PHR_YEAST
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 03-AUG-2022, entry version 193.
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; 43.
DR DIP; DIP-6327N; -.
DR IntAct; P05066; 24.
DR MINT; P05066; -.
DR STRING; 4932.YOR386W; -.
DR iPTMnet; P05066; -.
DR MaxQB; P05066; -.
DR PaxDb; P05066; -.
DR PRIDE; P05066; -.
DR EnsemblFungi; YOR386W_mRNA; YOR386W; YOR386W.
DR GeneID; 854568; -.
DR KEGG; sce:YOR386W; -.
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; WQWSASS; -.
DR BioCyc; YEAST:G3O-33848-MON; -.
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:0000719; P:photoreactive repair; TAS:SGD.
DR GO; GO:0009416; P:response to light stimulus; IBA:GO_Central.
DR Gene3D; 3.40.50.620; -; 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; PTHR11455; 1.
DR Pfam; PF00875; DNA_photolyase; 1.
DR Pfam; PF03441; FAD_binding_7; 1.
DR PRINTS; PR00147; DNAPHOTLYASE.
DR SUPFAM; SSF48173; SSF48173; 1.
DR SUPFAM; SSF52425; SSF52425; 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
