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Protein

Deoxyribodipyrimidine photo-lyase, mitochondrial

Gene

PHR1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: 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

Protein has several cofactor binding sites:

Absorptioni

Abs(max)=377 nm

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei326FADBy similarity1
Sitei416Electron transfer via tryptophanyl radicalBy similarity1
Sitei469Electron transfer via tryptophanyl radicalBy similarity1
Sitei492Electron transfer via tryptophanyl radicalBy similarity1
Binding sitei514DNABy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi338 – 342FADBy similarity5
Nucleotide bindingi482 – 484FADBy similarity3

GO - Molecular functioni

  • deoxyribodipyrimidine photo-lyase activity Source: SGD
  • DNA binding Source: UniProtKB-KW
  • mRNA binding Source: SGD
  • nucleotide binding Source: UniProtKB-KW

GO - Biological processi

  • photoreactive repair Source: SGD
  • 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
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOR386W.
SGDiS000005913. PHR1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi387W → A: Reduces substrate binding 100-fold. Reduces quantum yield for dimer photolysis 3-fold. 1 Publication1
Mutagenesisi463K → A: Reduces substrate binding 100-fold. 1 Publication1
Mutagenesisi507R → A: Reduces substrate binding 100-fold. 1 Publication1
Mutagenesisi517K → A: Reduces substrate binding 10-fold. 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_0000024051? – 565Deoxyribodipyrimidine photo-lyase, mitochondrial
Transit peptidei1 – ?Mitochondrion

Proteomic databases

MaxQBiP05066.
PRIDEiP05066.

PTM databases

iPTMnetiP05066.

Interactioni

Subunit structurei

Monomer.By similarity

Protein-protein interaction databases

BioGridi34767. 15 interactors.
DIPiDIP-6327N.
IntActiP05066. 14 interactors.
MINTiMINT-688138.

Structurei

3D structure databases

ProteinModelPortaliP05066.
SMRiP05066.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini75 – 226Photolyase/cryptochrome alpha/betaAdd BLAST152

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni384 – 391Interaction with DNABy similarity8
Regioni451 – 452Interaction with DNABy similarity2

Sequence similaritiesi

Belongs to the DNA photolyase class-1 family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

GeneTreeiENSGT00500000044813.
HOGENOMiHOG000245621.
InParanoidiP05066.
KOiK01669.
OMAiGGWGFCS.
OrthoDBiEOG092C14L6.

Family and domain databases

Gene3Di3.40.50.620. 1 hit.
InterProiIPR005101. Cryptochr/Photolyase_FAD-bd.
IPR002081. Cryptochrome/DNA_photolyase_1.
IPR018394. DNA_photolyase_1_CS_C.
IPR006050. DNA_photolyase_N.
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

        10         20         30         40         50
MKRTVISSSN AYASKRSRLD IEHDFEQYHS LNKKYYPRPI TRTGANQFNN
60 70 80 90 100
KSRAKPMEIV EKLQKKQKTS FENVSTVMHW FRNDLRLYDN VGLYKSVALF
110 120 130 140 150
QQLRQKNAKA KLYAVYVINE DDWRAHMDSG WKLMFIMGAL KNLQQSLAEL
160 170 180 190 200
HIPLLLWEFH TPKSTLSNSK EFVEFFKEKC MNVSSGTGTI ITANIEYQTD
210 220 230 240 250
ELYRDIRLLE NEDHRLQLKY YHDSCIVAPG LITTDRGTNY SVFTPWYKKW
260 270 280 290 300
VLYVNNYKKS TSEICHLHII EPLKYNETFE LKPFQYSLPD EFLQYIPKSK
310 320 330 340 350
WCLPDVSEEA ALSRLKDFLG TKSSKYNNEK DMLYLGGTSG LSVYITTGRI
360 370 380 390 400
STRLIVNQAF QSCNGQIMSK ALKDNSSTQN FIKEVAWRDF YRHCMCNWPY
410 420 430 440 450
TSMGMPYRLD TLDIKWENNP VAFEKWCTGN TGIPIVDAIM RKLLYTGYIN
460 470 480 490 500
NRSRMITASF LSKNLLIDWR WGERWFMKHL IDGDSSSNVG GWGFCSSTGI
510 520 530 540 550
DAQPYFRVFN MDIQAKKYDP QMIFVKQWVP ELISSENKRP ENYPKPLVDL
560
KHSRERALKV YKDAM
Length:565
Mass (Da):66,274
Last modified:August 13, 1987 - v1
Checksum:iCD4FC3DA6128B97C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti77V → A in AAA34875 (PubMed:3000886).Curated1
Sequence conflicti165T → S in AAA34875 (PubMed:3000886).Curated1
Sequence conflicti169S → T in AAA34875 (PubMed:3000886).Curated1
Sequence conflicti200D → S in AAA34875 (PubMed:3000886).Curated1
Sequence conflicti351S → R in AAA34875 (PubMed:3000886).Curated1
Sequence conflicti365G → E in AAA34875 (PubMed:3000886).Curated1
Sequence conflicti473E → K in AAA34875 (PubMed:3000886).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

ProteinModelPortaliP05066.
SMRiP05066.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34767. 15 interactors.
DIPiDIP-6327N.
IntActiP05066. 14 interactors.
MINTiMINT-688138.

PTM databases

iPTMnetiP05066.

Proteomic databases

MaxQBiP05066.
PRIDEiP05066.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YOR386W.
SGDiS000005913. PHR1.

Phylogenomic databases

GeneTreeiENSGT00500000044813.
HOGENOMiHOG000245621.
InParanoidiP05066.
KOiK01669.
OMAiGGWGFCS.
OrthoDBiEOG092C14L6.

Enzyme and pathway databases

BioCyciYEAST:G3O-33848-MONOMER.

Miscellaneous databases

PROiP05066.

Family and domain databases

Gene3Di3.40.50.620. 1 hit.
InterProiIPR005101. Cryptochr/Photolyase_FAD-bd.
IPR002081. Cryptochrome/DNA_photolyase_1.
IPR018394. DNA_photolyase_1_CS_C.
IPR006050. DNA_photolyase_N.
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]
ProtoNetiSearch...

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: November 2, 2016
This is version 161 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.1 Publication

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.