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Protein

DNA damage-binding protein 1

Gene

Ddb1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

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

Pathway:iprotein ubiquitination

This protein is involved in the pathway protein ubiquitination, which is part of Protein modification.
View all proteins of this organism that are known to be involved in the pathway protein ubiquitination and in Protein modification.

GO - Molecular functioni

  • damaged DNA binding Source: RGD

GO - Biological processi

Complete GO annotation...

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 Componenti: 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

Complete GO annotation...

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.

Interactioni

Subunit structurei

Component of the UV-DDB complex which includes DDB1 and DDB2; the heterodimer dimerizes to give rise to a heterotetramer when bound to damaged DNA. 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, CRBN, DCAF1, DCAF4, DCAF5, DCAF6, DCAF7, DCAF8, DCAF9, DCAF10, DCAF11, DCAF12, DCAF15, DCAF16, DCAF17, DDA1, DET1, DTL, ERCC8, FBXW5, FBXW8, GRWD1, KATNB1, NLE1, NUP43, PAFAH1B1, PHIP, PWP1, RBBP4, RBBP5, RBBP7, RFWD2, SNRNP40, VPRBP, WDR5, WDR5B, WDR12, WDR26, WDR39, WDR42, WDR53, WDR59, WDR61, 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). Interacts with TRPC4AP (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.
IPR031297. DDB1.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR017986. WD40_repeat_dom.
[Graphical view]
PANTHERiPTHR10644:SF3. PTHR10644:SF3. 1 hit.
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

« Hide

        10         20         30         40         50
MSYNYVVTAQ KPTAVNGCVT GHFTSAEDIN LLIAKNTRLE IYVVTAEGLR
60 70 80 90 100
PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI
110 120 130 140 150
ITRAHGNVQD RIGRPSETGI IGIIDPECRM IGLRLYDGLF KVIPLDRDNK
160 170 180 190 200
ELKAFNIRLE ELHVIDVKFL YGCQAPTICF VYQDPQGRHV KTYEVSLREK
210 220 230 240 250
EFNKGPWKQE NVEAEASMVI AVPEPFGGAI IIGQESITYH NGDKYLAIAP
260 270 280 290 300
PIIKQSTIVC HNRVDPNGSR YLLGDMEGRL FMLLLEKEEQ MDGTVTLKDL
310 320 330 340 350
RVELLGETSI AECLTYLDNG VVFVGSRLGD SQPVKLNVDS NEQGSYVVAM
360 370 380 390 400
ETFTNLGPIV DMCVVDLERQ GQGQLVTCSG AFKEGSLRII RNGIGIHEHA
410 420 430 440 450
SIDLPGIKGL WPLRSDPNRE TDDTLVLSFV GQTRVLMLNG EEVEETELMG
460 470 480 490 500
FVDDQQTFFC GNVAHQQLIQ ITSASVRLVS QEPKALVSEW KEPRAKNISV
510 520 530 540 550
ASCNSSQVVV AVGRALYYLQ IHPQELRQIS HTEMEHEVAC LDVTPLGDSN
560 570 580 590 600
GLSPLCAIGL WTDISARILK LPSFELLHKE MLGGEIIPRS ILMTTFESSH
610 620 630 640 650
YLLCALGDGA LFYFGLNIET GLLSDRKKVT LGTQPTVLRT FRSLSTTNVF
660 670 680 690 700
ACSDRPTVIY SSNHKLVFSN VNLKEVNYMC PLNSDGYPDS LALANTSTLT
710 720 730 740 750
IGTMNEIQKL HIRTVPIYES PRKICYQEVS QCFGVLSTRI EVQDTSGGTT
760 770 780 790 800
ALRPSASTQA LSSSVSSSKL FSSSAAPHET SFGEEVEVHN LLIIDQHTFE
810 820 830 840 850
VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE AEPKQGRIVV
860 870 880 890 900
FQYSGGKLQT VAEKEVKGAV YSMVEFNGKL LASINSTVRL YEWTTEKELR
910 920 930 940 950
TECNHYNNIM ALYLKTKGDF ILVGDLMRSV LLLAYKPMEG NFEEIARDFN
960 970 980 990 1000
PNWMSAVEIL DDDNFLGAEN AFNLFVCQKD SAATTDEERQ HLQEVGLFHL
1010 1020 1030 1040 1050
GEFVNVFCHG SLVMQNLGET STPTQGSVLL GTVNGMIGLV TSLSESWYNL
1060 1070 1080 1090 1100
LLDMQNRLNK VIKSVGKIEH SFWRSFHTER KTEPATGFID GDLIESFLDI
1110 1120 1130 1140
SRPKMQEVVA NLQYDDGSGM KREATADDLI KVVEELTRIH
Length:1,140
Mass (Da):126,862
Last modified:March 1, 2001 - v1
Checksum:i8A1873506C384263
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ277077 mRNA. Translation: CAB89874.2.
UniGeneiRn.8402.

Genome annotation databases

UCSCiRGD:621889. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ277077 mRNA. Translation: CAB89874.2.
UniGeneiRn.8402.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

PTM databases

PhosphoSiteiQ9ESW0.

Proteomic databases

PaxDbiQ9ESW0.
PRIDEiQ9ESW0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

UCSCiRGD:621889. rat.

Organism-specific databases

RGDi621889. Ddb1.

Phylogenomic databases

eggNOGiNOG247734.
HOGENOMiHOG000007241.
HOVERGENiHBG005460.
InParanoidiQ9ESW0.
PhylomeDBiQ9ESW0.

Enzyme and pathway databases

UniPathwayiUPA00143.

Miscellaneous databases

PROiQ9ESW0.

Family and domain databases

Gene3Di2.130.10.10. 3 hits.
InterProiIPR004871. Cleavage/polyA-sp_fac_asu_C.
IPR031297. DDB1.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR017986. WD40_repeat_dom.
[Graphical view]
PANTHERiPTHR10644:SF3. PTHR10644:SF3. 1 hit.
PfamiPF03178. CPSF_A. 1 hit.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 2 hits.
ProtoNetiSearch...

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: July 22, 2015
This is version 87 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.