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Literature summary for 1.14.11.66 extracted from

  • Zoabi, M.; Nadar-Ponniah, P.T.; Khoury-Haddad, H.; Usaj, M.; Budowski-Tal, I.; Haran, T.; Henn, A.; Mandel-Gutfreund, Y.; Ayoub, N.
    RNA-dependent chromatin localization of KDM4D lysine demethylase promotes H3K9me3 demethylation (2014), Nucleic Acids Res., 42, 13026-13038 .
    View publication on PubMedView publication on EuropePMC
Search for more literature for 1.14.11.66

Activating Compound

Activating Compound Comment Organism Structure
ascorbate required for activity Homo sapiens
additional information RNA interaction with KDM4D N-terminus is essential for KDM4D association with chromatin Homo sapiens

Cloned(Commentary)

Cloned (Comment) Organism
expressed in Escherichia coli BL21(DE3) cells Homo sapiens
gene KDM4D, functional recombinant expression of wild-type and mutant His6-tagged full-length enzyme in Escherichia coli strain BL21(DE3). To establish the U2OS-TetON stable cell line that conditionally expresses myc-KDM4D or EGFP-KDM4D-1H4R-HRK-FL, fragments including the myc-KDM4D or EGFP-KDM4D-1H4R-HRK-FL are subcloned into pTRE2-puro plasmid. The resulting pTRE2-puro-myc-KDM4D and pTRE2-puro-EGFP-KDM4D-1H4R-HRK-FL vectors are transfected into U2OS-Tet-ON cells. REcombinant expression of the His-tagged N-terminus, residues 1.350, of the enzyme, expressing the His-tagged C-terminus of KDM4D proves unsuccessful Homo sapiens

Protein Variants

Protein Variants Comment Organism
N202M site-directed mutagenesis, a KDM4D demethylase-dead mutant, that binds RNA like the wild-type enzyme Homo sapiens

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
 additional information determination of RNA binding kinetics of recombinant His-tagged full-length enzyme and N-terminal region of KDM4D, KD with 100 nt RNA is about 20 nM and 80 nM, respectively, while it is 15 nM for the catalytically inactive enzyme mutant KDM4D-N202M. The constants are higher for fluorescein labeled 22 nt RNA with 126 nM for the recombinant His-tagged full-length enzyme and 1217 nM for the N-terminal region of KDM4D, overview Homo sapiens

Localization

Localization Comment Organism GeneOntology No. Textmining
chromatin KDM4D is recruited to chromatin and recognizes its histone substrates Homo sapiens 785
-
nucleus
-
 Homo sapiens 5634
-

Metals/Ions

Metals/Ions Comment Organism Structure
Fe2+ required for activity Homo sapiens
Fe2+ 0.05 mM used in assay conditions Homo sapiens

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
[histone H3]-N6,N6,N6-trimethyl-L-lysine 9 + 2-oxoglutarate + O2 Homo sapiens
-
 [histone H3]-N6,N6-dimethyl-L-lysine 9 + succinate + formaldehyde + CO2
-
 ?
[histone H3]-N6,N6,N6-trimethyl-L-lysine9 + 2 2-oxoglutarate + 2 O2 Homo sapiens overall reaction [histone H3]-N6-methyl-L-lysine9 + 2 succinate + 2 formaldehyde + 2 CO2
-
 ?
[histone H3]-N6,N6,N6-trimethyl-L-lysine9 + 2-oxoglutarate + O2 Homo sapiens
-
 [histone H3]-N6,N6-dimethyl-L-lysine9 + succinate + formaldehyde + CO2
-
 ?
[histone H3]-N6,N6-dimethyl-L-lysine 9 + 2-oxoglutarate + O2 Homo sapiens
-
 [histone H3]-N6-methyl-L-lysine 9 + succinate + formaldehyde + CO2
-
 ?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2 Homo sapiens
-
 [histone H3]-N6-methyl-L-lysine9 + succinate + formaldehyde + CO2
-
 ?

Organism

Organism UniProt Comment Textmining
Homo sapiens
-
-
-
Homo sapiens Q6B0I6
-
-

Purification (Commentary)

Purification (Comment) Organism
Ni-NTA resin column chromatography Homo sapiens
recombinant wild-type and mutant benzonae-treated His6-tagged full-length enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography Homo sapiens

Source Tissue

Source Tissue Comment Organism Textmining
U2-OS cell
-
 Homo sapiens
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information the lysine demethylase KDM4D specifically catalyzes the demethylation of H3K9me2/me3. KDM4D lysine demethylase is an RNA-binding protein, KDM4D-RNA interaction analysis, detailed overview. KDM4D has two non-canonical RNA binding domains. The N-terminal region of KDM4D (His-KDM4D1-350) binds RNA (isolated from HEK-293 cells) in vitro Homo sapiens ?
-
 ?
additional information the enzyme binds RNA independently of its demethylase activity. RNA interactions with the enzyme's N-terminal region are critical for its association with chromatin and subsequently for demethylating [histone H3]-N6,N6,N6-trimethyl-L-lysine9 cells Homo sapiens ?
-
-
[histone H3]-N6,N6,N6-trimethyl-L-lysine 9 + 2-oxoglutarate + O2
-
 Homo sapiens [histone H3]-N6,N6-dimethyl-L-lysine 9 + succinate + formaldehyde + CO2
-
 ?
[histone H3]-N6,N6,N6-trimethyl-L-lysine9 + 2 2-oxoglutarate + 2 O2 overall reaction Homo sapiens [histone H3]-N6-methyl-L-lysine9 + 2 succinate + 2 formaldehyde + 2 CO2
-
 ?
[histone H3]-N6,N6,N6-trimethyl-L-lysine9 + 2-oxoglutarate + O2
-
 Homo sapiens [histone H3]-N6,N6-dimethyl-L-lysine9 + succinate + formaldehyde + CO2
-
 ?
[histone H3]-N6,N6-dimethyl-L-lysine 9 + 2-oxoglutarate + O2
-
 Homo sapiens [histone H3]-N6-methyl-L-lysine 9 + succinate + formaldehyde + CO2
-
 ?
[histone H3]-N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2
-
 Homo sapiens [histone H3]-N6-methyl-L-lysine9 + succinate + formaldehyde + CO2
-
 ?

Synonyms

Synonyms Comment Organism
KDM4D
-
 Homo sapiens

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
 assay at Homo sapiens

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.3
-
 assay at Homo sapiens

General Information

General Information Comment Organism
additional information KDM4D is recruited to chromatin and recognizes its histone substrates. KDM4D binds RNA (isolated from HEK-293T cells) independently of its demethylase activity, and contains two non-canonical RNA binding domains: the first is within the N-terminal spanning amino acids 115 to 236, and the second is within the C-terminal spanning amino acids 348 to 523 of KDM4D. Three surface residues on KDM4D close to the JmjC domain, His115, Arg123 and Lys127, are aligned to specific residues on the cleavage factor known to bind RNA, interaction analysis, overview. RNA interactions with KDM4D N-terminal region are critical for its association with chromatin and subsequently for demethylating H3K9me3 in cells Homo sapiens
physiological function lysine methylation can be erased by the activity of the Jumonji C (JmjC)-domain-containing proteins that demethylate lysine through an amine oxidative reaction in the presence of iron and 2-oxoglutarate. KDM4D specifically catalyzes the demethylation of H3K9me2/me3. RNA interaction with KDM4D N-terminus is essential for KDM4D association with chromatin Homo sapiens