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Literature summary for 1.14.11.67 extracted from
- Physical and functional interactions between the histone H3K4 demethylase KDM5A and the nucleosome remodeling and deacetylase (NuRD) complex (2014), J. Biol. Chem., 289, 28956-28970 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene KDM5A | Caenorhabditis elegans |
| gene KDM5A, cloned from a HeLa gene library, recombinant expression of N-terminally FLAG-tagged KDM5A in HeLa cells and HEK-293T cells, quantitative RT-PCR expression analysis | Homo sapiens |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| additional information | siRNA-mediated knockdown of KDM5A, and CHD4 or SIN3B in HeLa cells, and analysis of the changes in gene expression by microarray analysis. At least 435 genes (corresponding to 468 probes) are dysregulated in the KDM5A-knockdown cells. 66 and 63% of the KDM5A-regulated genes are also dysregulated in CHD4-and SIN3B-knockdown cells, respectively, and 47% of the KDM5A-regulated genes are affected by either CHD4 or SIN3B knockdown. Among the 435 KDM5A-regulated genes, 40% are upregulated, although more than half are downregulated. A similar proportion of genes is downregulated in response to SIN3B knockdown | Homo sapiens |
Localization
| Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|---|---|---|---|
| chromatin | - |
Caenorhabditis elegans | 785 | - |
| chromatin | - |
Homo sapiens | 785 | - |
| nucleus | - |
Caenorhabditis elegans | 5634 | - |
| nucleus | - |
Homo sapiens | 5634 | - |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Fe2+ | required for catalysis | Caenorhabditis elegans |  |
| Fe2+ | required for catalysis | Homo sapiens | |
Molecular Weight [Da]
| Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|
| 192000 | - |
- |
Homo sapiens |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2 | Caenorhabditis elegans | - |
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2 | - |
? | |
| histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2 | Homo sapiens | - |
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2 | - |
? | |
| histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2 | Caenorhabditis elegans | - |
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2 | - |
? | |
| histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2 | Homo sapiens | - |
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2 | - |
? | |
| additional information | Caenorhabditis elegans | KDM5A, a histone H3K4 demethylase, physically interacts with the nucleosome remodeling and deacetylase (NuRD) complex | ? | - |
? | |
| additional information | Homo sapiens | KDM5A, a histone H3K4 demethylase, physically interacts with the nucleosome remodeling and deacetylase (NuRD) complex | ? | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Caenorhabditis elegans | Q23541 | - |
- |
| Homo sapiens | P29375 | - |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant N-terminally FLAG-tagged KDM5A from HeLa cell nuclear extract by gel filtration and immunoaffinity chromatography, the enzyme copurifies with the SIN3B-HDAC complex, and with additional proteins including CHD4, MTA2, GATAD2A, ZMYND8A, ZNF592, and ZNF687. CHD4, MTA2, and GATAD2A are known components of the NuRD (nucleosome remodeling and deacetylase) complex | Homo sapiens |
Source Tissue
| Source Tissue | Comment | Organism | Textmining |
|---|---|---|---|
| HeLa cell | - |
Homo sapiens | - |
| U2-OS cell | - |
Homo sapiens | - |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2 | - |
Caenorhabditis elegans | histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2 | - |
? | |
| histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2 | - |
Homo sapiens | histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2 | - |
? | |
| histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2 | - |
Caenorhabditis elegans | histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2 | - |
? | |
| histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2 | - |
Homo sapiens | histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2 | - |
? | |
| additional information | KDM5A, a histone H3K4 demethylase, physically interacts with the nucleosome remodeling and deacetylase (NuRD) complex | Caenorhabditis elegans | ? | - |
? | |
| additional information | KDM5A, a histone H3K4 demethylase, physically interacts with the nucleosome remodeling and deacetylase (NuRD) complex | Homo sapiens | ? | - |
? | |
| additional information | no activity with monomethylated H3K4 | Caenorhabditis elegans | ? | - |
? | |
| additional information | no activity with monomethylated H3K4 | Homo sapiens | ? | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| H3K4 demethylase | - |
Caenorhabditis elegans |
| H3K4 demethylase | - |
Homo sapiens |
| histone H3K4 demethylase | - |
Caenorhabditis elegans |
| histone H3K4 demethylase | - |
Homo sapiens |
| Jarid1a | - |
Caenorhabditis elegans |
| Jarid1a | - |
Homo sapiens |
| KDM5A | - |
Caenorhabditis elegans |
| KDM5A | - |
Homo sapiens |
| RBP2 | - |
Caenorhabditis elegans |
| RBP2 | - |
Homo sapiens |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | the enzyme is a member of the KDM5 protein family | Caenorhabditis elegans |
| evolution | the enzyme is a member of the KDM5 protein family | Homo sapiens |
| malfunction | the rbr-2(tm1231) mutant exhibits complex defects in vulval development, the rbr-2(tm1231) mutant displays the Muv or vulvaless phenotype, overview | Caenorhabditis elegans |
| additional information | enzyme KDM5A uses distinct domains to associate with the SIN3B and NuRD complexes | Homo sapiens |
| physiological function | histone H3K4 methylation is linked to transcriptional activation. KDM5A, a histone H3K4 demethylase, physically interacts with the nucleosome remodeling and deacetylase (NuRD) complex, KDM5A and the NuRD complex cooperatively function to control developmentally regulated genes, and KDM5A and the NuRD complex cooperatively regulate H3K4me2/3 levels. CHD4 modulates H3K4 methylation levels at the promoter and coding regions of target genes | Homo sapiens |
| physiological function | histone H3K4 methylation is linked to transcriptional activation. KDM5A, a histone H3K4 demethylase, physically interacts with the nucleosome remodeling and deacetylase (NuRD) complex, KDM5A and the NuRD complex cooperatively function to control developmentally regulated genes. Caenorhabditis elegans homologues of KDM5, RBR-2, and CHD4 functions cooperatively with NuRD in vulval development, functional interaction between KDM5 and the NuRD complex during developmental processes | Caenorhabditis elegans |
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