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Protein

Methyl-CpG-binding domain protein 3

Gene

MBD3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Acts as transcriptional repressor and plays a role in gene silencing. Does not bind to DNA by itself (PubMed:12124384). Binds to DNA with a preference for sites containing methylated CpG dinucleotides (in vitro). Binds to a lesser degree DNA containing unmethylated CpG dinucleotides (PubMed:24307175). Recruits histone deacetylases and DNA methyltransferases.6 Publications

GO - Molecular functioni

  • chromatin binding Source: Ensembl
  • DNA binding Source: ProtInc
  • histone deacetylase activity Source: Reactome
  • methyl-CpG binding Source: UniProtKB

GO - Biological processi

Keywordsi

Molecular functionDNA-binding
Biological processTranscription, Transcription regulation

Enzyme and pathway databases

ReactomeiR-HSA-3214815 HDACs deacetylate histones
R-HSA-427389 ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
R-HSA-6804758 Regulation of TP53 Activity through Acetylation
R-HSA-73762 RNA Polymerase I Transcription Initiation
R-HSA-8943724 Regulation of PTEN gene transcription
SIGNORiO95983

Names & Taxonomyi

Protein namesi
Recommended name:
Methyl-CpG-binding domain protein 3
Alternative name(s):
Methyl-CpG-binding protein MBD3
Gene namesi
Name:MBD3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 19

Organism-specific databases

EuPathDBiHostDB:ENSG00000071655.17
HGNCiHGNC:6918 MBD3
MIMi603573 gene
neXtProtiNX_O95983

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi30H → K: No effect. Confers strong binding to methylated CpG (in vitro); when associated with Y-34. 2 Publications1
Mutagenesisi34F → A: Augments DNA binding activity, irrespective of DNA methylation. 2 Publications1
Mutagenesisi34F → Y: Confers weak binding to methylated CpG (in vitro). Confers strong binding to methylated CpG (in vitro); when associated with K-30. 2 Publications1

Organism-specific databases

DisGeNETi53615
OpenTargetsiENSG00000071655
PharmGKBiPA30661

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000962621 – 291Methyl-CpG-binding domain protein 3Add BLAST291

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei56PhosphoserineCombined sources1
Cross-linki73Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei85PhosphoserineCombined sources1
Cross-linki90Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki92Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei144PhosphoserineCombined sources1

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiO95983
MaxQBiO95983
PaxDbiO95983
PeptideAtlasiO95983
PRIDEiO95983
ProteomicsDBi51159
51160 [O95983-2]

PTM databases

iPTMnetiO95983
PhosphoSitePlusiO95983

Expressioni

Gene expression databases

BgeeiENSG00000071655
CleanExiHS_MBD3
ExpressionAtlasiO95983 baseline and differential
GenevisibleiO95983 HS

Organism-specific databases

HPAiCAB013265

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.6 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi119788, 90 interactors
ComplexPortaliCPX-922 MBD3/NuRD nucleosome remodeling and deacetylase complex
CORUMiO95983
DIPiDIP-46517N
IntActiO95983, 77 interactors
MINTiO95983
STRINGi9606.ENSP00000156825

Structurei

Secondary structure

1291
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 7Combined sources4
Beta strandi16 – 21Combined sources6
Turni26 – 29Combined sources4
Beta strandi31 – 36Combined sources6
Helixi46 – 53Combined sources8
Turni54 – 56Combined sources3
Turni64 – 67Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2MB7NMR-A1-70[»]
6CC8X-ray1.95A/B1-71[»]
6CCGX-ray1.90A/B1-71[»]
6CEUX-ray2.00A/B1-71[»]
6CEVX-ray2.00A/B1-71[»]
ProteinModelPortaliO95983
SMRiO95983
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 72MBDPROSITE-ProRule annotationAdd BLAST72

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili216 – 245Sequence analysisAdd BLAST30

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi272 – 281Poly-Glu10

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiENOG410INB5 Eukaryota
ENOG410XSPC LUCA
GeneTreeiENSGT00410000025376
HOGENOMiHOG000013073
HOVERGENiHBG052417
InParanoidiO95983
KOiK11591
OMAiRQRMRYD
OrthoDBiEOG091G0I05
PhylomeDBiO95983
TreeFamiTF325032

Family and domain databases

InterProiView protein in InterPro
IPR016177 DNA-bd_dom_sf
IPR032343 MBD2/MBD3_p55-bd
IPR037965 MBD3
IPR025884 MeCpG-bd_2/3_C_dom
IPR001739 Methyl_CpG_DNA-bd
PANTHERiPTHR12396:SF12 PTHR12396:SF12, 1 hit
PfamiView protein in Pfam
PF01429 MBD, 1 hit
PF14048 MBD_C, 1 hit
PF16564 MBDa, 1 hit
SMARTiView protein in SMART
SM00391 MBD, 1 hit
SUPFAMiSSF54171 SSF54171, 1 hit
PROSITEiView protein in PROSITE
PS50982 MBD, 1 hit

Sequences (2)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: O95983-1) [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 MSKMNKSRQR VRYDSSNQVK GKPDLNTALP
110 120 130 140 150
VRQTASIFKQ PVTKITNHPS NKVKSDPQKA VDQPRQLFWE KKLSGLNAFD
160 170 180 190 200
IAEELVKTMD LPKGLQGVGP GCTDETLLSA IASALHTSTM PITGQLSAAV
210 220 230 240 250
EKNPGVWLNT TQPLCKAFMV TDEDIRKQEE LVQQVRKRLE EALMADMLAH
260 270 280 290
VEELARDGEA PLDKACAEDD DEEDEEEEEE EPDPDPEMEH V
Length:291
Mass (Da):32,844
Last modified:May 1, 1999 - v1
Checksum:iB62134DD1BEB636B
GO
Isoform 2 (identifier: O95983-2) [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:259
Mass (Da):29,014
Checksum:i2578753C1E5D6A0B
GO

Sequence cautioni

The sequence AAH32443 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0110815 – 36Missing in isoform 2. 1 PublicationAdd BLAST32

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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
CCDSiCCDS12072.1 [O95983-1]
CCDS62481.1 [O95983-2]
RefSeqiNP_001268382.1, NM_001281453.1 [O95983-1]
NP_001268383.1, NM_001281454.1 [O95983-2]
UniGeneiHs.178728
Hs.595754

Genome annotation databases

EnsembliENST00000156825; ENSP00000156825; ENSG00000071655 [O95983-2]
ENST00000434436; ENSP00000412302; ENSG00000071655 [O95983-1]
GeneIDi53615
KEGGihsa:53615
UCSCiuc002ltj.5 human [O95983-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiMBD3_HUMAN
AccessioniPrimary (citable) accession number: O95983
Secondary accession number(s): A8K4B7
, D6W5Z2, Q6PIL9, Q6PJZ9, Q86XF4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: May 1, 1999
Last modified: June 20, 2018
This is version 154 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references

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