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Q3U1J4

- DDB1_MOUSE

UniProt

Q3U1J4 - DDB1_MOUSE

Protein

DNA damage-binding protein 1

Gene

Ddb1

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 81 (01 Oct 2014)
      Sequence version 2 (20 Mar 2007)
      Previous versions | rss
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    Functioni

    Required for DNA repair. Binds to DDB2 to form the UV-damaged DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The functional specificity of the DCX E3 ubiquitin-protein ligase complex is determined by the variable substrate recognition component recruited by DDB1. DCX(DDB2) (also known as DDB1-CUL4-ROC1, CUL4-DDB-ROC1 and CUL4-DDB-RBX1) may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. DCX(DDB2) also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. DCX(DTL) plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication. DCX(ERCC8) (the CSA complex) plays a role in transcription-coupled repair (TCR). May also play a role in ubiquitination of CDKN1B/p27kip when associated with CUL4 and SKP2 By similarity.By similarity

    Pathwayi

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW

    GO - Biological processi

    1. DNA repair Source: UniProtKB-KW
    2. negative regulation of apoptotic process Source: MGI
    3. proteasome-mediated ubiquitin-dependent protein catabolic process Source: UniProtKB
    4. protein ubiquitination involved in ubiquitin-dependent protein catabolic process Source: Ensembl
    5. regulation of mitotic cell cycle phase transition Source: Ensembl
    6. Wnt signaling pathway Source: MGI

    Keywords - Biological processi

    DNA damage, DNA repair, Ubl conjugation pathway

    Keywords - Ligandi

    DNA-binding

    Enzyme and pathway databases

    UniPathwayiUPA00143.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA damage-binding protein 1
    Alternative name(s):
    DDB p127 subunit
    Damage-specific DNA-binding protein 1
    UV-damaged DNA-binding factor
    Gene namesi
    Name:Ddb1
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 19

    Organism-specific databases

    MGIiMGI:1202384. Ddb1.

    Subcellular locationi

    Cytoplasm By similarity. Nucleus By similarity
    Note: Primarily cytoplasmic. Translocates to the nucleus following UV irradiation and subsequently accumulates at sites of DNA damage By similarity.By similarity

    GO - Cellular componenti

    1. Cul4A-RING E3 ubiquitin ligase complex Source: UniProtKB
    2. Cul4B-RING E3 ubiquitin ligase complex Source: UniProtKB
    3. Cul4-RING E3 ubiquitin ligase complex Source: UniProtKB
    4. cytoplasm Source: UniProtKB
    5. nucleus Source: UniProtKB

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11RemovedBy similarity
    Chaini2 – 11401139DNA damage-binding protein 1PRO_0000281036Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylserineBy similarity
    Modified residuei1067 – 10671N6-acetyllysineBy similarity

    Post-translational modificationi

    Phosphorylated by ABL1.1 Publication
    Ubiquitinated by CUL4A. Subsequently degraded by ubiquitin-dependent proteolysis By similarity.By similarity

    Keywords - PTMi

    Acetylation, Phosphoprotein, Ubl conjugation

    Proteomic databases

    MaxQBiQ3U1J4.
    PaxDbiQ3U1J4.
    PRIDEiQ3U1J4.

    Expressioni

    Tissue specificityi

    Ubiquitously expressed. Expressed in pregnant, lactating and involuting mammary gland.1 Publication

    Developmental stagei

    Ubiquitously expressed at E8.5, E9.5, E12.5, and E19.5.1 Publication

    Gene expression databases

    BgeeiQ3U1J4.
    CleanExiMM_DDB1.
    GenevestigatoriQ3U1J4.

    Interactioni

    Subunit structurei

    Component of the UV-DDB complex which includes DDB1 and DDB2. The UV-DDB complex interacts with monoubiquitinated histone H2A and binds to XPC via the DDB2 subunit. Component of numerous DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which consist of a core of DDB1, CUL4A or CUL4B and RBX1. DDB1 may recruit specific substrate targeting subunits to the DCX complex. These substrate targeting subunits are generally known as DCAF (DDB1- and CUL4-associated factor) or CDW (CUL4-DDB1-associated WD40-repeat) proteins. Interacts with AMBRA1, ATG16L1, BTRC, DCAF1, DCAF17, DCAF16, DCAF15, DDA1, DET1, DTL, ERCC8, FBXW5, FBXW8, GRWD1, DCAF6, KATNB1, NLE1, NUP43, PAFAH1B1, PHIP, PWP1, RBBP4, RBBP5, RBBP7, RFWD2, SNRNP40, VPRBP, WDR5, WDR5B, WDR12, DCAF4, DCAF5, DCAF11, WDR26, DCAF10, WDR39, DCAF12, WDR42, DCAF8, WDR53, WDR59, WDR61, DCAF7, WSB1, WSB2, LRWD1 and WDTC1. DCX complexes may associate with the COP9 signalosome, and this inhibits the E3 ubiquitin-protein ligase activity of the complex. Interacts with NF2, TSC1 and TSC2. Interacts with AGO1 and AGO2. Associates with the E3 ligase complex containing DYRK2, EDD/UBR5, DDB1 and VPRBP proteins (EDVP complex). Interacts directly with DYRK2 By similarity.By similarity

    Protein-protein interaction databases

    BioGridi199074. 37 interactions.
    IntActiQ3U1J4. 36 interactions.
    MINTiMINT-4131128.

    Structurei

    3D structure databases

    ProteinModelPortaliQ3U1J4.
    SMRiQ3U1J4. Positions 1-707, 709-1140.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni2 – 768767Interaction with CDT1By similarityAdd
    BLAST
    Regioni13 – 356344WD repeat beta-propeller ABy similarityAdd
    BLAST
    Regioni391 – 708318WD repeat beta-propeller B; Interaction with CUL4ABy similarityAdd
    BLAST
    Regioni709 – 1043335WD repeat beta-propeller CBy similarityAdd
    BLAST
    Regioni771 – 1140370Interaction with CDT1 and CUL4ABy similarityAdd
    BLAST

    Domaini

    The core of the protein consists of three WD40 beta-propeller domains.By similarity

    Sequence similaritiesi

    Belongs to the DDB1 family.Curated

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiNOG247734.
    GeneTreeiENSGT00530000063396.
    HOVERGENiHBG005460.
    InParanoidiQ3U1J4.
    KOiK10610.
    OMAiMCPLNSE.
    OrthoDBiEOG7X0VG9.
    PhylomeDBiQ3U1J4.
    TreeFamiTF105840.

    Family and domain databases

    Gene3Di2.130.10.10. 3 hits.
    InterProiIPR004871. Cleavage/polyA-sp_fac_asu_C.
    IPR011047. Quinonprotein_ADH-like_supfam.
    IPR015943. WD40/YVTN_repeat-like_dom.
    [Graphical view]
    PfamiPF03178. CPSF_A. 1 hit.
    [Graphical view]
    SUPFAMiSSF50998. SSF50998. 2 hits.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q3U1J4-1 [UniParc]FASTAAdd to Basket

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    MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR     50
    PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI 100
    ITRAHGNVQD RIGRPSETGI IGIIDPECRM IGLRLYDGLF KVIPLDRDNK 150
    ELKAFNIRLE ELHVIDVKFL YGCQAPTICF VYQDPQGRHV KTYEVSLREK 200
    EFNKGPWKQE NVEAEASMVI AVPEPFGGAI IIGQESITYH NGDKYLAIAP 250
    PIIKQSTIVC HNRVDPNGSR YLLGDMEGRL FMLLLEKEEQ MDGTVTLKDL 300
    RVELLGETSI AECLTYLDNG VVFVGSRLGD SQLVKLNVDS NEQGSYVVAM 350
    ETFTNLGPIV DMCVVDLERQ GQGQLVTCSG AFKEGSLRII RNGIGIHEHA 400
    SIDLPGIKGL WPLRSDPGRE TDDTLVLSFV GQTRVLMLNG EEVEETELMG 450
    FVDDQQTFFC GNVAHQQLIQ ITSASVRLVS QEPKALVSEW KEPQGKNISV 500
    ASCNSSQVVV AVGRALYYLQ IHPQELRQIS HTEMEHEVAC LDITPLGDSN 550
    GLSPLCAIGL WTDISARILK LPSFELLHKE MLGGEIIPRS ILMTTFESSH 600
    YLLCALGDGA LFYFGLNIET GLLSDRKKVT LGTQPTVLRT FRSLSTTNVF 650
    ACSDRPTVIY SSNHKLVFSN VNLKEVNYMC PLNSDGYPDS LALANNSTLT 700
    IGTIDEIQKL HIRTVPLYES PRKICYQEVS QCFGVLSSRI EVQDSSGGTT 750
    ALRPSASTQA LSSSVSSSKL FSSSTAPHET SFGEEVEVHN LLIIDQHTFE 800
    VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE AEPKQGRIVV 850
    FQYSDGKLQT VAEKEVKGAV YSMVEFNGKL LASINSTVRL YEWTTEKELR 900
    TECNHYNNIM ALYLKTKGDF ILVGDLMRSV LLLAYKPMEG NFEEIARDFN 950
    PNWMSAVEIL DDDNFLGAEN AFNLFVCQKD SAATTDEERQ HLQEVGLFHL 1000
    GEFVNVFCHG SLVMQNLGEA STPTQGSVLF GTVNGMIGLV TSLSESWYNL 1050
    LLDMQNRLNK VIKSVGKIEH SFWRSFHTER KTEPATGFID GDLIESFLDI 1100
    SRPKMQEVVA NLQYDDGSGM KREATADDLI KVVEELTRIH 1140
    Length:1,140
    Mass (Da):126,853
    Last modified:March 20, 2007 - v2
    Checksum:i9799298D52E60AE4
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti40 – 401E → K in AAD42230. 1 PublicationCurated
    Sequence conflicti297 – 2971L → P in AAD42230. 1 PublicationCurated
    Sequence conflicti600 – 6001H → R in AAD42230. 1 PublicationCurated
    Sequence conflicti601 – 6011Y → C in BAE32502. (PubMed:16141072)Curated
    Sequence conflicti689 – 6891D → N in BAE27231. (PubMed:16141072)Curated
    Sequence conflicti715 – 7151V → D in BAE32502. (PubMed:16141072)Curated
    Sequence conflicti795 – 7951D → G in BAE32502. (PubMed:16141072)Curated
    Sequence conflicti845 – 8451Q → L in BAE32502. (PubMed:16141072)Curated
    Sequence conflicti979 – 9791K → R in BAE33503. (PubMed:16141072)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB026432 mRNA. Translation: BAA84699.1.
    AF159853 mRNA. Translation: AAD42230.1.
    AK146522 mRNA. Translation: BAE27231.1.
    AK152228 mRNA. Translation: BAE31055.1.
    AK154303 mRNA. Translation: BAE32502.1.
    AK155020 mRNA. Translation: BAE32993.1.
    AK155920 mRNA. Translation: BAE33503.1.
    AK157491 mRNA. Translation: BAE34102.1.
    BC002210 mRNA. Translation: AAH02210.1.
    BC009661 mRNA. Translation: AAH09661.1.
    CCDSiCCDS37915.1.
    PIRiJC7152.
    RefSeqiNP_056550.1. NM_015735.1.
    UniGeneiMm.289915.
    Mm.466856.

    Genome annotation databases

    EnsembliENSMUST00000025649; ENSMUSP00000025649; ENSMUSG00000024740.
    GeneIDi13194.
    KEGGimmu:13194.
    UCSCiuc008gqm.1. mouse.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB026432 mRNA. Translation: BAA84699.1 .
    AF159853 mRNA. Translation: AAD42230.1 .
    AK146522 mRNA. Translation: BAE27231.1 .
    AK152228 mRNA. Translation: BAE31055.1 .
    AK154303 mRNA. Translation: BAE32502.1 .
    AK155020 mRNA. Translation: BAE32993.1 .
    AK155920 mRNA. Translation: BAE33503.1 .
    AK157491 mRNA. Translation: BAE34102.1 .
    BC002210 mRNA. Translation: AAH02210.1 .
    BC009661 mRNA. Translation: AAH09661.1 .
    CCDSi CCDS37915.1.
    PIRi JC7152.
    RefSeqi NP_056550.1. NM_015735.1.
    UniGenei Mm.289915.
    Mm.466856.

    3D structure databases

    ProteinModelPortali Q3U1J4.
    SMRi Q3U1J4. Positions 1-707, 709-1140.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 199074. 37 interactions.
    IntActi Q3U1J4. 36 interactions.
    MINTi MINT-4131128.

    Proteomic databases

    MaxQBi Q3U1J4.
    PaxDbi Q3U1J4.
    PRIDEi Q3U1J4.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000025649 ; ENSMUSP00000025649 ; ENSMUSG00000024740 .
    GeneIDi 13194.
    KEGGi mmu:13194.
    UCSCi uc008gqm.1. mouse.

    Organism-specific databases

    CTDi 1642.
    MGIi MGI:1202384. Ddb1.

    Phylogenomic databases

    eggNOGi NOG247734.
    GeneTreei ENSGT00530000063396.
    HOVERGENi HBG005460.
    InParanoidi Q3U1J4.
    KOi K10610.
    OMAi MCPLNSE.
    OrthoDBi EOG7X0VG9.
    PhylomeDBi Q3U1J4.
    TreeFami TF105840.

    Enzyme and pathway databases

    UniPathwayi UPA00143 .

    Miscellaneous databases

    ChiTaRSi DDB1. mouse.
    NextBioi 283320.
    PROi Q3U1J4.
    SOURCEi Search...

    Gene expression databases

    Bgeei Q3U1J4.
    CleanExi MM_DDB1.
    Genevestigatori Q3U1J4.

    Family and domain databases

    Gene3Di 2.130.10.10. 3 hits.
    InterProi IPR004871. Cleavage/polyA-sp_fac_asu_C.
    IPR011047. Quinonprotein_ADH-like_supfam.
    IPR015943. WD40/YVTN_repeat-like_dom.
    [Graphical view ]
    Pfami PF03178. CPSF_A. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50998. SSF50998. 2 hits.
    ProtoNeti Search...

    Publicationsi

    1. "cDNA cloning, tissue expression, and chromosomal assignment of a mouse gene, encoding a 127 kDa UV-damaged DNA binding protein which is defective in XPE cells."
      Seki N., Hayashi A., Hattori A., Kozuma S., Sasaki M., Suzuki Y., Sugano S., Muramatsu M., Saito T.
      DNA Res. 6:319-322(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
      Tissue: Fetal brain.
    2. Zhang L., Sabatinos S.A., Richardson C.D.
      Submitted (JUN-1999) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Tissue: Spleen.
    3. "The transcriptional landscape of the mammalian genome."
      Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
      , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
      Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: C57BL/6J and NOD.
      Tissue: Amnion, Bone marrow and Spleen.
    4. "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].
      Tissue: Mammary tumor.
    5. "Interaction between UV-damaged DNA binding activity proteins and the c-Abl tyrosine kinase."
      Cong F., Tang J., Hwang B.J., Vuong B.Q., Chu G., Goff S.P.
      J. Biol. Chem. 277:34870-34878(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH DDB2, PHOSPHORYLATION.
    6. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Liver.

    Entry informationi

    Entry nameiDDB1_MOUSE
    AccessioniPrimary (citable) accession number: Q3U1J4
    Secondary accession number(s): Q3U4D0
    , Q3U8G3, Q3UJC4, Q99LV3, Q9QYK0, Q9WV39
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 20, 2007
    Last sequence update: March 20, 2007
    Last modified: October 1, 2014
    This is version 81 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3