Structure of a double-stranded DNA (64) photoproduct in complex with the 64M-5 antibody Fab

DNA photoproducts with (64) pyrimidinepyrimidone adducts formed by ultraviolet radiation have been implicated in mutagenesis and cancer. The crystal structure of double-stranded DNA containing the (64) photoproduct in complex with the anti-(64)-photoproduct antibody 64M-5 Fab was determined at 2.5 angstrom resolution. The T(64)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(64)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(64)T segment are kinked by 87 degrees. The 64M-5 Fab recognizes the T(64)T segment dissociated from the complementary strand, indicating that the (64) 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 (64) photolyase and nucleotide-excision repair protein DDB1DDB2. 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 (64) photoproducts recognized by proteins.