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(6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
(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
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(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
(6-4) photoproduct (in DNA)
pyrimidine residues (in DNA)
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?
C(6-4)C photoproduct (in DNA)
2 cytosine residues (in DNA)
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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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?
T(6-4)T photoproduct (in DNA)
2 thymidine residues (in DNA)
T(6-4)T photoproduct (in DNA)
2 thymine residues (in DNA)
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?
T(6-4)T photoproduct (in DNA)
thymidine residues (in DNA)
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?
additional information
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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)TT
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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)
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)
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)
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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)
(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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(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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(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)
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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)
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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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
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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
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additional information
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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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additional information
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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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(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
cyclobutadipyrimidine in DNA
2 pyrimidine residues in DNA
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?
T(6-4)T photoproduct (in DNA)
2 thymine residues (in DNA)
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?
additional information
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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)
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)
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)
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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)
(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)
(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)
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-
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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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-
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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-
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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-
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?
(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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-
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(6-4) photoproduct (in DNA)
2 pyrimidine residues (in DNA)
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-
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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)
Xiphophorus maculatus Jp 163 B
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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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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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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
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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
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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
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evolution
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the energy transfer from cofactor 6,7-dimethyl-8-ribityllumazine (DMRL) to FAD might represent a phylogenetically ancient process
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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
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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
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evolution
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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
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evolution
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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. 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
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malfunction
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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
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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. 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
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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
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malfunction
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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
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malfunction
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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
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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
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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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the photolyase repairs UV-induced DNA damage
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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
-
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
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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
-
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
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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
-
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
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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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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
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
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
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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
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site-directed mutagenesis, Tyr391 replacement by alanine blocks photoreduction
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Y391F
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site-directed mutagenesis, Tyr391 replacement by phenylalanine does not block photoreduction
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Y391W
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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
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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
-
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
-
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
-
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
-
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
-
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
-
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
-
H365N
mutant shows no repair activity
K281G
-
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
-
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
L355A
-
large decrease in the affinity to the (6-4) photoproduct substrate, suggesting a hydrophobic interaction with the (6-4)photoproduct
Q288A
-
repair activity is not reduced
W291A
-
some enzymatic activity is retained
W398A
-
some enzymatic activity is retained
Y391F
-
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
-
site-directed mutagenesis, the mutant shows highly reduced light-induced spectral changes compared to wild-type
Y399F
-
site-directed mutagenesis, the mutant Y391F shows slightly reduced light-induced spectral changes compared to wild-type
Y424F
-
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
-
almost complete loss of repair activity
H354A
-
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
-
almost complete loss of repair activity, suggesting that His354 and His358 are essential for catalytic activity
H358A
-
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
-
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
-
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
-
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
-
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
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
-
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
-
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
-
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
-
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
-
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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Arabidopsis thaliana (O48652), Drosophila melanogaster (Q0E8P0), Xenopus laevis (Q9I910)
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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
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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)
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