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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)DescriptionActionsGraphical viewLength
Binding sitei197FAD1 Publication1
Binding sitei201DNABy similarity1
Binding sitei241FAD1 Publication1
Binding sitei248FAD1 Publication1
Sitei275Electron transfer via tryptophanyl radicalBy similarity1
Binding sitei310FAD1 Publication1
Sitei328Electron transfer via tryptophanyl radicalBy similarity1
Sitei351Electron transfer via tryptophanyl radicalBy similarity1
Binding sitei373DNABy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi209 – 213FAD1 Publication5
Nucleotide bindingi341 – 343FAD1 Publication3

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

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)DescriptionActionsGraphical viewLength
Mutagenesisi201R → A: Reduces CPD repair activity by 20%. 1
Mutagenesisi240K → A: Reduces CPD repair activity by 20%. 1
Mutagenesisi247W → A: Reduces CPD repair activity by 20%. 1
Mutagenesisi311R → A: Strongly reduces interaction with DNA. 1 Publication1
Mutagenesisi353W → A: Strongly reduces interaction with DNA. Reduces CPD repair activity by 80%. 1 Publication1
Mutagenesisi366R → A: Strongly reduces interaction with DNA. 1 Publication1

Chemistry databases

DrugBankiDB03147. Flavin adenine dinucleotide.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000851151 – 420Deoxyribodipyrimidine photo-lyaseAdd BLAST420

Interactioni

Subunit structurei

Monomer.By similarity

Structurei

Secondary structure

1420
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 7Combined sources4
Beta strandi14 – 16Combined sources3
Helixi18 – 24Combined sources7
Beta strandi29 – 35Combined sources7
Helixi37 – 40Combined sources4
Helixi44 – 63Combined sources20
Beta strandi68 – 73Combined sources6
Helixi75 – 85Combined sources11
Beta strandi89 – 94Combined sources6
Helixi99 – 111Combined sources13
Beta strandi116 – 119Combined sources4
Helixi136 – 140Combined sources5
Helixi179 – 192Combined sources14
Helixi194 – 196Combined sources3
Helixi197 – 200Combined sources4
Helixi213 – 217Combined sources5
Helixi223 – 233Combined sources11
Helixi236 – 257Combined sources22
Helixi259 – 262Combined sources4
Helixi268 – 270Combined sources3
Helixi279 – 286Combined sources8
Helixi293 – 305Combined sources13
Helixi310 – 322Combined sources13
Helixi328 – 338Combined sources11
Helixi344 – 354Combined sources11
Helixi359 – 361Combined sources3
Helixi370 – 377Combined sources8
Beta strandi379 – 381Combined sources3
Helixi382 – 387Combined sources6
Beta strandi392 – 395Combined sources4
Helixi403 – 418Combined sources16

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP61497.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini2 – 124Photolyase/cryptochrome alpha/betaAdd BLAST123

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni244 – 251Interaction with DNABy similarity8
Regioni310 – 311Interaction with DNABy similarity2

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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Chemistry databases

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

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: November 2, 2016
This is version 92 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.