title: Structural Changes of the Active Center during the Photoactivation of Xenopus (6-4) Photolyase.
abstract: Photolyases (PHRs) repair the UV-induced photoproducts, cyclobutane pyrimidine dimer (CPD) or pyrimidine-pyrimidone (6-4) photoproduct [(6-4) PP], restoring normal bases to maintain genetic integrity. CPD and (6-4) PP are repaired by substrate-specific PHRs, CPD PHR and (6-4) PHR, respectively. Flavin adenine dinucleotide (FAD) is the chromophore of both PHRs, and the resting oxidized form (FAD(ox)), at least under in vitro purified conditions, is first photoconverted to the neutral semiquinoid radical (FADH(•)) form, followed by photoconversion into the enzymatically active fully reduced (FADH(-)) form. Previously, we reported light-induced difference Fourier transform infrared (FTIR) spectra corresponding to the photoactivation process of Xenopus (6-4) PHR. Spectral differences between the absence and presence of (6-4) PP were observed in the photoactivation process. To identify the FTIR signals where these differences appeared, we compared the FTIR spectra of photoactivation (i) in the presence and absence of (6-4) PP, (ii) of (13)C labeling, (15)N labeling, and [(14)N]His/(15)N labeling, and (iii) of H354A and H358A mutants. We successfully assigned the vibrational bands for (6-4) PP, the α-helix and neutral His residue(s). In particular, we assigned three bands to the C ═ O groups of (6-4) PP in the three different redox states of FAD. Furthermore, the changed hydrogen bonding environments of C ═ O groups of (6-4) PP suggested restructuring of the binding pocket of the DNA lesion in the process of photoactivation.
authors.affiliation: Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.
authors.forename: Daichi
authors.initials: D
authors.lastname: Yamada
authors.affiliation: Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan.
authors.forename: Junpei
authors.initials: J
authors.lastname: Yamamoto
authors.affiliation: Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Iwata
authors.affiliation: Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States.|Life Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.
authors.forename: Kenichi
authors.initials: K
authors.lastname: Hitomi
authors.affiliation: Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States.
authors.forename: Elizabeth D
authors.initials: ED
authors.lastname: Getzoff
authors.affiliation: Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan.
authors.forename: Shigenori
authors.initials: S
authors.lastname: Iwai
authors.affiliation: Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.
authors.forename: Hideki
authors.initials: H
authors.lastname: Kandori
mesh_terms: D019943:Amino Acid Substitution; D000818:Animals; D020134:Catalytic Domain; D004255:Deoxyribodipyrimidine Photo-Lyase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D005182:Flavin-Adenine Dinucleotide / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020125:Mutation, Missense; D011740:Pyrimidine Dimers / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D029867:Xenopus Proteins / Q000737:chemistry* / Q000235:genetics / Q000276:immunology; D014982:Xenopus laevis
chemical_list: D011740:Pyrimidine Dimers; D029867:Xenopus Proteins; D005182:Flavin-Adenine Dinucleotide; D004255:Deoxyribodipyrimidine Photo-Lyase