Deoxyribodipyrimidine photo-lyase, mitochondrial precursor - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P05066 (PHR_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 132. 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, mitochondrial
EC=4.1.99.3

Alternative name(s):
DNA photolyase
Photoreactivating enzyme

Gene names

Name:	PHR1
Ordered Locus Names:	YOR386W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length	565 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
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 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.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Cellular component	Mitochondrion Nucleus
Domain	Transit peptide
Ligand	Chromophore DNA-binding FAD Flavoprotein Nucleotide-binding
Molecular function	Lyase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	photoreactive repair Traceable author statement PubMed 10915863. Source: SGD protein-chromophore linkage Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	mitochondrion Inferred from direct assay PubMed 14576278 PubMed 16823961. Source: SGD nucleus Traceable author statement PubMed 10915863. Source: SGD
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW deoxyribodipyrimidine photo-lyase activity Inferred from direct assay PubMed 2911265. Source: SGD mRNA binding Inferred from direct assay PubMed 21124907. Source: SGD 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

Transit peptide

1 – ?

Mitochondrion

Chain

? – 565

Deoxyribodipyrimidine photo-lyase, mitochondrial

PRO_0000024051

Regions

Domain

75 – 226

152

Photolyase/cryptochrome alpha/beta

Nucleotide binding

338 – 342

FAD By similarity

Nucleotide binding

482 – 484

FAD By similarity

Region

384 – 391

Interaction with DNA By similarity

Region

451 – 452

Interaction with DNA By similarity

Sites

Binding site

326

FAD By similarity

Binding site

514

DNA By similarity

Site

416

Electron transfer via tryptophanyl radical By similarity

Site

469

Electron transfer via tryptophanyl radical By similarity

Site

492

Electron transfer via tryptophanyl radical By similarity

Experimental info

Mutagenesis

387

W → A: Reduces substrate binding 100-fold. Reduces quantum yield for dimer photolysis 3-fold. Ref.6

Mutagenesis

463

K → A: Reduces substrate binding 100-fold. Ref.6

Mutagenesis

507

R → A: Reduces substrate binding 100-fold. Ref.6

Mutagenesis

517

K → A: Reduces substrate binding 10-fold.

Sequence conflict

V → A in AAA34875. Ref.2

Sequence conflict

165

T → S in AAA34875. Ref.2

Sequence conflict

169

S → T in AAA34875. Ref.2

Sequence conflict

200

D → S in AAA34875. Ref.2

Sequence conflict

351

S → R in AAA34875. Ref.2

Sequence conflict

365

G → E in AAA34875. Ref.2

Sequence conflict

473

E → K in AAA34875. Ref.2

Sequences

Sequence

Length

Mass (Da)

Tools

P05066 [UniParc].

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

FASTA

565

66,274

        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' referencesShow '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. Kleine K. Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[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.
PIR	S67298.
RefSeq	NP_015031.1. NM_001183806.1.
3D structure databases
ProteinModelPortal	P05066.
SMR	P05066. Positions 303-551.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-6327N.
IntAct	P05066. 15 interactions.
MINT	MINT-688138.
STRING	4932.YOR386W.
Proteomic databases
PaxDb	P05066.
PeptideAtlas	P05066.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YOR386W; YOR386W; YOR386W.
GeneID	854568.
KEGG	sce:YOR386W.
Organism-specific databases
CYGD	YOR386w.
SGD	S000005913. PHR1.
Phylogenomic databases
eggNOG	COG0415.
GeneTree	ENSGT00500000044813.
HOGENOM	HOG000245621.
KO	K01669.
OMA	CEDANAR.
OrthoDB	EOG4XPTQ3.
Enzyme and pathway databases
BioCyc	YEAST:G3O-33848-MONOMER.
Gene expression databases
Genevestigator	P05066.
GermOnline	YOR386W. Saccharomyces cerevisiae.
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
NextBio	977015.

Entry information

Entry name

PHR_YEAST

Accession

Primary (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:	May 29, 2013
This is version 132 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

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

Yeast chromosome XV

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

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

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