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Information on EC 4.1.99.3 - deoxyribodipyrimidine photo-lyase and Organism(s) Arabidopsis thaliana and UniProt Accession Q9SB00
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4.1.99.3 deoxyribodipyrimidine photo-lyaseIUBMB Comments
A flavoprotein (FAD), containing a second chromophore group. The enzyme catalyses the reactivation by light of irradiated DNA. A similar reactivation of irradiated RNA is probably due to a separate enzyme.
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The taxonomic range for the selected organisms is: Arabidopsis thaliana
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
ssdna, primase, photolyase, dna photolyase, cryptochrome 1, cpd photolyase, cry-dash, cpd-photolyase, cyclobutane pyrimidine dimer photolyase, cryptochrome dash, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
AtCry3
CPD photolyase
cry3
cryptochrome 3
DASH-type cryptochrome, the enzyme catalyzes light-driven DNA repair like conventional photolyases but lacks an efficient flipping mechanism for interaction with cyclobutane pyrimidine dimer lesions within duplex DNA
deoxyribodipyrimidine photolyase
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deoxyribonucleate pyrimidine dimer lyase (photosensitive)
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deoxyribonucleic cyclobutane dipyrimidine photolyase
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deoxyribonucleic photolyase
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dipyrimidine photolyase (photosensitive)
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-
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DNA cyclobutane dipyrimidine photolyase
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-
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DNA photolyase
DNA-photoreactivating enzyme
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-
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lyase, deoxyribonucleate pyrimidine dimer
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photolyase
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photoreactivating enzyme
-
-
-
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phr A photolyase
-
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PhrB photolyase
-
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PRE
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DNA photolyase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA)
photo-induced intramolecular electron transfer in photolyases and initial electron-transfer bifurcation in repair complexes. Seven electron-transfer reactions in 10 elementary steps in all classes of CPD photolyases. Unified electron-transfer pathway through a conserved structural configuration that bifurcates to favor direct tunneling in prokaryotes and a two step hopping mechanism in eukaryotes. Complete photocycles of CPD repair by class I and class II PLs, overview
cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA)
the repair of CPD reveals seven electron-transfer (ET) reactions among ten elementary steps by a cyclic ET radical mechanism through bifurcating ET pathways, a direct tunneling route mediated by the intervening adenine and a two-step hopping path bridged by the intermediate adenine from the cofactor to damaged DNA, through the conserved folded flavin at the active site. Repair photocycle of the PLs and development of a unified repair mechanism for all CPD PLs with the critical, bifurcating electron transfer pathways through the folded flavin cofactor in the conserved active site structure, overview
cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA)
photo-induced intramolecular electron transfer in photolyases and initial electron-transfer bifurcation in repair complexes. Seven electron-transfer reactions in 10 elementary steps in all classes of CPD photolyases. Unified electron-transfer pathway through a conserved structural configuration that bifurcates to favor direct tunneling in prokaryotes and a two step hopping mechanism in eukaryotes. Complete photocycles of CPD repair by class I and class II PLs, overview
cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA)
the repair of CPD reveals seven electron-transfer (ET) reactions among ten elementary steps by a cyclic ET radical mechanism through bifurcating ET pathways, a direct tunneling route mediated by the intervening adenine and a two-step hopping path bridged by the intermediate adenine from the cofactor to damaged DNA, through the conserved folded flavin at the active site. Repair photocycle of the PLs and development of a unified repair mechanism for all CPD PLs with the critical, bifurcating electron transfer pathways through the folded flavin cofactor in the conserved active site structure, overview
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C-C-bond cleavage
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-
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SYSTEMATIC NAME
IUBMB Comments
deoxyribocyclobutadipyrimidine pyrimidine-lyase
A flavoprotein (FAD), containing a second chromophore group. The enzyme catalyses the reactivation by light of irradiated DNA. A similar reactivation of irradiated RNA is probably due to a separate enzyme.
CAS REGISTRY NUMBER
COMMENTARY
37290-70-3
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
cyclobutadipyrimidine in DNA
2 pyrimidine residues in DNA
two photolyases specific for photoreactivation of either cyclobutane pyrimidine dimers or pyrimidine (6-4)pyrimidones
-
?
cyclobutadipyrimidine in DNA
?
compared to the wild-type the rate of cyclobutane pyrimidine dimer accumulation is increased in the uvr2-1 mutant but decreases in the CPD photolyase overexpressors. Under conditions without UV-B, overexpression of photolyase does not have any negative effect on growth
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-
?
cyclobutadipyrimidine (in DNA)
2 pyrimidine residues (in DNA)
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-
-
?
cyclobutadipyrimidine (in DNA)
2 pyrimidine residues (in DNA)
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-
-
?
cyclobutadipyrimidine (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
cyclobutadipyrimidine (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
cyclobutadipyrimidine (in DNA)
2 pyrimidine residues (in DNA)
enzyme AtCRY3 is specific for single-stranded DNA substrates
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-
?
cyclobutadipyrimidine in DNA
2 pyrimidine residues in DNA
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-
-
?
cyclobutadipyrimidine in DNA
2 pyrimidine residues in DNA
-
repairs cyclobutylpyrimidine dimers by a light-driven electron transfer
-
?
cyclobutadipyrimidine in DNA
2 pyrimidine residues in DNA
-
AtCry3 repairs the dimer but only in ssDNA
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-
?
cyclobutadipyrimidine in DNA
pyrimidine residues in DNA
the enzyme repairs specifically cyclobutane pyrimidine dimers in UV-damaged single-stranded DNA, the enzyme catalyzes light-driven DNA repair like conventional photolyases but lacks an efficient flipping mechanism for interaction with cyclobutane pyrimidine dimer lesions within duplex DNA
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-
?
additional information
?
-
light-dependent repair of UV-induced damage products in DNA by direct reversal of base damage rather than via excision repair pathways
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?
additional information
?
-
-
light-dependent repair of UV-induced damage products in DNA by direct reversal of base damage rather than via excision repair pathways
-
?
additional information
?
-
-
pre-inoculation UV-C (254 nm) treatment of normally susceptible Arabidopsis thaliana accessions induces prolonged, dose-dependent resistance to virulent isolates of the phytopathogenic oomycete Hyaloperonospora parasitica with cyclobutane pyrimidine dimers and (6-4) photoproducts playing a key role in this response
-
-
?
additional information
?
-
-
CPD-photolyase is a DNA repair protein, the electron-transport chain of Cry1 involves a Tyr residue as initial electron donor. For Cry3, weak but unspecific DNA binding, for Cry1, DNA binding cannot be detected. Cry2, whose surface largely resembles that of Cry1, does bind to DNA. Cry3 does repair cyclobutane-pyrimidine-dimers when the lesion is located in a preflipped out state such as in bulges of dsDNA. DASH cryptochromes are single-strand-specific CPD-photolyases
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
cyclobutadipyrimidine in DNA
2 pyrimidine residues in DNA
-
-
-
?
cyclobutadipyrimidine (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
cyclobutadipyrimidine (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
cyclobutadipyrimidine (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
cyclobutadipyrimidine (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
additional information
?
-
light-dependent repair of UV-induced damage products in DNA by direct reversal of base damage rather than via excision repair pathways
-
?
additional information
?
-
-
light-dependent repair of UV-induced damage products in DNA by direct reversal of base damage rather than via excision repair pathways
-
?
additional information
?
-
-
pre-inoculation UV-C (254 nm) treatment of normally susceptible Arabidopsis thaliana accessions induces prolonged, dose-dependent resistance to virulent isolates of the phytopathogenic oomycete Hyaloperonospora parasitica with cyclobutane pyrimidine dimers and (6-4) photoproducts playing a key role in this response
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pterin
contains not only reduced FAD but also a reduced pterin, or a cofactor with similar properties, as a chromophore
FADH2
-
the isoalloxazine ring is sandwiched between a salt bridge comprising an arginine and an aspartate residue
FAD
dependent on, adopts a uniquely folded configuration at the active site that plays a critical functional role in DNA repair, overview. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. Photolyase utilizes FADH-, not FAD- radical as the active state
FAD
the enzyme uses a fully reduced flavin, FADH-, cofactor to repair sunlight-induced DNA lesions
5,10-methenyltetrahydrofolate
-
an electron transfer pathway exists in DASH cryptochrome, where the 5,10-methenyltetrahydrofolate cofactor is photoreduced to 5,10-methylenetetrahydrofolate. Reduction requires the intact tryptophan triad. DASH cryptochrome forms 5,10-methylenetetrahydrofolate when treated with UV-A. Light-driven formation of 5,10-methylenetetrahydrofolate by DASH cryptochrome can be coupled with the formation of NADPH in the presence of 5,10-methylenetetrahydrofolate dehydrogenase
FAD
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binds the flavin cofactor in a pocket that is conserved in terms of its electronic properties
FAD
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Cry1, which does not bind to DNA, possesses a strongly reduced surface charge around the FAD binding pocket
FAD
-
photoreduction of FAD under blue light irradiation is faster in photolyase than in Arabidopsis cry3
FAD
dependent on, adopts a uniquely folded configuration at the active site that plays a critical functional role in DNA repair, overview. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. Photolyase utilizes FADH-, not FAD- radical as the active state
FAD
the enzyme uses a fully reduced flavin, FADH-, cofactor to repair sunlight-induced DNA lesions
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
CPD but not 6-4PP enzyme activity exhibits a lagperiod in photoreactivation after 3 days dark exposure
-
additional information
-
CPD but not 6-4PP enzyme activity exhibits a lagperiod in photoreactivation after 3 days dark exposure
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
AtCry1 shows no photorepair activity under any condition
additional information
-
it is shown by in vitro and in vivo by photoreactivation assays and electrophoretic mobility shift assays that AtCry3, as a member of the Cry-DASH enzymes, is specific for cyclobutane pyrimidine dimers in ssDNA
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
15 - 37
decrease in photoreactivation capacity with increasing temperature
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
physiological function
evolution
metabolism
physiological function
evolution
CPD photolyases are highly diversified and can be subdivided into three classes (I to III), as well as single-stranded DNA (ssDNA)-specific PLs. Unrooted phylogenetic tree of the PL-CRY protein family and representative members.The class II PL is distant from the other subfamilies, critical active-site residues that vary between the class I PLs and the other subfamilies, overview
evolution
the enzyme belongs to the enzyme superfamily of photolyase/cryptochromes. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. The unified, bifurcated electron transfer mechanism elucidates the molecular origin of various repair quantum yields of different photolyases from three life kingdoms. Classes of photolyases and structures of CPD and 6-4 photolyases, overview. The diverse subfamily of CPD photolyases consists of classes I, II and III, and ssDNA PLs
physiological function
overexpression of CPD photolyase strongly enhances the repair of cyclobutane pyrimidine dimers and results in a moderate increase of biomass production under elevated UV-B
physiological function
CPD photolyase is a blue-light-activated enzyme that repairs ultraviolet-induced DNA damage which occurs in the form of cyclobutane pyrimidine dimers (CPDs). The enzyme uses a fully reduced flavin (FADH-) cofactor to repair sunlight-induced DNA lesions
physiological function
CPD photolyase, a flavoenzyme containing flavin adenine dinucleotide (FAD) molecule as a catalytic cofactor, repairs UV-induced DNA damage of cyclobutane pyrimidine dimer (CPD) photoproduct using blue light. The FAD cofactor, conserved in the whole protein superfamily of photolyase/cryptochromes, adopts a unique folded configuration at the active site that plays a critical functional role in DNA repair
evolution
CPD photolyases are highly diversified and can be subdivided into three classes (I to III), as well as single-stranded DNA (ssDNA)-specific PLs. Unrooted phylogenetic tree of the PL-CRY protein family and representative members.The class II PL is distant from the other subfamilies, critical active-site residues that vary between the class I PLs and the other subfamilies, overview
evolution
the enzyme belongs to the enzyme superfamily of photolyase/cryptochromes. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. The unified, bifurcated electron transfer mechanism elucidates the molecular origin of various repair quantum yields of different photolyases from three life kingdoms. Classes of photolyases and structures of CPD and 6-4 photolyases, overview. The diverse subfamily of CPD photolyases consists of classes I, II and III, and ssDNA PLs
metabolism
-
photoreduction kinetics of class II photolyases are very similar to those of the other classes with even higher photoreduction rates in class II as compared to class I. W399-W378-W406 electron-transfer pathway is conserved among class II CPD photolyase enzymes
metabolism
-
third electron transfer pathway exists in members of the photolyase family, e.g. DASH cryptochrome, that remained undiscovered so far
physiological function
CPD photolyase is a blue-light-activated enzyme that repairs ultraviolet-induced DNA damage which occurs in the form of cyclobutane pyrimidine dimers (CPDs). The enzyme uses a fully reduced flavin (FADH-) cofactor to repair sunlight-induced DNA lesions
physiological function
CPD photolyase, a flavoenzyme containing flavin adenine dinucleotide (FAD) molecule as a catalytic cofactor, repairs UV-induced DNA damage of cyclobutane pyrimidine dimer (CPD) photoproduct using blue light. The FAD cofactor, conserved in the whole protein superfamily of photolyase/cryptochromes, adopts a unique folded configuration at the active site that plays a critical functional role in DNA repair
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). PHR_ARATH
496
0
57055
Swiss-Prot
other Location (Reliability: 4)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
cry3 cocrystallized with a thymine dimer-comprising oligonucleotide containing a synthetic CPD-like lesion. When cocrystals are exposed to UV-A at 180 K, a decrease in absorption at 380 nm together with the accumulation of semiquinoid and probably also fully reduced FAD is observed. Initial strong fluorescence emission of 5,10-methenyltetrahydrofolate at 440-460 nm seen for cry3 in solution is decreased in the crystal
-
crystallized in 85 mM Na-citrate, pH 4.6, 170 mM NH4- acetate, 21.5% (w/v) PEG 4000, and 15% (v/v) glycerol
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
W356F
-
photobleaching of 5,10-methenyltetrahydrofolate under UV-A irradiation is strongly reduced in the mutant compared with wild-type. The amount of 5,10-methenyltetrahydrofolate after UV-A irradiation is reduced by 64% for wild-type and by 20% for the mutant. Increase in the amount of oxidized FAD under UV-A irradiation due to electron donation to 5,10-methenyltetrahydrofolate by residual FADH- but a lack of photoreduction of the flavin caused by the interrupted tryptophan triad
W432F
-
photobleaching of 5,10-methenyltetrahydrofolate under UV-A irradiation is strongly reduced in the mutant compared with wild-type
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-70°C, 0.05 M sodium phosphate, pH 7.0, 0.1 M NaCl, 20% (v/v) glycerol
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
coding region of the CPD photolyase gene under the control of the CaMV 35S tandem promoter placed together with a hygromycin resistance gene on the T-DNA of a binary vector and overexpressed in transgenic Arabidopsis lines
AtCry1 belonging to the cryptochrome/photolyase class of enzymes called Cry-DASH proteins is shown to possess no photorepair activity under any condition
-
AtCry3 belonging to the cryptochrome/photolyase class of enzymes called Cry-DASH proteins is shown to be photolyases with high degree of specificity for cyclobutane pyrimidine dimers in ssDNA
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
biotechnology
-
a new class of photolyases with specificity for cyclobutane pyrimidine dimers in ssDNA is defined. Members of these branch are found in bacteria, plants, and animals, and are designated Cry-DASH, because of the lack of significant photorepair activity on dsDNA
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kleiner, O.; Butenandt, J.; Carell, T.; Batschauer, A.
Class II DNA photolyase from Arabidopsis thaliana contains FAD as a cofactor
Eur. J. Biochem.
264
161-167
1999
Arabidopsis thaliana
Waterworth, W.M.; Jiang, Q.; West, C.E.; Nikaido, M.; Bray, C.M.
Characterization of Arabidopsis photolyase enzymes and analysis of their role in protection from ultraviolet-B radiation
J. Exp. Bot.
53
1005-1015
2002
Arabidopsis thaliana (Q9SB00), Arabidopsis thaliana
Essen, L.O.; Klar, T.
Light-driven DNA repair by photolyases
Cell. Mol. Life Sci.
63
1266-1277
2006
Arabidopsis thaliana, Aspergillus nidulans, Potorous tridactylus, Escherichia coli (P00914)
Selby, C.P.; Sancar, A.
A cryptochrome/photolyase class of enzymes with single-stranded DNA-specific photolyase activity
Proc. Natl. Acad. Sci. USA
103
17696-17700
2006
Arabidopsis thaliana, Bacillus subtilis, Vibrio cholerae serotype O1, Xenopus laevis
Kunz, B.A.; Dando, P.K.; Grice, D.M.; Mohr, P.G.; Schenk, P.M.; Cahill, D.M.
UV-induced DNA damage promotes resistance to the biotrophic pathogen Hyaloperonospora parasitica in Arabidopsis
Plant Physiol.
148
1021-1031
2008
Arabidopsis thaliana
Pokorny, R.; Klar, T.; Hennecke, U.; Carell, T.; Batschauer, A.; Essen, L.O.
Recognition and repair of UV lesions in loop structures of duplex DNA by DASH-type cryptochrome
Proc. Natl. Acad. Sci. USA
105
21023-21027
2008
Arabidopsis thaliana (Q84RJ5)
Mueller, M.; Carell, T.
Structural biology of DNA photolyases and cryptochromes
Curr. Opin. Struct. Biol.
19
277-285
2009
Synechococcus elongatus PCC 7942 = FACHB-805, Arabidopsis thaliana, Homo sapiens, Sulfurisphaera tokodaii, Escherichia coli (P00914), Thermus thermophilus (P61497)
Okafuji, A.; Biskup, T.; Hitomi, K.; Getzoff, E.D.; Kaiser, G.; Batschauer, A.; Bacher, A.; Hidema, J.; Teranishi, M.; Yamamoto, K.; Schleicher, E.; Weber, S.
Light-induced activation of class II cyclobutane pyrimidine dimer photolyases
DNA Repair
9
495-505
2010
Arabidopsis thaliana, Escherichia coli, Oryza sativa
Moldt, J.; Pokorny, R.; Orth, C.; Linne, U.; Geisselbrecht, Y.; Marahiel, M.A.; Essen, L.O.; Batschauer, A.
Photoreduction of the folate cofactor in members of the photolyase family
J. Biol. Chem.
284
21670-21683
2009
Arabidopsis thaliana, Escherichia coli
Kaiser, G.; Kleiner, O.; Beisswenger, C.; Batschauer, A.
Increased DNA repair in Arabidopsis plants overexpressing CPD photolyase
Planta
230
505-515
2009
Arabidopsis thaliana (Q9SB00), Arabidopsis thaliana
Zhang, M.; Wang, L.; Zhong, D.
Photolyase dynamics and electron-transfer mechanisms of DNA repair
Arch. Biochem. Biophys.
632
158-174
2017
Caulobacter vibrioides (A0A0H3C7H5), Escherichia coli (P00914), Synechococcus elongatus PCC 7942 = FACHB-805 (P05327), Arabidopsis thaliana (Q84KJ5), Arabidopsis thaliana (Q9SB00), Methanosarcina mazei (Q8PYK9), Synechococcus elongatus PCC 7942 = FACHB-805 ATCC 27144 / PCC 6301 / SAUG 1402/1 (P05327), Caulobacter vibrioides NA1000/CB15N (A0A0H3C7H5), Methanosarcina mazei ATCC BAA-159 (Q8PYK9)
Zhang, M.; Wang, L.; Shu, S.; Sancar, A.; Zhong, D.
Bifurcating electron-transfer pathways in DNA photolyases determine the repair quantum yield
Science
354
209-213
2016
Caulobacter vibrioides (A0A0H3C7H5), Escherichia coli (P00914), Synechococcus elongatus PCC 7942 = FACHB-805 (P05327), Drosophila melanogaster (Q24443), Arabidopsis thaliana (Q84KJ5), Arabidopsis thaliana (Q9SB00), Caulobacter vibrioides NA1000 / CB15N (A0A0H3C7H5), Synechococcus elongatus PCC 7942 = FACHB-805 ATCC 27144 / PCC 6301 / SAUG 1402/1 (P05327)
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