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Literature summary 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

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

Cloned(Commentary)

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

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.14.11.67 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

EC Number Protein Variants Comment Organism
1.14.11.67 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
1.14.11.67 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
1.14.11.67 H394A site directed mutagenesis of a Fe2+ binding active site residue, inactive mutant Oryza sativa
1.14.11.67 H482A site directed mutagenesis of a Fe2+ binding active site residue, inactive mutant Oryza sativa
1.14.11.67 K412A site directed mutagenesis, the mutation abolishes the demethylation activity of H3K4 in all three methylation states Oryza sativa
1.14.11.67 additional information T-DNA insertion and RNAi mutation sof gene JMJ703, phenotypes, overview Oryza sativa
1.14.11.67 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
1.14.11.67 Y321A site directed mutagenesis decreases H3K4me1 demethylase activity but does not affect H3K4me2 and H3K4me3 demethylase activity Oryza sativa
1.14.11.67 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

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

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
1.14.11.67 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)

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

Organism

EC Number Organism UniProt Comment Textmining
1.14.11.67 Oryza sativa Q53WJ1
-
-

Purification (Commentary)

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

Source Tissue

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

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.14.11.67 histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
-
 Oryza sativa histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
-
 ?
1.14.11.67 histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
-
 Oryza sativa histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
 ?
1.14.11.67 histone H3 N6-methyl-L-lysine4 + 2-oxoglutarate + O2
-
 Oryza sativa histone H3 L-lysine4 + succinate + formaldehyde + CO2
-
 ?
1.14.11.67 additional information JMJ703 specifically reverses all three forms of H3K4me, mono-, di-, or trimethylated state histone 3, in rice Oryza sativa ?
-
 ?
1.14.11.67 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

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

General Information

EC Number General Information Comment Organism
1.14.11.67 malfunction loss of the enzyme reduces cell division rate of the stem and the size of plant stature Oryza sativa
1.14.11.67 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
1.14.11.67 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