PHRA_AGRFC
ID PHRA_AGRFC Reviewed; 479 AA.
AC A9CJC9;
DT 04-FEB-2015, integrated into UniProtKB/Swiss-Prot.
DT 15-JAN-2008, sequence version 1.
DT 03-AUG-2022, entry version 74.
DE RecName: Full=Deoxyribodipyrimidine photo-lyase {ECO:0000305};
DE EC=4.1.99.3 {ECO:0000269|PubMed:22066008};
DE AltName: Full=Cyclobutane pyrimidine dimer photolyase {ECO:0000305|PubMed:22066008};
DE Short=CPD photolyase {ECO:0000305|PubMed:22066008};
DE AltName: Full=DNA photolyase PhrA {ECO:0000303|PubMed:22066008};
DE AltName: Full=Photoreactivating enzyme PhrA;
GN Name=phrA {ECO:0000303|PubMed:22066008};
GN OrderedLocusNames=Atu1218 {ECO:0000312|EMBL:AAK87020.1};
OS Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens
OS (strain C58)).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium;
OC Agrobacterium tumefaciens complex.
OX NCBI_TaxID=176299;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C58 / ATCC 33970;
RX PubMed=11743193; DOI=10.1126/science.1066804;
RA Wood D.W., Setubal J.C., Kaul R., Monks D.E., Kitajima J.P., Okura V.K.,
RA Zhou Y., Chen L., Wood G.E., Almeida N.F. Jr., Woo L., Chen Y.,
RA Paulsen I.T., Eisen J.A., Karp P.D., Bovee D. Sr., Chapman P.,
RA Clendenning J., Deatherage G., Gillet W., Grant C., Kutyavin T., Levy R.,
RA Li M.-J., McClelland E., Palmieri A., Raymond C., Rouse G.,
RA Saenphimmachak C., Wu Z., Romero P., Gordon D., Zhang S., Yoo H., Tao Y.,
RA Biddle P., Jung M., Krespan W., Perry M., Gordon-Kamm B., Liao L., Kim S.,
RA Hendrick C., Zhao Z.-Y., Dolan M., Chumley F., Tingey S.V., Tomb J.-F.,
RA Gordon M.P., Olson M.V., Nester E.W.;
RT "The genome of the natural genetic engineer Agrobacterium tumefaciens
RT C58.";
RL Science 294:2317-2323(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C58 / ATCC 33970;
RX PubMed=11743194; DOI=10.1126/science.1066803;
RA Goodner B., Hinkle G., Gattung S., Miller N., Blanchard M., Qurollo B.,
RA Goldman B.S., Cao Y., Askenazi M., Halling C., Mullin L., Houmiel K.,
RA Gordon J., Vaudin M., Iartchouk O., Epp A., Liu F., Wollam C., Allinger M.,
RA Doughty D., Scott C., Lappas C., Markelz B., Flanagan C., Crowell C.,
RA Gurson J., Lomo C., Sear C., Strub G., Cielo C., Slater S.;
RT "Genome sequence of the plant pathogen and biotechnology agent
RT Agrobacterium tumefaciens C58.";
RL Science 294:2323-2328(2001).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND DISRUPTION PHENOTYPE.
RC STRAIN=C58 / ATCC 33970;
RX PubMed=22066008; DOI=10.1371/journal.pone.0026775;
RA Oberpichler I., Pierik A.J., Wesslowski J., Pokorny R., Rosen R.,
RA Vugman M., Zhang F., Neubauer O., Ron E.Z., Batschauer A., Lamparter T.;
RT "A photolyase-like protein from Agrobacterium tumefaciens with an iron-
RT sulfur cluster.";
RL PLoS ONE 6:E26775-E26775(2011).
CC -!- FUNCTION: Photolyase involved in the repair of UV radiation-induced DNA
CC damage. By using blue-light energy, catalyzes the photoreactivation of
CC cyclobutane pyrimidine dimers (CPDs), which are formed between adjacent
CC bases on the same DNA strand upon exposure to ultraviolet radiation.
CC Can repair CPD lesions in ssDNA as well as in dsDNA.
CC {ECO:0000269|PubMed:22066008}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in
CC DNA).; EC=4.1.99.3; Evidence={ECO:0000269|PubMed:22066008};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:22066008};
CC Note=Binds 1 FAD per subunit. {ECO:0000269|PubMed:22066008};
CC -!- COFACTOR:
CC Name=(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate;
CC Xref=ChEBI:CHEBI:15636; Evidence={ECO:0000269|PubMed:22066008};
CC Note=Binds 1 5,10-methenyltetrahydrofolate (MTHF) per subunit, that
CC serves as photoantenna. {ECO:0000269|PubMed:22066008};
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene show an attenuated
CC photoreactivation after treatment with UV-B irradiation.
CC {ECO:0000269|PubMed:22066008}.
CC -!- SIMILARITY: Belongs to the DNA photolyase class-3 family.
CC {ECO:0000305|PubMed:22066008}.
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DR EMBL; AE007869; AAK87020.1; -; Genomic_DNA.
DR PIR; AG2726; AG2726.
DR PIR; C97508; C97508.
DR RefSeq; NP_354235.1; NC_003062.2.
DR RefSeq; WP_010971478.1; NC_003062.2.
DR PDB; 4U63; X-ray; 1.67 A; A=2-479.
DR PDBsum; 4U63; -.
DR AlphaFoldDB; A9CJC9; -.
DR SMR; A9CJC9; -.
DR STRING; 176299.Atu1218; -.
DR EnsemblBacteria; AAK87020; AAK87020; Atu1218.
DR KEGG; atu:Atu1218; -.
DR PATRIC; fig|176299.10.peg.1239; -.
DR eggNOG; COG0415; Bacteria.
DR HOGENOM; CLU_010348_2_2_5; -.
DR OMA; WQWSASS; -.
DR PhylomeDB; A9CJC9; -.
DR BioCyc; AGRO:ATU1218-MON; -.
DR Proteomes; UP000000813; Chromosome circular.
DR GO; GO:0003904; F:deoxyribodipyrimidine photo-lyase activity; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0071949; F:FAD binding; IDA:UniProtKB.
DR GO; GO:0000719; P:photoreactive repair; IMP:UniProtKB.
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; Reference proteome.
FT CHAIN 1..479
FT /note="Deoxyribodipyrimidine photo-lyase"
FT /id="PRO_0000431764"
FT DOMAIN 6..132
FT /note="Photolyase/cryptochrome alpha/beta"
FT /evidence="ECO:0000305"
FT REGION 277..284
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT REGION 343..344
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT BINDING 226
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P00914"
FT BINDING 230
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000250"
FT BINDING 238..242
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P00914"
FT BINDING 277..284
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P00914"
FT BINDING 374..376
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P00914"
FT BINDING 406
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000250"
FT SITE 308
FT /note="Electron transfer via tryptophanyl radical"
FT /evidence="ECO:0000250|UniProtKB:P00914"
FT SITE 361
FT /note="Electron transfer via tryptophanyl radical"
FT /evidence="ECO:0000250|UniProtKB:P00914"
FT SITE 384
FT /note="Electron transfer via tryptophanyl radical"
FT /evidence="ECO:0000250|UniProtKB:P00914"
FT STRAND 8..14
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 22..30
FT /evidence="ECO:0007829|PDB:4U63"
FT STRAND 34..40
FT /evidence="ECO:0007829|PDB:4U63"
FT STRAND 42..45
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 49..68
FT /evidence="ECO:0007829|PDB:4U63"
FT STRAND 74..78
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 80..91
FT /evidence="ECO:0007829|PDB:4U63"
FT STRAND 95..99
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 104..119
FT /evidence="ECO:0007829|PDB:4U63"
FT STRAND 123..127
FT /evidence="ECO:0007829|PDB:4U63"
FT TURN 135..137
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 149..158
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 184..187
FT /evidence="ECO:0007829|PDB:4U63"
FT TURN 196..199
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 200..203
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 208..219
FT /evidence="ECO:0007829|PDB:4U63"
FT TURN 220..225
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 226..229
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 242..246
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 252..257
FT /evidence="ECO:0007829|PDB:4U63"
FT TURN 258..261
FT /evidence="ECO:0007829|PDB:4U63"
FT TURN 263..265
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 268..290
FT /evidence="ECO:0007829|PDB:4U63"
FT TURN 292..296
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 301..303
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 312..319
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 326..338
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 343..354
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 361..371
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 379..388
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 403..410
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 415..420
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 422..424
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 429..432
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 435..437
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 440..446
FT /evidence="ECO:0007829|PDB:4U63"
FT TURN 450..452
FT /evidence="ECO:0007829|PDB:4U63"
FT HELIX 461..476
FT /evidence="ECO:0007829|PDB:4U63"
SQ SEQUENCE 479 AA; 53885 MW; 65EF130E31AB6F15 CRC64;
MSLKTAPVIV WFRKDLRLSD NLALLAAVEH GGPVIPVYIR EKSAGPLGGA QEWWLHHSLA
ALSSSLEKAG GRLVLASGDA ERILRDLISE TGADTVVWNR RYDPTGMATD KALKQKLRDD
GLTVRSFSGQ LLHEPSRLQT KSGGPYRVYT PFWRALEGSD EPHAPADPPK SLTAPKVWPK
SEKLSNWKLL PTKPDWAKDF SDIWTPGETG ALDKLDDFID GALKGYEEGR DFPAKPATSL
LSPHLAAGEI SPAAVWHATK GLSRHIASND ISRFRKEIVW REFCYHLLFH FPELGEKNWN
DSFDAFSWRD DEKSFKAWTR GMTGYPIVDA GMRQLWQHGT MHNRVRMIVA SFLIKHLLID
WRKGEKWFRD TLVDADPASN AANWQWVAGS GADASPFFRI FNPILQGEKF DGDGDYVRRF
VPELEKLERK YIHKPFEAPK DALKKAGVEL GKTYPLPIVD HGKARERALA AYAAVKKTT
