Q3U1J4 (DDB1_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:

Ddb1

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	1140 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.5
Pathway	Protein modification; protein ubiquitination.
Subunit structure	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 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 EIF2C1 and EIF2C2. Associates with the E3 ligase complex containing DYRK2, EDD/UBR5, DDB1 and VPRBP proteins (EDVP complex). Interacts directly with DYRK2 By similarity. Ref.5
Subcellular location	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.
Tissue specificity	Ubiquitously expressed. Expressed in pregnant, lactating and involuting mammary gland. Ref.1
Developmental stage	Ubiquitously expressed at E8.5, E9.5, E12.5, and E19.5. Ref.1
Post-translational modification	Phosphorylated by ABL1. Ref.5 Ubiquitinated by CUL4A. Subsequently degraded by ubiquitin-dependent proteolysis By similarity.
Sequence similarities	Belongs to the DDB1 family.

Ontologies

Keywords
Biological process	DNA damage DNA repair Ubl conjugation pathway
Cellular component	Cytoplasm Nucleus
Ligand	DNA-binding
PTM	Acetylation Phosphoprotein Ubl conjugation
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW Wnt receptor signaling pathway Inferred from direct assay PubMed 19056892. Source: MGI cell cycle checkpoint Inferred from electronic annotation. Source: Compara proteasomal ubiquitin-dependent protein catabolic process Inferred from sequence or structural similarity. Source: UniProtKB protein ubiquitination involved in ubiquitin-dependent protein catabolic process Inferred from electronic annotation. Source: Compara
Cellular_component	Cul4A-RING ubiquitin ligase complex Inferred from sequence or structural similarity. Source: UniProtKB Cul4B-RING ubiquitin ligase complex Inferred from sequence or structural similarity. Source: UniProtKB cytoplasm Inferred from sequence or structural similarity. Source: UniProtKB nucleus Inferred from sequence or structural similarity. Source: UniProtKB
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1140	1140	DNA damage-binding protein 1		PRO_0000281036
Regions
	Region	1 – 768	768	Interaction with CDT1 By similarity
	Region	391 – 709	319	Interaction with CUL4A By similarity
	Region	771 – 1140	370	Interaction with CDT1 and CUL4A By similarity
Amino acid modifications
	Modified residue	8	1	Phosphothreonine Ref.6
	Modified residue	757	1	Phosphoserine Ref.7
	Modified residue	766	1	Phosphoserine Ref.7
	Modified residue	1067	1	N6-acetyllysine By similarity
Experimental info
	Sequence conflict	40	1	E → K in AAD42230. Ref.2
	Sequence conflict	297	1	L → P in AAD42230. Ref.2
	Sequence conflict	600	1	H → R in AAD42230. Ref.2
	Sequence conflict	601	1	Y → C in BAE32502. Ref.3
	Sequence conflict	689	1	D → N in BAE27231. Ref.3
	Sequence conflict	715	1	V → D in BAE32502. Ref.3
	Sequence conflict	795	1	D → G in BAE32502. Ref.3
	Sequence conflict	845	1	Q → L in BAE32502. Ref.3
	Sequence conflict	979	1	K → R in BAE33503. Ref.3

Sequences

	Sequence		Length	Mass (Da)
	Q3U1J4 [UniParc]. Last modified March 20, 2007. Version 2. Checksum: 9799298D52E60AE4	FASTA	1,140	126,853
	10 20 30 40 50 60 MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK 70 80 90 100 110 120 IAVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI 130 140 150 160 170 180 IGIIDPECRM IGLRLYDGLF KVIPLDRDNK ELKAFNIRLE ELHVIDVKFL YGCQAPTICF 190 200 210 220 230 240 VYQDPQGRHV KTYEVSLREK EFNKGPWKQE NVEAEASMVI AVPEPFGGAI IIGQESITYH 250 260 270 280 290 300 NGDKYLAIAP PIIKQSTIVC HNRVDPNGSR YLLGDMEGRL FMLLLEKEEQ MDGTVTLKDL 310 320 330 340 350 360 RVELLGETSI AECLTYLDNG VVFVGSRLGD SQLVKLNVDS NEQGSYVVAM ETFTNLGPIV 370 380 390 400 410 420 DMCVVDLERQ GQGQLVTCSG AFKEGSLRII RNGIGIHEHA SIDLPGIKGL WPLRSDPGRE 430 440 450 460 470 480 TDDTLVLSFV GQTRVLMLNG EEVEETELMG FVDDQQTFFC GNVAHQQLIQ ITSASVRLVS 490 500 510 520 530 540 QEPKALVSEW KEPQGKNISV ASCNSSQVVV AVGRALYYLQ IHPQELRQIS HTEMEHEVAC 550 560 570 580 590 600 LDITPLGDSN GLSPLCAIGL WTDISARILK LPSFELLHKE MLGGEIIPRS ILMTTFESSH 610 620 630 640 650 660 YLLCALGDGA LFYFGLNIET GLLSDRKKVT LGTQPTVLRT FRSLSTTNVF ACSDRPTVIY 670 680 690 700 710 720 SSNHKLVFSN VNLKEVNYMC PLNSDGYPDS LALANNSTLT IGTIDEIQKL HIRTVPLYES 730 740 750 760 770 780 PRKICYQEVS QCFGVLSSRI EVQDSSGGTT ALRPSASTQA LSSSVSSSKL FSSSTAPHET 790 800 810 820 830 840 SFGEEVEVHN LLIIDQHTFE VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE 850 860 870 880 890 900 AEPKQGRIVV FQYSDGKLQT VAEKEVKGAV YSMVEFNGKL LASINSTVRL YEWTTEKELR 910 920 930 940 950 960 TECNHYNNIM ALYLKTKGDF ILVGDLMRSV LLLAYKPMEG NFEEIARDFN PNWMSAVEIL 970 980 990 1000 1010 1020 DDDNFLGAEN AFNLFVCQKD SAATTDEERQ HLQEVGLFHL GEFVNVFCHG SLVMQNLGEA 1030 1040 1050 1060 1070 1080 STPTQGSVLF GTVNGMIGLV TSLSESWYNL LLDMQNRLNK VIKSVGKIEH SFWRSFHTER 1090 1100 1110 1120 1130 1140 KTEPATGFID GDLIESFLDI SRPKMQEVVA NLQYDDGSGM KREATADDLI KVVEELTRIH

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"Protein phosphorylation and expression profiling by Yin-yang multidimensional liquid chromatography (Yin-yang MDLC) mass spectrometry." Dai J., Jin W.-H., Sheng Q.-H., Shieh C.-H., Wu J.-R., Zeng R. J. Proteome Res. 6:250-262(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-8, MASS SPECTROMETRY. Tissue: Liver.
[7]	"Large-scale phosphorylation analysis of mouse liver." Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-757 AND SER-766, MASS SPECTROMETRY. Tissue: Liver.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
IPI	IPI00316740.
PIR	JC7152.
RefSeq	NP_056550.1. NM_015735.1.
UniGene	Mm.289915. Mm.466856.
3D structure databases
HSSP	HSSP built from PDB template 2B5N based on UniProtKB Q16531.
ProteinModelPortal	Q3U1J4.
SMR	Q3U1J4. Positions 1-707, 709-1140.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q3U1J4. 34 interactions.
Proteomic databases
PaxDb	Q3U1J4.
PRIDE	Q3U1J4.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSMUST00000025649; ENSMUSP00000025649; ENSMUSG00000024740.
GeneID	13194.
KEGG	mmu:13194.
UCSC	uc008gqm.1. mouse.
Organism-specific databases
CTD	1642.
MGI	MGI:1202384. Ddb1.
Phylogenomic databases
eggNOG	NOG247734.
GeneTree	ENSGT00530000063396.
HOVERGEN	HBG005460.
InParanoid	Q3U1J4.
KO	K10610.
OMA	CALGDGS.
Enzyme and pathway databases
UniPathway	UPA00143.
Gene expression databases
ArrayExpress	Q3U1J4.
Bgee	Q3U1J4.
CleanEx	MM_DDB1.
Genevestigator	Q3U1J4.
Family and domain databases
Gene3D	2.130.10.10. 3 hits.
InterPro	IPR004871. Cleavage/polyA-sp_fac_asu_C. IPR015943. WD40/YVTN_repeat-like_dom. [Graphical view]
Pfam	PF03178. CPSF_A. 1 hit. [Graphical view]
ProtoNet	Search...
Other
ChiTaRS	DDB1. mouse.
NextBio	283320.
SOURCE	Search...

Entry information

Entry name

DDB1_MOUSE

Accession

Primary (citable) accession number: Q3U1J4
Secondary accession number(s): Q3U4D0 , Q3U8G3, Q3UJC4, Q99LV3, Q9QYK0, Q9WV39

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 20, 2007
Last sequence update:	March 20, 2007
Last modified:	April 3, 2013
This is version 67 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program