ID UVR3_ORYSJ Reviewed; 551 AA.
AC Q0E2Y1; A0A0P0VG67; B9F3X5; Q6Z6D9;
DT 05-OCT-2010, integrated into UniProtKB/Swiss-Prot.
DT 13-OCT-2009, sequence version 1.
DT 27-MAR-2024, entry version 76.
DE RecName: Full=(6-4)DNA photolyase;
DE EC=4.1.99.13;
GN Name=UVR3; OrderedLocusNames=Os02g0204400, LOC_Os02g10990;
GN ORFNames=OSJNBb0056C19.3, P0544H11.19;
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 [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 [2]
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 [3]
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 [4]
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).
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) (By similarity). {ECO:0000250}.
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; Evidence={ECO:0000250};
CC Note=Binds 1 FAD per subunit. {ECO:0000250};
CC -!- SIMILARITY: Belongs to the DNA photolyase class-1 family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAD16007.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAD38427.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AP005008; BAD16007.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP005915; BAD38427.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008208; BAF08157.2; -; Genomic_DNA.
DR EMBL; AP014958; BAS77547.1; -; Genomic_DNA.
DR EMBL; CM000139; EEE56527.1; -; Genomic_DNA.
DR RefSeq; XP_015623929.1; XM_015768443.1.
DR AlphaFoldDB; Q0E2Y1; -.
DR SMR; Q0E2Y1; -.
DR STRING; 39947.Q0E2Y1; -.
DR PaxDb; 39947-Q0E2Y1; -.
DR EnsemblPlants; Os02t0204400-00; Os02t0204400-00; Os02g0204400.
DR GeneID; 4328669; -.
DR Gramene; Os02t0204400-00; Os02t0204400-00; Os02g0204400.
DR KEGG; osa:4328669; -.
DR eggNOG; KOG0133; Eukaryota.
DR HOGENOM; CLU_010348_3_4_1; -.
DR InParanoid; Q0E2Y1; -.
DR OMA; WHRTDLR; -.
DR OrthoDB; 124765at2759; -.
DR Proteomes; UP000000763; Chromosome 2.
DR Proteomes; UP000007752; Chromosome 2.
DR Proteomes; UP000059680; Chromosome 2.
DR Genevisible; Q0E2Y1; OS.
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; IEA:UniProtKB-EC.
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; IEA:EnsemblPlants.
DR GO; GO:0009411; P:response to UV; IEA:EnsemblPlants.
DR Gene3D; 1.25.40.80; -; 2.
DR Gene3D; 1.10.579.10; DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3; 1.
DR Gene3D; 3.40.50.620; HUPs; 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; CRYPTOCHROME; 1.
DR PANTHER; PTHR11455:SF9; CRYPTOCHROME-1; 1.
DR Pfam; PF00875; DNA_photolyase; 1.
DR Pfam; PF03441; FAD_binding_7; 1.
DR SUPFAM; SSF48173; Cryptochrome/photolyase FAD-binding domain; 1.
DR SUPFAM; SSF52425; Cryptochrome/photolyase, N-terminal domain; 1.
DR PROSITE; PS51645; PHR_CRY_ALPHA_BETA; 1.
PE 3: Inferred from homology;
KW DNA damage; DNA repair; DNA-binding; FAD; Flavoprotein; Lyase;
KW Nucleotide-binding; Reference proteome.
FT CHAIN 1..551
FT /note="(6-4)DNA photolyase"
FT /id="PRO_0000397887"
FT DOMAIN 13..157
FT /note="Photolyase/cryptochrome alpha/beta"
FT REGION 374..379
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT REGION 508..551
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 508..526
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 527..551
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 254
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000250"
FT BINDING 255
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 268..272
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 309..313
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 312
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000250"
FT BINDING 372..375
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 378
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 407..409
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 413
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 419
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000250"
FT SITE 340
FT /note="Electron transfer via tryptophanyl radical"
FT /evidence="ECO:0000250"
FT SITE 394
FT /note="Electron transfer via tryptophanyl radical"
FT /evidence="ECO:0000250"
FT SITE 417
FT /note="Electron transfer via tryptophanyl radical"
FT /evidence="ECO:0000250"
FT CONFLICT 40
FT /note="A -> V (in Ref. 4; EEE56527)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 551 AA; 62264 MW; 37C2FE84F92C34C8 CRC64;
MDAAATAATA TAAAAMVWFR KGLRVHDNPA LDAARRGGAA ARLYPVFVLD PRYLRPDQAA
PSPGSARAGV ARVRFLLESL SDLDARLRRL GSRLLLLRAR DDGDVAGTVC AALKDWNIGK
LCFESDTEPY ALARDKKVMD FAAASGIDVF SPVSHTLFDP AEIIEKNGGR PPMTYQSFVA
IAGEPPEPIM EEYSELPPVG DTGEYELLPV PRVEELGYGD ISQEDLSLFR GGETEALKRM
RESLHDKEWV AKFEKPKGDP SAFLKPATTV LSPYLKFGCL SSRYFYHCIQ DIYRSTKKHT
NPPVSLTGQL LWRDFFYTVA FGTPNFDQMK GNKICKQIPW TENEELFPAW RDGRTGYPWI
DAIMIQLRKW GWMHHLARHS VACFLTRGDL FIHWEKGRDV FERLLIDSDW AINNGNWMWL
SCSSFFYQYH RIYSPTSFGK KYDPNGNYIR HFIPVLKDMP KEYIYEPWTA PLSIQKKANC
IIGKDYPKPV VDHAIASKEC KKMMGEAYAS NRLDDDKPDK GKSSNSSRRK LSAGSQVTPN
SSKTKQLKRS S
//
