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Conserved domains on  [gi|334188017|ref|NP_001190421|]
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methyl-CPG-binding domain protein 02 [Arabidopsis thaliana]

Protein Classification

methyl-CpG-binding domain-containing protein( domain architecture ID 10539299)

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

Gene Ontology:  GO:0008270|GO:0008327
PubMed:  15888682|12665246

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MeCP2_MBD cd01396
MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the ...
 122-201 1.41e-27

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: 101.30  E-value: 1.41e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188017 122 KPNISRPPAGWQRLLRIRGEGGTRFADVYYVAPSGKKLRSTVEVQKYLNDNSEyigEGVKLSQFSFQIPKPLQDDYVRKR 201
Cdd:cd01396    1 KPEDPRLPPGWKRELVPRKSGSAGKFDVYYISPTGKKFRSKVELARYLEKNGP---TSLDLSDFDFTVPKKLGLGSPRRH 77
zf-CW pfam07496
CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four ...
 59-110 7.68e-11

CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialized mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteriztic of vertebrates, higher plants and other animals in which these domain is found.


:

Pssm-ID: 462181  Cd Length: 46  Bit Score: 56.16  E-value: 7.68e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 334188017   59 FTVQCASCFKWRLMPSMQKYEEIREqllenPFFCDTAREWKpDISCDVPADI 110
Cdd:pfam07496   1 YWVQCDSCLKWRRLPTEIDPYELPE-----PWYCSMNPDPK-YNSCDAPEEI 46
 
Name Accession Description Interval E-value
MeCP2_MBD cd01396
MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the ...
 122-201 1.41e-27

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: 101.30  E-value: 1.41e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188017 122 KPNISRPPAGWQRLLRIRGEGGTRFADVYYVAPSGKKLRSTVEVQKYLNDNSEyigEGVKLSQFSFQIPKPLQDDYVRKR 201
Cdd:cd01396    1 KPEDPRLPPGWKRELVPRKSGSAGKFDVYYISPTGKKFRSKVELARYLEKNGP---TSLDLSDFDFTVPKKLGLGSPRRH 77
MBD pfam01429
Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one ...
 118-187 1.32e-11

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: 58.91  E-value: 1.32e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334188017  118 WAIDKPNISRPPAGWQRLLRIRGEGGTRF-ADVYYVAPSGKKLRSTVEVQKYLNDNSEYigeGVKLSQFSF 187
Cdd:pfam01429   1 IERKREDRLPLPPGWRREERQRKSGSKAGkVDVFYYSPTGKKLRSKSEVARYLEANGGT---SPKLEDFSF 68
zf-CW pfam07496
CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four ...
 59-110 7.68e-11

CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialized mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteriztic of vertebrates, higher plants and other animals in which these domain is found.


Pssm-ID: 462181  Cd Length: 46  Bit Score: 56.16  E-value: 7.68e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 334188017   59 FTVQCASCFKWRLMPSMQKYEEIREqllenPFFCDTAREWKpDISCDVPADI 110
Cdd:pfam07496   1 YWVQCDSCLKWRRLPTEIDPYELPE-----PWYCSMNPDPK-YNSCDAPEEI 46
MBD smart00391
Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, ...
 129-195 1.26e-09

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: 53.53  E-value: 1.26e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 334188017   129 PAGWQRLLRIR--GEGGTRFaDVYYVAPSGKKLRSTVEVQKYLNDNSEYIgegVKLSQFSFQIPKPLQD 195
Cdd:smart00391   9 PCGWRRETKQRksGRSAGKF-DVYYISPCGKKLRSKSELARYLHKNGDLS---LDLECFDFNATVPVGP 73
 
Name Accession Description Interval E-value
MeCP2_MBD cd01396
MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the ...
 122-201 1.41e-27

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: 101.30  E-value: 1.41e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188017 122 KPNISRPPAGWQRLLRIRGEGGTRFADVYYVAPSGKKLRSTVEVQKYLNDNSEyigEGVKLSQFSFQIPKPLQDDYVRKR 201
Cdd:cd01396    1 KPEDPRLPPGWKRELVPRKSGSAGKFDVYYISPTGKKFRSKVELARYLEKNGP---TSLDLSDFDFTVPKKLGLGSPRRH 77
MBD cd00122
MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of ...
 122-187 2.05e-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: 82.37  E-value: 2.05e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 334188017 122 KPNISRPPaGWQRLLRIRGEGGTRFADVYYVAPSGKKLRSTVEVQKYLNDNSEyigEGVKLSQFSF 187
Cdd:cd00122    1 PLRDPLPP-GWKRELVIRKSGSAGKGDVYYYSPCGKKLRSKPEVARYLEKTGP---SSLDLENFSF 62
MBD pfam01429
Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one ...
 118-187 1.32e-11

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: 58.91  E-value: 1.32e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334188017  118 WAIDKPNISRPPAGWQRLLRIRGEGGTRF-ADVYYVAPSGKKLRSTVEVQKYLNDNSEYigeGVKLSQFSF 187
Cdd:pfam01429   1 IERKREDRLPLPPGWRREERQRKSGSKAGkVDVFYYSPTGKKLRSKSEVARYLEANGGT---SPKLEDFSF 68
zf-CW pfam07496
CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four ...
 59-110 7.68e-11

CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialized mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteriztic of vertebrates, higher plants and other animals in which these domain is found.


Pssm-ID: 462181  Cd Length: 46  Bit Score: 56.16  E-value: 7.68e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 334188017   59 FTVQCASCFKWRLMPSMQKYEEIREqllenPFFCDTAREWKpDISCDVPADI 110
Cdd:pfam07496   1 YWVQCDSCLKWRRLPTEIDPYELPE-----PWYCSMNPDPK-YNSCDAPEEI 46
MBD smart00391
Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, ...
 129-195 1.26e-09

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: 53.53  E-value: 1.26e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 334188017   129 PAGWQRLLRIR--GEGGTRFaDVYYVAPSGKKLRSTVEVQKYLNDNSEYIgegVKLSQFSFQIPKPLQD 195
Cdd:smart00391   9 PCGWRRETKQRksGRSAGKF-DVYYISPCGKKLRSKSELARYLHKNGDLS---LDLECFDFNATVPVGP 73
HAT_MBD cd01397
Methyl-CpG binding domains (MBD) present in putative chromatin remodelling factor such as ...
 129-198 3.94e-09

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.


Pssm-ID: 238691 [Multi-domain]  Cd Length: 73  Bit Score: 52.02  E-value: 3.94e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188017 129 PAGWQRLLRIRGEGGTRFADVYYVAPSGKKLRSTVEVQKYLNDNSeyiGEGVKLSQFSFQIPKPLQDDYV 198
Cdd:cd01397    7 ELGWRRETRIRGLGGRIQGEVAYYAPCGKKLRQYPEVIKYLSKNG---ISLLSRENFSFSARAPVGDFYE 73
HMT_MBD cd01395
Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as ...
 131-169 1.14e-03

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.


Pssm-ID: 238689  Cd Length: 60  Bit Score: 36.59  E-value: 1.14e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 334188017 131 GWQRLLRIRGEGGTRFAdVYYVAPSGKKLRSTVEVQKYL 169
Cdd:cd01395    9 GFQRMKYRARVGKVKKH-VIYKAPCGRSLRNMSEVHRYL 46
 
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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