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Conserved domains on  [gi|157389003|ref|NP_653215|]
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methyl-CpG-binding domain protein 3-like 2 [Homo sapiens]

Protein Classification

MBDa and MBD_C domain-containing protein( domain architecture ID 11244107)

MBDa and MBD_C domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MBDa super family cl48299
p55-binding region of Methyl-CpG-binding domain proteins MBD; MBDa is a second MBD domain of ...
 48-97 5.81e-26

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.


The actual alignment was detected with superfamily member pfam16564:

Pssm-ID: 465179  Cd Length: 68  Bit Score: 95.02  E-value: 5.81e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 157389003   48 LPMRLTSCIFRRPVTRIRSHPDNQVRRRKGDEHLEKPQQLCAYRRLQALQ 97
Cdd:pfam16564  18 LPIRLTSCIFKQPVTRITSHPGNKVRYRPKEGTLEKPQQLCWEKRLQGLQ 67
MBD_C super family cl16567
C-terminal domain of methyl-CpG binding protein 2 and 3; CpG-methylation is a frequently ...
 102-193 5.56e-20

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.


The actual alignment was detected with superfamily member pfam14048:

Pssm-ID: 464072  Cd Length: 94  Bit Score: 80.37  E-value: 5.56e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157389003  102 QGEGSSPLHLESVLSILAPGTAGESLDRAGAERVRSPLEPTPGRFPA-VAGGPTPGMGCQLPPPLSGQ-LVTPADIRRQA 179
Cdd:pfam14048   1 DGELLSTLDLPKSLKPIGPGITDETLLQSLATALHSSPQPITGQTASsDALEKNPGVGLNPDQPLCKQfVITEEDIRRQE 80

                          90
                  ....*....|....
gi 157389003  180 RRVKKARERLAKAL 193
Cdd:pfam14048  81 ERVKKARKRLAEAL 94
 
Name Accession Description Interval E-value
MBDa pfam16564
p55-binding region of Methyl-CpG-binding domain proteins MBD; MBDa is a second MBD domain of ...
 48-97 5.81e-26

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: 95.02  E-value: 5.81e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 157389003   48 LPMRLTSCIFRRPVTRIRSHPDNQVRRRKGDEHLEKPQQLCAYRRLQALQ 97
Cdd:pfam16564  18 LPIRLTSCIFKQPVTRITSHPGNKVRYRPKEGTLEKPQQLCWEKRLQGLQ 67
MBD_C pfam14048
C-terminal domain of methyl-CpG binding protein 2 and 3; CpG-methylation is a frequently ...
 102-193 5.56e-20

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: 80.37  E-value: 5.56e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157389003  102 QGEGSSPLHLESVLSILAPGTAGESLDRAGAERVRSPLEPTPGRFPA-VAGGPTPGMGCQLPPPLSGQ-LVTPADIRRQA 179
Cdd:pfam14048   1 DGELLSTLDLPKSLKPIGPGITDETLLQSLATALHSSPQPITGQTASsDALEKNPGVGLNPDQPLCKQfVITEEDIRRQE 80

                          90
                  ....*....|....
gi 157389003  180 RRVKKARERLAKAL 193
Cdd:pfam14048  81 ERVKKARKRLAEAL 94
 
Name Accession Description Interval E-value
MBDa pfam16564
p55-binding region of Methyl-CpG-binding domain proteins MBD; MBDa is a second MBD domain of ...
 48-97 5.81e-26

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: 95.02  E-value: 5.81e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 157389003   48 LPMRLTSCIFRRPVTRIRSHPDNQVRRRKGDEHLEKPQQLCAYRRLQALQ 97
Cdd:pfam16564  18 LPIRLTSCIFKQPVTRITSHPGNKVRYRPKEGTLEKPQQLCWEKRLQGLQ 67
MBD_C pfam14048
C-terminal domain of methyl-CpG binding protein 2 and 3; CpG-methylation is a frequently ...
 102-193 5.56e-20

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: 80.37  E-value: 5.56e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157389003  102 QGEGSSPLHLESVLSILAPGTAGESLDRAGAERVRSPLEPTPGRFPA-VAGGPTPGMGCQLPPPLSGQ-LVTPADIRRQA 179
Cdd:pfam14048   1 DGELLSTLDLPKSLKPIGPGITDETLLQSLATALHSSPQPITGQTASsDALEKNPGVGLNPDQPLCKQfVITEEDIRRQE 80

                          90
                  ....*....|....
gi 157389003  180 RRVKKARERLAKAL 193
Cdd:pfam14048  81 ERVKKARKRLAEAL 94
 
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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