ID   PHR_ECOLI               Reviewed;         472 AA.
AC   P00914;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   21-JUL-1986, sequence version 1.
DT   02-SEP-2026, entry version 197.
DE   RecName: Full=Deoxyribodipyrimidine photo-lyase;
DE            EC=4.1.99.3;
DE   AltName: Full=DNA photolyase;
DE   AltName: Full=Photoreactivating enzyme;
GN   Name=phrB; Synonyms=phr; OrderedLocusNames=b0708, JW0698;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
OC   Enterobacterales; Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=6325460; DOI=10.1016/s0021-9258(18)91118-x;
RA   Sancar G.B., Smith F.W., Lorence M.C., Rupert C.S., Sancar A.;
RT   "Sequences of the Escherichia coli photolyase gene and protein.";
RL   J. Biol. Chem. 259:6033-6038(1984).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RA   Begley T.P.;
RL   Submitted (JAN-1991) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA   Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA   Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA   Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA   Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA   Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA   Horiuchi T.;
RT   "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT   the 12.7-28.0 min region on the linkage map.";
RL   DNA Res. 3:137-155(1996).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA   Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA   Shao Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1462(1997).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT   and W3110.";
RL   Mol. Syst. Biol. 2:E1-E5(2006).
RN   [6]
RP   REVIEW.
RA   Sancar G.B., Sancar A.;
RT   "Structure and function of DNA photolyases.";
RL   Trends Biochem. Sci. 12:259-261(1987).
RN   [7]
RP   MUTAGENESIS OF TRP-278.
RX   PubMed=2200511; DOI=10.1021/bi00476a009;
RA   Li Y.F., Sancar A.;
RT   "Active site of Escherichia coli DNA photolyase: mutations at Trp277 alter
RT   the selectivity of the enzyme without affecting the quantum yield of
RT   photorepair.";
RL   Biochemistry 29:5698-5706(1990).
RN   [8]
RP   MUTAGENESIS OF TRP-383, AND ELECTRON TRANSFER CHAIN.
RX   PubMed=12835419; DOI=10.1073/pnas.1531645100;
RA   Byrdin M., Eker A.P., Vos M.H., Brettel K.;
RT   "Dissection of the triple tryptophan electron transfer chain in Escherichia
RT   coli DNA photolyase: Trp382 is the primary donor in photoactivation.";
RL   Proc. Natl. Acad. Sci. U.S.A. 100:8676-8681(2003).
RN   [9]
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).
RN   [10]
RP   X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH FAD AND MTHF,
RP   COFACTOR, AND SUBUNIT.
RX   PubMed=7604260; DOI=10.1126/science.7604260;
RA   Park H.-W., Kim S.-T., Sancar A., Deisenhofer J.;
RT   "Crystal structure of DNA photolyase from Escherichia coli.";
RL   Science 268:1866-1872(1995).
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; Evidence={ECO:0000269|PubMed:7604260};
CC       Note=Binds 1 5,10-methenyltetrahydrofolate (MTHF) non-covalently per
CC       subunit. {ECO:0000269|PubMed:7604260};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Absorption:
CC         Abs(max)=384 nm;
CC   -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:7604260}.
CC   -!- INTERACTION:
CC       P00914; P68739: nfi; NbExp=2; IntAct=EBI-555781, EBI-551698;
CC   -!- MISCELLANEOUS: There are only 10-20 molecules of photolyase per E.coli
CC       cell.
CC   -!- MISCELLANEOUS: Upon absorption of visible light electrons are
CC       transferred from Trp-307 through Trp-360 to Trp 383, and from there to
CC       FADH, giving rise to the fully reduced catalytic FADH(-).
CC   -!- SIMILARITY: Belongs to the DNA photolyase class-1 family.
CC       {ECO:0000305}.
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DR   EMBL; K01299; AAA24388.1; -; Genomic_DNA.
DR   EMBL; X57399; CAB56782.1; -; Genomic_DNA.
DR   EMBL; U00096; AAC73802.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAA35367.1; -; Genomic_DNA.
DR   PIR; A01137; WZECD.
DR   RefSeq; NP_415236.1; NC_000913.3.
DR   RefSeq; WP_000207142.1; NZ_CP009789.1.
DR   PDB; 1DNP; X-ray; 2.30 A; A/B=2-472.
DR   AlphaFoldDB; P00914; -.
DR   SMR; P00914; -.
DR   BioGRID; 4259920; 175.
DR   BioGRID; 851344; 1.
DR   DIP; DIP-10505N; -.
DR   FunCoup; P00914; 492.
DR   IntAct; P00914; 12.
DR   STRING; 511145.b0708; -.
DR   DrugBank; DB03147; Flavin adenine dinucleotide.
DR   jPOST; P00914; -.
DR   PaxDb; 511145-b0708; -.
DR   EnsemblBacteria; AAC73802; AAC73802; b0708.
DR   GeneID; 947005; -.
DR   KEGG; ecj:JW0698; -.
DR   KEGG; eco:b0708; -.
DR   KEGG; ecoc:C3026_03540; -.
DR   PATRIC; fig|1411691.4.peg.1565; -.
DR   EchoBASE; EB0729; -.
DR   eggNOG; COG0415; Bacteria.
DR   HOGENOM; CLU_010348_2_2_6; -.
DR   InParanoid; P00914; -.
DR   OMA; YTVFTPY; -.
DR   OrthoDB; 9772484at2; -.
DR   PhylomeDB; P00914; -.
DR   BioCyc; EcoCyc:EG10736-MONOMER; -.
DR   BioCyc; MetaCyc:EG10736-MONOMER; -.
DR   BRENDA; 4.1.99.3; 2026.
DR   SABIO-RK; P00914; -.
DR   EvolutionaryTrace; P00914; -.
DR   PRO; PR:P00914; -.
DR   Proteomes; UP000000625; Chromosome.
DR   AbasyAtlas; P00914; -.
DR   GO; GO:0003684; F:damaged DNA binding; IDA:EcoCyc.
DR   GO; GO:0003904; F:deoxyribodipyrimidine photo-lyase activity; IDA:EcoCyc.
DR   GO; GO:0000719; P:photoreactive repair; IDA:EcoCyc.
DR   GO; GO:0007603; P:phototransduction, visible light; IDA:EcoCyc.
DR   GO; GO:0009416; P:response to light stimulus; IBA:GO_Central.
DR   FunFam; 1.10.579.10:FF:000003; Deoxyribodipyrimidine photo-lyase; 1.
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   NCBIfam; NF007955; PRK10674.1; 1.
DR   PANTHER; PTHR11455; CRYPTOCHROME; 1.
DR   PANTHER; PTHR11455:SF9; CRYPTOCHROME CIRCADIAN CLOCK 5 ISOFORM X1; 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.
DR   PDBsum; 1DNP; -.
PE   1: Evidence at protein level;
KW   3D-structure; Chromophore; DNA damage; DNA repair; DNA-binding; FAD;
KW   Flavoprotein; Lyase; Nucleotide-binding; Reference proteome.
FT   CHAIN           1..472
FT                   /note="Deoxyribodipyrimidine photo-lyase"
FT                   /id="PRO_0000085108"
FT   DOMAIN          2..134
FT                   /note="Photolyase/cryptochrome alpha/beta"
FT   REGION          275..282
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000250"
FT   REGION          342..343
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000250"
FT   BINDING         109
FT                   /ligand="(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate"
FT                   /ligand_id="ChEBI:CHEBI:15636"
FT                   /evidence="ECO:0000269|PubMed:7604260,
FT                   ECO:0007744|PDB:1DNP"
FT   BINDING         110
FT                   /ligand="(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate"
FT                   /ligand_id="ChEBI:CHEBI:15636"
FT                   /evidence="ECO:0000269|PubMed:7604260,
FT                   ECO:0007744|PDB:1DNP"
FT   BINDING         223
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000269|PubMed:7604260"
FT   BINDING         227
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /evidence="ECO:0000250"
FT   BINDING         235..239
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000269|PubMed:7604260"
FT   BINDING         272
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000269|PubMed:7604260"
FT   BINDING         275..282
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000269|PubMed:7604260"
FT   BINDING         373..375
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000269|PubMed:7604260"
FT   BINDING         405
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /evidence="ECO:0000250"
FT   SITE            307
FT                   /note="Electron transfer via tryptophanyl radical"
FT   SITE            360
FT                   /note="Electron transfer via tryptophanyl radical"
FT   SITE            383
FT                   /note="Electron transfer via tryptophanyl radical"
FT   MUTAGEN         278
FT                   /note="W->X: Reduces DNA-binding affinity."
FT                   /evidence="ECO:0000269|PubMed:2200511"
FT   MUTAGEN         383
FT                   /note="W->F: Abolishes photolyase activity."
FT                   /evidence="ECO:0000269|PubMed:12835419"
FT   STRAND          3..7
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           18..23
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   STRAND          24..26
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   STRAND          29..37
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           39..44
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           49..68
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   STRAND          73..77
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           81..95
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   STRAND          99..103
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           108..120
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   STRAND          124..129
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   STRAND          132..135
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           151..163
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           169..176
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           182..185
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   TURN            198..200
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           205..217
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           219..226
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           239..244
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           249..259
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           261..265
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           270..288
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           290..294
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           300..304
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           311..319
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           325..337
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           342..350
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           351..355
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           360..368
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           376..386
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           402..409
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   TURN            410..412
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           414..419
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           421..423
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           430..432
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           434..439
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   TURN            440..442
FT                   /evidence="ECO:0007829|PDB:1DNP"
FT   HELIX           454..468
FT                   /evidence="ECO:0007829|PDB:1DNP"
SQ   SEQUENCE   472 AA;  53667 MW;  B06048703F18F7AE CRC64;
     MTTHLVWFRQ DLRLHDNLAL AAACRNSSAR VLALYIATPR QWATHNMSPR QAELINAQLN
     GLQIALAEKG IPLLFREVDD FVASVEIVKQ VCAENSVTHL FYNYQYEVNE RARDVEVERA
     LRNVVCEGFD DSVILPPGAV MTGNHEMYKV FTPFKNAWLK RLREGMPECV AAPKVRSSGS
     IEPSPSITLN YPRQSFDTAH FPVEEKAAIA QLRQFCQNGA GEYEQQRDFP AVEGTSRLSA
     SLATGGLSPR QCLHRLLAEQ PQALDGGAGS VWLNELIWRE FYRHLITYHP SLCKHRPFIA
     WTDRVQWQSN PAHLQAWQEG KTGYPIVDAA MRQLNSTGWM HNRLRMITAS FLVKDLLIDW
     REGERYFMSQ LIDGDLAANN GGWQWAASTG TDAAPYFRIF NPTTQGEKFD HEGEFIRQWL
     PELRDVPGKV VHEPWKWAQK AGVTLDYPQP IVEHKEARVQ TLAAYEAARK GK
//