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Information on EC 4.1.99.13 - (6-4)DNA photolyase
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4.1.99.13 (6-4)DNA photolyaseIUBMB Comments
A flavoprotein (FAD). The overall repair reaction consists of two distinct steps, one of which is light-independent and the other one light-dependent. In the initial light-independent step, a 6-iminium ion is thought to be generated via proton transfer induced by two histidines highly conserved among the (6-4) photolyases. This intermediate spontaneously rearranges to form an oxetane intermediate by intramolecular nucleophilic attack. In the subsequent light-driven reaction, one electron is believed to be transferred from the fully reduced FAD cofactor (FADH-) to the oxetane intermediate thus forming a neutral FADH radical and an anionic oxetane radical, which spontaneously fractures. The excess electron is then back-transferred to the flavin radical restoring the fully reduced flavin cofactor and a pair of pyrimidine bases .
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Word Map
- 4.1.99.13
- photoproducts
-
cyclobutane
-
uv-induced
-
cryptochromes
-
photoreactivation
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light-dependent
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pyrimidone
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blue-light
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photorepair
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oxetane
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pyrimidine-pyrimidone
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photoreduction
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photolesion
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dash
- ostreococcus
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four-membered
- fadox
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photoreception
- cry-dashs
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dewar
- cryptochrome-dash
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
(6-4) photolyase, (6-4) phr, (6-4)photolyase, 6-4 photolyase, nf-10, otcpf1, 6-4ciphr, 6-4pp-photolyase, prokaryotic (6-4) photolyase, h64prh, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
(6-4) photolyase
(6-4) PHR
(6-4) PL
(6-4) PP-specific PL
(6-4)-Phr
6-4 DNA photolyase
6-4 photolyase
bacterial (6-4) photolyase
CmPHR1
Cry1
CryB
deoxyribodipyrimidine photolyase-related protein
PhrB
prokaryotic (6-4) photolyase
RSP_3077
TRIREDRAFT_77473
(6-4) photolyase
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(6-4) photolyase
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6-4 DNA photolyase
Xiphophorus maculatus Jp 163 B
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6-4 photolyase
Xiphophorus maculatus Jp 163 B
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deoxyribodipyrimidine photolyase-related protein
Cereibacter sphaeroides ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158
UniProt
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
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(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
A mechanism is proposed in which the histidines residues His 354 and His 358 catalyze the formation of the four-membered ring intermediate in the repair process of this enzyme. When deuterium oxide is used as a solvent, the repair activity is decreased. The proton transfer shown by this isotope effect supports the proposed mechanism
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(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
The overall repair reaction consists of two distinct steps, one of which is light-independent and the other one light-dependent. In the initial light-independent step, a 6-iminium ion is thought to be generated via proton transfer induced by two histidines highly conserved among the (6-4) photolyases.This intermediate spontaneously rearranges to form an oxetane intermediate by intramolecular nucleophilic attack. In the subsequent light-driven reaction, one electron is believed to be transferred from the fully reduced FAD cofactor (FADH-) to the oxetane intermediate thus forming a neutral FADH radical and an anionic oxetane radical, which spontaneously fractures. The excess electron is then back-transferred to the flavin radical restoring the fully reduced flavin cofactor and a pair of pyrimidine bases
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(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
The overall repair reaction consists of two distinct steps, one of which is light-independent and the other one light-dependent. In the initial light-independent step, a 6-iminium ion is thought to be generated via proton transfer induced by two histidines highly conserved among the (6-4) photolyases.This intermediate spontaneously rearranges to form an oxetane intermediate by intramolecular nucleophilic attack. In the subsequent light-driven reaction, one electron is believed to be transferred from the fully reduced FAD cofactor (FADH-) to the oxetane intermediate thus forming a neutral FADH radical and an anionic oxetane radical, which spontaneously fractures. The excess electron is then back-transferred to the flavin radical restoring the fully reduced flavin cofactor and a pair of pyrimidine bases
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(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
The overall repair reaction consists of two distinct steps, one of which is light-independent and the other one light-dependent. In the initial light-independent step, a 6-iminium ion is thought to be generated via proton transfer induced by two histidines highly conserved among the (6-4) photolyases.This intermediate spontaneously rearranges to form an oxetane intermediate by intramolecular nucleophilic attack. In the subsequent light-driven reaction, one electron is believed to be transferred from the fully reduced FAD cofactor (FADH-) to the oxetane intermediate thus forming a neutral FADH radical and an anionic oxetane radical, which spontaneously fractures. The excess electron is then back-transferred to the flavin radical restoring the fully reduced flavin cofactor and a pair of pyrimidine bases
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(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
The overall repair reaction consists of two distinct steps, one of which is light-independent and the other one light-dependent. In the initial light-independent step, a 6-iminium ion is thought to be generated via proton transfer induced by two histidines highly conserved among the (6-4) photolyases.This intermediate spontaneously rearranges to form an oxetane intermediate by intramolecular nucleophilic attack. In the subsequent light-driven reaction, one electron is believed to be transferred from the fully reduced FAD cofactor (FADH-) to the oxetane intermediate thus forming a neutral FADH radical and an anionic oxetane radical, which spontaneously fractures. The excess electron is then back-transferred to the flavin radical restoring the fully reduced flavin cofactor and a pair of pyrimidine bases
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(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
The overall repair reaction consists of two distinct steps, one of which is light-independent and the other one light-dependent. In the initial light-independent step, a 6-iminium ion is thought to be generated via proton transfer induced by two histidines highly conserved among the (6-4) photolyases.This intermediate spontaneously rearranges to form an oxetane intermediate by intramolecular nucleophilic attack. In the subsequent light-driven reaction, one electron is believed to be transferred from the fully reduced FAD cofactor (FADH-) to the oxetane intermediate thus forming a neutral FADH radical and an anionic oxetane radical, which spontaneously fractures. The excess electron is then back-transferred to the flavin radical restoring the fully reduced flavin cofactor and a pair of pyrimidine bases
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(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
The overall repair reaction consists of two distinct steps, one of which is light-independent and the other one light-dependent. In the initial light-independent step, a 6-iminium ion is thought to be generated via proton transfer induced by two histidines highly conserved among the (6-4) photolyases.This intermediate spontaneously rearranges to form an oxetane intermediate by intramolecular nucleophilic attack. In the subsequent light-driven reaction, one electron is believed to be transferred from the fully reduced FAD cofactor (FADH-) to the oxetane intermediate thus forming a neutral FADH radical and an anionic oxetane radical, which spontaneously fractures. The excess electron is then back-transferred to the flavin radical restoring the fully reduced flavin cofactor and a pair of pyrimidine bases
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(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
Fourier transform infrared spectroscopy is applied to (6-4)DNA photolyase. Differences in FTIR spectra that correspond to (6-4)DNA photolyase photoactivation, substrate binding, and light-dependent DNA repair processes are reported. The presence of DNA carrying a single (6-4) PP uniquely influences vibrations of the protein backbone and a protonated carboxylic acid, whereas photoactivation produces IR spectral changes for the FAD cofactor and the surrounding protein. Difference FTIR spectra for the light-dependent DNA damage repair reaction directly show significant DNA structural changes in the (6-4) lesion and the neighboring phosphate group. Time-dependent illumination of samples with different enzyme:substrate stoichiometries successfully distinguish signals characteristic of structural changes in the protein and the DNA resulting from binding and catalysis
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(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
repair of Dewar valence isomers by (6-4) photolyases involves the rearrangement of the Dewar lesions into the corresponding (6-4) lesions. This reaction requires electron injection. (6-4) photolyases have two catalytic functions: Splitting (6-4) lesions and catalyzing the formal 4pi sigmatropic rearrangement of Dewar isomers to (6-4) lesions
(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
time-resolved measurements are performed of radical formation, diffusion, and protein conformational changes during light-dependent repair by full-length (6-4) photolyase on DNA carrying a single UV-induced damage. The (6-4) photolyase shows significant volume changes after blue-light activation, indicating protein conformational changes distant from the flavin cofactor. A drastic diffusion change is observed only in the presence of both (6-4) photolyase and damaged DNA, and not for (6-4) photolyase alone or with undamaged DNA
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(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
ultrafast spectroscopy is used to show that the key step in the repair photocycle is a cyclic proton transfer between the enzyme and the substrate. By femtosecond synchronization of the enzymatic dynamics with the repair function, direct electron transfer from the excited flavin cofactor to the 6-4 photoproduct is observed in 225 ps but fast back electron transfer in 50 ps without repair. The catalytic proton transfer between a histidine residue in the active site and the 6-4 photoproduct, induced by the initial photoinduced electron transfer from the excited flavin cofactor to 6-4 photoproduct, occurs in 425 ps and leads to 6-4 photoproduct repair in tens of nanoseconds
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(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
using quantum mechanics/molecular mechanics studies, a repair mechanism is proposed, which involves two photoexcitations. The flavin chromophore, initially being in its reduced anionic form, is photoexcited and donates an electron to the (6-4) form of the photolesion. The photolesion is then protonated by the neighboring histidine residue and forms a radical intermediate. A second photoexcitation of the flavin promotes another electron transfer to the oxetane. Proton donation from the same histidine residue allows for the splitting of the four-membered ring, hence opening an efficient pathway to the final repaired form
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(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
repair photocycle of (6-4) thymine photoproduct by (6-4) photolyase, which involves light absorption by the 8-HDF cofactor and transfer of the excitation energy to the FADH-. Intermolecular Coulombic decay resulting in an electron transfer from FADH? to the dimer initiating the splitting process, mechanism, detailed overview. The mechanism requires the C5-OH transfer from C5 of the 5' thymine to the C4' of the 3' thymine followed by H transfer to the N3' of the 3' thymine. Of two conserved histidine residues, only His365 is protonated
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(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
in the formation of the (6-4) PPs, a Paterno-Buechi reaction first yields an oxetane-bridged (or azetidine-bridged for cytosine at 3') intermediate. This structure is thermodynamically unstable and rearranges to form a (6-4) PP. During this reaction, the O4' (or N4'H) in the 3' component is transferred to the 5'-component and has thus to be returned to 3' during the repair reaction. Reaction mechanism of repair of (6-4) lesions by (6-4) photolyase, detailed overview. The repair-active redox state of the FAD cofactor is fully reduced FADH- and (6-4) PP-containing substrates are bound in a specific manner. No thermal oxetane formation
(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
photoreduction of PhrB differs from the typical pattern because the amino acid of the electron cascade next to FAD is a tyrosine (Tyr391), whereas photolyases and cryptochromes of other groups have a tryptophan as direct electron donor of FAD. Residues Trp342 and Trp390 are essential for charge transfer, Trp342 is located at the periphery of PhrB, while Trp390 connects Trp342 and Tyr391. Charge transfer occurs via the triad 391-390-342. Charge transfer simulations reveal an unusual stabilization of the positive charge on site 391 compared to other photolyases or cryptochromes. Water molecules near Tyr391 offer a polar environment which stabilizes the positive charge on this site, thereby lowering the energetic barrier intrinsic to tyrosine. This opens a second charge transfer channel in addition to tunnelling through the tyrosine barrier, based on hopping and therefore transient oxidation of Tyr391, which enables a fast charge transfer similar to proteins utilizing a tryptophan-triad
(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
reaction mechanism of repair of (6-4) lesions by (6-4) photolyase, detailed overview. The repair-active redox state of the FAD cofactor is fully reduced FADH- and (6-4) PP-containing substrates are bound in a specific manner
(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
reaction mechanism of repair of (6-4) lesions by (6-4) photolyase, detailed overview. The repair-active redox state of the FAD cofactor is fully reduced FADH- and (6-4) PP-containing substrates are bound in a specific manner. Occurrence of a two-photon mechanism for the repair of a T(6-4)T lesion by the (6-4) PL of Xenopus laevis
(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
two histidines in the active center, H354 and H358, must work in a concerted manner in the active center of the wild-type enzyme, which significantly raises the repair efficiency, molecular mechanism of the repair reaction by enzyme (6-4) PHR, overview
(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
photoreduction of PhrB differs from the typical pattern because the amino acid of the electron cascade next to FAD is a tyrosine (Tyr391), whereas photolyases and cryptochromes of other groups have a tryptophan as direct electron donor of FAD. Residues Trp342 and Trp390 are essential for charge transfer, Trp342 is located at the periphery of PhrB, while Trp390 connects Trp342 and Tyr391. Charge transfer occurs via the triad 391-390-342. Charge transfer simulations reveal an unusual stabilization of the positive charge on site 391 compared to other photolyases or cryptochromes. Water molecules near Tyr391 offer a polar environment which stabilizes the positive charge on this site, thereby lowering the energetic barrier intrinsic to tyrosine. This opens a second charge transfer channel in addition to tunnelling through the tyrosine barrier, based on hopping and therefore transient oxidation of Tyr391, which enables a fast charge transfer similar to proteins utilizing a tryptophan-triad
Agrobacterium fabrum C58 / ATCC 33970
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SYSTEMATIC NAME
IUBMB Comments
(6-4) photoproduct pyrimidine-lyase
A flavoprotein (FAD). The overall repair reaction consists of two distinct steps, one of which is light-independent and the other one light-dependent. In the initial light-independent step, a 6-iminium ion is thought to be generated via proton transfer induced by two histidines highly conserved among the (6-4) photolyases. This intermediate spontaneously rearranges to form an oxetane intermediate by intramolecular nucleophilic attack. In the subsequent light-driven reaction, one electron is believed to be transferred from the fully reduced FAD cofactor (FADH-) to the oxetane intermediate thus forming a neutral FADH radical and an anionic oxetane radical, which spontaneously fractures. The excess electron is then back-transferred to the flavin radical restoring the fully reduced flavin cofactor and a pair of pyrimidine bases [2].
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CAS REGISTRY NUMBER
COMMENTARY
37290-70-3
not distinguished from DNA photolyase, spore photoproduct lyase
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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
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?
cyclobutadipyrimidine in herring sperm DNA
2 pyrimidine residues in herring sperm DNA
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?
deoxyoligonucleotide containing (6-4) photoproduct + H2O
deoxyoligonucleotide containing 2 pyrimidine residues
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?
Dewar photoproduct
?
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although the affinity of the enzyme for the Dewar photoproduct-containing duplex is similar to that for the (6-4) photoproduct containing substrate a repair rate could not be shown. These results indicate that the (6-4) photolyase binds the DNA containing the Dewar photoproduct and induces a structural change in DNA to some extent, suggesting a difference in the binding mode compared to the (6-4) photoproduct
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?
T(6-4)C photoproduct (in DNA)
2 thymidine + cytosine (in DNA)
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?
T(6-4)C photoproduct (in DNA)
T-C (in DNA)
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A T(6-4)C photoproduct is synthesized. Differences from T(6-4)T is formation of cytosine hydrates by UV irradiation, and acylation of the amino function with the capping reagent. The capping step is omitted to improve the yield of the desired oligonucleotides. (6-4) photolyase restores the pyrimidines in T(6-4)C to their original structures
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?
T(6-4)T photoproduct (in DNA)
2 thymidine resdiues (in DNA)
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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(6-4)TT
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
Agrobacterium fabrum C58 / ATCC 33970
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
PhrB is active with ssDNA and dsDNA TT (6-4) photoproducts
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
substrates are single stranded or double stranded DNA probe comprising the AGGT(6-4)TGGC or GCGGT(6-4)TGGCG paired with TCGCCAACCGCT. PhrB is active with ssDNA and dsDNA TT (6-4) photoproducts, substrate binding structure, detailed overview. Arg183 is part of the loop region connecting alpha7 and alpha8
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
Agrobacterium tumefaciens C58 / ATCC 33970
PhrB is active with ssDNA and dsDNA TT (6-4) photoproducts
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
Agrobacterium tumefaciens C58 / ATCC 33970
substrates are single stranded or double stranded DNA probe comprising the AGGT(6-4)TGGC or GCGGT(6-4)TGGCG paired with TCGCCAACCGCT. PhrB is active with ssDNA and dsDNA TT (6-4) photoproducts, substrate binding structure, detailed overview. Arg183 is part of the loop region connecting alpha7 and alpha8
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
Cereibacter sphaeroides ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
(6-4) photolyases repair (6-4) pyrimidine-pyrimidone photoproducts. CmPHR1 exhibits a repair activity of both (6-4)-ssDNA and (6-4)-dsDNA. Cryptochromes CmPHR2 and CmPHR5 show CPD repair activity only on ssDNA, and have no repair activity when CPD-damaged dsDNA is used as a substrate
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
substrate is radio-labeled 48-bp DNA substrates that contains CPD or (6-4) damages within MseI restriction sites (TTAA), pyrimidine(6-4)pyrimidone photoptoducts
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
(6-4) photolyases repair (6-4) pyrimidine-pyrimidone photoproducts. CmPHR1 exhibits a repair activity of both (6-4)-ssDNA and (6-4)-dsDNA. Cryptochromes CmPHR2 and CmPHR5 show CPD repair activity only on ssDNA, and have no repair activity when CPD-damaged dsDNA is used as a substrate
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
substrate is radio-labeled 48-bp DNA substrates that contains CPD or (6-4) damages within MseI restriction sites (TTAA), pyrimidine(6-4)pyrimidone photoptoducts
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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substrate is a 10-mer oligonucleotide d(HHHHT(6-4)TTHHH), i.e. DHT (6-4)PP 10-mer, where H represents non-absorbing dihydrothymine
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
i.e. (6-4) PP
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
Xiphophorus maculatus Jp 163 B
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?
T(6-4)T photoproduct (in DNA)
2 thymidine residues (in DNA)
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?
additional information
?
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analysis of the repair of a T(6-4)T lesion by the (6-4) PL of Arabidopsis thaliana (At64) by ultrafast fluorescence and transient absorption spectroscopy between 315 and 800 nm. About 90% of the FADH- radicals formed by this primary electron transfer are re-reduced very quickly
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?
additional information
?
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the repair function requires to transfer a functional group (OH in the case T(6-4)T) from the 5' to the 3' base, in addition to intradimer bond cleavage
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?
additional information
?
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the repair function requires to transfer a functional group (OH in the case T(6-4)T) from the 5' to the 3' base, in addition to intradimer bond cleavage
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?
additional information
?
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the repair function requires to transfer a functional group (OH in the case T(6-4)T) from the 5' to the 3' base, in addition to intradimer bond cleavage
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?
additional information
?
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binding and catalytic properties of the enzyme are investigated using natural substrates, T[6-4]T and T[6-4]C, and the Dewar isomer of (6-4) photoproduct and substrate analogs s5T[6-4]T/thietane, mes5T[6-4]T, and the N-methyl-3T thietane analog of the oxetane intermediate. The enzyme binds to the natural substrates and to mes5T[6-4]T with high affinity and produces a DNase I footprint of about 20 base pairs around the photolesion. Of the four substrates that bind with high affinity to the enzyme, T[6-4]T and T[6-4]C are repaired with relatively high quantum yields compared with the Dewar isomer and the mes5T[6-4]T which are repaired with 300-400-fold lower quantum yield
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?
additional information
?
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enzyme catalyzes the light-dependent repair of (6-4) photoproducts in Drosophilia melanogaster
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?
additional information
?
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can not repair T(Dew)T lesion, direct electron injection into the lesion may be the first step of the repair reaction performed by (6-4) DNA photolyase
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?
additional information
?
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by electrophoretic mobility shift assay it is demonstrated that NF-10 binds to UV-irradiated double-stranded DNA but not to unirradiated DNA
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?
additional information
?
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cyclobutane pyrimidine dimer-photolyase (EC 4.1.99.3) or 6-4PP-photolyase are able to prevent UV-induced apoptosis in cells deficient for nucleotide excision repair to a similar extent, while in nucleotide excision repair-proficient cells UV-induced apoptosis is prevented only by cyclobutane pyrimidine dimer-photolyase, with no effects observed when pyrimidine-(6-4)-pyrimidone photoproducts are removed by the specific photolyase. Both cyclobutane pyrimidine dimers and pyrimidine-(6-4)-pyrimidone photoproducts contribute to UV-induced apoptosis in nucleotide excision repair-deficient cells, while in nucleotide excision repair-proficient cells, cyclobutane pyrimidine dimers are the only lesions responsible for UV-killing, probably due to the rapid repair of pyrimidine-(6-4)-pyrimidone photoproducts by nucleotide excision repair
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?
additional information
?
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Cry1, heterologously expressed and purified from Escherichia coli, is capable of binding to undamaged and 6-4PP damaged DNA. Cry1 repairs 6-4PP, but not CPD and Dewar DNA lesions
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?
additional information
?
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Cry1, heterologously expressed and purified from Escherichia coli, is capable of binding to undamaged and 6-4PP damaged DNA. Cry1 repairs 6-4PP, but not CPD and Dewar DNA lesions
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?
additional information
?
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(6-4) photolyase is examined by optical spectroscopy, electron paramagnetic resonance, and pulsed electron nuclear double resonance spectroscopy. It is suggested that His354 and His358 catalyze the formation of the oxetane intermediate that precedes light-initiated DNA repair. At pH 9.5 where the enzyme repair activity is highest His358 is deprotonated, whereas His354 is protonated, acting as the proton donor that initiates oxetane formation from the (6-4) photoproduct
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?
additional information
?
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2-thio analog of the the (6-4) photoproduct, in which the carbonyl group at the C2 of the 3'pyrimidone is replaced with a thiocarbonyl group, is not repaired by the (6-4) photolyase. Cationic imine analogue of the (6-4) photoproduct, in which the carbonyl group at the C2 of the 3'pyrimidone is replaced with an imine (T(6-4)TNH2), is not repaired by the (6-4) photolyase, even in the presence of a 10 molar excess of the enzyme. 3'carbonyl group of the (6-4) photoproduct is involved in the recognition and reaction of the (6-4) photolyse
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?
additional information
?
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imine analogue of the (6-4) photoproduct (T(6-4)TNH2), in which the carbonyl group is replaced with an iminium cation, is not repaired by the (6-4) photolyase, even in the presence of a 10fold molar excess of the enzyme, although the enzyme binds to the oligonucleotide with considerable affinity. Carbonyl group of the 3' pyrimidone ring plays an important role in the (6-4) photolyase reaction
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?
additional information
?
-
inability of (6-4) PL to repair the Dewar photoproduct T(Dew) T lesion (formed via an electrocyclic reaction of the 3' pyrimidone ring in (6-4) PPs upon photoexcitation in the 325-nm band of the (6-4) PP), which cannot be attributed to poor substrate binding, as a high affinity for T(Dew)T-containing substrates has been demonstrated. Rather, reversion of the T(Dew)T to the T(6-4)T lesion appears to be inhibited, either by an unfavorable electron transfer from photoexcited FADH- to T(Dew)T. QM/MM calculations of the absorption spectra of different potential reaction intermediates
-
-
?
additional information
?
-
polarizable molecular dynamics simulations and constrained density functional theory calculations reveal the energetics of charge migration along the tryptophan tetrad. Migration toward the fourth tryptophan is thermodynamically favorable. Electron transfer mechanisms occur either through an incoherent hopping mechanism or through a multiple sites tunneling process. The Jortner-Bixon formulation of electron transfer (ET) theory is employed to characterize the hopping mechanism, interplay between electron transfer and relaxation of protein and solvent, overview. Electron transfer in (6-4) photolyase proceeds out of equilibrium. Multiple site tunneling is modeled with the recently proposed flickering resonance mechanism
-
-
?
additional information
?
-
-
polarizable molecular dynamics simulations and constrained density functional theory calculations reveal the energetics of charge migration along the tryptophan tetrad. Migration toward the fourth tryptophan is thermodynamically favorable. Electron transfer mechanisms occur either through an incoherent hopping mechanism or through a multiple sites tunneling process. The Jortner-Bixon formulation of electron transfer (ET) theory is employed to characterize the hopping mechanism, interplay between electron transfer and relaxation of protein and solvent, overview. Electron transfer in (6-4) photolyase proceeds out of equilibrium. Multiple site tunneling is modeled with the recently proposed flickering resonance mechanism
-
-
?
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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
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
Agrobacterium fabrum C58 / ATCC 33970
-
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
PhrB is active with ssDNA and dsDNA TT (6-4) photoproducts
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
Agrobacterium tumefaciens C58 / ATCC 33970
PhrB is active with ssDNA and dsDNA TT (6-4) photoproducts
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
Cereibacter sphaeroides ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158
-
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
(6-4) photolyases repair (6-4) pyrimidine-pyrimidone photoproducts. CmPHR1 exhibits a repair activity of both (6-4)-ssDNA and (6-4)-dsDNA. Cryptochromes CmPHR2 and CmPHR5 show CPD repair activity only on ssDNA, and have no repair activity when CPD-damaged dsDNA is used as a substrate
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
(6-4) photolyases repair (6-4) pyrimidine-pyrimidone photoproducts. CmPHR1 exhibits a repair activity of both (6-4)-ssDNA and (6-4)-dsDNA. Cryptochromes CmPHR2 and CmPHR5 show CPD repair activity only on ssDNA, and have no repair activity when CPD-damaged dsDNA is used as a substrate
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
-
-
-
?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
Xiphophorus maculatus Jp 163 B
-
-
-
-
?
additional information
?
-
the repair function requires to transfer a functional group (OH in the case T(6-4)T) from the 5' to the 3' base, in addition to intradimer bond cleavage
-
-
?
additional information
?
-
-
the repair function requires to transfer a functional group (OH in the case T(6-4)T) from the 5' to the 3' base, in addition to intradimer bond cleavage
-
-
?
additional information
?
-
the repair function requires to transfer a functional group (OH in the case T(6-4)T) from the 5' to the 3' base, in addition to intradimer bond cleavage
-
-
?
additional information
?
-
-
cyclobutane pyrimidine dimer-photolyase (EC 4.1.99.3) or 6-4PP-photolyase are able to prevent UV-induced apoptosis in cells deficient for nucleotide excision repair to a similar extent, while in nucleotide excision repair-proficient cells UV-induced apoptosis is prevented only by cyclobutane pyrimidine dimer-photolyase, with no effects observed when pyrimidine-(6-4)-pyrimidone photoproducts are removed by the specific photolyase. Both cyclobutane pyrimidine dimers and pyrimidine-(6-4)-pyrimidone photoproducts contribute to UV-induced apoptosis in nucleotide excision repair-deficient cells, while in nucleotide excision repair-proficient cells, cyclobutane pyrimidine dimers are the only lesions responsible for UV-killing, probably due to the rapid repair of pyrimidine-(6-4)-pyrimidone photoproducts by nucleotide excision repair
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
[4Fe-4S] cluster
the iron-sulfur cluster is an indispensable cofactor for the structural integrity of the enzyme protein
6,7-dimethyl-8-ribityllumazine
the PhrB structure contains 6,7-dimethyl-8-ribityllumazine as an antenna chromophore, binding site-structure, overview
6,7-dimethyl-8-ribityllumazine
DMRL, serves as an antenna chromophore for photoreduction and DNA repair in the wild-type enzyme
FAD
-
-
FAD
-
Resonance Raman spectra of (6-4) photolyase having neutral semiquinoid and oxidized forms of FAD. Density functional theory (DFT) calculations are carried out on the neutral semiquinone. The marker band of a neutral semiquinone at 1606 cm-1 in H2O, splits into two comparable bands at 1594 and 1608 cm-1 in D2O, and similarly, that at 1522 cm-1 in H2O does into three bands at 1456, 1508, and 1536 cm-1 in D2O. This D2O effect is recognized only after being oxidized once and photoreduced to form a semiquinone again, but not by simple H/D exchange of solvent. Some Raman bands of the oxidized form are observed at significantly low frequencies (1621, 1576 cm-1) and with band splittings (1508/1493, 1346/1320 cm-1). These Raman spectral characteristics indicate strong H-bonding interactions (at N5-H, N1), a fairly hydrophobic environment, and an electron-lacking feature in benzene ring of the FAD cofactor, which seems to specifically control the reactivity of (6-4) photolyase
FAD
-
FAD cofactor photoactivation in (64) photolyase occurs via two sequential single-electron reduction steps with a tyrosine residue acting as final electron donor
FAD
non-covalently bound to the enzyme. Flavin to apoprotein molecular ratio of 64%. FAD is present in three different redox states: the fully oxidized form (FADox, 82%), the neutral semiquinone (14%) and the fully reduced anion (4%)
FAD
in the structure of (6-4) photolyase, there is a phosphate anion bound to Glu-243 and Trp-238, close to FAD
FAD
an essential cofactor, the enzyme contains FAD at a concentration of less than 0.2%
FAD
chromophore, assumes a prototypical U-shaped conformation
FAD
-
for activation of Xenopus (6-4) PHR, FADox is first converted to a neutral radical form by light-induced one-electron and one-proton transfers and then into a fully reduced form by light-induced one electron transfer, mechanism, overview
FAD
-
transition from the oxidized to the semi-reduced form of FAD is characterized by absorbance decreases at around 450 nm and 370 nm, and an increase at 580 nm
Fe-S cluster
a cubane-type Fe-S cluster, residue Tyr424 of PhrB is part of the DNA-binding site and provides an electron link to the Fe-S cluster
additional information
-
the enzyme protein expressed in Escherichia coli does not bind a second chromophore, such as 5,10-methenyltetrahydrofolate, MTHF
-
additional information
the protein harbors three cofactors: the enzymatically active FAD chromophore, a second chromophore, 6,7-dimethyl-8-ribityllumazine (DMRL) and a cubane-type Fe-S cluster
-
additional information
-
the protein harbors three cofactors: the enzymatically active FAD chromophore, a second chromophore, 6,7-dimethyl-8-ribityllumazine (DMRL) and a cubane-type Fe-S cluster
-
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe2+
Na+
additional information
Fe2+
-
Fe-S cluster, the Fe-S cluster is required for structural stability, integrity and correct folding of PhrB
Fe2+
the prokaryotic enzyme contains a a [4Fe-4S] cluster bound to the catalytic domain
additional information
-
NH4Cl or NaH2PO4 increase activity of the enzyme. CH3COONa or Na2CO3 strongly decrease the enzymes activity. Maximum activity occurs in the presence of NaH2PO4, which is increased eight times than that in the presence of Na2CO3. When the ions that possess stronger ability to donate a proton are added to enzyme reaction buffer, the rate of photoreactivation increases
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Dithionite
-
reduction of the FAD cofactor with dithionite increases the quantum yield of repair
additional information
repair is triggered by non-saturating 100-ps laser flashes
-
additional information
repair is triggered by non-saturating 100-ps laser flashes
-
additional information
-
for activation of Xenopus (6-4) PHR, FADox is first converted to a neutral radical form by light-induced one-electron and one-proton transfers and then into a fully reduced form by light-induced one electron transfer, four different redox states for the FAD chromophore of PHR, mechanism, overview
-
additional information
repair is triggered by non-saturating 100-ps laser flashes
-
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Carcinoma
Tranilast (N-3,4-dimethoxycinamoyl anthranilic acid): a novel inhibitor of invasion-stimulating interaction between gastric cancer cells and orthotopic fibroblasts.
Stomach Neoplasms
Tranilast and cisplatin as an experimental combination therapy for scirrhous gastric cancer.
Xeroderma Pigmentosum
Purification of a novel UV-damaged-DNA binding protein highly specific for (6-4) photoproduct.
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
enzyme does not show any detectable photolyase activity
additional information
-
(6-4) photolyase binds to T[6-4]T in double stranded DNA with high affinity (KD= 10*exp-9) and to T[6-4]T in single-stranded DNA with slightly lower-affinity (KD= 2*10 exp-8). Majority of the T[64]T-(6-4) photolyase complex dissociates very slowly (koff= 2.9* 10exp-5/sec). Its absolute action spectrum without a second chromophore in the 350-600 nm region closely matches the absorption spectrum of the enzyme
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
10
-
(6-4) photolyase in the alkaline treated algae cells exhibit much more efficient repair than that in the normally cultured algae cells
7.4
7.5
8.5
8.5
-
maximum activity occurs at pH 8.5 and is 2.4fold higher than that at pH 7.0
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6 - 9
-
wild-type, K281G mutant and K281R mutant show no differences in this pH range. Highest activity is reached at pH 9.0
8.5 - 9
9 - 11
-
in this pH range wild-type, K281G mutant and K281R mutant show different activities: The activity of K281G mutant declines sharply and less than 30% of the activity is retained at pH 11.0, whereas K281R mutant and the wild-type shows more tolerance to the high pH (9.0-11.0), and at pH 11.0, 78.5% and 62.3% of the activity are retained, respectively
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
15
25
additional information
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Agrobacterium fabrum C58 / ATCC 33970
isolated from the floating ice near the Zhongshan Research Station of Antarctica
UniProt
brenda
and F1 interspecies hybrids made by crossing these two parental lines, i.e. Xiphophorus maculatus Jp 163 B × Xiphophorus couchianus
-
-
brenda
and F1 interspecies hybrids made by crossing these two parental lines, i.e. Xiphophorus maculatus Jp 163 B × Xiphophorus couchianus
-
-
brenda
Xiphophorus maculatus Jp 163 B
and F1 interspecies hybrids made by crossing these two parental lines, i.e. Xiphophorus maculatus Jp 163 B × Xiphophorus couchianus
-
-
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
by Northern blot analysis it is demonstrated that the transcript is expressed at highest level only in adult ovary
brenda
-
exposure of the cells to blue light, but not red light, for 12 h results in more than 20fold increase of the (6-4) photolyase mRNA
brenda
additional information
-
testes exhibit very high basal expression values in the F1 interspecies hybrid for photolyase 6-4 about 100fold higher than liver
brenda
-
testes exhibit very high basal expression values in the F1 interspecies hybrid for photolyase 6-4 about 100fold higher than liver
brenda
additional information
gene is strongly expressed in the upper part of the animal and not in the middle part or the base
brenda
additional information
-
gene is strongly expressed in the upper part of the animal and not in the middle part or the base
brenda
additional information
-
it is found that the 6-4 photoreactivating activity is constitutively expressed prior to as well as during the period of repair
brenda
additional information
-
expression levels of (64) photolyase in 24 h dark-maintained algae increase rapidly after 8-h exposure to white light, and also increase after being treated with NaCl for 8 h
brenda
additional information
-
by Northern blot analysis an ubiquitous expression pattern is demonstrated
brenda
additional information
-
by Northern blot analysis it is demonstrated that the transcript is expressed in multiple tissues
brenda
additional information
-
immunoblot analysis using a monoclonal antibody reveals that the NF-10 protein is expressed in cell lines from all complementation groups of xeroderma pigmentosum
brenda
additional information
-
tissue expression pattern, overview. The expression of 6-4 photolyase in F1 interspecies hybrids appears to be about 3-4fold above the parental line expression in the skin and eyes. In the brain and gill, the F1 interspecies hybrid 6-4 photolyase expression is similar to that of Xiphophorus couchianus, and both the F1 and Xiphophorus couchianus exhibit a greater than 5fold higher basal expression in the heart compared to Xiphophorus maculatus. The 6-4 photolyase becomes dramatically dysregulated in testis compared to either parent exhibiting substantial upregulated basal expression (over 30fold compared to Xiphophoruscouchianus and over 50fold for Xiphophorus maculatus). Liver shows much reduced 6-4 basal expression
brenda
additional information
-
tissue expression pattern, overview. The expression of 6-4 photolyase in F1 interspecies hybrids appears to be about 3-4fold above the parental line expression in the skin and eyes. In the brain and gill, the F1 interspecies hybrid 6-4 photolyase expression is similar to that of Xiphophorus couchianus, and both the F1 and Xiphophorus couchianus exhibit a greater than 5fold higher basal expression in the heart compared to Xiphophorus maculatus. The 6-4 photolyase becomes dramatically dysregulated in testis compared to either parent exhibiting substantial upregulated basal expression (over 30fold compared to Xiphophoruscouchianus and over 50fold for Xiphophorus maculatus). Liver shows much reduced 6-4 basal expression
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
physiological function
additional information
evolution
(6-4)photolyases are broadly distributed in prokaryotes. the PhrB-like photolyases branched at the base of the evolution of the cryptochrome/photolyase family. The prokaryotic (6-4) photolyases are the ancestors of the cryptochrome/photolyase family
evolution
the enzyme belongs to the photolyase/cryptochrome family, a large family of flavoproteins that possess different functions and use blue light as an energy source, phylogenetic analysis. Of the seven members of this gene family, three (CmPHR2, CmPHR5 and CmPHR6) fall within the clade of cryptochrome DASH, three (CmPHR3, CmPHR4 and CmPHR7) group with plant cryptochromes, and one (CmPHR1) is a homologue of (6-4) photolyase. Photolyases repair UV-induced DNA damage, whereas cryptochromes regulate the growth and development of plants in a blue-light dependent manner
evolution
cryptochromes and photolyases are flavoproteins that undergo cascades of electron/hole transfers after excitation of the flavin cofactor. Animal (6-4) photolyases, as well as animal cryptochromes, feature a chain of four tryptophan residues, while other members of the family contain merely a tryptophan triad
evolution
photolyases are efficient DNA repair enzymes that specifically repair either cyclobutane pyrimidine dimers or (6-4) photoproducts in a light-dependent cleavage reaction. The closely related classical cryptochrome blue light photoreceptors do not repair DNA lesions, instead they are involved in regulatory processes. CryB of Rhodobacter sphaeroides has been described as a cryptochrome that affects light-dependent and singlet oxygen-dependent gene expression and is unusual in terms of its cofactor composition. Evidence for a repair activity of (6-4) photoproducts by CryB is described suggesting a dual character combining the functions of cryptochromes and photolyases
evolution
-
PhrB from Agrobacterium fabrum represents a distinct group of prokaryotic (6-4) photolyases which contain an iron-sulfur cluster and a DMRL chromophore. The family of photolyases and cryptochromes may be divided into seven major phylogenetic groups: CPD photolyases class I, II and III, Cry-DASH proteins, eukaryotic (6-4) photolyases and animal cryptochromes, plant cryptochromes and prokaryotic FeS-BCP (Fe-S bacterial cryptochromes and photolyases) proteins. The terms CPD- and (6-4) photolyases refer to the kind of lesions that are repaired by these proteins, which are cyclopyrimidine dimers and (6-4) photoproducts, respectively. Both kinds of repair are triggered by a rapid electron transfer from the excited flavin adenine dinucleotide (FAD) chromophore to the DNA lesion. A second light reaction, termed photoreduction, results in the transition of oxidized or semi-reduced FAD to fully reduced FAD in photolyases or from oxidized to semi reduced FAD in plant cryptochromes. During photoreduction, electrons are transmitted from the surface via Trp or Tyr residues of the protein to the FAD chromophore. The classical photoreduction pathways in which electrons travel via three conserved Trp residues is realized in most photolyases and in cryptochromes. The group of FeS-BCP proteins is most distantly related to the other members of the cryptochrome/photolyase family. Two members of this group are CryB from Rhodobacter sphaeroides and PhrB from Agrobacterium fabrum. Among FeS-BCP members, amino acid residues in the active center are highly conserved. Loss of the cluster during the early evolution of the other photolyases
evolution
the bacterial (6-4) photolyase PhrB belongs to a phylogenetically ancient group. Photoreduction of PhrB differs from the typical pattern because the amino acid of the electron cascade next to FAD is a tyrosine (Tyr391), whereas photolyases and cryptochromes of other groups have a tryptophan as direct electron donor of FAD. Evolution of the first site of the redox chain has just been possible by tuning the protein structure and environment to manage a downhill hole transfer process from FAD to solvent
evolution
the energy transfer from cofactor 6,7-dimethyl-8-ribityllumazine (DMRL) to FAD might represent a phylogenetically ancient process
evolution
the Trichoderma reesei Cry1 protein is a member of the cryptochrome/photolyase family with 6-4 photoproduct repair activity. The two major types of DNA damage are cyclobutane pyrimidine dimers (CPD) and 6-4 photoproducts (6-4PP), which are repaired under illumination by CPD and 6-4 photolyases, respectively. Phylogenetic analysis and tree, overview
evolution
Agrobacterium fabrum C58 / ATCC 33970
-
the bacterial (6-4) photolyase PhrB belongs to a phylogenetically ancient group. Photoreduction of PhrB differs from the typical pattern because the amino acid of the electron cascade next to FAD is a tyrosine (Tyr391), whereas photolyases and cryptochromes of other groups have a tryptophan as direct electron donor of FAD. Evolution of the first site of the redox chain has just been possible by tuning the protein structure and environment to manage a downhill hole transfer process from FAD to solvent
-
evolution
Agrobacterium fabrum C58 / ATCC 33970
-
the energy transfer from cofactor 6,7-dimethyl-8-ribityllumazine (DMRL) to FAD might represent a phylogenetically ancient process
-
evolution
Agrobacterium tumefaciens C58 / ATCC 33970
-
(6-4)photolyases are broadly distributed in prokaryotes. the PhrB-like photolyases branched at the base of the evolution of the cryptochrome/photolyase family. The prokaryotic (6-4) photolyases are the ancestors of the cryptochrome/photolyase family
-
evolution
-
the enzyme belongs to the photolyase/cryptochrome family, a large family of flavoproteins that possess different functions and use blue light as an energy source, phylogenetic analysis. Of the seven members of this gene family, three (CmPHR2, CmPHR5 and CmPHR6) fall within the clade of cryptochrome DASH, three (CmPHR3, CmPHR4 and CmPHR7) group with plant cryptochromes, and one (CmPHR1) is a homologue of (6-4) photolyase. Photolyases repair UV-induced DNA damage, whereas cryptochromes regulate the growth and development of plants in a blue-light dependent manner
-
evolution
-
the Trichoderma reesei Cry1 protein is a member of the cryptochrome/photolyase family with 6-4 photoproduct repair activity. The two major types of DNA damage are cyclobutane pyrimidine dimers (CPD) and 6-4 photoproducts (6-4PP), which are repaired under illumination by CPD and 6-4 photolyases, respectively. Phylogenetic analysis and tree, overview
-
evolution
Cereibacter sphaeroides ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158
-
photolyases are efficient DNA repair enzymes that specifically repair either cyclobutane pyrimidine dimers or (6-4) photoproducts in a light-dependent cleavage reaction. The closely related classical cryptochrome blue light photoreceptors do not repair DNA lesions, instead they are involved in regulatory processes. CryB of Rhodobacter sphaeroides has been described as a cryptochrome that affects light-dependent and singlet oxygen-dependent gene expression and is unusual in terms of its cofactor composition. Evidence for a repair activity of (6-4) photoproducts by CryB is described suggesting a dual character combining the functions of cryptochromes and photolyases
-
malfunction
-
in contrast to transgenic mice expressing Potorous tridactylus CPD-photolyase transgenic mice expressing Arabidopsis thaliana (6-4) photolyase do not show any altered circadian behaviour
malfunction
both enzyme mutants H354A and H358A of Xenopus (6-4) PHR maintain their repair activity, although the efficiency is much lower than that of the wild-type. Two histidines must work in a concerted manner in the active center of the wild-type enzyme, which significantly raises the repair efficiency
malfunction
conidia of cry1 mutants show decreased photorepair capacity of DNA damage caused by UV light. In contrast, strains overexpressing Cry1 show increased repair, as compared to the parental strain even in the dark
malfunction
impairment of one of the two light absorbing cofactors, FAD or 6,7-dimethyl-8-ribityllumazine, only marginally affect the final survival rate but strongly decelerate photoreactivation kinetics. The impairment of both of them together through mutagenesis decreases CryB-dependent photoreactivation to the level of the DELTAcryB knockout strain. Survival rates of different Rhodobacter sphaeroides mutant strains after UV light treatment, overview
malfunction
-
mutants on cysteines that coordinate the Fe-S cluster of PhrB are either insoluble or not expressed. The same result is found for proteins with a truncated C-terminus, in which one of the Fe-S binding cysteines is mutated and for expression in minimal medium with limited Fe concentrations. The replacement of the highly conserved His366 results in loss of DNA repair activity. Leu370, which is also highly conserved, is not essential for repair, the L370M mutant has a lower repair activity. Mutants in which Tyr430 is replaced are characterized by a lower DNA repair activity. Tyr424 mutants are inactive
malfunction
replacement of Tyr391 by phenylalanine does not block photoreduction, while replacement by alanine blocks photoreduction, replacement of Tyr391 by Trp results in loss of FAD and DMRL chromophores
malfunction
Agrobacterium fabrum C58 / ATCC 33970
-
replacement of Tyr391 by phenylalanine does not block photoreduction, while replacement by alanine blocks photoreduction, replacement of Tyr391 by Trp results in loss of FAD and DMRL chromophores
-
malfunction
-
conidia of cry1 mutants show decreased photorepair capacity of DNA damage caused by UV light. In contrast, strains overexpressing Cry1 show increased repair, as compared to the parental strain even in the dark
-
malfunction
Cereibacter sphaeroides ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158
-
impairment of one of the two light absorbing cofactors, FAD or 6,7-dimethyl-8-ribityllumazine, only marginally affect the final survival rate but strongly decelerate photoreactivation kinetics. The impairment of both of them together through mutagenesis decreases CryB-dependent photoreactivation to the level of the DELTAcryB knockout strain. Survival rates of different Rhodobacter sphaeroides mutant strains after UV light treatment, overview
-
physiological function
the photolyase repairs UV-induced DNA damage
physiological function
Cry1 protein is a member of the cryptochrome/photolyase family with 6-4 photoproduct repair activity, it uses UV-visible light to repair DNA damage caused by UV radiation. The type of DNA damages, which are repaired under illumination by 6-4 photolyase, are 6-4 photoproducts (6-4PP). Cry1 is involved in the process of photoreactivation in Trichoderma reesei but has no participation in aspects related to growth at least under the tested conditions
physiological function
exposure of DNA to ultraviolet (UV) light from the sun or from other sources causes the formation of harmful and carcinogenic crosslinks between adjacent pyrimidine nucleobases, namely cyclobutane pyrimidine dimers and pyrimidine(6-4)pyrimidone photoproducts. Unique flavoenzymes, called DNA photolyases, utilize blue light, that is photons of lower energy than those of the damaging light, to repair these lesions. The chemically challenging repair of the (6-4) photoproducts by (6-4) photolyase and reaction mechanisms, overview
physiological function
exposure of DNA to ultraviolet (UV) light from the sun or from other sources causes the formation of harmful and carcinogenic crosslinks between adjacent pyrimidine nucleobases, namely cyclobutane pyrimidine dimers and pyrimidine(6-4)pyrimidone photoproducts. Unique flavoenzymes, called DNA photolyases, utilize blue light, that is photons of lower energy than those of the damaging light, to repair these lesions. The chemically challenging repair of the (6-4) photoproducts by (6-4) photolyase and reaction mechanisms, overview
physiological function
exposure of DNA to ultraviolet (UV) light from the sun or from other sources causes the formation of harmful and carcinogenic crosslinks between adjacent pyrimidine nucleobases, namely cyclobutane pyrimidine dimers and pyrimidine(6-4)pyrimidone photoproducts. Unique flavoenzymes, called DNA photolyases, utilize blue light, that is photons of lower energy than those of the damaging light, to repair these lesions. The chemically challenging repair of the (6-4) photoproducts by (6-4) photolyase and reaction mechanisms, overview
physiological function
photolyases are efficient DNA repair enzymes that specifically repair either cyclobutane pyrimidine dimers or (6-4) photoproducts in a light-dependent cleavage reaction. CryB of Rhodobacter sphaeroides has been described as a cryptochrome that affects light-dependent and singlet oxygen-dependent gene expression and is unusual in terms of its cofactor composition. Evidence for a repair activity of (6-4) photoproducts by CryB is described suggesting a dual character combining the functions of cryptochromes and photolyases. The reduction of FAD via the conserved tryptophan W338, which is crucial for in vitro reduction and consequently DNA repair, is not required for in vivo photoreactivation, suggesting that this reduction pathway to FAD is dispensable in the cellular environment
physiological function
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photolyases are flavoproteins that repair UV-damaged DNA in a light-dependent fashion, photolyases can repair pyrimidine dimers on the DNA that are formed during UV irradiation
physiological function
PhrB from Agrobacterium fabrum is a prokaryotic photolyase which repairs (6-4) UV DNA photoproducts
physiological function
psychrophilic microalga, Chlamydomonas sp. ICE-L, isolated from floating ice in the Antarctic, one of the most highly UV exposed ecosystems on Earth, displays an efficient DNA photorepair capacity, enzyme 6-4CiPhr is a photolyase with 6-4PP repair activity
physiological function
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UVB-induced DNA lesions in Xiphophorus fishes are thought to primarily be repaired via light dependent CPD and 6-4PP specific photolyases, cf. EC 4.1.99.3
physiological function
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UVB-induced DNA lesions in Xiphophorus fishes are thought to primarily be repaired via light dependent CPD and 6-4PP specific photolyases, cf. EC 4.1.99.3
physiological function
Agrobacterium fabrum C58 / ATCC 33970
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PhrB from Agrobacterium fabrum is a prokaryotic photolyase which repairs (6-4) UV DNA photoproducts
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physiological function
Xiphophorus maculatus Jp 163 B
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UVB-induced DNA lesions in Xiphophorus fishes are thought to primarily be repaired via light dependent CPD and 6-4PP specific photolyases, cf. EC 4.1.99.3
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physiological function
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Cry1 protein is a member of the cryptochrome/photolyase family with 6-4 photoproduct repair activity, it uses UV-visible light to repair DNA damage caused by UV radiation. The type of DNA damages, which are repaired under illumination by 6-4 photolyase, are 6-4 photoproducts (6-4PP). Cry1 is involved in the process of photoreactivation in Trichoderma reesei but has no participation in aspects related to growth at least under the tested conditions
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physiological function
Cereibacter sphaeroides ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158
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photolyases are efficient DNA repair enzymes that specifically repair either cyclobutane pyrimidine dimers or (6-4) photoproducts in a light-dependent cleavage reaction. CryB of Rhodobacter sphaeroides has been described as a cryptochrome that affects light-dependent and singlet oxygen-dependent gene expression and is unusual in terms of its cofactor composition. Evidence for a repair activity of (6-4) photoproducts by CryB is described suggesting a dual character combining the functions of cryptochromes and photolyases. The reduction of FAD via the conserved tryptophan W338, which is crucial for in vitro reduction and consequently DNA repair, is not required for in vivo photoreactivation, suggesting that this reduction pathway to FAD is dispensable in the cellular environment
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additional information
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quantum mechanical/molecular mechanics simulations using X-ray structure of the enzyme-DNA complex, overview
additional information
the His365-His366-X-X-Arg369 motif is located within the proposed DNA lesion contact site of PhrB. This motif is structurally conserved in eukaryotic (6-4) photolyases for which the second His is essential for the (6-4) photolyase function. His366 in PhrB is stabilized by van der Waals contacts with Leu370 and Met410. The enzyme has a C-terminal extension
additional information
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the His365-His366-X-X-Arg369 motif is located within the proposed DNA lesion contact site of PhrB. This motif is structurally conserved in eukaryotic (6-4) photolyases for which the second His is essential for the (6-4) photolyase function. His366 in PhrB is stabilized by van der Waals contacts with Leu370 and Met410. The enzyme has a C-terminal extension
additional information
effects of crucial amino acids involved in cofactor or DNA lesion binding on the light-dependent recovery of cells after UV light exposure (in vivo photoreactivation), overview. The iron-sulfur cluster is essential for the structural integrity of CryB
additional information
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effects of crucial amino acids involved in cofactor or DNA lesion binding on the light-dependent recovery of cells after UV light exposure (in vivo photoreactivation), overview. The iron-sulfur cluster is essential for the structural integrity of CryB
additional information
homology modeling using the crystal structure of a photolyase from Drosophila melanogaster in complex with 6--4 thymine dimer, PDB ID 3CVU, as a template
additional information
important role of residue His354 in the repair reaction of enzyme (6-4) PHR
additional information
in Xenopus laevis (6-4) photolyase, the fourth residue of a chain of four tryptophan residues is effectively involved in photoreduction
additional information
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in Xenopus laevis (6-4) photolyase, the fourth residue of a chain of four tryptophan residues is effectively involved in photoreduction
additional information
residues H354 and H358 are important in catalysis of Xenopus laevis (6-4) PL
additional information
residues H365 and H369 are important in catalysis of enzyme (6-4) PL, structure of a complex between the (6-4) PL of Drosophila melanogaster and a double-stranded DNA substrate containing a T(6-4)T lesion, overview
additional information
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role of particular amino acid residues in photorepair and photoreduction, during which the FAD chromophore converts from the oxidized to the enzymatically active, reduced form. Important function of highly conserved tyrosines in prokaryotic (6-4) photolyases, Tyr424 is essential for lesion binding and repair, and Tyr430 is required for efficient repair. Residues Trp342 and Trp390 as electron transmitters. Significant role of His366 in the protonation of the lesion during DNA repair
additional information
tunnelling matrix calculations show that tyrosine or phenylalanine can be involved in a productive bridged electron transfer between FAD and Trp390, in line with experimental findings, structure modeling of wild-type and mutant enzymes. Unusual stabilization of the positive charge on site 391 compared to other photolyases or cryptochromes. Mutational analyses of oligonucleotide sequences for DNA repair studies. Charge migration pathway from the protein surface Trp342 to FAD via Trp390 and Tyr391, light induced consecutive electron transfers, structures. Model structures and molecular dynamics simulations, overview
additional information
two highly conserved Tyr residues at positions 424 and 430 form an electron bridge between the DNA lesion and the Fe-S cluster, Tyr424 of PhrB is part of the DNA-binding site
additional information
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two highly conserved Tyr residues at positions 424 and 430 form an electron bridge between the DNA lesion and the Fe-S cluster, Tyr424 of PhrB is part of the DNA-binding site
additional information
two His residues are important in catalysis of enzyme (6-4) PL
additional information
Agrobacterium fabrum C58 / ATCC 33970
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tunnelling matrix calculations show that tyrosine or phenylalanine can be involved in a productive bridged electron transfer between FAD and Trp390, in line with experimental findings, structure modeling of wild-type and mutant enzymes. Unusual stabilization of the positive charge on site 391 compared to other photolyases or cryptochromes. Mutational analyses of oligonucleotide sequences for DNA repair studies. Charge migration pathway from the protein surface Trp342 to FAD via Trp390 and Tyr391, light induced consecutive electron transfers, structures. Model structures and molecular dynamics simulations, overview
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additional information
Agrobacterium fabrum C58 / ATCC 33970
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two highly conserved Tyr residues at positions 424 and 430 form an electron bridge between the DNA lesion and the Fe-S cluster, Tyr424 of PhrB is part of the DNA-binding site
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additional information
Agrobacterium tumefaciens C58 / ATCC 33970
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the His365-His366-X-X-Arg369 motif is located within the proposed DNA lesion contact site of PhrB. This motif is structurally conserved in eukaryotic (6-4) photolyases for which the second His is essential for the (6-4) photolyase function. His366 in PhrB is stabilized by van der Waals contacts with Leu370 and Met410. The enzyme has a C-terminal extension
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additional information
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homology modeling using the crystal structure of a photolyase from Drosophila melanogaster in complex with 6--4 thymine dimer, PDB ID 3CVU, as a template
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additional information
Cereibacter sphaeroides ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158
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effects of crucial amino acids involved in cofactor or DNA lesion binding on the light-dependent recovery of cells after UV light exposure (in vivo photoreactivation), overview. The iron-sulfur cluster is essential for the structural integrity of CryB
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Show AA Sequence and Transmembrane Helices (165 entries)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
62000
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
the N-terminal region of Cry1 contains a conserved DNA photolyase domain (Pfam00875) between amino acid positions 6 and 173, and a FAD-binding domain (Pfam03441) in the amino acid positions 239 to 549, involved in binding a light harvesting cofactor, while the C-terminal domain (residues 550 to 628) does not show similarity to any known domain, homology structure modeling, structure comparisons, overview
additional information
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the N-terminal region of Cry1 contains a conserved DNA photolyase domain (Pfam00875) between amino acid positions 6 and 173, and a FAD-binding domain (Pfam03441) in the amino acid positions 239 to 549, involved in binding a light harvesting cofactor, while the C-terminal domain (residues 550 to 628) does not show similarity to any known domain, homology structure modeling, structure comparisons, overview
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant PhrBI51W mutant, is crystallized by hanging drop vapor diffusion method, mixing of 5 mg/ml protein in 12.5 mM Tris, 1.25 mM EDTA, 2.5% w/v glycerol, and 75 mM sodium chloride, pH 7.8, with reservoir solution containing 5% PEG 400 and 100 mM 2-(N-morpholino) ethanesulfonic acid, pH 6.5, in a 1:1 ratio, X-ray diffraction structure determination and analysis at 2.15 A resolution, molecular replacement using the wild-type PhrBWT structure, PDB ID 4DJA, as the initial search model. Purified recombinant PhrBY424F mutant is crystallized by sitting drop vapor diffusion method, mixing 0.004 ml of 4-6 mg/ml protein in 12.5 mM Tris, 1.25 mM EDTA, 2.5% w/v glycerol, and 75 mM sodium chloride, pH 7.8, with an equal volume of reservoir solution containing 5% w/v PEG 400, 100 mM 2-(N-morpholino) ethanesulfonic acid, pH 6.0, and equilibration against 1 mLl of reservoir solution at 16°C, in darkness, 3-7 days, X-ray diffraction structure determination and analysis at 2.50 A resolution
purified recombinant His-tagged enzyme, hanging drop vapor diffusion method, mixing of 0.005 ml of protein in 12.5 mM Tris (hydroxymethyl) amino methane, 1.25 mM EDTA, 2.5% v/v glycerol, 75 mM sodium chloride, pH 7.8, with 0.005 ml of reservoir solution containing 2-6% w/v PEG400, 100 mM 2-(N-morpholino) ethanesulfonic acid buffer, pH 6.0, 25°C, 3-7 days, X-ray diffraction structure determination and analysis at 1.45-1.95 A resolution
determination of a crystal structure of Drosophila melanogaster (6-4) PL (Dm64) bound to a 15-mer DNA duplex containing a central T(6-4)T lesion
T(6-4)C lesion containing DNA duplex in complex with the (6-4) photolyase, by the hanging-drop vapour diffusion method, at 18°C, to 2.95 A resolution. Lesion is flipped out of the opened DNA duplex into the active site of the enzyme
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to study how the enzyme recognizes the T(6-4)C and T(Dew)C lesion analogues in the active site, DNA duplexes are crystallized together with the (6-4) photolyase
two crystal structures of the (6-4) photolyase bound to lesion containing DNA before and after repair, repair does not involve oxetane formation before light-induced electron transfer. The histidine 369, supposed to activate the acylimine, is in a position that does not allow efficient proton donation and hence activation of this substructure
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C350S
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site-directed mutagenesis, mutation of a Cys residue of the Fe-S cluster, the mutant protein is not expressed in Escherichia coli under conditions where the wild-type protein is expressed as soluble protein
C438S
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site-directed mutagenesis, mutation of a Cys residue of the Fe-S cluster, the mutant protein is not expressed in Escherichia coli under conditions where the wild-type protein is expressed as soluble protein
C441S
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site-directed mutagenesis, mutation of a Cys residue of the Fe-S cluster, the mutant protein is not expressed in Escherichia coli under conditions where the wild-type protein is expressed as soluble protein
H366A
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site-directed mutagenesis, in the mutant repair activity is lost
H366N/L370M
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site-directed mutagenesis, in the mutant repair activity is lost
I51W
site-directed mutagenesis, the mutant PhrBI51W shows loss of the DMRL chromophore (due to structural rearrangements of the residues in the DMRL binding pocket), reduced photoreduction, and reduced DNA repair capacity compared to wild-type. The mutation only affects local protein environments, whereas the overall fold remains unchanged. The crystal structure of PhrBI51W shows how the bulky Trp leads to structural rearrangements in the DMRL chromophore pocket. Structure analysis of mutant PhrBI51W
W342F
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site-directed mutagenesis, the mutant shows highly reduced light-induced spectral changes compared to wild-type
W390F
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site-directed mutagenesis, the mutant shows highly reduced light-induced spectral changes compared to wild-type
W390F/Y391F
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site-directed mutagenesis, the mutant shows highly reduced light-induced spectral changes compared to wild-type
Y391A
site-directed mutagenesis, Tyr391 replacement by alanine blocks photoreduction
Y391F
Y391W
site-directed mutagenesis, replacement of Tyr391 by Trp results in loss of FAD and DMRL chromophores, Trp might participate in the electron transfer cascade
Y399F
Y424F
Y430F
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site-directed mutagenesis, photoreduction of the mutant is indistinguishable from the wild-type, DNA binding assays are performed with single-stranded oligonucleotides with or without (-4)TT lesion, the mutant repair activity is 70% reduced compared to wild-type
Y460F
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site-directed mutagenesis, photoreduction of the mutant is indistinguishable from the wild-type, DNA binding assays are performed with single-stranded oligonucleotides with or without (6-4)TT lesion, the mutant repair activity is unaltered compared to wild-type
I51W
Agrobacterium fabrum C58 / ATCC 33970
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site-directed mutagenesis, the mutant PhrBI51W shows loss of the DMRL chromophore (due to structural rearrangements of the residues in the DMRL binding pocket), reduced photoreduction, and reduced DNA repair capacity compared to wild-type. The mutation only affects local protein environments, whereas the overall fold remains unchanged. The crystal structure of PhrBI51W shows how the bulky Trp leads to structural rearrangements in the DMRL chromophore pocket. Structure analysis of mutant PhrBI51W
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Y391A
Agrobacterium fabrum C58 / ATCC 33970
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site-directed mutagenesis, Tyr391 replacement by alanine blocks photoreduction
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Y391F
Agrobacterium fabrum C58 / ATCC 33970
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site-directed mutagenesis, Tyr391 replacement by phenylalanine does not block photoreduction
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Y391W
Agrobacterium fabrum C58 / ATCC 33970
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site-directed mutagenesis, replacement of Tyr391 by Trp results in loss of FAD and DMRL chromophores, Trp might participate in the electron transfer cascade
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Y424F
Agrobacterium fabrum C58 / ATCC 33970
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site-directed mutagenesis, the PhrBY424F mutant shows reduced binding of lesion DNA and loss of DNA repair compared to wild-type. The mutation only affects local protein environments, whereas the overall fold remains unchanged. The crystal structure of PhrBY424F reveals a water network extending to His366, which are part of the lesion-binding site. Structure analysis of mutant PhrBY424F
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H364A
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compared to wild-type mutant similar electron transfer dynamics in the range of 70-260 ps but decay to zero without any long plateaus, H364 is irreplaceable: Steady-state quantum yield measurements reveal a total lack of repair with the mutant
H364D
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compared to wild-type mutant similar electron transfer dynamics in the range of 70-260 ps but decay to zero without any long plateaus, H364 is irreplaceable: Steady-state quantum yield measurements reveal a total lack of repair with the mutant
H364K
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compared to wild-type mutant similar electron transfer dynamics in the range of 70-260 ps but decay to zero without any long plateaus, H364 is irreplaceable: Steady-state quantum yield measurements reveal a total lack of repair with the mutant
H364M
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compared to wild-type mutant similar electron transfer dynamics in the range of 70-260 ps but decay to zero without any long plateaus, H364 is irreplaceable: Steady-state quantum yield measurements reveal a total lack of repair with the mutant
H364N
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compared to wild-type mutant similar electron transfer dynamics in the range of 70-260 ps but decay to zero without any long plateaus, H364 is irreplaceable: Steady-state quantum yield measurements reveal a total lack of repair with the mutant
H364Y
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compared to wild-type mutant similar electron transfer dynamics in the range of 70-260 ps but decay to zero without any long plateaus, H364 is irreplaceable: Steady-state quantum yield measurements reveal a total lack of repair with the mutant
C434A/C437A
site-directed mutagenesis, the mutant cells show altered survival rates compaired to wild-type cells
E37F
site-directed mutagenesis, the mutant cells show altered survival rates compaired to wild-type cells
E37F/L366H
site-directed mutagenesis, the mutant cells show altered survival rates compaired to wild-type cells
E37F/W388F
site-directed mutagenesis, the mutant cells show altered survival rates compaired to wild-type cells
H362A
site-directed mutagenesis of an active site residue, the mutant cells show altered survival rates compaired to wild-type cells, in vivo and in vitro inactive mutant, no influence of an altered cofactor composition on the lack of repair. The position of H362 in the active centre next to FAD and the amino acids is involved in FAD reduction
L366A
site-directed mutagenesis, the mutant cells show altered survival rates compaired to wild-type cells, the mutant shows reduced in vitro repair activity compared to wild-type, and highly reduced FAD content
L366F
site-directed mutagenesis, the mutant cells show altered survival rates compaired to wild-type cells, the mutant shows reduced in vitro repair activity compared to wild-type, and highly reduced FAD content
L366H
site-directed mutagenesis, the mutant cells show altered survival rates compaired to wild-type cells, the mutant shows reduced in vitro repair activity compared to wild-type, and highly reduced FAD content
Q302A
site-directed mutagenesis of an active site residue, the mutant cells show altered survival rates compaired to wild-type cells
S431V
removal of the C-terminal roof-like subdomain of CryB including the [4Fe4S] cluster, two variants: variant CryBDELTAD432-V508 and CryBS431VDELTAS431-P507, both variants show highly reduced production and activity compared to wild-type
W388F
site-directed mutagenesis, the mutant cells show altered survival rates compaired to wild-type cells. The cofactor composition of CryB W338F does not differ from that of the wild-type protein. Considering the requirement of W338 for full reduction of FAD in vitro, the in vivo functionality of CryB W338F is remarkable
Y387F
site-directed mutagenesis, the mutant cells show altered survival rates compaired to wild-type cells, the mutant has a slightly reduced FAD content compared to wild-type
Y391F
site-directed mutagenesis, the mutant cells show altered survival rates compaired to wild-type cells, the mutant has a slightly reduced FAD content compared to wild-type
H362A
Cereibacter sphaeroides ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158
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site-directed mutagenesis of an active site residue, the mutant cells show altered survival rates compaired to wild-type cells, in vivo and in vitro inactive mutant, no influence of an altered cofactor composition on the lack of repair. The position of H362 in the active centre next to FAD and the amino acids is involved in FAD reduction
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S431V
Cereibacter sphaeroides ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158
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removal of the C-terminal roof-like subdomain of CryB including the [4Fe4S] cluster, two variants: variant CryBDELTAD432-V508 and CryBS431VDELTAS431-P507, both variants show highly reduced production and activity compared to wild-type
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Y387F
Cereibacter sphaeroides ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158
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site-directed mutagenesis, the mutant cells show altered survival rates compaired to wild-type cells, the mutant has a slightly reduced FAD content compared to wild-type
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Y391F
Cereibacter sphaeroides ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158
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site-directed mutagenesis, the mutant cells show altered survival rates compaired to wild-type cells, the mutant has a slightly reduced FAD content compared to wild-type
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K281G
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a single T(6-4)T photoproduct in a 10-mer oligonucleotide is photoreactivated by this mutant. Mutant shows similar capacity of photoreactivation compared to wild-type. Over the pH range 6-9 no difference to wild-type. Over the pH range 9-11 the activity of K281G mutant declines sharply and less than 30% of the activity is retained at pH 11.0
K281R
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a single T(6-4)T photoproduct in a 10-mer oligonucleotide is photoreactivated by this mutant. Mutant shows similar capacity of photoreactivation compared to wild-type. Over the pH range 6-9 no difference to wild-type. Over the pH range 9-11 the K281R mutant and the wild-type show more tolerance to the high pH (9.0-11.0), and at pH 11.0, 78.5% and 62.3% of the activity are retained, respectively
H354A
H358A
L355A
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large decrease in the affinity to the (6-4) photoproduct substrate, suggesting a hydrophobic interaction with the (6-4)photoproduct
additional information
Y391F
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site-directed mutagenesis, the mutant Y391F shows wild-type-like light-induced spectral changes
Y391F
site-directed mutagenesis, Tyr391 replacement by phenylalanine does not block photoreduction
Y399F
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site-directed mutagenesis, the mutant shows highly reduced light-induced spectral changes compared to wild-type
Y399F
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site-directed mutagenesis, the mutant Y391F shows slightly reduced light-induced spectral changes compared to wild-type
Y424F
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site-directed mutagenesis, photoreduction of the mutant is indistinguishable from the wild-type, DNA binding assays are performed with single-stranded oligonucleotides with or without (6-4)TT lesion, the mutant repair activity is lost
Y424F
site-directed mutagenesis, the PhrBY424F mutant shows reduced binding of lesion DNA and loss of DNA repair compared to wild-type. The mutation only affects local protein environments, whereas the overall fold remains unchanged. The crystal structure of PhrBY424F reveals a water network extending to His366, which are part of the lesion-binding site. Structure analysis of mutant PhrBY424F
H354A
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mutation of a conserved His residue: mutant is inactive in photorepair
H354A
site-directed mutagenesis, the mutant shows reduced repair activity compared to the wild-type enzyme
H354A
site-directed mutagenesis, unlike for the wild-type, the difference FTIR spectrum of H354A coincides with the zero line, mutant H358A to possesses limited repair activity
H358A
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almost complete loss of repair activity, suggesting that His354 and His358 are essential for catalytic activity
H358A
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mutation of a conserved His residue: mutant is inactive in photorepair
H358A
site-directed mutagenesis, unlike for the wild-type, the difference FTIR spectrum of enzyme mutant H358A is close to the zero line, mutant H358A to possesses highly limited repair activity
additional information
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mutants on cysteines that coordinate the Fe-S cluster of PhrB are either insoluble or not expressed. The same result is found for proteins with a truncated C-terminus, in which one of the Fe-S binding cysteines is mutated and for expression in minimal medium with limited Fe concentrations. Construction of two truncated versions of PhrB, designated PhrB-C and PhrB-D, which consist of amino acids 1-432 and 1-476, respectively. In PhrB-C, three of the Fe-S coordinating Cys residues aremissing, in PhrB-D, all Cys residues are present but the two C-terminal helices are missing. PhrB-C is insoluble under all tested conditions, whereas PhrB-D is partially soluble. With expression of PhrB by Escherichia coli cells growing in minimal medium without iron, PhrB is also insoluble. Thus, all conditions that might lead to a protein without Fe-S cluster result in very poor protein expression or insoluble protein
additional information
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light-dependent repair of UV-induced (6-4) photoproducts is investigated in an excision repair-deficient Arabidopsis mutant. It is demonstrated that (6-4) photoproducts are efficiently eliminated in a light-dependent manner which occurs in the presence of blue light (435 nm) but not upon exposure to light of longer wavelengths
additional information
construction of a knockout strain of cryB, termed 2.4.1DELTAcryB, which shows no detectable photoreduction of its FAD cofactor in vitro, but is able to maintain photoreactivation of Rhodobacter sphaeroides cells, in contrast, its in vitro repair activity is lost due to the inability to accumulate the repair-competent FADH- state under the assay conditions. In vivo photoreactivation is also functional when binding of FAD or the antenna chromophore is impaired, or when only low amounts of both are present. The impairment of one of the two light absorbing cofactors at a time through mutagenesis strongly influences the kinetics of photoreactivation, and the combination of both mutation completely abolishes CryB-dependent photoreactivation. The misfolding of the protein when trying to remove the iron-sulfur cluster by amino acid exchanges demonstrates its structural relevance for the protein. Survival rates of different Rhodobacter sphaeroides mutant strains after UV light treatment, and absorbance spectra of purified His-tagged CryB variants, overview
additional information
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construction of a knockout strain of cryB, termed 2.4.1DELTAcryB, which shows no detectable photoreduction of its FAD cofactor in vitro, but is able to maintain photoreactivation of Rhodobacter sphaeroides cells, in contrast, its in vitro repair activity is lost due to the inability to accumulate the repair-competent FADH- state under the assay conditions. In vivo photoreactivation is also functional when binding of FAD or the antenna chromophore is impaired, or when only low amounts of both are present. The impairment of one of the two light absorbing cofactors at a time through mutagenesis strongly influences the kinetics of photoreactivation, and the combination of both mutation completely abolishes CryB-dependent photoreactivation. The misfolding of the protein when trying to remove the iron-sulfur cluster by amino acid exchanges demonstrates its structural relevance for the protein. Survival rates of different Rhodobacter sphaeroides mutant strains after UV light treatment, and absorbance spectra of purified His-tagged CryB variants, overview
additional information
Cereibacter sphaeroides ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158
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construction of a knockout strain of cryB, termed 2.4.1DELTAcryB, which shows no detectable photoreduction of its FAD cofactor in vitro, but is able to maintain photoreactivation of Rhodobacter sphaeroides cells, in contrast, its in vitro repair activity is lost due to the inability to accumulate the repair-competent FADH- state under the assay conditions. In vivo photoreactivation is also functional when binding of FAD or the antenna chromophore is impaired, or when only low amounts of both are present. The impairment of one of the two light absorbing cofactors at a time through mutagenesis strongly influences the kinetics of photoreactivation, and the combination of both mutation completely abolishes CryB-dependent photoreactivation. The misfolding of the protein when trying to remove the iron-sulfur cluster by amino acid exchanges demonstrates its structural relevance for the protein. Survival rates of different Rhodobacter sphaeroides mutant strains after UV light treatment, and absorbance spectra of purified His-tagged CryB variants, overview
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additional information
expressing 6-4CiPhr in a photolyase-deficient Escherichia coli strain improves survival rate of the strain
additional information
construction of a theoretical 3D model shows that the protein has a FAD-binding domain. Although the amino acids identity between Dunaliella salina (6-4)photolyase and Escherichia coli CPD photolyase is just 23%, the backbone structure shows a high similarity in overall folding, suggesting a parallel photoreversal mechanism in the two enzymes
additional information
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construction of a theoretical 3D model shows that the protein has a FAD-binding domain. Although the amino acids identity between Dunaliella salina (6-4)photolyase and Escherichia coli CPD photolyase is just 23%, the backbone structure shows a high similarity in overall folding, suggesting a parallel photoreversal mechanism in the two enzymes
additional information
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expression of H64PRH does not show any photoreactivating effects on the survival of UV-irradiated Escherichia coli. Using a gel shift assay with with un-irradiated and UV-irradiated DNA probes it is shown that H64PRH protein does not possess any binding activity to either DNA probe
additional information
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the predicted amino acid sequence of the human protein has 48% identity with the Drosophila (6-4)photolyase over the entire protein
additional information
construction of a cry1 gene replacement mutants and cry1 overexpressing strains, (DELTAcry1, OEcry1, DELTAblr1 and DELTAenv1 strains). The mutant strains and the parental strain QM9414 are grown under continuous exposure to blue light or in the dark for 72 h at 28°C. The results show that neither the gene replacement mutant nor the overexpressing strain have any colony morphology alterations, and conidiated normally, the two independent gene replacement mutants and overexpressing strains show the same unaltered behavior compared to wild-type
additional information
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construction of a cry1 gene replacement mutants and cry1 overexpressing strains, (DELTAcry1, OEcry1, DELTAblr1 and DELTAenv1 strains). The mutant strains and the parental strain QM9414 are grown under continuous exposure to blue light or in the dark for 72 h at 28°C. The results show that neither the gene replacement mutant nor the overexpressing strain have any colony morphology alterations, and conidiated normally, the two independent gene replacement mutants and overexpressing strains show the same unaltered behavior compared to wild-type
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additional information
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sequencing of the cDNA clone reveals an open reading frame of encoding a protein of 526 amino acids (60600 Da) cDNA shows 58-54% amino acid identity to Drosophila (6-4)photolyase and its human homologue and 20-24% identity to the class I CPD photolyase
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
activity is unstable and it is lost upon storage at -20° or -70°C for 2-3 months
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glycerol to a final concentration of 50% (v/v) is added to the photolyase, storage at -70°C
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protein in aliquots is kept at -20°C until further use or stored at -80°C. The protein sample remained active after 6 months storage
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
(6-4) photoproduct DNA photolyase activity is detected in Crotalus atrox fibroblast. Activity is considerably enhanced when a UV-damaged DNA affinity column is used for purification. However, the activity is unstable and it is lost during purification or upon storage at -20° or -70°C for 2-3 months
-
by fractionation of crude cell extracts with Heparin agarose and UV DNA affinity column chromatography
-
by using a glutathione sepharose column and a Hi Trap Q column. Concentrated fusion protein is cleaved with thrombin from bovine plasma by incubation overnight at 4°C. For chromophore determination, the eluate from the glutathione sepharose column is purified through a Q sepharose column, omitting gel filtration procedure, and concentrated by ultrafiltration
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by using a glutathione-sepharose column and UV-irradiated DNA affinity column, fusion protein is cleaved with thrombin
-
by using affinity chromatography and UV-irradiated DNA attached beads
-
by using glutathione-sepharose columns
fusion protein is applied to amylose column. At this point the protein is above 90% pure. Further purification can be obtained by applying the eluted material to a 10 ml heparin-agarose column. Maltose-binding protein is removed by treatment with factor Xa protease
-
fusion protein is purified through a 20-ml amylose column and through heparin-agarose column
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NF-1 is isolated from nuclear extracts prepared from HeLa cell culture using a heparin column, an anion exchange Fractogel EMD TMAE-650 (S) column and a FPLC MonoS HR5/5 column
-
protein is isolated from whole cell extracts from Xenopus laevis, purified by using a sepharose column and a UV-damaged DNA affinity column
-
purified to near homogeneity from Drosophila embryonic cells by using NH4SO4 precipitation, SP sepharose column, UV DNA affinity beads, heparin sepharose column and Mono S column
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recombinant GST-tagged enzyme from Escherichia coli by glutathione affinity chromatography, and recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain C41(DE3) by nickel affinity and heparin affinity chromatography
recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography and gel filtration under dim light conditions or in darkness
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli by nickel affinity and heparin affinity chromatography, followed by gel filtration
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain ER2566 by nickel affinity chromatography and gel filtration
recombinant N-terminally His-tagged enzyme from Escherichia coli strain BL21(DE3) by metal affinity and heparin affinity chromatography
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
a cDNA of (6-4)photolyase from Dunaliella salina is cloned, sequenced and its amino acid sequence is deduced
DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic analysis, quantitative real-time PCR enzyme expression analysis
due to insolubility problems (6-4) photolyases is overexpressed as a fusion protein in Escherichia coli. Plasmid pXZ1997, a derivative of pMal-c2 containing the Drosophila melanogaster phr(6-4) cDNA fused in frame to the malE gene encoding maltose-binding protein (MBP), is propagated in Escherichia coli strain UNC523 (phr::kan uvrA::Tn10) selecting for ampicillin resistance. Cells are cultured in 2 liter of LB to A600: 0.60.8. IPTG is added to 0.3 mM, and incubation continued for 6 h prior to harvesting the cells by centrifugation.
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expressed in Escherichia coli
expressed in Escherichia coli, fusion protein with glutathione S-transferase
expression of N-terminally His-tagged enzyme in Escherichia coli strain BL21(DE3)
-
gene 6-4CiPhr, transcriptome analysis and cloning, DNA and amino acid sequence determination and analysis, phylogenetic tree, real-time PCR enzyme expression analysis, functional recombinant expression of C-terminally His-tagged enzyme in a photolyase-deficient Escherichia coli strain
gene phrB, recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain ER2566
gene RSP_3077 or cryB, recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strains BL21(DE3)pLysS or Rosetta(DE3)pRARE
phylogenetic analysis, DNA and amino acid sequence determination and analysis, expression of isozymes in Escherichia coli strain UNC 523 from pMal-c2x vector
recombinant expression of GST-tagged enzyme in Escherichia coli, and recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain C41(DE3). Photorepair difference FTIR spectra of Xenopus laevis (6-4) PHR using His-tagged sample and GST-tagged sample, overview
recombinant expression of His-tagged enzyme in Escherichia coli
recombinant expression of wild-type and mutant enzymes in Escherichia coli
-
DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic analysis, quantitative real-time PCR enzyme expression analysis
-
DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic analysis, quantitative real-time PCR enzyme expression analysis
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
cry1 mRNA accumulates in response to blue-light in a blr1-dependent manner and is modulated by Envoy
mRNA level of Ds64PHR in 24 h dark-grown algae cells increases in response to the exposure of UV-C. The mRNA levels of Ds64PHR increases after alkaline treatment
-
photolyase gene expression patterns before and after exposure to fluorescent light in Xiphophorus maculatus, Xiphophorus couchianus, and for F1 interspecies hybrids produced from crossing these two parental lines (Xiphophorus maculatus Jp 163 B Xiphophorus couchianus)
under UVB exposure, transcription of 6-4CiPhr is upregulated continuously within 6 h, achieving a maximum of 62.7fold at 6 h
cry1 mRNA accumulates in response to blue-light in a blr1-dependent manner and is modulated by Envoy
cry1 mRNA accumulates in response to blue-light in a blr1-dependent manner and is modulated by Envoy
-
-
photolyase gene expression patterns before and after exposure to fluorescent light in Xiphophorus maculatus, Xiphophorus couchianus, and for F1 interspecies hybrids produced from crossing these two parental lines (Xiphophorus maculatus Jp 163 B Xiphophorus couchianus)
-
photolyase gene expression patterns before and after exposure to fluorescent light in Xiphophorus maculatus, Xiphophorus couchianus, and for F1 interspecies hybrids produced from crossing these two parental lines (Xiphophorus maculatus Jp 163 B Xiphophorus couchianus)
-
photolyase gene expression patterns before and after exposure to fluorescent light in Xiphophorus maculatus, Xiphophorus couchianus, and for F1 interspecies hybrids produced from crossing these two parental lines (Xiphophorus maculatus Jp 163 B Xiphophorus couchianus)
Xiphophorus maculatus Jp 163 B
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Schroder, H.C.; Krasko, A.; Gundacker, D.; Leys, S.P.; Muller, I.M.; Muller, W.E.
Molecular and functional analysis of the (6-4) photolyase from the hexactinellid Aphrocallistes vastus
Biochim. Biophys. Acta
1651
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2003
Aphrocallistes vastus (Q86RA1), Aphrocallistes vastus
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Hitomi, K.; Nakamura, H.; Kim, S.T.; Mizukoshi, T.; Ishikawa, T.; Iwai, S.; Todo, T.
Role of two histidines in the (6-4) photolyase reaction
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2001
Xenopus laevis
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Weber, S.; Kay, C.W.; Mogling, H.; Mobius, K.; Hitomi, K.; Todo, T.
Photoactivation of the flavin cofactor in Xenopus laevis (6 - 4) photolyase: observation of a transient tyrosyl radical by time-resolved electron paramagnetic resonance
Proc. Natl. Acad. Sci. USA
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1319-1322
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Xenopus laevis
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Yi, Y.; Yi, C.; Qian, L.; Min, L.; Long, C.; Linhan, B.; Zhirong, Y.; Dairong, Q.
Cloning and sequence analysis of the gene encoding (6-4) photolyase from Dunaliella salina
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2006
Dunaliella salina (Q52Z99), Dunaliella salina
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Yan Lv, X.; Rong Qiao, D.; Xiong, Y.; Xu, H.; You, F.F.; Cao, Y.; He, X.
Photoreactivation of (6-4) photolyase in Dunaliella salina
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Dunaliella salina
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Drosophila melanogaster
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Binding and catalytic properties of Xenopus (6-4) photolyase
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Xenopus laevis
brenda
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Xenopus laevis
brenda
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Characteristic structure and environment in FAD cofactor of (6-4) photolyase along function revealed by resonance Raman spectroscopy
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Arabidopsis thaliana
brenda
Sancar, G.B.; Sancar, A.
Purification and characterization of DNA photolyases
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2006
Drosophila melanogaster
brenda
Todo, T.; Tsuji, H.; Otoshi, E.; Hitomi, K.; Kim, S.T.; Ikenaga, M.
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Mutat. Res.
384
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1997
Homo sapiens
brenda
Todo, T.; Ryo, H.; Borden, A.; Lawrence, C.; Sakaguchi, K.; Hirata, H.; Nomura, T.
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385
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Drosophila melanogaster
brenda
Todo, T.; Takemori, H.; Ryo, H.; Ihara, M.; Matsunaga, T.; Nikaido, O.; Sato, K.; Nomura, T.
A new photoreactivating enzyme that specifically repairs ultraviolet light-induced (6-4)photoproducts
Nature
361
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1993
Drosophila melanogaster
brenda
Wakasugi, M.; Abe, Y.; Yoshida, Y.; Matsunaga, T.; Nikaido, O.
Purification of a novel UV-damaged-DNA binding protein highly specific for (6-4) photoproduct
Nucleic Acids Res.
24
1099-1004
1996
Homo sapiens
brenda
Todo, T.; Kim, S.T.; Hitomi, K.; Otoshi, E.; Inui, T.; Morioka, H.; Kobayashi, H.; Ohtsuka, E.; Toh, H.; Ikenaga, M.
Flavin adenine dinucleotide as a chromophore of the Xenopus (6-4)photolyase
Nucleic Acids Res.
25
764-768
1997
Xenopus laevis
brenda
Yamamoto, J.; Hitomi, K.; Todo, T.; Iwai, S.
Synthesis of oligonucleotides containing the Dewar valence isomer of the (6-4) photoproduct and their application to (6-4) photolyase studies
Nucleic Acids Symp. Ser.
50
61-62
2006
Xenopus laevis
brenda
Iwai, S.; Mizukoshi, T.; Hitomi, K.; Todo, T.
Chemical synthesis of oligonucleotides containing the (6-4) photoproduct at the thymine-cytosine site and its repair by (6-4) photolyase
Nucleosides Nucleotides
18
1325-1327
1999
Xenopus laevis
brenda
Kim, S.T.; Malhotra, K.; Taylor, J.S.; Sancar, A.
Purification and partial characterization of (6-4) photoproduct DNA photolyase from Xenopus laevis
Photochem. Photobiol.
63
292-295
1996
Crotalus atrox, Xenopus laevis
brenda
Chen, J.J.; Mitchell, D.L.; Britt, A.B.
A light-dependent pathway for the elimination of UV-induced pyrimidine (6-4) pyrimidinone photoproducts in Arabidopsis
Plant Cell
6
1311-1317
1994
Arabidopsis thaliana
brenda
Todo, T.; Ryo, H.; Yamamoto, K.; Toh, H.; Inui, T.; Ayaki, H.; Nomura, T.; Ikenaga, M.
Similarity among the Drosophila (6-4)photolyase, a human photolyase homolog, and the DNA photolyase-blue-light photoreceptor family
Science
272
109-112
1996
Drosophila melanogaster, Homo sapiens
brenda
Fukushima, N.; Naito, Y.; Ryoji, M.
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383
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Xenopus laevis
brenda
de Lima-Bessa, K.M.; Armelini, M.G.; Chigancas, V.; Jacysyn, J.F.; Amarante-Mendes, G.P.; Sarasin, A.; Menck, C.F.
CPDs and 6-4PPs play different roles in UV-induced cell death in normal and NER-deficient human cells
DNA Repair
7
303-312
2008
Homo sapiens
brenda
Usman, A.; Brazard, J.; Martin, M.M.; Plaza, P.; Heijde, M.; Zabulon, G.; Bowler, C.
Spectroscopic characterization of a (6-4) photolyase from the green alga Ostreococcus tauri
J. Photochem. Photobiol. B Biol.
96
38-48
2009
Ostreococcus tauri (Q5IFN1), Ostreococcus tauri
brenda
Hitomi, K.; DiTacchio, L.; Arvai, A.S.; Yamamoto, J.; Kim, S.T.; Todo, T.; Tainer, J.A.; Iwai, S.; Panda, S.; Getzoff, E.D.
Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes
Proc. Natl. Acad. Sci. USA
106
6962-6967
2009
Arabidopsis thaliana (O48652), Arabidopsis thaliana
brenda
Yamamoto, J.; Hitomi, K.; Hayashi, R.; Getzoff, E.D.; Iwai, S.
Role of the carbonyl group of the (6-4) photoproduct in the (6-4) photolyase reaction
Biochemistry
48
9306-9312
2009
Xenopus laevis
brenda
Glas, A.F.; Schneider, S.; Maul, M.J.; Hennecke, U.; Carell, T.
Crystal structure of the T(6-4)C lesion in complex with a (6-4) DNA photolyase and repair of UV-induced (6-4) and Dewar photolesions
Chemistry
15
10387-10396
2009
Drosophila melanogaster
brenda
Mueller, M.; Carell, T.
Structural biology of DNA photolyases and cryptochromes
Curr. Opin. Struct. Biol.
19
277-285
2009
Drosophila melanogaster, Arabidopsis thaliana (O48652)
brenda
Yamamoto, J.; Hitomi, K.; Hayashi, R.; Getzoff, E.D.; Iwai, S.
Recognition and reaction mechanisms of the (6-4) photolyase as determined by using a (6-4) photoproduct analog
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53
221-222
2009
Xenopus laevis
brenda
Zhang, Y.; Iwata, T.; Yamamoto, J.; Hitomi, K.; Iwai, S.; Todo, T.; Getzoff, E.D.; Kandori, H.
FTIR study of light-dependent activation and DNA repair processes of (6-4) photolyase
Biochemistry
50
3591-3598
2011
Xenopus laevis
brenda
Zhang, F.; Xu, H.; Cao, Y.; Wen, T.; Lin, J.; Ma, G.; Qiao, D.; Cao, Y.
Role of Lys281 in the Dunaliella salina (6-4) photolyase reaction
Curr. Microbiol.
62
146-151
2011
Dunaliella salina
brenda
Sadeghian, K.; Bocola, M.; Merz, T.; Schuetz, M.
Theoretical study on the repair mechanism of the (6-4) photolesion by the (6-4) photolyase
J. Am. Chem. Soc.
132
16285-16295
2010
Drosophila melanogaster
brenda
Glas, A.; Kaya, E.; Schneider, S.; Heil, K.; Fazio, D.; Maul, M.; Carell, T.
DNA (6-4) photolyases reduce dewar isomers for isomerization into (6-4) lesions
J. Am. Chem. Soc.
132
3254-3255
2010
Drosophila melanogaster (Q8SXK5)
brenda
Kondoh, M.; Hitomi, K.; Yamamoto, J.; Todo, T.; Iwai, S.; Getzoff, E.D.; Terazima, M.
Light-induced conformational change and product release in DNA repair by (6-4) photolyase
J. Am. Chem. Soc.
133
2183-2191
2011
Xenopus laevis
brenda
Li, J.; Liu, Z.; Tan, C.; Guo, X.; Wang, L.; Sancar, A.; Zhong, D.
Dynamics and mechanism of repair of ultraviolet-induced (6-4) photoproduct by photolyase
Nature
466
887-890
2010
Arabidopsis thaliana
brenda
Chaves, I.; Nijman, R.M.; Biernat, M.A.; Bajek, M.I.; Brand, K.; da Silva, A.C.; Saito, S.; Yagita, K.; Eker, A.P.; van der Horst, G.T.
The potorous CPD photolyase rescues a cryptochrome-deficient mammalian circadian clock
PLoS ONE
6
e23447
2011
Arabidopsis thaliana
brenda
Yamamoto, J.; Martin, R.; Iwai, S.; Plaza, P.; Brettel, K.
Repair of the (6-4) photoproduct by DNA photolyase requires two photons
Angew. Chem. Int. Ed. Engl.
52
7432-7436
2013
Xenopus laevis
brenda
Yamada, D.; Zhang, Y.; Iwata, T.; Hitomi, K.; Getzoff, E.D.; Kandori, H.
Fourier-transform infrared study of the photoactivation process of Xenopus (6-4) photolyase
Biochemistry
51
5774-5783
2012
Xenopus laevis
brenda
Faraji, S.; Groenhof, G.; Dreuw, A.
Combined QM/MM investigation on the light-driven electron-induced repair of the (6-4) thymine dimer catalyzed by DNA photolyase
J. Phys. Chem. B
117
10071-10079
2013
Drosophila melanogaster
brenda
Asimgil, H.; Kavakli, I.H.
Purification and characterization of five members of photolyase/cryptochrome family from Cyanidioschyzon merolae
Plant Sci.
185-186
190-198
2012
Cyanidioschyzon merolae (M1V623), Cyanidioschyzon merolae, Cyanidioschyzon merolae 10D (M1V623)
brenda
Zhang, F.; Scheerer, P.; Oberpichler, I.; Lamparter, T.; Krauss, N.
Crystal structure of a prokaryotic (6-4) photolyase with an Fe-S cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore
Proc. Natl. Acad. Sci. USA
110
7217-7222
2013
Agrobacterium tumefaciens (A9CH39), Agrobacterium tumefaciens, Agrobacterium tumefaciens C58 / ATCC 33970 (A9CH39)
brenda
Yamada, D.; Iwata, T.; Yamamoto, J.; Hitomi, K.; Todo, T.; Iwai, S.; Getzoff, E.D.; Kandori, H.
Structural role of two histidines in the (6-4) photolyase reaction
Biophys. Physicobiol.
12
139-144
2015
Xenopus laevis (Q9I910)
brenda
Holub, D.; Ma, H.; Krauss, N.; Lamparter, T.; Elstner, M.; Gillet, N.
Functional role of an unusual tyrosine residue in the electron transfer chain of a prokaryotic (6-4) photolyase
Chem. Sci.
9
1259-1272
2018
Agrobacterium fabrum (A9CH39), Agrobacterium fabrum C58 / ATCC 33970 (A9CH39)
brenda
Walter, D.; Boswell, M.; Volk de Garcia, S.; Walter, S.; Breitenfeldt, E.; Boswell, W.; Walter, R.
Characterization and differential expression of CPD and 6-4 DNA photolyases in Xiphophorus species and interspecies hybrids
Comp. Biochem. Physiol. C
163
77-85
2014
Xiphophorus couchianus, Xiphophorus maculatus, Xiphophorus maculatus Jp 163 B
brenda
von Zadow, A.; Ignatz, E.; Pokorny, R.; Essen, L.O.; Klug, G.
Rhodobacter sphaeroides CryB is a bacterial cryptochrome with (6-4) photolyase activity
FEBS J.
283
4291-4309
2016
Cereibacter sphaeroides (Q3IXP1), Cereibacter sphaeroides, Cereibacter sphaeroides ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 (Q3IXP1)
brenda
Cailliez, F.; Mueller, P.; Firmino, T.; Pernot, P.; de la Lande, A.
Energetics of photoinduced charge migration within the tryptophan tetrad of an animal (6-4) photolyase
J. Am. Chem. Soc.
138
1904-1915
2016
Xenopus laevis (Q9I910), Xenopus laevis
brenda
An, M.; Zheng, Z.; Qu, C.; Wang, X.; Chen, H.; Shi, C.; Miao, J.
The first (6-4) photolyase with DNA damage repair activity from the Antarctic microalga Chlamydomonas sp. ICE-L
Mutat. Res.
809
13-19
2018
Chlamydomonas sp. ICE-L (A0A2Z5J5J9)
brenda
Zhang, F.; Ma, H.; Bowatte, K.; Kwiatkowski, D.; Mittmann, E.; Qasem, H.; Krauss, N.; Zeng, X.; Ren, Z.; Scheerer, P.; Yang, X.; Lamparter, T.
Crystal structures of bacterial (6-4) photolyase mutants with impaired DNA repair activity
Photochem. Photobiol.
93
304-314
2017
Agrobacterium fabrum (A9CH39), Agrobacterium fabrum, Agrobacterium fabrum C58 / ATCC 33970 (A9CH39)
brenda
Yamamoto, J.; Plaza, P.; Brettel, K.
Repair of (6-4) lesions in DNA by (6-4) photolyase 20 years of quest for the photoreaction mechanism
Photochem. Photobiol.
93
51-66
2017
Arabidopsis thaliana (O48652), Drosophila melanogaster (Q0E8P0), Xenopus laevis (Q9I910)
brenda
Graf, D.; Wesslowski, J.; Ma, H.; Scheerer, P.; Krauss, N.; Oberpichler, I.; Zhang, F.; Lamparter, T.
Key amino acids in the bacterial (6-4) photolyase PhrB from Agrobacterium fabrum
PLoS ONE
10
e0140955
2015
Agrobacterium fabrum
brenda
Guzman-Moreno, J.; Flores-Martinez, A.; Brieba, L.G.; Herrera-Estrella, A.
The Trichoderma reesei Cry1 protein is a member of the cryptochrome/photolyase family with 6-4 photoproduct repair activity
PLoS ONE
9
e100625
2014
Trichoderma reesei (G0RI60), Trichoderma reesei QM6a (G0RI60)
brenda
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