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(6-4)DNA photolyase (EC 4.1.99.13) (Protein UV repair defective 3)

 UVR3_ARATH              Reviewed;         556 AA.
O48652; Q2V3V6;
05-OCT-2010, integrated into UniProtKB/Swiss-Prot.
05-OCT-2010, sequence version 2.
30-AUG-2017, entry version 100.
RecName: Full=(6-4)DNA photolyase;
EC=4.1.99.13;
AltName: Full=Protein UV repair defective 3;
Name=UVR3; OrderedLocusNames=At3g15620; ORFNames=SJ11.2;
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 [MRNA], FUNCTION, AND COFACTOR.
STRAIN=cv. Landsberg erecta;
PubMed=9421527; DOI=10.1093/nar/26.2.638;
Nakajima S., Sugiyama M., Iwai S., Hitomi K., Otoshi E., Kim S.T.,
Jiang C.Z., Todo T., Britt A.B., Yamamoto K.;
"Cloning and characterization of a gene (UVR3) required for
photorepair of 6-4 photoproducts in Arabidopsis thaliana.";
Nucleic Acids Res. 26:638-644(1998).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=cv. Columbia;
Sakamoto A., Tanaka A., Tano S., Nakajima S., Yamamoto K.,
Watanabe H.;
"The genomic organization of the Arabidopsis 6-4 photolyase gene.";
(er) Plant Gene Register PGR98-180(1998).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10819329; DOI=10.1093/dnares/7.2.131;
Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
"Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
features of the regions of 4,504,864 bp covered by sixty P1 and TAC
clones.";
DNA Res. 7:131-135(2000).
[4]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
The Arabidopsis Information Portal (Araport);
Submitted (MAY-2016) to the EMBL/GenBank/DDBJ databases.
[5]
TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, AND INDUCTION BY LIGHT.
PubMed=11971912; DOI=10.1093/jexbot/53.371.1005;
Waterworth W.M., Jiang Q., West C.E., Nikaido M., Bray C.M.;
"Characterization of Arabidopsis photolyase enzymes and analysis of
their role in protection from ultraviolet-B radiation.";
J. Exp. Bot. 53:1005-1015(2002).
[6]
FUNCTION.
PubMed=17164245; DOI=10.1074/jbc.M604734200;
Schleicher E., Hitomi K., Kay C.W., Getzoff E.D., Todo T., Weber S.;
"Electron nuclear double resonance differentiates complementary roles
for active site histidines in (6-4) photolyase.";
J. Biol. Chem. 282:4738-4747(2007).
[7]
X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) IN COMPLEX WITH FAD, AND
MUTAGENESIS OF LYS-263; THR-276; HIS-383; HIS-387 AND ARG-439.
PubMed=19359474; DOI=10.1073/pnas.0809180106;
Hitomi K., DiTacchio L., Arvai A.S., Yamamoto J., Kim S.T., Todo T.,
Tainer J.A., Iwai S., Panda S., Getzoff E.D.;
"Functional motifs in the (6-4) photolyase crystal structure make a
comparative framework for DNA repair photolyases and clock
cryptochromes.";
Proc. Natl. Acad. Sci. U.S.A. 106:6962-6967(2009).
-!- FUNCTION: Involved in repair of UV radiation-induced DNA damage.
Catalyzes the photoreactivation of pyrimidine [6-4] pyrimidone
photoproduct (6-4 products). Binds specifically to DNA containing
6-4 products and repairs these lesions in a visible light-
dependent manner. Not required for repair of cyclobutane
pyrimidine dimer (CPD). {ECO:0000269|PubMed:17164245,
ECO:0000269|PubMed:9421527}.
-!- CATALYTIC ACTIVITY: (6-4) photoproduct (in DNA) = 2 pyrimidine
residues (in DNA).
-!- COFACTOR:
Name=FAD; Xref=ChEBI:CHEBI:57692;
Evidence={ECO:0000269|PubMed:9421527};
Note=Binds 1 FAD per subunit. {ECO:0000269|PubMed:9421527};
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=O48652-1; Sequence=Displayed;
Name=2;
IsoId=O48652-2; Sequence=VSP_039720, VSP_039721;
Note=Derived from EST data. No experimental confirmation
available.;
-!- TISSUE SPECIFICITY: Expressed in siliques, flowers and leaves. Not
detected in roots. {ECO:0000269|PubMed:11971912}.
-!- DEVELOPMENTAL STAGE: Expressed at all developmental stages.
{ECO:0000269|PubMed:11971912}.
-!- INDUCTION: Not induced by white or UV-B light.
{ECO:0000269|PubMed:11971912}.
-!- SIMILARITY: Belongs to the DNA photolyase class-1 family.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=BAA24449.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
Sequence=BAA34711.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; AB003687; BAA24449.1; ALT_INIT; mRNA.
EMBL; AB017331; BAA34711.1; ALT_INIT; Genomic_DNA.
EMBL; AB017071; BAB02293.1; -; Genomic_DNA.
EMBL; CP002686; AEE75703.1; -; Genomic_DNA.
EMBL; CP002686; AEE75704.1; -; Genomic_DNA.
RefSeq; NP_001030703.1; NM_001035626.2. [O48652-2]
RefSeq; NP_566520.1; NM_112432.2. [O48652-1]
UniGene; At.188; -.
PDB; 3FY4; X-ray; 2.70 A; A/B/C=20-556.
PDBsum; 3FY4; -.
ProteinModelPortal; O48652; -.
SMR; O48652; -.
STRING; 3702.AT3G15620.1; -.
PaxDb; O48652; -.
EnsemblPlants; AT3G15620.1; AT3G15620.1; AT3G15620. [O48652-1]
EnsemblPlants; AT3G15620.2; AT3G15620.2; AT3G15620. [O48652-2]
GeneID; 820804; -.
Gramene; AT3G15620.1; AT3G15620.1; AT3G15620.
Gramene; AT3G15620.2; AT3G15620.2; AT3G15620.
KEGG; ath:AT3G15620; -.
Araport; AT3G15620; -.
TAIR; locus:2093217; AT3G15620.
eggNOG; KOG0133; Eukaryota.
eggNOG; COG0415; LUCA.
HOGENOM; HOG000245622; -.
InParanoid; O48652; -.
KO; K02295; -.
OMA; CRMIVAS; -.
OrthoDB; EOG0936062H; -.
PhylomeDB; O48652; -.
BioCyc; ARA:GQT-2758-MONOMER; -.
BioCyc; MetaCyc:MONOMER-15021; -.
BRENDA; 4.1.99.13; 399.
EvolutionaryTrace; O48652; -.
PRO; PR:O48652; -.
Proteomes; UP000006548; Chromosome 3.
Genevisible; O48652; AT.
GO; GO:0003914; F:DNA (6-4) photolyase activity; IDA:TAIR.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
GO; GO:0009411; P:response to UV; IMP:TAIR.
Gene3D; 3.40.50.620; -; 1.
InterPro; IPR005101; Cryptochr/Photolyase_FAD-bd.
InterPro; IPR006050; DNA_photolyase_N.
InterPro; IPR014729; Rossmann-like_a/b/a_fold.
Pfam; PF00875; DNA_photolyase; 1.
Pfam; PF03441; FAD_binding_7; 1.
SUPFAM; SSF48173; SSF48173; 1.
SUPFAM; SSF52425; SSF52425; 1.
PROSITE; PS51645; PHR_CRY_ALPHA_BETA; 1.
1: Evidence at protein level;
3D-structure; Alternative splicing; Complete proteome; DNA damage;
DNA repair; DNA-binding; FAD; Flavoprotein; Lyase; Nucleotide-binding;
Reference proteome.
CHAIN 1 556 (6-4)DNA photolyase.
/FTId=PRO_0000397886.
DOMAIN 24 162 Photolyase/cryptochrome alpha/beta.
NP_BIND 276 280 FAD. {ECO:0000269|PubMed:19359474}.
NP_BIND 317 321 FAD. {ECO:0000269|PubMed:19359474}.
NP_BIND 380 383 FAD. {ECO:0000269|PubMed:19359474}.
NP_BIND 415 417 FAD. {ECO:0000269|PubMed:19359474}.
REGION 382 387 Interaction with DNA. {ECO:0000250}.
BINDING 262 262 Phosphate; via amide nitrogen and
carbonyl oxygen.
BINDING 263 263 FAD. {ECO:0000269|PubMed:19359474}.
BINDING 320 320 DNA. {ECO:0000250}.
BINDING 386 386 FAD. {ECO:0000269|PubMed:19359474}.
BINDING 421 421 FAD. {ECO:0000269|PubMed:19359474}.
BINDING 427 427 DNA. {ECO:0000250}.
SITE 348 348 Electron transfer via tryptophanyl
radical. {ECO:0000250}.
SITE 402 402 Electron transfer via tryptophanyl
radical. {ECO:0000250}.
SITE 425 425 Electron transfer via tryptophanyl
radical. {ECO:0000250}.
VAR_SEQ 437 445 FNRIYSPIS -> ALSPFCFSF (in isoform 2).
{ECO:0000305}.
/FTId=VSP_039720.
VAR_SEQ 446 556 Missing (in isoform 2). {ECO:0000305}.
/FTId=VSP_039721.
MUTAGEN 263 263 K->R: No effect on DNA repair activity.
{ECO:0000269|PubMed:19359474}.
MUTAGEN 276 276 T->P: No effect on DNA repair activity.
{ECO:0000269|PubMed:19359474}.
MUTAGEN 383 383 H->A: Loss of DNA repair activity.
{ECO:0000269|PubMed:19359474}.
MUTAGEN 387 387 H->A: Loss of DNA repair activity.
{ECO:0000269|PubMed:19359474}.
MUTAGEN 439 439 R->H,A: No effect on DNA repair activity.
{ECO:0000269|PubMed:19359474}.
STRAND 25 32 {ECO:0000244|PDB:3FY4}.
HELIX 40 46 {ECO:0000244|PDB:3FY4}.
STRAND 52 58 {ECO:0000244|PDB:3FY4}.
HELIX 60 63 {ECO:0000244|PDB:3FY4}.
STRAND 69 73 {ECO:0000244|PDB:3FY4}.
HELIX 79 98 {ECO:0000244|PDB:3FY4}.
STRAND 104 108 {ECO:0000244|PDB:3FY4}.
HELIX 110 118 {ECO:0000244|PDB:3FY4}.
STRAND 123 128 {ECO:0000244|PDB:3FY4}.
HELIX 134 149 {ECO:0000244|PDB:3FY4}.
STRAND 153 155 {ECO:0000244|PDB:3FY4}.
STRAND 160 163 {ECO:0000244|PDB:3FY4}.
HELIX 165 171 {ECO:0000244|PDB:3FY4}.
STRAND 173 175 {ECO:0000244|PDB:3FY4}.
HELIX 180 187 {ECO:0000244|PDB:3FY4}.
TURN 191 194 {ECO:0000244|PDB:3FY4}.
TURN 221 225 {ECO:0000244|PDB:3FY4}.
HELIX 228 230 {ECO:0000244|PDB:3FY4}.
HELIX 241 251 {ECO:0000244|PDB:3FY4}.
HELIX 255 259 {ECO:0000244|PDB:3FY4}.
HELIX 263 265 {ECO:0000244|PDB:3FY4}.
HELIX 280 284 {ECO:0000244|PDB:3FY4}.
HELIX 290 302 {ECO:0000244|PDB:3FY4}.
TURN 310 312 {ECO:0000244|PDB:3FY4}.
HELIX 314 329 {ECO:0000244|PDB:3FY4}.
TURN 332 335 {ECO:0000244|PDB:3FY4}.
HELIX 352 359 {ECO:0000244|PDB:3FY4}.
HELIX 366 378 {ECO:0000244|PDB:3FY4}.
HELIX 383 393 {ECO:0000244|PDB:3FY4}.
TURN 394 398 {ECO:0000244|PDB:3FY4}.
HELIX 402 412 {ECO:0000244|PDB:3FY4}.
HELIX 418 428 {ECO:0000244|PDB:3FY4}.
STRAND 431 433 {ECO:0000244|PDB:3FY4}.
TURN 443 446 {ECO:0000244|PDB:3FY4}.
HELIX 447 449 {ECO:0000244|PDB:3FY4}.
HELIX 455 460 {ECO:0000244|PDB:3FY4}.
HELIX 462 464 {ECO:0000244|PDB:3FY4}.
TURN 469 473 {ECO:0000244|PDB:3FY4}.
HELIX 475 477 {ECO:0000244|PDB:3FY4}.
HELIX 480 486 {ECO:0000244|PDB:3FY4}.
TURN 490 492 {ECO:0000244|PDB:3FY4}.
HELIX 501 521 {ECO:0000244|PDB:3FY4}.
TURN 522 524 {ECO:0000244|PDB:3FY4}.
HELIX 528 541 {ECO:0000244|PDB:3FY4}.
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


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