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Protein

Deoxyribodipyrimidine photo-lyase

Gene

phr

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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 (By similarity).By similarity

Catalytic activityi

Cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA).

Cofactori

FADNote: Binds 1 FAD per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei197 – 1971FAD1 Publication
Binding sitei201 – 2011DNABy similarity
Binding sitei241 – 2411FAD1 Publication
Binding sitei248 – 2481FAD1 Publication
Sitei275 – 2751Electron transfer via tryptophanyl radicalBy similarity
Binding sitei310 – 3101FAD1 Publication
Sitei328 – 3281Electron transfer via tryptophanyl radicalBy similarity
Sitei351 – 3511Electron transfer via tryptophanyl radicalBy similarity
Binding sitei373 – 3731DNABy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi209 – 2135FAD1 Publication
Nucleotide bindingi341 – 3433FAD1 Publication

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

BioCyciTTHE300852:GH8R-2125-MONOMER.
BRENDAi4.1.99.3. 2305.

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
Ordered Locus Names:TTHB102
Encoded oniPlasmid pTT271 Publication
OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Taxonomic identifieri300852 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
Proteomesi
  • UP000000532 Componenti: Plasmid pTT27

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi201 – 2011R → A: Reduces CPD repair activity by 20%.
Mutagenesisi240 – 2401K → A: Reduces CPD repair activity by 20%.
Mutagenesisi247 – 2471W → A: Reduces CPD repair activity by 20%.
Mutagenesisi311 – 3111R → A: Strongly reduces interaction with DNA. 1 Publication
Mutagenesisi353 – 3531W → A: Strongly reduces interaction with DNA. Reduces CPD repair activity by 80%. 1 Publication
Mutagenesisi366 – 3661R → A: Strongly reduces interaction with DNA. 1 Publication

Chemistry

DrugBankiDB03147. Flavin adenine dinucleotide.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 420420Deoxyribodipyrimidine photo-lyasePRO_0000085115Add
BLAST

Interactioni

Subunit structurei

Monomer.By similarity

Structurei

Secondary structure

1
420
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 74Combined sources
Beta strandi14 – 163Combined sources
Helixi18 – 247Combined sources
Beta strandi29 – 357Combined sources
Helixi37 – 404Combined sources
Helixi44 – 6320Combined sources
Beta strandi68 – 736Combined sources
Helixi75 – 8511Combined sources
Beta strandi89 – 946Combined sources
Helixi99 – 11113Combined sources
Beta strandi116 – 1194Combined sources
Helixi136 – 1405Combined sources
Helixi179 – 19214Combined sources
Helixi194 – 1963Combined sources
Helixi197 – 2004Combined sources
Helixi213 – 2175Combined sources
Helixi223 – 23311Combined sources
Helixi236 – 25722Combined sources
Helixi259 – 2624Combined sources
Helixi268 – 2703Combined sources
Helixi279 – 2868Combined sources
Helixi293 – 30513Combined sources
Helixi310 – 32213Combined sources
Helixi328 – 33811Combined sources
Helixi344 – 35411Combined sources
Helixi359 – 3613Combined sources
Helixi370 – 3778Combined sources
Beta strandi379 – 3813Combined sources
Helixi382 – 3876Combined sources
Beta strandi392 – 3954Combined sources
Helixi403 – 41816Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1IQRX-ray2.10A1-420[»]
1IQUX-ray2.20A1-420[»]
2J07X-ray1.95A1-420[»]
2J08X-ray2.61A1-420[»]
2J09X-ray2.00A1-420[»]
ProteinModelPortaliP61497.
SMRiP61497. Positions 2-420.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP61497.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini2 – 124123Photolyase/cryptochrome alpha/betaAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni244 – 2518Interaction with DNABy similarity
Regioni310 – 3112Interaction with DNABy similarity

Sequence similaritiesi

Belongs to the DNA photolyase class-1 family.Curated

Phylogenomic databases

HOGENOMiHOG000245621.
KOiK01669.
OMAiWRIGARY.
PhylomeDBiP61497.

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.

P61497-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGPLLVWHRG DLRLHDHPAL LEALARGPVV GLVVLDPNNL KTTPRRRAWF
60 70 80 90 100
LENVRALREA YRARGGALWV LEGLPWEKVP EAARRLKAKA VYALTSHTPY
110 120 130 140 150
GRYRDGRVRE ALPVPLHLLP APHLLPPDLP RAYRVYTPFS RLYRGAAPPL
160 170 180 190 200
PPPEALPKGP EEGEIPREDP GLPLPEPGEE AALAGLRAFL EAKLPRYAEE
210 220 230 240 250
RDRLDGEGGS RLSPYFALGV LSPRLAAWEA ERRGGEGARK WVAELLWRDF
260 270 280 290 300
SYHLLYHFPW MAERPLDPRF QAFPWQEDEA LFQAWYEGKT GVPLVDAAMR
310 320 330 340 350
ELHATGFLSN RARMNAAQFA VKHLLLPWKR CEEAFRHLLL DGDRAVNLQG
360 370 380 390 400
WQWAGGLGVD AAPYFRVFNP VLQGERHDPE GRWLKRWAPE YPSYAPKDPV
410 420
VDLEEARRRY LRLARDLARG
Length:420
Mass (Da):47,901
Last modified:May 24, 2004 - v1
Checksum:i773968AC2D300893
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB064548 Genomic DNA. Translation: BAB61864.2.
AP008227 Genomic DNA. Translation: BAD71898.1.
RefSeqiWP_011229192.1. NC_006462.1.
YP_145341.1. NC_006462.1.

Genome annotation databases

EnsemblBacteriaiBAD71898; BAD71898; BAD71898.
GeneIDi3169528.
KEGGittj:TTHB102.
PATRICi23959128. VBITheThe93045_2045.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB064548 Genomic DNA. Translation: BAB61864.2.
AP008227 Genomic DNA. Translation: BAD71898.1.
RefSeqiWP_011229192.1. NC_006462.1.
YP_145341.1. NC_006462.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1IQRX-ray2.10A1-420[»]
1IQUX-ray2.20A1-420[»]
2J07X-ray1.95A1-420[»]
2J08X-ray2.61A1-420[»]
2J09X-ray2.00A1-420[»]
ProteinModelPortaliP61497.
SMRiP61497. Positions 2-420.
ModBaseiSearch...
MobiDBiSearch...

Chemistry

DrugBankiDB03147. Flavin adenine dinucleotide.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD71898; BAD71898; BAD71898.
GeneIDi3169528.
KEGGittj:TTHB102.
PATRICi23959128. VBITheThe93045_2045.

Phylogenomic databases

HOGENOMiHOG000245621.
KOiK01669.
OMAiWRIGARY.
PhylomeDBiP61497.

Enzyme and pathway databases

BioCyciTTHE300852:GH8R-2125-MONOMER.
BRENDAi4.1.99.3. 2305.

Miscellaneous databases

EvolutionaryTraceiP61497.

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_THET8
AccessioniPrimary (citable) accession number: P61497
Secondary accession number(s): P37250, Q53W60
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 24, 2004
Last sequence update: May 24, 2004
Last modified: September 7, 2016
This is version 90 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Plasmid, Reference proteome

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.