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Protein

Methyl-CpG-binding domain protein 3

Gene

Mbd3

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Acts as transcriptional repressor and plays a role in gene silencing. Does not bind DNA by itself. Binds to DNA with a preference for sites containing methylated CpG dinucleotides (in vitro). Binds to a lesser degree DNA containing unmethylated CpG dinucleotides (By similarity). Recruits histone deacetylases and DNA methyltransferases.By similarity1 Publication

GO - Molecular functioni

GO - Biological processi

  • aging Source: Ensembl
  • ATP-dependent chromatin remodeling Source: MGI
  • brain development Source: Ensembl
  • embryonic organ development Source: Ensembl
  • heart development Source: Ensembl
  • histone acetylation Source: MGI
  • in utero embryonic development Source: MGI
  • methylation-dependent chromatin silencing Source: MGI
  • negative regulation of transcription from RNA polymerase II promoter Source: MGI
  • regulation of DNA methylation Source: Ensembl
  • response to estradiol Source: Ensembl
  • response to nutrient levels Source: Ensembl
  • tissue development Source: MGI
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-MMU-73762. RNA Polymerase I Transcription Initiation.

Names & Taxonomyi

Protein namesi
Recommended name:
Methyl-CpG-binding domain protein 3
Alternative name(s):
Methyl-CpG-binding protein MBD3
Gene namesi
Name:Mbd3
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 10

Organism-specific databases

MGIiMGI:1333812. Mbd3.

Subcellular locationi

  • Nucleus 2 Publications
  • Chromosome By similarity

  • Note: Detected on chromatin, at promoter regions of active genes (By similarity). Nuclear, in discrete foci.By similarity

GO - Cellular componenti

  • chromatin Source: MGI
  • cytoplasm Source: MGI
  • heterochromatin Source: MGI
  • nuclear chromatin Source: MGI
  • nucleus Source: MGI
  • NuRD complex Source: MGI
  • protein complex Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 285285Methyl-CpG-binding domain protein 3PRO_0000096263Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei56 – 561PhosphoserineCombined sources
Modified residuei85 – 851PhosphoserineBy similarity
Modified residuei144 – 1441PhosphoserineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9Z2D8.
MaxQBiQ9Z2D8.
PaxDbiQ9Z2D8.
PRIDEiQ9Z2D8.

PTM databases

PhosphoSiteiQ9Z2D8.

Expressioni

Tissue specificityi

Highly expressed in brain, heart, kidney, liver, lung, skeletal muscle, spleen and testis. Detected at lower levels in embryonic stem cells.1 Publication

Gene expression databases

BgeeiQ9Z2D8.
CleanExiMM_MBD3.
ExpressionAtlasiQ9Z2D8. baseline and differential.
GenevisibleiQ9Z2D8. MM.

Interactioni

Subunit structurei

Heterodimer with MBD2. Part of the NuRD and the MeCP1 complex. Interacts with BCL6, HDAC1, MTA2, DNMT1, p66-alpha and p66-beta (By similarity).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
MecomP144045EBI-1994598,EBI-1994523

Protein-protein interaction databases

BioGridi201332. 15 interactions.
DIPiDIP-46518N.
IntActiQ9Z2D8. 11 interactions.
MINTiMINT-4101368.
STRINGi10090.ENSMUSP00000089948.

Structurei

3D structure databases

ProteinModelPortaliQ9Z2D8.
SMRiQ9Z2D8. Positions 1-69, 216-249.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 6969MBDPROSITE-ProRule annotationAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili221 – 27959Sequence analysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi229 – 28355Glu-richAdd
BLAST

Sequence similaritiesi

Contains 1 MBD (methyl-CpG-binding) domain.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG4161. Eukaryota.
ENOG4111HPQ. LUCA.
GeneTreeiENSGT00410000025376.
HOGENOMiHOG000013073.
HOVERGENiHBG052417.
InParanoidiQ9Z2D8.
KOiK11591.
OMAiQDQEMEH.
PhylomeDBiQ9Z2D8.
TreeFamiTF325032.

Family and domain databases

Gene3Di3.30.890.10. 2 hits.
InterProiIPR016177. DNA-bd_dom.
IPR032343. MBD2/MBD3_p55-bd.
IPR025884. MeCpG-bd_2/3_C_dom.
IPR001739. Methyl_CpG_DNA-bd.
[Graphical view]
PfamiPF01429. MBD. 1 hit.
PF14048. MBD_C. 1 hit.
PF16564. MBDa. 1 hit.
[Graphical view]
SMARTiSM00391. MBD. 1 hit.
[Graphical view]
SUPFAMiSSF54171. SSF54171. 1 hit.
PROSITEiPS50982. MBD. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9Z2D8-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MERKRWECPA LPQGWEREEV PRRSGLSAGH RDVFYYSPSG KKFRSKPQLA
60 70 80 90 100
RYLGGSMDLS TFDFRTGKML MNKMNKSRQR VRYDSSNQVK GKPDLNTALP
110 120 130 140 150
VRQTASIFKQ PVTKITNHPS NKVKSDPQKA VDQPRQLFWE KKLSGLSAFD
160 170 180 190 200
IAEELVRTMD LPKGLQGVGP GCTDETLLSA IASALHTSTL PITGQLSAAV
210 220 230 240 250
EKNPGVWLNT AQPLCKAFMV TDDDIRKQEE LVQQVRKRLE EALMADMLAH
260 270 280
VEELARDGEA PLDKACAEEE EEEEEEEEEP EPERV
Length:285
Mass (Da):32,168
Last modified:May 1, 1999 - v1
Checksum:iE4E57BD48463643F
GO
Isoform 2 (identifier: Q9Z2D8-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     5-36: Missing.

Note: No experimental confirmation available.
Show »
Length:253
Mass (Da):28,338
Checksum:iAD85860066812B03
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei5 – 3632Missing in isoform 2. 1 PublicationVSP_011082Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF072248 mRNA. Translation: AAC68877.1.
AF120995 Genomic DNA. Translation: AAD48909.1.
BC038264 mRNA. Translation: AAH38264.1.
CCDSiCCDS24020.1. [Q9Z2D8-1]
CCDS78860.1. [Q9Z2D8-2]
RefSeqiNP_001293072.1. NM_001306143.1. [Q9Z2D8-2]
NP_038623.1. NM_013595.3. [Q9Z2D8-1]
UniGeneiMm.7142.

Genome annotation databases

EnsembliENSMUST00000092295; ENSMUSP00000089948; ENSMUSG00000035478. [Q9Z2D8-1]
ENSMUST00000105349; ENSMUSP00000100986; ENSMUSG00000035478. [Q9Z2D8-2]
GeneIDi17192.
KEGGimmu:17192.
UCSCiuc007gda.1. mouse. [Q9Z2D8-2]
uc007gdb.1. mouse. [Q9Z2D8-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF072248 mRNA. Translation: AAC68877.1.
AF120995 Genomic DNA. Translation: AAD48909.1.
BC038264 mRNA. Translation: AAH38264.1.
CCDSiCCDS24020.1. [Q9Z2D8-1]
CCDS78860.1. [Q9Z2D8-2]
RefSeqiNP_001293072.1. NM_001306143.1. [Q9Z2D8-2]
NP_038623.1. NM_013595.3. [Q9Z2D8-1]
UniGeneiMm.7142.

3D structure databases

ProteinModelPortaliQ9Z2D8.
SMRiQ9Z2D8. Positions 1-69, 216-249.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi201332. 15 interactions.
DIPiDIP-46518N.
IntActiQ9Z2D8. 11 interactions.
MINTiMINT-4101368.
STRINGi10090.ENSMUSP00000089948.

PTM databases

PhosphoSiteiQ9Z2D8.

Proteomic databases

EPDiQ9Z2D8.
MaxQBiQ9Z2D8.
PaxDbiQ9Z2D8.
PRIDEiQ9Z2D8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000092295; ENSMUSP00000089948; ENSMUSG00000035478. [Q9Z2D8-1]
ENSMUST00000105349; ENSMUSP00000100986; ENSMUSG00000035478. [Q9Z2D8-2]
GeneIDi17192.
KEGGimmu:17192.
UCSCiuc007gda.1. mouse. [Q9Z2D8-2]
uc007gdb.1. mouse. [Q9Z2D8-1]

Organism-specific databases

CTDi53615.
MGIiMGI:1333812. Mbd3.

Phylogenomic databases

eggNOGiKOG4161. Eukaryota.
ENOG4111HPQ. LUCA.
GeneTreeiENSGT00410000025376.
HOGENOMiHOG000013073.
HOVERGENiHBG052417.
InParanoidiQ9Z2D8.
KOiK11591.
OMAiQDQEMEH.
PhylomeDBiQ9Z2D8.
TreeFamiTF325032.

Enzyme and pathway databases

ReactomeiR-MMU-73762. RNA Polymerase I Transcription Initiation.

Miscellaneous databases

ChiTaRSiMbd3. mouse.
NextBioi291538.
PROiQ9Z2D8.
SOURCEiSearch...

Gene expression databases

BgeeiQ9Z2D8.
CleanExiMM_MBD3.
ExpressionAtlasiQ9Z2D8. baseline and differential.
GenevisibleiQ9Z2D8. MM.

Family and domain databases

Gene3Di3.30.890.10. 2 hits.
InterProiIPR016177. DNA-bd_dom.
IPR032343. MBD2/MBD3_p55-bd.
IPR025884. MeCpG-bd_2/3_C_dom.
IPR001739. Methyl_CpG_DNA-bd.
[Graphical view]
PfamiPF01429. MBD. 1 hit.
PF14048. MBD_C. 1 hit.
PF16564. MBDa. 1 hit.
[Graphical view]
SMARTiSM00391. MBD. 1 hit.
[Graphical view]
SUPFAMiSSF54171. SSF54171. 1 hit.
PROSITEiPS50982. MBD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE (ISOFORM 1), FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
  2. "Genomic structure and chromosomal mapping of the murine and human mbd1, mbd2, mbd3, and mbd4 genes."
    Hendrich B., Abbott C., McQueen H., Chambers D., Cross S.H., Bird A.
    Mamm. Genome 10:906-912(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: 129.
  3. "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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Strain: C57BL/6J.
    Tissue: Mammary tumor.
  4. "Role of human ribosomal RNA (rRNA) promoter methylation and of methyl-CpG-binding protein MBD2 in the suppression of rRNA gene expression."
    Ghoshal K., Majumder S., Datta J., Motiwala T., Bai S., Sharma S.M., Frankel W., Jacob S.T.
    J. Biol. Chem. 279:6783-6793(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  5. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-56, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Brown adipose tissue, Heart, Kidney, Lung and Spleen.

Entry informationi

Entry nameiMBD3_MOUSE
AccessioniPrimary (citable) accession number: Q9Z2D8
Secondary accession number(s): Q792D3, Q8CFJ1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: May 1, 1999
Last modified: April 13, 2016
This is version 123 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.