title: Structure of a double-stranded DNA (6-4) photoproduct in complex with the 64M-5 antibody Fab.
abstract: DNA photoproducts with (6-4) pyrimidine-pyrimidone adducts formed by ultraviolet radiation have been implicated in mutagenesis and cancer. The crystal structure of double-stranded DNA containing the (6-4) photoproduct in complex with the anti-(6-4)-photoproduct antibody 64M-5 Fab was determined at 2.5 Å resolution. The T(6-4)T segment and the 5'-side adjacent adenosine are flipped out of the duplex and are accommodated in the concave antigen-binding pocket composed of six complementarity-determining regions (CDRs). A loop comprised of CDR L1 residues is inserted between the flipped-out T(6-4)T segment and the complementary DNA. The separation of strands by the insertion of the loop facilitates extensive and specific recognition of the photoproduct. The DNA helices flanking the T(6-4)T segment are kinked by 87°. The 64M-5 Fab recognizes the T(6-4)T segment dissociated from the complementary strand, indicating that the (6-4) photoproduct can be detected in double-stranded DNA as well as in single-stranded DNA using the 64M-5 antibody. The structure and recognition mode of the 64M-5 antibody were compared with those of the DNA (6-4) photolyase and nucleotide-excision repair protein DDB1-DDB2. These proteins have distinctive binding-site structures that are appropriate for their functions, and the flipping out of the photolesion and the kinking of the DNA are common to mutagenic (6-4) photoproducts recognized by proteins.
authors.affiliation: School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan. h-yokoya@u-shizuoka-ken.ac.jp
authors.forename: Hideshi
authors.initials: H
authors.lastname: Yokoyama
authors.forename: Ryuta
authors.initials: R
authors.lastname: Mizutani
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Satow
mesh_terms: D000915:Antibody Affinity; D022801:Complementarity Determining Regions / Q000737:chemistry; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000528:radiation effects; D018076:DNA, Complementary / Q000737:chemistry; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000528:radiation effects; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D011740:Pyrimidine Dimers / Q000737:chemistry* / Q000276:immunology; D014466:Ultraviolet Rays
chemical_list: D022801:Complementarity Determining Regions; D018076:DNA, Complementary; D004277:DNA, Single-Stranded; D007140:Immunoglobulin Fab Fragments; D011740:Pyrimidine Dimers; C058406:pyrimidine-pyrimidone dimer; D004247:DNA
keywords: DNA (6–4) photoproduct; antibodies; antigen-binding fragment; nucleotide flipping; ultraviolet light