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Literature summary for 1.14.11.67 extracted from

  • Chen, Q.; Chen, X.; Wang, Q.; Zhang, F.; Lou, Z.; Zhang, Q.; Zhou, D.X.
    Structural basis of a histone H3 lysine 4 demethylase required for stem elongation in rice (2013), PLoS Genet., 9, e1003239.
    View publication on PubMedView publication on EuropePMC

Activating Compound

Activating Compound Comment Organism Structure
N-oxalylglycine required, essential for the demethylase activity in vivo Oryza sativa

Cloned(Commentary)

Cloned (Comment) Organism
gene JMJ703, functional transient overexpression of the FLAG:HA-tagged JmjN-JmjC-zinc finger region in Nicotiana tabacum leaf nuclei Oryza sativa

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant enzyme, free or in complex with N-oxalylglycine, X-ray diffraction structure determination and analysis at 2.35 A resolution Oryza sativa

Protein Variants

Protein Variants Comment Organism
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 Oryza sativa
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 Oryza sativa
H394A site directed mutagenesis of a Fe2+ binding active site residue, inactive mutant Oryza sativa
H482A site directed mutagenesis of a Fe2+ binding active site residue, inactive mutant Oryza sativa
K412A site directed mutagenesis, the mutation abolishes the demethylation activity of H3K4 in all three methylation states Oryza sativa
additional information T-DNA insertion and RNAi mutation sof gene JMJ703, phenotypes, overview Oryza sativa
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 Oryza sativa
Y321A site directed mutagenesis decreases H3K4me1 demethylase activity but does not affect H3K4me2 and H3K4me3 demethylase activity Oryza sativa
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 Oryza sativa

Localization

Localization Comment Organism GeneOntology No. Textmining
nucleus
-
Oryza sativa 5634
-

Metals/Ions

Metals/Ions Comment Organism Structure
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 Oryza sativa

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2 Oryza sativa
-
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2 Oryza sativa
-
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
?
histone H3 N6-methyl-L-lysine4 + 2-oxoglutarate + O2 Oryza sativa
-
histone H3 L-lysine4 + succinate + formaldehyde + CO2
-
?
additional information Oryza sativa JMJ703 specifically reverses all three forms of H3K4me, mono-, di-, or trimethylated state histone 3, in rice ?
-
?

Organism

Organism UniProt Comment Textmining
Oryza sativa Q53WJ1
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant FLAG:HA-tagged JmjN-JmjC-zinc finger region from Nicotiana tabacum leaf nuclei byy affinity chromatography Oryza sativa

Source Tissue

Source Tissue Comment Organism Textmining
epidermal cell
-
Oryza sativa
-
leaf
-
Oryza sativa
-
stem
-
Oryza sativa
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
-
Oryza sativa histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
-
Oryza sativa histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
?
histone H3 N6-methyl-L-lysine4 + 2-oxoglutarate + O2
-
Oryza sativa histone H3 L-lysine4 + succinate + formaldehyde + CO2
-
?
additional information JMJ703 specifically reverses all three forms of H3K4me, mono-, di-, or trimethylated state histone 3, in rice Oryza sativa ?
-
?
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 Oryza sativa ?
-
?

Synonyms

Synonyms Comment Organism
histone H3 lysine 4 demethylase
-
Oryza sativa
JMJ703
-
Oryza sativa

General Information

General Information Comment Organism
malfunction loss of the enzyme reduces cell division rate of the stem and the size of plant stature Oryza sativa
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 Oryza sativa
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 Oryza sativa