Binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binds hemi-methylated DNA as well. Recruits histone deacetylases and DNA methyltransferases. Acts as transcriptional repressor and plays a role in gene silencing. May enhance the activation of some unmethylated cAMP-responsive promoters. Homo sapiens (taxid: 9606)
>sp|Q9Z2E1|MBD2_MOUSE Methyl-CpG-binding domain protein 2 OS=Mus musculus GN=Mbd2 PE=2 SV=2
Binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binds hemi-methylated DNA as well. Recruits histone deacetylases and DNA methyltransferases. Acts as transcriptional repressor and plays a role in gene silencing. May enhance the activation of some unmethylated cAMP-responsive promoters (By similarity). Selectively represses transcription activity of methylated rRNA promoters.
Mus musculus (taxid: 10090)
>sp|O95983|MBD3_HUMAN Methyl-CpG-binding domain protein 3 OS=Homo sapiens GN=MBD3 PE=1 SV=1
Does not bind DNA by itself. Recruits histone deacetylases and DNA methyltransferases. Acts as transcriptional repressor and plays a role in gene silencing.
Homo sapiens (taxid: 9606)
>sp|Q9Z2D8|MBD3_MOUSE Methyl-CpG-binding domain protein 3 OS=Mus musculus GN=Mbd3 PE=1 SV=1
Does not bind DNA by itself. Recruits histone deacetylases and DNA methyltransferases. Acts as transcriptional repressor and plays a role in gene silencing.
Mus musculus (taxid: 10090)
>sp|Q9Z2E2|MBD1_MOUSE Methyl-CpG-binding domain protein 1 OS=Mus musculus GN=Mbd1 PE=1 SV=2
Score = 57.8 bits (138), Expect = 2e-08, Method: Composition-based stats.
Identities = 26/63 (41%), Positives = 37/63 (58%)
Query: 25 ECPQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGNIPGVSFDFRS 84
+CP L PGW R E R G S G+ D++Y SP G+K+R++ E+ + + FDFR
Sbjct: 7 DCPALGPGWKRRESFRKSGASFGRSDIYYQSPTGEKIRSKVELTRYLGPACDLTLFDFRQ 66
Query: 85 GKL 87
G L
Sbjct: 67 GTL 69
Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Isoform 1 can also repress transcription from unmethylated promoters.
Mus musculus (taxid: 10090)
>sp|Q9UIS9|MBD1_HUMAN Methyl-CpG-binding domain protein 1 OS=Homo sapiens GN=MBD1 PE=1 SV=2
Score = 53.9 bits (128), Expect = 3e-07, Method: Composition-based stats.
Identities = 24/63 (38%), Positives = 36/63 (57%)
Query: 25 ECPQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGNIPGVSFDFRS 84
+CP L PGW R EV R G + G+ D +Y SP G ++R++ E+ + + FDF+
Sbjct: 7 DCPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLGPACDLTLFDFKQ 66
Query: 85 GKL 87
G L
Sbjct: 67 GIL 69
Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Isoform 1 and isoform 2 can also repress transcription from unmethylated promoters.
Homo sapiens (taxid: 9606)
>sp|Q9LTJ1|MBD6_ARATH Methyl-CpG-binding domain-containing protein 6 OS=Arabidopsis thaliana GN=MBD6 PE=1 SV=1
Transcriptional regulator that binds CpG, CpNpN and CpNpG (N is A, T, or C) islands in promoters regardless the DNA methylation status. Plays probably a role in gene silencing. May associate with histone deacetylase proteins (HDAC). Required for nucleolar dominance that consist in the silencing of rRNA genes inherited from one progenitor in genetic hybrids. Recruited to rRNA genes in a DRM2-dependent manner.
Arabidopsis thaliana (taxid: 3702)
>sp|Q9SNC0|MBD5_ARATH Methyl-CpG-binding domain-containing protein 5 OS=Arabidopsis thaliana GN=MBD5 PE=1 SV=1
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 29 LPPGWYREEVTRNKGLSVGKVDVFYYSP-CGKKLRTRSEVLQVIRGNIP 76
LPP W E R G G VD FYY P G+K R+++EVL + P
Sbjct: 35 LPPDWRTEIRVRTSGTKAGTVDKFYYEPITGRKFRSKNEVLYYLEHGTP 83
Transcriptional regulator that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. In addition, binds specifically methylated m(5)CpNpN but not m(5)CpNpG (N is A, T or C). Plays probably a role in gene silencing.
Arabidopsis thaliana (taxid: 3702)
Close Homologs in the Non-Redundant Database Detected by BLAST
The Methyl-CpG binding domain (MBD) binds to DNA that contains one or more symmetrically methylated CpGs. DNA methylation in animals is associated with alterations in chromatin structure and silencing of gene expression. MBD has negligible non-specific affinity for DNA. In vitro foot-printing with MeCP2 showed the MBD can protect a 12 nucleotide region surrounding a methyl CpG pair. MBDs are found in several Methyl-CpG binding proteins and also DNA demethylase. Length = 75
>gnl|CDD|238690 cd01396, MeCP2_MBD, MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD)
Score = 65.1 bits (159), Expect = 1e-15
Identities = 31/69 (44%), Positives = 39/69 (56%), Gaps = 5/69 (7%)
Query: 23 RYECPQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGNIPGV---- 78
+ E P+LPPGW RE V R K S GK DV+Y SP GKK R++ E+ + + N P
Sbjct: 1 KPEDPRLPPGWKRELVPR-KSGSAGKFDVYYISPTGKKFRSKVELARYLEKNGPTSLDLS 59
Query: 79 SFDFRSGKL 87
FDF K
Sbjct: 60 DFDFTVPKK 68
The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. Length = 77
Score = 63.9 bits (156), Expect = 4e-15
Identities = 29/73 (39%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 21 KKRYECPQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGN----IP 76
P LP GW RE R G S GK DV+Y SPCGKKLR++SE+ + + N +
Sbjct: 1 GDPLRLP-LPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLD 59
Query: 77 GVSFDFRSGKLNS 89
FDF +
Sbjct: 60 LECFDFNATVPVG 72
Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain. Length = 77
>gnl|CDD|238069 cd00122, MBD, MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD)
Score = 61.2 bits (149), Expect = 3e-14
Identities = 31/63 (49%), Positives = 37/63 (58%), Gaps = 6/63 (9%)
Query: 24 YECPQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGNIPGV----S 79
P LPPGW RE V R G S GK DV+YYSPCGKKLR++ EV + + P +
Sbjct: 2 LRDP-LPPGWKRELVIRKSG-SAGKGDVYYYSPCGKKLRSKPEVARYLEKTGPSSLDLEN 59
Query: 80 FDF 82
F F
Sbjct: 60 FSF 62
The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family. Length = 62
>gnl|CDD|238691 cd01397, HAT_MBD, Methyl-CpG binding domains (MBD) present in putative chromatin remodelling factor such as BAZ2A; BAZ2A contains a MBD, DDT, PHD-type zinc finger and Bromo domain suggesting that BAZ2A might be associated with histone acetyltransferase (HAT) activity
Score = 42.0 bits (99), Expect = 1e-06
Identities = 20/48 (41%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 29 LPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGNIP 76
L GW RE R G + + +V YY+PCGKKLR EV++ + N
Sbjct: 6 LELGWRRETRIRGLGGRI-QGEVAYYAPCGKKLRQYPEVIKYLSKNGI 52
The Drosophila melanogaster toutatis protein, a putative subunit of the chromatin-remodeling complex, and other such proteins in this group share a similar domain architecture with BAZ2A, as does the Caenorhabditis elegans flectin homolog. Length = 73
The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
>PF01429 MBD: Methyl-CpG binding domain; InterPro: IPR001739 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 [, ]. The MBD folds into an alpha/beta sandwich structure comprising a layer of twisted beta sheet, backed by another layer formed by the alpha1 helix and a hairpin loop at the C terminus. These layers are both amphipathic, with the alpha1 helix and the beta sheet lying parallel and the hydrophobic faces tightly packed against each other. The beta sheet is composed of two long inner strands (beta2 and beta3) sandwiched by two shorter outer strands (beta1 and beta4) [].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 2KY8_A 1UB1_A 1D9N_A 1IG4_A 1QK9_A 3C2I_A.
>cd00122 MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD)
The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.
>cd01397 HAT_MBD Methyl-CpG binding domains (MBD) present in putative chromatin remodelling factor such as BAZ2A; BAZ2A contains a MBD, DDT, PHD-type zinc finger and Bromo domain suggesting that BAZ2A might be associated with histone acetyltransferase (HAT) activity
The Drosophila melanogaster toutatis protein, a putative subunit of the chromatin-remodeling complex, and other such proteins in this group share a similar domain architecture with BAZ2A, as does the Caenorhabditis elegans flectin homolog.
>cd01395 HMT_MBD Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated transcriptional repression
SETDB1 and other proteins in this group have a similar domain architecture. SETDB1 is a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins.
>PF00397 WW: WW domain; InterPro: IPR001202 Synonym(s): Rsp5 or WWP domain The WW domain is a short conserved region in a number of unrelated proteins, which folds as a stable, triple stranded beta-sheet
This short domain of approximately 40 amino acids, may be repeated up to four times in some proteins [, , , ]. The name WW or WWP derives from the presence of two signature tryptophan residues that are spaced 20-23 amino acids apart and are present in most WW domains known to date, as well as that of a conserved Pro. The WW domain binds to proteins with particular proline-motifs, [AP]-P-P-[AP]-Y, and/or phosphoserine- phosphothreonine-containing motifs [, ]. It is frequently associated with other domains typical for proteins in signal transduction processes. A large variety of proteins containing the WW domain are known. These include; dystrophin, a multidomain cytoskeletal protein; utrophin, a dystrophin-like protein of unknown function; vertebrate YAP protein, substrate of an unknown serine kinase; Mus musculus (Mouse) NEDD-4, involved in the embryonic development and differentiation of the central nervous system; Saccharomyces cerevisiae (Baker's yeast) RSP5, similar to NEDD-4 in its molecular organisation; Rattus norvegicus (Rat) FE65, a transcription-factor activator expressed preferentially in liver; Nicotiana tabacum (Common tobacco) DB10 protein, amongst others.; GO: 0005515 protein binding; PDB: 2JXW_A 2DK1_A 2JOC_A 2JO9_A 1YIU_A 1O6W_A 2JMF_A 1TK7_A 2KYK_A 2L5F_A ....
Solution Structure Of The Matrix Attachment Region-
7e-05
>pdb|2KY8|A Chain A, Solution Structure And Dynamic Analysis Of Chicken Mbd2 Methyl Binding Domain Bound To A Target Methylated Dna Sequence Length = 72
>2ysg_A Syntaxin-binding protein 4; synip, STXBP4, WW domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.22.1.1
>2ysh_A GAS-7, growth-arrest-specific protein 7; WW domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.22.1.1
>2dwv_A Salvador homolog 1 protein; WW domain, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}
>2ysb_A Salvador homolog 1 protein; WW domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: k.22.1.1
