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Protein

Methyl-CpG-binding domain protein 4

Gene

Mbd4

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

Functioni

Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase activity and is specific for G:T mismatches within methylated and unmethylated CpG sites. Can also remove uracil or 5-fluorouracil in G:U mismatches. Has no lyase activity. Was first identified as methyl-CpG-binding protein.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei534 – 5341By similarity

GO - Molecular functioni

GO - Biological processi

  • base-excision repair Source: InterPro
  • cellular response to DNA damage stimulus Source: MGI
  • DNA methylation Source: MGI
  • DNA repair Source: GO_Central
  • intrinsic apoptotic signaling pathway in response to DNA damage Source: MGI
  • mitotic G2 DNA damage checkpoint Source: MGI
  • response to radiation Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiREACT_338868. Displacement of DNA glycosylase by APEX1.
REACT_342323. Cleavage of the damaged pyrimidine.

Names & Taxonomyi

Protein namesi
Recommended name:
Methyl-CpG-binding domain protein 4 (EC:3.2.2.-)
Alternative name(s):
Methyl-CpG-binding protein MBD4
Mismatch-specific DNA N-glycosylase
Gene namesi
Name:Mbd4
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Unplaced

Organism-specific databases

MGIiMGI:1333850. Mbd4.

Subcellular locationi

  • Nucleus 1 Publication

  • Note: Nuclear, in discrete foci.

GO - Cellular componenti

  • chromatin Source: MGI
  • cytoplasm Source: MGI
  • nucleoplasm Source: MGI
  • nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 554554Methyl-CpG-binding domain protein 4PRO_0000096265Add
BLAST

Proteomic databases

PaxDbiQ9Z2D7.
PRIDEiQ9Z2D7.

PTM databases

PhosphoSiteiQ9Z2D7.

Expressioni

Gene expression databases

BgeeiQ9Z2D7.
CleanExiMM_MBD4.
ExpressionAtlasiQ9Z2D7. baseline and differential.
GenevestigatoriQ9Z2D7.

Interactioni

Subunit structurei

Interacts with MLH1.By similarity

Protein-protein interaction databases

BioGridi201333. 2 interactions.

Structurei

Secondary structure

1
554
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi78 – 836Combined sources
Turni88 – 914Combined sources
Beta strandi93 – 986Combined sources
Beta strandi104 – 1074Combined sources
Helixi108 – 11811Combined sources
Helixi125 – 1273Combined sources
Helixi423 – 4264Combined sources
Helixi430 – 44011Combined sources
Helixi445 – 45814Combined sources
Helixi462 – 4676Combined sources
Helixi470 – 4767Combined sources
Helixi478 – 4803Combined sources
Helixi483 – 49917Combined sources
Helixi505 – 5073Combined sources
Helixi513 – 52210Combined sources
Helixi527 – 5293Combined sources
Helixi535 – 55117Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NGNX-ray2.10A400-554[»]
3VXVX-ray2.00A69-136[»]
3VXXX-ray2.20A69-136[»]
3VYBX-ray2.40A69-136[»]
3VYQX-ray2.52A/D63-136[»]
4EVVX-ray2.39A411-554[»]
4EW0X-ray2.39A411-554[»]
4EW4X-ray2.79A411-554[»]
ProteinModelPortaliQ9Z2D7.
SMRiQ9Z2D7. Positions 71-135, 411-554.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9Z2D7.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini63 – 13573MBDPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiNOG264445.
HOGENOMiHOG000113489.
HOVERGENiHBG052418.
InParanoidiQ9Z2D7.
KOiK10801.
OrthoDBiEOG74N5J9.
PhylomeDBiQ9Z2D7.
TreeFamiTF329176.

Family and domain databases

Gene3Di1.10.340.30. 1 hit.
3.30.890.10. 1 hit.
InterProiIPR016177. DNA-bd_dom.
IPR011257. DNA_glycosylase.
IPR003265. HhH-GPD_domain.
IPR017352. MBD4.
IPR001739. Methyl_CpG_DNA-bd.
[Graphical view]
PANTHERiPTHR15074:SF2. PTHR15074:SF2. 1 hit.
PfamiPF00730. HhH-GPD. 1 hit.
PF01429. MBD. 1 hit.
[Graphical view]
PIRSFiPIRSF038005. Methyl_CpG_bd_MBD4. 1 hit.
SMARTiSM00391. MBD. 1 hit.
[Graphical view]
SUPFAMiSSF48150. SSF48150. 1 hit.
SSF54171. SSF54171. 1 hit.
PROSITEiPS50982. MBD. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9Z2D7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MESPNLGDNR VRGESLVPDP PWDRCKEDIA VGLGGVGEDG KDLVISSERS
60 70 80 90 100
SLLQEPTAST LSSTTATEGH KPVPCGWERV VKQRLSGKTA GKFDVYFISP
110 120 130 140 150
QGLKFRSKRS LANYLLKNGE TFLKPEDFNF TVLPKGSINP GYKHQSLAAL
160 170 180 190 200
TSLQPNETDV SKQNLKTRSK WKTDVLPLPS GTSESPESSG LSNSNSACLL
210 220 230 240 250
LREHRDIQDV DSEKRRKSKR KVTVLKGTAS QKTKQKCRKS LLESTQRNRK
260 270 280 290 300
RASVVQKVGA DRELVPQESQ LNRTLCPADA CARETVGLAG EEKSPSPGLD
310 320 330 340 350
LCFIQVTSGT TNKFHSTEAA GEANREQTFL ESEEIRSKGD RKGEAHLHTG
360 370 380 390 400
VLQDGSEMPS CSQAKKHFTS ETFQEDSIPR TQVEKRKTSL YFSSKYNKEA
410 420 430 440 450
LSPPRRKSFK KWTPPRSPFN LVQEILFHDP WKLLIATIFL NRTSGKMAIP
460 470 480 490 500
VLWEFLEKYP SAEVARAADW RDVSELLKPL GLYDLRAKTI IKFSDEYLTK
510 520 530 540 550
QWRYPIELHG IGKYGNDSYR IFCVNEWKQV HPEDHKLNKY HDWLWENHEK

LSLS
Length:554
Mass (Da):62,578
Last modified:May 1, 1999 - v1
Checksum:i792D37CB180291F5
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti129 – 1291N → D in AAH24812 (PubMed:15489334).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF072249 mRNA. Translation: AAC68878.1.
AF120996 Genomic DNA. Translation: AAD56595.1.
BC024812 mRNA. Translation: AAH24812.1.
CCDSiCCDS39603.1.
RefSeqiNP_034904.2. NM_010774.2.
UniGeneiMm.259308.

Genome annotation databases

GeneIDi17193.
KEGGimmu:17193.
UCSCiuc009dje.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF072249 mRNA. Translation: AAC68878.1.
AF120996 Genomic DNA. Translation: AAD56595.1.
BC024812 mRNA. Translation: AAH24812.1.
CCDSiCCDS39603.1.
RefSeqiNP_034904.2. NM_010774.2.
UniGeneiMm.259308.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NGNX-ray2.10A400-554[»]
3VXVX-ray2.00A69-136[»]
3VXXX-ray2.20A69-136[»]
3VYBX-ray2.40A69-136[»]
3VYQX-ray2.52A/D63-136[»]
4EVVX-ray2.39A411-554[»]
4EW0X-ray2.39A411-554[»]
4EW4X-ray2.79A411-554[»]
ProteinModelPortaliQ9Z2D7.
SMRiQ9Z2D7. Positions 71-135, 411-554.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi201333. 2 interactions.

PTM databases

PhosphoSiteiQ9Z2D7.

Proteomic databases

PaxDbiQ9Z2D7.
PRIDEiQ9Z2D7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi17193.
KEGGimmu:17193.
UCSCiuc009dje.2. mouse.

Organism-specific databases

CTDi8930.
MGIiMGI:1333850. Mbd4.

Phylogenomic databases

eggNOGiNOG264445.
HOGENOMiHOG000113489.
HOVERGENiHBG052418.
InParanoidiQ9Z2D7.
KOiK10801.
OrthoDBiEOG74N5J9.
PhylomeDBiQ9Z2D7.
TreeFamiTF329176.

Enzyme and pathway databases

ReactomeiREACT_338868. Displacement of DNA glycosylase by APEX1.
REACT_342323. Cleavage of the damaged pyrimidine.

Miscellaneous databases

EvolutionaryTraceiQ9Z2D7.
NextBioi291542.
PROiQ9Z2D7.
SOURCEiSearch...

Gene expression databases

BgeeiQ9Z2D7.
CleanExiMM_MBD4.
ExpressionAtlasiQ9Z2D7. baseline and differential.
GenevestigatoriQ9Z2D7.

Family and domain databases

Gene3Di1.10.340.30. 1 hit.
3.30.890.10. 1 hit.
InterProiIPR016177. DNA-bd_dom.
IPR011257. DNA_glycosylase.
IPR003265. HhH-GPD_domain.
IPR017352. MBD4.
IPR001739. Methyl_CpG_DNA-bd.
[Graphical view]
PANTHERiPTHR15074:SF2. PTHR15074:SF2. 1 hit.
PfamiPF00730. HhH-GPD. 1 hit.
PF01429. MBD. 1 hit.
[Graphical view]
PIRSFiPIRSF038005. Methyl_CpG_bd_MBD4. 1 hit.
SMARTiSM00391. MBD. 1 hit.
[Graphical view]
SUPFAMiSSF48150. SSF48150. 1 hit.
SSF54171. 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, FUNCTION, 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].
  4. "Mismatch repair in methylated DNA. Structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4."
    Wu P., Qiu C., Sohail A., Zhang X., Bhagwat A.S., Cheng X.
    J. Biol. Chem. 278:5285-5291(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 411-554.

Entry informationi

Entry nameiMBD4_MOUSE
AccessioniPrimary (citable) accession number: Q9Z2D7
Secondary accession number(s): Q792D2, Q8R3R3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: May 1, 1999
Last modified: May 27, 2015
This is version 116 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

3D-structure, Complete proteome, Reference proteome

Documents

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

External Data

Dasty 3

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 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.