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Literature summary for 1.14.11.65 extracted from
- Features of the PHF8/KIAA1718 histone demethylase (2010), Cell Res., 20, 861-862.
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| PHF8 | Homo sapiens |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Fe2+ | in presence of Fe2+ and 2-oxoglutarate, Fe2+ sits in the center of the c-PHF8 catalytic core, which consists of nine hydrophobic residues. Binding of 2-oxoglutarate to Fe2+ does not drastically change the conformation, however it causes the side chain of Y257 to turn towards the substrate binding channel, to be in a position to contact the methyl group of K9me2 | Homo sapiens |  |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| histone H3 N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2 | Homo sapiens | PHF8 is able to demethylate H3K9me2 and H3K9me1 | histone H3 N6-methyl-L-lysine9 + succinate + formaldehyde + CO2 | - |
? | |
| histone H3 N6-methyl-L-lysine9 + 2-oxoglutarate + O2 | Homo sapiens | - |
histone H3 L-lysine9 + succinate + formaldehyde + CO2 | - |
? | |
| additional information | Homo sapiens | the PHD domain of human PHF8 interacts with the catalytic core in a manner similar to ceKIAA1718 of Caenorhabditis elegans, and the C-terminal coiled-coil region interacts with the catalytic core. JHDM1a binds methyl H3K36, while PHF8 does not | ? | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Homo sapiens | - |
- |
- |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| histone H3 N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2 | PHF8 is able to demethylate H3K9me2 and H3K9me1 | Homo sapiens | histone H3 N6-methyl-L-lysine9 + succinate + formaldehyde + CO2 | - |
? | |
| histone H3 N6,N6-dimethyl-L-lysine9 + 2-oxoglutarate + O2 | PHF8 is able to demethylate H3K9me2 and H3K9me1. The PHD domain adjacent to the catalytic domain in PHF8 may recognize methyl H3K9 and contribute to its demethylation | Homo sapiens | histone H3 N6-methyl-L-lysine9 + succinate + formaldehyde + CO2 | - |
? | |
| histone H3 N6-methyl-L-lysine9 + 2-oxoglutarate + O2 | - |
Homo sapiens | histone H3 L-lysine9 + succinate + formaldehyde + CO2 | - |
? | |
| additional information | the PHD domain of human PHF8 interacts with the catalytic core in a manner similar to ceKIAA1718 of Caenorhabditis elegans, and the C-terminal coiled-coil region interacts with the catalytic core. JHDM1a binds methyl H3K36, while PHF8 does not | Homo sapiens | ? | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| More | the PHD domain adjacent to the catalytic domain in PHF8 may recognize methyl H3K9 and contribute to its demethylation. PHF8 consists of 16 alpha-helices and 12 beta-strands, arranged in a similar manner to a known JmjC-domain-containing histone demethylase, JHDM1a. In the presence of Fe2+ and 2-oxoglutarate, Fe2+ sits in the center of the c-PHF8 catalytic core, which consists of nine hydrophobic residues | Homo sapiens |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| PHF8 | - |
Homo sapiens |
| PHF8/KIAA1718 histone demethylase | - |
Homo sapiens |
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