PHRB_AGRFC
ID PHRB_AGRFC Reviewed; 507 AA.
AC A9CH39;
DT 04-FEB-2015, integrated into UniProtKB/Swiss-Prot.
DT 15-JAN-2008, sequence version 1.
DT 03-AUG-2022, entry version 68.
DE RecName: Full=(6-4) photolyase {ECO:0000303|PubMed:23589886};
DE EC=4.1.99.13 {ECO:0000269|PubMed:23589886};
DE AltName: Full=(6-4)DNA photolyase {ECO:0000305};
DE AltName: Full=DNA photolyase PhrB {ECO:0000303|PubMed:22066008};
DE AltName: Full=Photoreactivating enzyme PhrB;
GN Name=phrB {ECO:0000303|PubMed:22066008};
GN OrderedLocusNames=Atu4765 {ECO:0000312|EMBL:AAK88685.1};
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 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).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) IN COMPLEX WITH FAD;
RP 6,7-DIMETHYL-8-RIBITYLLUMAZINE AND IRON-SULFUR (4FE-4S), FUNCTION,
RP CATALYTIC ACTIVITY, AND COFACTOR.
RC STRAIN=C58 / ATCC 33970;
RX PubMed=23589886; DOI=10.1073/pnas.1302377110;
RA Zhang F., Scheerer P., Oberpichler I., Lamparter T., Krauss N.;
RT "Crystal structure of a prokaryotic (6-4) photolyase with an Fe-S cluster
RT and a 6,7-dimethyl-8-ribityllumazine antenna chromophore.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:7217-7222(2013).
CC -!- FUNCTION: Photolyase involved in the repair of UV-induced (6-4) lesions
CC in DNA. Catalyzes the photoreactivation of (6-4) pyrimidine-pyrimidone
CC photoproducts by using blue-light energy. Can repair (6-4)
CC photoproducts in ssDNA as well as in dsDNA.
CC {ECO:0000269|PubMed:23589886}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA).;
CC EC=4.1.99.13; Evidence={ECO:0000269|PubMed:23589886};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:22066008, ECO:0000269|PubMed:23589886};
CC Note=Binds 1 FAD per subunit. {ECO:0000269|PubMed:23589886};
CC -!- COFACTOR:
CC Name=6,7-dimethyl-8-(1-D-ribityl)lumazine; Xref=ChEBI:CHEBI:58201;
CC Evidence={ECO:0000269|PubMed:23589886};
CC Note=Binds 6,7-dimethyl-8-ribityllumazine (DMRL) as antenna
CC chromophore. {ECO:0000269|PubMed:23589886};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:23589886, ECO:0000305|PubMed:22066008};
CC Note=Binds 1 [4Fe-4S] cluster per subunit.
CC {ECO:0000269|PubMed:23589886};
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene show a strongly
CC attenuated photoreactivation after treatment with UV-B irradiation.
CC {ECO:0000269|PubMed:22066008}.
CC -!- SIMILARITY: Belongs to the iron-sulfur bacterial
CC cryptochrome/photolyase (FeS-BCP) family.
CC {ECO:0000305|PubMed:22066008}.
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DR EMBL; AE007870; AAK88685.1; -; Genomic_DNA.
DR PIR; AI3142; AI3142.
DR PIR; C98145; C98145.
DR RefSeq; NP_355900.1; NC_003063.2.
DR PDB; 4DJA; X-ray; 1.45 A; A=1-507.
DR PDB; 5KCM; X-ray; 2.15 A; A/B=1-507.
DR PDB; 5LFA; X-ray; 2.50 A; A=1-507.
DR PDB; 6DD6; X-ray; 2.30 A; A=1-507.
DR PDBsum; 4DJA; -.
DR PDBsum; 5KCM; -.
DR PDBsum; 5LFA; -.
DR PDBsum; 6DD6; -.
DR AlphaFoldDB; A9CH39; -.
DR SMR; A9CH39; -.
DR STRING; 176299.Atu4765; -.
DR PRIDE; A9CH39; -.
DR DNASU; 1136639; -.
DR EnsemblBacteria; AAK88685; AAK88685; Atu4765.
DR KEGG; atu:Atu4765; -.
DR PATRIC; fig|176299.10.peg.4572; -.
DR eggNOG; COG3046; Bacteria.
DR HOGENOM; CLU_031632_1_0_5; -.
DR OMA; GMSQYAD; -.
DR PhylomeDB; A9CH39; -.
DR BioCyc; AGRO:ATU4765-MON; -.
DR BRENDA; 4.1.99.13; 14964.
DR Proteomes; UP000000813; Chromosome linear.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:UniProtKB.
DR GO; GO:0003914; F:DNA (6-4) photolyase 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:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000719; P:photoreactive repair; IDA:UniProtKB.
DR Gene3D; 3.40.50.620; -; 1.
DR InterPro; IPR036134; Crypto/Photolyase_FAD-like_sf.
DR InterPro; IPR007357; PhrB-like.
DR InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR Pfam; PF04244; DPRP; 1.
DR SUPFAM; SSF48173; SSF48173; 1.
PE 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; Chromophore; DNA damage; DNA repair; DNA-binding;
KW FAD; Flavoprotein; Iron; Iron-sulfur; Lyase; Metal-binding;
KW Nucleotide-binding; Reference proteome.
FT CHAIN 1..507
FT /note="(6-4) photolyase"
FT /id="PRO_0000431763"
FT BINDING 9..10
FT /ligand="6,7-dimethyl-8-(1-D-ribityl)lumazine"
FT /ligand_id="ChEBI:CHEBI:58201"
FT /evidence="ECO:0000269|PubMed:23589886,
FT ECO:0007744|PDB:4DJA"
FT BINDING 32..40
FT /ligand="6,7-dimethyl-8-(1-D-ribityl)lumazine"
FT /ligand_id="ChEBI:CHEBI:58201"
FT /evidence="ECO:0000269|PubMed:23589886,
FT ECO:0007744|PDB:4DJA"
FT BINDING 105
FT /ligand="6,7-dimethyl-8-(1-D-ribityl)lumazine"
FT /ligand_id="ChEBI:CHEBI:58201"
FT /evidence="ECO:0000269|PubMed:23589886,
FT ECO:0007744|PDB:4DJA"
FT BINDING 265..269
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:23589886,
FT ECO:0007744|PDB:4DJA"
FT BINDING 273
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:23589886,
FT ECO:0007744|PDB:4DJA"
FT BINDING 350
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:23589886,
FT ECO:0007744|PDB:4DJA"
FT BINDING 363..366
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:23589886,
FT ECO:0007744|PDB:4DJA"
FT BINDING 397
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:23589886,
FT ECO:0007744|PDB:4DJA"
FT BINDING 406
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:23589886,
FT ECO:0007744|PDB:4DJA"
FT BINDING 438
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:23589886,
FT ECO:0007744|PDB:4DJA"
FT BINDING 441
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:23589886,
FT ECO:0007744|PDB:4DJA"
FT BINDING 454
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:23589886,
FT ECO:0007744|PDB:4DJA"
FT STRAND 3..6
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 17..19
FT /evidence="ECO:0007829|PDB:4DJA"
FT TURN 24..26
FT /evidence="ECO:0007829|PDB:4DJA"
FT STRAND 28..32
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 35..39
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 45..64
FT /evidence="ECO:0007829|PDB:4DJA"
FT STRAND 68..72
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 83..94
FT /evidence="ECO:0007829|PDB:4DJA"
FT STRAND 97..102
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 107..114
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 116..120
FT /evidence="ECO:0007829|PDB:4DJA"
FT STRAND 122..127
FT /evidence="ECO:0007829|PDB:4DJA"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 136..143
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 151..162
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 172..174
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 179..181
FT /evidence="ECO:0007829|PDB:5KCM"
FT HELIX 202..214
FT /evidence="ECO:0007829|PDB:4DJA"
FT STRAND 218..220
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 231..244
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 246..248
FT /evidence="ECO:0007829|PDB:4DJA"
FT TURN 249..254
FT /evidence="ECO:0007829|PDB:4DJA"
FT STRAND 260..262
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 269..272
FT /evidence="ECO:0007829|PDB:4DJA"
FT TURN 273..275
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 279..291
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 297..308
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 310..321
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 323..327
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 340..343
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 349..361
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 366..371
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 373..379
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 384..394
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 400..408
FT /evidence="ECO:0007829|PDB:4DJA"
FT TURN 409..412
FT /evidence="ECO:0007829|PDB:4DJA"
FT TURN 414..419
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 428..434
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 437..440
FT /evidence="ECO:0007829|PDB:4DJA"
FT STRAND 442..444
FT /evidence="ECO:0007829|PDB:4DJA"
FT STRAND 448..450
FT /evidence="ECO:0007829|PDB:6DD6"
FT HELIX 455..466
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 468..471
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 475..477
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 478..485
FT /evidence="ECO:0007829|PDB:4DJA"
FT HELIX 489..507
FT /evidence="ECO:0007829|PDB:4DJA"
SQ SEQUENCE 507 AA; 57864 MW; 9DB788BDA687ECF5 CRC64;
MSQLVLILGD QLSPSIAALD GVDKKQDTIV LCEVMAEASY VGHHKKKIAF IFSAMRHFAE
ELRGEGYRVR YTRIDDADNA GSFTGEVKRA IDDLTPSRIC VTEPGEWRVR SEMDGFAGAF
GIQVDIRSDR RFLSSHGEFR NWAAGRKSLT MEYFYREMRR KTGLLMNGEQ PVGGRWNFDA
ENRQPARPDL LRPKHPVFAP DKITKEVIDT VERLFPDNFG KLENFGFAVT RTDAERALSA
FIDDFLCNFG ATQDAMLQDD PNLNHSLLSF YINCGLLDAL DVCKAAERAY HEGGAPLNAV
EGFIRQIIGW REYMRGIYWL AGPDYVDSNF FENDRSLPVF YWTGKTHMNC MAKVITETIE
NAYAHHIQRL MITGNFALLA GIDPKAVHRW YLEVYADAYE WVELPNVIGM SQFADGGFLG
TKPYAASGNY INRMSDYCDT CRYDPKERLG DNACPFNALY WDFLARNREK LKSNHRLAQP
YATWARMSED VRHDLRAKAA AFLRKLD
