DDB1_RAT
ID DDB1_RAT Reviewed; 1140 AA.
AC Q9ESW0;
DT 20-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 25-MAY-2022, entry version 117.
DE RecName: Full=DNA damage-binding protein 1;
DE AltName: Full=Damage-specific DNA-binding protein 1;
GN Name=Ddb1;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=Sprague-Dawley; TISSUE=Brain;
RA Chao C.C.;
RL Submitted (AUG-2000) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-1125, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22673903; DOI=10.1038/ncomms1871;
RA Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C.,
RA Olsen J.V.;
RT "Quantitative maps of protein phosphorylation sites across 14 different rat
RT organs and tissues.";
RL Nat. Commun. 3:876-876(2012).
CC -!- FUNCTION: Protein, which is both involved in DNA repair and protein
CC ubiquitination, as part of the UV-DDB complex and DCX (DDB1-CUL4-X-box)
CC complexes, respectively. Core component of the UV-DDB complex (UV-
CC damaged DNA-binding protein complex), a complex that recognizes UV-
CC induced DNA damage and recruit proteins of the nucleotide excision
CC repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB
CC complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-
CC 4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also
CC functions as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3
CC ubiquitin-protein ligase complexes which mediate the ubiquitination and
CC subsequent proteasomal degradation of target proteins. The functional
CC specificity of the DCX E3 ubiquitin-protein ligase complex is
CC determined by the variable substrate recognition component recruited by
CC DDB1. DCX(DDB2) (also known as DDB1-CUL4-ROC1, CUL4-DDB-ROC1 and CUL4-
CC DDB-RBX1) may ubiquitinate histone H2A, histone H3 and histone H4 at
CC sites of UV-induced DNA damage. The ubiquitination of histones may
CC facilitate their removal from the nucleosome and promote subsequent DNA
CC repair. DCX(DDB2) also ubiquitinates XPC, which may enhance DNA-binding
CC by XPC and promote NER. DCX(DTL) plays a role in PCNA-dependent
CC polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in
CC response to radiation-induced DNA damage and during DNA replication.
CC DCX(ERCC8) (the CSA complex) plays a role in transcription-coupled
CC repair (TCR). The DDB1-CUL4A-DTL E3 ligase complex regulates the
CC circadian clock function by mediating the ubiquitination and
CC degradation of CRY1 (By similarity). DDB1-mediated CRY1 degradation
CC promotes FOXO1 protein stability and FOXO1-mediated gluconeogenesis in
CC the liver (By similarity). {ECO:0000250|UniProtKB:Q16531,
CC ECO:0000250|UniProtKB:Q3U1J4}.
CC -!- PATHWAY: Protein modification; protein ubiquitination.
CC {ECO:0000250|UniProtKB:Q16531}.
CC -!- SUBUNIT: Component of the UV-DDB complex which includes DDB1 and DDB2;
CC the heterodimer dimerizes to give rise to a heterotetramer when bound
CC to damaged DNA. The UV-DDB complex interacts with monoubiquitinated
CC histone H2A and binds to XPC via the DDB2 subunit. Component of
CC numerous DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes
CC which consist of a core of DDB1, CUL4A or CUL4B and RBX1. DDB1 may
CC recruit specific substrate targeting subunits to the DCX complex. These
CC substrate targeting subunits are generally known as DCAF (DDB1- and
CC CUL4-associated factor) or CDW (CUL4-DDB1-associated WD40-repeat)
CC proteins. Interacts with AMBRA1, ATG16L1, BTRC, CRBN, DCAF1, DCAF4,
CC DCAF5, DCAF6, DCAF7, DCAF8, DCAF9, DCAF10, DCAF11, DCAF12, DCAF15,
CC DCAF16, DCAF17, DDA1, DET1, DTL, ERCC8, FBXW5, FBXW8, GRWD1, KATNB1,
CC NLE1, NUP43, PAFAH1B1, PHIP, PWP1, RBBP4, RBBP5, RBBP7, COP1, SNRNP40,
CC DCAF1, WDR5, WDR5B, WDR12, WDR26, WDR39, WDR42, WDR53, WDR59, WDR61,
CC WSB1, WSB2, LRWD1 and WDTC1. DCX complexes may associate with the COP9
CC signalosome, and this inhibits the E3 ubiquitin-protein ligase activity
CC of the complex. Interacts with NF2, TSC1 and TSC2. Interacts with AGO1
CC and AGO2. Associates with the E3 ligase complex containing DYRK2,
CC EDD/UBR5, DDB1 and DCAF1 proteins (EDVP complex). Interacts directly
CC with DYRK2. DCX(DTL) complex interacts with FBXO11; does not
CC ubiquitinate and degradate FBXO11. Interacts with TRPC4AP (By
CC similarity). Interacts with CRY1 and CRY2 (By similarity). The DDB1-
CC CUL4A complex interacts with CRY1 (By similarity). May also interact
CC with DCUN1D1, DCUN1D2, DCUN1D3 and DCUN1D5 (By similarity).
CC {ECO:0000250|UniProtKB:Q16531, ECO:0000250|UniProtKB:Q3U1J4}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q16531}. Nucleus
CC {ECO:0000250|UniProtKB:Q16531}. Note=Primarily cytoplasmic.
CC Translocates to the nucleus following UV irradiation and subsequently
CC accumulates at sites of DNA damage. {ECO:0000250|UniProtKB:Q16531}.
CC -!- DOMAIN: The core of the protein consists of three WD40 beta-propeller
CC domains. {ECO:0000250|UniProtKB:Q16531}.
CC -!- PTM: Phosphorylated by ABL1. {ECO:0000250|UniProtKB:Q3U1J4}.
CC -!- PTM: Ubiquitinated by CUL4A. Subsequently degraded by ubiquitin-
CC dependent proteolysis. {ECO:0000250|UniProtKB:Q16531}.
CC -!- PTM: Acetylated, promoting interaction with CUL4 (CUL4A or CUL4B) and
CC subsequent formation of DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein
CC ligase complexes. Deacetylation by SIRT7 impairs the interaction with
CC CUL4 (CUL4A or CUL4B) and formation of DCX (DDB1-CUL4-X-box) E3
CC ubiquitin-protein ligase complexes. {ECO:0000250|UniProtKB:Q16531}.
CC -!- SIMILARITY: Belongs to the DDB1 family. {ECO:0000305}.
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DR EMBL; AJ277077; CAB89874.2; -; mRNA.
DR AlphaFoldDB; Q9ESW0; -.
DR SMR; Q9ESW0; -.
DR IntAct; Q9ESW0; 2.
DR MINT; Q9ESW0; -.
DR STRING; 10116.ENSRNOP00000028188; -.
DR iPTMnet; Q9ESW0; -.
DR PhosphoSitePlus; Q9ESW0; -.
DR jPOST; Q9ESW0; -.
DR PaxDb; Q9ESW0; -.
DR PRIDE; Q9ESW0; -.
DR UCSC; RGD:621889; rat.
DR RGD; 621889; Ddb1.
DR eggNOG; KOG1897; Eukaryota.
DR InParanoid; Q9ESW0; -.
DR PhylomeDB; Q9ESW0; -.
DR Reactome; R-RNO-110314; Recognition of DNA damage by PCNA-containing replication complex.
DR Reactome; R-RNO-5696394; DNA Damage Recognition in GG-NER.
DR Reactome; R-RNO-5696395; Formation of Incision Complex in GG-NER.
DR Reactome; R-RNO-5696400; Dual Incision in GG-NER.
DR Reactome; R-RNO-6781823; Formation of TC-NER Pre-Incision Complex.
DR Reactome; R-RNO-6782135; Dual incision in TC-NER.
DR Reactome; R-RNO-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR Reactome; R-RNO-8951664; Neddylation.
DR UniPathway; UPA00143; -.
DR PRO; PR:Q9ESW0; -.
DR Proteomes; UP000002494; Unplaced.
DR GO; GO:0080008; C:Cul4-RING E3 ubiquitin ligase complex; ISS:UniProtKB.
DR GO; GO:0031464; C:Cul4A-RING E3 ubiquitin ligase complex; ISS:UniProtKB.
DR GO; GO:0031465; C:Cul4B-RING E3 ubiquitin ligase complex; ISS:UniProtKB.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0032991; C:protein-containing complex; ISO:RGD.
DR GO; GO:0035861; C:site of double-strand break; IBA:GO_Central.
DR GO; GO:0097602; F:cullin family protein binding; ISO:RGD.
DR GO; GO:0003684; F:damaged DNA binding; IMP:RGD.
DR GO; GO:0044877; F:protein-containing complex binding; ISO:RGD.
DR GO; GO:0030674; F:protein-macromolecule adaptor activity; ISO:RGD.
DR GO; GO:0071987; F:WD40-repeat domain binding; ISO:RGD.
DR GO; GO:0051702; P:biological process involved in interaction with symbiont; ISO:RGD.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; ISO:RGD.
DR GO; GO:0006281; P:DNA repair; IBA:GO_Central.
DR GO; GO:0035518; P:histone H2A monoubiquitination; ISO:RGD.
DR GO; GO:0043066; P:negative regulation of apoptotic process; ISO:RGD.
DR GO; GO:0046726; P:positive regulation by virus of viral protein levels in host cell; ISO:RGD.
DR GO; GO:0045722; P:positive regulation of gluconeogenesis; ISS:UniProtKB.
DR GO; GO:0045732; P:positive regulation of protein catabolic process; ISO:RGD.
DR GO; GO:0045070; P:positive regulation of viral genome replication; ISO:RGD.
DR GO; GO:0010498; P:proteasomal protein catabolic process; ISO:RGD.
DR GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; ISS:UniProtKB.
DR GO; GO:0016567; P:protein ubiquitination; ISS:UniProtKB.
DR GO; GO:0042752; P:regulation of circadian rhythm; ISS:UniProtKB.
DR GO; GO:1901990; P:regulation of mitotic cell cycle phase transition; ISO:RGD.
DR GO; GO:0048511; P:rhythmic process; IEA:UniProtKB-KW.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; ISS:UniProtKB.
DR GO; GO:0070914; P:UV-damage excision repair; ISO:RGD.
DR GO; GO:0019076; P:viral release from host cell; ISO:RGD.
DR GO; GO:0016055; P:Wnt signaling pathway; ISO:RGD.
DR Gene3D; 2.130.10.10; -; 3.
DR InterPro; IPR004871; Cleavage/polyA-sp_fac_asu_C.
DR InterPro; IPR018846; Cleavage/polyA-sp_fac_asu_N.
DR InterPro; IPR031297; DDB1.
DR InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
DR InterPro; IPR036322; WD40_repeat_dom_sf.
DR PANTHER; PTHR10644:SF3; PTHR10644:SF3; 1.
DR Pfam; PF03178; CPSF_A; 1.
DR Pfam; PF10433; MMS1_N; 1.
DR SUPFAM; SSF50978; SSF50978; 1.
PE 1: Evidence at protein level;
KW Acetylation; Biological rhythms; Cytoplasm; DNA damage; DNA repair;
KW DNA-binding; Isopeptide bond; Nucleus; Phosphoprotein; Reference proteome;
KW Repeat; Ubl conjugation; Ubl conjugation pathway.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250|UniProtKB:Q16531"
FT CHAIN 2..1140
FT /note="DNA damage-binding protein 1"
FT /id="PRO_0000281038"
FT REGION 2..768
FT /note="Interaction with CDT1"
FT /evidence="ECO:0000250"
FT REGION 13..356
FT /note="WD repeat beta-propeller A"
FT /evidence="ECO:0000250"
FT REGION 391..708
FT /note="WD repeat beta-propeller B; Interaction with CUL4A"
FT /evidence="ECO:0000250"
FT REGION 709..1043
FT /note="WD repeat beta-propeller C"
FT /evidence="ECO:0000250"
FT REGION 771..1140
FT /note="Interaction with CDT1 and CUL4A"
FT /evidence="ECO:0000250"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0000250|UniProtKB:Q16531"
FT MOD_RES 1067
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q16531"
FT MOD_RES 1125
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT CROSSLNK 1121
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q16531"
SQ SEQUENCE 1140 AA; 126862 MW; 8A1873506C384263 CRC64;
MSYNYVVTAQ KPTAVNGCVT GHFTSAEDIN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK
IAVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI
IGIIDPECRM IGLRLYDGLF KVIPLDRDNK ELKAFNIRLE ELHVIDVKFL YGCQAPTICF
VYQDPQGRHV KTYEVSLREK EFNKGPWKQE NVEAEASMVI AVPEPFGGAI IIGQESITYH
NGDKYLAIAP PIIKQSTIVC HNRVDPNGSR YLLGDMEGRL FMLLLEKEEQ MDGTVTLKDL
RVELLGETSI AECLTYLDNG VVFVGSRLGD SQPVKLNVDS NEQGSYVVAM ETFTNLGPIV
DMCVVDLERQ GQGQLVTCSG AFKEGSLRII RNGIGIHEHA SIDLPGIKGL WPLRSDPNRE
TDDTLVLSFV GQTRVLMLNG EEVEETELMG FVDDQQTFFC GNVAHQQLIQ ITSASVRLVS
QEPKALVSEW KEPRAKNISV ASCNSSQVVV AVGRALYYLQ IHPQELRQIS HTEMEHEVAC
LDVTPLGDSN GLSPLCAIGL WTDISARILK LPSFELLHKE MLGGEIIPRS ILMTTFESSH
YLLCALGDGA LFYFGLNIET GLLSDRKKVT LGTQPTVLRT FRSLSTTNVF ACSDRPTVIY
SSNHKLVFSN VNLKEVNYMC PLNSDGYPDS LALANTSTLT IGTMNEIQKL HIRTVPIYES
PRKICYQEVS QCFGVLSTRI EVQDTSGGTT ALRPSASTQA LSSSVSSSKL FSSSAAPHET
SFGEEVEVHN LLIIDQHTFE VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE
AEPKQGRIVV FQYSGGKLQT VAEKEVKGAV YSMVEFNGKL LASINSTVRL YEWTTEKELR
TECNHYNNIM ALYLKTKGDF ILVGDLMRSV LLLAYKPMEG NFEEIARDFN PNWMSAVEIL
DDDNFLGAEN AFNLFVCQKD SAATTDEERQ HLQEVGLFHL GEFVNVFCHG SLVMQNLGET
STPTQGSVLL GTVNGMIGLV TSLSESWYNL LLDMQNRLNK VIKSVGKIEH SFWRSFHTER
KTEPATGFID GDLIESFLDI SRPKMQEVVA NLQYDDGSGM KREATADDLI KVVEELTRIH
