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Conserved domains on  [gi|2277788472|ref|NP_001397036|]
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methyl-CpG-binding domain protein 4 isoform 3 [Mus musculus]

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, ...
66-132 2.37e-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: 102.06  E-value: 2.37e-26
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2277788472   66 ATEGHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFDFTV 132
Cdd:smart00391   1 GDPLRLPLPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLDLECFDFNA 67
Nth super family cl43050
Endonuclease III [Replication, recombination and repair];
399-469 3.58e-08

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: 53.56  E-value: 3.58e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2277788472 399 EILFHDPWKLLIATIFLNRTSGKMAIPVLWEFLEKYPSAEVARAADWRDVSELLKPLGLYDLRAKTIIKFS 469
Cdd:COG0177    14 ELDYRDPFELLVATILSAQTTDERVNKATPRLFARYPTPEALAAADLEELEELIRPIGLYRNKAKNIIALA 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, ...
66-132 2.37e-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: 102.06  E-value: 2.37e-26
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2277788472   66 ATEGHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFDFTV 132
Cdd:smart00391   1 GDPLRLPLPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLDLECFDFNA 67
MeCP2_MBD cd01396
MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the ...
72-144 8.81e-25

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: 97.44  E-value: 8.81e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2277788472  72 PVPCGWERVVKQRLSGkTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFDFTVLPKGSINPGYKH 144
Cdd:cd01396     6 RLPPGWKRELVPRKSG-SAGKFDVYYISPTGKKFRSKVELARYLEKNGPTSLDLSDFDFTVPKKLGLGSPRRH 77
MBD pfam01429
Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one ...
64-135 4.29e-23

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: 92.81  E-value: 4.29e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2277788472  64 TTATEGHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFDFTVLPK 135
Cdd:pfam01429   2 ERKREDRLPLPPGWRREERQRKSGSKAGKVDVFYYSPTGKKLRSKSEVARYLEANGGTSPKLEDFSFTVRSE 73
Nth COG0177
Endonuclease III [Replication, recombination and repair];
399-469 3.58e-08

Endonuclease III [Replication, recombination and repair];


Pssm-ID: 439947 [Multi-domain]  Cd Length: 198  Bit Score: 53.56  E-value: 3.58e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2277788472 399 EILFHDPWKLLIATIFLNRTSGKMAIPVLWEFLEKYPSAEVARAADWRDVSELLKPLGLYDLRAKTIIKFS 469
Cdd:COG0177    14 ELDYRDPFELLVATILSAQTTDERVNKATPRLFARYPTPEALAAADLEELEELIRPIGLYRNKAKNIIALA 84
ENDO3c cd00056
endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), ...
406-489 3.95e-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: 41.07  E-value: 3.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277788472 406 WKLLIATIFLNRTSGKMAIPVLWEFLEKY-PSAEVARAADWRDVSELLKPLGlYDLRAKTIIKFS----DEYLTKQWRYP 480
Cdd:cd00056     1 FEVLVSEILSQQTTDKAVNKAYERLFERYgPTPEALAAADEEELRELIRSLG-YRRKAKYLKELAraivEGFGGLVLDDP 79
                          90
                  ....*....|....*
gi 2277788472 481 ------IELHGIGKY 489
Cdd:cd00056    80 dareelLALPGVGRK 94
HhH-GPD pfam00730
HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of ...
410-523 4.15e-04

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: 40.73  E-value: 4.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277788472 410 IATIFLNRTSGKMAIPVLWEFLEK-YPSAEVARAADWRDVSELLKPLGLYDLRAKTIIKFS----DEYLTKQWRYPIELH 484
Cdd:pfam00730   1 VSAILSQQTSDKAVNKITERLFEKfFPTPEDLADADEEELRELIRGLGFYRRKAKYLKELArilvEGYGGEVPLDEEELE 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2277788472 485 ----GIGKYGNDSYRIFCVNEWKQVHPED---HKLNKYHDWLWENH 523
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, ...
66-132 2.37e-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: 102.06  E-value: 2.37e-26
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2277788472   66 ATEGHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFDFTV 132
Cdd:smart00391   1 GDPLRLPLPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLDLECFDFNA 67
MeCP2_MBD cd01396
MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the ...
72-144 8.81e-25

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: 97.44  E-value: 8.81e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2277788472  72 PVPCGWERVVKQRLSGkTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFDFTVLPKGSINPGYKH 144
Cdd:cd01396     6 RLPPGWKRELVPRKSG-SAGKFDVYYISPTGKKFRSKVELARYLEKNGPTSLDLSDFDFTVPKKLGLGSPRRH 77
MBD pfam01429
Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one ...
64-135 4.29e-23

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: 92.81  E-value: 4.29e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2277788472  64 TTATEGHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFDFTVLPK 135
Cdd:pfam01429   2 ERKREDRLPLPPGWRREERQRKSGSKAGKVDVFYYSPTGKKLRSKSEVARYLEANGGTSPKLEDFSFTVRSE 73
MBD cd00122
MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of ...
68-130 4.60e-23

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: 92.39  E-value: 4.60e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2277788472  68 EGHKPVPCGWERVVKQRLSGkTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFDF 130
Cdd:cd00122     1 PLRDPLPPGWKRELVIRKSG-SAGKGDVYYYSPCGKKLRSKPEVARYLEKTGPSSLDLENFSF 62
Nth COG0177
Endonuclease III [Replication, recombination and repair];
399-469 3.58e-08

Endonuclease III [Replication, recombination and repair];


Pssm-ID: 439947 [Multi-domain]  Cd Length: 198  Bit Score: 53.56  E-value: 3.58e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2277788472 399 EILFHDPWKLLIATIFLNRTSGKMAIPVLWEFLEKYPSAEVARAADWRDVSELLKPLGLYDLRAKTIIKFS 469
Cdd:COG0177    14 ELDYRDPFELLVATILSAQTTDERVNKATPRLFARYPTPEALAAADLEELEELIRPIGLYRNKAKNIIALA 84
ENDO3c cd00056
endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), ...
406-489 3.95e-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: 41.07  E-value: 3.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277788472 406 WKLLIATIFLNRTSGKMAIPVLWEFLEKY-PSAEVARAADWRDVSELLKPLGlYDLRAKTIIKFS----DEYLTKQWRYP 480
Cdd:cd00056     1 FEVLVSEILSQQTTDKAVNKAYERLFERYgPTPEALAAADEEELRELIRSLG-YRRKAKYLKELAraivEGFGGLVLDDP 79
                          90
                  ....*....|....*
gi 2277788472 481 ------IELHGIGKY 489
Cdd:cd00056    80 dareelLALPGVGRK 94
HhH-GPD pfam00730
HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of ...
410-523 4.15e-04

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: 40.73  E-value: 4.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277788472 410 IATIFLNRTSGKMAIPVLWEFLEK-YPSAEVARAADWRDVSELLKPLGLYDLRAKTIIKFS----DEYLTKQWRYPIELH 484
Cdd:pfam00730   1 VSAILSQQTSDKAVNKITERLFEKfFPTPEDLADADEEELRELIRGLGFYRRKAKYLKELArilvEGYGGEVPLDEEELE 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2277788472 485 ----GIGKYGNDSYRIFCVNEWKQVHPED---HKLNKYHDWLWENH 523
Cdd:pfam00730  81 allkGVGRWTAEAVLIFALGRPDPLPVVDthvRRVLKRLGLIKEKP 126
HAT_MBD cd01397
Methyl-CpG binding domains (MBD) present in putative chromatin remodelling factor such as ...
72-130 4.92e-04

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: 38.92  E-value: 4.92e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277788472  72 PVPCGWERVVKQR-LSGKTAGkfDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFDF 130
Cdd:cd01397     5 PLELGWRRETRIRgLGGRIQG--EVAYYAPCGKKLRQYPEVIKYLSKNGISLLSRENFSF 62
HMT_MBD cd01395
Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as ...
70-130 3.05e-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: 36.20  E-value: 3.05e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2277788472  70 HKPVPCGWERVVKQRLSGKTagKFDVYFISPQGLKFRSKRSLANYLLKNgETFLKPEDFDF 130
Cdd:cd01395     3 HTPLLCGFQRMKYRARVGKV--KKHVIYKAPCGRSLRNMSEVHRYLRET-CSFLTVDNFSF 60
 
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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