Crystal structure of the 64M-2 antibody Fab fragment in complex with a DNAdT(6-4)T photoproduct formed by ultraviolet radiation

DNA photoproducts with (6-4) pyrimidine-pyrimidone adducts formed by ultrav iolet radiation are implicated in mutagenesis and cancer, particularly skin cancer. The crystal structure of the Fab fragment of the murine 64M-2 anti body specific to DNA T(6-4)T photoproducts is determined as a complex with dT(6-4)T, a (6-4) pyrimidine-pyrimidone photodimer of dTpT, at 2.4 Angstrom resolution to a crystallographic R-factor of 0.199 and an R-free value of 0.279. The 64M-2 Fab molecule is in an extended arrangement with an elbow a ngle of 174 degrees, and its five complementarity-determining regions, exce pt L2, are involved in the ligand binding. The bound dT(6-4)T ligand adopti ng a ring structure with (6-4) linked 5' thymine-3' pyrimidone bases is ful ly accommodated in an antigen-binding pocket of about 15 Angstrom x 10 Angs trom. The 5'-thymine and 3'-pyrimidone bases are in half-chair and planar c onformations, respectively, and are nearly perpendicular to each other. The 5'-thymine base is hydrogen-bonded to Arg95H and Ser96H, and is in van der Waals contact with Tyr100iH. The S'-pyrimidone base is hydrogen-bonded to His35H, and is in contact with Trp33H. Three water molecules are located at the interface between the bases and the Fab residues. Hydrogen bonds invol ving these water molecules also contribute to Fab recognition of the dT(6-4 )T bases. The sugar-phosphate backbone connecting the bases is surrounded b y residues His27dL, Tyr32L, Ser92L, Trp33H, and Scr58H, but is not hydrogen -bonded to these residues. (C) 2000 Academic Press.