TF Info Page for MBD3 (MBD)


Assessment Binding Mode Motif Status Notes Comments
Likely to be sequence specific TF 3 Low specificity DNA-binding protein No motif The MBD domain of MBD3 is thought to be primarily responsible for interaction with HDAC1 and MTA2, members of the NuRD complex (PMID: 12124384). More recently, studies have shown that it retains the ability to bind methylated CpG sites in vitro (PMID: 24307175) with lower affinity than other MBD proteins (e.g., MBD2), but does not distinguish between hydroxymethylated and unmethylated sites. Coupled with in vivo ChIP experiments, it appears that MBD3 binds unmethylated CpG sites in vivo after be


Description: methyl-CpG binding domain protein 3 [Source:HGNC Symbol;Acc:HGNC:6918]
Entrez Summary DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. This gene belongs to a family of nuclear proteins which are characterized by the presence of a methyl-CpG binding domain (MBD). The encoded protein is a subunit of the NuRD, a multisubunit complex containing nucleosome remodeling and histone deacetylase activities. Unlike the other family members, the encoded protein is not capable of binding to methylated DNA. The protein mediates the association of metastasis-associated protein 2 with the core histone deacetylase complex. Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jul 2013]
Ensembl ID: ENSG00000071655
External Link: CisBP
Interpro IPR001739; IPR016177; IPR025884; ;
Protein Domain: ENSP00000156825
Protein Domain: ENSP00000412302
Protein Domain: ENSP00000464718
Protein: ENSP00000156825DBD: Methyl-CpG DNA-bindingOther: MBD_C
Protein: ENSP00000412302DBD: Methyl-CpG DNA-bindingOther: MBD_C
Protein: ENSP00000464718DBD: Methyl-CpG DNA-bindingOther: MBD_C, MBDa, RasGAP

Previous Annotations

Source Annotation
TF-CAT classification No
Vaquerizas 2009 TF classification
"a" Has direct evidence of TF function;
"b" Has evidence for an orthologous TF;
"c" contains likely DBDs, but has no functional evidence;
"x" is an unlikely TF such as predicted gene, genes with likely non-specific DBDs or that have function outside transcription;
"other" category contains proteins without clear DBDs they curated from external sources.
CisBP considers it as a TF? Yes
TFclass considers it as a TF? No
Has GO:0003700 "transcription factor activity, sequence-specific DNA binding" No
Initial Assessment
1a1 Protein has a high confidence PWM (HT-SELEX, PBM or B1H model) or there is a crystal structure that supports sequence specific DNA binding;
1a2 There is high confidence data for a close ortholog (as defined in CisBP);
2a1 There is lower confidence direct evidence, such as a Jaspar, Hocomoco or Transfac model;
2a2 There is lower confidence evidence for an close ortholog;
3a There is decent circumstantial evidence for its role as a TF or not;
4a Two or more datasets predict it as a TF;
5a One of the source datasets predicts is as a TF
3a, decent circumstantial evidence for its role as
TF has conditional DNA-binding requirements


Published Motif Data

Source Annotation Motif Evidence


Structure PDB Not_Covered

Experimental History

Method Constructs
Tried in PBM?
(Whether the protein was tried in PBM or not)
Tried in HT-SELEX
(Whether the protein was tried in HT-SELEX or not, and if so, then what kind of clones were tested)
Other Information?
(Tried with another method and failed?)

External Contribution