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Database: UniProt
Entry: Q2YDS1
LinkDB: Q2YDS1
Original site: Q2YDS1 
ID   DDB2_DANRE              Reviewed;         496 AA.
AC   Q2YDS1; Q1LUF7; Q1LUF8;
DT   23-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT   23-SEP-2008, sequence version 2.
DT   07-APR-2021, entry version 106.
DE   RecName: Full=DNA damage-binding protein 2;
DE   AltName: Full=Damage-specific DNA-binding protein 2;
GN   Name=ddb2; ORFNames=si:dkey-45f10.3;
OS   Danio rerio (Zebrafish) (Brachydanio rerio).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC   Danionidae; Danioninae; Danio.
OX   NCBI_TaxID=7955;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Tuebingen;
RX   PubMed=23594743; DOI=10.1038/nature12111;
RA   Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA   Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA   Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA   White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA   Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA   Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA   Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA   Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA   Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA   Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA   Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA   Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA   Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA   Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA   Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA   McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA   Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA   Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA   Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA   Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA   Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA   Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA   Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA   Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA   Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA   Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA   Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA   Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA   de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA   Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT   "The zebrafish reference genome sequence and its relationship to the human
RT   genome.";
RL   Nature 496:498-503(2013).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC   TISSUE=Olfactory epithelium;
RG   NIH - Zebrafish Gene Collection (ZGC) project;
RL   Submitted (NOV-2005) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 60-423 IN COMPLEX WITH DDB1,
RP   SUBUNIT, AND WD REPEATS.
RX   PubMed=19109893; DOI=10.1016/j.cell.2008.10.045;
RA   Scrima A., Konickova R., Czyzewski B.K., Kawasaki Y., Jeffrey P.D.,
RA   Groisman R., Nakatani Y., Iwai S., Pavletich N.P., Thoma N.H.;
RT   "Structural basis of UV DNA-damage recognition by the DDB1-DDB2 complex.";
RL   Cell 135:1213-1223(2008).
RN   [4]
RP   X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) OF 60-423 IN COMPLEXES WITH DDB1 AND
RP   RBX1, AND SUBUNIT.
RX   PubMed=22118460; DOI=10.1016/j.cell.2011.10.035;
RA   Fischer E.S., Scrima A., Bohm K., Matsumoto S., Lingaraju G.M., Faty M.,
RA   Yasuda T., Cavadini S., Wakasugi M., Hanaoka F., Iwai S., Gut H.,
RA   Sugasawa K., Thoma N.H.;
RT   "The molecular basis of CRL4DDB2/CSA ubiquitin ligase architecture,
RT   targeting, and activation.";
RL   Cell 147:1024-1039(2011).
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 the substrate recognition module for the DCX (DDB2-CUL4-X-
CC       box) E3 ubiquitin-protein ligase complex DDB2-CUL4-ROC1 (also known as
CC       CUL4-DDB-ROC1 and CUL4-DDB-RBX1). The DDB2-CUL4-ROC1 complex may
CC       ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-
CC       induced DNA damage. The ubiquitination of histones may facilitate their
CC       removal from the nucleosome and promote subsequent DNA repair.
CC       {ECO:0000250|UniProtKB:Q92466}.
CC   -!- PATHWAY: Protein modification; protein ubiquitination.
CC   -!- SUBUNIT: Component of the UV-DDB complex which includes ddb1 and ddb2
CC       (PubMed:19109893). Component of a DCX (DDB1-CUL4-X-box) E3 ubiquitin-
CC       protein ligase complex that includes cul4a, or cul4b, ddb1, ddb2 and
CC       rbx1 (PubMed:22118460). A large number of other DCX complexes may also
CC       exist in which an alternate substrate targeting subunit replaces ddb2.
CC       These targeting subunits are generally known as DCAF (ddb1- and cul4-
CC       associated factor) or CDW (cul4-ddb1-associated WD40-repeat) proteins
CC       (By similarity). {ECO:0000250, ECO:0000269|PubMed:19109893,
CC       ECO:0000269|PubMed:22118460}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q92466}.
CC       Note=Accumulates at sites of DNA damage following UV irradiation.
CC       {ECO:0000250|UniProtKB:Q92466}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=Q2YDS1-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q2YDS1-2; Sequence=VSP_035462;
CC   -!- DOMAIN: The DWD box is required for interaction with ddb1.
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.
CC   -!- SIMILARITY: Belongs to the WD repeat DDB2/WDR76 family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAI10097.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC       Sequence=CAK11059.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=CAK11060.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; BX942814; CAK11059.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; BX942814; CAK11060.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; BC110096; AAI10097.1; ALT_INIT; mRNA.
DR   PDB; 3EI1; X-ray; 2.80 A; B=60-423.
DR   PDB; 3EI2; X-ray; 2.60 A; B=60-423.
DR   PDB; 3EI3; X-ray; 2.30 A; B=60-423.
DR   PDB; 4A08; X-ray; 3.00 A; B=60-423.
DR   PDB; 4A09; X-ray; 3.10 A; B=60-423.
DR   PDB; 4A0A; X-ray; 3.60 A; B=60-423.
DR   PDB; 4A0B; X-ray; 3.80 A; B/D=60-423.
DR   PDB; 4A0K; X-ray; 5.93 A; D=60-423.
DR   PDB; 4A0L; X-ray; 7.40 A; B/D=60-423.
DR   PDBsum; 3EI1; -.
DR   PDBsum; 3EI2; -.
DR   PDBsum; 3EI3; -.
DR   PDBsum; 4A08; -.
DR   PDBsum; 4A09; -.
DR   PDBsum; 4A0A; -.
DR   PDBsum; 4A0B; -.
DR   PDBsum; 4A0K; -.
DR   PDBsum; 4A0L; -.
DR   SMR; Q2YDS1; -.
DR   DIP; DIP-53463N; -.
DR   IntAct; Q2YDS1; 2.
DR   STRING; 7955.ENSDARP00000091438; -.
DR   Ensembl; ENSDART00000060302; ENSDARP00000060301; ENSDARG00000041140. [Q2YDS1-1]
DR   Ensembl; ENSDART00000180316; ENSDARP00000152759; ENSDARG00000114723. [Q2YDS1-1]
DR   ZFIN; ZDB-GENE-050419-169; ddb2.
DR   eggNOG; KOG4328; Eukaryota.
DR   GeneTree; ENSGT00510000047881; -.
DR   HOGENOM; CLU_036401_0_0_1; -.
DR   InParanoid; Q2YDS1; -.
DR   OMA; FIKGKGP; -.
DR   PhylomeDB; Q2YDS1; -.
DR   TreeFam; TF331587; -.
DR   Reactome; R-DRE-5689880; Ub-specific processing proteases.
DR   Reactome; R-DRE-5696394; DNA Damage Recognition in GG-NER.
DR   Reactome; R-DRE-5696395; Formation of Incision Complex in GG-NER.
DR   Reactome; R-DRE-5696400; Dual Incision in GG-NER.
DR   Reactome; R-DRE-8951664; Neddylation.
DR   UniPathway; UPA00143; -.
DR   EvolutionaryTrace; Q2YDS1; -.
DR   PRO; PR:Q2YDS1; -.
DR   Proteomes; UP000000437; Chromosome 18.
DR   Bgee; ENSDARG00000041140; Expressed in female gonad and 40 other tissues.
DR   ExpressionAtlas; Q2YDS1; baseline and differential.
DR   GO; GO:0080008; C:Cul4-RING E3 ubiquitin ligase complex; IEA:InterPro.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0003684; F:damaged DNA binding; IEA:InterPro.
DR   GO; GO:0006281; P:DNA repair; IBA:GO_Central.
DR   GO; GO:0016567; P:protein ubiquitination; IEA:UniProtKB-UniPathway.
DR   GO; GO:0009411; P:response to UV; IBA:GO_Central.
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; IPR019775; WD40_repeat_CS.
DR   InterPro; IPR017986; WD40_repeat_dom.
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; 1.
DR   PROSITE; PS50082; WD_REPEATS_2; 1.
DR   PROSITE; PS50294; WD_REPEATS_REGION; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Alternative splicing; DNA damage; DNA repair; DNA-binding;
KW   Nucleus; Reference proteome; Repeat; Ubl conjugation pathway; WD repeat.
FT   CHAIN           1..496
FT                   /note="DNA damage-binding protein 2"
FT                   /id="PRO_0000351090"
FT   REPEAT          118..153
FT                   /note="WD 1"
FT   REPEAT          161..196
FT                   /note="WD 2"
FT   REPEAT          205..240
FT                   /note="WD 3"
FT   REPEAT          246..289
FT                   /note="WD 4"
FT   REPEAT          292..332
FT                   /note="WD 5"
FT   REPEAT          346..386
FT                   /note="WD 6"
FT   REPEAT          396..420
FT                   /note="WD 7"
FT   REGION          337..339
FT                   /note="Photolesion recognition"
FT   MOTIF           258..276
FT                   /note="DWD box"
FT   VAR_SEQ         155..203
FT                   /note="MGPGDAITGMKFNQFNTNQLFVSSIWGATTLRDFSGSVIQVFAKTDSWD ->
FT                   KGAGDFIGCPRDSSKVFVASGDGTVSVQSFEGLQSQILSRTPDCGHDHHDLC (in
FT                   isoform 2)"
FT                   /evidence="ECO:0000305"
FT                   /id="VSP_035462"
FT   CONFLICT        45
FT                   /note="S -> T (in Ref. 2; AAI10097)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        146
FT                   /note="L -> Q (in Ref. 2; AAI10097)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        180
FT                   /note="W -> R (in Ref. 2; AAI10097)"
FT                   /evidence="ECO:0000305"
FT   HELIX           71..79
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   HELIX           85..100
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          104..109
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          116..121
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          128..134
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          138..142
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          149..152
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          156..158
FT                   /evidence="ECO:0007744|PDB:3EI2"
FT   STRAND          160..167
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          170..178
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   TURN            179..181
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          182..187
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   TURN            188..190
FT                   /evidence="ECO:0007744|PDB:4A08"
FT   STRAND          192..197
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          206..212
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   TURN            213..216
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          217..222
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          225..231
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          236..241
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          243..245
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          247..252
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          254..256
FT                   /evidence="ECO:0007744|PDB:4A08"
FT   STRAND          259..264
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          267..273
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   HELIX           274..276
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          279..281
FT                   /evidence="ECO:0007744|PDB:3EI1"
FT   STRAND          283..288
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          293..298
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   TURN            300..302
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          305..319
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          322..325
FT                   /evidence="ECO:0007744|PDB:3EI1"
FT   STRAND          327..331
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          349..357
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   TURN            362..364
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          372..376
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   TURN            377..379
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          382..386
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          397..400
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          404..411
FT                   /evidence="ECO:0007744|PDB:3EI3"
FT   STRAND          414..419
FT                   /evidence="ECO:0007744|PDB:3EI3"
SQ   SEQUENCE   496 AA;  55863 MW;  0B4435B115B15D9D CRC64;
     MARGRAQTDS AASKQTKTVN SKKRPNEETP QPSTKKLKAK QQHKSKQKEE TYIQASVKWT
     GGQKKVGQTS ILHYIYKSSL GQSIHAQLRQ CLQEPFIRSL KSYKLHRTAS PFDRRVTSLE
     WHPTHPTTVA VGSKGGDIIL WDYDVLNKTS FIQGMGPGDA ITGMKFNQFN TNQLFVSSIW
     GATTLRDFSG SVIQVFAKTD SWDYWYCCVD VSVSRQMLAT GDSTGRLLLL GLDGHEIFKE
     KLHKAKVTHA EFNPRCDWLM ATSSVDATVK LWDLRNIKDK NSYIAEMPHE KPVNAAYFNP
     TDSTKLLTTD QRNEIRVYSS YDWSKPDQII IHPHRQFQHL TPIKATWHPM YDLIVAGRYP
     DDQLLLNDKR TIDIYDANSG GLVHQLRDPN AAGIISLNKF SPTGDVLASG MGFNILIWNR
     EDTLSSVNRK QTIVTGEDVG GRAGGSRSQR SSQQRPSRDR RAAADEAKLK KKLSATETKS
     KTKSKTESKT SKSKKK
//
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