Crystal Structure of DNA Photolyase from Escherichia Coli

Photolyase repairs ultraviolet (UV) damage to DNA by splitting the cyclobutane ring of the major UV photoproduct, the cis,syn-cyclobutane pyrimidine dimer (PyrPyr). The reaction is initiated by blue light and proceeds through long-range energy transfer, single electron transfer, and enzyme catalysis by a radical mechanism. The three-dimensional crystallographic structure of DNA photolyase from Escherichia coli is presented and the atomic model was refined to an R value of 0.172 at 2.3 $\AA$ resolution. The polypeptide chain of 471 amino acids is folded into an amino-terminal α/β domain resembling dinucleotide binding domains and a carboxyl-terminal helical domain; a loop of 72 residues connects the domains. The light-harvesting cofactor 5,10-methenyltetrahydrofolylpolyglutamate (MTHF) binds in a cleft between the two domains. Energy transfer from MTHF to the catalytic cofactor flavin adenine dinucleotide (FAD) occurs over a distance of 16.8 $\AA$. The FAD adopts a U-shaped conformation between two helix clusters in the center of the helical domain and is accessible through a hole in the surface of this domain. Dimensions and polarity of the hole match those of a PyrPyr dinucleotide, suggesting that the PyrPyr "flips out" of the helix to fit into this hole, and that electron transfer between the flavin and the PyrPyr occurs over van der Waals contact distance.