Structural comparison study of (6-4) photolyase from Vibrio cholerae

Upon Ultraviolet (UV) irradiation to the DNA, pyrimidine dimers are formed. These mutagenic lesions are either in form of cyclobutene pyrimidine dimers (CPD) or (6-4) photoproducts ((6-4) PPs). Photolyases (PLs) are DNA repair enzymes that use blue light energy to catalyze pyrimidine dimers back to their original state. PLs are named after their specific substrates and their repair functions. (6-4) PLs repair (6-4) PPs with the help of catalytic cofactor flavin adenine dinucleotide (FAD) and an additional antenna chromophore. Bacterial (6-4) PLs contain another cofactor called [4Fe-4S] cluster with an unknown function. In this study, the crystal structure of (6-4) photolyase from Vibrio cholerae (O1 bivar Tor str. N16961) (Vc) has been identified at 2.5 Å resolution. The presence and location of FAD, 6,7-dimethyl-8-ribityllumazine (DMRL), and [4Fe-4S] cofactors were shown by the electron clouds. Their interactions with the Vc(6-4) PL were investigated with the comparison of other structurally available bacterial (6-4) PLs and Drosophila melanogaster (Dm) (6-4) PL. The comparison revealed a conserved water molecule that might be stabilizing the DMRL in bacterial PLs, which makes tighter interaction in Vc(6- 4) PL. In a conserved motif located at the catalytic domain, a different conformation was observed between Vc(6-4) PL and Dm(6-4) PL residue. A disordered region in the Vc(6- 4) PL was observed and suggested as a DNA binding site. A structural comparison with Dm(6-4) PL revealed that Vc(6-4) PL has two additional helixes in C-terminal. Further computational studies suggest either DNA binds to Vc(6-4) PL in a different manner than Dm(6-4) PL or Vc(6-4) PL might be subjected to a conformational change upon DNA binding.