Cloned (Comment) | Organism |
---|---|
gene rph1 | Saccharomyces cerevisiae |
Protein Variants | Comment | Organism |
---|---|---|
H235A | catalytically deficient mutant | Saccharomyces cerevisiae |
General Stability | Organism |
---|---|
the JmjN domain is important in maintaining protein stability and the repressive effect of Rph1 | Saccharomyces cerevisiae |
Inhibitors | Comment | Organism | Structure |
---|---|---|---|
additional information | expression of GTT1, UGX2, CTT1, and HSP26 is highly induced by H2O2 treatment and causes the dissociation of Rph1 from the promoters of these genes | Saccharomyces cerevisiae |
Localization | Comment | Organism | GeneOntology No. | Textmining |
---|---|---|---|---|
chromatin | Rph1 is associated with a specific chromatin locus. Release of Rph1 from chromatin also required the phosphorylation at S652 | Saccharomyces cerevisiae | 785 | - |
nucleus | - |
Saccharomyces cerevisiae | 5634 | - |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2 | Saccharomyces cerevisiae | - |
histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2 | - |
? | |
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2 | Saccharomyces cerevisiae BY4742 | - |
histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2 | - |
? | |
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2 | Saccharomyces cerevisiae | - |
histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2 | - |
? | |
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2 | Saccharomyces cerevisiae BY4742 | - |
histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2 | - |
? | |
additional information | Saccharomyces cerevisiae | Rph1 is a histone demethylase specific to tri-methylated-H3K36. Rph1 binds to the URS of PHR1 through ZF domains and modulates chromatin modifications in specific regions of the PHR1 promoter | ? | - |
? | |
additional information | Saccharomyces cerevisiae BY4742 | Rph1 is a histone demethylase specific to tri-methylated-H3K36. Rph1 binds to the URS of PHR1 through ZF domains and modulates chromatin modifications in specific regions of the PHR1 promoter | ? | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Saccharomyces cerevisiae | - |
- |
- |
Saccharomyces cerevisiae | - |
gene rph1 | - |
Saccharomyces cerevisiae BY4742 | - |
gene rph1 | - |
Posttranslational Modification | Comment | Organism |
---|---|---|
phosphoprotein | Rph1 is phosphorylated under oxidative stress, which leads to Rph1 dissociation and transcriptional activation. Rad53 may be the key kinase essential for Rph1 phosphorylation on oxidative stress with H2O2 treatment | Saccharomyces cerevisiae |
phosphoprotein | the crucial checkpoint protein Rad53 acts as an upstream regulator of Rph1 and dominates the phosphorylation of Rph1 that is required for efficient PHR1 expression and the dissociation of Rph1. Release of Rph1 from chromatin also required the phosphorylation at S652 | Saccharomyces cerevisiae |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2 | - |
Saccharomyces cerevisiae | histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2 | - |
? | |
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2 | - |
Saccharomyces cerevisiae BY4742 | histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2 | - |
? | |
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2 | - |
Saccharomyces cerevisiae | histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2 | - |
? | |
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2 | - |
Saccharomyces cerevisiae BY4742 | histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2 | - |
? | |
additional information | Rph1 is a histone demethylase specific to tri-methylated-H3K36. Rph1 binds to the URS of PHR1 through ZF domains and modulates chromatin modifications in specific regions of the PHR1 promoter | Saccharomyces cerevisiae | ? | - |
? | |
additional information | Rph1 is a histone demethylase specific to tri-methylated-H3K36. Rph1 binds to the URS of PHR1 through ZF domains and modulates chromatin modifications in specific regions of the PHR1 promoter | Saccharomyces cerevisiae BY4742 | ? | - |
? |
Synonyms | Comment | Organism |
---|---|---|
histone H3K36 demethylase | - |
Saccharomyces cerevisiae |
Rph1/KDM4 | - |
Saccharomyces cerevisiae |
Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
---|---|---|---|
30 | - |
assay at | Saccharomyces cerevisiae |
pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|
8 | - |
assay at | Saccharomyces cerevisiae |
Organism | Comment | Expression |
---|---|---|
Saccharomyces cerevisiae | checkpoint kinase Rad53 negatively modulates Rph1 protein level | down |
Saccharomyces cerevisiae | the crucial checkpoint protein Rad53 acts as an upstream regulator of Rph1 and dominates the phosphorylation of Rph1 that is required for efficient PHR1 expression and the dissociation of Rph1 | down |
Saccharomyces cerevisiae | Rph1 is phosphorylated under oxidative stress, which leads to Rph1 dissociation and transcriptional activation. Rad53 may be the key kinase essential for Rph1 phosphorylation on oxidative stress with H2O2 treatment | up |
General Information | Comment | Organism |
---|---|---|
evolution | Rph1 is a histone demethylase containing a Jumonji C (JmjC) domain and belongs to the C2H2 zinc-finger protein family | Saccharomyces cerevisiae |
malfunction | histone H3K36A mutant shows increased UV sensitivity. Deletion of rph1 leads to approximately 2fold enhancement of PHR1 under normal conditions. Overexpression of Rph1 reduces the expression of PHR1 and increased UV sensitivity. The catalytically deficient mutant H235A of Rph1 diminishes the repressive transcriptional effect on PHR1 expression, which indicates that histone demethylase activity contributes to transcriptional repression | Saccharomyces cerevisiae |
malfunction | more than 75% of Rph1-regulated genes show increased expression in the rph1-deletion mutant | Saccharomyces cerevisiae |
additional information | Rph1 is a labile protein, and Rad53 negatively modulates Rph1 protein level. The JmjN domain is important in maintaining protein stability and the repressive effect of Rph1. Binding motif 5'-CCCCTWA-3', which resembles the stress response element, is overrepresented in the promoters of Rph1-repressed genes. JmjN and ZF domains of Rph1 are required for its function. Rph1 binds to gene promoters and is dissociated with DNA damage | Saccharomyces cerevisiae |
physiological function | histone H3K36 demethylase Rph1/KDM4 regulates the expression of the photoreactivation gene PHR1, the demethylation at H3K36 is linked to UV sensitivity. Overexpression of Rph1 and H3K36A mutant reduced histone acetylation at the URS, which implies a crosstalk between histone demethylation and acetylation at the PHR1 promoter. Rph1 is a repressor of the DNA repair gene PHR1. Rph1 is dissociated from the PHR1 promoter in response to DNA damage. Rad53 regulates the expression of PHR1 and dissociation of Rph1 in response to DNA damage. Activated Rad53 complex phosphorylates Rph1 and S652A-mutated Rph1 impairs the dissociation in response to DNA damage | Saccharomyces cerevisiae |
physiological function | Rph1 might be a regulatory node connecting different signaling pathways responding to environmental stresses. Rph1 is mainly a transcriptional repressor. Rph1-regulated genes respond to DNA damage and environmental stress. Microarray analysis, overview | Saccharomyces cerevisiae |