Crystal structure of DNA photolyase from Escherichia coli

Science. 1995 Jun 30;268(5219):1866-72. doi: 10.1126/science.7604260.


Photolyase repairs ultraviolet (UV) damage to DNA by splitting the cyclobutane ring of the major UV photoproduct, the cis, syn-cyclobutane pyrimidine dimer (Pyr <> Pyr). 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 A resolution. The polypeptide chain of 471 amino acids is folded into an amino-terminal alpha/beta 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 A. 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 Pyr <> Pyr dinucleotide, suggesting that the Pyr <> Pyr "flips out" of the helix to fit into this hole, and that electron transfer between the flavin and the Pyr <> Pyr occurs over van der Waals contact distance.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Computer Graphics
  • Crystallography, X-Ray
  • DNA Damage
  • DNA Repair
  • DNA, Bacterial / metabolism
  • Deoxyribodipyrimidine Photo-Lyase / chemistry*
  • Deoxyribodipyrimidine Photo-Lyase / metabolism
  • Electron Transport
  • Escherichia coli / enzymology*
  • Flavin-Adenine Dinucleotide / metabolism
  • Folic Acid / analogs & derivatives
  • Folic Acid / metabolism
  • Hydrogen Bonding
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Folding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Pyrimidine Dimers / metabolism


  • DNA, Bacterial
  • Pyrimidine Dimers
  • Flavin-Adenine Dinucleotide
  • 5,11-methenyltetrahydrohomofolate
  • Folic Acid
  • Deoxyribodipyrimidine Photo-Lyase