-
no activity with monomethylated H3K4
-
-
-
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
?
-
-
KDM1A catalyzes the oxidative demethylation of histone H3K4me1/2 and H3K9me1/2 as well as non-histone substrates
-
-
-
additional information
?
-
-
KDM5A, a histone H3K4 demethylase, physically interacts with the nucleosome remodeling and deacetylase (NuRD) complex
-
-
-
additional information
?
-
-
KDM5B associates with the deacetylase NuRD complex
-
-
-
additional information
?
-
-
LSD1 directly binds to the promoter of P21 where it catalyzes H3K4me2 demethylation. FEZF1-AS1, a 2564 bp RNA overexpressed in gastric cancer, epigenetically represses the expression of P21 via binding with LSD1
-
-
-
additional information
?
-
no activity with histone H3 N6-dimethyl-L-lysine4
-
-
-
additional information
?
-
no activity with histone H3 N6-dimethyl-L-lysine4
-
-
-
additional information
?
-
no activity with histone H3 N6-dimethyl-L-lysine4
-
-
-
additional information
?
-
-
the enzyme also catalyzes the demethylation of histone H3 N6,N6-dimethyl-L-lysine9 and histone H3 N6-methyl-L-lysine9. Histone H3 is the preferred histone substrate of KDM1A compared to histones H2A, H2B, and H4. KDM1A likely contains a histone H3 secondary specificity element on the enzyme surface that contributes significantly to its recognition of substrates and products. Kinetic analysis of full-length histone products against KDM1A. KDM1A requires a minimal substrate corresponding to the first 21 residues of the N-terminal histone H3 tail for efficient demethylation activity
-
-
-
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
?
-
-
LSD1 demethylates mono- and dimethylated H3K4 and H3K9, but does not alter trimethylated H3K4 and H3K9
-
-
-
additional information
?
-
-
protein-protein interaction anaysis of wild-type and mutants and interactional domains between Rbp2 and Piasy, overview
-
-
-
additional information
?
-
-
no activity with histone H3 N6,N6,N6-dimethyl-L-lysine4
-
-
-
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
-
-
-
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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-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 L-lysine4 + succinate + formaldehyde + CO2
P29375, Q9BY66, Q9UGL1
-
-
-
?
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
O64752
-
-
-
?
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
O64752
-
-
-
?
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
Q23541
-
-
-
?
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
P29375, Q9BY66, Q9UGL1
-
-
-
?
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
O60341
-
-
-
?
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
Q6ZQ88
-
-
-
?
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
Q10RP4
SE14 catalyzes H3K4me3 demethylation in the promoter region of RFT1
-
-
?
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
P47156
yeast Jhd2 demethylates histone H3 Lys4 near the rDNA locus, Jhd2 demethylates H3K4 within the rDNA regions in vivo
-
-
?
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
P29375, Q9BY66, Q9UGL1
-
-
-
?
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
O60341
-
-
-
?
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
Q6ZQ88
-
-
-
?
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
-
-
-
-
?
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
?
-
-
KDM5A, a histone H3K4 demethylase, physically interacts with the nucleosome remodeling and deacetylase (NuRD) complex
-
-
-
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
?
-
-
KDM1A catalyzes the oxidative demethylation of histone H3K4me1/2 and H3K9me1/2 as well as non-histone substrates
-
-
-
additional information
?
-
-
KDM5A, a histone H3K4 demethylase, physically interacts with the nucleosome remodeling and deacetylase (NuRD) complex
-
-
-
additional information
?
-
-
KDM5B associates with the deacetylase NuRD complex
-
-
-
additional information
?
-
-
LSD1 directly binds to the promoter of P21 where it catalyzes H3K4me2 demethylation. FEZF1-AS1, a 2564 bp RNA overexpressed in gastric cancer, epigenetically represses the expression of P21 via binding with LSD1
-
-
-
additional information
?
-
P29375
no activity with histone H3 N6-dimethyl-L-lysine4
-
-
-
additional information
?
-
Q9BY66
no activity with histone H3 N6-dimethyl-L-lysine4
-
-
-
additional information
?
-
Q9UGL1
no activity with histone H3 N6-dimethyl-L-lysine4
-
-
-
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
?
-
-
LSD1 demethylates mono- and dimethylated H3K4 and H3K9, but does not alter trimethylated H3K4 and H3K9
-
-
-
additional information
?
-
-
protein-protein interaction anaysis of wild-type and mutants and interactional domains between Rbp2 and Piasy, 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
-
-
-
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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
-
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe2+
Fe2+
required for acatalysis; required for acatalysis; required for catalysis; required for catalysis
Fe2+
-
dependent on, active site bound, required for activity; dependent on, active site bound, required for activity
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
(2-hydroxyacetyl)-L-alanyl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucine
-
-
(2-hydroxyacetyl)-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucine
-
-
(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
-
-
(2Z)-N-ethyl-N'-[4-[(4-[[(2Z)-4-(ethylamino)but-2-en-1-yl]amino]butyl)amino]butyl]but-2-ene-1,4-diamine
-
-
(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
2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)-N-ethylisonicotinamide
-
2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)-N-methylisonicotinamide
-
2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinamide
; the potent and selective KDM5A-D inhibitor stops cellular demethylation of H3K4me3 at transcription start sites and proliferation of MM1S myeloma cells; the potent and selective KDM5A-D inhibitor stops cellular demethylation of H3K4me3 at transcription start sites and proliferation of MM1S myeloma cells; the potent and selective KDM5A-D inhibitor stops cellular demethylation of H3K4me3 at transcription start sites and proliferation of MM1S myeloma cells. Analysis of enzyme-inhibitor binding structure from crystal structure analysis, overview
2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinic acid
-
2-(piperazin-1-ylmethyl)isonicotinic acid
; the potent and selective KDM5A-D inhibitor stops cellular demethylation of H3K4me3 at transcription start sites and proliferation of MM1S myeloma cells
3-((2-(pyridin-2-yl)-6-(1,2,4,5-tetrahydro-3H-benzo[d]azepin-3-yl)pyrimidin-4-yl)amino)propanoic acid
-
;
4-((methyl((1-(4-oxo-3,4-dihydropyrido[3,4-d]pyrimidin-8-yl)-1H-pyrazol-4-yl)methyl)amino)methyl)benzonitrile
-
-
4-((methyl(2-(1-(4-oxo-3,4-dihydropyrido[3,4-d]pyrimidin-8-yl)-1H-pyrazol-4-yl)ethyl)amino)methyl)benzonitrile
-
-
4-(1-(2-(1-(4-oxo-3,4-dihydropyrido[3,4-d]pyrimidin-8-yl)-1H-pyrazol-4-yl)ethyl)piperidin-4-yl)benzonitrile
-
;
8-(4-(((3,4-dichlorobenzyl)(methyl)amino)methyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-((dimethylamino)methyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-((methyl(4-(methylsulfonyl)benzyl)amino)methyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
-
8-(4-((methyl(4-(methylsulfonyl)benzyl)amino)methyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one52g
-
-
-
8-(4-(2-((4-fluorobenzyl) (methyl)amino)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-((5-cyclopropyl-1,2,4-oxadiazol-3-yl)methyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-(2,4-difluorophenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-(2-chlorophenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-(3,4-dichlorobenzyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-(3,5-dichlorophenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
; substitution from C4 of the pyrazole moiety allows access to the histone peptide substrate binding site, incorporation of a conformationally constrained 4-phenylpiperidine linker gives derivatives such as 8-(4-(2-(4-(3-chlorophenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one which demonstrates equipotent activity versus the KDM4 (JMJD2) and KDM5 (JARID1) subfamily demethylases, selectivity over representative exemplars of the KDM2, KDM3, and KDM6 subfamilies, and cellular permeability in the Caco-2 assay
8-(4-(2-(4-(3,5-difluorophenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-(3-(trifluoromethyl)phenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-(3-chlorophenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
; substitution from C4 of the pyrazole moiety allows access to the histone peptide substrate binding site, incorporation of a conformationally constrained 4-phenylpiperidine linker gives derivatives such as 8-(4-(2-(4-(3-chlorophenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one which demonstrates equipotent activity versus the KDM4 (JMJD2) and KDM5 (JARID1) subfamily demethylases, selectivity over representative exemplars of the KDM2, KDM3, and KDM6 subfamilies, cellular permeability in the Caco-2 assay, and inhibition of H3K9Me3 and H3K4Me3 demethylation in a cell-based assay
8-(4-(2-(4-(3-methoxybenzyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-(4-(methylsulfonyl)phenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-(4-(trifluoromethyl)benzyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-(4-chlorobenzyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-(4-chlorophenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-(4-fluorobenzyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-(4-fluorophenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-(4-methoxyphenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-(benzo[d][1,3]dioxol-5-ylmethyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-(pyridin-3-ylmethyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-(pyridin-4-yl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-(thiophen-2-yl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-benzylpiperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(2-(4-phenylpiperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(piperidin-1-ylmethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
8-(4-(pyrrolidin-1-ylmethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
;
Cd2+
-
at 0.001-0.005 mM, cadmium increases global histone H3 methylation, H3K4me3 and H3K9me2, by inhibiting the activities of histone demethylases, and aberrant histone methylation that occurs early (48 h) and at 4 weeks is associated with cadmium-induced transformation of BEAS-2B cells at the early stage
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
ethyl 2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinate
-
GSK-J1
-
a selective inhibitor of the KDM6/KDM5 subfamilies. Docking study and identification of critical residues for binding of the inhibitor to the reconstituted KDM5 Jumonji domain; a selective inhibitor of the KDM6/KDM5 subfamilies. Docking study and identification of critical residues for binding of the inhibitor to the reconstituted KDM5 Jumonji domain. GSK-J1 inhibits the demethylase activity of KDM5C with 8.5fold increased potency compared with that of KDM5B at 1 mM 2-oxoglutarate. Also inhibits the enzyme mutant KDM5BDELTAAP; a selective inhibitor of the KDM6/KDM5 subfamilies. Docking study and identification of critical residues for binding of the inhibitor to the reconstituted KDM5 Jumonji domain. GSK-J1 inhibits the demethylase activity of KDM5C with 8.5fold increased potency compared with that of KDM5B at 1 mM 2-oxoglutarate. Also inhibits the enzyme mutant KDM5CDELTAAP
-
histone H3
-
full-length histone H3, H3_1-135, which lacks any posttranslational modifications, is a tight-binding, competitive inhibitor of KDM1A demethylation activity. Full-length H3 rapidly reaches equilibrium with KDM1A and shows 100fold increased binding affinity compared to a 21-mer H3-derived peptide
-
JIB-04
-
a pan-inhibitor of the Jumonji demethylase superfamily; a pan-inhibitor of the Jumonji demethylase superfamily, that is about 8fold more potent against KDM5B than against KDM5C. Also inhibits the enzyme mutant KDM5BDELTAAP; a pan-inhibitor of the Jumonji demethylase superfamily, that is about 8fold more potent against KDM5B than against KDM5C. Also inhibits the enzyme mutant KDM5CDELTAAP
-
L-alanyl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucine
-
-
L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucine
-
-
L-homoseryseryl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucyl-(N6-(L-homoseryl))-L-lysine
-
enzyme binding structure, overview
-
L-seryl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucine
-
enzyme binding structure, 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-(hydroxyacetyl)-L-alanyl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-N6-(hydroxyacetyl)-L-lysyl-L-glutaminyl-L-leucine
-
-
N-(hydroxyacetyl)-L-alanyl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-N6-(hydroxyacetyl)-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucine
-
-
N-ethyl-N'-[[2-([[4-([[2-([[4-(ethylamino)butyl]amino]methyl)cyclopropyl]methyl]amino)butyl]amino]methyl)cyclopropyl]methyl]butane-1,4-diamine
-
-
N2-L-alanyl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-N6-(2-hydroxyacetyl)-L-lysyl-L-glutaminyl-L-leucine
-
-
N2-L-alanyl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-N6-(2-hydroxyacetyl)-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucine
-
-
N2-L-seryl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-(N6-(L-seryl))-L-lysyl-L-glutaminyl-L-leucine
-
-
N2-L-seryl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucyl-(N6-(L-seryl))-L-lysine-amide
-
enzyme binding structure, overview
N2-L-seryl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucyl-L-alanyl-L-threonyl-(N6-(L-seryl))-L-lysine-amide
-
-
NURF-1
-
an H3K4me3-binding protein and member of the chromatin-remodeling complex NURF, is required for promoting aberrant wsp-1 transcription in rbr-2 mutants and its ablation restores wild-type expression of wsp-1 and axon guidance
-
peptide H3K4M
-
the modified H3 peptide with substitution of Lys4 to Met [H3K4M] is known to be a potent competitive inhibitor of LSD1
-
Pargyline
-
i.e. N-methyl-N-propargylbenzylamine, the LSD1 inhibitor prevents demethylation of Dnmt1-C by LSD1
Tranylcypromine
-
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
-
additional information
-
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
-
(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
-
additional information
-
no other core histones exhibited inhibition of KDM1A demethylation activity. Kinetic analysis of full-length histone products against KDM1A
-
additional information
-
structural analysis of homoserine-substituted inhibitor peptide-bound LSD1-CoREST complex, overview
-
additional information
-
structural characterization of the linked JmjN-JmjC domain for the KDM5 family for the design of KDM5 demethylase inhibitors with improved potency and selectivity; structural characterization of the linked JmjN-JmjC domain for the KDM5 family for the design of KDM5 demethylase inhibitors with improved potency and selectivity; structural characterization of the linked JmjN-JmjC domain for the KDM5 family for the design of KDM5 demethylase inhibitors with improved potency and selectivity, hypothetical modeling of the N-terminal half of KDM5, overview
-
additional information
-
discovery and synthesis of N-substituted 4-(pyridin-2-yl)thiazole-2-amine derivatives and their subsequent optimization, guided by structure-based design, to give 8-(1H-pyrazol-3-yl)pyrido[3,4-d]pyrimidin-4(3H)-ones, a series of potent JmjC histone N-methyl lysine demethylase (KDM) inhibitors which bind to Fe(II) in the active site. No inhibition by 4-(pyridin-2-yl)thiazol-2-amine; discovery and synthesis of N-substituted 4-(pyridin-2-yl)thiazole-2-amine derivatives and their subsequent optimization, guided by structure-based design, to give 8-(1H-pyrazol-3-yl)pyrido[3,4-d]pyrimidin-4(3H)-ones, a series of potent JmjC histone N-methyl lysine demethylase (KDM) inhibitors which bind to Fe(II) in the active site. No inhibition by 4-(pyridin-2-yl)thiazol-2-amine, 4-((methyl((1-(4-oxo-3,4-dihydropyrido[3,4-d]pyrimidin-8-yl)-1H-pyrazol-4-yl)methyl)amino)methyl)benzonitrile, and 4-((methyl(2-(1-(4-oxo-3,4-dihydropyrido[3,4-d]pyrimidin-8-yl)-1H-pyrazol-4-yl)ethyl)amino)methyl)benzonitrile, poor inhibition by 8-((4-phenylpiperazin-1-yl)methyl)pyrido[3,4-d]pyrimidin-4(3H)-one
-
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
HP1a
-
Suv(Var)3-9/KMT1 interacts with HP1 that binds [histone H3]-N6,N6-trimethyl-L-lysine9
-
N-oxalylglycine
required, essential for the demethylase activity in vivo
additional information
-
transient hyperglycemia induces recruitment of LSD1 to gene regulation sites/promoters
-
additional information
-
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
-
interleukin-1beta enhances recruitment of LSD1 to mPGES-1 promoter
-
additional information
-
transient hyperglycemia induces recruitment of LSD1 to gene regulation sites/promoters
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
Michaelis-Menten kinetics of wild-type and mutant enzymes; Michaelis-Menten kinetics of wild-type and mutant enzymes
-
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.5
(2-hydroxyacetyl)-L-alanyl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucine
-
pH 7.5, 25°C
0.17
(2-hydroxyacetyl)-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucine
-
pH 7.5, 25°C
0.000098
L-alanyl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucine
-
pH 7.5, 25°C
0.5
L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucine
-
pH 7.5, 25°C
0.0063
L-homoseryseryl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucyl-(N6-(L-homoseryl))-L-lysine
-
pH 7.5, 25°C
-
0.00003
L-seryl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucine
-
pH 7.5, 25°C
0.5
N-(hydroxyacetyl)-L-alanyl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-N6-(hydroxyacetyl)-L-lysyl-L-glutaminyl-L-leucine
-
pH 7.5, 25°C
0.5
N-(hydroxyacetyl)-L-alanyl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-N6-(hydroxyacetyl)-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucine
-
pH 7.5, 25°C
0.0014
N2-L-alanyl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-N6-(2-hydroxyacetyl)-L-lysyl-L-glutaminyl-L-leucine
-
pH 7.5, 25°C
0.0098
N2-L-alanyl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-N6-(2-hydroxyacetyl)-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucine
-
pH 7.5, 25°C
0.00038
N2-L-seryl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-(N6-(L-seryl))-L-lysyl-L-glutaminyl-L-leucine
-
pH 7.5, 25°C
0.00006
N2-L-seryl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucyl-(N6-(L-seryl))-L-lysine-amide
-
pH 7.5, 25°C
0.00029
N2-L-seryl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucyl-L-alanyl-L-threonyl-(N6-(L-seryl))-L-lysine-amide
-
pH 7.5, 25°C
additional information
additional information
-
kinetic analysis of full-length histone products against KDM1A
-
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.000098
2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)-N-ethylisonicotinamide
Homo sapiens;
Q9BY66
pH and temperature not specified in the publication
0.00027
2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)-N-methylisonicotinamide
Homo sapiens;
Q9BY66
pH and temperature not specified in the publication
0.000019 - 0.000071
2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinamide
0.000007
2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinic acid
Homo sapiens;
Q9BY66
pH and temperature not specified in the publication
0.00098
2-(piperazin-1-ylmethyl)isonicotinic acid
Homo sapiens;
Q9BY66
pH and temperature not specified in the publication
0.000048
ethyl 2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinate
Homo sapiens;
Q9BY66
pH and temperature not specified in the publication
0.000019
2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinamide
Homo sapiens;
Q9BY66
pH and temperature not specified in the publication
0.000069
2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinamide
Homo sapiens;
Q9BY66
pH and temperature not specified in the publication; pH and temperature not specified in the publication
0.000071
2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinamide
Homo sapiens;
Q9BY66
pH and temperature not specified in the publication
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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
7.5
8.5
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
22
37
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
histone H3-K4 demethylase is restricted to the corpus luteum
-
LSD1 is strongly expressed in poorly differentiated neuroblastomas, real-time reverse transcription-PCR expression analysis
-
histone H3 lysine 4 demethylase JARID1B is up-regulated in prostate cancer. JARID1B associates with androgen receptor and regulates its transcriptional activity
-
lysine-specific demethylase 1 colocalizes with androgen receptor
-
lysine-specific demethylase 1 colocalizes with androgen receptor
-
the highest expression of LSD1 occurs in postmitotic retinal cells during the peak period of rod photoreceptor differentiation. LSD1 appears to be absent at the outer margin of the retina, enzyme distribution, overview
-
JMJ703 is expressed at relatively high levels in leaves of 7 d-after-germination in seedlings compared with all of the other tissues tested
-
Beko cell, spontaneous T-cell lymphoma cell line derived from T-cell receptor beta knockout mice, only KDM5A and KDM5C are expressed
additional information
-
the distributions of H3-K4 mono-, di-, and tri-methylated histones exhibit exactly the same pattern as the LSD1 protein, immunofluoresecence histochemic analysis, overview
-
the distributions of H3-K4 mono-, di-, and tri-methylated histones exhibit exactly the same pattern as the LSD1 protein, immunofluoresecence histochemic analysis, overview
-
-
BALB c nu/nu athymic nude mice are implanted with the human colorectal cancer HCT-116 cells
-
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
additional information
expression of gene JMJ15 is relatively low and is limited to a number of tissues during vegetative growth but is higher in young floral organs. JMJ15 displays a highly tissue-specific expression pattern
additional information
-
expression of gene JMJ15 is relatively low and is limited to a number of tissues during vegetative growth but is higher in young floral organs. JMJ15 displays a highly tissue-specific expression pattern
-
additional information
-
RBR-2 is ubiquitously expressed in embryos and larvae
additional information
-
the expression level of KDM5B is significantly lower in breast cancer estrogen receptor lacking ER- cells compared to ER+ cells, e.g. lower expression levels of KDM5B in the triple-negative breast cancer patients compared with patients with the ER+/PR+ subtype
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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
-
KDM5B colocalizes with HDAC1 and CHD4 at chromatin in K-562 cells
-
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
-
additional information
-
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
-
from N- to C-terminus, KDM1A is composed of an unstructured region that contains the nuclear localization signal and three structured domains: a SWI3p, Rsc8p, and Moira (SWIRM) domain, an amine oxidase domain (AOD), and an unprecedented intervening domain within the AOD colloquially known as the tower. The tower domain of KDM1A is composed of two antiparallel alpha-helices (termed TalphaA and TalphaB) that form a coiled coil and extend approximately 100 A from the AOD
additional information
-
KDM5 domain structure and functional analysis, overview; KDM5 domain structure and functional analysis, overview; KDM5 domain structure and functional analysis, overview
additional information
-
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 in complex with inhibitor KDOAM-25, sitting drop vapor diffusion method, mixing of 50 nl of 8.1 mg/ml protein in solution with 1 mM KDOAM-25 and 4 mM MnCl2, is mixed with ,precipitant solution consisting of 1.6 M Na/K phosphate, and 0.1 M HEPES, pH 7.5, and 20 nL of KDM5B seeds of crystals obtained from the same condition, 4°C, X-ray diffraction structure determination and analysis at 2.0 A resolution, modeling
purified recombinant truncated enzyme LSD1 comprising residues 172-833 in complex with recombinant human CoREST residues 308-440, and peptide inhibitors 9, N2-L-seryl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucyl-(N6-(L-seryl))-L-lysine-amide, and L-homoseryseryl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucyl-(N6-(L-homoseryl))-L-lysine, by hanging drop vapor diffusion method, mixing of 0.001 ml of 9 mg/m protein solution with 0.001 ml of reservoir solution containing 100 mM N-(carbamoylmethyl)iminodiacetic acid, pH 5.5, and 1.18-1.28M potassium sodium tartrate tetrahydrate, 20°C, crystals are soaked in a solution containing 100 mM N-(carbamoylmethyl) iminodiacetic acid buffer, pH 5.5, with 1.14 M potassium sodium tartrate tetrahydrate, 10% glycerol, and 2 mM LSD1 inhibitor peptide L-seryl-L-arginyl-L-threonyl-L-methionyl-L-glutaminyl-L-threonyl-L-alanyl-L-arginyl-L-lysyl-L-seryl-L-threonylglycylglycyl-L-lysyl-L-alanyl-L-prolyl-L-arginyl-L-lysyl-L-glutaminyl-L-leucine, 11 or 13 for 2 h, X-ray diffraction structure determination and analysis at 2.53-2.69 A resolution
-
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-SUMO-tagged enzyme from Escherichia coli strain BL21(DE3)C+ by nickel affinity chromatography, tag cleavage overnight by Ulp-1 protease, followed by anion exchange chromatography, gel filtration, and ultrafiltration; recombinant His-SUMO-tagged enzyme from Escherichia coli strain BL21(DE3)C+ by nickel affinity chromatography, tag cleavage overnight by Ulp-1 protease, followed by anion exchange chromatography, gel filtration, and ultrafiltration; recombinant His-SUMO-tagged enzyme from Escherichia coli strain BL21(DE3)C+ by nickel affinity chromatography, tag cleavage overnight by Ulp-1 protease, followed by anion exchange chromatography, gel filtration, and ultrafiltration. Deletion of DELTAAP has no effect on kinetics of KDM5C
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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 FLAG-tagged KDM5A from HeLa cell nuclear extract by gel filtration and immunoaffinity chromatography, the enzyme copurifies with the SIN3B-HDAC complex, and with additional proteins including CHD4, MTA2, GATAD2A, ZMYND8A, ZNF592, and ZNF687. CHD4, MTA2, and GATAD2A are known components of the NuRD (nucleosome remodeling and deacetylase) complex
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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 JHD2, recombinant expression of HA-tagged wild-type Jhd2 and H427A mutant in yeast cells
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gene JMJ15, quantitative RT-PCR enzyme expression analysis, pJMJ15-GUS and 35S-JMJ15-FLAG-HA constructs are transformed into Agrobacterium tumefaciens strain GV3101 and then transformed into plants using the floral dip method
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 KDM5A, cloned from a HeLa gene library, recombinant expression of N-terminally FLAG-tagged KDM5A in HeLa cells and HEK-293T cells, quantitative RT-PCR expression analysis
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gene KDM5A, recombinant coexpression of wild-type and mutant FLAG-tagged Piasy and HA-tagged Rbp2 from pcDNA3.1(+) HA expression vector and p33 Flag CMV7.1 expression vector, respectively, in HEK-293T cells
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gene KDM5A, recombinant expression of soluble His-SUMO-tagged enzyme in Escherichia coli strain BL21(DE3)C+; gene KDM5B, recombinant expression of soluble His-SUMO-tagged enzyme in Escherichia coli strain BL21(DE3)C+; gene KDM5C, recombinant expression ofsoluble His-SUMO-tagged enzyme in Escherichia coli strain BL21(DE3)C+
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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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gene rbr2, generation of transgenic lines in which RBR-2::GFP expression is driven by the rbr-2 promoter showing that RBR-2 is ubiquitously expressed in embryos and larvae, gene rbr-2 interacts with many neuronal genes, overview
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gene SE14, map-based cloning of Se14, DNA and amino acid sequence determination and analysis, sequence comparisons, fine mapping of the Se14 locus on the short arm of chromosome 3, genetic interaction of the Se14 locus with other flowering time genes loci and gene expression analysis
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
D328A
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site-directed mutagenesis, a loss-of-function mutations in the PHD1 finger domain
L326W
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site-directed mutagenesis, a loss-of-function mutations in the PHD1 finger domain
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
W1502A
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site-directed mutagenesis, a loss-of-function mutations in the PHD3 finger domain
K1096R
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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
construction of JMJ15 T-DNA insertion mutants, phenotypes, overview
additional information
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construction of JMJ15 T-DNA insertion mutants, phenotypes, overview
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additional information
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generation of a rbr-2(tm3141) mutant, expression of wild-type rbr-2 gene completely rescues the PVQ defects
additional information
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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
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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
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LSD1 knockdown by siRNA inhibits 8-oxo-guanine production
additional information
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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
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the enzyme is knocked out by expression of specific siRNA for LSD1 in chondrocytes
additional information
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siRNA-mediated knockdown of KDM5A, and CHD4 or SIN3B in HeLa cells, and analysis of the changes in gene expression by microarray analysis. At least 435 genes (corresponding to 468 probes) are dysregulated in the KDM5A-knockdown cells. 66 and 63% of the KDM5A-regulated genes are also dysregulated in CHD4-and SIN3B-knockdown cells, respectively, and 47% of the KDM5A-regulated genes are affected by either CHD4 or SIN3B knockdown. Among the 435 KDM5A-regulated genes, 40% are upregulated, although more than half are downregulated. A similar proportion of genes is downregulated in response to SIN3B knockdown
additional information
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internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes; internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes. Generation of a KDM5B(1-755)DELTAAP mutant by deleting ARID and PHD1 (AP) domains by connecting residues 100 and 363. The DELTAAP constructs represent the domain arrangement of the conventional Jumonji domain followed by a C-terminal helical zinc binding domain. Deletion of DELTAAP has no effect on kinetics of KDM5C; internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes. Generation of a KDM5C(1-789)DELTAAP mutant by deleting ARID and PHD1 (AP) domains by connecting residues 100 and 363. The DELTAAP constructs represent the domain arrangement of the conventional Jumonji domain followed by a C-terminal helical zinc binding domain
additional information
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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
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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
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hairpin RNA enzyme LSD1 knockdown, RNAi rescue experiments by expressing the human LSD1 cDNA
additional information
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RBP2 enzyme knockout by transfection of siRNA, that targets Rbp2, into Piasy+/+ MEFs
additional information
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RNAi knockdown of LSD1 expression to undetectable levels in about 90% of OP-6 cells in culture, LSD1 depletion does not appear to interfere with the ability of OP-6 cells to switch from one odorant receptor gene to another during culturing, LSD1 seems not to be required for de novo odorant receptor activation events. LSD1 depletion disrupts monoallelic and monogenic odorant receptor expression in OP-6 cells. LSD1 depletion has a gradual and subtle impact on H3K4 methylation in a systematic way across all tested odorant receptor loci, while no a significant or systematic difference in H3K9me3 at odorant receptor loci in LSD1-depleted cells is observed
additional information
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hairpin RNA enzyme LSD1 knockdown, RNAi rescue experiments by expressing the human LSD1 cDNA
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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
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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
generation of Se14-deficient mutant line HS112, an early flowering time mutant, Diurnal expression of flowering time genes in the wild-type and HS112, overview
additional information
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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
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generation of an enzyme mutant jhd2DELTA, jhd2DELTA profoundly enhances rDNA silencing. Overexpression of wild-type Jhd2 significantly reduces H3K4me3 levels, whereas overexpression of jhd2-H427A has little effect on H3K4me3
additional information
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generation of enzyme mutant Jhd2DELTA MSY724 cells
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