NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|938320031|ref|NP_001303266|]
View 

methyl-CpG-binding protein 2 isoform 3 [Homo sapiens]

Protein Classification

methyl-CpG-binding domain-containing protein( domain architecture ID 10647783)

methyl-CpG-binding domain (MBD)-containing protein may act as a transcriptional regulator

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
MBD smart00391
Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, ...
 1-76 2.62e-26

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: 100.52  E-value: 2.62e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 938320031     1 MYDDPtLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDTSLDPNDFDFTVTGRGSPSRRE 76
Cdd:smart00391   3 PLRLP-LPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLDLECFDFNATVPVGPKFTP 77
 
Name Accession Description Interval E-value
MBD smart00391
Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, ...
 1-76 2.62e-26

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: 100.52  E-value: 2.62e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 938320031     1 MYDDPtLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDTSLDPNDFDFTVTGRGSPSRRE 76
Cdd:smart00391   3 PLRLP-LPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLDLECFDFNATVPVGPKFTP 77
MeCP2_MBD cd01396
MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the ...
 1-75 1.18e-23

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: 93.21  E-value: 1.18e-23
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 938320031   1 MYDDPTLPEGWTRKLKQRKSGrSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDTSLDPNDFDFTV---TGRGSPSRR 75
Cdd:cd01396    1 KPEDPRLPPGWKRELVPRKSG-SAGKFDVYYISPTGKKFRSKVELARYLEKNGPTSLDLSDFDFTVpkkLGLGSPRRH 77
MBD pfam01429
Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one ...
 3-66 1.12e-15

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: 71.24  E-value: 1.12e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 938320031    3 DDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDTSLDPNDFDFTV 66
Cdd:pfam01429   7 DRLPLPPGWRREERQRKSGSKAGKVDVFYYSPTGKKLRSKSEVARYLEANGGTSPKLEDFSFTV 70
 
Name Accession Description Interval E-value
MBD smart00391
Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, ...
 1-76 2.62e-26

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: 100.52  E-value: 2.62e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 938320031     1 MYDDPtLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDTSLDPNDFDFTVTGRGSPSRRE 76
Cdd:smart00391   3 PLRLP-LPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLDLECFDFNATVPVGPKFTP 77
MeCP2_MBD cd01396
MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the ...
 1-75 1.18e-23

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: 93.21  E-value: 1.18e-23
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 938320031   1 MYDDPTLPEGWTRKLKQRKSGrSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDTSLDPNDFDFTV---TGRGSPSRR 75
Cdd:cd01396    1 KPEDPRLPPGWKRELVPRKSG-SAGKFDVYYISPTGKKFRSKVELARYLEKNGPTSLDLSDFDFTVpkkLGLGSPRRH 77
MBD cd00122
MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of ...
 1-64 2.47e-20

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: 83.91  E-value: 2.47e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 938320031   1 MYDDPtLPEGWTRKLKQRKSGrSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDTSLDPNDFDF 64
Cdd:cd00122    1 PLRDP-LPPGWKRELVIRKSG-SAGKGDVYYYSPCGKKLRSKPEVARYLEKTGPSSLDLENFSF 62
MBD pfam01429
Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one ...
 3-66 1.12e-15

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: 71.24  E-value: 1.12e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 938320031    3 DDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDTSLDPNDFDFTV 66
Cdd:pfam01429   7 DRLPLPPGWRREERQRKSGSKAGKVDVFYYSPTGKKLRSKSEVARYLEANGGTSPKLEDFSFTV 70
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH