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Q3U1J4

- DDB1_MOUSE

UniProt

Q3U1J4 - DDB1_MOUSE

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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

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: Ensembl

GO - Biological processi

  1. histone H2A monoubiquitination Source: Ensembl
  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. UV-damage excision repair Source: Ensembl
  7. Wnt signaling pathway Source: MGI
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):
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. extracellular space Source: Ensembl
  6. extracellular vesicular exosome Source: Ensembl
  7. nucleus Source: UniProtKB
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_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 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN 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 SQLVKLNVDS NEQGSYVVAM
360 370 380 390 400
ETFTNLGPIV DMCVVDLERQ GQGQLVTCSG AFKEGSLRII RNGIGIHEHA
410 420 430 440 450
SIDLPGIKGL WPLRSDPGRE TDDTLVLSFV GQTRVLMLNG EEVEETELMG
460 470 480 490 500
FVDDQQTFFC GNVAHQQLIQ ITSASVRLVS QEPKALVSEW KEPQGKNISV
510 520 530 540 550
ASCNSSQVVV AVGRALYYLQ IHPQELRQIS HTEMEHEVAC LDITPLGDSN
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 LALANNSTLT
710 720 730 740 750
IGTIDEIQKL HIRTVPLYES PRKICYQEVS QCFGVLSSRI EVQDSSGGTT
760 770 780 790 800
ALRPSASTQA LSSSVSSSKL FSSSTAPHET SFGEEVEVHN LLIIDQHTFE
810 820 830 840 850
VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE AEPKQGRIVV
860 870 880 890 900
FQYSDGKLQT 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 SLVMQNLGEA STPTQGSVLF 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):126,853
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

« Hide 'large scale' publications
  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 29, 2014
This is version 82 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