Crystallization (Comment) | Organism |
---|---|
catalytic core of Rph1, hanging drop vapour diffusion method, X-ray diffraction structure determination and analysis at 2.5 A resolution | Saccharomyces cerevisiae |
KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
---|---|---|---|---|---|
additional information | - |
additional information | binding affinities of c-Rph1 with H3K36 and H3K9 peptides, overview | Saccharomyces cerevisiae |
Metals/Ions | Comment | Organism | Structure |
---|---|---|---|
Ni2+ | the Ni2+ ion at the active site is chelated by conserved residues and the cofactor 2-oxoglutarate | Saccharomyces cerevisiae |
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-dimethyl-L-lysine36 + 2-oxoglutarate + O2 | Saccharomyces cerevisiae | - |
histone H3 N6-methyl-L-lysine36 + succinate + formaldehyde + CO2 | - |
? | |
histone H3 N6-methyl-L-lysine36 + 2-oxoglutarate + O2 | Saccharomyces cerevisiae | - |
histone H3 L-lysine36 + succinate + formaldehyde + CO2 | - |
? | |
additional information | Saccharomyces cerevisiae | Rph1 is a histone demethylase that can specifically demethylate tri- and dimethylated Lys36 of histone H3. 2-Oxoglutarate forms hydrogen-bonding interactions with the side chains of conserved residues. The substrate-binding cleft of Rph1 is formed with several structural elements of the JmjC domain, the long beta-hairpin and the mixed structural motif, and the methylated Lys36 of H3 is recognized by several conserved residues of the JmjC domain. Molecular basis for the substrate specificity of Rph1, overview | ? | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Saccharomyces cerevisiae | P39956 | - |
- |
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 | calf thymus type II-A histones | Saccharomyces cerevisiae | 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 | calf thymus type II-A histones | Saccharomyces cerevisiae | histone H3 N6-methyl-L-lysine36 + succinate + formaldehyde + CO2 | - |
? | |
histone H3 N6-methyl-L-lysine36 + 2-oxoglutarate + O2 | - |
Saccharomyces cerevisiae | histone H3 L-lysine36 + succinate + formaldehyde + CO2 | - |
? | |
histone H3 N6-methyl-L-lysine36 + 2-oxoglutarate + O2 | calf thymus type II-A histones | Saccharomyces cerevisiae | histone H3 L-lysine36 + succinate + formaldehyde + CO2 | - |
? | |
additional information | Rph1 is a histone demethylase that can specifically demethylate tri- and dimethylated Lys36 of histone H3. 2-Oxoglutarate forms hydrogen-bonding interactions with the side chains of conserved residues. The substrate-binding cleft of Rph1 is formed with several structural elements of the JmjC domain, the long beta-hairpin and the mixed structural motif, and the methylated Lys36 of H3 is recognized by several conserved residues of the JmjC domain. Molecular basis for the substrate specificity of Rph1, overview | Saccharomyces cerevisiae | ? | - |
? |
Subunits | Comment | Organism |
---|---|---|
More | the structure of c-Rph1 is composed of a JmjN, Jumonji N, domain, a long beta-hairpin, a mixed structural motif and a JmjC domain | Saccharomyces cerevisiae |
Synonyms | Comment | Organism |
---|---|---|
Rph1 | - |
Saccharomyces cerevisiae |
Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
---|---|---|---|
30 | - |
assay at | Saccharomyces cerevisiae |
pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|
7.5 | - |
assay at | Saccharomyces cerevisiae |
General Information | Comment | Organism |
---|---|---|
physiological function | c-Rph1, the catalytic core of Rph1, is responsible for the demethylase activity, which is essential for the transcription elongation of some actively transcribed genes | Saccharomyces cerevisiae |