Structures of the antibody 64M-5 Fab and its complex with dT(6–4)T indicate induced-fit and high-affinity mechanisms

DNA photoproducts with (6–4) pyrimidine–pyrimidone adducts produced by ultraviolet light are mutagenic and carcinogenic. The crystal structures of the anti-(6–4) photoproduct antibody 64M-5 Fab and of its complex with dT(6–4)T were determined at 2.5 and 2.0 Å resolution, respectively. A comparison between the dT(6–4)T-liganded and unliganded structures indicates that the side chain of His93L is greatly rotated and shifted on binding to dT(6–4)T, leading to the formation of an electrostatic interaction with the phosphate moiety of dT(6–4)T, which shows a remarkable induced fit. Based on a comparison of the dT(6–4)T-liganded structures of the 64M-5 and 64M-2 Fabs, the electrostatic interaction between the side chain of His93L in 64M-5 and the phosphate moiety of dT(6–4)T is lost for Leu93L in 64M-2, while Arg90L in 64M-5 instead of Gln90L in 64M-2 stabilizes the conformation of complementarity-determining region (CDR) L3. These differences contribute to the higher affinity of 64M-5 for dT(6–4)T compared with that of 64M-2.