Deoxyribodipyrimidine photo-lyase - Escherichia coli (strain K12)

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P00914 (PHR_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 130. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Deoxyribodipyrimidine photo-lyase
EC=4.1.99.3

Alternative name(s):
DNA photolyase
Photoreactivating enzyme

Gene names

Name:	phrB
Synonyms:	phr
Ordered Locus Names:	b0708, JW0698

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	472 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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 activity	Cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA).
Cofactor	Binds 1 FAD per subunit. Binds 1 5,10-methenyltetrahydrofolate non-covalently per subunit.
Subunit structure	Monomer. Ref.10
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^-.
Sequence similarities	Belongs to the DNA photolyase class-1 family. Contains 1 photolyase/cryptochrome alpha/beta domain.
Biophysicochemical properties	Absorption: Abs(max)=384 nm

Ontologies

Keywords
Biological process	DNA damage DNA repair
Ligand	Chromophore DNA-binding FAD Flavoprotein Nucleotide-binding
Molecular function	Lyase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW protein-chromophore linkage Inferred from direct assay PubMed 2895469 PubMed 6363715. Source: EcoCyc
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW deoxyribodipyrimidine photo-lyase activity Inferred from direct assay PubMed 6363715. Source: EcoCyc nucleotide binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 472

472

Deoxyribodipyrimidine photo-lyase

PRO_0000085108

Regions

Domain

2 – 134

133

Photolyase/cryptochrome alpha/beta

Nucleotide binding

235 – 239

FAD

Nucleotide binding

275 – 282

FAD

Nucleotide binding

373 – 375

FAD

Region

109 – 110

MTF binding

Region

275 – 282

Interaction with DNA By similarity

Region

342 – 343

Interaction with DNA By similarity

Sites

Binding site

223

FAD

Binding site

227

DNA By similarity

Binding site

272

FAD

Binding site

405

DNA By similarity

Site

307

Electron transfer via tryptophanyl radical

Site

360

Electron transfer via tryptophanyl radical

Site

383

Electron transfer via tryptophanyl radical

Experimental info

Mutagenesis

278

W → X: Reduces DNA-binding affinity. Ref.7

Mutagenesis

383

W → F: Abolishes photolyase activity. Ref.8

Secondary structure

472

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P00914 [UniParc].

Last modified July 21, 1986. Version 1.
Checksum: B06048703F18F7AE
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FASTA

472

53,667

        10         20         30         40         50         60 
MTTHLVWFRQ DLRLHDNLAL AAACRNSSAR VLALYIATPR QWATHNMSPR QAELINAQLN 

        70         80         90        100        110        120 
GLQIALAEKG IPLLFREVDD FVASVEIVKQ VCAENSVTHL FYNYQYEVNE RARDVEVERA 

       130        140        150        160        170        180 
LRNVVCEGFD DSVILPPGAV MTGNHEMYKV FTPFKNAWLK RLREGMPECV AAPKVRSSGS 

       190        200        210        220        230        240 
IEPSPSITLN YPRQSFDTAH FPVEEKAAIA QLRQFCQNGA GEYEQQRDFP AVEGTSRLSA 

       250        260        270        280        290        300 
SLATGGLSPR QCLHRLLAEQ PQALDGGAGS VWLNELIWRE FYRHLITYHP SLCKHRPFIA 

       310        320        330        340        350        360 
WTDRVQWQSN PAHLQAWQEG KTGYPIVDAA MRQLNSTGWM HNRLRMITAS FLVKDLLIDW 

       370        380        390        400        410        420 
REGERYFMSQ LIDGDLAANN GGWQWAASTG TDAAPYFRIF NPTTQGEKFD HEGEFIRQWL 

       430        440        450        460        470 
PELRDVPGKV VHEPWKWAQK AGVTLDYPQP IVEHKEARVQ TLAAYEAARK GK

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. Horiuchi T. DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

K01299 Genomic DNA. Translation: AAA24388.1.
X57399 Genomic DNA. Translation: CAB56782.1.
U00096 Genomic DNA. Translation: AAC73802.1.
AP009048 Genomic DNA. Translation: BAA35367.1.

PIR

WZECD. A01137.

RefSeq

NP_415236.1. NC_000913.2.
YP_488988.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DNP	X-ray	2.30	A/B	2-472	[»]

ProteinModelPortal

P00914.

SMR

P00914. Positions 2-470.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10505N.

IntAct

P00914. 11 interactions.

MINT

MINT-1302006.

STRING

511145.b0708.

Proteomic databases

PaxDb

P00914.

PRIDE

P00914.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73802; AAC73802; b0708.
BAA35367; BAA35367; BAA35367.

GeneID

12930926.
947005.

KEGG

ecj:Y75_p0688.
eco:b0708.

PATRIC

32116611. VBIEscCol129921_0738.

Organism-specific databases

EchoBASE

EB0729.

EcoGene

EG10736. phrB.

Phylogenomic databases

eggNOG

COG0415.

HOGENOM

HOG000245621.

K01669.

OMA

CKVDFWL.

ProtClustDB

PRK10674.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10736-MONOMER.
ECOL316407:JW0698-MONOMER.
MetaCyc:EG10736-MONOMER.

SABIO-RK

P00914.

Gene expression databases

Genevestigator

P00914.

Family and domain databases

Gene3D

3.40.50.620. 1 hit.

InterPro

IPR002081. Cryptochrome/DNA_photolyase_1.
IPR018394. DNA_photolyase_1_CS_C.
IPR006050. DNA_photolyase_N.
IPR005101. Photolyase_FAD-bd/Cryptochr_C.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]

Pfam

PF00875. DNA_photolyase. 1 hit.
PF03441. FAD_binding_7. 1 hit.
[Graphical view]

PRINTS

PR00147. DNAPHOTLYASE.

SUPFAM

SSF52425. DNA_photolyase_N. 1 hit.
SSF48173. Photolyase_FAD-bd/Cryptochr_C. 1 hit.

PROSITE

PS00394. DNA_PHOTOLYASES_1_1. 1 hit.
PS00691. DNA_PHOTOLYASES_1_2. 1 hit.
PS51645. PHR_CRY_ALPHA_BETA. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P00914.

Entry information

Entry name

PHR_ECOLI

Accession

Primary (citable) accession number: P00914

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 21, 1986
Last modified:	May 1, 2013
This is version 130 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents