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Literature summary for 1.14.11.65 extracted from
- Genome-wide studies of histone demethylation catalysed by the fission yeast homologues of mammalian LSD1 (2007), PLoS ONE, 2, e386 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene lsd1, recombinant expression of GST-tagged Smw1 in Escherichia coli strain Rosetta, recombinant expression of TAP-tagged Swm1 in Schizosaccharomyces pombe | Schizosaccharomyces pombe |
| gene lsd2, recombinant expression of TAP-tagged Swm2 in Schizosaccharomyces pombe | Schizosaccharomyces pombe |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| additional information | deletion of the swm1+ gene alters the expression patterns of several genes, overview | Schizosaccharomyces pombe |
Localization
| Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|---|---|---|---|
| chromatin | - |
Schizosaccharomyces pombe | 785 | - |
| nucleosome | - |
Schizosaccharomyces pombe | 786 | - |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| [histone H3]-N6,N6-dimethyl-L-lysine 9 + 2-oxoglutarate + O2 | Schizosaccharomyces pombe | - |
[histone H3]-N6-methyl-L-lysine 9 + succinate + formaldehyde + CO2 | - |
? |  |
| [histone H3]-N6,N6-dimethyl-L-lysine 9 + 2-oxoglutarate + O2 | Schizosaccharomyces pombe ATCC 24843 | - |
[histone H3]-N6-methyl-L-lysine 9 + succinate + formaldehyde + CO2 | - |
? | |
| [histone H3]-N6,N6-dimethyl-L-lysine 9 + 2-oxoglutarate + O2 | Schizosaccharomyces pombe 972 | - |
[histone H3]-N6-methyl-L-lysine 9 + succinate + formaldehyde + CO2 | - |
? | |
| [histone H3]-N6-methyl-L-lysine 9 + 2-oxoglutarate + O2 | Schizosaccharomyces pombe | - |
[histone H3]-L-lysine 9 + succinate + formaldehyde + CO2 | - |
? | |
| [histone H3]-N6-methyl-L-lysine 9 + 2-oxoglutarate + O2 | Schizosaccharomyces pombe ATCC 24843 | - |
[histone H3]-L-lysine 9 + succinate + formaldehyde + CO2 | - |
? | |
| [histone H3]-N6-methyl-L-lysine 9 + 2-oxoglutarate + O2 | Schizosaccharomyces pombe 972 | - |
[histone H3]-L-lysine 9 + succinate + formaldehyde + CO2 | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Schizosaccharomyces pombe | Q10135 | - |
- |
| Schizosaccharomyces pombe | Q9Y802 | - |
- |
| Schizosaccharomyces pombe 972 | Q9Y802 | - |
- |
| Schizosaccharomyces pombe ATCC 24843 | Q9Y802 | - |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant GST-tagged Smw1 from Escherichia coli strain Rosetta by glutathione affinity chromatography | Schizosaccharomyces pombe |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | lack of in-vitro H3K4 demethylase activity of the Swm1/2 complex | Schizosaccharomyces pombe | ? | - |
? | |
| additional information | lack of in-vitro H3K4 demethylase activity of the Swm1/2 complex | Schizosaccharomyces pombe ATCC 24843 | ? | - |
? | |
| additional information | lack of in-vitro H3K4 demethylase activity of the Swm1/2 complex | Schizosaccharomyces pombe 972 | ? | - |
? | |
| [histone H3]-N6,N6-dimethyl-L-lysine 9 + 2-oxoglutarate + O2 | - |
Schizosaccharomyces pombe | [histone H3]-N6-methyl-L-lysine 9 + succinate + formaldehyde + CO2 | - |
? | |
| [histone H3]-N6,N6-dimethyl-L-lysine 9 + 2-oxoglutarate + O2 | substrates are calf thymus bulk histones, chicken poly-nucleosomes, calf thymus histone H3, or recombinant Xenopus laevis H3 | Schizosaccharomyces pombe | [histone H3]-N6-methyl-L-lysine 9 + succinate + formaldehyde + CO2 | - |
? | |
| [histone H3]-N6,N6-dimethyl-L-lysine 9 + 2-oxoglutarate + O2 | - |
Schizosaccharomyces pombe ATCC 24843 | [histone H3]-N6-methyl-L-lysine 9 + succinate + formaldehyde + CO2 | - |
? | |
| [histone H3]-N6,N6-dimethyl-L-lysine 9 + 2-oxoglutarate + O2 | substrates are calf thymus bulk histones, chicken poly-nucleosomes, calf thymus histone H3, or recombinant Xenopus laevis H3 | Schizosaccharomyces pombe ATCC 24843 | [histone H3]-N6-methyl-L-lysine 9 + succinate + formaldehyde + CO2 | - |
? | |
| [histone H3]-N6,N6-dimethyl-L-lysine 9 + 2-oxoglutarate + O2 | - |
Schizosaccharomyces pombe 972 | [histone H3]-N6-methyl-L-lysine 9 + succinate + formaldehyde + CO2 | - |
? | |
| [histone H3]-N6,N6-dimethyl-L-lysine 9 + 2-oxoglutarate + O2 | substrates are calf thymus bulk histones, chicken poly-nucleosomes, calf thymus histone H3, or recombinant Xenopus laevis H3 | Schizosaccharomyces pombe 972 | [histone H3]-N6-methyl-L-lysine 9 + succinate + formaldehyde + CO2 | - |
? | |
| [histone H3]-N6-methyl-L-lysine 9 + 2-oxoglutarate + O2 | - |
Schizosaccharomyces pombe | [histone H3]-L-lysine 9 + succinate + formaldehyde + CO2 | - |
? | |
| [histone H3]-N6-methyl-L-lysine 9 + 2-oxoglutarate + O2 | substrates are calf thymus bulk histones, chicken poly-nucleosomes, calf thymus histone H3, or recombinant Xenopus laevis H3 | Schizosaccharomyces pombe | [histone H3]-L-lysine 9 + succinate + formaldehyde + CO2 | - |
? | |
| [histone H3]-N6-methyl-L-lysine 9 + 2-oxoglutarate + O2 | - |
Schizosaccharomyces pombe ATCC 24843 | [histone H3]-L-lysine 9 + succinate + formaldehyde + CO2 | - |
? | |
| [histone H3]-N6-methyl-L-lysine 9 + 2-oxoglutarate + O2 | substrates are calf thymus bulk histones, chicken poly-nucleosomes, calf thymus histone H3, or recombinant Xenopus laevis H3 | Schizosaccharomyces pombe ATCC 24843 | [histone H3]-L-lysine 9 + succinate + formaldehyde + CO2 | - |
? | |
| [histone H3]-N6-methyl-L-lysine 9 + 2-oxoglutarate + O2 | - |
Schizosaccharomyces pombe 972 | [histone H3]-L-lysine 9 + succinate + formaldehyde + CO2 | - |
? | |
| [histone H3]-N6-methyl-L-lysine 9 + 2-oxoglutarate + O2 | substrates are calf thymus bulk histones, chicken poly-nucleosomes, calf thymus histone H3, or recombinant Xenopus laevis H3 | Schizosaccharomyces pombe 972 | [histone H3]-L-lysine 9 + succinate + formaldehyde + CO2 | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| More | domain structure, overview | Schizosaccharomyces pombe |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| LSD1 | - |
Schizosaccharomyces pombe |
| LSD2 | - |
Schizosaccharomyces pombe |
| lysine-specific histone demethylase 1 | - |
Schizosaccharomyces pombe |
| lysine-specific histone demethylase 2 | - |
Schizosaccharomyces pombe |
| SPAC23E2.02 | locus name | Schizosaccharomyces pombe |
| SPBC146.09c | locus name | Schizosaccharomyces pombe |
| SWIRM1 | - |
Schizosaccharomyces pombe |
| SWIRM2 | - |
Schizosaccharomyces pombe |
| Swm1 | - |
Schizosaccharomyces pombe |
| Swm1/2 complex | - |
Schizosaccharomyces pombe |
| Swm2 | - |
Schizosaccharomyces pombe |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 37 | - |
assay at | Schizosaccharomyces pombe |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 8 | - |
assay at | Schizosaccharomyces pombe |
General Information
| General Information | Comment | Organism |
|---|---|---|
| malfunction | genome-wide changes in patterns of histone methylation are correlated with gene expression upon deletion of the swm1+ gene. In vivo, loss of Swm1 increases the global levels of both H3K9me2 and H3K4me2. A significant accumulation of H3K4me2 is observed at genes that are up-regulated in a swm1 deletion strain. In addition, H3K9me2 accumulates at some genes known to be direct Swm1/2 targets that are down-regulated in the swm1DELTA strain. The lack of in-vitro H3K4 demethylase activity of the Swm1/2 complex, suggests that the increased H3K4me2 levels results from either increased H3K4 methylation via Set1, or the incorporation of H3K4 methylated histones during transcription | Schizosaccharomyces pombe |
| malfunction | in vivo, loss of Swm1 increases the global levels of both H3K9me2 and H3K4me2. A significant accumulation of H3K4me2 is observed at genes that are up-regulated in a swm1 deletion strain. In addition, H3K9me2 accumulates at some genes known to be direct Swm1/2 targets that are down-regulated in the swm1DELTA strain | Schizosaccharomyces pombe |
| metabolism | genetic exist links between lysine-specific demethylases, the histone deacetylase Clr6, and the chromatin remodeller Hrp1. Complex interactions between histone demethylase, deacetylase and chromatin remodelling activities in the regulation of gene expression | Schizosaccharomyces pombe |
| physiological function | fission yeast proteins Swm1 and Swm2 (after SWIRM1 and SWIRM2), associate together in a complex. This complex specifically demethylates lysine 9 in histone H3 (H3K9) and both up- and down-regulates expression of different groups of genes.Lack of in-vitro H3K4 demethylase activity of the Swm1/2 complex suggesting that the increased H3K4me2 levels results from either increased H3K4 methylation via Set1, or the incorporation of H3K4 methylated histones during transcription | Schizosaccharomyces pombe |
| physiological function | Swm1 and Swm2 (after SWIRM1 and SWIRM2), associate together in a complex. This complex specifically demethylates lysine 9 in histone H3 (H3K9) and both up- and down-regulates expression of different groups of genes. In vitro, bacterially expressed Swm1 also possesses lysine 9 demethylase activity | Schizosaccharomyces pombe |
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Release 2023.1 (January 2023)
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