UVR3_ARATH
ID UVR3_ARATH Reviewed; 556 AA.
AC O48652; Q2V3V6;
DT 05-OCT-2010, integrated into UniProtKB/Swiss-Prot.
DT 05-OCT-2010, sequence version 2.
DT 03-AUG-2022, entry version 123.
DE RecName: Full=(6-4)DNA photolyase;
DE EC=4.1.99.13;
DE AltName: Full=Protein UV repair defective 3;
GN Name=UVR3; OrderedLocusNames=At3g15620; ORFNames=SJ11.2;
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 [MRNA], FUNCTION, AND COFACTOR.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=9421527; DOI=10.1093/nar/26.2.638;
RA Nakajima S., Sugiyama M., Iwai S., Hitomi K., Otoshi E., Kim S.T.,
RA Jiang C.Z., Todo T., Britt A.B., Yamamoto K.;
RT "Cloning and characterization of a gene (UVR3) required for photorepair of
RT 6-4 photoproducts in Arabidopsis thaliana.";
RL Nucleic Acids Res. 26:638-644(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=cv. Columbia;
RA Sakamoto A., Tanaka A., Tano S., Nakajima S., Yamamoto K., Watanabe H.;
RT "The genomic organization of the Arabidopsis 6-4 photolyase gene.";
RL (er) Plant Gene Register PGR98-180(1998).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(2000).
RN [4]
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 [5]
RP TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, AND INDUCTION BY LIGHT.
RX PubMed=11971912; DOI=10.1093/jexbot/53.371.1005;
RA Waterworth W.M., Jiang Q., West C.E., Nikaido M., Bray C.M.;
RT "Characterization of Arabidopsis photolyase enzymes and analysis of their
RT role in protection from ultraviolet-B radiation.";
RL J. Exp. Bot. 53:1005-1015(2002).
RN [6]
RP FUNCTION.
RX PubMed=17164245; DOI=10.1074/jbc.m604734200;
RA Schleicher E., Hitomi K., Kay C.W., Getzoff E.D., Todo T., Weber S.;
RT "Electron nuclear double resonance differentiates complementary roles for
RT active site histidines in (6-4) photolyase.";
RL J. Biol. Chem. 282:4738-4747(2007).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) IN COMPLEX WITH FAD, AND MUTAGENESIS
RP OF LYS-263; THR-276; HIS-383; HIS-387 AND ARG-439.
RX PubMed=19359474; DOI=10.1073/pnas.0809180106;
RA Hitomi K., DiTacchio L., Arvai A.S., Yamamoto J., Kim S.T., Todo T.,
RA Tainer J.A., Iwai S., Panda S., Getzoff E.D.;
RT "Functional motifs in the (6-4) photolyase crystal structure make a
RT comparative framework for DNA repair photolyases and clock cryptochromes.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:6962-6967(2009).
CC -!- FUNCTION: Involved in repair of UV radiation-induced DNA damage.
CC Catalyzes the photoreactivation of pyrimidine [6-4] pyrimidone
CC photoproduct (6-4 products). Binds specifically to DNA containing 6-4
CC products and repairs these lesions in a visible light-dependent manner.
CC Not required for repair of cyclobutane pyrimidine dimer (CPD).
CC {ECO:0000269|PubMed:17164245, ECO:0000269|PubMed:9421527}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA).;
CC EC=4.1.99.13;
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:9421527};
CC Note=Binds 1 FAD per subunit. {ECO:0000269|PubMed:9421527};
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=O48652-1; Sequence=Displayed;
CC Name=2;
CC IsoId=O48652-2; Sequence=VSP_039720, VSP_039721;
CC -!- TISSUE SPECIFICITY: Expressed in siliques, flowers and leaves. Not
CC detected in roots. {ECO:0000269|PubMed:11971912}.
CC -!- DEVELOPMENTAL STAGE: Expressed at all developmental stages.
CC {ECO:0000269|PubMed:11971912}.
CC -!- INDUCTION: Not induced by white or UV-B light.
CC {ECO:0000269|PubMed:11971912}.
CC -!- SIMILARITY: Belongs to the DNA photolyase class-1 family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA24449.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=BAA34711.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AB003687; BAA24449.1; ALT_INIT; mRNA.
DR EMBL; AB017331; BAA34711.1; ALT_INIT; Genomic_DNA.
DR EMBL; AB017071; BAB02293.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75703.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75704.1; -; Genomic_DNA.
DR RefSeq; NP_001030703.1; NM_001035626.2. [O48652-2]
DR RefSeq; NP_566520.1; NM_112432.2. [O48652-1]
DR PDB; 3FY4; X-ray; 2.70 A; A/B/C=20-556.
DR PDBsum; 3FY4; -.
DR AlphaFoldDB; O48652; -.
DR SMR; O48652; -.
DR STRING; 3702.AT3G15620.1; -.
DR PaxDb; O48652; -.
DR PRIDE; O48652; -.
DR ProteomicsDB; 228566; -. [O48652-1]
DR EnsemblPlants; AT3G15620.1; AT3G15620.1; AT3G15620. [O48652-1]
DR EnsemblPlants; AT3G15620.2; AT3G15620.2; AT3G15620. [O48652-2]
DR GeneID; 820804; -.
DR Gramene; AT3G15620.1; AT3G15620.1; AT3G15620. [O48652-1]
DR Gramene; AT3G15620.2; AT3G15620.2; AT3G15620. [O48652-2]
DR KEGG; ath:AT3G15620; -.
DR Araport; AT3G15620; -.
DR TAIR; locus:2093217; AT3G15620.
DR eggNOG; KOG0133; Eukaryota.
DR HOGENOM; CLU_010348_3_4_1; -.
DR InParanoid; O48652; -.
DR OMA; WQWSASS; -.
DR OrthoDB; 378952at2759; -.
DR PhylomeDB; O48652; -.
DR BioCyc; MetaCyc:MON-15021; -.
DR BRENDA; 4.1.99.13; 399.
DR EvolutionaryTrace; O48652; -.
DR PRO; PR:O48652; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; O48652; baseline and differential.
DR Genevisible; O48652; AT.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003904; F:deoxyribodipyrimidine photo-lyase activity; IBA:GO_Central.
DR GO; GO:0003914; F:DNA (6-4) photolyase activity; IDA:TAIR.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
DR GO; GO:0071949; F:FAD binding; IBA:GO_Central.
DR GO; GO:0032922; P:circadian regulation of gene expression; IBA:GO_Central.
DR GO; GO:0043153; P:entrainment of circadian clock by photoperiod; IBA:GO_Central.
DR GO; GO:0006290; P:pyrimidine dimer repair; IMP:TAIR.
DR GO; GO:0009411; P:response to UV; IMP:TAIR.
DR Gene3D; 3.40.50.620; -; 1.
DR InterPro; IPR036134; Crypto/Photolyase_FAD-like_sf.
DR InterPro; IPR036155; Crypto/Photolyase_N_sf.
DR InterPro; IPR005101; Cryptochr/Photolyase_FAD-bd.
DR InterPro; IPR002081; Cryptochrome/DNA_photolyase_1.
DR InterPro; IPR006050; DNA_photolyase_N.
DR InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR PANTHER; PTHR11455; PTHR11455; 1.
DR Pfam; PF00875; DNA_photolyase; 1.
DR Pfam; PF03441; FAD_binding_7; 1.
DR SUPFAM; SSF48173; SSF48173; 1.
DR SUPFAM; SSF52425; SSF52425; 1.
DR PROSITE; PS51645; PHR_CRY_ALPHA_BETA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; DNA damage; DNA repair; DNA-binding;
KW FAD; Flavoprotein; Lyase; Nucleotide-binding; Reference proteome.
FT CHAIN 1..556
FT /note="(6-4)DNA photolyase"
FT /id="PRO_0000397886"
FT DOMAIN 24..162
FT /note="Photolyase/cryptochrome alpha/beta"
FT REGION 382..387
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT REGION 534..556
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 262
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT BINDING 263
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:19359474"
FT BINDING 276..280
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:19359474"
FT BINDING 317..321
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:19359474"
FT BINDING 320
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000250"
FT BINDING 380..383
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:19359474"
FT BINDING 386
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:19359474"
FT BINDING 415..417
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:19359474"
FT BINDING 421
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:19359474"
FT BINDING 427
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000250"
FT SITE 348
FT /note="Electron transfer via tryptophanyl radical"
FT /evidence="ECO:0000250"
FT SITE 402
FT /note="Electron transfer via tryptophanyl radical"
FT /evidence="ECO:0000250"
FT SITE 425
FT /note="Electron transfer via tryptophanyl radical"
FT /evidence="ECO:0000250"
FT VAR_SEQ 437..445
FT /note="FNRIYSPIS -> ALSPFCFSF (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_039720"
FT VAR_SEQ 446..556
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_039721"
FT MUTAGEN 263
FT /note="K->R: No effect on DNA repair activity."
FT /evidence="ECO:0000269|PubMed:19359474"
FT MUTAGEN 276
FT /note="T->P: No effect on DNA repair activity."
FT /evidence="ECO:0000269|PubMed:19359474"
FT MUTAGEN 383
FT /note="H->A: Loss of DNA repair activity."
FT /evidence="ECO:0000269|PubMed:19359474"
FT MUTAGEN 387
FT /note="H->A: Loss of DNA repair activity."
FT /evidence="ECO:0000269|PubMed:19359474"
FT MUTAGEN 439
FT /note="R->H,A: No effect on DNA repair activity."
FT /evidence="ECO:0000269|PubMed:19359474"
FT STRAND 25..32
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 40..46
FT /evidence="ECO:0007829|PDB:3FY4"
FT STRAND 52..58
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 60..63
FT /evidence="ECO:0007829|PDB:3FY4"
FT STRAND 69..73
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 79..98
FT /evidence="ECO:0007829|PDB:3FY4"
FT STRAND 104..108
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 110..118
FT /evidence="ECO:0007829|PDB:3FY4"
FT STRAND 123..128
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 134..149
FT /evidence="ECO:0007829|PDB:3FY4"
FT STRAND 153..155
FT /evidence="ECO:0007829|PDB:3FY4"
FT STRAND 160..163
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 165..171
FT /evidence="ECO:0007829|PDB:3FY4"
FT STRAND 173..175
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 180..187
FT /evidence="ECO:0007829|PDB:3FY4"
FT TURN 191..194
FT /evidence="ECO:0007829|PDB:3FY4"
FT TURN 221..225
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 228..230
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 241..251
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 255..259
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 263..265
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 280..284
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 290..302
FT /evidence="ECO:0007829|PDB:3FY4"
FT TURN 310..312
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 314..329
FT /evidence="ECO:0007829|PDB:3FY4"
FT TURN 332..335
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 352..359
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 366..378
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 383..393
FT /evidence="ECO:0007829|PDB:3FY4"
FT TURN 394..398
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 402..412
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 418..428
FT /evidence="ECO:0007829|PDB:3FY4"
FT STRAND 431..433
FT /evidence="ECO:0007829|PDB:3FY4"
FT TURN 443..446
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 447..449
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 455..460
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 462..464
FT /evidence="ECO:0007829|PDB:3FY4"
FT TURN 469..473
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 475..477
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 480..486
FT /evidence="ECO:0007829|PDB:3FY4"
FT TURN 490..492
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 501..521
FT /evidence="ECO:0007829|PDB:3FY4"
FT TURN 522..524
FT /evidence="ECO:0007829|PDB:3FY4"
FT HELIX 528..541
FT /evidence="ECO:0007829|PDB:3FY4"
SQ SEQUENCE 556 AA; 63790 MW; 3110841DBA33CAC8 CRC64;
MQRFCVCSPS SYRLNPITSM ATGSGSLIWF RKGLRVHDNP ALEYASKGSE FMYPVFVIDP
HYMESDPSAF SPGSSRAGVN RIRFLLESLK DLDSSLKKLG SRLLVFKGEP GEVLVRCLQE
WKVKRLCFEY DTDPYYQALD VKVKDYASST GVEVFSPVSH TLFNPAHIIE KNGGKPPLSY
QSFLKVAGEP SCAKSELVMS YSSLPPIGDI GNLGISEVPS LEELGYKDDE QADWTPFRGG
ESEALKRLTK SISDKAWVAN FEKPKGDPSA FLKPATTVMS PYLKFGCLSS RYFYQCLQNI
YKDVKKHTSP PVSLLGQLLW REFFYTTAFG TPNFDKMKGN RICKQIPWNE DHAMLAAWRD
GKTGYPWIDA IMVQLLKWGW MHHLARHCVA CFLTRGDLFI HWEQGRDVFE RLLIDSDWAI
NNGNWMWLSC SSFFYQFNRI YSPISFGKKY DPDGKYIRHF LPVLKDMPKQ YIYEPWTAPL
SVQTKANCIV GKDYPKPMVL HDSASKECKR KMGEAYALNK KMDGKVDEEN LRDLRRKLQK
DEHEESKIRN QRPKLK
