PHR_SYNP6
ID PHR_SYNP6 Reviewed; 484 AA.
AC P05327; Q5N288;
DT 01-NOV-1988, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 4.
DT 03-AUG-2022, entry version 152.
DE RecName: Full=Deoxyribodipyrimidine photo-lyase;
DE EC=4.1.99.3;
DE AltName: Full=DNA photolyase;
DE AltName: Full=Photoreactivating enzyme;
GN Name=phr; Synonyms=phrA; OrderedLocusNames=syc1392_c;
OS Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (Anacystis
OS nidulans).
OC Bacteria; Cyanobacteria; Synechococcales; Synechococcaceae; Synechococcus.
OX NCBI_TaxID=269084;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2837735; DOI=10.1093/nar/16.10.4447;
RA Yasui A., Takao M., Oikawa A., Kiener A., Walsh C.T., Eker A.P.M.;
RT "Cloning and characterization of a photolyase gene from the cyanobacterium
RT Anacystis nidulans.";
RL Nucleic Acids Res. 16:4447-4463(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27144 / PCC 6301 / SAUG 1402/1;
RX PubMed=17211581; DOI=10.1007/s11120-006-9122-4;
RA Sugita C., Ogata K., Shikata M., Jikuya H., Takano J., Furumichi M.,
RA Kanehisa M., Omata T., Sugiura M., Sugita M.;
RT "Complete nucleotide sequence of the freshwater unicellular cyanobacterium
RT Synechococcus elongatus PCC 6301 chromosome: gene content and
RT organization.";
RL Photosyn. Res. 93:55-67(2007).
RN [3]
RP PROTEIN SEQUENCE OF 2-26.
RX PubMed=2110564; DOI=10.1016/s0021-9258(19)39031-3;
RA Eker A.P.M., Kooiman P., Hessels J.K.C., Yasui A.;
RT "DNA photoreactivating enzyme from the cyanobacterium Anacystis nidulans.";
RL J. Biol. Chem. 265:8009-8015(1990).
RN [4]
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 [5]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH FAD AND 8-HDF.
RX PubMed=9360600; DOI=10.1038/nsb1197-887;
RA Tamada T., Kitadokoro K., Higuchi Y., Inaka K., Yasui A., de Ruiter P.E.,
RA Eker A.P., Miki K.;
RT "Crystal structure of DNA photolyase from Anacystis nidulans.";
RL Nat. Struct. Biol. 4:887-891(1997).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH FAD, AND SUBUNIT.
RX PubMed=15213381; DOI=10.1107/s0907444904009321;
RA Kort R., Komori H., Adachi S., Miki K., Eker A.;
RT "DNA apophotolyase from Anacystis nidulans: 1.8 A structure, 8-HDF
RT reconstitution and X-ray-induced FAD reduction.";
RL Acta Crystallogr. D 60:1205-1213(2004).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 1-475 IN COMPLEX WITH FAD; 8-HDF
RP AND DAMAGED DNA.
RX PubMed=15576622; DOI=10.1126/science.1101598;
RA Mees A., Klar T., Gnau P., Hennecke U., Eker A.P.M., Carell T.,
RA Essen L.-O.;
RT "Crystal structure of a photolyase bound to a CPD-like DNA lesion after in
RT situ repair.";
RL Science 306:1789-1793(2004).
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=coenzyme F420-(gamma-Glu)n; Xref=ChEBI:CHEBI:133980;
CC Note=Binds 1 coenzyme F420 non-covalently per subunit.;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Absorption:
CC Abs(max)=440 nm;
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:15213381,
CC ECO:0000269|PubMed:15576622, ECO:0000269|PubMed:9360600}.
CC -!- SIMILARITY: Belongs to the DNA photolyase class-1 family.
CC {ECO:0000305}.
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DR EMBL; X07230; CAA30190.1; -; Genomic_DNA.
DR EMBL; AP008231; BAD79582.1; -; Genomic_DNA.
DR RefSeq; WP_011243704.1; NC_006576.1.
DR PDB; 1OWL; X-ray; 1.80 A; A=1-484.
DR PDB; 1OWM; X-ray; 2.30 A; A=1-484.
DR PDB; 1OWN; X-ray; 2.30 A; A=1-484.
DR PDB; 1OWO; X-ray; 2.30 A; A=1-484.
DR PDB; 1OWP; X-ray; 2.30 A; A=1-484.
DR PDB; 1QNF; X-ray; 1.80 A; A=1-484.
DR PDB; 1TEZ; X-ray; 1.80 A; A/B/C/D=2-475.
DR PDBsum; 1OWL; -.
DR PDBsum; 1OWM; -.
DR PDBsum; 1OWN; -.
DR PDBsum; 1OWO; -.
DR PDBsum; 1OWP; -.
DR PDBsum; 1QNF; -.
DR PDBsum; 1TEZ; -.
DR AlphaFoldDB; P05327; -.
DR SMR; P05327; -.
DR STRING; 269084.syc1392_c; -.
DR DrugBank; DB03147; Flavin adenine dinucleotide.
DR PRIDE; P05327; -.
DR EnsemblBacteria; BAD79582; BAD79582; syc1392_c.
DR KEGG; syc:syc1392_c; -.
DR eggNOG; COG0415; Bacteria.
DR OMA; WQWSASS; -.
DR BRENDA; 4.1.99.3; 325.
DR EvolutionaryTrace; P05327; -.
DR Proteomes; UP000001175; Chromosome.
DR GO; GO:0003904; F:deoxyribodipyrimidine photo-lyase activity; IEA:UniProtKB-EC.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
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; IPR019947; Photolyase_8HDF.
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 TIGRFAMs; TIGR03556; photolyase_8HDF; 1.
DR PROSITE; PS00394; DNA_PHOTOLYASES_1_1; 1.
DR PROSITE; PS51645; PHR_CRY_ALPHA_BETA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chromophore; Direct protein sequencing; DNA damage;
KW DNA repair; DNA-binding; FAD; Flavoprotein; Lyase; Nucleotide-binding.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:2110564"
FT CHAIN 2..484
FT /note="Deoxyribodipyrimidine photo-lyase"
FT /id="PRO_0000085112"
FT DOMAIN 3..132
FT /note="Photolyase/cryptochrome alpha/beta"
FT REGION 141..148
FT /note="DNA-binding"
FT REGION 283..290
FT /note="Interaction with DNA"
FT REGION 349..350
FT /note="Interaction with DNA"
FT BINDING 36..38
FT /ligand="coenzyme F420-(gamma-Glu)n"
FT /ligand_id="ChEBI:CHEBI:133980"
FT BINDING 51
FT /ligand="coenzyme F420-(gamma-Glu)n"
FT /ligand_id="ChEBI:CHEBI:133980"
FT BINDING 101..109
FT /ligand="coenzyme F420-(gamma-Glu)n"
FT /ligand_id="ChEBI:CHEBI:133980"
FT BINDING 228
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:15213381,
FT ECO:0000269|PubMed:15576622, ECO:0000269|PubMed:9360600"
FT BINDING 232
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT BINDING 240..247
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:15213381,
FT ECO:0000269|PubMed:15576622, ECO:0000269|PubMed:9360600"
FT BINDING 248
FT /ligand="coenzyme F420-(gamma-Glu)n"
FT /ligand_id="ChEBI:CHEBI:133980"
FT BINDING 346..352
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:15213381,
FT ECO:0000269|PubMed:15576622, ECO:0000269|PubMed:9360600"
FT BINDING 380..382
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:15213381,
FT ECO:0000269|PubMed:15576622, ECO:0000269|PubMed:9360600"
FT BINDING 386
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:15213381,
FT ECO:0000269|PubMed:15576622, ECO:0000269|PubMed:9360600"
FT BINDING 411
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT BINDING 472
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT SITE 314
FT /note="Electron transfer via tryptophanyl radical"
FT /evidence="ECO:0000250"
FT SITE 367
FT /note="Electron transfer via tryptophanyl radical"
FT /evidence="ECO:0000250"
FT SITE 390
FT /note="Electron transfer via tryptophanyl radical"
FT /evidence="ECO:0000250"
FT CONFLICT 259
FT /note="R -> Q (in Ref. 1; CAA30190)"
FT /evidence="ECO:0000305"
FT CONFLICT 352
FT /note="W -> R (in Ref. 1; CAA30190)"
FT /evidence="ECO:0000305"
FT CONFLICT 446
FT /note="G -> E (in Ref. 1; CAA30190)"
FT /evidence="ECO:0000305"
FT STRAND 5..8
FT /evidence="ECO:0007829|PDB:1OWL"
FT STRAND 15..17
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 19..27
FT /evidence="ECO:0007829|PDB:1OWL"
FT STRAND 31..37
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 39..42
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 49..69
FT /evidence="ECO:0007829|PDB:1OWL"
FT STRAND 73..78
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 80..90
FT /evidence="ECO:0007829|PDB:1OWL"
FT STRAND 94..99
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 104..119
FT /evidence="ECO:0007829|PDB:1OWL"
FT STRAND 123..127
FT /evidence="ECO:0007829|PDB:1OWL"
FT STRAND 130..133
FT /evidence="ECO:0007829|PDB:1OWL"
FT TURN 135..137
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 149..158
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 176..182
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 183..185
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 194..196
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 210..222
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 224..227
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 228..231
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 244..248
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 254..267
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 271..296
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 298..302
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 308..311
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 318..325
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 332..344
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 349..361
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 368..375
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 383..392
FT /evidence="ECO:0007829|PDB:1OWL"
FT TURN 393..395
FT /evidence="ECO:0007829|PDB:1OWL"
FT STRAND 397..399
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 408..415
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 420..425
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 427..429
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 434..439
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 444..447
FT /evidence="ECO:0007829|PDB:1OWL"
FT HELIX 457..474
FT /evidence="ECO:0007829|PDB:1OWL"
SQ SEQUENCE 484 AA; 54462 MW; 2DAC6D9CFD515E3D CRC64;
MAAPILFWHR RDLRLSDNIG LAAARAQSAQ LIGLFCLDPQ ILQSADMAPA RVAYLQGCLQ
ELQQRYQQAG SRLLLLQGDP QHLIPQLAQQ LQAEAVYWNQ DIEPYGRDRD GQVAAALKTA
GIRAVQLWDQ LLHSPDQILS GSGNPYSVYG PFWKNWQAQP KPTPVATPTE LVDLSPEQLT
AIAPLLLSEL PTLKQLGFDW DGGFPVEPGE TAAIARLQEF CDRAIADYDP QRNFPAEAGT
SGLSPALKFG AIGIRQAWRA ASAAHALSRS DEARNSIRVW QQELAWREFY QHALYHFPSL
ADGPYRSLWQ QFPWENREAL FTAWTQAQTG YPIVDAAMRQ LTETGWMHNR CWMIVASFLT
KDLIIDWRRG EQFFMQHLVD GDLAANNGGW QWSASSGMDP KPLRIFNPAS QAKKFDATAT
YIKRWLPELR HVHPKDLISG EITPIGRRGY PAPIVNHNLR QKQFKALYNQ LKAAIAEPEA
EPDS
