Reviewed, UniProtKB/Swiss-Prot P05066 (PHR_YEAST)

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 (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [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. Ref.6
Sequence similarities	Belongs to the DNA photolyase class-1 family. Contains 1 DNA photolyase domain.
Biophysicochemical properties	Absorption: Has a fluorescence excitation maximum at 390 nm and an emission maximum at 475 nm. Abs(max)=377 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
Gene Ontology (GO)
Biological process	photoreactive repair Traceable author statement. Source: SGD protein-chromophore linkage Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	mitochondrion Inferred from direct assay. Source: SGD nucleus Traceable author statement. Source: SGD
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW deoxyribodipyrimidine photo-lyase activity Inferred from direct assay. Source: SGD nucleotide binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
MSD1	P15179	1	EBI-13385,EBI-18659
PRP40	P33203	1	EBI-13385,EBI-701

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 – 262	188	DNA photolyase
	Nucleotide binding	338 – 342	5	FAD By similarity
	Nucleotide binding	482 – 484	3	FAD By similarity
	Region	384 – 391	8	Interaction with DNA By similarity
	Region	451 – 452	2	Interaction with DNA By similarity
Sites
	Binding site	326	1	FAD By similarity
	Binding site	514	1	DNA By similarity
	Site	416	1	Electron transfer via tryptophanyl radical By similarity
	Site	469	1	Electron transfer via tryptophanyl radical By similarity
	Site	492	1	Electron transfer via tryptophanyl radical By similarity
Experimental info
	Mutagenesis	387	1	W → A: Reduces substrate binding 100-fold. Reduces quantum yield for dimer photolysis 3-fold. Ref.5
	Mutagenesis	463	1	K → A: Reduces substrate binding 100-fold. Ref.5
	Mutagenesis	507	1	R → A: Reduces substrate binding 100-fold. Ref.5
	Mutagenesis	517	1	K → A: Reduces substrate binding 10-fold.
	Sequence conflict	77	1	V → A in AAA34875. Ref.2
	Sequence conflict	165	1	T → S in AAA34875. Ref.2
	Sequence conflict	169	1	S → T in AAA34875. Ref.2
	Sequence conflict	200	1	D → S in AAA34875. Ref.2
	Sequence conflict	351	1	S → R in AAA34875. Ref.2
	Sequence conflict	365	1	G → E in AAA34875. Ref.2
	Sequence conflict	473	1	E → K in AAA34875. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	P05066-1 [UniParc]. Last modified August 13, 1987. Version 1. Checksum: CD4FC3DA6128B97C	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

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: 3906569] [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: 3000886] [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: 3316199] [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: 9169874] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[5]	"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: 8344951] [Abstract] Cited for: MUTAGENESIS OF TRP-387; LYS-463 AND ARG-507.
[6]	"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: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[7]	"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: 15721603] [Abstract] Cited for: REVIEW.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	X03183 Genomic DNA. Translation: CAA26944.1. M11578 Genomic DNA. Translation: AAA34875.1. Z75294 Genomic DNA. Translation: CAA99718.1.
PIR	S67298.
RefSeq	NP_015031.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
DIP	DIP:6327N.
IntAct	P05066. 15 interactions.
STRING	P05066.
Proteomic databases
PeptideAtlas	P05066.
PRIDE	P05066.
Genome annotation databases
Ensembl	YOR386W; YOR386W; YOR386W; Saccharomyces cerevisiae. [Genome view]
GeneID	854568.
KEGG	sce:YOR386W.
NMPDR	fig|4932.3.peg.6152.
Organism-specific databases
CYGD	YOR386w.
SGD	S000005913. PHR1.
Phylogenomic databases
HOGENOM	P05066.
OMA	AWRDFYK
OrthoDB	EOG9BK6MT
Enzyme and pathway databases
BRENDA	4.1.99.3. 250.
Gene expression databases
ArrayExpress	P05066.
Genevestigator	P05066.
GermOnline	YOR386W. Saccharomyces cerevisiae.
Family and domain databases
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]
Gene3D	G3DSA:3.40.50.620. Rossmann-like_a/b/a_fold. 1 hit.
Pfam	PF00875. DNA_photolyase. 1 hit. PF03441. FAD_binding_7. 1 hit. [Graphical view]
PRINTS	PR00147. DNAPHOTLYASE.
PROSITE	PS00394. DNA_PHOTOLYASES_1_1. 1 hit. PS00691. DNA_PHOTOLYASES_1_2. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	977015.

Entry information

Entry name

PHR_YEAST

Accession

Primary (citable) accession number: P05066

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 13, 1987
Last sequence update:	August 13, 1987
Last modified:	November 24, 2009
This is version 104 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)