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5,10-methenyltetrahydrofolate
5,10-methenyltetrahydropterolypolyglutamate
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5,10-methylenetetrahydrofolate
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antenna pigment in Escherichia coli absorbs blue/near UV light and transfers the excitation energy fast and efficiently to FADH-
7,8-didemethyl-8-hydroxy-5-deazaflavin
7,8-didemethyl-8-hydroxy-5-deazariboflavin
8-hydroxy-5-deazariboflavin
8-hydroxy-7,8-didemethyl-5-deazariboflavin
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antenna pigment in Anacystis nidulans absorbs blue/near UV light and transfers the excitation energy fast and efficiently to FADH-
8-iodo-8-demethylriboflavin
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8-iodoflavin
chromophore binding site of Thermus photolyase is reconstited also with a novel synthetic flavin, 8-iodoflavin
ATP
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stimulates, utilization of ATP for the photorepair process of the pyrimidine dimer containing DNA, not only an allosteric effector
deazaflavin
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antenna cofactor
5,10-methenyltetrahydrofolate
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5,10-methenyltetrahydrofolate
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5,10-methenyltetrahydrofolate
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5,10-methenyltetrahydrofolate
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5,10-methenyltetrahydrofolate
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5,10-methenyltetrahydrofolate
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5,10-methenyltetrahydrofolate
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5,10-methenyltetrahydrofolate
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5,10-methenyltetrahydrofolate
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acts as a light-harvesting pigment
5,10-methenyltetrahydrofolate
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an electron transfer pathway exists in DASH cryptochrome, where the 5,10-methenyltetrahydrofolate cofactor is photoreduced to 5,10-methylenetetrahydrofolate. Reduction requires the intact tryptophan triad. DASH cryptochrome forms 5,10-methylenetetrahydrofolate when treated with UV-A. Light-driven formation of 5,10-methylenetetrahydrofolate by DASH cryptochrome can be coupled with the formation of NADPH in the presence of 5,10-methylenetetrahydrofolate dehydrogenase
5,10-methenyltetrahydrofolate
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an electron transfer pathway exists in photolyase, where the 5,10-methenyltetrahydrofolate cofactor is photoreduced to 5,10-methylenetetrahydrofolate. Reduction requires the intact tryptophan triad. Photolyase forms 5,10-methylenetetrahydrofolate when treated with UV-A. Light-driven formation of 5,10-methylenetetrahydrofolate by photolyase can be coupled with the formation of NADPH in the presence of 5,10-methylenetetrahydrofolate dehydrogenase
5,10-methenyltetrahydrofolate
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antenna cofactor
5,10-methenyltetrahydrofolate
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bound at the interface between N-terminal and C-terminal domain
5,10-methenyltetrahydrofolate
bound at the interface between N-terminal and C-terminal domain
5,10-methenyltetrahydrofolate
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Cry3
5,10-methenyltetrahydrofolate
FAD and 5,10-methenyltetrahydrofolate act as chromophore and antenna molecules, respectively
5,10-methenyltetrahydrofolate
observed in the cleft between the two domains, where it interacts with two critical amino acid residues, Cys292 and Lys293
5-deazaflavin
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prosthetic group
7,8-didemethyl-8-hydroxy-5-deazaflavin
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part of the chromophore
7,8-didemethyl-8-hydroxy-5-deazaflavin
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essential chromogenic part of the cofactor
7,8-didemethyl-8-hydroxy-5-deazariboflavin
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7,8-didemethyl-8-hydroxy-5-deazariboflavin
chromophore binding site of Thermus photolyase is reconstited also with 7,8-didemethyl-8-hydroxy-5-deazariboflavin (8-HDF). However, in the genome sequence of Thermus thermophilus it is found that the genes essential for the biosynthesis of 8-HDF are missing
8-hydroxy-5-deazaflavin
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cofactor
8-hydroxy-5-deazaflavin
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light-harvesting chromophore, not essential for correct folding of the enzyme
8-hydroxy-5-deazaflavin
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contains the chromophore 8-hydroxy-5-deazaflavin
8-hydroxy-5-deazariboflavin
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bound at the interface between N-terminal and C-terminal domain
8-hydroxy-5-deazariboflavin
bound at the interface between N-terminal and C-terminal domain
8-hydroxy-5-deazariboflavin
photolyase can bind next to the natural cofactor 8-hydroxy-5-deazariboflavin also FMN
FAD
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FAD
enzyme contains two chromophore cofactors: FAD is a catalytic cofactor which directly contributes to the repair of a pyrimidine-dimer, the other is an unidentified light harvesting cofactor, which absorbs visible light and transfers energy to the catalytic cofactor
FAD
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only FAD as cofactor, no second cofactor detectable
FAD
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is indispensable for catalytic activity
FAD
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the photoexcited FAD cofactor is reduced from the semiquinone or fully oxidized state to the catalytically active FADH- state
FAD
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the photolyase in its native state contains FAD in the two-electron reduced and deprotonated FADH- form, during purification under aerobic conditions, FADH- is oxidized to the rather stable blue neutral radical
FAD
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the photolyase in its native state contains FAD in the two-electron reduced and deprotonated FADH- form, during purification under aerobic conditions, FADH- is oxidized to the rather stable blue neutral radical
FAD
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the purified enzyme binds a FAD, which is in the neutral radical semiquinone form
FAD
the repair reaction involves electron transfer to the cyclobutane pyrimidine dimers from the photoexcited FAD cofactor in its fully reduced form
FAD
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a second FAD molecule is present in the antenna pigment binding pocket
FAD
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alpha-helical domain is harboring the FAD cofactor, essential for catalysis
FAD
alpha-helical domain is harboring the FAD cofactor, essential for catalysis
FAD
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binds the flavin cofactor in a pocket that is conserved in terms of its electronic properties
FAD
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binds the flavin cofactor in a pocket that is conserved in terms of its electronic properties. W399-W378-W406 may function as potential electron donors to the flavin and are possible candidate tryptophans for light-induced electron transfer
FAD
critical W382 residue relative to the flavin for efficient vectorial electron transfer leading to photoreduction
FAD
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Cry1, which does not bind to DNA, possesses a strongly reduced surface charge around the FAD binding pocket
FAD
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large kinetic isotope and pH effects on the rate constants for FAD semiquinone oxidation, which reveal that proton transfer is rate-limiting. Photolyase-specific residues, Trp392 and Gly389, independently ensure a high kinetic barrier to semiquinone reactivity in photolyase, possibly through interactions with the adenine moiety of FAD and/or adjusting the polarity of the binding site. These residues have a much greater impact on semiquinone reactivity than the more FAD proximal Met353 or Ser395
FAD
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photoreduction of FAD under blue light irradiation is faster in photolyase than in Arabidopsis cry3
FAD
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photoreduction of FAD under blue light irradiation is faster in photolyase than in Arabidopsis cry3
FAD
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photolyase's essential cofactor is a non-covalently bound flavin adenine dinucleotide in fully reduced state (FADH-)
FAD
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photolyase's essential cofactor is a non-covalently bound flavin adenine dinucleotide in fully reduced state (FADH-)
FAD
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the physiological form of the enzyme contains a fully reduced FAD (FADH-) that is required for its activity both in vivo and in vitro. It binds a cyclobutane pyrimidine dimer (CPD) in DNA independent of light and flips the dimer out of the double helix into the active site cavity to make a stable enzyme-substrate complex. Enzyme usually purified with FAD in the blue neutral radical form. The purified enzyme can hold its radical flavin cofactor unoxidized in aerobic conditions for several days
FAD
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absorption spectra of FADH+, FADH radical, and FADH- of wild-type and mutant enzymes, overview. All three flavin species and decays to zero upon completion of repair
FAD
FAD and 5,10-methenyltetrahydrofolate act as chromophore and antenna molecules, respectively. The Ver3 chromophore always remains partly (including the semiquinone state) or fully reduced under all experimental conditions tested
FAD
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light-induced reduction of FAD, and transfer of an electron from the photoexcited reduced FAD to the damaged DNA for cleaving the dimers
FAD
the C-terminal domain frames a concave pocket that holds the FAD cofactor in the U-shaped conformation. The U-shaped FAD is positioned with the isoalloxazine ring buried and the adenine ring solvent-exposed beneath the substrate binding pocket. A salt bridge (Arg396 to Asp427) across the isoalloxazine ring orients the guanidinium to stabilize a semiquinone radical at the C4a position. Cofactor binding and interactions with the enzyme, overview
FAD
the enzyme appears to utilize an unusual, conserved tryptophan dyad as electron transfer pathway to the catalytic FAD cofactor
FAD
the enzyme is capable to photoreduce its catalytic FAD to the active FADH- form. The C-terminal FAD-binding subdomain contains the catalytic cofactor FAD in the U-shaped conformation. FAD-binding site and electron transfer pathway in class II photolyases, overview
FAD
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the FAD binding region is required for the catalytic activity of DNA photolyase
FAD
bound in a C-terminal alpha-helix cavity, the C-terminal alpha-helical domain consists of 14 alpha-helices. FAD is held in a U-shaped conformation by interaction with 14 conserved amino acid residues
FAD
catalytic cofactor, 4 different redox states of flavin, overview
FAD
dependent on, adopts a uniquely folded configuration at the active site that plays a critical functional role in DNA repair, overview. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. Photolyase utilizes FADH-, not FAD- radical as the active state
FAD
dependent on, adopts a uniquely folded configuration at the active site that plays a critical functional role in DNA repair, overview. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. Photolyase utilizes FADH-, not FAD- radical as the active state
FAD
dependent on, adopts a uniquely folded configuration at the active site that plays a critical functional role in DNA repair, overview. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. Photolyase utilizes FADH-, not FAD- radical as the active state
FAD
dependent on, adopts a uniquely folded configuration at the active site that plays a critical functional role in DNA repair, overview. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. Photolyase utilizes FADH-, not FAD- radical as the active state
FAD
dependent on, adopts a uniquely folded configuration at the active site that plays a critical functional role in DNA repair, overview. Dynamics of flavin cofactor and its repair photocycles by different classes of photolyases, overview. Photolyase utilizes FADH-, not FAD- radical as the active state. Using femtosecond (fs)-resolved spectroscopy and site-directed mutagenesis, the dynamics of class I PL from Escherichia coli (EcPL) in four redox states are investigated
FAD
enzyme SsPL is an unusual photolyase in that it contains two FAD cofactors. One FAD cofactor is part of the active site of the protein and required for both DNA binding and repair. The second cofactor, the putative accessory chromophore, may play a role as a light-harvesting pigment, it is always present in the fully oxidized FAD state. The active site cycles between FADH-, the fully reduced form required for activity, and FADH radical, the one-electron oxidized or semiquinone form, SsPL is isolated with the active site mainly in the FADHยท state. The accessory FAD does not appear to readily undergo any reduction-oxidation chemistry, and it is always found in the fully oxidized state
FAD
four redox states of FAD are relevant for the various functions of DNA photolyases: fully reduced FADH- required for DNA photorepair, and the two semireduced radical states FAD- radical and FADH radical formed in electron transfer reactions. Absorption spectra of wild-type EcPL and MTHF antenna-free mutant E109A/N378D EcPL, transient absorption kinetics on nano- and microsecond time scales at six characteristic wavelengths, spectral analysis of transient absorption kinetics, overview
FAD
involved in catalysis, cold-adapted DNA photolyase binds a catalytic flavin adenine dinucleotide (FAD) cofactor noncovalently. UV/Vis and fluorescence spectroscopy reveal that the FAD-binding site in this psychrophilic protein is unique compared to meso/thermophilic PLs. FAD-binding pocket of the CpPL model, overview
FAD
reduced anionic flavin adenine dinucleotide (FADH-) is the critical cofactor in DNA photolyase (PL) for the repair of cyclobutane pyrimidine dimers (CPD) in UV-damaged DNA
FAD
steady-state spectra of flavin at various redox states and active-site solvation dynamics in photolyases, overview
FAD
the adenine moiety of FADH- bridges between the electron donating isoalloxazine ring and CPD via two hydrogen bonds, suggesting the presence of electron transfer pathways via adenine
FAD
the enzyme uses a fully reduced flavin, FADH-, cofactor to repair sunlight-induced DNA lesions
FAD
the enzyme uses a fully reduced flavin, FADH-, cofactor to repair sunlight-induced DNA lesions
FAD
the enzyme uses a fully reduced flavin, FADH-, cofactor to repair sunlight-induced DNA lesions
FAD
the enzyme uses a fully reduced flavin, FADH-, cofactor to repair sunlight-induced DNA lesions
FAD
the enzyme uses a fully reduced flavin, FADH-, cofactor to repair sunlight-induced DNA lesions
FADH2
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FADH2
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enzyme contains FADH2 and a second chromophore. Enzyme with a photodecomposed second chromophore retains full activity
FADH2
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purified enzyme contains a stable neutral radical FAD that is not active in dimer repair. Dimer repair observed with the enzyme containing FAD in the radical form at shorter wavelength is probably photoreduction of the radical FAD followed by dimer repair by enzyme-bound FADH2
FADH2
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enzyme contains FAD
FADH2
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enzyme contains FAD
FADH2
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electron donation by excited states of enzyme-bound FADH2 is the mechanism of flavin photosensitized dimer repair by DNA photolyase
FADH2
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purified enzyme contains FAD
FADH2
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catalytic cofactor
FADH2
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computational calculations demonstrate that the localization of the FADH-donor state on the flavin ring enhances the electronic coupling between the flavin and the dimer by permitting shorter electron-transfer pathways to the dimer that have single through-space jumps. Therefore, in photolyase, the photo-excitation itself enhances the electron transfer rate by moving the electron towards the dimer
FADH2
results indicate that both charge recombination of the primary charge separation state FADH-W382 and electron transfer from W359 to W382 occur with time constants below 4 ps, considerably faster than the initial W382-FADH electron-transfer step.
FADH2
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the isoalloxazine ring is sandwiched between a salt bridge comprising an arginine and an aspartate residue
FADH2
the isoalloxazine ring is sandwiched between a salt bridge comprising an arginine and an aspartate residue: R344/D372 and short polypeptide stretches: A377-N378/G381-W382. Another conserved interaction is a hydrogen bond formed between the N5 nitrogen of the isoalloxazine group and a conserved asparagine: N378
FADH2
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the isoalloxazine ring is sandwiched between a salt bridge comprising an arginine and an aspartate residue: R352/D380 and short polypeptide stretches: A385-N386/G389-W390. Another conserved interaction is a hydrogen bond formed between the N5 nitrogen of the isoalloxazine group and a conserved asparagine: N386. Mutagenesis and ultrafast kinetic spectroscopy revealed a consecutive chain of three conserved tryptophan residues with the order: Y469 -(?)- W314- W367- W390- FAD(H)
FADH2
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contains the chromophore FADH2
FADH2
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contains the chromophore FADH2
FADH2
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the catalytic activity of the enzyme requires fully reduced FAD
FADH2
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the photoactivation of FADH- immediately preceding the electron transfer is a key step in the repair mechanism
FADH2
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uses the anionic state of flavin, FADH-,as cofactor
FADH2
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heterogeneous dynamics continuously tune local configurations to optimize photolyase's function through resonance energy transfer from the antenna to the cofactor for energy efficiency and then electron transfer between the cofactor and the substrate for repair of damaged DNA
FADH2
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photoreduction of FADH proceeds along the conserved tryptophan triad W306-W359-W382
flavin
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prosthetic group
flavin
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enzyme contains a stable flavin radical, the one-electron reduction potential of the excited quartet state of the flavin radical must be at least 1.23 V more positive than the ground state
flavin
flavin-mononucleotide (FMN), crystal strucutre analysis reveals the binding of flavin mononucleotide as an antenna chromophore
flavin
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requires fully reduced flavin for photorepair of DNA, full oxidation to FAD is not necessary for biological function, the reaction mechanism involves electron transfer to the substrate from the excited state of the flavin in its fully reduced state FADH- with subsequent electron return within a nanosecond
flavin
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requires fully reduced flavin for photorepair of DNA, full oxidation to FAD is not necessary for biological function, the reaction mechanism involves electron transfer to the substrate from the excited state of the flavin in its fully reduced state FADH- with subsequent electron return within a nanosecond
FMN
increases the light absorption efficiency of the enzyme, direct electron transfer between FMN and the enzyme is not likely to occur. FMN acts as a highly efficient light harvester that gathers light and transfers the energy to FAD
FMN
photolyase can bind next to the natural cofactor 8-hydroxy-5-deazariboflavin also FMN
folate
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folate
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enzyme contains folate
methenyltetrahydrofolate
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methenyltetrahydrofolate
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methenyltetrahydrofolate
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methenyltetrahydrofolate
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the enzyme utilizes the the antenna cofactor to harvest light energy for the repair of thymine dimers in DNA. For this purpose, the enzyme evolved to bind the cofactor and red-shift its absorption maximum by 25 nm
methenyltetrahydrofolate
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contains the chromophore methenyltetrahydrofolate
methenyltetrahydrofolate
is the solar panel or photoantenna of the enzyme
methenyltetrahydrofolate
MTHF, the molecule is bound as an antenna molecule and found in substoichiometric amounts
pterin
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cofactor
pterin
contains not only reduced FAD but also a reduced pterin, or a cofactor with similar properties, as a chromophore
additional information
light-driven blue light flavophotoreceptors all operate from the excited state, whether singlet oxidized (e.g., BLUF and LOV domains) or doublet semiquinone
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additional information
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light-driven blue light flavophotoreceptors all operate from the excited state, whether singlet oxidized (e.g., BLUF and LOV domains) or doublet semiquinone
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additional information
FAD analogues containing either an ethano- or etheno-bridged Ade between the AN1 and AN6 atoms (e-FAD and epsilon-FAD, respectively) are used to reconstitute apo-PL, giving e-PL and epsilon-PL, respectively. The reconstitution yield of e-PL is very poor, suggesting that the hydrophobicity of the ethano group prevents its uptake, while epsilon-PL shows 50% reconstitution yield. The substrate binding constants for epsilon-PL and rPL are identical. epsilon-PL shows a 15% higher steady-state repair yield compared to FAD-reconstituted photolyase (rPL). Evaluation of an epsilon-Ade radical intermediate versus a superexchange mechanism, preparation of apophotolyase (apo-PL) and reconstitution of apo-PL with FAD, e-FAD and epsilon-FAD, overview. Incorporation of the more hydrophobic e-FAD is so inefficient that it can not be made in sufficient quantities to study further. Ligand binding structure analysis
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additional information
recombinant CpPL (rCpPL) binds two different second cofactor molecules, flavin mononucleotide (FMN) when overexpressed and purified from Escherichia coli BL21(DE3) inclusion bodies, and a folate (possibly MTHF) when overexpressed and purified from Escherichia coli Arctic Express (DE3) cells as a His6-tagged protein or in strain BL21-DE3 cells as a maltose-binding-protein fusion protein. CpPL might be somewhat promiscuous in antenna cofactor binding
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