title: Eukaryotic class II cyclobutane pyrimidine dimer photolyase structure reveals basis for improved ultraviolet tolerance in plants.
abstract: Ozone depletion increases terrestrial solar ultraviolet B (UV-B; 280-315 nm) radiation, intensifying the risks plants face from DNA damage, especially covalent cyclobutane pyrimidine dimers (CPD). Without efficient repair, UV-B destroys genetic integrity, but plant breeding creates rice cultivars with more robust photolyase (PHR) DNA repair activity as an environmental adaptation. So improved strains of Oryza sativa (rice), the staple food for Asia, have expanded rice cultivation worldwide. Efficient light-driven PHR enzymes restore normal pyrimidines to UV-damaged DNA by using blue light via flavin adenine dinucleotide to break pyrimidine dimers. Eukaryotes duplicated the photolyase gene, producing PHRs that gained functions and adopted activities that are distinct from those of prokaryotic PHRs yet are incompletely understood. Many multicellular organisms have two types of PHR: (6-4) PHR, which structurally resembles bacterial CPD PHRs but recognizes different substrates, and Class II CPD PHR, which is remarkably dissimilar in sequence from bacterial PHRs despite their common substrate. To understand the enigmatic DNA repair mechanisms of PHRs in eukaryotic cells, we determined the first crystal structure of a eukaryotic Class II CPD PHR from the rice cultivar Sasanishiki. Our 1.7 Å resolution PHR structure reveals structure-activity relationships in Class II PHRs and tuning for enhanced UV tolerance in plants. Structural comparisons with prokaryotic Class I CPD PHRs identified differences in the binding site for UV-damaged DNA substrate. Convergent evolution of both flavin hydrogen bonding and a Trp electron transfer pathway establish these as critical functional features for PHRs. These results provide a paradigm for light-dependent DNA repair in higher organisms.
authors.affiliation: Graduate School of Engineering Science, Osaka University, Machikaneyama-cho 1-3, Toyonaka, Osaka 560-8531, Japan.
authors.forename: Kenichi
authors.initials: K
authors.lastname: Hitomi
authors.forename: Andrew S
authors.initials: AS
authors.lastname: Arvai
authors.forename: Junpei
authors.initials: J
authors.lastname: Yamamoto
authors.forename: Chiharu
authors.initials: C
authors.lastname: Hitomi
authors.forename: Mika
authors.initials: M
authors.lastname: Teranishi
authors.forename: Tokuhisa
authors.initials: T
authors.lastname: Hirouchi
authors.forename: Kazuo
authors.initials: K
authors.lastname: Yamamoto
authors.forename: Shigenori
authors.initials: S
authors.lastname: Iwai
authors.forename: John A
authors.initials: JA
authors.lastname: Tainer
authors.forename: Jun
authors.initials: J
authors.lastname: Hidema
authors.forename: Elizabeth D
authors.initials: ED
authors.lastname: Getzoff
mesh_terms: D020816:Amino Acid Motifs; D001483:Base Sequence; D001665:Binding Sites; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry; D004260:DNA Repair; D004255:Deoxyribodipyrimidine Photo-Lyase / Q000737:chemistry* / Q000235:genetics; D024202:Electrophoretic Mobility Shift Assay; D005182:Flavin-Adenine Dinucleotide / Q000737:chemistry; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012275:Oryza / Q000201:enzymology* / Q000235:genetics; D010766:Phosphorylation; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry* / Q000235:genetics; D011110:Polymorphism, Genetic; D011485:Protein Binding; D040681:Structural Homology, Protein; D013499:Surface Properties; D014466:Ultraviolet Rays
chemical_list: D010940:Plant Proteins; D005182:Flavin-Adenine Dinucleotide; D004247:DNA; D004255:Deoxyribodipyrimidine Photo-Lyase