Q9ESW0 (DDB1_RAT) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA damage-binding protein 1

Alternative name(s):
Damage-specific DNA-binding protein 1

Gene names

Name:

Ddb1

Organism

Rattus norvegicus (Rat) [Reference proteome]

Taxonomic identifier

10116 [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 › Rattus

Protein attributes

Sequence length	1140 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript 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.
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, 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.
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.
Post-translational modification	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 Traceable author statement PubMed 12145536. Source: RGD proteasomal ubiquitin-dependent protein catabolic process Inferred from sequence or structural similarity. Source: UniProtKB protein ubiquitination Inferred from electronic annotation. Source: UniProtKB-UniPathway
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	damaged DNA binding Inferred from mutant phenotype PubMed 12145536. Source: RGD
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_0000281038
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 By similarity
	Modified residue	757	1	Phosphoserine By similarity
	Modified residue	766	1	Phosphoserine By similarity
	Modified residue	1067	1	N6-acetyllysine By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q9ESW0 [UniParc]. Last modified March 1, 2001. Version 1. Checksum: 8A1873506C384263	FASTA	1,140	126,862
	10 20 30 40 50 60 MSYNYVVTAQ KPTAVNGCVT GHFTSAEDIN 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 SQPVKLNVDS NEQGSYVVAM ETFTNLGPIV 370 380 390 400 410 420 DMCVVDLERQ GQGQLVTCSG AFKEGSLRII RNGIGIHEHA SIDLPGIKGL WPLRSDPNRE 430 440 450 460 470 480 TDDTLVLSFV GQTRVLMLNG EEVEETELMG FVDDQQTFFC GNVAHQQLIQ ITSASVRLVS 490 500 510 520 530 540 QEPKALVSEW KEPRAKNISV ASCNSSQVVV AVGRALYYLQ IHPQELRQIS HTEMEHEVAC 550 560 570 580 590 600 LDVTPLGDSN 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 LALANTSTLT IGTMNEIQKL HIRTVPIYES 730 740 750 760 770 780 PRKICYQEVS QCFGVLSTRI EVQDTSGGTT ALRPSASTQA LSSSVSSSKL FSSSAAPHET 790 800 810 820 830 840 SFGEEVEVHN LLIIDQHTFE VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE 850 860 870 880 890 900 AEPKQGRIVV FQYSGGKLQT 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 SLVMQNLGET 1030 1040 1050 1060 1070 1080 STPTQGSVLL GTVNGMIGLV TSLSESWYNL LLDMQNRLNK VIKSVGKIEH SFWRSFHTER 1090 1100 1110 1120 1130 1140 KTEPATGFID GDLIESFLDI SRPKMQEVVA NLQYDDGSGM KREATADDLI KVVEELTRIH

References

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

Cross-references

Sequence databases
EMBL GenBank DDBJ	AJ277077 mRNA. Translation: CAB89874.2.
IPI	IPI00324451.
UniGene	Rn.8402.
3D structure databases
HSSP	HSSP built from PDB template 2B5M based on UniProtKB Q16531.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9ESW0. 1 interaction.
MINT	MINT-4784948.
STRING	10116.ENSRNOP00000028188.
PTM databases
PhosphoSite	Q9ESW0.
Proteomic databases
PaxDb	Q9ESW0.
PRIDE	Q9ESW0.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
UCSC	RGD:621889. rat.
Organism-specific databases
RGD	621889. Ddb1.
Phylogenomic databases
eggNOG	NOG247734.
HOGENOM	HOG000007241.
HOVERGEN	HBG005460.
InParanoid	Q9ESW0.
Enzyme and pathway databases
UniPathway	UPA00143.
Gene expression databases
ArrayExpress	Q9ESW0.
Genevestigator	Q9ESW0.
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...

Entry information

Entry name

DDB1_RAT

Accession

Primary (citable) accession number: Q9ESW0

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 20, 2007
Last sequence update:	March 1, 2001
Last modified:	April 3, 2013
This is version 71 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program