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Conserved domains on  [gi|4505121|ref|NP_003916|]
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methyl-CpG-binding domain protein 4 isoform 1 [Homo sapiens]

Protein Classification

Graphical summary

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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, ...
 79-155 8.95e-30

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: 112.08  E-value: 8.95e-30
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4505121      79 GTECRKSVPCGWERVVKQRLFGKTAGRFDVYFISPQGLKFRSKSSLANYLHKNGETSLKPEDFDFTVLSKRGIKSRY 155
Cdd:smart00391   1 GDPLRLPLPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLDLECFDFNATVPVGPKFTP 77
Nth super family cl43050
Endonuclease III [Replication, recombination and repair];
453-520 4.86e-07

Endonuclease III [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0177:

Pssm-ID: 439947 [Multi-domain]  Cd Length: 198  Bit Score: 50.48  E-value: 4.86e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 4505121  453 FHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFS 520
Cdd:COG0177  17 YRDPFELLVATILSAQTTDERVNKATPRLFARYPTPEALAAADLEELEELIRPIGLYRNKAKNIIALA 84
 
Name Accession Description Interval E-value
MBD smart00391
Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, ...
 79-155 8.95e-30

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: 112.08  E-value: 8.95e-30
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4505121      79 GTECRKSVPCGWERVVKQRLFGKTAGRFDVYFISPQGLKFRSKSSLANYLHKNGETSLKPEDFDFTVLSKRGIKSRY 155
Cdd:smart00391   1 GDPLRLPLPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLDLECFDFNATVPVGPKFTP 77
MeCP2_MBD cd01396
MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the ...
 87-156 2.40e-24

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: 96.67  E-value: 2.40e-24
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505121   87 PCGWERVVKQRLFGkTAGRFDVYFISPQGLKFRSKSSLANYLHKNGETSLKPEDFDFTVLSKRGIKSRYK 156
Cdd:cd01396   8 PPGWKRELVPRKSG-SAGKFDVYYISPTGKKFRSKVELARYLEKNGPTSLDLSDFDFTVPKKLGLGSPRR 76
MBD pfam01429
Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one ...
 80-151 3.09e-24

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: 96.27  E-value: 3.09e-24
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4505121     80 TECRKSVPCGWERVVKQRLFGKTAGRFDVYFISPQGLKFRSKSSLANYLHKNGETSLKPEDFDFTVLSKRGI 151
Cdd:pfam01429   5 REDRLPLPPGWRREERQRKSGSKAGKVDVFYYSPTGKKLRSKSEVARYLEANGGTSPKLEDFSFTVRSEVGR 76
Nth COG0177
Endonuclease III [Replication, recombination and repair];
453-520 4.86e-07

Endonuclease III [Replication, recombination and repair];


Pssm-ID: 439947 [Multi-domain]  Cd Length: 198  Bit Score: 50.48  E-value: 4.86e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 4505121  453 FHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFS 520
Cdd:COG0177  17 YRDPFELLVATILSAQTTDERVNKATPRLFARYPTPEALAAADLEELEELIRPIGLYRNKAKNIIALA 84
ENDO3c cd00056
endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), ...
 457-540 8.06e-04

endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases


Pssm-ID: 238013 [Multi-domain]  Cd Length: 158  Bit Score: 40.30  E-value: 8.06e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505121  457 WKLLIATIFLNRTSGKMAIPVLWKFLEKY-PSAEVARTADWRDVSELLKPLGlYDLRAKTIVKFS----DEYLTKQWKYP 531
Cdd:cd00056   1 FEVLVSEILSQQTTDKAVNKAYERLFERYgPTPEALAAADEEELRELIRSLG-YRRKAKYLKELAraivEGFGGLVLDDP 79

                        90
                ....*....|....*
gi 4505121  532 ------IELHGIGKY 540
Cdd:cd00056  80 dareelLALPGVGRK 94
HhH-GPD pfam00730
HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of ...
 461-574 7.41e-03

HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.


Pssm-ID: 425841 [Multi-domain]  Cd Length: 141  Bit Score: 37.26  E-value: 7.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505121    461 IATIFLNRTSGKMAIPVLWKFLEK-YPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFS----DEYLTKQWKYPIELH 535
Cdd:pfam00730   1 VSAILSQQTSDKAVNKITERLFEKfFPTPEDLADADEEELRELIRGLGFYRRKAKYLKELArilvEGYGGEVPLDEEELE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 4505121    536 ----GIGKYGNDSYRIFCVNEWKQVHPED---HKLNKYHDWLWENH 574
Cdd:pfam00730  81 allkGVGRWTAEAVLIFALGRPDPLPVVDthvRRVLKRLGLIKEKP 126
 
Name Accession Description Interval E-value
MBD smart00391
Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, ...
 79-155 8.95e-30

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: 112.08  E-value: 8.95e-30
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4505121      79 GTECRKSVPCGWERVVKQRLFGKTAGRFDVYFISPQGLKFRSKSSLANYLHKNGETSLKPEDFDFTVLSKRGIKSRY 155
Cdd:smart00391   1 GDPLRLPLPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLDLECFDFNATVPVGPKFTP 77
MeCP2_MBD cd01396
MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the ...
 87-156 2.40e-24

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: 96.67  E-value: 2.40e-24
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505121   87 PCGWERVVKQRLFGkTAGRFDVYFISPQGLKFRSKSSLANYLHKNGETSLKPEDFDFTVLSKRGIKSRYK 156
Cdd:cd01396   8 PPGWKRELVPRKSG-SAGKFDVYYISPTGKKFRSKVELARYLEKNGPTSLDLSDFDFTVPKKLGLGSPRR 76
MBD pfam01429
Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one ...
 80-151 3.09e-24

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: 96.27  E-value: 3.09e-24
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4505121     80 TECRKSVPCGWERVVKQRLFGKTAGRFDVYFISPQGLKFRSKSSLANYLHKNGETSLKPEDFDFTVLSKRGI 151
Cdd:pfam01429   5 REDRLPLPPGWRREERQRKSGSKAGKVDVFYYSPTGKKLRSKSEVARYLEANGGTSPKLEDFSFTVRSEVGR 76
MBD cd00122
MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of ...
 87-143 1.56e-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: 85.45  E-value: 1.56e-20
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 4505121   87 PCGWERVVKQRLFGkTAGRFDVYFISPQGLKFRSKSSLANYLHKNGETSLKPEDFDF 143
Cdd:cd00122   7 PPGWKRELVIRKSG-SAGKGDVYYYSPCGKKLRSKPEVARYLEKTGPSSLDLENFSF 62
Nth COG0177
Endonuclease III [Replication, recombination and repair];
453-520 4.86e-07

Endonuclease III [Replication, recombination and repair];


Pssm-ID: 439947 [Multi-domain]  Cd Length: 198  Bit Score: 50.48  E-value: 4.86e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 4505121  453 FHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFS 520
Cdd:COG0177  17 YRDPFELLVATILSAQTTDERVNKATPRLFARYPTPEALAAADLEELEELIRPIGLYRNKAKNIIALA 84
ENDO3c cd00056
endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), ...
 457-540 8.06e-04

endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases


Pssm-ID: 238013 [Multi-domain]  Cd Length: 158  Bit Score: 40.30  E-value: 8.06e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505121  457 WKLLIATIFLNRTSGKMAIPVLWKFLEKY-PSAEVARTADWRDVSELLKPLGlYDLRAKTIVKFS----DEYLTKQWKYP 531
Cdd:cd00056   1 FEVLVSEILSQQTTDKAVNKAYERLFERYgPTPEALAAADEEELRELIRSLG-YRRKAKYLKELAraivEGFGGLVLDDP 79

                        90
                ....*....|....*
gi 4505121  532 ------IELHGIGKY 540
Cdd:cd00056  80 dareelLALPGVGRK 94
HAT_MBD cd01397
Methyl-CpG binding domains (MBD) present in putative chromatin remodelling factor such as ...
 81-143 5.51e-03

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: 35.84  E-value: 5.51e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 4505121   81 ECRKSVPCGWERVVKQRLFGktaGRF--DVYFISPQGLKFRSKSSLANYLHKNGETSLKPEDFDF 143
Cdd:cd01397   1 ELRVPLELGWRRETRIRGLG---GRIqgEVAYYAPCGKKLRQYPEVIKYLSKNGISLLSRENFSF 62
HhH-GPD pfam00730
HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of ...
 461-574 7.41e-03

HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.


Pssm-ID: 425841 [Multi-domain]  Cd Length: 141  Bit Score: 37.26  E-value: 7.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505121    461 IATIFLNRTSGKMAIPVLWKFLEK-YPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFS----DEYLTKQWKYPIELH 535
Cdd:pfam00730   1 VSAILSQQTSDKAVNKITERLFEKfFPTPEDLADADEEELRELIRGLGFYRRKAKYLKELArilvEGYGGEVPLDEEELE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 4505121    536 ----GIGKYGNDSYRIFCVNEWKQVHPED---HKLNKYHDWLWENH 574
Cdd:pfam00730  81 allkGVGRWTAEAVLIFALGRPDPLPVVDthvRRVLKRLGLIKEKP 126
 
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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