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DNA damage-binding protein 1a (UV-damaged DNA-binding protein 1a) (DDB1a)

 DDB1A_ARATH             Reviewed;        1088 AA.
Q9M0V3; Q0WL42; Q8VY31;
23-NOV-2004, integrated into UniProtKB/Swiss-Prot.
01-OCT-2000, sequence version 1.
22-NOV-2017, entry version 129.
RecName: Full=DNA damage-binding protein 1a;
AltName: Full=UV-damaged DNA-binding protein 1a;
Short=DDB1a;
Name=DDB1A; OrderedLocusNames=At4g05420; ORFNames=C6L9.100;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10617198; DOI=10.1038/47134;
Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G.,
Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N.,
Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M.,
Weichselgartner M., de Simone V., Obermaier B., Mache R., Mueller M.,
Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T.,
Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I.,
Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P.,
Langham S.-A., McCullagh B., Bilham L., Robben J.,
van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F.,
Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E.,
Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W.,
Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P.,
Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H.,
De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R.,
van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S.,
Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R.,
Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S.,
Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H.,
Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S.,
Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A.,
Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R.,
Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S.,
Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E.,
Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A.,
Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T.,
Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C.,
Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S.,
Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K.,
Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L.,
Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J.,
Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J.,
Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D.,
Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D.,
Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C.,
Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C.,
Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R.,
Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S.,
Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A.,
Chen E., Marra M.A., Martienssen R., McCombie W.R.;
"Sequence and analysis of chromosome 4 of the plant Arabidopsis
thaliana.";
Nature 402:769-777(1999).
[2]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
The Arabidopsis Information Portal (Araport);
Submitted (MAY-2016) to the EMBL/GenBank/DDBJ databases.
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 362-1088.
STRAIN=cv. Columbia;
Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J.,
Hayashizaki Y., Shinozaki K.;
"Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
[5]
INTERACTION WITH DET1.
PubMed=12225661; DOI=10.1016/S0960-9822(02)01106-5;
Schroeder D.F., Gahrtz M., Maxwell B.B., Cook R.K., Kan J.M.,
Alonso J.M., Ecker J.R., Chory J.;
"De-etiolated 1 and damaged DNA binding protein 1 interact to regulate
Arabidopsis photomorphogenesis.";
Curr. Biol. 12:1462-1472(2002).
[6]
COMPONENT OF CDD COMPLEX WITH COP10 AND DET1.
PubMed=15342494; DOI=10.1101/gad.1229504;
Yanagawa Y., Sullivan J.A., Komatsu S., Gusmaroli G., Suzuki G.,
Yin J., Ishibashi T., Saijo Y., Rubio V., Kimura S., Wang J.,
Deng X.-W.;
"Arabidopsis COP10 forms a complex with DDB1 and DET1 in vivo and
enhances the activity of ubiquitin conjugating enzymes.";
Genes Dev. 18:2172-2181(2004).
[7]
INTERACTION WITH CUL4, AND IDENTIFICATION IN THE CUL4-RBX1-CDD E3
LIGASE COMPLEX.
PubMed=16844902; DOI=10.1105/tpc.106.043224;
Chen H., Shen Y., Tang X., Yu L., Wang J., Guo L., Zhang Y., Zhang H.,
Feng S., Strickland E., Zheng N., Deng X.-W.;
"Arabidopsis CULLIN4 forms an E3 ubiquitin ligase with RBX1 and the
CDD complex in mediating light control of development.";
Plant Cell 18:1991-2004(2006).
[8]
INTERACTION WITH CUL4 AND WITH DDB2.
PubMed=16792691; DOI=10.1111/j.1365-313X.2006.02810.x;
Bernhardt A., Lechner E., Hano P., Schade V., Dieterle M., Anders M.,
Dubin M.J., Benvenuto G., Bowler C., Genschik P., Hellmann H.;
"CUL4 associates with DDB1 and DET1 and its downregulation affects
diverse aspects of development in Arabidopsis thaliana.";
Plant J. 47:591-603(2006).
[9]
COMPONENT OF THE UV-DDB COMPLEX.
PubMed=17409070; DOI=10.1534/genetics.107.070359;
Al Khateeb W.M., Schroeder D.F.;
"DDB2, DDB1A and DET1 exhibit complex interactions during Arabidopsis
development.";
Genetics 176:231-242(2007).
[10]
FUNCTION, INTERACTION WITH CUL4 AND DDB2, AND SUBCELLULAR LOCATION.
PubMed=18551167; DOI=10.1371/journal.pgen.1000093;
Molinier J., Lechner E., Dumbliauskas E., Genschik P.;
"Regulation and role of Arabidopsis CUL4-DDB1A-DDB2 in maintaining
genome integrity upon UV stress.";
PLoS Genet. 4:E1000093-E1000093(2008).
[11]
INTERACTION WITH PRL1 AND RAE1, AND COMPONENT OF THE
CUL4-RBX1-DDB1-PRL1 COMPLEX.
PubMed=18223036; DOI=10.1105/tpc.107.055418;
Lee J.H., Terzaghi W., Gusmaroli G., Charron J.B., Yoon H.J., Chen H.,
He Y.J., Xiong Y., Deng X.W.;
"Characterization of Arabidopsis and rice DWD proteins and their roles
as substrate receptors for CUL4-RING E3 ubiquitin ligases.";
Plant Cell 20:152-167(2008).
[12]
INTERACTION WITH WDR55.
PubMed=22447688; DOI=10.1105/tpc.111.089425;
Bjerkan K.N., Jung-Romeo S., Jurgens G., Genschik P., Grini P.E.;
"Arabidopsis WD repeat domain55 Interacts with DNA damaged binding
protein1 and is required for apical patterning in the embryo.";
Plant Cell 24:1013-1033(2012).
-!- FUNCTION: Component of light signal transduction machinery.
Involved in repression of photomorphogenesis in darkness by
participating in the CDD complex, a complex probably required to
regulate the activity of ubiquitin conjugating enzymes (E2s).
Repression of photomorphogenesis is probably mediated by
ubiquitination and subsequent degradation of photomorphogenesis-
promoting factors such as HY5, HYH and LAF1. Plays a role in DNA
repair by forming with DDB2 the UV-damaged DNA-binding protein
complex (UV-DDB). Component of the CUL4-RBX1-DDB1-PRL1 E3
ubiquitin-protein ligase complex. {ECO:0000269|PubMed:18551167}.
-!- PATHWAY: Protein modification; protein ubiquitination.
-!- SUBUNIT: Component of the CDD complex, at least composed of DET1,
COP10 and DDB1A. Component of the CUL4-RBX1-CDD complex. Component
of the CUL4-RBX1-DDB1-PRL1 E3 ubiquitin-protein ligase complex.
Component of the UV-DDB complex, which is composed of DDB1A and
DDB2. Interacts with RAE1 (PubMed:16844902, PubMed:18223036).
Interacts with WDR55 (PubMed:22447688).
{ECO:0000269|PubMed:16844902, ECO:0000269|PubMed:18223036,
ECO:0000269|PubMed:22447688}.
-!- INTERACTION:
Q8H177:At1g65030; NbExp=2; IntAct=EBI-1632780, EBI-1632868;
Q9LJD7:COP10; NbExp=5; IntAct=EBI-1632780, EBI-2429853;
Q8LGH4:CUL4; NbExp=11; IntAct=EBI-1632780, EBI-541750;
Q9M086:DCAF1; NbExp=6; IntAct=EBI-1632780, EBI-2429941;
Q6NQ88:DDB2; NbExp=2; IntAct=EBI-8565056, EBI-2028926;
Q9M1E5:F9K21.200; NbExp=2; IntAct=EBI-1632780, EBI-1632891;
O22467:MSI1; NbExp=3; IntAct=EBI-8565056, EBI-632891;
O22469:MSI3; NbExp=2; IntAct=EBI-1632780, EBI-1632794;
O22607:MSI4; NbExp=2; IntAct=EBI-1632780, EBI-9661079;
Q8L4M1:THO6; NbExp=2; IntAct=EBI-1632780, EBI-941035;
Q9SZQ5:VIP3; NbExp=2; IntAct=EBI-1632780, EBI-1632819;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:18551167}.
Nucleus {ECO:0000269|PubMed:18551167}. Note=Translocates to the
nucleus upon exposure to UV.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=1;
Comment=A number of isoforms are produced. According to EST
sequences.;
Name=1;
IsoId=Q9M0V3-1; Sequence=Displayed;
-!- SIMILARITY: Belongs to the DDB1 family. {ECO:0000305}.
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EMBL; AL161503; CAB81084.1; -; Genomic_DNA.
EMBL; CP002687; AEE82517.1; -; Genomic_DNA.
EMBL; AY074257; AAL66955.1; -; mRNA.
EMBL; BT001905; AAN71904.1; -; mRNA.
EMBL; AK230366; BAF02165.1; -; mRNA.
PIR; B85068; B85068.
RefSeq; NP_192451.1; NM_116781.3. [Q9M0V3-1]
UniGene; At.32663; -.
UniGene; At.47587; -.
ProteinModelPortal; Q9M0V3; -.
SMR; Q9M0V3; -.
BioGrid; 11201; 37.
DIP; DIP-40455N; -.
IntAct; Q9M0V3; 23.
STRING; 3702.AT4G05420.1; -.
iPTMnet; Q9M0V3; -.
PaxDb; Q9M0V3; -.
EnsemblPlants; AT4G05420.1; AT4G05420.1; AT4G05420. [Q9M0V3-1]
GeneID; 825890; -.
Gramene; AT4G05420.1; AT4G05420.1; AT4G05420.
KEGG; ath:AT4G05420; -.
Araport; AT4G05420; -.
TAIR; locus:2115909; AT4G05420.
eggNOG; KOG1897; Eukaryota.
eggNOG; ENOG410XPF6; LUCA.
HOGENOM; HOG000007241; -.
InParanoid; Q9M0V3; -.
KO; K10610; -.
OMA; GIGIQEH; -.
OrthoDB; EOG093600TR; -.
PhylomeDB; Q9M0V3; -.
BRENDA; 6.3.2.19; 399.
Reactome; R-ATH-110314; Recognition of DNA damage by PCNA-containing replication complex.
Reactome; R-ATH-5696394; DNA Damage Recognition in GG-NER.
Reactome; R-ATH-5696395; Formation of Incision Complex in GG-NER.
Reactome; R-ATH-5696400; Dual Incision in GG-NER.
Reactome; R-ATH-6781823; Formation of TC-NER Pre-Incision Complex.
Reactome; R-ATH-6782135; Dual incision in TC-NER.
Reactome; R-ATH-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
Reactome; R-ATH-8951664; Neddylation.
UniPathway; UPA00143; -.
PRO; PR:Q9M0V3; -.
Proteomes; UP000006548; Chromosome 4.
ExpressionAtlas; Q9M0V3; baseline and differential.
Genevisible; Q9M0V3; AT.
GO; GO:0080008; C:Cul4-RING E3 ubiquitin ligase complex; IPI:TAIR.
GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
GO; GO:0005829; C:cytosol; IDA:TAIR.
GO; GO:0005634; C:nucleus; IDA:TAIR.
GO; GO:0003684; F:damaged DNA binding; IBA:GO_Central.
GO; GO:0006289; P:nucleotide-excision repair; IBA:GO_Central.
GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; IBA:GO_Central.
GO; GO:0016567; P:protein ubiquitination; IEA:UniProtKB-UniPathway.
GO; GO:0009585; P:red, far-red light phototransduction; IEA:UniProtKB-KW.
Gene3D; 2.130.10.10; -; 2.
InterPro; IPR004871; Cleavage/polyA-sp_fac_asu_C.
InterPro; IPR031297; DDB1.
InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
InterPro; IPR036322; WD40_repeat_dom_sf.
PANTHER; PTHR10644:SF3; PTHR10644:SF3; 1.
Pfam; PF03178; CPSF_A; 1.
SUPFAM; SSF50978; SSF50978; 2.
1: Evidence at protein level;
Alternative splicing; Complete proteome; Cytoplasm; DNA damage;
DNA repair; DNA-binding; Nucleus; Phytochrome signaling pathway;
Reference proteome; Ubl conjugation pathway.
CHAIN 1 1088 DNA damage-binding protein 1a.
/FTId=PRO_0000079837.
SEQUENCE 1088 AA; 121306 MW; 79071E5BC62A197E CRC64;
MSSWNYVVTA HKPTSVTHSC VGNFTSPQEL NLIVAKCTRI EIHLLTPQGL QPMLDVPIYG
RIATLELFRP HGEAQDFLFI ATERYKFCVL QWDPESSELI TRAMGDVSDR IGRPTDNGQI
GIIDPDCRLI GLHLYDGLFK VIPFDNKGQL KEAFNIRLEE LQVLDIKFLF GCAKPTIAVL
YQDNKDARHV KTYEVSLKDK DFVEGPWSQN SLDNGADLLI PVPPPLCGVL IIGEETIVYC
SASAFKAIPI RPSITKAYGR VDVDGSRYLL GDHAGMIHLL VITHEKEKVT GLKIELLGET
SIASTISYLD NAVVFVGSSY GDSQLVKLNL HPDAKGSYVE VLERYINLGP IVDFCVVDLE
RQGQGQVVTC SGAFKDGSLR VVRNGIGINE QASVELQGIK GMWSLKSSID EAFDTFLVVS
FISETRILAM NLEDELEETE IEGFLSQVQT LFCHDAVYNQ LVQVTSNSVR LVSSTTRELR
DEWHAPAGFT VNVATANASQ VLLATGGGHL VYLEIGDGKL TEVQHALLEY EVSCLDINPI
GDNPNYSQLA AVGMWTDISV RIFSLPELTL ITKEQLGGEI IPRSVLLCAF EGISYLLCAL
GDGHLLNFQM DTTTGQLKDR KKVSLGTQPI TLRTFSSKSA THVFAASDRP TVIYSSNKKL
LYSNVNLKEV SHMCPFNSAA FPDSLAIARE GELTIGTIDD IQKLHIRTIP LGEHARRICH
QEQTRTFGIC SLGNQSNSEE SEMHFVRLLD DQTFEFMSTY PLDSFEYGCS ILSCSFTEDK
NVYYCVGTAY VLPEENEPTK GRILVFIVED GRLQLIAEKE TKGAVYSLNA FNGKLLAAIN
QKIQLYKWML RDDGTRELQS ECGHHGHILA LYVQTRGDFI VVGDLMKSIS LLLYKHEEGA
IEERARDYNA NWMSAVEILD DDIYLGAENN FNLLTVKKNS EGATDEERGR LEVVGEYHLG
EFVNRFRHGS LVMRLPDSEI GQIPTVIFGT VNGVIGVIAS LPQEQYTFLE KLQSSLRKVI
KGVGGLSHEQ WRSFNNEKRT AEARNFLDGD LIESFLDLSR NKMEDISKSM NVQVEELCKR
VEELTRLH


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