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IPR001739 is a Methyl-CpG DNA binding.
<p>Methylation at CpG dinucleotide, the most common DNA modification in eukaryotes, has been correlated with gene silencing associated with various phenomena such as genomic imprinting, transposon and chromosome X inactivation, differentiation, and cancer. Effects of DNA methylation are mediated through proteins which bind to symmetrically methylated CpGs. Such proteins contain a specific domain of ~70 residues, the methyl-CpG-binding domain (MBD), which is linked to additional domains associated with chromatin, such as the bromodomain, the AT hook motif, the SET domain, or the PHD finger. MBD-containing proteins appear to act as structural proteins, which recruit a variety of histone deacetylase (HDAC) complexes and chromatin remodelling factors, leading to chromatin compaction and, consequently, to transcriptional repression. The MBD of MeCP2, MBD1, MBD2, MBD4 and BAZ2 mediates binding to DNA, in case of MeCP2, MBD1 and MBD2 preferentially to methylated CpG. In case of human MBD3 and SETDB1 the MBD has been shown to mediate protein-protein interactions [[cite:PUB00015393], [cite:PUB00015391]].</p> <p>The MBD folds into an α/β-sandwich structure comprising a layer of twisted β-sheet, backed by another layer formed by the α1 helix and a hairpin loop at the C terminus. These layers are both amphipathic, with the α1 helix and the β-sheet lying parallel and the hydrophobic faces tightly packed against each other. The β-sheet is composed of two long inner strands (β2 and β3) sandwiched by two shorter outer strands (β1 and β4) [[cite:PUB00015392]].</p>
This description is obtained from EB-eye REST.
GO predictions are based solely on the InterPro-to-GO mappings published by EMBL-EBI, which are in turn based on the mapping of predicted domains to the InterPro dataset. The InterPro-to-GO mapping was last updated on , while the GO metadata was last updated on .
| GO term | Namespace | Name | Definition | Relationships |
|---|---|---|---|---|
| Molecular function | DNA binding | Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). | ||
| Cellular component | Host cell nucleus | A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction. |
| Transcript | Name | Description | Predicted domains | Domain count |
|---|---|---|---|---|
| – | Methyl-CpG binding [Medicago truncatula] gi|124359618|gb|ABD32284.2| | 8 | ||
| – | Methyl-CpG binding [Medicago truncatula] gi|124359618|gb|ABD32284.2| | 9 | ||
| – | PREDICTED: methyl-CpG-binding domain-containing protein 7-like [Glycine max] gi|356520740|ref|XP_003529018.1| | 9 | ||
| – | Methyl binding domain protein [Populus trichocarpa] gi|224134745|ref|XP_002321896.1| | 10 | ||
| – | PREDICTED: methyl-CpG-binding domain-containing protein 2-like [Glycine max] gi|356520885|ref|XP_003529090.1| | 13 | ||
| – | Uncharacterized protein TCM_042767 [Theobroma cacao] gi|508726253|gb|EOY18150.1| | 4 | ||
| – | Uncharacterized protein TCM_042767 [Theobroma cacao] gi|508726253|gb|EOY18150.1| | 5 | ||
| – | PREDICTED: methyl-CpG-binding domain-containing protein 9-like [Cicer arietinum] gi|502090713|ref|XP_004489317.1| | 32 | ||
| – | PREDICTED: methyl-CpG-binding domain-containing protein 10-like [Cicer arietinum] gi|502147866|ref|XP_004506946.1| | 9 | ||
| – | PREDICTED: methyl-CpG-binding domain-containing protein 10-like [Cicer arietinum] gi|502151520|ref|XP_004508481.1| | 9 | ||
| – | Uncharacterized protein TCM_016211 [Theobroma cacao] gi|508777412|gb|EOY24668.1| | 8 | ||
| – | Uncharacterized protein TCM_016211 [Theobroma cacao] gi|508777412|gb|EOY24668.1| | 8 | ||
| – | PREDICTED: methyl-CpG-binding domain-containing protein 2-like [Glycine max] gi|356520885|ref|XP_003529090.1| | 13 | ||
| – | PREDICTED: methyl-CpG-binding domain-containing protein 4-like [Cicer arietinum] gi|502118026|ref|XP_004496064.1| | 7 | ||
| – | PREDICTED: methyl-CpG-binding domain-containing protein 4-like [Cicer arietinum] gi|502118026|ref|XP_004496064.1| | 12 | ||
| – | Methyl-CpG-binding domain protein; TAIR: AT5G52230.1 methyl-CPG-binding domain protein 13; Swiss-Prot: sp|Q9LTJ8|MBD13_ARATH Methyl-CpG-binding domain-containing protein 13; TrEMBL-Plants: tr|K7MIH7|K7MIH7_SOYBN Uncharacterized protein; Found in the gene: LotjaGi2g1v0145200 | 11 | ||
| – | Methyl-CpG-binding domain protein; TAIR: AT5G35330.1 methyl-CPG-binding domain protein 02; Swiss-Prot: sp|Q8LA53|MBD2_ARATH Methyl-CpG-binding domain-containing protein 2; TrEMBL-Plants: tr|A0A151T2U3|A0A151T2U3_CAJCA Uncharacterized protein; Found in the gene: LotjaGi2g1v0234500 | 15 | ||
| – | Methyl-CpG-binding domain-containing protein 9; TAIR: AT3G01460.1 methyl-CPG-binding domain 9; Swiss-Prot: sp|Q9SGH2|MBD9_ARATH Methyl-CpG-binding domain-containing protein 9; TrEMBL-Plants: tr|I1M022|I1M022_SOYBN Uncharacterized protein; Found in the gene: LotjaGi2g1v0248100 | 32 | ||
| – | Methyl-CpG-binding domain protein; TAIR: AT5G59800.1 methyl-CPG-binding domain 7; Swiss-Prot: sp|Q9FJF4|MBD7_ARATH Methyl-CpG-binding domain-containing protein 7; TrEMBL-Plants: tr|I1KJG1|I1KJG1_SOYBN Uncharacterized protein; Found in the gene: LotjaGi3g1v0280400 | 9 | ||
| – | Methyl-CpG-binding domain protein; TAIR: AT5G59800.1 methyl-CPG-binding domain 7; Swiss-Prot: sp|Q9FJF4|MBD7_ARATH Methyl-CpG-binding domain-containing protein 7; TrEMBL-Plants: tr|A0A0B2P285|A0A0B2P285_GLYSO Methyl-CpG-binding domain-containing protein 7; Found in the gene: LotjaGi3g1v0280400 | 9 | ||
| – | Methyl-CpG-binding domain protein; TAIR: AT5G59800.1 methyl-CPG-binding domain 7; Swiss-Prot: sp|Q9FJF4|MBD7_ARATH Methyl-CpG-binding domain-containing protein 7; TrEMBL-Plants: tr|I3SW30|I3SW30_LOTJA Uncharacterized protein; Found in the gene: LotjaGi3g1v0280500 | 9 | ||
| – | Methyl-CpG-binding domain protein; TAIR: AT1G15340.1 methyl-CPG-binding domain 10; Swiss-Prot: sp|Q9XI36|MBD10_ARATH Methyl-CpG-binding domain-containing protein 10; TrEMBL-Plants: tr|I3SMM8|I3SMM8_LOTJA Uncharacterized protein; Found in the gene: LotjaGi3g1v0356500 | 9 | ||
| – | Methyl-CpG-binding domain protein; TAIR: AT1G15340.1 methyl-CPG-binding domain 10; Swiss-Prot: sp|Q9XI36|MBD10_ARATH Methyl-CpG-binding domain-containing protein 10; TrEMBL-Plants: tr|I3SMM8|I3SMM8_LOTJA Uncharacterized protein; Found in the gene: LotjaGi3g1v0356500 | 9 | ||
| – | Methyl-CpG-binding domain protein; TAIR: AT3G15790.1 methyl-CPG-binding domain 11; Swiss-Prot: sp|Q9LW00|MBD11_ARATH Methyl-CpG-binding domain-containing protein 11; TrEMBL-Plants: tr|A0A1J7I076|A0A1J7I076_LUPAN Uncharacterized protein; Found in the gene: LotjaGi4g1v0272500 | 11 | ||
| – | Methyl-CpG-binding domain protein; TAIR: AT3G15790.1 methyl-CPG-binding domain 11; Swiss-Prot: sp|Q9LW00|MBD11_ARATH Methyl-CpG-binding domain-containing protein 11; TrEMBL-Plants: tr|A0A1J7I076|A0A1J7I076_LUPAN Uncharacterized protein; Found in the gene: LotjaGi4g1v0272500 | 11 | ||
| – | Methyl-CpG-binding domain protein; TAIR: AT5G52230.1 methyl-CPG-binding domain protein 13; Swiss-Prot: sp|Q9LTJ8|MBD13_ARATH Methyl-CpG-binding domain-containing protein 13; TrEMBL-Plants: tr|A0A0B2QVK9|A0A0B2QVK9_GLYSO Methyl-CpG-binding domain-containing protein 13; Found in the gene: LotjaGi4g1v0423500 | 11 | ||
| – | Methyl-CpG-binding domain protein; TAIR: AT5G52230.1 methyl-CPG-binding domain protein 13; Swiss-Prot: sp|Q9LTJ8|MBD13_ARATH Methyl-CpG-binding domain-containing protein 13; TrEMBL-Plants: tr|A0A0B2QVK9|A0A0B2QVK9_GLYSO Methyl-CpG-binding domain-containing protein 13; Found in the gene: LotjaGi4g1v0423500 | 11 | ||
| – | Methyl-CpG-binding domain protein; TAIR: AT5G52230.1 methyl-CPG-binding domain protein 13; Swiss-Prot: sp|Q9LTJ8|MBD13_ARATH Methyl-CpG-binding domain-containing protein 13; TrEMBL-Plants: tr|A0A0B2QVK9|A0A0B2QVK9_GLYSO Methyl-CpG-binding domain-containing protein 13; Found in the gene: LotjaGi4g1v0423500 | 11 | ||
| – | Methyl-CpG-binding domain protein; TAIR: AT5G52230.1 methyl-CPG-binding domain protein 13; Swiss-Prot: sp|Q9LTJ8|MBD13_ARATH Methyl-CpG-binding domain-containing protein 13; TrEMBL-Plants: tr|I1KP74|I1KP74_SOYBN Uncharacterized protein; Found in the gene: LotjaGi4g1v0423500 | 11 | ||
| – | Methyl-CpG-binding domain protein; TAIR: AT3G63030.1 methyl-CPG-binding domain 4; Swiss-Prot: sp|Q9LYB9|MBD4_ARATH Methyl-CpG-binding domain-containing protein 4; TrEMBL-Plants: tr|I3SHA3|I3SHA3_LOTJA Uncharacterized protein; Found in the gene: LotjaGi5g1v0259700 | 13 | ||
| – | Methyl-CpG-binding domain protein; TAIR: AT3G63030.1 methyl-CPG-binding domain 4; Swiss-Prot: sp|Q9LYB9|MBD4_ARATH Methyl-CpG-binding domain-containing protein 4; TrEMBL-Plants: tr|I3SU39|I3SU39_LOTJA Uncharacterized protein; Found in the gene: LotjaGi5g1v0259800 | 15 | ||
| – | Methyl-CpG-binding domain-containing protein 8; TAIR: AT1G22310.1 methyl-CPG-binding domain 8; Swiss-Prot: sp|Q9LME6|MBD8_ARATH Methyl-CpG-binding domain-containing protein 8; TrEMBL-Plants: tr|V7BR06|V7BR06_PHAVU Uncharacterized protein; Found in the gene: LotjaGi6g1v0351800 | 12 |
A list of co-occurring predicted domains within the L. japonicus gene space:
| Predicted domain | Source | Observations | Saturation (%) |
|---|---|---|---|
| SSF54171 | SUPERFAMILY | 1 | 3.13 |