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Protein

Deoxyribodipyrimidine photo-lyase

Gene

phrB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in repair of UV radiation-induced DNA damage. Catalyzes the light-dependent monomerization (300-600 nm) of cyclobutyl pyrimidine dimers (in cis-syn configuration), which are formed between adjacent bases on the same DNA strand upon exposure to ultraviolet radiation.

Catalytic activityi

Cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA).

Cofactori

Protein has several cofactor binding sites:

Absorptioni

Abs(max)=384 nm

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei223 – 2231FAD1 Publication
Binding sitei227 – 2271DNABy similarity
Binding sitei272 – 2721FAD1 Publication
Sitei307 – 3071Electron transfer via tryptophanyl radical
Sitei360 – 3601Electron transfer via tryptophanyl radical
Sitei383 – 3831Electron transfer via tryptophanyl radical
Binding sitei405 – 4051DNABy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi235 – 2395FAD1 Publication
Nucleotide bindingi275 – 2828FAD1 Publication
Nucleotide bindingi373 – 3753FAD1 Publication

GO - Molecular functioni

  • deoxyribodipyrimidine photo-lyase activity Source: EcoCyc
  • DNA binding Source: UniProtKB-KW
  • nucleotide binding Source: UniProtKB-KW

GO - Biological processi

  • DNA repair Source: UniProtKB-KW
  • protein-chromophore linkage Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

Chromophore, DNA-binding, FAD, Flavoprotein, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10736-MONOMER.
ECOL316407:JW0698-MONOMER.
MetaCyc:EG10736-MONOMER.
BRENDAi4.1.99.3. 2026.
SABIO-RKP00914.

Names & Taxonomyi

Protein namesi
Recommended name:
Deoxyribodipyrimidine photo-lyase (EC:4.1.99.3)
Alternative name(s):
DNA photolyase
Photoreactivating enzyme
Gene namesi
Name:phrB
Synonyms:phr
Ordered Locus Names:b0708, JW0698
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10736. phrB.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi278 – 2781W → X: Reduces DNA-binding affinity. 1 Publication
Mutagenesisi383 – 3831W → F: Abolishes photolyase activity. 1 Publication

Chemistry

DrugBankiDB03147. Flavin adenine dinucleotide.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 472472Deoxyribodipyrimidine photo-lyasePRO_0000085108Add
BLAST

Proteomic databases

PaxDbiP00914.
PRIDEiP00914.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

BioGridi4259920. 163 interactions.
DIPiDIP-10505N.
IntActiP00914. 11 interactions.
MINTiMINT-1302006.
STRINGi511145.b0708.

Structurei

Secondary structure

1
472
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 75Combined sources
Helixi18 – 236Combined sources
Beta strandi24 – 263Combined sources
Beta strandi29 – 379Combined sources
Helixi39 – 446Combined sources
Helixi49 – 6820Combined sources
Beta strandi73 – 775Combined sources
Helixi81 – 9515Combined sources
Beta strandi99 – 1035Combined sources
Helixi108 – 12013Combined sources
Beta strandi124 – 1296Combined sources
Beta strandi132 – 1354Combined sources
Helixi151 – 16313Combined sources
Turni198 – 2003Combined sources
Helixi205 – 21713Combined sources
Helixi219 – 2268Combined sources
Helixi239 – 2446Combined sources
Helixi249 – 25911Combined sources
Helixi261 – 2655Combined sources
Helixi270 – 28819Combined sources
Helixi290 – 2945Combined sources
Helixi300 – 3045Combined sources
Helixi311 – 3199Combined sources
Helixi325 – 33713Combined sources
Helixi342 – 35413Combined sources
Helixi360 – 37011Combined sources
Helixi376 – 38611Combined sources
Helixi402 – 4098Combined sources
Turni410 – 4123Combined sources
Helixi414 – 4196Combined sources
Helixi421 – 4233Combined sources
Helixi430 – 4323Combined sources
Helixi434 – 4396Combined sources
Turni440 – 4423Combined sources
Helixi454 – 46815Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DNPX-ray2.30A/B2-472[»]
ProteinModelPortaliP00914.
SMRiP00914. Positions 2-470.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00914.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini2 – 134133Photolyase/cryptochrome alpha/betaAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni109 – 1102MTF binding
Regioni275 – 2828Interaction with DNABy similarity
Regioni342 – 3432Interaction with DNABy similarity

Sequence similaritiesi

Belongs to the DNA photolyase class-1 family.Curated

Phylogenomic databases

eggNOGiENOG4105CVP. Bacteria.
COG0415. LUCA.
HOGENOMiHOG000245621.
InParanoidiP00914.
KOiK01669.
OMAiWGERYFR.
OrthoDBiEOG6XWV2B.
PhylomeDBiP00914.

Family and domain databases

Gene3Di3.40.50.620. 1 hit.
InterProiIPR005101. Cryptochr/Photolyase_FAD-bd.
IPR002081. Cryptochrome/DNA_photolyase_1.
IPR018394. DNA_photolyase_1_CS_C.
IPR006050. DNA_photolyase_N.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]
PfamiPF00875. DNA_photolyase. 1 hit.
PF03441. FAD_binding_7. 1 hit.
[Graphical view]
PRINTSiPR00147. DNAPHOTLYASE.
SUPFAMiSSF48173. SSF48173. 1 hit.
SSF52425. SSF52425. 1 hit.
PROSITEiPS00394. DNA_PHOTOLYASES_1_1. 1 hit.
PS00691. DNA_PHOTOLYASES_1_2. 1 hit.
PS51645. PHR_CRY_ALPHA_BETA. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P00914-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTTHLVWFRQ DLRLHDNLAL AAACRNSSAR VLALYIATPR QWATHNMSPR
60 70 80 90 100
QAELINAQLN GLQIALAEKG IPLLFREVDD FVASVEIVKQ VCAENSVTHL
110 120 130 140 150
FYNYQYEVNE RARDVEVERA LRNVVCEGFD DSVILPPGAV MTGNHEMYKV
160 170 180 190 200
FTPFKNAWLK RLREGMPECV AAPKVRSSGS IEPSPSITLN YPRQSFDTAH
210 220 230 240 250
FPVEEKAAIA QLRQFCQNGA GEYEQQRDFP AVEGTSRLSA SLATGGLSPR
260 270 280 290 300
QCLHRLLAEQ PQALDGGAGS VWLNELIWRE FYRHLITYHP SLCKHRPFIA
310 320 330 340 350
WTDRVQWQSN PAHLQAWQEG KTGYPIVDAA MRQLNSTGWM HNRLRMITAS
360 370 380 390 400
FLVKDLLIDW REGERYFMSQ LIDGDLAANN GGWQWAASTG TDAAPYFRIF
410 420 430 440 450
NPTTQGEKFD HEGEFIRQWL PELRDVPGKV VHEPWKWAQK AGVTLDYPQP
460 470
IVEHKEARVQ TLAAYEAARK GK
Length:472
Mass (Da):53,667
Last modified:July 21, 1986 - v1
Checksum:iB06048703F18F7AE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
K01299 Genomic DNA. Translation: AAA24388.1.
X57399 Genomic DNA. Translation: CAB56782.1.
U00096 Genomic DNA. Translation: AAC73802.1.
AP009048 Genomic DNA. Translation: BAA35367.1.
PIRiA01137. WZECD.
RefSeqiNP_415236.1. NC_000913.3.
WP_000207142.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73802; AAC73802; b0708.
BAA35367; BAA35367; BAA35367.
GeneIDi947005.
KEGGiecj:JW0698.
eco:b0708.
PATRICi32116611. VBIEscCol129921_0738.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
K01299 Genomic DNA. Translation: AAA24388.1.
X57399 Genomic DNA. Translation: CAB56782.1.
U00096 Genomic DNA. Translation: AAC73802.1.
AP009048 Genomic DNA. Translation: BAA35367.1.
PIRiA01137. WZECD.
RefSeqiNP_415236.1. NC_000913.3.
WP_000207142.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DNPX-ray2.30A/B2-472[»]
ProteinModelPortaliP00914.
SMRiP00914. Positions 2-470.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259920. 163 interactions.
DIPiDIP-10505N.
IntActiP00914. 11 interactions.
MINTiMINT-1302006.
STRINGi511145.b0708.

Chemistry

DrugBankiDB03147. Flavin adenine dinucleotide.

Proteomic databases

PaxDbiP00914.
PRIDEiP00914.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73802; AAC73802; b0708.
BAA35367; BAA35367; BAA35367.
GeneIDi947005.
KEGGiecj:JW0698.
eco:b0708.
PATRICi32116611. VBIEscCol129921_0738.

Organism-specific databases

EchoBASEiEB0729.
EcoGeneiEG10736. phrB.

Phylogenomic databases

eggNOGiENOG4105CVP. Bacteria.
COG0415. LUCA.
HOGENOMiHOG000245621.
InParanoidiP00914.
KOiK01669.
OMAiWGERYFR.
OrthoDBiEOG6XWV2B.
PhylomeDBiP00914.

Enzyme and pathway databases

BioCyciEcoCyc:EG10736-MONOMER.
ECOL316407:JW0698-MONOMER.
MetaCyc:EG10736-MONOMER.
BRENDAi4.1.99.3. 2026.
SABIO-RKP00914.

Miscellaneous databases

EvolutionaryTraceiP00914.
PROiP00914.

Family and domain databases

Gene3Di3.40.50.620. 1 hit.
InterProiIPR005101. Cryptochr/Photolyase_FAD-bd.
IPR002081. Cryptochrome/DNA_photolyase_1.
IPR018394. DNA_photolyase_1_CS_C.
IPR006050. DNA_photolyase_N.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]
PfamiPF00875. DNA_photolyase. 1 hit.
PF03441. FAD_binding_7. 1 hit.
[Graphical view]
PRINTSiPR00147. DNAPHOTLYASE.
SUPFAMiSSF48173. SSF48173. 1 hit.
SSF52425. SSF52425. 1 hit.
PROSITEiPS00394. DNA_PHOTOLYASES_1_1. 1 hit.
PS00691. DNA_PHOTOLYASES_1_2. 1 hit.
PS51645. PHR_CRY_ALPHA_BETA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sequences of the Escherichia coli photolyase gene and protein."
    Sancar G.B., Smith F.W., Lorence M.C., Rupert C.S., Sancar A.
    J. Biol. Chem. 259:6033-6038(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Begley T.P.
    Submitted (JAN-1991) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "Structure and function of DNA photolyases."
    Sancar G.B., Sancar A.
    Trends Biochem. Sci. 12:259-261(1987)
    Cited for: REVIEW.
  7. "Active site of Escherichia coli DNA photolyase: mutations at Trp277 alter the selectivity of the enzyme without affecting the quantum yield of photorepair."
    Li Y.F., Sancar A.
    Biochemistry 29:5698-5706(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF TRP-278.
  8. "Dissection of the triple tryptophan electron transfer chain in Escherichia coli DNA photolyase: Trp382 is the primary donor in photoactivation."
    Byrdin M., Eker A.P., Vos M.H., Brettel K.
    Proc. Natl. Acad. Sci. U.S.A. 100:8676-8681(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF TRP-383, ELECTRON TRANSFER CHAIN.
  9. "Light-driven enzymatic catalysis of DNA repair: a review of recent biophysical studies on photolyase."
    Weber S.
    Biochim. Biophys. Acta 1707:1-23(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  10. "Crystal structure of DNA photolyase from Escherichia coli."
    Park H.-W., Kim S.-T., Sancar A., Deisenhofer J.
    Science 268:1866-1872(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH FAD AND MTF, SUBUNIT.

Entry informationi

Entry nameiPHR_ECOLI
AccessioniPrimary (citable) accession number: P00914
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: April 13, 2016
This is version 149 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

There are only 10-20 molecules of photolyase per E.coli cell.
Upon absorption of visible light electrons are transferred from Trp-307 through Trp-360 to Trp 383, and from there to FADH, giving rise to the fully reduced catalytic FADH-.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.