4.1.99.13: (6-4)DNA photolyase
This is an abbreviated version!
For detailed information about (6-4)DNA photolyase, go to the full flat file.
Word Map on EC 4.1.99.13
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4.1.99.13
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photoproducts
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cyclobutane
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uv-induced
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cryptochromes
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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
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ostreococcus
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four-membered
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fadox
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photoreception
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cry-dashs
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dewar
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cryptochrome-dash
- 4.1.99.13
- photoproducts
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cyclobutane
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uv-induced
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cryptochromes
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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
Reaction
= 2 pyrimidine residues (in DNA)
Synonyms
(6-4) DNA photolyase, (6-4) photolyase, (6-4) PHR, (6-4) PL, (6-4) PP-specific PL, (6-4)-Phr, (6-4)photolyase, 6-4 DNA photolyase, 6-4 photolyase, 6-4CiPhr, 6-4PP-photolyase, animal (6-4) photolyase, At64, At64PHR, bacterial (6-4) photolyase, CmPHR1, Cry1, CryB, deoxyribodipyrimidine photolyase-related protein, Dm64, DNA photolyase, Ds64PHR, H64PRH, human (6-4) photolyase homologous protein, NF-10, OtCPF1, phr (6-4), PhrB, PL-(6-4), prokaryotic (6-4) photolyase, RSP_3077, TRIREDRAFT_77473, XELAEV_18035355mg, Xl64phr
ECTree
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General Information
General Information on EC 4.1.99.13 - (6-4)DNA photolyase
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evolution
malfunction
physiological function
additional information
(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
Agrobacterium fabrum C58 / ATCC 33970
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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
Agrobacterium fabrum C58 / ATCC 33970
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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
Agrobacterium tumefaciens C58 / ATCC 33970
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(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
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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
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. 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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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
Agrobacterium fabrum C58 / ATCC 33970
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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
Cereibacter sphaeroides ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158
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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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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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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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