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Protein

Deoxyribodipyrimidine photo-lyase

Gene

phrB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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.

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-.

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

Keywordsi

Molecular functionDNA-binding, Lyase
Biological processDNA damage, DNA repair
LigandChromophore, FAD, Flavoprotein, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10736-MONOMER
MetaCyc:EG10736-MONOMER
BRENDAi4.1.99.3 2026
SABIO-RKiP00914

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

Binary interactionsi

WithEntry#Exp.IntActNotes
nfiP687392EBI-555781,EBI-551698

Protein-protein interaction databases

BioGridi4259920, 166 interactors
DIPiDIP-10505N
IntActiP00914, 12 interactors
STRINGi316385.ECDH10B_0775

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
OMAiCRMIVAS
PhylomeDBiP00914

Family and domain databases

Gene3Di3.40.50.620, 2 hits
InterProiView protein in InterPro
IPR036134 Crypto/Photolyase_FAD-like_sf
IPR036155 Crypto/Photolyase_N_sf
IPR005101 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
PfamiView protein in Pfam
PF00875 DNA_photolyase, 1 hit
PF03441 FAD_binding_7, 1 hit
PRINTSiPR00147 DNAPHOTLYASE
SUPFAMiSSF48173 SSF48173, 1 hit
SSF52425 SSF52425, 1 hit
PROSITEiView protein in PROSITE
PS00394 DNA_PHOTOLYASES_1_1, 1 hit
PS00691 DNA_PHOTOLYASES_1_2, 1 hit
PS51645 PHR_CRY_ALPHA_BETA, 1 hit

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
PATRICifig|1411691.4.peg.1565

Similar proteinsi

Entry informationi

Entry nameiPHR_ECOLI
AccessioniPrimary (citable) accession number: P00914
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: March 28, 2018
This is version 160 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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

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