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Q9ESW0

- DDB1_RAT

UniProt

Q9ESW0 - DDB1_RAT

Protein

DNA damage-binding protein 1

Gene

Ddb1

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 82 (01 Oct 2014)
      Sequence version 1 (01 Mar 2001)
      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. damaged DNA binding Source: RGD

    GO - Biological processi

    1. DNA repair Source: RGD
    2. proteasome-mediated ubiquitin-dependent protein catabolic process Source: UniProtKB
    3. protein ubiquitination Source: UniProtKB-UniPathway

    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):
    Damage-specific DNA-binding protein 1
    Gene namesi
    Name:Ddb1
    OrganismiRattus norvegicus (Rat)
    Taxonomic identifieri10116 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
    ProteomesiUP000002494: Unplaced

    Organism-specific databases

    RGDi621889. 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_0000281038Add
    BLAST

    Amino acid modifications

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

    Post-translational modificationi

    Ubiquitinated by CUL4A. Subsequently degraded by ubiquitin-dependent proteolysis By similarity.By similarity

    Keywords - PTMi

    Acetylation, Ubl conjugation

    Proteomic databases

    PaxDbiQ9ESW0.
    PRIDEiQ9ESW0.

    PTM databases

    PhosphoSiteiQ9ESW0.

    Expressioni

    Gene expression databases

    GenevestigatoriQ9ESW0.

    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, 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

    IntActiQ9ESW0. 2 interactions.
    MINTiMINT-4784948.
    STRINGi10116.ENSRNOP00000028188.

    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.
    HOGENOMiHOG000007241.
    HOVERGENiHBG005460.
    InParanoidiQ9ESW0.
    PhylomeDBiQ9ESW0.

    Family and domain databases

    Gene3Di2.130.10.10. 3 hits.
    InterProiIPR004871. Cleavage/polyA-sp_fac_asu_C.
    IPR015943. WD40/YVTN_repeat-like_dom.
    IPR017986. WD40_repeat_dom.
    [Graphical view]
    PfamiPF03178. CPSF_A. 1 hit.
    [Graphical view]
    SUPFAMiSSF50978. SSF50978. 2 hits.

    Sequencei

    Sequence statusi: Complete.

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

    Q9ESW0-1 [UniParc]FASTAAdd to Basket

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    MSYNYVVTAQ KPTAVNGCVT GHFTSAEDIN 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 SQPVKLNVDS NEQGSYVVAM 350
    ETFTNLGPIV DMCVVDLERQ GQGQLVTCSG AFKEGSLRII RNGIGIHEHA 400
    SIDLPGIKGL WPLRSDPNRE TDDTLVLSFV GQTRVLMLNG EEVEETELMG 450
    FVDDQQTFFC GNVAHQQLIQ ITSASVRLVS QEPKALVSEW KEPRAKNISV 500
    ASCNSSQVVV AVGRALYYLQ IHPQELRQIS HTEMEHEVAC LDVTPLGDSN 550
    GLSPLCAIGL WTDISARILK LPSFELLHKE MLGGEIIPRS ILMTTFESSH 600
    YLLCALGDGA LFYFGLNIET GLLSDRKKVT LGTQPTVLRT FRSLSTTNVF 650
    ACSDRPTVIY SSNHKLVFSN VNLKEVNYMC PLNSDGYPDS LALANTSTLT 700
    IGTMNEIQKL HIRTVPIYES PRKICYQEVS QCFGVLSTRI EVQDTSGGTT 750
    ALRPSASTQA LSSSVSSSKL FSSSAAPHET SFGEEVEVHN LLIIDQHTFE 800
    VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE AEPKQGRIVV 850
    FQYSGGKLQT VAEKEVKGAV YSMVEFNGKL LASINSTVRL YEWTTEKELR 900
    TECNHYNNIM ALYLKTKGDF ILVGDLMRSV LLLAYKPMEG NFEEIARDFN 950
    PNWMSAVEIL DDDNFLGAEN AFNLFVCQKD SAATTDEERQ HLQEVGLFHL 1000
    GEFVNVFCHG SLVMQNLGET STPTQGSVLL GTVNGMIGLV TSLSESWYNL 1050
    LLDMQNRLNK VIKSVGKIEH SFWRSFHTER KTEPATGFID GDLIESFLDI 1100
    SRPKMQEVVA NLQYDDGSGM KREATADDLI KVVEELTRIH 1140
    Length:1,140
    Mass (Da):126,862
    Last modified:March 1, 2001 - v1
    Checksum:i8A1873506C384263
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ277077 mRNA. Translation: CAB89874.2.
    UniGeneiRn.8402.

    Genome annotation databases

    UCSCiRGD:621889. rat.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ277077 mRNA. Translation: CAB89874.2 .
    UniGenei Rn.8402.

    3D structure databases

    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi Q9ESW0. 2 interactions.
    MINTi MINT-4784948.
    STRINGi 10116.ENSRNOP00000028188.

    PTM databases

    PhosphoSitei Q9ESW0.

    Proteomic databases

    PaxDbi Q9ESW0.
    PRIDEi Q9ESW0.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    UCSCi RGD:621889. rat.

    Organism-specific databases

    RGDi 621889. Ddb1.

    Phylogenomic databases

    eggNOGi NOG247734.
    HOGENOMi HOG000007241.
    HOVERGENi HBG005460.
    InParanoidi Q9ESW0.
    PhylomeDBi Q9ESW0.

    Enzyme and pathway databases

    UniPathwayi UPA00143 .

    Miscellaneous databases

    PROi Q9ESW0.

    Gene expression databases

    Genevestigatori Q9ESW0.

    Family and domain databases

    Gene3Di 2.130.10.10. 3 hits.
    InterProi IPR004871. Cleavage/polyA-sp_fac_asu_C.
    IPR015943. WD40/YVTN_repeat-like_dom.
    IPR017986. WD40_repeat_dom.
    [Graphical view ]
    Pfami PF03178. CPSF_A. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50978. SSF50978. 2 hits.
    ProtoNeti Search...

    Publicationsi

    1. Chao C.C.
      Submitted (AUG-2000) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Strain: Sprague-Dawley.
      Tissue: Brain.

    Entry informationi

    Entry nameiDDB1_RAT
    AccessioniPrimary (citable) accession number: Q9ESW0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 20, 2007
    Last sequence update: March 1, 2001
    Last modified: October 1, 2014
    This is version 82 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

    Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3