Methyl-CpG-binding domain protein 4

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Q9Z2D7 (MBD4_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 99. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

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) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	554 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

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.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Cellular component	Nucleus
Ligand	DNA-binding
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA methylation Traceable author statement PubMed 11336497. Source: MGI G2 DNA damage checkpoint Inferred from mutant phenotype PubMed 14614141. Source: MGI base-excision repair Inferred from electronic annotation. Source: InterPro intrinsic apoptotic signaling pathway in response to DNA damage Inferred from mutant phenotype PubMed 14562041. Source: MGI response to radiation Inferred from mutant phenotype PubMed 14562041. Source: MGI
Cellular_component	chromatin Inferred from direct assay Ref.1. Source: MGI cytoplasm Inferred from direct assay PubMed 17546630. Source: MGI nucleus Inferred from direct assay PubMed 17546630 Ref.1. Source: MGI
Molecular_function	DNA binding Inferred from direct assay Ref.1. Source: MGI pyrimidine-specific mismatch base pair DNA N-glycosylase activity Inferred from electronic annotation. Source: Compara
Complete GO annotation...

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...

Sequences

Sequence

Length

Mass (Da)

Tools

Q9Z2D7 [UniParc].

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

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

« Hide

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] [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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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

IPI

IPI00321709.

RefSeq

NP_034904.2. NM_010774.2.

UniGene

Mm.259308.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NGN	X-ray	2.10	A	400-554	[»]
3VXV	X-ray	2.00	A	69-136	[»]
3VXX	X-ray	2.20	A	69-136	[»]
3VYB	X-ray	2.40	A	69-136	[»]
3VYQ	X-ray	2.52	A/D	63-136	[»]
4EVV	X-ray	2.39	A	411-554	[»]
4EW0	X-ray	2.39	A	411-554	[»]
4EW4	X-ray	2.79	A	411-554	[»]

ProteinModelPortal

Q9Z2D7.

SMR

Q9Z2D7. Positions 73-132, 411-554.

ModBase

Search...

PTM databases

PhosphoSite

Q9Z2D7.

Proteomic databases

PaxDb

Q9Z2D7.

PRIDE

Q9Z2D7.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENSMUST00000032469; ENSMUSP00000032469; ENSMUSG00000030322.

GeneID

17193.

KEGG

mmu:17193.

UCSC

uc009dje.2. mouse.

Organism-specific databases

CTD

8930.

MGI

MGI:1333850. Mbd4.

Phylogenomic databases

eggNOG

NOG264445.

GeneTree

ENSGT00530000063687.

HOGENOM

HOG000113489.

HOVERGEN

HBG052418.

InParanoid

Q9Z2D7.

K10801.

OrthoDB

EOG48GW3R.

Gene expression databases

ArrayExpress

Q9Z2D7.

Bgee

Q9Z2D7.

CleanEx

MM_MBD4.

Genevestigator

Q9Z2D7.

GermOnline

ENSMUSG00000030322. Mus musculus.

Family and domain databases

Gene3D

1.10.340.30. 1 hit.
3.30.890.10. 1 hit.

InterPro

IPR016177. DNA-bd_integrase-typ.
IPR011257. DNA_glycosylase.
IPR003265. HhH-GPD_domain.
IPR017352. Me_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]

SUPFAM

SSF54171. DNA-binding_integrase-type. 1 hit.
SSF48150. DNA_glycsylse. 1 hit.

PROSITE

PS50982. MBD. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q9Z2D7.

NextBio

291542.

SOURCE

Search...

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 1, 2013
This is version 99 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

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

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

PTM databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents