ID   PHR_YEAST               Reviewed;         565 AA.
AC   P05066; D6W379;
DT   13-AUG-1987, integrated into UniProtKB/Swiss-Prot.
DT   13-AUG-1987, sequence version 1.
DT   27-MAR-2024, entry version 200.
DE   RecName: Full=Deoxyribodipyrimidine photo-lyase, mitochondrial;
DE            EC=4.1.99.3;
DE   AltName: Full=DNA photolyase;
DE   AltName: Full=Photoreactivating enzyme;
DE   Flags: Precursor;
GN   Name=PHR1; OrderedLocusNames=YOR386W;
OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC   Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX   NCBI_TaxID=559292;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=3906569; DOI=10.1093/nar/13.22.8231;
RA   Sancar G.B.;
RT   "Sequence of the Saccharomyces cerevisiae PHR1 gene and homology of the
RT   PHR1 photolyase to E. coli photolyase.";
RL   Nucleic Acids Res. 13:8231-8246(1985).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=3000886; DOI=10.1016/0378-1119(85)90190-8;
RA   Yasui A., Langeveld S.A.;
RT   "Homology between the photoreactivation genes of Saccharomyces cerevisiae
RT   and Escherichia coli.";
RL   Gene 36:349-355(1985).
RN   [3]
RP   CHARACTERIZATION.
RX   PubMed=3316199; DOI=10.1016/s0021-9258(18)47748-4;
RA   Sancar G.B., Smith F.W., Heelis P.F.;
RT   "Purification of the yeast PHR1 photolyase from an Escherichia coli
RT   overproducing strain and characterization of the intrinsic chromophores of
RT   the enzyme.";
RL   J. Biol. Chem. 262:15457-15465(1987).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169874;
RA   Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J.,
RA   Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A.,
RA   Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B.,
RA   Dang V.-D., de Haan M., Delius H., Durand P., Fairhead C., Feldmann H.,
RA   Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E.,
RA   Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA   Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA   Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA   Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C.,
RA   Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G.,
RA   Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B.,
RA   Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B.,
RA   Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F.,
RA   Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E.,
RA   Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I.,
RA   Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H.,
RA   Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL   Nature 387:98-102(1997).
RN   [5]
RP   GENOME REANNOTATION.
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=24374639; DOI=10.1534/g3.113.008995;
RA   Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA   Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA   Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT   "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL   G3 (Bethesda) 4:389-398(2014).
RN   [6]
RP   MUTAGENESIS OF TRP-387; LYS-463 AND ARG-507.
RX   PubMed=8344951; DOI=10.1016/s0021-9258(19)85476-5;
RA   Baer M.E., Sancar G.B.;
RT   "The role of conserved amino acids in substrate binding and discrimination
RT   by photolyase.";
RL   J. Biol. Chem. 268:16717-16724(1993).
RN   [7]
RP   LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX   PubMed=14562106; DOI=10.1038/nature02046;
RA   Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA   O'Shea E.K., Weissman J.S.;
RT   "Global analysis of protein expression in yeast.";
RL   Nature 425:737-741(2003).
RN   [8]
RP   REVIEW.
RX   PubMed=15721603; DOI=10.1016/j.bbabio.2004.02.010;
RA   Weber S.;
RT   "Light-driven enzymatic catalysis of DNA repair: a review of recent
RT   biophysical studies on photolyase.";
RL   Biochim. Biophys. Acta 1707:1-23(2005).
CC   -!- FUNCTION: Involved in repair of UV radiation-induced DNA damage.
CC       Catalyzes the light-dependent monomerization (300-600 nm) of cyclobutyl
CC       pyrimidine dimers (in cis-syn configuration), which are formed between
CC       adjacent bases on the same DNA strand upon exposure to ultraviolet
CC       radiation.
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       Note=Binds 1 FAD per subunit.;
CC   -!- COFACTOR:
CC       Name=(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate;
CC         Xref=ChEBI:CHEBI:15636;
CC       Note=Binds 1 5,10-methenyltetrahydrofolate (MTHF) non-covalently per
CC       subunit.;
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Absorption:
CC         Abs(max)=377 nm;
CC         Note=Has a fluorescence excitation maximum at 390 nm and an emission
CC         maximum at 475 nm.;
CC   -!- SUBUNIT: Monomer. {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Nucleus. Mitochondrion.
CC   -!- MISCELLANEOUS: There are only 150-300 molecules of photolyase per yeast
CC       cell.
CC   -!- MISCELLANEOUS: Present with 688 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the DNA photolyase class-1 family.
CC       {ECO:0000305}.
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DR   EMBL; X03183; CAA26944.1; -; Genomic_DNA.
DR   EMBL; M11578; AAA34875.1; -; Genomic_DNA.
DR   EMBL; Z75294; CAA99718.1; -; Genomic_DNA.
DR   EMBL; BK006948; DAA11145.1; -; Genomic_DNA.
DR   PIR; S67298; S67298.
DR   RefSeq; NP_015031.1; NM_001183806.1.
DR   AlphaFoldDB; P05066; -.
DR   SMR; P05066; -.
DR   BioGRID; 34767; 49.
DR   DIP; DIP-6327N; -.
DR   IntAct; P05066; 24.
DR   MINT; P05066; -.
DR   STRING; 4932.YOR386W; -.
DR   iPTMnet; P05066; -.
DR   MaxQB; P05066; -.
DR   PaxDb; 4932-YOR386W; -.
DR   PeptideAtlas; P05066; -.
DR   EnsemblFungi; YOR386W_mRNA; YOR386W; YOR386W.
DR   GeneID; 854568; -.
DR   KEGG; sce:YOR386W; -.
DR   AGR; SGD:S000005913; -.
DR   SGD; S000005913; PHR1.
DR   VEuPathDB; FungiDB:YOR386W; -.
DR   eggNOG; KOG0133; Eukaryota.
DR   GeneTree; ENSGT00940000166153; -.
DR   HOGENOM; CLU_010348_2_1_1; -.
DR   InParanoid; P05066; -.
DR   OMA; TPYKNAW; -.
DR   OrthoDB; 124765at2759; -.
DR   BioCyc; YEAST:G3O-33848-MONOMER; -.
DR   BioGRID-ORCS; 854568; 0 hits in 10 CRISPR screens.
DR   PRO; PR:P05066; -.
DR   Proteomes; UP000002311; Chromosome XV.
DR   RNAct; P05066; Protein.
DR   GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR   GO; GO:0005739; C:mitochondrion; HDA:SGD.
DR   GO; GO:0005634; C:nucleus; HDA:SGD.
DR   GO; GO:0003904; F:deoxyribodipyrimidine photo-lyase activity; IDA:SGD.
DR   GO; GO:0003677; F:DNA binding; IBA:GO_Central.
DR   GO; GO:0071949; F:FAD binding; IBA:GO_Central.
DR   GO; GO:0003729; F:mRNA binding; IDA:SGD.
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:0000719; P:photoreactive repair; TAS:SGD.
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; IPR005101; Cryptochr/Photolyase_FAD-bd.
DR   InterPro; IPR002081; Cryptochrome/DNA_photolyase_1.
DR   InterPro; IPR018394; DNA_photolyase_1_CS_C.
DR   InterPro; IPR006050; DNA_photolyase_N.
DR   InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR   PANTHER; PTHR11455; CRYPTOCHROME; 1.
DR   PANTHER; PTHR11455:SF18; DEOXYRIBODIPYRIMIDINE PHOTO-LYASE, MITOCHONDRIAL; 1.
DR   Pfam; PF00875; DNA_photolyase; 1.
DR   Pfam; PF03441; FAD_binding_7; 1.
DR   PRINTS; PR00147; DNAPHOTLYASE.
DR   SUPFAM; SSF48173; Cryptochrome/photolyase FAD-binding domain; 1.
DR   SUPFAM; SSF52425; Cryptochrome/photolyase, N-terminal domain; 1.
DR   PROSITE; PS00394; DNA_PHOTOLYASES_1_1; 1.
DR   PROSITE; PS00691; DNA_PHOTOLYASES_1_2; 1.
DR   PROSITE; PS51645; PHR_CRY_ALPHA_BETA; 1.
PE   1: Evidence at protein level;
KW   Chromophore; DNA damage; DNA repair; DNA-binding; FAD; Flavoprotein; Lyase;
KW   Mitochondrion; Nucleotide-binding; Nucleus; Reference proteome;
KW   Transit peptide.
FT   TRANSIT         1..?
FT                   /note="Mitochondrion"
FT   CHAIN           ?..565
FT                   /note="Deoxyribodipyrimidine photo-lyase, mitochondrial"
FT                   /id="PRO_0000024051"
FT   DOMAIN          75..226
FT                   /note="Photolyase/cryptochrome alpha/beta"
FT   REGION          384..391
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000250"
FT   REGION          451..452
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000250"
FT   BINDING         326
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   BINDING         338..342
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   BINDING         482..484
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   BINDING         514
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /evidence="ECO:0000250"
FT   SITE            416
FT                   /note="Electron transfer via tryptophanyl radical"
FT                   /evidence="ECO:0000250"
FT   SITE            469
FT                   /note="Electron transfer via tryptophanyl radical"
FT                   /evidence="ECO:0000250"
FT   SITE            492
FT                   /note="Electron transfer via tryptophanyl radical"
FT                   /evidence="ECO:0000250"
FT   MUTAGEN         387
FT                   /note="W->A: Reduces substrate binding 100-fold. Reduces
FT                   quantum yield for dimer photolysis 3-fold."
FT                   /evidence="ECO:0000269|PubMed:8344951"
FT   MUTAGEN         463
FT                   /note="K->A: Reduces substrate binding 100-fold."
FT                   /evidence="ECO:0000269|PubMed:8344951"
FT   MUTAGEN         507
FT                   /note="R->A: Reduces substrate binding 100-fold."
FT                   /evidence="ECO:0000269|PubMed:8344951"
FT   MUTAGEN         517
FT                   /note="K->A: Reduces substrate binding 10-fold."
FT   CONFLICT        77
FT                   /note="V -> A (in Ref. 2; AAA34875)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        165
FT                   /note="T -> S (in Ref. 2; AAA34875)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        169
FT                   /note="S -> T (in Ref. 2; AAA34875)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        200
FT                   /note="D -> S (in Ref. 2; AAA34875)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        351
FT                   /note="S -> R (in Ref. 2; AAA34875)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        365
FT                   /note="G -> E (in Ref. 2; AAA34875)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        473
FT                   /note="E -> K (in Ref. 2; AAA34875)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   565 AA;  66274 MW;  CD4FC3DA6128B97C CRC64;
     MKRTVISSSN AYASKRSRLD IEHDFEQYHS LNKKYYPRPI TRTGANQFNN KSRAKPMEIV
     EKLQKKQKTS FENVSTVMHW FRNDLRLYDN VGLYKSVALF QQLRQKNAKA KLYAVYVINE
     DDWRAHMDSG WKLMFIMGAL KNLQQSLAEL HIPLLLWEFH TPKSTLSNSK EFVEFFKEKC
     MNVSSGTGTI ITANIEYQTD ELYRDIRLLE NEDHRLQLKY YHDSCIVAPG LITTDRGTNY
     SVFTPWYKKW VLYVNNYKKS TSEICHLHII EPLKYNETFE LKPFQYSLPD EFLQYIPKSK
     WCLPDVSEEA ALSRLKDFLG TKSSKYNNEK DMLYLGGTSG LSVYITTGRI STRLIVNQAF
     QSCNGQIMSK ALKDNSSTQN FIKEVAWRDF YRHCMCNWPY TSMGMPYRLD TLDIKWENNP
     VAFEKWCTGN TGIPIVDAIM RKLLYTGYIN NRSRMITASF LSKNLLIDWR WGERWFMKHL
     IDGDSSSNVG GWGFCSSTGI DAQPYFRVFN MDIQAKKYDP QMIFVKQWVP ELISSENKRP
     ENYPKPLVDL KHSRERALKV YKDAM
//