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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)DescriptionActionsGraphical viewLength
Binding sitei51F4201
Binding sitei228FAD3 Publications1
Binding sitei232DNA1
Binding sitei248F4201
Sitei314Electron transfer via tryptophanyl radicalBy similarity1
Sitei367Electron transfer via tryptophanyl radicalBy similarity1
Binding sitei386FAD3 Publications1
Sitei390Electron transfer via tryptophanyl radicalBy similarity1
Binding sitei411DNA1
Binding sitei472DNA1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi240 – 247FAD3 Publications8
Nucleotide bindingi346 – 352FAD3 Publications7
Nucleotide bindingi380 – 382FAD3 Publications3

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

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 lineageiBacteriaCyanobacteriaSynechococcalesSynechococcaceaeSynechococcus
Proteomesi
  • UP000001175 Componenti: Chromosome

Pathology & Biotechi

Chemistry databases

DrugBankiDB03147. Flavin adenine dinucleotide.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000851122 – 484Deoxyribodipyrimidine photo-lyaseAdd BLAST483

Proteomic databases

PRIDEiP05327.

Interactioni

Subunit structurei

Monomer.3 Publications

Protein-protein interaction databases

STRINGi269084.syc1392_c.

Structurei

Secondary structure

1484
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 8Combined sources4
Beta strandi15 – 17Combined sources3
Helixi19 – 27Combined sources9
Beta strandi31 – 37Combined sources7
Helixi39 – 42Combined sources4
Helixi49 – 69Combined sources21
Beta strandi73 – 78Combined sources6
Helixi80 – 90Combined sources11
Beta strandi94 – 99Combined sources6
Helixi104 – 119Combined sources16
Beta strandi123 – 127Combined sources5
Beta strandi130 – 133Combined sources4
Turni135 – 137Combined sources3
Helixi149 – 158Combined sources10
Helixi176 – 182Combined sources7
Helixi183 – 185Combined sources3
Helixi194 – 196Combined sources3
Helixi210 – 222Combined sources13
Helixi224 – 227Combined sources4
Helixi228 – 231Combined sources4
Helixi244 – 248Combined sources5
Helixi254 – 267Combined sources14
Helixi271 – 296Combined sources26
Helixi298 – 302Combined sources5
Helixi308 – 311Combined sources4
Helixi318 – 325Combined sources8
Helixi332 – 344Combined sources13
Helixi349 – 361Combined sources13
Helixi368 – 375Combined sources8
Helixi383 – 392Combined sources10
Turni393 – 395Combined sources3
Beta strandi397 – 399Combined sources3
Helixi408 – 415Combined sources8
Helixi420 – 425Combined sources6
Helixi427 – 429Combined sources3
Helixi434 – 439Combined sources6
Helixi444 – 447Combined sources4
Helixi457 – 474Combined sources18

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP05327.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini3 – 132Photolyase/cryptochrome alpha/betaAdd BLAST130

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni36 – 38F420 binding3
Regioni101 – 109F420 binding9
Regioni141 – 148DNA binding8
Regioni283 – 290Interaction with DNA8
Regioni349 – 350Interaction with DNA2

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)DescriptionActionsGraphical viewLength
Sequence conflicti259R → Q in CAA30190 (PubMed:2837735).Curated1
Sequence conflicti352W → R in CAA30190 (PubMed:2837735).Curated1
Sequence conflicti446G → E in CAA30190 (PubMed:2837735).Curated1

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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi269084.syc1392_c.

Chemistry databases

DrugBankiDB03147. Flavin adenine dinucleotide.

Proteomic databases

PRIDEiP05327.

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.

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: November 2, 2016
This is version 133 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.