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Literature summary extracted from

  • Nishibuchi, G.; Shibata, Y.; Hayakawa, T.; Hayakawa, N.; Ohtani, Y.; Sinmyozu, K.; Tagami, H.; Nakayama, J.
    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 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.14.11.67 gene KDM5A Caenorhabditis elegans
1.14.11.67 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

EC Number Protein Variants Comment Organism
1.14.11.67 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

EC Number Localization Comment Organism GeneOntology No. Textmining
1.14.11.67 chromatin
-
 Caenorhabditis elegans 785
-
1.14.11.67 chromatin
-
 Homo sapiens 785
-
1.14.11.67 nucleus
-
 Caenorhabditis elegans 5634
-
1.14.11.67 nucleus
-
 Homo sapiens 5634
-

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
1.14.11.67 Fe2+ required for catalysis Caenorhabditis elegans
1.14.11.67 Fe2+ required for catalysis Homo sapiens

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
1.14.11.67 192000
-
-
 Homo sapiens

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.14.11.67 histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2 Caenorhabditis elegans
-
 histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
-
 ?
1.14.11.67 histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2 Homo sapiens
-
 histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
-
 ?
1.14.11.67 histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2 Caenorhabditis elegans
-
 histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
 ?
1.14.11.67 histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2 Homo sapiens
-
 histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
 ?
1.14.11.67 additional information Caenorhabditis elegans KDM5A, a histone H3K4 demethylase, physically interacts with the nucleosome remodeling and deacetylase (NuRD) complex ?
-
 ?
1.14.11.67 additional information Homo sapiens KDM5A, a histone H3K4 demethylase, physically interacts with the nucleosome remodeling and deacetylase (NuRD) complex ?
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
1.14.11.67 Caenorhabditis elegans Q23541
-
-
1.14.11.67 Homo sapiens P29375
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.14.11.67 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

EC Number Source Tissue Comment Organism Textmining
1.14.11.67 HeLa cell
-
 Homo sapiens
-
1.14.11.67 U2-OS cell
-
 Homo sapiens
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.14.11.67 histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
-
 Caenorhabditis elegans histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
-
 ?
1.14.11.67 histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
-
 Homo sapiens histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
-
 ?
1.14.11.67 histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
-
 Caenorhabditis elegans histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
 ?
1.14.11.67 histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
-
 Homo sapiens histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
 ?
1.14.11.67 additional information KDM5A, a histone H3K4 demethylase, physically interacts with the nucleosome remodeling and deacetylase (NuRD) complex Caenorhabditis elegans ?
-
 ?
1.14.11.67 additional information KDM5A, a histone H3K4 demethylase, physically interacts with the nucleosome remodeling and deacetylase (NuRD) complex Homo sapiens ?
-
 ?
1.14.11.67 additional information no activity with monomethylated H3K4 Caenorhabditis elegans ?
-
 ?
1.14.11.67 additional information no activity with monomethylated H3K4 Homo sapiens ?
-
 ?

Synonyms

EC Number Synonyms Comment Organism
1.14.11.67 H3K4 demethylase
-
 Caenorhabditis elegans
1.14.11.67 H3K4 demethylase
-
 Homo sapiens
1.14.11.67 histone H3K4 demethylase
-
 Caenorhabditis elegans
1.14.11.67 histone H3K4 demethylase
-
 Homo sapiens
1.14.11.67 Jarid1a
-
 Caenorhabditis elegans
1.14.11.67 Jarid1a
-
 Homo sapiens
1.14.11.67 KDM5A
-
 Caenorhabditis elegans
1.14.11.67 KDM5A
-
 Homo sapiens
1.14.11.67 RBP2
-
 Caenorhabditis elegans
1.14.11.67 RBP2
-
 Homo sapiens

General Information

EC Number General Information Comment Organism
1.14.11.67 evolution the enzyme is a member of the KDM5 protein family Caenorhabditis elegans
1.14.11.67 evolution the enzyme is a member of the KDM5 protein family Homo sapiens
1.14.11.67 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
1.14.11.67 additional information enzyme KDM5A uses distinct domains to associate with the SIN3B and NuRD complexes Homo sapiens
1.14.11.67 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
1.14.11.67 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