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Information on EC 1.14.11.67 - [histone H3]-trimethyl-L-lysine4 demethylase and Organism(s) Oryza sativa and UniProt Accession Q53WJ1

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IUBMB Comments
Requires iron(II). This entry describes a group of enzymes that demethylate N-methylated L-lysine residues at position 4 of histone H3 (H3K4). The enzymes are dioxygenases and act by hydroxylating the methyl group, forming an unstable hemiaminal that leaves as formaldehyde. They can act on tri-, di-, and mono-methylated forms.
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Oryza sativa
UNIPROT: Q53WJ1
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The taxonomic range for the selected organisms is: Oryza sativa
The enzyme appears in selected viruses and cellular organisms
Synonyms
kdm5b, jarid2, kdm5c, jarid1b, kdm5a, fbxl10, lysine-specific demethylase, jarid1c, jarid1a, kdm5d, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
histone H3 lysine 4 demethylase
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SYSTEMATIC NAME
IUBMB Comments
[histone H3]-N6,N6,N6-trimethyl-L-lysine4,2-oxoglutarate:oxygen oxidoreductase
Requires iron(II). This entry describes a group of enzymes that demethylate N-methylated L-lysine residues at position 4 of histone H3 (H3K4). The enzymes are dioxygenases and act by hydroxylating the methyl group, forming an unstable hemiaminal that leaves as formaldehyde. They can act on tri-, di-, and mono-methylated forms.
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
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
show the reaction diagram
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
show the reaction diagram
-
-
-
?
histone H3 N6-methyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 L-lysine4 + succinate + formaldehyde + CO2
show the reaction diagram
-
-
-
?
additional information
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
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
show the reaction diagram
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
show the reaction diagram
-
-
-
?
histone H3 N6-methyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 L-lysine4 + succinate + formaldehyde + CO2
show the reaction diagram
-
-
-
?
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
N-oxalylglycine
required, essential for the demethylase activity in vivo
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
UniProt
Manually annotated by BRENDA team
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
loss of the enzyme reduces cell division rate of the stem and the size of plant stature
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
additional information
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme, free or in complex with N-oxalylglycine, X-ray diffraction structure determination and analysis at 2.35 A resolution
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant FLAG:HA-tagged JmjN-JmjC-zinc finger region from Nicotiana tabacum leaf nuclei byy affinity chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene JMJ703, functional transient overexpression of the FLAG:HA-tagged JmjN-JmjC-zinc finger region in Nicotiana tabacum leaf nuclei
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
PLoS Genet.
9
e1003239
2013
Oryza sativa (Q53WJ1), Oryza sativa
Manually annotated by BRENDA team