IUCrJ (Sep 2018)

Twist and turn: a revised structural view on the unpaired bubble of class II CPD photolyase in complex with damaged DNA

  • Manuel Maestre-Reyna,
  • Junpei Yamamoto,
  • Wei-Cheng Huang,
  • Ming-Daw Tsai,
  • Lars-Oliver Essen,
  • Yoshitaka Bessho

Journal volume & issue
Vol. 5, no. 5
pp. 608 – 618


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Cyclobutane pyrimidine dimer (CPD) photolyases harness the energy of blue light to repair UV-induced DNA CPDs. Upon binding, CPD photolyases cause the photodamage to flip out of the duplex DNA and into the catalytic site of the enzyme. This process, called base-flipping, induces a kink in the DNA, as well as an unpaired bubble, which are stabilized by a network of protein–nucleic acid interactions. Previously, several co-crystal structures have been reported in which the binding mode of CPD photolyases has been studied in detail. However, in all cases the internucleoside linkage of the photodamage site was a chemically synthesized formacetal analogue and not the natural phosphodiester. Here, the first crystal structure and conformational analysis via molecular-dynamics simulations of a class II CPD photolyase in complex with photodamaged DNA that contains a natural cyclobutane pyrimidine dimer with an intra-lesion phosphodiester linkage are presented. It is concluded that a highly conserved bubble-intruding region (BIR) mediates stabilization of the open form of CPD DNA when complexed with class II CPD photolyases.