DNA photoreactivating enzyme from the cyanobacterium Anacystis nidulans.

Eker, A.P.M.; Kooiman, P.; Hessels, J.K.C.; Yasui, Akira

doi:10.1016/s0021-9258(19)39031-3

Cited by 157 publications

(62 citation statements)

References 39 publications

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“…After the 8-HDF uptake, the loop translocation induced by the through-space interaction (π-π or CH-π) between Phe41 in Xl64 or Ile50 in Dm64 and the deazaisoalloxazine ring takes place to close the entrance of the binding site, to ensure the apolar circumstance of 8-HDF. Noteworthy, the amino acid residues important for the 8-HDF uptake and function are well conserved in Anacystis nidulans CPD photolyase, which is also known as an 8-HDF binding protein [23] (Fig. S10).…”

Section: Dna Repair Of Xl64 Proteins Bearing 8-hdfmentioning

confidence: 99%

“…Contrary to the exclusively conserved catalytic chromophore, several types of the auxiliary chromophore are known to function as the light-harvesting chromophore (LHC) in PLs. The examples are 5,10-methenytetrahydrofolate (MTHF) in bacterial PL [17], FAD or flavin mononucleotide (FMN) in thermophilic bacterial PLs [20,21], 6,7-dimethyl-8-ribityllumazine (DMRL) in bacterial PLs [19], and 8-hydroxy-7,8-didemethyl-5-deazariboflavin (8-HDF) in class II CPD-PL [22], class I PL in cyanobacteria [23], algae cryptochrome/photolyase families (CPF) [18,24], and insect (6-4)PL [24]. Regardless of the chemical structures of LHCs, their fluorescence overlaps the FADHabsorption, leading to the enhanced light-driven DNA repair via FRET.…”

Section: Introductionmentioning

confidence: 99%

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Key interactions with deazariboflavin cofactor for light-driven energy transfer in Xenopus (6–4) photolyase

Morimoto

Hosokawa

Miyamoto

et al. 2021

Photochem Photobiol Sci

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Photolyases are flavoenzymes responsible for light-driven repair of carcinogenic crosslinks formed in DNA by UV exposure. They possess two non-covalently bound chromophores: flavin adenine dinucleotide (FAD) as a catalytic center and an auxiliary antenna chromophore that harvests photons and transfers solar energy to the catalytic center. Although the energy transfer reaction has been characterized by time-resolved spectroscopy, it is strikingly important to understand how well natural biological systems organize the chromophores for the efficient energy transfer. Here, we comprehensively characterized the binding of 8-hydroxy-7,8-didemethyl-5-deazariboflavin (8-HDF) to Xenopus (6–4) photolyase. In silico simulations indicated that a hydrophobic amino acid residue located at the entrance of the binding site dominates translocation of a loop upon binding of 8-HDF, and a mutation of this residue caused dysfunction of the efficient energy transfer in the DNA repair reaction. Mutational analyses of the protein combined with modification of the chromophore suggested that Coulombic interactions between positively charged residues in the protein and the phenoxide moiety in 8-HDF play a key role in accommodation of 8-HDF in the proper direction. This study provides a clear evidence that Xenopus (6–4) photolyase can utilize 8-HDF as the light-harvesting chromophore. The obtained new insights into binding of the natural antenna molecule will be helpful for the development of artificial light-harvesting chromophores and future characterization of the energy transfer in (6–4) photolyase by spectroscopic studies.

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Section: Dna Repair Of Xl64 Proteins Bearing 8-hdfmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Key interactions with deazariboflavin cofactor for light-driven energy transfer in Xenopus (6–4) photolyase

Morimoto

Hosokawa

Miyamoto

et al. 2021

Photochem Photobiol Sci

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“…The buffers were made in MilliQ-filtered, deionized water. Photolyase, obtained from Anacystis nidulans (Eker et al, 1990;Tamada et al, 1997), was added to a final concentration of 0.12 ng/l in the reaction buffer.…”

Section: Sample Preparationmentioning

confidence: 99%

Direct Visualization of Dynamic Protein-DNA Interactions with a Dedicated Atomic Force Microscope

Noort

Werf

Eker

et al. 1998

Biophysical Journal

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Photolyase DNA interactions and the annealing of restriction fragment ends are directly visualized with the atomic force microscope (AFM). To be able to interact with proteins, DNA must be loosely bound to the surface. When MgCl2 is used to immobilize DNA to mica, DNA is attached to the surface at distinct sites. The pieces of DNA in between are free to move over the surface and are available for protein interaction. After implementation of a number of instrumental improvements, the molecules can be visualized routinely, under physiological conditions and with molecular resolution. Images are acquired reproducibly without visible damage for at least 30 min, at a scan rate of 2 x 2 microm2/min and a root mean square noise of less than 0.2 nm. Nonspecific photolyase DNA complexes were visualized, showing association, dissociation, and movement of photolyase over the DNA. The latter result suggests a sliding mechanism by which photolyase can scan DNA for damaged sites. The experiments illustrate the potential that AFM presents for modern molecular biology.

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“…The digested DNA was separated on an agarose gel and the 1150 and 735 bp fragments, from the cDNA sequence of the human XPB gene, were isolated by electroelution. DNA photolyase from Anacystis nidulans was purified to apparent homogeneity as described previously (6). As a substrate for photolyase 1150 bp DNA was irradiated with~3800 J/m 2 UV (254 nm), introducing damage, mainly pyrimidine dimers, at random sites.…”

Section: Sample Preparationmentioning

confidence: 99%

DNA bending by photolyase in specific and non-specific complexes studied by atomic force microscopy

Noort

Orsini

Eker³

et al. 1999

Nucleic Acids Research

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Specific and non-specific complexes of DNA and photolyase are visualised by atomic force microscopy. As a substrate for photolyase a 1150 bp DNA restriction fragment was UV-irradiated to produce damaged sites at random positions. Comparison with a 735 bp undamaged DNA fragment made it possible to separate populations of specific and non-specific photolyase complexes on the 1150 bp fragment, relieving the need for highly defined substrates. Thus it was possible to compare DNA bending for specific and non-specific interactions. Non-specific complexes show no significant bending but increased rigidity compared to naked DNA, whereas specific complexes show DNA bending of on average 36 degrees and higher flexibility. A model obtained by docking shows that photolyase can accommodate a 36 degrees bent DNA in the vicinity of the active site.

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DNA photoreactivating enzyme from the cyanobacterium Anacystis nidulans.

Cited by 157 publications

References 39 publications

Key interactions with deazariboflavin cofactor for light-driven energy transfer in Xenopus (6–4) photolyase

Key interactions with deazariboflavin cofactor for light-driven energy transfer in Xenopus (6–4) photolyase

Direct Visualization of Dynamic Protein-DNA Interactions with a Dedicated Atomic Force Microscope

DNA bending by photolyase in specific and non-specific complexes studied by atomic force microscopy

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