DDB2_ARATH
ID DDB2_ARATH Reviewed; 557 AA.
AC Q6NQ88; Q9LUY5;
DT 26-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 25-MAY-2022, entry version 140.
DE RecName: Full=Protein DAMAGED DNA-BINDING 2;
DE AltName: Full=UV-damaged DNA-binding protein 2;
GN Name=DDB2; OrderedLocusNames=At5g58760; ORFNames=MZN1.20;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10718197; DOI=10.1093/dnares/7.1.31;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence
RT features of the regions of 3,076,755 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:31-63(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP INTERACTION WITH DDB1A.
RX PubMed=16792691; DOI=10.1111/j.1365-313x.2006.02810.x;
RA Bernhardt A., Lechner E., Hano P., Schade V., Dieterle M., Anders M.,
RA Dubin M.J., Benvenuto G., Bowler C., Genschik P., Hellmann H.;
RT "CUL4 associates with DDB1 and DET1 and its downregulation affects diverse
RT aspects of development in Arabidopsis thaliana.";
RL Plant J. 47:591-603(2006).
RN [6]
RP COMPONENT OF THE UV-DDB COMPLEX.
RX PubMed=17409070; DOI=10.1534/genetics.107.070359;
RA Al Khateeb W.M., Schroeder D.F.;
RT "DDB2, DDB1A and DET1 exhibit complex interactions during Arabidopsis
RT development.";
RL Genetics 176:231-242(2007).
RN [7]
RP FUNCTION, INTERACTION WITH CUL4 AND DDB1A, SUBCELLULAR LOCATION, AND
RP MUTAGENESIS OF ARG-343.
RX PubMed=18551167; DOI=10.1371/journal.pgen.1000093;
RA Molinier J., Lechner E., Dumbliauskas E., Genschik P.;
RT "Regulation and role of Arabidopsis CUL4-DDB1A-DDB2 in maintaining genome
RT integrity upon UV stress.";
RL PLoS Genet. 4:E1000093-E1000093(2008).
RN [8]
RP DWD MOTIF.
RX PubMed=18223036; DOI=10.1105/tpc.107.055418;
RA Lee J.H., Terzaghi W., Gusmaroli G., Charron J.B., Yoon H.J., Chen H.,
RA He Y.J., Xiong Y., Deng X.W.;
RT "Characterization of Arabidopsis and rice DWD proteins and their roles as
RT substrate receptors for CUL4-RING E3 ubiquitin ligases.";
RL Plant Cell 20:152-167(2008).
RN [9]
RP FUNCTION, TISSUE SPECIFICITY, AND INDUCTION BY UV-B.
RX PubMed=20128879; DOI=10.1111/j.1365-313x.2010.04157.x;
RA Biedermann S., Hellmann H.;
RT "The DDB1a interacting proteins ATCSA-1 and DDB2 are critical factors for
RT UV-B tolerance and genomic integrity in Arabidopsis thaliana.";
RL Plant J. 62:404-415(2010).
CC -!- FUNCTION: May function as the substrate recognition module for a DCX
CC (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex including DDB1A
CC and CUL4 (By similarity). Required for DNA repair. Binds to DDB1A to
CC form the UV-damaged DNA-binding protein complex (the UV-DDB complex).
CC The UV-DDB complex may recognize UV-induced DNA damage and recruit
CC proteins of the nucleotide excision repair pathway (the NER pathway) to
CC initiate DNA repair (PubMed:18551167). Involved in UV-B tolerance and
CC genome integrity. In association with ATCSA-1, is necessary for repair
CC of UV-B-induced DNA lesions (PubMed:20128879). {ECO:0000250,
CC ECO:0000269|PubMed:18551167, ECO:0000269|PubMed:20128879}.
CC -!- PATHWAY: Protein modification; protein ubiquitination.
CC -!- SUBUNIT: Component of the UV-DDB complex, which is composed of DDB1A
CC and DDB2. Interacts with CUL4. {ECO:0000269|PubMed:16792691,
CC ECO:0000269|PubMed:18551167}.
CC -!- INTERACTION:
CC Q6NQ88; Q9M0V3-1: DDB1A; NbExp=2; IntAct=EBI-2028926, EBI-8565056;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:18551167}.
CC Note=Broadly distributed over chromatin.
CC -!- TISSUE SPECIFICITY: Expressed in roots and flowers. Expressed at low
CC levels in stems. {ECO:0000269|PubMed:20128879}.
CC -!- INDUCTION: Induced transiently by UV-B. {ECO:0000269|PubMed:20128879}.
CC -!- DOMAIN: The DWD box is required for interaction with DDB1A.
CC {ECO:0000250}.
CC -!- DOMAIN: Interblade loops of the WD repeat region mediate most of the
CC interaction with DNA. A hairpin between blades 5 and 6 inserts into DNA
CC minor groove and mediates recognition of lesions and separation of the
CC damaged and undamaged strands (By similarity). {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the WD repeat DDB2/WDR76 family. {ECO:0000305}.
CC -!- CAUTION: Although the DWD box motif has been suggested to mediate
CC interaction of DDB2 with DDB1A, mutagenesis experiments have to date
CC failed to demonstrate a role for this motif. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA97344.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AB020755; BAA97344.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED97095.1; -; Genomic_DNA.
DR EMBL; BT010570; AAQ65193.1; -; mRNA.
DR EMBL; AK175124; BAD42887.1; -; mRNA.
DR RefSeq; NP_200684.2; NM_125263.5.
DR AlphaFoldDB; Q6NQ88; -.
DR BioGRID; 21234; 1.
DR IntAct; Q6NQ88; 2.
DR MINT; Q6NQ88; -.
DR STRING; 3702.AT5G58760.1; -.
DR iPTMnet; Q6NQ88; -.
DR PaxDb; Q6NQ88; -.
DR PRIDE; Q6NQ88; -.
DR ProteomicsDB; 224587; -.
DR EnsemblPlants; AT5G58760.1; AT5G58760.1; AT5G58760.
DR GeneID; 835990; -.
DR Gramene; AT5G58760.1; AT5G58760.1; AT5G58760.
DR KEGG; ath:AT5G58760; -.
DR Araport; AT5G58760; -.
DR TAIR; locus:2178808; AT5G58760.
DR eggNOG; KOG4328; Eukaryota.
DR HOGENOM; CLU_025710_0_0_1; -.
DR InParanoid; Q6NQ88; -.
DR OrthoDB; 559605at2759; -.
DR PhylomeDB; Q6NQ88; -.
DR UniPathway; UPA00143; -.
DR PRO; PR:Q6NQ88; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q6NQ88; baseline and differential.
DR Genevisible; Q6NQ88; AT.
DR GO; GO:0080008; C:Cul4-RING E3 ubiquitin ligase complex; ISS:TAIR.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0003684; F:damaged DNA binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IMP:TAIR.
DR GO; GO:0016567; P:protein ubiquitination; IEA:UniProtKB-UniPathway.
DR GO; GO:0009411; P:response to UV; IBA:GO_Central.
DR GO; GO:0010224; P:response to UV-B; IMP:TAIR.
DR Gene3D; 2.130.10.10; -; 1.
DR InterPro; IPR033312; DDB2.
DR InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
DR InterPro; IPR001680; WD40_repeat.
DR InterPro; IPR036322; WD40_repeat_dom_sf.
DR PANTHER; PTHR15169; PTHR15169; 1.
DR Pfam; PF00400; WD40; 2.
DR SMART; SM00320; WD40; 5.
DR SUPFAM; SSF50978; SSF50978; 1.
DR PROSITE; PS00678; WD_REPEATS_1; 2.
DR PROSITE; PS50082; WD_REPEATS_2; 2.
DR PROSITE; PS50294; WD_REPEATS_REGION; 1.
PE 1: Evidence at protein level;
KW DNA damage; DNA repair; DNA-binding; Metal-binding; Nucleus;
KW Reference proteome; Repeat; Ubl conjugation pathway; WD repeat; Zinc;
KW Zinc-finger.
FT CHAIN 1..557
FT /note="Protein DAMAGED DNA-BINDING 2"
FT /id="PRO_0000318605"
FT REPEAT 169..209
FT /note="WD 1"
FT /evidence="ECO:0000255"
FT REPEAT 213..255
FT /note="WD 2"
FT /evidence="ECO:0000255"
FT REPEAT 265..304
FT /note="WD 3"
FT /evidence="ECO:0000255"
FT REPEAT 310..350
FT /note="WD 4"
FT /evidence="ECO:0000255"
FT REPEAT 355..395
FT /note="WD 5"
FT /evidence="ECO:0000255"
FT REPEAT 415..458
FT /note="WD 6"
FT /evidence="ECO:0000255"
FT REPEAT 461..500
FT /note="WD 7"
FT /evidence="ECO:0000255"
FT ZN_FING 100..117
FT /note="CCHC-type"
FT /evidence="ECO:0000255"
FT REGION 1..55
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 515..538
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 328..343
FT /note="DWD box"
FT /evidence="ECO:0000305|PubMed:18223036"
FT COMPBIAS 1..18
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 24..42
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 343
FT /note="R->H: Does not impair interaction with DDB1A."
FT /evidence="ECO:0000269|PubMed:18551167"
SQ SEQUENCE 557 AA; 62829 MW; 5C4C32E25166D7C0 CRC64;
MSSTRSRRKR DPEIVIARDT DSELSSSEEE EEEEDNYPFS ESEEEDEAVK NGGKIELEKN
KAKGKAPITV KLIKKVCKVC KQPGHEAGFK GATYIDCPMK PCFLCKMPGH TTMSCPHRVV
TDHGILPTSH RNTKNPIDFV FKRQLQPRIP PIKPKYVIPD QVHCAVIRYH SRRVTCLEFH
PTKNNILLSG DKKGQIGVWD FGKVYEKNVY GNIHSVQVNN MRFSPTNDDM VYSASSDGTI
GYTDLETGTS STLLNLNPDG WQGANSWKML YGMDINSEKG VVLAADNFGF LHMIDHRTNN
STGEPILIHK QGSKVCGLDC NPVQPELLLS CGNDHFARIW DMRKLQPKAS LHDLAHKRVV
NSAYFSPSSG TKILTTCQDN RIRIWDSIFG NLDLPSREIV HSNDFNRHLT PFKAEWDPKD
TSESLIVIGR YISENYNGTA LHPIDFIDAS NGQLVAEVMD PNITTITPVN KLHPRDDVLA
SGSSRSLFIW RPQDNTEMVE EKKDKKIIIC YGDSKKKGKK QKRGSDDEDD EDDIFSSKGK
NIKVNKYQAK TTKKTKT
