PHR_ECOLI
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 03-AUG-2022, entry version 181.
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; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC 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_SSZK01000033.1.
DR PDB; 1DNP; X-ray; 2.30 A; A/B=2-472.
DR PDBsum; 1DNP; -.
DR AlphaFoldDB; P00914; -.
DR SMR; P00914; -.
DR BioGRID; 4259920; 166.
DR BioGRID; 851344; 1.
DR DIP; DIP-10505N; -.
DR IntAct; P00914; 12.
DR STRING; 511145.b0708; -.
DR DrugBank; DB03147; Flavin adenine dinucleotide.
DR jPOST; P00914; -.
DR PaxDb; P00914; -.
DR PRIDE; P00914; -.
DR EnsemblBacteria; AAC73802; AAC73802; b0708.
DR EnsemblBacteria; BAA35367; BAA35367; BAA35367.
DR GeneID; 947005; -.
DR KEGG; ecj:JW0698; -.
DR KEGG; eco:b0708; -.
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; WQWSASS; -.
DR PhylomeDB; P00914; -.
DR BioCyc; EcoCyc:EG10736-MON; -.
DR BioCyc; MetaCyc:EG10736-MON; -.
DR BRENDA; 4.1.99.3; 2026.
DR SABIO-RK; P00914; -.
DR EvolutionaryTrace; P00914; -.
DR PRO; PR:P00914; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0003684; F:damaged DNA binding; IDA:EcoCyc.
DR GO; GO:0003904; F:deoxyribodipyrimidine photo-lyase activity; IDA:EcoCyc.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
DR GO; GO:0071949; F:FAD binding; IBA:GO_Central.
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 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 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 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..354
FT /evidence="ECO:0007829|PDB:1DNP"
FT HELIX 360..370
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
