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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)DescriptionActionsGraphical viewLength
Binding sitei223FAD1 Publication1
Binding sitei227DNABy similarity1
Binding sitei272FAD1 Publication1
Sitei307Electron transfer via tryptophanyl radical1
Sitei360Electron transfer via tryptophanyl radical1
Sitei383Electron transfer via tryptophanyl radical1
Binding sitei405DNABy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi235 – 239FAD1 Publication5
Nucleotide bindingi275 – 282FAD1 Publication8
Nucleotide bindingi373 – 375FAD1 Publication3

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10736. phrB.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi278W → X: Reduces DNA-binding affinity. 1 Publication1
Mutagenesisi383W → F: Abolishes photolyase activity. 1 Publication1

Chemistry databases

DrugBankiDB03147. Flavin adenine dinucleotide.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000851081 – 472Deoxyribodipyrimidine photo-lyaseAdd BLAST472

Proteomic databases

PaxDbiP00914.
PRIDEiP00914.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

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

Structurei

Secondary structure

1472
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 7Combined sources5
Helixi18 – 23Combined sources6
Beta strandi24 – 26Combined sources3
Beta strandi29 – 37Combined sources9
Helixi39 – 44Combined sources6
Helixi49 – 68Combined sources20
Beta strandi73 – 77Combined sources5
Helixi81 – 95Combined sources15
Beta strandi99 – 103Combined sources5
Helixi108 – 120Combined sources13
Beta strandi124 – 129Combined sources6
Beta strandi132 – 135Combined sources4
Helixi151 – 163Combined sources13
Turni198 – 200Combined sources3
Helixi205 – 217Combined sources13
Helixi219 – 226Combined sources8
Helixi239 – 244Combined sources6
Helixi249 – 259Combined sources11
Helixi261 – 265Combined sources5
Helixi270 – 288Combined sources19
Helixi290 – 294Combined sources5
Helixi300 – 304Combined sources5
Helixi311 – 319Combined sources9
Helixi325 – 337Combined sources13
Helixi342 – 354Combined sources13
Helixi360 – 370Combined sources11
Helixi376 – 386Combined sources11
Helixi402 – 409Combined sources8
Turni410 – 412Combined sources3
Helixi414 – 419Combined sources6
Helixi421 – 423Combined sources3
Helixi430 – 432Combined sources3
Helixi434 – 439Combined sources6
Turni440 – 442Combined sources3
Helixi454 – 468Combined sources15

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP00914.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini2 – 134Photolyase/cryptochrome alpha/betaAdd BLAST133

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni109 – 110MTF binding2
Regioni275 – 282Interaction with DNABy similarity8
Regioni342 – 343Interaction with DNABy similarity2

Sequence similaritiesi

Belongs to the DNA photolyase class-1 family.Curated

Phylogenomic databases

eggNOGiENOG4105CVP. Bacteria.
COG0415. LUCA.
HOGENOMiHOG000245621.
InParanoidiP00914.
KOiK01669.
OMAiWGERYFR.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DNPX-ray2.30A/B2-472[»]
ProteinModelPortaliP00914.
SMRiP00914.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Chemistry databases

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.
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...

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: November 2, 2016
This is version 152 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.