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Conserved domains on  [gi|1370478223|ref|XP_024308757|]
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methyl-CpG-binding domain protein 5 isoform X4 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PWWP super family cl02554
PWWP (Pro-Trp-Trp-Pro) domain; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, ...
 1616-1698 7.02e-31

PWWP (Pro-Trp-Trp-Pro) domain; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids and is composed of a five-stranded antiparallel beta-barrel followed by a helical region. It is found in numerous proteins that are involved in cell division, growth, and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. PWWP domains specifically recognize DNA and histone methylated lysines at the level of the nucleosome. Based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.


The actual alignment was detected with superfamily member cd20141:

Pssm-ID: 470613  Cd Length: 92  Bit Score: 117.03  E-value: 7.02e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370478223 1616 FNVGDLVWGQIKGLTSWPGKLVREDDV--------HNSCQQSPEEGKVEPEKLKTLTEGLEAYSRVRKRNRKLRgrrkee 1687
Cdd:cd20141      1 FNVGDLVWGQIRGFPSWPGKLVSENDVgktnegkvWVSWFGDHSFGQVEPDKLKTLSEGLEAHHRARKRTRKGR------ 74

                           90
                   ....*....|.
gi 1370478223 1688 kaeKGRCHLEQ 1698
Cdd:cd20141     75 ---KLNNHLEA 82
MBD super family cl00110
MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of ...
 21-79 1.98e-04

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.


The actual alignment was detected with superfamily member smart00391:

Pssm-ID: 469618  Cd Length: 77  Bit Score: 41.59  E-value: 1.98e-04
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1370478223    21 VPVGWQRRVDQ---------NGVLYVSPSGSLLSCLEQVKTYLLTDGTCKCGLECplilpkvFNFDPG 79
Cdd:smart00391    8 LPCGWRRETKQrksgrsagkFDVYYISPCGKKLRSKSELARYLHKNGDLSLDLEC-------FDFNAT 68
 
Name Accession Description Interval E-value
PWWP_MBD5 cd20141
PWWP domain found in methyl-CpG-binding domain protein 5 (MBD5) and similar proteins; MBD5, is ...
 1616-1698 7.02e-31

PWWP domain found in methyl-CpG-binding domain protein 5 (MBD5) and similar proteins; MBD5, is a methyl-CpG-binding protein that binds to heterochromatin. It does not interact with either methylated or unmethylated DNA. MBD5 acts as a transcriptional regulator responsible for 2q23.1 deletion syndrome. It belongs to the MBD family proteins, which play central roles in transcriptional regulation and development. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438969  Cd Length: 92  Bit Score: 117.03  E-value: 7.02e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370478223 1616 FNVGDLVWGQIKGLTSWPGKLVREDDV--------HNSCQQSPEEGKVEPEKLKTLTEGLEAYSRVRKRNRKLRgrrkee 1687
Cdd:cd20141      1 FNVGDLVWGQIRGFPSWPGKLVSENDVgktnegkvWVSWFGDHSFGQVEPDKLKTLSEGLEAHHRARKRTRKGR------ 74

                           90
                   ....*....|.
gi 1370478223 1688 kaeKGRCHLEQ 1698
Cdd:cd20141     75 ---KLNNHLEA 82
MBD smart00391
Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, ...
 21-79 1.98e-04

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: 41.59  E-value: 1.98e-04
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1370478223    21 VPVGWQRRVDQ---------NGVLYVSPSGSLLSCLEQVKTYLLTDGTCKCGLECplilpkvFNFDPG 79
Cdd:smart00391    8 LPCGWRRETKQrksgrsagkFDVYYISPCGKKLRSKSELARYLHKNGDLSLDLEC-------FDFNAT 68
PWWP pfam00855
PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain ...
 1619-1691 2.26e-04

PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyzes all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organizing higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression.


Pssm-ID: 459964 [Multi-domain]  Cd Length: 92  Bit Score: 41.64  E-value: 2.26e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370478223 1619 GDLVWGQIKGLTSWPGKLVREDDVHNSCQQSP--------------EEGKVEPEKLKTLTEGLEAYSRVRKRNRKLRGRR 1684
Cdd:pfam00855    1 GDLVWAKLKGYPWWPARVVDPEELPENVLKPKkkdgeylvrffgdsEFAWVKPKDLKPFDEGDEFEYLKKKKKKKKKKAF 80


                   ....*....
gi 1370478223 1685 KE--EKAEK 1691
Cdd:pfam00855   81 KKalEEAEE 89
 
Name Accession Description Interval E-value
PWWP_MBD5 cd20141
PWWP domain found in methyl-CpG-binding domain protein 5 (MBD5) and similar proteins; MBD5, is ...
 1616-1698 7.02e-31

PWWP domain found in methyl-CpG-binding domain protein 5 (MBD5) and similar proteins; MBD5, is a methyl-CpG-binding protein that binds to heterochromatin. It does not interact with either methylated or unmethylated DNA. MBD5 acts as a transcriptional regulator responsible for 2q23.1 deletion syndrome. It belongs to the MBD family proteins, which play central roles in transcriptional regulation and development. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438969  Cd Length: 92  Bit Score: 117.03  E-value: 7.02e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370478223 1616 FNVGDLVWGQIKGLTSWPGKLVREDDV--------HNSCQQSPEEGKVEPEKLKTLTEGLEAYSRVRKRNRKLRgrrkee 1687
Cdd:cd20141      1 FNVGDLVWGQIRGFPSWPGKLVSENDVgktnegkvWVSWFGDHSFGQVEPDKLKTLSEGLEAHHRARKRTRKGR------ 74

                           90
                   ....*....|.
gi 1370478223 1688 kaeKGRCHLEQ 1698
Cdd:cd20141     75 ---KLNNHLEA 82
PWWP cd05162
PWWP (Pro-Trp-Trp-Pro) domain; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, ...
 1619-1680 2.41e-06

PWWP (Pro-Trp-Trp-Pro) domain; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids and is composed of a five-stranded antiparallel beta-barrel followed by a helical region. It is found in numerous proteins that are involved in cell division, growth, and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. PWWP domains specifically recognize DNA and histone methylated lysines at the level of the nucleosome. Based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.


Pssm-ID: 438958 [Multi-domain]  Cd Length: 86  Bit Score: 47.11  E-value: 2.41e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1370478223 1619 GDLVWGQIKGLTSWPGKLVREDDVHNSCQQSPEEGK-------------VEPEKLKTLTEGLEAYSRVRKRNRKL 1680
Cdd:cd05162      1 GDLVWAKLKGYPWWPARVVDPEELPEEVGKKKKKGGvlvqffgdndyawVKSKNIKPFEEGFKKEFKKKKKKSKK 75
PWWP_GLYR1 cd05836
PWWP domain found in glyoxylate reductase 1 (GLYR1) and similar proteins; GLYR1, also called ...
 1616-1638 6.69e-05

PWWP domain found in glyoxylate reductase 1 (GLYR1) and similar proteins; GLYR1, also called 3-hydroxyisobutyrate dehydrogenase-like protein, cytokine-like nuclear factor N-PAC, nuclear protein NP60, or nuclear protein of 60 kDa, is a putative oxidoreductase that is recruited on chromatin and promotes KDM1B demethylase activity. It recognizes and binds trimethylated 'Lys-36' of histone H3 (H3K36me3). GLYR1 enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In addition to the PWWP domain, GLYR1 also contains an AT-hook and a C-terminal NAD-binding domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438961 [Multi-domain]  Cd Length: 86  Bit Score: 42.98  E-value: 6.69e-05
                           10        20
                   ....*....|....*....|...
gi 1370478223 1616 FNVGDLVWGQIKGLTSWPGKLVR 1638
Cdd:cd05836      1 FKIGDLVWAKMKGFPPWPGKIVN 23
MBD smart00391
Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, ...
 21-79 1.98e-04

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: 41.59  E-value: 1.98e-04
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1370478223    21 VPVGWQRRVDQ---------NGVLYVSPSGSLLSCLEQVKTYLLTDGTCKCGLECplilpkvFNFDPG 79
Cdd:smart00391    8 LPCGWRRETKQrksgrsagkFDVYYISPCGKKLRSKSELARYLHKNGDLSLDLEC-------FDFNAT 68
PWWP pfam00855
PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain ...
 1619-1691 2.26e-04

PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyzes all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organizing higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression.


Pssm-ID: 459964 [Multi-domain]  Cd Length: 92  Bit Score: 41.64  E-value: 2.26e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370478223 1619 GDLVWGQIKGLTSWPGKLVREDDVHNSCQQSP--------------EEGKVEPEKLKTLTEGLEAYSRVRKRNRKLRGRR 1684
Cdd:pfam00855    1 GDLVWAKLKGYPWWPARVVDPEELPENVLKPKkkdgeylvrffgdsEFAWVKPKDLKPFDEGDEFEYLKKKKKKKKKKAF 80


                   ....*....
gi 1370478223 1685 KE--EKAEK 1691
Cdd:pfam00855   81 KKalEEAEE 89
PWWP_DNMT3 cd05835
PWWP domain found in the DNA (cytosine-5)-methyltransferase 3 (DNMT3) family; The DNMT3 family ...
 1617-1652 2.65e-04

PWWP domain found in the DNA (cytosine-5)-methyltransferase 3 (DNMT3) family; The DNMT3 family includes DNMT3A and DNMT3B, which are required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNMT3A, also called DNA methyltransferase HsaIIIA, DNA MTase HsaIIIA, or M.HsaIIIA, modifies DNA in a non-processive manner and also methylates non-CpG sites. It may preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. DNMT3A is recruited to trimethylated 'Lys-36' of histone H3 (H3K36me3) sites. DNMT3B, also called DNA methyltransferase HsaIIIB, DNA MTase HsaIIIB, or M.HsaIIIB, may preferentially methylate nucleosomal DNA within the nucleosome core region. DNMT3B may function as a transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Members of this family contains a PWWP domain that is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by DNMT3B is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of DNMT3B has been identified in patients with ICF (immunodeficiency, centromeric instability, and facial anomalie) syndrome , a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA.


Pssm-ID: 438960 [Multi-domain]  Cd Length: 89  Bit Score: 41.48  E-value: 2.65e-04
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1370478223 1617 NVGDLVWGQIKGLTSWPGKLVReddvHNSCQQSPEE 1652
Cdd:cd05835      1 KIGDLVWAKLKGSPWWPGIVVS----HKDCGQKPPA 32
PWWP_PWWP2 cd20140
PWWP domain found in the PWWP domain-containing protein 2 (PWWP2) family; The PWWP2 family ...
 1614-1637 5.32e-04

PWWP domain found in the PWWP domain-containing protein 2 (PWWP2) family; The PWWP2 family includes PWWP2A and its paralog PWWP2B. PWWP2A is a H2A.Z-specific chromatin binding protein which may play an important role in the neural crest stem cell migration and differentiation during early development. It is also required for proper mitosis progression. PWWP2A and PWWP2B form a stable complex with NuRD subunits MTA1/2/3:HDAC1/2:RBBP4/7, but not with MBD2/3, p66alpha/beta, and CHD3/4. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438968  Cd Length: 92  Bit Score: 40.71  E-value: 5.32e-04
                           10        20
                   ....*....|....*....|....
gi 1370478223 1614 RTFNVGDLVWGQIKGLTSWPGKLV 1637
Cdd:cd20140      2 RTLRVGDIVWGKIHGFPWWPGRIL 25
PWWP_DNMT3A cd20154
PWWP domain found in DNA (cytosine-5)-methyltransferase 3A (DNMT3A); DNMT3A, also called DNA ...
 1614-1637 1.16e-03

PWWP domain found in DNA (cytosine-5)-methyltransferase 3A (DNMT3A); DNMT3A, also called DNA methyltransferase HsaIIIA, DNA MTase HsaIIIA, or M.HsaIIIA, is required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. It modifies DNA in a non-processive manner and also methylates non-CpG sites. It may preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. DNMT3A is recruited to trimethylated 'Lys-36' of histone H3 (H3K36me3) sites. It contains a PWWP domain that binds methylated histone.


Pssm-ID: 438982  Cd Length: 134  Bit Score: 40.72  E-value: 1.16e-03
                           10        20
                   ....*....|....*....|....
gi 1370478223 1614 RTFNVGDLVWGQIKGLTSWPGKLV 1637
Cdd:cd20154      4 RGFGIGELVWGKLRGFSWWPGRIV 27
PWWP_PWWP2B cd20153
PWWP domain found in PWWP domain-containing protein 2B (PWWP2B); PWWP2B is a paralog of PWWP2A, ...
 1614-1696 1.43e-03

PWWP domain found in PWWP domain-containing protein 2B (PWWP2B); PWWP2B is a paralog of PWWP2A, a H2A.Z-specific chromatin binding protein which may play an important role in the neural crest stem cell migration and differentiation during early development. PWWP2A and PWWP2B form a stable complex with NuRD subunits MTA1/2/3:HDAC1/2:RBBP4/7, but not with MBD2/3, p66alpha/beta, and CHD3/4. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438981  Cd Length: 116  Bit Score: 40.33  E-value: 1.43e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370478223 1614 RTFNVGDLVWGQIKGLTSWPGKLV-----REDDVHNSCQQ-------SPEEGKVEPEKLKTLTEgleaYSRVRkRNRKLR 1681
Cdd:cd20153     12 RTVSVGDIVWGKIHGFPWWPARVLsislsQKEDGEPSWQEakvswfgSPTTSLLSVSKLSPFSE----FFKLR-FNRKKK 86

                           90
                   ....*....|....*..
gi 1370478223 1682 G--RRKEEKAEKGRCHL 1696
Cdd:cd20153     87 GmyRKAITEAAKAAEHL 103
 
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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