Crystal structure of Vibrio cholerae (6-4) photolyase with DNA binding region

Photolyases (PLs) are the enzymes that reverse UV-Induced DNA damages by using blue-light as an energy source. Among those photolyases (6-4) PLs are the enzymes that repair (6-4) lesioned photoproduct. Here, we determined Vibrio cholerae ( Vc ) crystal structure of (6-4) PL at 2.5 Å resolution. Our high-resolution structure revealed that the presence of two well-known cofactors, flavin adenine dinucleotide (FAD) and or 6,7-dimethyl 8-ribityl-lumazin (DMRL), stably interact with an α -helical and an α / β and domains, respectively. Additionally, it has also a third cofactor with distinct electron clouds corresponding to [4Fe-4S] cluster. Asp106 makes a hydrogen bond with the water and DMRL, which indicates further stabilization of the photoantenna DMRL to Vc (6-4) PL. Further analysis of Vc (6-4) PL structure revealed a possible region responsible for the DNA binding. The region located between residues 478-484 may binds the lesioned DNA and Arg483 forms a salt bridge with DNA to stabilize further Vc (6-4) PL with its substrate. Our comparative analysis revealed that DNA lesion could not bind to the Vc (6-4) PL in a similar fashion to the Dm (6-4) PL without a significant conformational change in the protein. The 23 rd helix of the bacterial (6-4) PLs seems to have a remarkable plasticity and conformational changes facilitate the DNA binding.

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