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P05066

- PHR_YEAST

UniProt

P05066 - PHR_YEAST

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Protein

Deoxyribodipyrimidine photo-lyase, mitochondrial

Gene
PHR1, YOR386W
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - 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

Binds 1 FAD per subunit.
Binds 1 5,10-methenyltetrahydrofolate non-covalently per subunit.

Absorptioni

Abs(max)=377 nm

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei326 – 3261FAD By similarity
Sitei416 – 4161Electron transfer via tryptophanyl radical By similarity
Sitei469 – 4691Electron transfer via tryptophanyl radical By similarity
Sitei492 – 4921Electron transfer via tryptophanyl radical By similarity
Binding sitei514 – 5141DNA By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi338 – 3425FAD By similarity
Nucleotide bindingi482 – 4843FAD By similarity

GO - Molecular functioni

  1. deoxyribodipyrimidine photo-lyase activity Source: SGD
  2. DNA binding Source: UniProtKB-KW
  3. mRNA binding Source: SGD
  4. nucleotide binding Source: UniProtKB-KW

GO - Biological processi

  1. photoreactive repair Source: SGD
  2. protein-chromophore linkage Source: UniProtKB-KW
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

BioCyciYEAST:G3O-33848-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Deoxyribodipyrimidine photo-lyase, mitochondrial (EC:4.1.99.3)
Alternative name(s):
DNA photolyase
Photoreactivating enzyme
Gene namesi
Name:PHR1
Ordered Locus Names:YOR386W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XV

Organism-specific databases

CYGDiYOR386w.
SGDiS000005913. PHR1.

Subcellular locationi

GO - Cellular componenti

  1. mitochondrion Source: UniProtKB-SubCell
  2. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi387 – 3871W → A: Reduces substrate binding 100-fold. Reduces quantum yield for dimer photolysis 3-fold. 1 Publication
Mutagenesisi463 – 4631K → A: Reduces substrate binding 100-fold. 1 Publication
Mutagenesisi507 – 5071R → A: Reduces substrate binding 100-fold. 1 Publication
Mutagenesisi517 – 5171K → A: Reduces substrate binding 10-fold.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini? – 565Deoxyribodipyrimidine photo-lyase, mitochondrialPRO_0000024051
Transit peptidei1 – ?Mitochondrion

Proteomic databases

MaxQBiP05066.
PaxDbiP05066.
PeptideAtlasiP05066.

Expressioni

Gene expression databases

GenevestigatoriP05066.

Interactioni

Subunit structurei

Monomer By similarity.

Protein-protein interaction databases

BioGridi34767. 14 interactions.
DIPiDIP-6327N.
IntActiP05066. 14 interactions.
MINTiMINT-688138.
STRINGi4932.YOR386W.

Structurei

3D structure databases

ProteinModelPortaliP05066.
SMRiP05066. Positions 75-562.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini75 – 226152Photolyase/cryptochrome alpha/betaAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni384 – 3918Interaction with DNA By similarity
Regioni451 – 4522Interaction with DNA By similarity

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0415.
GeneTreeiENSGT00500000044813.
HOGENOMiHOG000245621.
KOiK01669.
OMAiYIRAFVP.
OrthoDBiEOG7K3TWX.

Family and domain databases

Gene3Di3.40.50.620. 1 hit.
InterProiIPR002081. 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]
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.

Sequence processingi: The displayed sequence is further processed into a mature form.

P05066-1 [UniParc]FASTAAdd to Basket

« Hide

MKRTVISSSN AYASKRSRLD IEHDFEQYHS LNKKYYPRPI TRTGANQFNN    50
KSRAKPMEIV EKLQKKQKTS FENVSTVMHW FRNDLRLYDN VGLYKSVALF 100
QQLRQKNAKA KLYAVYVINE DDWRAHMDSG WKLMFIMGAL KNLQQSLAEL 150
HIPLLLWEFH TPKSTLSNSK EFVEFFKEKC MNVSSGTGTI ITANIEYQTD 200
ELYRDIRLLE NEDHRLQLKY YHDSCIVAPG LITTDRGTNY SVFTPWYKKW 250
VLYVNNYKKS TSEICHLHII EPLKYNETFE LKPFQYSLPD EFLQYIPKSK 300
WCLPDVSEEA ALSRLKDFLG TKSSKYNNEK DMLYLGGTSG LSVYITTGRI 350
STRLIVNQAF QSCNGQIMSK ALKDNSSTQN FIKEVAWRDF YRHCMCNWPY 400
TSMGMPYRLD TLDIKWENNP VAFEKWCTGN TGIPIVDAIM RKLLYTGYIN 450
NRSRMITASF LSKNLLIDWR WGERWFMKHL IDGDSSSNVG GWGFCSSTGI 500
DAQPYFRVFN MDIQAKKYDP QMIFVKQWVP ELISSENKRP ENYPKPLVDL 550
KHSRERALKV YKDAM 565
Length:565
Mass (Da):66,274
Last modified:August 13, 1987 - v1
Checksum:iCD4FC3DA6128B97C
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti77 – 771V → A in AAA34875. 1 Publication
Sequence conflicti165 – 1651T → S in AAA34875. 1 Publication
Sequence conflicti169 – 1691S → T in AAA34875. 1 Publication
Sequence conflicti200 – 2001D → S in AAA34875. 1 Publication
Sequence conflicti351 – 3511S → R in AAA34875. 1 Publication
Sequence conflicti365 – 3651G → E in AAA34875. 1 Publication
Sequence conflicti473 – 4731E → K in AAA34875. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X03183 Genomic DNA. Translation: CAA26944.1.
M11578 Genomic DNA. Translation: AAA34875.1.
Z75294 Genomic DNA. Translation: CAA99718.1.
BK006948 Genomic DNA. Translation: DAA11145.1.
PIRiS67298.
RefSeqiNP_015031.1. NM_001183806.1.

Genome annotation databases

EnsemblFungiiYOR386W; YOR386W; YOR386W.
GeneIDi854568.
KEGGisce:YOR386W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X03183 Genomic DNA. Translation: CAA26944.1 .
M11578 Genomic DNA. Translation: AAA34875.1 .
Z75294 Genomic DNA. Translation: CAA99718.1 .
BK006948 Genomic DNA. Translation: DAA11145.1 .
PIRi S67298.
RefSeqi NP_015031.1. NM_001183806.1.

3D structure databases

ProteinModelPortali P05066.
SMRi P05066. Positions 75-562.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 34767. 14 interactions.
DIPi DIP-6327N.
IntActi P05066. 14 interactions.
MINTi MINT-688138.
STRINGi 4932.YOR386W.

Proteomic databases

MaxQBi P05066.
PaxDbi P05066.
PeptideAtlasi P05066.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YOR386W ; YOR386W ; YOR386W .
GeneIDi 854568.
KEGGi sce:YOR386W.

Organism-specific databases

CYGDi YOR386w.
SGDi S000005913. PHR1.

Phylogenomic databases

eggNOGi COG0415.
GeneTreei ENSGT00500000044813.
HOGENOMi HOG000245621.
KOi K01669.
OMAi YIRAFVP.
OrthoDBi EOG7K3TWX.

Enzyme and pathway databases

BioCyci YEAST:G3O-33848-MONOMER.

Miscellaneous databases

NextBioi 977015.
PROi P05066.

Gene expression databases

Genevestigatori P05066.

Family and domain databases

Gene3Di 3.40.50.620. 1 hit.
InterProi 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 ]
Pfami PF00875. DNA_photolyase. 1 hit.
PF03441. FAD_binding_7. 1 hit.
[Graphical view ]
PRINTSi PR00147. DNAPHOTLYASE.
SUPFAMi SSF48173. SSF48173. 1 hit.
SSF52425. SSF52425. 1 hit.
PROSITEi PS00394. DNA_PHOTOLYASES_1_1. 1 hit.
PS00691. DNA_PHOTOLYASES_1_2. 1 hit.
PS51645. PHR_CRY_ALPHA_BETA. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. 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. 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.

Entry informationi

Entry nameiPHR_YEAST
AccessioniPrimary (citable) accession number: P05066
Secondary accession number(s): D6W379
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: August 13, 1987
Last modified: June 11, 2014
This is version 141 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

There are only 150-300 molecules of photolyase per yeast cell.
Present with 688 molecules/cell in log phase SD medium.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

External Data

Dasty 3

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