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Protein

Deoxyribodipyrimidine photo-lyase

Gene

phr

Organism
Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (Anacystis nidulans)
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)=440 nm

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei51 – 511F420
Binding sitei228 – 2281FAD3 Publications
Binding sitei232 – 2321DNA
Binding sitei248 – 2481F420
Sitei314 – 3141Electron transfer via tryptophanyl radicalBy similarity
Sitei367 – 3671Electron transfer via tryptophanyl radicalBy similarity
Binding sitei386 – 3861FAD3 Publications
Sitei390 – 3901Electron transfer via tryptophanyl radicalBy similarity
Binding sitei411 – 4111DNA
Binding sitei472 – 4721DNA

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi240 – 2478FAD3 Publications
Nucleotide bindingi346 – 3527FAD3 Publications
Nucleotide bindingi380 – 3823FAD3 Publications

GO - Molecular functioni

GO - Biological processi

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

BioCyciSELO269084:GCDQ-1424-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Deoxyribodipyrimidine photo-lyase (EC:4.1.99.3)
Alternative name(s):
DNA photolyase
Photoreactivating enzyme
Gene namesi
Name:phr
Synonyms:phrA
Ordered Locus Names:syc1392_c
OrganismiSynechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (Anacystis nidulans)
Taxonomic identifieri269084 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechococcus
Proteomesi
  • UP000001175 Componenti: Chromosome

Pathology & Biotechi

Chemistry

DrugBankiDB03147. Flavin adenine dinucleotide.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 484483Deoxyribodipyrimidine photo-lyasePRO_0000085112Add
BLAST

Interactioni

Subunit structurei

Monomer.3 Publications

Protein-protein interaction databases

STRINGi269084.syc1392_c.

Structurei

Secondary structure

1
484
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 84Combined sources
Beta strandi15 – 173Combined sources
Helixi19 – 279Combined sources
Beta strandi31 – 377Combined sources
Helixi39 – 424Combined sources
Helixi49 – 6921Combined sources
Beta strandi73 – 786Combined sources
Helixi80 – 9011Combined sources
Beta strandi94 – 996Combined sources
Helixi104 – 11916Combined sources
Beta strandi123 – 1275Combined sources
Beta strandi130 – 1334Combined sources
Turni135 – 1373Combined sources
Helixi149 – 15810Combined sources
Helixi176 – 1827Combined sources
Helixi183 – 1853Combined sources
Helixi194 – 1963Combined sources
Helixi210 – 22213Combined sources
Helixi224 – 2274Combined sources
Helixi228 – 2314Combined sources
Helixi244 – 2485Combined sources
Helixi254 – 26714Combined sources
Helixi271 – 29626Combined sources
Helixi298 – 3025Combined sources
Helixi308 – 3114Combined sources
Helixi318 – 3258Combined sources
Helixi332 – 34413Combined sources
Helixi349 – 36113Combined sources
Helixi368 – 3758Combined sources
Helixi383 – 39210Combined sources
Turni393 – 3953Combined sources
Beta strandi397 – 3993Combined sources
Helixi408 – 4158Combined sources
Helixi420 – 4256Combined sources
Helixi427 – 4293Combined sources
Helixi434 – 4396Combined sources
Helixi444 – 4474Combined sources
Helixi457 – 47418Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1OWLX-ray1.80A1-484[»]
1OWMX-ray2.30A1-484[»]
1OWNX-ray2.30A1-484[»]
1OWOX-ray2.30A1-484[»]
1OWPX-ray2.30A1-484[»]
1QNFX-ray1.80A1-484[»]
1TEZX-ray1.80A/B/C/D2-475[»]
ProteinModelPortaliP05327.
SMRiP05327. Positions 1-475.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP05327.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 132130Photolyase/cryptochrome alpha/betaAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni36 – 383F420 binding
Regioni101 – 1099F420 binding
Regioni141 – 1488DNA binding
Regioni283 – 2908Interaction with DNA
Regioni349 – 3502Interaction with DNA

Sequence similaritiesi

Belongs to the DNA photolyase class-1 family.Curated

Phylogenomic databases

eggNOGiENOG4105CVP. Bacteria.
COG0415. LUCA.
HOGENOMiHOG000245621.
KOiK01669.
OMAiHDVEVYD.
OrthoDBiPOG091H03PR.

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.
IPR019947. Photolyase_8HDF.
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.
TIGRFAMsiTIGR03556. photolyase_8HDF. 1 hit.
PROSITEiPS00394. DNA_PHOTOLYASES_1_1. 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.

P05327-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAAPILFWHR RDLRLSDNIG LAAARAQSAQ LIGLFCLDPQ ILQSADMAPA
60 70 80 90 100
RVAYLQGCLQ ELQQRYQQAG SRLLLLQGDP QHLIPQLAQQ LQAEAVYWNQ
110 120 130 140 150
DIEPYGRDRD GQVAAALKTA GIRAVQLWDQ LLHSPDQILS GSGNPYSVYG
160 170 180 190 200
PFWKNWQAQP KPTPVATPTE LVDLSPEQLT AIAPLLLSEL PTLKQLGFDW
210 220 230 240 250
DGGFPVEPGE TAAIARLQEF CDRAIADYDP QRNFPAEAGT SGLSPALKFG
260 270 280 290 300
AIGIRQAWRA ASAAHALSRS DEARNSIRVW QQELAWREFY QHALYHFPSL
310 320 330 340 350
ADGPYRSLWQ QFPWENREAL FTAWTQAQTG YPIVDAAMRQ LTETGWMHNR
360 370 380 390 400
CWMIVASFLT KDLIIDWRRG EQFFMQHLVD GDLAANNGGW QWSASSGMDP
410 420 430 440 450
KPLRIFNPAS QAKKFDATAT YIKRWLPELR HVHPKDLISG EITPIGRRGY
460 470 480
PAPIVNHNLR QKQFKALYNQ LKAAIAEPEA EPDS
Length:484
Mass (Da):54,462
Last modified:January 23, 2007 - v4
Checksum:i2DAC6D9CFD515E3D
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti259 – 2591R → Q in CAA30190 (PubMed:2837735).Curated
Sequence conflicti352 – 3521W → R in CAA30190 (PubMed:2837735).Curated
Sequence conflicti446 – 4461G → E in CAA30190 (PubMed:2837735).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X07230 Genomic DNA. Translation: CAA30190.1.
AP008231 Genomic DNA. Translation: BAD79582.1.
RefSeqiWP_011243704.1. NC_006576.1.

Genome annotation databases

EnsemblBacteriaiBAD79582; BAD79582; syc1392_c.
KEGGisyc:syc1392_c.
PATRICi32488703. VBISynElo117686_1605.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X07230 Genomic DNA. Translation: CAA30190.1.
AP008231 Genomic DNA. Translation: BAD79582.1.
RefSeqiWP_011243704.1. NC_006576.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1OWLX-ray1.80A1-484[»]
1OWMX-ray2.30A1-484[»]
1OWNX-ray2.30A1-484[»]
1OWOX-ray2.30A1-484[»]
1OWPX-ray2.30A1-484[»]
1QNFX-ray1.80A1-484[»]
1TEZX-ray1.80A/B/C/D2-475[»]
ProteinModelPortaliP05327.
SMRiP05327. Positions 1-475.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi269084.syc1392_c.

Chemistry

DrugBankiDB03147. Flavin adenine dinucleotide.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD79582; BAD79582; syc1392_c.
KEGGisyc:syc1392_c.
PATRICi32488703. VBISynElo117686_1605.

Phylogenomic databases

eggNOGiENOG4105CVP. Bacteria.
COG0415. LUCA.
HOGENOMiHOG000245621.
KOiK01669.
OMAiHDVEVYD.
OrthoDBiPOG091H03PR.

Enzyme and pathway databases

BioCyciSELO269084:GCDQ-1424-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP05327.

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.
IPR019947. Photolyase_8HDF.
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.
TIGRFAMsiTIGR03556. photolyase_8HDF. 1 hit.
PROSITEiPS00394. DNA_PHOTOLYASES_1_1. 1 hit.
PS51645. PHR_CRY_ALPHA_BETA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPHR_SYNP6
AccessioniPrimary (citable) accession number: P05327
Secondary accession number(s): Q5N288
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: January 23, 2007
Last modified: September 7, 2016
This is version 131 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

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.