PHR_ORYSJ
ID PHR_ORYSJ Reviewed; 506 AA.
AC Q6F6A2; A0A0P0XT34; C7J833; Q3LGA3; Q84LN6; Q8LM09;
DT 03-MAY-2011, integrated into UniProtKB/Swiss-Prot.
DT 16-AUG-2004, sequence version 1.
DT 03-AUG-2022, entry version 99.
DE RecName: Full=Deoxyribodipyrimidine photo-lyase;
DE EC=4.1.99.3;
DE AltName: Full=DNA photolyase;
DE AltName: Full=OsCPDII;
DE AltName: Full=Photoreactivating enzyme;
GN Name=PHR; OrderedLocusNames=Os10g0167600, LOC_Os10g08580;
GN ORFNames=OSJNAb0015J03.12;
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 [MRNA], AND FUNCTION.
RC STRAIN=cv. Sasanishiki;
RX PubMed=12764611; DOI=10.1007/s00438-003-0856-9;
RA Hirouchi T., Nakajima S., Najrana T., Tanaka M., Matsunaga T., Hidema J.,
RA Teranishi M., Fujino T., Kumagai T., Yamamoto K.;
RT "A gene for a Class II DNA photolyase from Oryza sativa: cloning of the
RT cDNA by dilution-amplification.";
RL Mol. Genet. Genomics 269:508-516(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=cv. Nohrin;
RX PubMed=15653803; DOI=10.1093/pcp/pch215;
RA Teranishi M., Iwamatsu Y., Hidema J., Kumagai T.;
RT "Ultraviolet-B sensitivities in Japanese lowland rice cultivars:
RT cyclobutane pyrimidine dimer photolyase activity and gene mutation.";
RL Plant Cell Physiol. 45:1848-1856(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RX PubMed=15965242; DOI=10.1534/genetics.105.044735;
RA Ueda T., Sato T., Hidema J., Hirouchi T., Yamamoto K., Kumagai T., Yano M.;
RT "qUVR-10, a major quantitative trait locus for ultraviolet-B resistance in
RT rice, encodes cyclobutane pyrimidine dimer photolyase.";
RL Genetics 171:1941-1950(2005).
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA], AND FUNCTION.
RC STRAIN=cv. Gulfmont;
RX PubMed=17895582; DOI=10.1266/ggs.82.311;
RA Ymamoto A., Hirouchi T., Mori T., Teranishi M., Hidema J., Morioka H.,
RA Kumagai T., Yamamoto K.;
RT "Biochemical and biological properties of DNA photolyases derived from
RT utraviolet-sensitive rice cultivars.";
RL Genes Genet. Syst. 82:311-319(2007).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12791992; DOI=10.1126/science.1083523;
RA Yu Y., Rambo T., Currie J., Saski C., Kim H.-R., Collura K., Thompson S.,
RA Simmons J., Yang T.-J., Nah G., Patel A.J., Thurmond S., Henry D.,
RA Oates R., Palmer M., Pries G., Gibson J., Anderson H., Paradkar M.,
RA Crane L., Dale J., Carver M.B., Wood T., Frisch D., Engler F.,
RA Soderlund C., Palmer L.E., Teytelman L., Nascimento L., De la Bastide M.,
RA Spiegel L., Ware D., O'Shaughnessy A., Dike S., Dedhia N., Preston R.,
RA Huang E., Ferraro K., Kuit K., Miller B., Zutavern T., Katzenberger F.,
RA Muller S., Balija V., Martienssen R.A., Stein L., Minx P., Johnson D.,
RA Cordum H., Mardis E., Cheng Z., Jiang J., Wilson R., McCombie W.R.,
RA Wing R.A., Yuan Q., Ouyang S., Liu J., Jones K.M., Gansberger K.,
RA Moffat K., Hill J., Tsitrin T., Overton L., Bera J., Kim M., Jin S.,
RA Tallon L., Ciecko A., Pai G., Van Aken S., Utterback T., Reidmuller S.,
RA Bormann J., Feldblyum T., Hsiao J., Zismann V., Blunt S., de Vazeille A.R.,
RA Shaffer T., Koo H., Suh B., Yang Q., Haas B., Peterson J., Pertea M.,
RA Volfovsky N., Wortman J., White O., Salzberg S.L., Fraser C.M., Buell C.R.,
RA Messing J., Song R., Fuks G., Llaca V., Kovchak S., Young S., Bowers J.E.,
RA Paterson A.H., Johns M.A., Mao L., Pan H., Dean R.A.;
RT "In-depth view of structure, activity, and evolution of rice chromosome
RT 10.";
RL Science 300:1566-1569(2003).
RN [6]
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 [7]
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 [8]
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 [9]
RP TISSUE SPECIFICITY.
RX PubMed=15150342; DOI=10.1093/nar/gkh591;
RA Kimura S., Tahira Y., Ishibashi T., Mori Y., Mori T., Hashimoto J.,
RA Sakaguchi K.;
RT "DNA repair in higher plants; photoreactivation is the major DNA repair
RT pathway in non-proliferating cells while excision repair (nucleotide
RT excision repair and base excision repair) is active in proliferating
RT cells.";
RL Nucleic Acids Res. 32:2760-2767(2004).
RN [10]
RP FUNCTION.
RX PubMed=17397507; DOI=10.1111/j.1365-313x.2007.03041.x;
RA Hidema J., Taguchi T., Ono T., Teranishi M., Yamamoto K., Kumagai T.;
RT "Increase in CPD photolyase activity functions effectively to prevent
RT growth inhibition caused by UVB radiation.";
RL Plant J. 50:70-79(2007).
RN [11]
RP FUNCTION, PHOSPHORYLATION AT SER-312, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RX PubMed=18235036; DOI=10.1104/pp.107.110189;
RA Teranishi M., Nakamura K., Morioka H., Yamamoto K., Hidema J.;
RT "The native cyclobutane pyrimidine dimer photolyase of rice is
RT phosphorylated.";
RL Plant Physiol. 146:1941-1951(2008).
RN [12]
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).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (1.71 ANGSTROMS) IN COMPLEX WITH FAD.
RX PubMed=22170053; DOI=10.1074/jbc.m111.244020;
RA Hitomi K., Arvai A.S., Yamamoto J., Hitomi C., Teranishi M., Hirouchi T.,
RA Yamamoto K., Iwai S., Tainer J.A., Hidema J., Getzoff E.D.;
RT "Eukaryotic class II cyclobutane pyrimidine dimer photolyase structure
RT reveals basis for improved ultraviolet tolerance in plants.";
RL J. Biol. Chem. 287:12060-12069(2012).
RN [14]
RP INDUCTION BY GAMMA IRRADIATION.
RX PubMed=25124817; DOI=10.1093/jhered/esu025;
RA Hayashi G., Shibato J., Imanaka T., Cho K., Kubo A., Kikuchi S., Satoh K.,
RA Kimura S., Ozawa S., Fukutani S., Endo S., Ichikawa K., Agrawal G.K.,
RA Shioda S., Fukumoto M., Rakwal R.;
RT "Unraveling low-level gamma radiation--responsive changes in expression of
RT early and late genes in leaves of rice seedlings at Iitate Village,
RT Fukushima.";
RL J. Hered. 105:723-738(2014).
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:12764611,
CC ECO:0000269|PubMed:15965242, ECO:0000269|PubMed:17397507,
CC ECO:0000269|PubMed:17895582, ECO:0000269|PubMed:18235036,
CC ECO:0000269|PubMed:20227927}.
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, ECO:0000269|PubMed:22170053};
CC Note=Binds 1 FAD per subunit. {ECO:0000269|PubMed:20227927,
CC ECO:0000269|PubMed:22170053};
CC -!- INTERACTION:
CC Q6F6A2; Q10B79-1: SPX4; NbExp=2; IntAct=EBI-16205114, EBI-16205145;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- TISSUE SPECIFICITY: Expressed in proliferating tissues. Highly
CC expressed in roots and shoot apical meristem (SAM). Expressed in
CC leaves, flag leaves, and panicle. {ECO:0000269|PubMed:15150342}.
CC -!- INDUCTION: Induced by gamma irradiation. {ECO:0000269|PubMed:25124817}.
CC -!- MISCELLANEOUS: Over-expression of PHR decreases growth inhibition, leaf
CC necrosis and CPDs accumulation under UV-B treatment.
CC -!- SIMILARITY: Belongs to the DNA photolyase class-2 family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAN04184.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAH94769.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB096003; BAC76449.2; -; mRNA.
DR EMBL; AB099694; BAD26607.1; -; Genomic_DNA.
DR EMBL; AB198744; BAE06248.1; -; Genomic_DNA.
DR EMBL; AB210109; BAE45635.1; -; mRNA.
DR EMBL; AC131375; AAN04184.1; ALT_SEQ; Genomic_DNA.
DR EMBL; DP000086; ABB46863.1; -; Genomic_DNA.
DR EMBL; AP008216; BAH94769.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014966; BAT10044.1; -; Genomic_DNA.
DR RefSeq; XP_015614933.1; XM_015759447.1.
DR PDB; 3UMV; X-ray; 1.70 A; A/B=1-506.
DR PDBsum; 3UMV; -.
DR AlphaFoldDB; Q6F6A2; -.
DR SMR; Q6F6A2; -.
DR DIP; DIP-62040N; -.
DR IntAct; Q6F6A2; 1.
DR STRING; 4530.OS10T0167600-01; -.
DR iPTMnet; Q6F6A2; -.
DR PaxDb; Q6F6A2; -.
DR PRIDE; Q6F6A2; -.
DR EnsemblPlants; Os10t0167600-02; Os10t0167600-02; Os10g0167600.
DR GeneID; 9272017; -.
DR Gramene; Os10t0167600-02; Os10t0167600-02; Os10g0167600.
DR KEGG; osa:9272017; -.
DR eggNOG; KOG0133; Eukaryota.
DR HOGENOM; CLU_026342_2_0_1; -.
DR InParanoid; Q6F6A2; -.
DR OrthoDB; 985150at2759; -.
DR BRENDA; 4.1.99.3; 8948.
DR Proteomes; UP000000763; Chromosome 10.
DR Proteomes; UP000059680; Chromosome 10.
DR ExpressionAtlas; Q6F6A2; baseline and differential.
DR Genevisible; Q6F6A2; OS.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003904; F:deoxyribodipyrimidine photo-lyase activity; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0071949; F:FAD binding; IDA:UniProtKB.
DR GO; GO:0006281; P:DNA repair; IDA:UniProtKB.
DR GO; GO:0000719; P:photoreactive repair; IBA:GO_Central.
DR GO; GO:0009650; P:UV protection; IDA:UniProtKB.
DR Gene3D; 3.40.50.620; -; 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 Pfam; PF00875; DNA_photolyase; 1.
DR SUPFAM; SSF48173; SSF48173; 1.
DR SUPFAM; SSF52425; SSF52425; 1.
DR TIGRFAMs; TIGR00591; phr2; 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 1: Evidence at protein level;
KW 3D-structure; DNA damage; DNA repair; DNA-binding; FAD; Flavoprotein;
KW Lyase; Nucleotide-binding; Nucleus; Phosphoprotein; Reference proteome.
FT CHAIN 1..506
FT /note="Deoxyribodipyrimidine photo-lyase"
FT /id="PRO_0000407852"
FT DOMAIN 38..171
FT /note="Photolyase/cryptochrome alpha/beta"
FT REGION 1..33
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 487..506
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..20
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 489..506
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 268
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:22170053,
FT ECO:0007744|PDB:3UMV"
FT BINDING 282..285
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:22170053,
FT ECO:0007744|PDB:3UMV"
FT BINDING 319..327
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P00914"
FT BINDING 390
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:22170053,
FT ECO:0007744|PDB:3UMV"
FT BINDING 421
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:22170053,
FT ECO:0007744|PDB:3UMV"
FT BINDING 427..429
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P00914"
FT BINDING 427
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:22170053,
FT ECO:0007744|PDB:3UMV"
FT SITE 378
FT /note="Electron transfer via tryptophanyl radical"
FT /evidence="ECO:0000255"
FT SITE 399
FT /note="Electron transfer via tryptophanyl radical"
FT /evidence="ECO:0000255"
FT SITE 406
FT /note="Electron transfer via tryptophanyl radical"
FT /evidence="ECO:0000255"
FT MOD_RES 312
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:18235036"
FT CONFLICT 126
FT /note="R -> Q (in Ref. 1; BAC76449)"
FT /evidence="ECO:0000305"
FT HELIX 23..25
FT /evidence="ECO:0007829|PDB:3UMV"
FT STRAND 26..30
FT /evidence="ECO:0007829|PDB:3UMV"
FT STRAND 40..46
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 54..65
FT /evidence="ECO:0007829|PDB:3UMV"
FT STRAND 70..75
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 82..84
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 87..106
FT /evidence="ECO:0007829|PDB:3UMV"
FT STRAND 111..116
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 120..127
FT /evidence="ECO:0007829|PDB:3UMV"
FT STRAND 131..135
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 141..157
FT /evidence="ECO:0007829|PDB:3UMV"
FT STRAND 161..166
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 174..177
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 185..193
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 196..199
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 222..231
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 246..254
FT /evidence="ECO:0007829|PDB:3UMV"
FT TURN 256..258
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 260..263
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 265..267
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 268..271
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 278..280
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 285..289
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 295..305
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 306..308
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 310..320
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 322..333
FT /evidence="ECO:0007829|PDB:3UMV"
FT TURN 335..338
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 340..342
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 345..353
FT /evidence="ECO:0007829|PDB:3UMV"
FT TURN 354..356
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 365..369
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 376..388
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 393..405
FT /evidence="ECO:0007829|PDB:3UMV"
FT STRAND 407..409
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 410..424
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 431..442
FT /evidence="ECO:0007829|PDB:3UMV"
FT TURN 453..455
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 463..469
FT /evidence="ECO:0007829|PDB:3UMV"
FT HELIX 472..489
FT /evidence="ECO:0007829|PDB:3UMV"
SQ SEQUENCE 506 AA; 56637 MW; 954450951EE78EA4 CRC64;
MPPTSVSPPR TAPGPANPSP AHPSRVRVIH PGGGKPGGPV VYWMLRDQRL ADNWALLHAA
GLAAASASPL AVAFALFPRP FLLSARRRQL GFLLRGLRRL AADAAARHLP FFLFTGGPAE
IPALVRRLGA STLVADFSPL RPVREALDAV VGDLRREAPG VAVHQVDAHN VVPVWTASAK
MEYSAKTFRG KVSKVMDEYL VEFPELPAVV PWDREQPEGV DWDALIARVC SEAENVPEID
WCEPGEEAAI EALLGSKDGF LTKRIKSYET DRNDPTKPRA LSGLSPYLHF GHISAQRCAL
EAKKCRHLSP KSVDAFLEEL VVRRELADNF CYYQPQYDSL SGAWEWARKT LMDHAADKRE
HIYTREQLEN AKTHDPLWNA SQLEMVHHGK MHGFMRMYWA KKILEWTSGP EEALSTAIYL
NDKYEIDGRD PSGYVGCMWS ICGLHDQGWK ERPVFGKIRY MNYAGCKRKF DVDAYISYVK
RLAGQSKKRN AEESPNPVVK LSKSQH
