DDB2_ORYSJ
ID DDB2_ORYSJ Reviewed; 584 AA.
AC Q84KJ3; Q9FU94;
DT 02-NOV-2016, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=DNA damage-binding protein 2 {ECO:0000305};
DE AltName: Full=UV-damaged DNA-binding protein 2 {ECO:0000305};
DE Short=OsUV-DDB2 {ECO:0000303|PubMed:12711392};
DE AltName: Full=WD40 repeat-containing protein 2 {ECO:0000305};
DE Short=OsWD40-2 {ECO:0000303|PubMed:22429805};
GN Name=DDB2 {ECO:0000305};
GN OrderedLocusNames=Os01g0141700 {ECO:0000312|EMBL:BAF03899.1},
GN LOC_Os01g04870 {ECO:0000305};
GN ORFNames=OsJ_00319 {ECO:0000312|EMBL:EEE53842.1},
GN P0019D06.8 {ECO:0000312|EMBL:BAB16450.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, INTERACTION WITH DDB1,
RP AND TISSUE SPECIFICITY.
RC STRAIN=cv. Nipponbare;
RX PubMed=12711392; DOI=10.1016/s0378-1119(03)00447-5;
RA Ishibashi T., Kimura S., Yamamoto T., Furukawa T., Takata K., Uchiyama Y.,
RA Hashimoto J., Sakaguchi K.;
RT "Rice UV-damaged DNA binding protein homologues are most abundant in
RT proliferating tissues.";
RL Gene 308:79-87(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12447438; DOI=10.1038/nature01184;
RA Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT "The genome sequence and structure of rice chromosome 1.";
RL Nature 420:312-316(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [8]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=22429805; DOI=10.1186/1471-2164-13-100;
RA Ouyang Y., Huang X., Lu Z., Yao J.;
RT "Genomic survey, expression profile and co-expression network analysis of
RT OsWD40 family in rice.";
RL BMC Genomics 13:100-100(2012).
CC -!- FUNCTION: Required for DNA repair. Binds to DDB1 to form the UV-damaged
CC DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex
CC may recognize UV-induced DNA damage and recruit proteins of the
CC nucleotide excision repair pathway (the NER pathway) to initiate DNA
CC repair (Probable). May function as the substrate recognition module for
CC a DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex (By
CC similarity). {ECO:0000250|UniProtKB:Q92466,
CC ECO:0000305|PubMed:12711392}.
CC -!- SUBUNIT: Component of the UV-DDB complex, which is composed of DDB1 and
CC DDB2. {ECO:0000269|PubMed:12711392}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q6NQ88}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q84KJ3-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q84KJ3-2; Sequence=VSP_058626;
CC -!- TISSUE SPECIFICITY: Expressed in proliferating tissues such as shoot
CC apical meristem (SAM), root tips and young leaves. Not detected in
CC mature leaves. {ECO:0000269|PubMed:12711392}.
CC -!- SIMILARITY: Belongs to the WD repeat DDB2/WDR76 family. {ECO:0000305}.
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DR EMBL; AB082381; BAC75824.1; -; mRNA.
DR EMBL; AP002483; BAB16450.1; -; Genomic_DNA.
DR EMBL; AP008207; BAF03899.1; -; Genomic_DNA.
DR EMBL; AP014957; BAS70324.1; -; Genomic_DNA.
DR EMBL; CM000138; EEE53842.1; -; Genomic_DNA.
DR EMBL; AK111907; BAG99473.1; -; mRNA.
DR EMBL; AK112097; BAG99549.1; -; mRNA.
DR RefSeq; XP_015622245.1; XM_015766759.1. [Q84KJ3-2]
DR AlphaFoldDB; Q84KJ3; -.
DR SMR; Q84KJ3; -.
DR STRING; 4530.OS01T0141700-01; -.
DR PRIDE; Q84KJ3; -.
DR EnsemblPlants; Os01t0141700-01; Os01t0141700-01; Os01g0141700. [Q84KJ3-2]
DR GeneID; 4325482; -.
DR Gramene; Os01t0141700-01; Os01t0141700-01; Os01g0141700. [Q84KJ3-2]
DR KEGG; osa:4325482; -.
DR eggNOG; KOG4328; Eukaryota.
DR InParanoid; Q84KJ3; -.
DR OMA; DSIFGNM; -.
DR OrthoDB; 559605at2759; -.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000007752; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
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; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IBA:GO_Central.
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; IPR036322; WD40_repeat_dom_sf.
DR PANTHER; PTHR15169; PTHR15169; 1.
DR Pfam; PF00400; WD40; 1.
DR SMART; SM00320; WD40; 5.
DR SUPFAM; SSF50978; SSF50978; 1.
DR PROSITE; PS00678; WD_REPEATS_1; 1.
DR PROSITE; PS50082; WD_REPEATS_2; 2.
DR PROSITE; PS50294; WD_REPEATS_REGION; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; DNA damage; DNA repair; DNA-binding; Metal-binding;
KW Nucleus; Reference proteome; Repeat; Ubl conjugation pathway; WD repeat;
KW Zinc; Zinc-finger.
FT CHAIN 1..584
FT /note="DNA damage-binding protein 2"
FT /id="PRO_0000438215"
FT REPEAT 192..232
FT /note="WD 1"
FT /evidence="ECO:0000255"
FT REPEAT 236..278
FT /note="WD 2"
FT /evidence="ECO:0000255"
FT REPEAT 288..327
FT /note="WD 3"
FT /evidence="ECO:0000255"
FT REPEAT 333..373
FT /note="WD 4"
FT /evidence="ECO:0000255"
FT REPEAT 378..418
FT /note="WD 5"
FT /evidence="ECO:0000255"
FT REPEAT 438..481
FT /note="WD 6"
FT /evidence="ECO:0000255"
FT REPEAT 484..523
FT /note="WD 7"
FT /evidence="ECO:0000255"
FT ZN_FING 122..140
FT /note="CCHC-type"
FT /evidence="ECO:0000255"
FT REGION 1..87
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 517..584
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 351..366
FT /note="DWD box"
FT /evidence="ECO:0000250|UniProtKB:Q6NQ88"
FT COMPBIAS 43..69
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 517..563
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 564..584
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 131
FT /note="Missing (in isoform 2)"
FT /id="VSP_058626"
SQ SEQUENCE 584 AA; 64825 MW; D74E18EF92840CBA CRC64;
MGPTTRARFV HNRRRRRRRG PYAAPDDDDE EEDQQEASSS SSSSDEGEED AEEEGSGEVD
DDDGEAAEPS GKEEEVSPVA AAARSGRKAS ITISLKKVCK VCKSTGHEAG FKGAVYIDCP
RKPCFLCKMP GGHTTLTCPH RVAMEHGVIP ASRRNTNTSL DYVFQSQVKG KIPMVKPQFL
IPNQLECGNI KFHQRRVTCL EFHPTKNNVL LSGDKKGLLG VWDYVKLHEK ITYDSVHSCI
LNSMKFDTTN DGLLYTASSD GTISSTDLDT GIGSSLLNLN PNGWNGPSTW RMIYGMDFNS
DKGLLLVADS FGFLHLLDRR LKARIGDPIL IHKKGSKVTS LHCNPAQPEV LLSSGNDHYA
RIWDTRKLEP NSAFVSLAHG RVVNSGYFSP QSGNKILTTC QDNRIRVWDY IFGNLESPSR
EIVHSHDFNR HLTPFKAEWD PKDHTETVAV IGRYISENYN GIALHPIDFI DTSTGKLLAE
VMDPDITTIS PVNKLHPRDD ILASGSSRSI FIWKPKTESD ATEERNREKA KEFVYGSGSR
KKSNGKHENS SDDDSDGSCD GKKKKKAKKT RFTHTIKGKG KSKV
