O95983 (MBD3_HUMAN) Reviewed, UniProtKB/Swiss-Prot
Last modified
January 25, 2012.
Version 90.
History...
Names·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
Names·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize orderNames and origin
| Protein names | Recommended name: Methyl-CpG-binding domain protein 3 Alternative name(s): Methyl-CpG-binding protein MBD3 | ||
| Gene names |
| ||
| Organism | Homo sapiens (Human) | ||
| Taxonomic identifier | 9606 [NCBI] | ||
| Taxonomic lineage | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Protein attributes
| Sequence length | 291 AA. |
| Sequence status | Complete. |
| Protein existence | Evidence at protein level |
General annotation (Comments)
| Function | Does not bind DNA by itself. Recruits histone deacetylases and DNA methyltransferases. Acts as transcriptional repressor and plays a role in gene silencing. Ref.1 Ref.6 Ref.8 |
| Subunit structure | Heterodimer with MBD2. Part of the NuRD and the MeCP1 complex. Binds HDAC1, MTA2, DNMT1, p66-alpha and p66-beta. Ref.6 |
| Subcellular location | |
| Sequence similarities | Contains 1 MBD (methyl-CpG-binding) domain. |
| Sequence caution | The sequence AAH32443.1 differs from that shown. Reason: Erroneous initiation. |
Ontologies
| Keywords | |
|---|---|
| Biological process | Transcription Transcription regulation |
| Cellular component | Nucleus |
| Coding sequence diversity | Alternative splicing |
| Domain | Coiled coil |
| PTM | Acetylation Phosphoprotein |
| Technical term | Complete proteome Reference proteome |
| Gene Ontology (GO) | |
| Biological process | transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW |
| Cellular component | NuRD complex Non-traceable author statement. Source: BHF-UCL |
| Molecular function | DNA binding Traceable author statement. Source: ProtInc protein bindingInferred from physical interaction Ref.9. Source: UniProtKB |
| Complete GO annotation... | |
Binary interactions
With | Entry | #Exp. | IntAct | Notes |
|---|---|---|---|---|
| DDX5 | P17844 | 4 | EBI-1783068,EBI-351962 |
Alternative products
| This entry describes 2 isoforms produced by alternative splicing. [Align] [Select] | ||||||
| Isoform 1 (identifier: O95983-1) This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. | ||||||
| Isoform 2 (identifier: O95983-2) The sequence of this isoform differs from the canonical sequence as follows: 5-36: Missing. | ||||||
| Note: No experimental confirmation available. |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||
Molecule processing | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 291 | 291 | Methyl-CpG-binding domain protein 3 | PRO_0000096262 | |||||
Regions | |||||||||
| Domain | 1 – 72 | 72 | MBD | ||||||
| Coiled coil | 216 – 245 | 30 | Potential | ||||||
| Compositional bias | 272 – 281 | 10 | Poly-Glu | ||||||
Amino acid modifications | |||||||||
| Modified residue | 4 | 1 | N6-acetyllysine Ref.13 | ||||||
| Modified residue | 56 | 1 | Phosphoserine Ref.11 Ref.12 | ||||||
| Modified residue | 109 | 1 | N6-acetyllysine Ref.13 | ||||||
| Modified residue | 141 | 1 | N6-acetyllysine Ref.13 | ||||||
| Modified residue | 144 | 1 | Phosphoserine Ref.12 | ||||||
Natural variations | |||||||||
| Alternative sequence | 5 – 36 | 32 | Missing in isoform 2. | VSP_011081 | |||||
Experimental info | |||||||||
| Mutagenesis | 30 | 1 | H → K: No effect. Confers strong binding to methylated CpG (in vitro); when associated with Y-30. Ref.8 | ||||||
| Mutagenesis | 34 | 1 | F → A: Augments DNA binding activity, irrespective of DNA methylation. Ref.8 | ||||||
| Mutagenesis | 34 | 1 | F → Y: Confers weak binding to methylated CpG (in vitro). Confers strong binding to methylated CpG (in vitro); when associated with K-30. Ref.8 | ||||||
Sequences
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References
| « Hide 'large scale' references | |
| [1] | "Identification and characterization of a family of mammalian methyl-CpG binding proteins." Hendrich B., Bird A. Mol. Cell. Biol. 18:6538-6547(1998) [PubMed: 9774669] [Abstract] Cited for: NUCLEOTIDE SEQUENCE (ISOFORM 1), FUNCTION, SUBCELLULAR LOCATION. |
| [2] | "Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. Sugano S.Nat. Genet. 36:40-45(2004) [PubMed: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). |
| [3] | "The DNA sequence and biology of human chromosome 19." Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V. Lucas S.M.Nature 428:529-535(2004) [PubMed: 15057824] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
| [4] | Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. Venter J.C.Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
| [5] | "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). Tissue: Brain, Cervix, Muscle and Uterus. |
| [6] | "MBD2-MBD3 complex binds to hemi-methylated DNA and forms a complex containing DNMT1 at the replication foci in late S phase." Tatematsu K., Yamazaki T., Ishikawa F. Genes Cells 5:677-688(2000) [PubMed: 10947852] [Abstract] Cited for: FUNCTION, HETERODIMERIZATION WITH MBD2, INTERACTION WITH DNMT1. |
| [7] | "Stable histone deacetylase complexes distinguished by the presence of SANT domain proteins CoREST/kiaa0071 and Mta-L1." Humphrey G.W., Wang Y., Russanova V.R., Hirai T., Qin J., Nakatani Y., Howard B.H. J. Biol. Chem. 276:6817-6824(2001) [PubMed: 11102443] [Abstract] Cited for: INTERACTION WITH THE HDAC1 COMPLEX, MASS SPECTROMETRY. |
| [8] | "The mCpG-binding domain of human MBD3 does not bind to mCpG but interacts with NuRD/Mi2 components HDAC1 and MTA2." Saito M., Ishikawa F. J. Biol. Chem. 277:35434-35439(2002) [PubMed: 12124384] [Abstract] Cited for: FUNCTION, INTERACTION WITH HDAC1; MTA2 AND THE NURD COMPLEX, MUTAGENESIS OF HIS-30 AND PHE-34. |
| [9] | "Two highly related p66 proteins comprise a new family of potent transcriptional repressors interacting with MBD2 and MBD3." Brackertz M., Boeke J., Zhang R., Renkawitz R. J. Biol. Chem. 277:40958-40966(2002) [PubMed: 12183469] [Abstract] Cited for: INTERACTION WITH P66ALPHA AND P66BETA. |
| [10] | "Identification and functional characterization of the p66/p68 components of the MeCP1 complex." Feng Q., Cao R., Xia L., Erdjument-Bromage H., Tempst P., Zhang Y. Mol. Cell. Biol. 22:536-546(2002) [PubMed: 11756549] [Abstract] Cited for: INTERACTION WITH P66BETA AND THE MECP1 COMPLEX. |
| [11] | "A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-56, MASS SPECTROMETRY. Tissue: Cervix carcinoma. |
| [12] | "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed: 19690332] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-56 AND SER-144, MASS SPECTROMETRY. Tissue: Leukemic T-cell. |
| [13] | "Lysine acetylation targets protein complexes and co-regulates major cellular functions." Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T., Olsen J.V., Mann M. Science 325:834-840(2009) [PubMed: 19608861] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-4; LYS-109 AND LYS-141, MASS SPECTROMETRY. |
| [14] | "Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed: 21269460] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. |
| + | Additional computationally mapped references. |
Cross-references
Sequence databases | |
|---|---|
| EMBL GenBank DDBJ | AF072247 mRNA. Translation: AAC68876.1. AK290882 mRNA. Translation: BAF83571.1. AC005943 Genomic DNA. Translation: AAC72104.1. CH471139 Genomic DNA. Translation: EAW69477.1. CH471139 Genomic DNA. Translation: EAW69478.1. CH471139 Genomic DNA. Translation: EAW69481.1. BC009372 mRNA. Translation: AAH09372.1. BC009438 mRNA. Translation: AAH09438.1. BC032443 mRNA. Translation: AAH32443.1. Different initiation. BC043619 mRNA. Translation: AAH43619.1. |
| IPI | IPI00439194. IPI00439195. |
| RefSeq | NP_003917.1. NM_003926.5. |
| UniGene | Hs.178728. |
3D structure databases | |
| ProteinModelPortal | O95983. |
| SMR | O95983. Positions 2-69, 216-249. |
| ModBase | Search... |
Protein-protein interaction databases | |
| IntAct | O95983. 10 interactions. |
| STRING | O95983. |
PTM databases | |
| PhosphoSite | O95983. |
Proteomic databases | |
| PRIDE | O95983. |
Protocols and materials databases | |
| StructuralBiologyKnowledgebase | Search... |
Genome annotation databases | |
| Ensembl | ENST00000156825; ENSP00000156825; ENSG00000071655. ENST00000355664; ENSP00000347886; ENSG00000071655. |
| GeneID | 53615. |
| KEGG | hsa:53615. |
| UCSC | uc002ltj.2. human. uc002ltk.2. human. |
Organism-specific databases | |
| CTD | 53615. |
| GeneCards | GC19M001576. |
| H-InvDB | HIX0014590. |
| HGNC | HGNC:6918. MBD3. |
| HPA | CAB013265. |
| MIM | 603573. gene. |
| neXtProt | NX_O95983. |
| PharmGKB | PA30661. |
| GenAtlas | Search... |
Phylogenomic databases | |
| eggNOG | prNOG12869. |
| GeneTree | ENSGT00410000025376. |
| HOGENOM | HBG315648. |
| HOVERGEN | HBG052417. |
| InParanoid | O95983. |
| OMA | RQRMRYD. |
| OrthoDB | EOG4GF3FS. |
| PhylomeDB | O95983. |
Enzyme and pathway databases | |
| Pathway_Interaction_DB | hdac_classi_pathway. Signaling events mediated by HDAC Class I. |
Gene expression databases | |
| ArrayExpress | O95983. |
| Bgee | O95983. |
| CleanEx | HS_MBD3. |
| Genevestigator | O95983. |
| GermOnline | ENSG00000071655. Homo sapiens. |
Family and domain databases | |
| InterPro | IPR016177. DNA-bd_integrase-typ. IPR001739. Methyl_CpG_DNA-bd. [Graphical view] |
| Gene3D | G3DSA:3.30.890.10. Methyl_CpG_DNA-bd. 1 hit. |
| KO | K11591. |
| Pfam | PF01429. MBD. 1 hit. [Graphical view] |
| SMART | SM00391. MBD. 1 hit. [Graphical view] |
| SUPFAM | SSF54171. DNA-binding_integrase-type. 1 hit. |
| PROSITE | PS50982. MBD. 1 hit. [Graphical view] |
| ProtoNet | Search... |
Other | |
| NextBio | 56092. |
| SOURCE | Search... |
Entry information
| Entry name | MBD3_HUMAN | ||||||||
| Accession | Primary (citable) accession number: O95983 Secondary accession number(s): A8K4B7 Q86XF4 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation program | Chordata Protein Annotation Program | ||||||||
| Disclaimer | Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care. | ||||||||
Relevant documents
| Human chromosome 19 Human chromosome 19: entries, gene names and cross-references to MIM |
| MIM cross-references Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot |
| SIMILARITY comments Index of protein domains and families |

Clusters with