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Q9Z2D7

- MBD4_MOUSE

UniProt

Q9Z2D7 - MBD4_MOUSE

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Protein
Methyl-CpG-binding domain protein 4
Gene
Mbd4
Organism
Mus musculus (Mouse)
Status
Reviewed - 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 – 5341 By similarity

GO - Molecular functioni

  1. DNA binding Source: MGI
  2. pyrimidine-specific mismatch base pair DNA N-glycosylase activity Source: Ensembl

GO - Biological processi

  1. DNA methylation Source: MGI
  2. base-excision repair Source: InterPro
  3. cellular response to DNA damage stimulus Source: MGI
  4. intrinsic apoptotic signaling pathway in response to DNA damage Source: MGI
  5. mitotic G2 DNA damage checkpoint Source: MGI
  6. 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_208690. Recognition and association of DNA glycosylase with site containing an affected pyrimidine.
REACT_220827. Displacement of DNA glycosylase by APE1.

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: Chromosome 6

Organism-specific databases

MGIiMGI:1333850. Mbd4.

Subcellular locationi

Nucleus
Note: Nuclear, in discrete foci.1 Publication

GO - Cellular componenti

  1. chromatin Source: MGI
  2. cytoplasm Source: MGI
  3. 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 4
PRO_0000096265Add
BLAST

Proteomic databases

PaxDbiQ9Z2D7.
PRIDEiQ9Z2D7.

PTM databases

PhosphoSiteiQ9Z2D7.

Expressioni

Gene expression databases

ArrayExpressiQ9Z2D7.
BgeeiQ9Z2D7.
CleanExiMM_MBD4.
GenevestigatoriQ9Z2D7.

Interactioni

Subunit structurei

Interacts with MLH1 By similarity.

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.

Miscellaneous databases

EvolutionaryTraceiQ9Z2D7.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini63 – 13573MBD
Add
BLAST

Sequence similaritiesi

Phylogenomic databases

eggNOGiNOG264445.
GeneTreeiENSGT00530000063687.
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. Me_CpG-bd_MBD4.
IPR001739. Methyl_CpG_DNA-bd.
[Graphical view]
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

MESPNLGDNR VRGESLVPDP PWDRCKEDIA VGLGGVGEDG KDLVISSERS    50
SLLQEPTAST LSSTTATEGH KPVPCGWERV VKQRLSGKTA GKFDVYFISP 100
QGLKFRSKRS LANYLLKNGE TFLKPEDFNF TVLPKGSINP GYKHQSLAAL 150
TSLQPNETDV SKQNLKTRSK WKTDVLPLPS GTSESPESSG LSNSNSACLL 200
LREHRDIQDV DSEKRRKSKR KVTVLKGTAS QKTKQKCRKS LLESTQRNRK 250
RASVVQKVGA DRELVPQESQ LNRTLCPADA CARETVGLAG EEKSPSPGLD 300
LCFIQVTSGT TNKFHSTEAA GEANREQTFL ESEEIRSKGD RKGEAHLHTG 350
VLQDGSEMPS CSQAKKHFTS ETFQEDSIPR TQVEKRKTSL YFSSKYNKEA 400
LSPPRRKSFK KWTPPRSPFN LVQEILFHDP WKLLIATIFL NRTSGKMAIP 450
VLWEFLEKYP SAEVARAADW RDVSELLKPL GLYDLRAKTI IKFSDEYLTK 500
QWRYPIELHG IGKYGNDSYR IFCVNEWKQV HPEDHKLNKY HDWLWENHEK 550
LSLS 554
Length:554
Mass (Da):62,578
Last modified:May 1, 1999 - v1
Checksum:i792D37CB180291F5
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti129 – 1291N → D in AAH24812. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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

EnsembliENSMUST00000032469; ENSMUSP00000032469; ENSMUSG00000030322.
GeneIDi17193.
KEGGimmu:17193.
UCSCiuc009dje.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF072249 mRNA. Translation: AAC68878.1 .
AF120996 Genomic DNA. Translation: AAD56595.1 .
BC024812 mRNA. Translation: AAH24812.1 .
CCDSi CCDS39603.1.
RefSeqi NP_034904.2. NM_010774.2.
UniGenei Mm.259308.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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 [» ]
ProteinModelPortali Q9Z2D7.
SMRi Q9Z2D7. Positions 71-135, 411-554.
ModBasei Search...
MobiDBi Search...

PTM databases

PhosphoSitei Q9Z2D7.

Proteomic databases

PaxDbi Q9Z2D7.
PRIDEi Q9Z2D7.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000032469 ; ENSMUSP00000032469 ; ENSMUSG00000030322 .
GeneIDi 17193.
KEGGi mmu:17193.
UCSCi uc009dje.2. mouse.

Organism-specific databases

CTDi 8930.
MGIi MGI:1333850. Mbd4.

Phylogenomic databases

eggNOGi NOG264445.
GeneTreei ENSGT00530000063687.
HOGENOMi HOG000113489.
HOVERGENi HBG052418.
InParanoidi Q9Z2D7.
KOi K10801.
OrthoDBi EOG74N5J9.
PhylomeDBi Q9Z2D7.
TreeFami TF329176.

Enzyme and pathway databases

Reactomei REACT_208690. Recognition and association of DNA glycosylase with site containing an affected pyrimidine.
REACT_220827. Displacement of DNA glycosylase by APE1.

Miscellaneous databases

EvolutionaryTracei Q9Z2D7.
NextBioi 291542.
PROi Q9Z2D7.
SOURCEi Search...

Gene expression databases

ArrayExpressi Q9Z2D7.
Bgeei Q9Z2D7.
CleanExi MM_MBD4.
Genevestigatori Q9Z2D7.

Family and domain databases

Gene3Di 1.10.340.30. 1 hit.
3.30.890.10. 1 hit.
InterProi IPR016177. DNA-bd_dom.
IPR011257. DNA_glycosylase.
IPR003265. HhH-GPD_domain.
IPR017352. Me_CpG-bd_MBD4.
IPR001739. Methyl_CpG_DNA-bd.
[Graphical view ]
Pfami PF00730. HhH-GPD. 1 hit.
PF01429. MBD. 1 hit.
[Graphical view ]
PIRSFi PIRSF038005. Methyl_CpG_bd_MBD4. 1 hit.
SMARTi SM00391. MBD. 1 hit.
[Graphical view ]
SUPFAMi SSF48150. SSF48150. 1 hit.
SSF54171. SSF54171. 1 hit.
PROSITEi PS50982. MBD. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: September 3, 2014
This is version 108 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

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