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Conserved domains on  [gi|1270530333|ref|NP_001344352|]
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methyl-CpG-binding domain protein 1 isoform 4 [Mus musculus]

Protein Classification

CXXC-type zinc finger protein( domain architecture ID 10477548)

CXXC-type zinc finger protein, such as human CXXC4 and CXXC5, contains eight conserved cysteine residues that bind to two zinc ions and plays important roles in epigenetic regulation by targeting various activities to CpG islands

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MBD pfam01429
Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one ...
 1-72 6.15e-22

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: 89.73  E-value: 6.15e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1270530333   1 MAESWQDCPALGPGWKRRESFRKSGASFGRSDIYYQSPTGEKIRSKVELTRYLGPAC----DLTLFDFRQGTLCHP 72
Cdd:pfam01429   1 IERKREDRLPLPPGWRREERQRKSGSKAGKVDVFYYSPTGKKLRSKSEVARYLEANGgtspKLEDFSFTVRSEVGR 76
zf-CXXC pfam02008
CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to ...
 357-403 4.80e-15

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.


:

Pssm-ID: 366873  Cd Length: 48  Bit Score: 69.31  E-value: 4.80e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1270530333 357 NQRQNRKCGACAACLRRMDCGRCDFCCDKPKFGGGNQKRQKCRWRQC 403
Cdd:pfam02008   2 NRRKRRRCGVCEGCQRPEDCGQCSFCLDMPKFGGPGKKKQKCRLRRC 48
zf-CXXC pfam02008
CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to ...
 243-288 1.91e-09

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.


:

Pssm-ID: 366873  Cd Length: 48  Bit Score: 53.51  E-value: 1.91e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1270530333 243 RIMEKSRGCGVCRGCQTQEDCGHCCICLRSPR---PGLKRQwRCLQRRC 288
Cdd:pfam02008   1 RNRRKRRRCGVCEGCQRPEDCGQCSFCLDMPKfggPGKKKQ-KCRLRRC 48
zf-CXXC pfam02008
CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to ...
 194-241 3.95e-09

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.


:

Pssm-ID: 366873  Cd Length: 48  Bit Score: 52.74  E-value: 3.95e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1270530333 194 QRMFKRVGCGDCAACLVKEDCGVCSTCRLQLPSDVASGLYCKCERRRC 241
Cdd:pfam02008   1 RNRRKRRRCGVCEGCQRPEDCGQCSFCLDMPKFGGPGKKKQKCRLRRC 48
 
Name Accession Description Interval E-value
MBD pfam01429
Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one ...
 1-72 6.15e-22

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: 89.73  E-value: 6.15e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1270530333   1 MAESWQDCPALGPGWKRRESFRKSGASFGRSDIYYQSPTGEKIRSKVELTRYLGPAC----DLTLFDFRQGTLCHP 72
Cdd:pfam01429   1 IERKREDRLPLPPGWRREERQRKSGSKAGKVDVFYYSPTGKKLRSKSEVARYLEANGgtspKLEDFSFTVRSEVGR 76
MeCP2_MBD cd01396
MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the ...
 5-66 1.08e-20

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: 86.27  E-value: 1.08e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1270530333   5 WQDCPALGPGWKRRESFRKSGaSFGRSDIYYQSPTGEKIRSKVELTRYLGP----ACDLTLFDFRQ 66
Cdd:cd01396     1 KPEDPRLPPGWKRELVPRKSG-SAGKFDVYYISPTGKKFRSKVELARYLEKngptSLDLSDFDFTV 65
MBD smart00391
Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, ...
 3-72 8.50e-20

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: 83.96  E-value: 8.50e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1270530333    3 ESWQDCPaLGPGWKRRESFRKSGASFGRSDIYYQSPTGEKIRSKVELTRYLGPACDLTL----FDFRQGTLCHP 72
Cdd:smart00391   1 GDPLRLP-LPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLdlecFDFNATVPVGP 73
zf-CXXC pfam02008
CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to ...
 357-403 4.80e-15

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.


Pssm-ID: 366873  Cd Length: 48  Bit Score: 69.31  E-value: 4.80e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1270530333 357 NQRQNRKCGACAACLRRMDCGRCDFCCDKPKFGGGNQKRQKCRWRQC 403
Cdd:pfam02008   2 NRRKRRRCGVCEGCQRPEDCGQCSFCLDMPKFGGPGKKKQKCRLRRC 48
zf-CXXC pfam02008
CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to ...
 243-288 1.91e-09

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.


Pssm-ID: 366873  Cd Length: 48  Bit Score: 53.51  E-value: 1.91e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1270530333 243 RIMEKSRGCGVCRGCQTQEDCGHCCICLRSPR---PGLKRQwRCLQRRC 288
Cdd:pfam02008   1 RNRRKRRRCGVCEGCQRPEDCGQCSFCLDMPKfggPGKKKQ-KCRLRRC 48
zf-CXXC pfam02008
CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to ...
 194-241 3.95e-09

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.


Pssm-ID: 366873  Cd Length: 48  Bit Score: 52.74  E-value: 3.95e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1270530333 194 QRMFKRVGCGDCAACLVKEDCGVCSTCRLQLPSDVASGLYCKCERRRC 241
Cdd:pfam02008   1 RNRRKRRRCGVCEGCQRPEDCGQCSFCLDMPKFGGPGKKKQKCRLRRC 48
 
Name Accession Description Interval E-value
MBD pfam01429
Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one ...
 1-72 6.15e-22

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: 89.73  E-value: 6.15e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1270530333   1 MAESWQDCPALGPGWKRRESFRKSGASFGRSDIYYQSPTGEKIRSKVELTRYLGPAC----DLTLFDFRQGTLCHP 72
Cdd:pfam01429   1 IERKREDRLPLPPGWRREERQRKSGSKAGKVDVFYYSPTGKKLRSKSEVARYLEANGgtspKLEDFSFTVRSEVGR 76
MeCP2_MBD cd01396
MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the ...
 5-66 1.08e-20

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: 86.27  E-value: 1.08e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1270530333   5 WQDCPALGPGWKRRESFRKSGaSFGRSDIYYQSPTGEKIRSKVELTRYLGP----ACDLTLFDFRQ 66
Cdd:cd01396     1 KPEDPRLPPGWKRELVPRKSG-SAGKFDVYYISPTGKKFRSKVELARYLEKngptSLDLSDFDFTV 65
MBD smart00391
Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, ...
 3-72 8.50e-20

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: 83.96  E-value: 8.50e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1270530333    3 ESWQDCPaLGPGWKRRESFRKSGASFGRSDIYYQSPTGEKIRSKVELTRYLGPACDLTL----FDFRQGTLCHP 72
Cdd:smart00391   1 GDPLRLP-LPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLdlecFDFNATVPVGP 73
zf-CXXC pfam02008
CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to ...
 357-403 4.80e-15

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.


Pssm-ID: 366873  Cd Length: 48  Bit Score: 69.31  E-value: 4.80e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1270530333 357 NQRQNRKCGACAACLRRMDCGRCDFCCDKPKFGGGNQKRQKCRWRQC 403
Cdd:pfam02008   2 NRRKRRRCGVCEGCQRPEDCGQCSFCLDMPKFGGPGKKKQKCRLRRC 48
MBD cd00122
MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of ...
 11-64 2.33e-14

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: 67.73  E-value: 2.33e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1270530333  11 LGPGWKRRESFRKSGASfGRSDIYYQSPTGEKIRSKVELTRYLG--PACDLTL--FDF 64
Cdd:cd00122     6 LPPGWKRELVIRKSGSA-GKGDVYYYSPCGKKLRSKPEVARYLEktGPSSLDLenFSF 62
zf-CXXC pfam02008
CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to ...
 243-288 1.91e-09

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.


Pssm-ID: 366873  Cd Length: 48  Bit Score: 53.51  E-value: 1.91e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1270530333 243 RIMEKSRGCGVCRGCQTQEDCGHCCICLRSPR---PGLKRQwRCLQRRC 288
Cdd:pfam02008   1 RNRRKRRRCGVCEGCQRPEDCGQCSFCLDMPKfggPGKKKQ-KCRLRRC 48
zf-CXXC pfam02008
CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to ...
 194-241 3.95e-09

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.


Pssm-ID: 366873  Cd Length: 48  Bit Score: 52.74  E-value: 3.95e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1270530333 194 QRMFKRVGCGDCAACLVKEDCGVCSTCRLQLPSDVASGLYCKCERRRC 241
Cdd:pfam02008   1 RNRRKRRRCGVCEGCQRPEDCGQCSFCLDMPKFGGPGKKKQKCRLRRC 48
 
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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