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P05066 (PHR_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 139. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Deoxyribodipyrimidine photo-lyase, mitochondrial

EC=4.1.99.3
Alternative name(s):
DNA photolyase
Photoreactivating enzyme
Gene names
Name:PHR1
Ordered Locus Names:YOR386W
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length565 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence 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 By similarity.

Subcellular location

Nucleus. Mitochondrion.

Miscellaneous

There are only 150-300 molecules of photolyase per yeast cell.

Present with 688 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the DNA photolyase class-1 family.

Contains 1 photolyase/cryptochrome alpha/beta domain.

Biophysicochemical properties

Absorption:

Abs(max)=377 nm

Has a fluorescence excitation maximum at 390 nm and an emission maximum at 475 nm.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – ?Mitochondrion
Chain? – 565Deoxyribodipyrimidine photo-lyase, mitochondrialPRO_0000024051

Regions

Domain75 – 226152Photolyase/cryptochrome alpha/beta
Nucleotide binding338 – 3425FAD By similarity
Nucleotide binding482 – 4843FAD By similarity
Region384 – 3918Interaction with DNA By similarity
Region451 – 4522Interaction with DNA By similarity

Sites

Binding site3261FAD By similarity
Binding site5141DNA By similarity
Site4161Electron transfer via tryptophanyl radical By similarity
Site4691Electron transfer via tryptophanyl radical By similarity
Site4921Electron transfer via tryptophanyl radical By similarity

Experimental info

Mutagenesis3871W → A: Reduces substrate binding 100-fold. Reduces quantum yield for dimer photolysis 3-fold. Ref.6
Mutagenesis4631K → A: Reduces substrate binding 100-fold. Ref.6
Mutagenesis5071R → A: Reduces substrate binding 100-fold. Ref.6
Mutagenesis5171K → A: Reduces substrate binding 10-fold.
Sequence conflict771V → A in AAA34875. Ref.2
Sequence conflict1651T → S in AAA34875. Ref.2
Sequence conflict1691S → T in AAA34875. Ref.2
Sequence conflict2001D → S in AAA34875. Ref.2
Sequence conflict3511S → R in AAA34875. Ref.2
Sequence conflict3651G → E in AAA34875. Ref.2
Sequence conflict4731E → K in AAA34875. Ref.2

Sequences

Sequence LengthMass (Da)Tools
P05066 [UniParc].

Last modified August 13, 1987. Version 1.
Checksum: CD4FC3DA6128B97C

FASTA56566,274
        10         20         30         40         50         60 
MKRTVISSSN AYASKRSRLD IEHDFEQYHS LNKKYYPRPI TRTGANQFNN KSRAKPMEIV 

        70         80         90        100        110        120 
EKLQKKQKTS FENVSTVMHW FRNDLRLYDN VGLYKSVALF QQLRQKNAKA KLYAVYVINE 

       130        140        150        160        170        180 
DDWRAHMDSG WKLMFIMGAL KNLQQSLAEL HIPLLLWEFH TPKSTLSNSK EFVEFFKEKC 

       190        200        210        220        230        240 
MNVSSGTGTI ITANIEYQTD ELYRDIRLLE NEDHRLQLKY YHDSCIVAPG LITTDRGTNY 

       250        260        270        280        290        300 
SVFTPWYKKW VLYVNNYKKS TSEICHLHII EPLKYNETFE LKPFQYSLPD EFLQYIPKSK 

       310        320        330        340        350        360 
WCLPDVSEEA ALSRLKDFLG TKSSKYNNEK DMLYLGGTSG LSVYITTGRI STRLIVNQAF 

       370        380        390        400        410        420 
QSCNGQIMSK ALKDNSSTQN FIKEVAWRDF YRHCMCNWPY TSMGMPYRLD TLDIKWENNP 

       430        440        450        460        470        480 
VAFEKWCTGN TGIPIVDAIM RKLLYTGYIN NRSRMITASF LSKNLLIDWR WGERWFMKHL 

       490        500        510        520        530        540 
IDGDSSSNVG GWGFCSSTGI DAQPYFRVFN MDIQAKKYDP QMIFVKQWVP ELISSENKRP 

       550        560 
ENYPKPLVDL KHSRERALKV YKDAM 

« Hide

References

« Hide 'large scale' references
[1]"Sequence of the Saccharomyces cerevisiae PHR1 gene and homology of the PHR1 photolyase to E. coli photolyase."
Sancar G.B.
Nucleic Acids Res. 13:8231-8246(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Homology between the photoreactivation genes of Saccharomyces cerevisiae and Escherichia coli."
Yasui A., Langeveld S.A.
Gene 36:349-355(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"Purification of the yeast PHR1 photolyase from an Escherichia coli overproducing strain and characterization of the intrinsic chromophores of the enzyme."
Sancar G.B., Smith F.W., Heelis P.F.
J. Biol. Chem. 262:15457-15465(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION.
[4]"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D. expand/collapse author list , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[5]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[6]"The role of conserved amino acids in substrate binding and discrimination by photolyase."
Baer M.E., Sancar G.B.
J. Biol. Chem. 268:16717-16724(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF TRP-387; LYS-463 AND ARG-507.
[7]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[8]"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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X03183 Genomic DNA. Translation: CAA26944.1.
M11578 Genomic DNA. Translation: AAA34875.1.
Z75294 Genomic DNA. Translation: CAA99718.1.
BK006948 Genomic DNA. Translation: DAA11145.1.
PIRS67298.
RefSeqNP_015031.1. NM_001183806.1.

3D structure databases

ProteinModelPortalP05066.
SMRP05066. Positions 76-564.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid34767. 14 interactions.
DIPDIP-6327N.
IntActP05066. 14 interactions.
MINTMINT-688138.
STRING4932.YOR386W.

Proteomic databases

PaxDbP05066.
PeptideAtlasP05066.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYOR386W; YOR386W; YOR386W.
GeneID854568.
KEGGsce:YOR386W.

Organism-specific databases

CYGDYOR386w.
SGDS000005913. PHR1.

Phylogenomic databases

eggNOGCOG0415.
GeneTreeENSGT00500000044813.
HOGENOMHOG000245621.
KOK01669.
OMANGTRENG.
OrthoDBEOG7K3TWX.

Enzyme and pathway databases

BioCycYEAST:G3O-33848-MONOMER.

Gene expression databases

GenevestigatorP05066.

Family and domain databases

Gene3D3.40.50.620. 1 hit.
InterProIPR002081. 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]
PfamPF00875. DNA_photolyase. 1 hit.
PF03441. FAD_binding_7. 1 hit.
[Graphical view]
PRINTSPR00147. DNAPHOTLYASE.
SUPFAMSSF48173. SSF48173. 1 hit.
SSF52425. SSF52425. 1 hit.
PROSITEPS00394. DNA_PHOTOLYASES_1_1. 1 hit.
PS00691. DNA_PHOTOLYASES_1_2. 1 hit.
PS51645. PHR_CRY_ALPHA_BETA. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio977015.
PROP05066.

Entry information

Entry namePHR_YEAST
AccessionPrimary (citable) accession number: P05066
Secondary accession number(s): D6W379
Entry history
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: August 13, 1987
Last modified: March 19, 2014
This is version 139 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XV

Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families