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Q9Z2D7

- MBD4_MOUSE

UniProt

Q9Z2D7 - MBD4_MOUSE

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
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    • History
      Entry version 109 (01 Oct 2014)
      Sequence version 1 (01 May 1999)
      Previous versions | rss
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    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

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

    GO - Biological processi

    1. base-excision repair Source: InterPro
    2. cellular response to DNA damage stimulus Source: MGI
    3. DNA methylation 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

    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 1 Publication
    Note: Nuclear, in discrete foci.

    GO - Cellular componenti

    1. chromatin Source: MGI
    2. cytoplasm Source: MGI
    3. nucleus Source: MGI

    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

    ArrayExpressiQ9Z2D7.
    BgeeiQ9Z2D7.
    CleanExiMM_MBD4.
    GenevestigatoriQ9Z2D7.

    Interactioni

    Subunit structurei

    Interacts with MLH1.By similarity

    Structurei

    Secondary structure

    1
    554
    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.
    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.
    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

    Experimental Info

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

    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

    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: October 1, 2014
    This is version 109 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