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Conserved domains on  [gi|527498242|ref|NP_001268383|]
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methyl-CpG-binding domain protein 3 isoform 2 [Homo sapiens]

Protein Classification

methyl-CpG-binding domain-containing protein; PHD zinc finger domain-containing N-acetyltransferase( domain architecture ID 10893177)

methyl-CpG-binding domain (MBD)-containing protein may act as a transcriptional regulator| PHD (plant homeodomain) zinc finger domain-containing N-acetyltransferase such as increased DNA methylation 1 (IDM1) which is a histone H3 acetyltransferase that binds methylated DNA at chromatin sites lacking histone H3K4 di- or trimethylation and catalyzes H3K18 and H3K23 acetylation; also contains a methyl-CpG-binding domain (MBD) and Jas domain(s)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MBD_C pfam14048
C-terminal domain of methyl-CpG binding protein 2 and 3; CpG-methylation is a frequently ...
 120-211 1.48e-46

C-terminal domain of methyl-CpG binding protein 2 and 3; CpG-methylation is a frequently occurring epigenetic modification of vertebrate genomes resulting in transcriptional repression. This domain was found at the C-terminus of the methyl-CpG-binding domain (MBD) containing proteins MBD2 and MBD3, the latter was shown to not bind directly to methyl-CpG DNA but rather interact with components of the NuRD/Mi2 complex, an abundant deacetylase complex. The domain is subject to structure determination by the Joint Center of Structural Genomics.


:

Pssm-ID: 464072  Cd Length: 94  Bit Score: 150.47  E-value: 1.48e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 527498242  120 AEELVKTMDLPKGLQGVGPGCTDETLLSAIASALHTSTMPITGQL--SAAVEKNPGVWLNTTQPLCKAFMVTDEDIRKQE 197
Cdd:pfam14048   1 DGELLSTLDLPKSLKPIGPGITDETLLQSLATALHSSPQPITGQTasSDALEKNPGVGLNPDQPLCKQFVITEEDIRRQE 80

                          90
                  ....*....|....
gi 527498242  198 ELVQQVRKRLEEAL 211
Cdd:pfam14048  81 ERVKKARKRLAEAL 94
MBDa pfam16564
p55-binding region of Methyl-CpG-binding domain proteins MBD; MBDa is a second MBD domain of ...
 50-116 4.10e-31

p55-binding region of Methyl-CpG-binding domain proteins MBD; MBDa is a second MBD domain of Methyl-CpG-binding domain proteins. region implicated in binding the RbAp46/48 (retinoblastoma protein-associated protein) homolog p55, which is one of the components of the MBD2-NuRD complex. The MBD2-NuRD complex is a nucleosome remodelling and deacetylation complex.


:

Pssm-ID: 465179  Cd Length: 68  Bit Score: 110.04  E-value: 4.10e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 527498242   50 RYDSSNQVKGKPDLNTALPVRQTASIFKQPVTKITNHPSNKVKSDP-QKAVDQPRQLFWEKKLSGLNA 116
Cdd:pfam16564   1 RQDQLDKAKRRPDLSTALPIRLTSCIFKQPVTRITSHPGNKVRYRPkEGTLEKPQQLCWEKRLQGLQA 68
MBD super family cl00110
MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of ...
 5-47 9.07e-12

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.


The actual alignment was detected with superfamily member cd01396:

Pssm-ID: 469618  Cd Length: 77  Bit Score: 59.31  E-value: 9.07e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 527498242   5 SPSGKKFRSKPQLARYLG----GSMDLSTFDFRTGKMLMsKMNKSRQ 47
Cdd:cd01396   32 SPTGKKFRSKVELARYLEkngpTSLDLSDFDFTVPKKLG-LGSPRRH 77
 
Name Accession Description Interval E-value
MBD_C pfam14048
C-terminal domain of methyl-CpG binding protein 2 and 3; CpG-methylation is a frequently ...
 120-211 1.48e-46

C-terminal domain of methyl-CpG binding protein 2 and 3; CpG-methylation is a frequently occurring epigenetic modification of vertebrate genomes resulting in transcriptional repression. This domain was found at the C-terminus of the methyl-CpG-binding domain (MBD) containing proteins MBD2 and MBD3, the latter was shown to not bind directly to methyl-CpG DNA but rather interact with components of the NuRD/Mi2 complex, an abundant deacetylase complex. The domain is subject to structure determination by the Joint Center of Structural Genomics.


Pssm-ID: 464072  Cd Length: 94  Bit Score: 150.47  E-value: 1.48e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 527498242  120 AEELVKTMDLPKGLQGVGPGCTDETLLSAIASALHTSTMPITGQL--SAAVEKNPGVWLNTTQPLCKAFMVTDEDIRKQE 197
Cdd:pfam14048   1 DGELLSTLDLPKSLKPIGPGITDETLLQSLATALHSSPQPITGQTasSDALEKNPGVGLNPDQPLCKQFVITEEDIRRQE 80

                          90
                  ....*....|....
gi 527498242  198 ELVQQVRKRLEEAL 211
Cdd:pfam14048  81 ERVKKARKRLAEAL 94
MBDa pfam16564
p55-binding region of Methyl-CpG-binding domain proteins MBD; MBDa is a second MBD domain of ...
 50-116 4.10e-31

p55-binding region of Methyl-CpG-binding domain proteins MBD; MBDa is a second MBD domain of Methyl-CpG-binding domain proteins. region implicated in binding the RbAp46/48 (retinoblastoma protein-associated protein) homolog p55, which is one of the components of the MBD2-NuRD complex. The MBD2-NuRD complex is a nucleosome remodelling and deacetylation complex.


Pssm-ID: 465179  Cd Length: 68  Bit Score: 110.04  E-value: 4.10e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 527498242   50 RYDSSNQVKGKPDLNTALPVRQTASIFKQPVTKITNHPSNKVKSDP-QKAVDQPRQLFWEKKLSGLNA 116
Cdd:pfam16564   1 RQDQLDKAKRRPDLSTALPIRLTSCIFKQPVTRITSHPGNKVRYRPkEGTLEKPQQLCWEKRLQGLQA 68
MeCP2_MBD cd01396
MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the ...
 5-47 9.07e-12

MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family 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.


Pssm-ID: 238690  Cd Length: 77  Bit Score: 59.31  E-value: 9.07e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 527498242   5 SPSGKKFRSKPQLARYLG----GSMDLSTFDFRTGKMLMsKMNKSRQ 47
Cdd:cd01396   32 SPTGKKFRSKVELARYLEkngpTSLDLSDFDFTVPKKLG-LGSPRRH 77
MBD smart00391
Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, ...
 4-44 6.09e-11

Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain


Pssm-ID: 128673  Cd Length: 77  Bit Score: 57.00  E-value: 6.09e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 527498242     4 KSPSGKKFRSKPQLARYLGGSMDLST----FDFRTGKMLMSKMNK 44
Cdd:smart00391  33 ISPCGKKLRSKSELARYLHKNGDLSLdlecFDFNATVPVGPKFTP 77
MBD pfam01429
Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one ...
 4-37 1.73e-05

Methyl-CpG binding domain; 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.


Pssm-ID: 396147 [Multi-domain]  Cd Length: 76  Bit Score: 41.96  E-value: 1.73e-05
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 527498242    4 KSPSGKKFRSKPQLARYL----GGSMDLSTFDFRTGKM 37
Cdd:pfam01429  36 YSPTGKKLRSKSEVARYLeangGTSPKLEDFSFTVRSE 73
 
Name Accession Description Interval E-value
MBD_C pfam14048
C-terminal domain of methyl-CpG binding protein 2 and 3; CpG-methylation is a frequently ...
 120-211 1.48e-46

C-terminal domain of methyl-CpG binding protein 2 and 3; CpG-methylation is a frequently occurring epigenetic modification of vertebrate genomes resulting in transcriptional repression. This domain was found at the C-terminus of the methyl-CpG-binding domain (MBD) containing proteins MBD2 and MBD3, the latter was shown to not bind directly to methyl-CpG DNA but rather interact with components of the NuRD/Mi2 complex, an abundant deacetylase complex. The domain is subject to structure determination by the Joint Center of Structural Genomics.


Pssm-ID: 464072  Cd Length: 94  Bit Score: 150.47  E-value: 1.48e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 527498242  120 AEELVKTMDLPKGLQGVGPGCTDETLLSAIASALHTSTMPITGQL--SAAVEKNPGVWLNTTQPLCKAFMVTDEDIRKQE 197
Cdd:pfam14048   1 DGELLSTLDLPKSLKPIGPGITDETLLQSLATALHSSPQPITGQTasSDALEKNPGVGLNPDQPLCKQFVITEEDIRRQE 80

                          90
                  ....*....|....
gi 527498242  198 ELVQQVRKRLEEAL 211
Cdd:pfam14048  81 ERVKKARKRLAEAL 94
MBDa pfam16564
p55-binding region of Methyl-CpG-binding domain proteins MBD; MBDa is a second MBD domain of ...
 50-116 4.10e-31

p55-binding region of Methyl-CpG-binding domain proteins MBD; MBDa is a second MBD domain of Methyl-CpG-binding domain proteins. region implicated in binding the RbAp46/48 (retinoblastoma protein-associated protein) homolog p55, which is one of the components of the MBD2-NuRD complex. The MBD2-NuRD complex is a nucleosome remodelling and deacetylation complex.


Pssm-ID: 465179  Cd Length: 68  Bit Score: 110.04  E-value: 4.10e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 527498242   50 RYDSSNQVKGKPDLNTALPVRQTASIFKQPVTKITNHPSNKVKSDP-QKAVDQPRQLFWEKKLSGLNA 116
Cdd:pfam16564   1 RQDQLDKAKRRPDLSTALPIRLTSCIFKQPVTRITSHPGNKVRYRPkEGTLEKPQQLCWEKRLQGLQA 68
MeCP2_MBD cd01396
MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the ...
 5-47 9.07e-12

MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family 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.


Pssm-ID: 238690  Cd Length: 77  Bit Score: 59.31  E-value: 9.07e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 527498242   5 SPSGKKFRSKPQLARYLG----GSMDLSTFDFRTGKMLMsKMNKSRQ 47
Cdd:cd01396   32 SPTGKKFRSKVELARYLEkngpTSLDLSDFDFTVPKKLG-LGSPRRH 77
MBD smart00391
Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, ...
 4-44 6.09e-11

Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain


Pssm-ID: 128673  Cd Length: 77  Bit Score: 57.00  E-value: 6.09e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 527498242     4 KSPSGKKFRSKPQLARYLGGSMDLST----FDFRTGKMLMSKMNK 44
Cdd:smart00391  33 ISPCGKKLRSKSELARYLHKNGDLSLdlecFDFNATVPVGPKFTP 77
MBD cd00122
MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of ...
 4-32 7.30e-08

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.


Pssm-ID: 238069  Cd Length: 62  Bit Score: 48.09  E-value: 7.30e-08
                         10        20        30
                 ....*....|....*....|....*....|...
gi 527498242   4 KSPSGKKFRSKPQLARYLG----GSMDLSTFDF 32
Cdd:cd00122   30 YSPCGKKLRSKPEVARYLEktgpSSLDLENFSF 62
MBD pfam01429
Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one ...
 4-37 1.73e-05

Methyl-CpG binding domain; 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.


Pssm-ID: 396147 [Multi-domain]  Cd Length: 76  Bit Score: 41.96  E-value: 1.73e-05
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 527498242    4 KSPSGKKFRSKPQLARYL----GGSMDLSTFDFRTGKM 37
Cdd:pfam01429  36 YSPTGKKLRSKSEVARYLeangGTSPKLEDFSFTVRSE 73
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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