Methyl-CpG-binding domain protein 4

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Reviewed, UniProtKB/Swiss-Prot Q9Z2D7 (MBD4_MOUSE)

Last modified May 26, 2009. Version 68. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

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 names

Name:

Mbd4

Organism

Mus musculus (Mouse)

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus

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Protein attributes

Sequence length	554 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	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. Ref.1
Subunit structure	Interacts with MLH1 By similarity.
Subcellular location	Nucleus. Note: Nuclear, in discrete foci. Ref.1
Sequence similarities	Contains 1 MBD (methyl-CpG-binding) domain.

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Ontologies

Keywords
Biological process	DNA damage DNA repair
Cellular component	Nucleus
Ligand	DNA-binding
Molecular function	Hydrolase
Technical term	3D-structure
Gene Ontology (GO)
Biological process	DNA damage response, signal transduction resulting in induction of apoptosis Inferred from mutant phenotype. Source: MGI DNA methylation Traceable author statement. Source: MGI base-excision repair Inferred from electronic annotation. Source: InterPro response to radiation Inferred from mutant phenotype. Source: MGI
Cellular component	chromatin Ref.1 Inferred from direct assay. Source: MGI cytoplasm Inferred from direct assay. Source: MGI nucleus Ref.1 Inferred from direct assay. Source: MGI
Molecular function	DNA binding Ref.1 Inferred from direct assay. Source: MGI hydrolase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 554

554

Methyl-CpG-binding domain protein 4

PRO_0000096265

Regions

Domain

63 – 135

MBD

Sites

Active site

534

By similarity

Experimental info

Sequence conflict

129

N → D in AAH24812. Ref.3

Secondary structure

554

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

Q9Z2D7-1 [UniParc].

Last modified May 1, 1999. Version 1.
Checksum: 792D37CB180291F5
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FASTA

554

62,578

        10         20         30         40         50         60 
MESPNLGDNR VRGESLVPDP PWDRCKEDIA VGLGGVGEDG KDLVISSERS SLLQEPTAST 

        70         80         90        100        110        120 
LSSTTATEGH KPVPCGWERV VKQRLSGKTA GKFDVYFISP QGLKFRSKRS LANYLLKNGE 

       130        140        150        160        170        180 
TFLKPEDFNF TVLPKGSINP GYKHQSLAAL TSLQPNETDV SKQNLKTRSK WKTDVLPLPS 

       190        200        210        220        230        240 
GTSESPESSG LSNSNSACLL LREHRDIQDV DSEKRRKSKR KVTVLKGTAS QKTKQKCRKS 

       250        260        270        280        290        300 
LLESTQRNRK RASVVQKVGA DRELVPQESQ LNRTLCPADA CARETVGLAG EEKSPSPGLD 

       310        320        330        340        350        360 
LCFIQVTSGT TNKFHSTEAA GEANREQTFL ESEEIRSKGD RKGEAHLHTG VLQDGSEMPS 

       370        380        390        400        410        420 
CSQAKKHFTS ETFQEDSIPR TQVEKRKTSL YFSSKYNKEA LSPPRRKSFK KWTPPRSPFN 

       430        440        450        460        470        480 
LVQEILFHDP WKLLIATIFL NRTSGKMAIP VLWEFLEKYP SAEVARAADW RDVSELLKPL 

       490        500        510        520        530        540 
GLYDLRAKTI IKFSDEYLTK QWRYPIELHG IGKYGNDSYR IFCVNEWKQV HPEDHKLNKY 

       550 
HDWLWENHEK LSLS

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References

	« Hide 'large scale' referencesShow '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, 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: 10441743] [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: 15489334] [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: 12456671] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 411-554.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

AF072249 mRNA. Translation: AAC68878.1.
AF120996 Genomic DNA. Translation: AAD56595.1.
BC024812 mRNA. Translation: AAH24812.1.

IPI

IPI00321709.

RefSeq

NP_034904.2.

UniGene

Mm.259308

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NGN	X-ray	2.10	A	400-554	[»]

ModBase

Search...

PTM databases

PhosphoSite

Q9Z2D7.

Genome annotation databases

Ensembl

ENSMUSG00000030322. Mus musculus. [Contig view]

GeneID

17193.

KEGG

mmu:17193.

Organism-specific databases

MGI

MGI:1333850. Mbd4.

Phylogenomic databases

HOGENOM

Q9Z2D7.

HOVERGEN

Q9Z2D7.

Gene expression databases

ArrayExpress

Q9Z2D7.

Bgee

Q9Z2D7.

CleanEx

MM_MBD4.

GermOnline

ENSMUSG00000030322. Mus musculus.

Family and domain databases

InterPro

IPR003265. HhH-GPD_domain.
IPR017352. Methyl_CpG-bd_MBD4.
IPR001739. Methyl_CpG_DNA-bd.
[Graphical view]

Pfam

PF00730. HhH-GPD. 1 hit.
PF01429. MBD. 1 hit.
[Graphical view]

PIRSF

PIRSF038005. Methyl_CpG_bd_MBD4. 1 hit.

SMART

SM00391. MBD. 1 hit.
[Graphical view]

PROSITE

PS50982. MBD. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

SOURCE

Search...

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Entry information

Entry name

MBD4_MOUSE

Accession

Primary (citable) accession number: Q9Z2D7
Secondary accession number(s): Q792D2, Q8R3R3

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 19, 2004
Last sequence update:	May 1, 1999
Last modified:	May 26, 2009
This is version 68 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

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Relevant documents

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families