ID PHR_ARATH Reviewed; 496 AA.
AC Q9SB00; O24374; Q94CC5; Q9LNA9;
DT 03-MAY-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 27-MAR-2024, entry version 129.
DE RecName: Full=Deoxyribodipyrimidine photo-lyase;
DE EC=4.1.99.3;
DE AltName: Full=AtCPDII;
DE AltName: Full=DNA photolyase;
DE AltName: Full=Photoreactivating enzyme 1;
DE AltName: Full=Protein UV RESISTANCE 2;
GN Name=PHR1; Synonyms=UVR2; OrderedLocusNames=At1g12370; ORFNames=F5O11.9;
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] (ISOFORM 1), FUNCTION, TISSUE SPECIFICITY,
RP INDUCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=9061951; DOI=10.1105/tpc.9.2.199;
RA Ahmad M., Jarillo J.A., Klimczak L.J., Landry L.G., Peng T., Last R.L.,
RA Cashmore A.R.;
RT "An enzyme similar to animal type II photolyases mediates photoreactivation
RT in Arabidopsis.";
RL Plant Cell 9:199-207(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RA Taylor R., Tobin A., Bray C.;
RT "The cloning and sequence analysis of a putative type II CPD photolyases
RT from Arabidopsis thaliana.";
RL Submitted (SEP-1996) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=8990208; DOI=10.1073/pnas.94.1.328;
RA Landry L.G., Stapleton A.E., Lim J., Hoffman P., Hays J.B., Walbot V.,
RA Last R.L.;
RT "An Arabidopsis photolyase mutant is hypersensitive to ultraviolet-B
RT radiation.";
RL Proc. Natl. Acad. Sci. U.S.A. 94:328-332(1997).
RN [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=9750104; DOI=10.1073/pnas.94.14.7441;
RA Jiang C.Z., Yee J., Mitchell D.L., Britt A.B.;
RT "Photorepair mutants of Arabidopsis.";
RL Proc. Natl. Acad. Sci. U.S.A. 94:7441-7445(1997).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=11069284; DOI=10.1073/pnas.230251897;
RA Ries G., Buchholz G., Frohnmeyer H., Hohn B.;
RT "UV-damage-mediated induction of homologous recombination in Arabidopsis is
RT dependent on photosynthetically active radiation.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:13425-13429(2000).
RN [9]
RP INDUCTION.
RX PubMed=12011338; DOI=10.1104/pp.010894;
RA Tanaka A., Sakamoto A., Ishigaki Y., Nikaido O., Sun G., Hase Y.,
RA Shikazono N., Tano S., Watanabe H.;
RT "An ultraviolet-B-resistant mutant with enhanced DNA repair in
RT Arabidopsis.";
RL Plant Physiol. 129:64-71(2002).
RN [10]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=19521716; DOI=10.1007/s00425-009-0962-y;
RA Kaiser G., Kleiner O., Beisswenger C., Batschauer A.;
RT "Increased DNA repair in Arabidopsis plants overexpressing CPD
RT photolyase.";
RL Planta 230:505-515(2009).
RN [11]
RP FUNCTION, AND COFACTOR.
RX PubMed=20227927; DOI=10.1016/j.dnarep.2010.01.014;
RA Okafuji A., Biskup T., Hitomi K., Getzoff E.D., Kaiser G., Batschauer A.,
RA Bacher A., Hidema J., Teranishi M., Yamamoto K., Schleicher E., Weber S.;
RT "Light-induced activation of class II cyclobutane pyrimidine dimer
RT photolyases.";
RL DNA Repair 9:495-505(2010).
CC -!- FUNCTION: Involved in repair of UV radiation-induced DNA damage.
CC Catalyzes the light-dependent monomerization (300-600 nm) of
CC cyclobutylpyrimidine dimers (CPDs), which are formed between adjacent
CC bases on the same DNA strand upon exposure to ultraviolet radiation.
CC Required for plant survival in the presence of UV-B light. Not involved
CC in the repair of (6-4) photoproducts. {ECO:0000269|PubMed:11069284,
CC ECO:0000269|PubMed:19521716, ECO:0000269|PubMed:20227927,
CC ECO:0000269|PubMed:8990208, ECO:0000269|PubMed:9061951,
CC ECO:0000269|PubMed:9750104}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in
CC DNA).; EC=4.1.99.3;
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:20227927};
CC Note=Binds 1 FAD per subunit. {ECO:0000269|PubMed:20227927};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:19521716}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9SB00-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9SB00-2; Sequence=VSP_040972;
CC -!- TISSUE SPECIFICITY: Highly expressed in flowers. Expressed in roots and
CC stems. {ECO:0000269|PubMed:9061951}.
CC -!- INDUCTION: By high-fluence white light, UV-A and UV-B.
CC {ECO:0000269|PubMed:12011338, ECO:0000269|PubMed:9061951}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under white light, but
CC inhibition of growth and leaf necrosis under white light and UV-B.
CC Increased accumulation of CPDs under UV-B.
CC {ECO:0000269|PubMed:11069284, ECO:0000269|PubMed:8990208,
CC ECO:0000269|PubMed:9061951, ECO:0000269|PubMed:9750104}.
CC -!- MISCELLANEOUS: Over-expression of PHR1 decreases CPDs accumulation
CC during UV-B treatment.
CC -!- SIMILARITY: Belongs to the DNA photolyase class-2 family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF79657.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF053365; AAC08008.1; -; mRNA.
DR EMBL; X99301; CAA67683.1; -; mRNA.
DR EMBL; AB010875; BAA74701.1; -; Genomic_DNA.
DR EMBL; AC025416; AAF79657.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE28871.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE28872.1; -; Genomic_DNA.
DR EMBL; AY034961; AAK59467.1; -; mRNA.
DR EMBL; AY113909; AAM44957.1; -; mRNA.
DR PIR; T52112; T52112.
DR RefSeq; NP_563906.1; NM_101109.1. [Q9SB00-2]
DR RefSeq; NP_849651.1; NM_179320.2. [Q9SB00-1]
DR AlphaFoldDB; Q9SB00; -.
DR SMR; Q9SB00; -.
DR STRING; 3702.Q9SB00; -.
DR PaxDb; 3702-AT1G12370-2; -.
DR ProteomicsDB; 235082; -. [Q9SB00-1]
DR EnsemblPlants; AT1G12370.1; AT1G12370.1; AT1G12370. [Q9SB00-2]
DR EnsemblPlants; AT1G12370.2; AT1G12370.2; AT1G12370. [Q9SB00-1]
DR GeneID; 837792; -.
DR Gramene; AT1G12370.1; AT1G12370.1; AT1G12370. [Q9SB00-2]
DR Gramene; AT1G12370.2; AT1G12370.2; AT1G12370. [Q9SB00-1]
DR KEGG; ath:AT1G12370; -.
DR Araport; AT1G12370; -.
DR TAIR; AT1G12370; PHR1.
DR eggNOG; KOG0133; Eukaryota.
DR HOGENOM; CLU_026342_2_0_1; -.
DR InParanoid; Q9SB00; -.
DR OMA; IHNYLRM; -.
DR OrthoDB; 1341644at2759; -.
DR PhylomeDB; Q9SB00; -.
DR BRENDA; 4.1.99.3; 399.
DR PRO; PR:Q9SB00; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9SB00; baseline and differential.
DR Genevisible; Q9SB00; AT.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003904; F:deoxyribodipyrimidine photo-lyase activity; IEA:UniProtKB-EC.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003913; F:DNA photolyase activity; IDA:TAIR.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0000719; P:photoreactive repair; IMP:TAIR.
DR GO; GO:0009650; P:UV protection; IMP:TAIR.
DR Gene3D; 1.25.40.80; -; 1.
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; IPR008148; DNA_photolyase_2.
DR InterPro; IPR032673; DNA_photolyase_2_CS.
DR InterPro; IPR006050; DNA_photolyase_N.
DR InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR NCBIfam; TIGR00591; phr2; 1.
DR PANTHER; PTHR10211:SF0; DEOXYRIBODIPYRIMIDINE PHOTO-LYASE; 1.
DR PANTHER; PTHR10211; DEOXYRIBODIPYRIMIDINE PHOTOLYASE; 1.
DR Pfam; PF00875; DNA_photolyase; 1.
DR SUPFAM; SSF48173; Cryptochrome/photolyase FAD-binding domain; 1.
DR SUPFAM; SSF52425; Cryptochrome/photolyase, N-terminal domain; 1.
DR PROSITE; PS01083; DNA_PHOTOLYASES_2_1; 1.
DR PROSITE; PS01084; DNA_PHOTOLYASES_2_2; 1.
DR PROSITE; PS51645; PHR_CRY_ALPHA_BETA; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; DNA damage; DNA repair; DNA-binding; FAD;
KW Flavoprotein; Lyase; Nucleotide-binding; Nucleus; Reference proteome.
FT CHAIN 1..496
FT /note="Deoxyribodipyrimidine photo-lyase"
FT /id="PRO_0000407851"
FT DOMAIN 28..160
FT /note="Photolyase/cryptochrome alpha/beta"
FT BINDING 256
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 269..273
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 307..315
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 307
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000255"
FT BINDING 415..417
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT SITE 366
FT /note="Electron transfer via tryptophanyl radical"
FT /evidence="ECO:0000255"
FT SITE 387
FT /note="Electron transfer via tryptophanyl radical"
FT /evidence="ECO:0000255"
FT SITE 394
FT /note="Electron transfer via tryptophanyl radical"
FT /evidence="ECO:0000255"
FT VAR_SEQ 365..370
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_040972"
FT CONFLICT 23
FT /note="L -> S (in Ref. 1; AAC08008 and 2; CAA67683)"
FT /evidence="ECO:0000305"
FT CONFLICT 303
FT /note="T -> I (in Ref. 1; AAC08008 and 2; CAA67683)"
FT /evidence="ECO:0000305"
FT CONFLICT 374
FT /note="V -> L (in Ref. 1; AAC08008 and 2; CAA67683)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 496 AA; 57055 MW; 0EEC0511BE8F5639 CRC64;
MASTVSVQPG RIRILKKGSW QPLDQTVGPV VYWMFRDQRL KDNWALIHAV DLANRTNAPV
AVVFNLFDQF LDAKARQLGF MLKGLRQLHH QIDSLQIPFF LLQGDAKETI PNFLTECGAS
HLVTDFSPLR EIRRCKDEVV KRTSDSLAIH EVDAHNVVPM WAASSKLEYS ARTIRGKINK
LLPDYLIEFP KLEPPKKKWT GMMDKKLVDW DSLIDKVVRE GAEVPEIEWC VPGEDAGIEV
LMGNKDGFLT KRLKNYSTDR NNPIKPKALS GLSPYLHFGQ VSAQRCALEA RKVRSTSPQA
VDTFLEELIV RRELSDNFCY YQPHYDSLKG AWEWARKSLM DHASDKREHI YSLEQLEKGL
TADPLWNASQ LEMVYQGKMH GFMRMYWAKK ILEWTKGPEE ALSISIYLNN KYEIDGRDPS
GYVGCMWSIC GVHDQGWKER PVFGKIRYMN YAGCKRKFNV DSYISYVKSL VSVTKKKRKA
EEQLTRDSVD PKITIV
//