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

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

doi:10.1107/s205225251800996x

Abstract

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.

Highlights

DNA photolyases are ancient and ubiquitous flavin adenine dinucleotide (FAD)-containing enzymes (Essen & Klar, 2006) which harness the energy of blue light to repair UV-induced DNA lesions in a sequence-independent manner
The crystal structure of the MmCPDII complex containing native Cyclobutane pyrimidine dimer (CPD), i.e. presenting a phosphodiester linkage within the CPD moiety, here designated PDM (PDB entry 5zcw) was determined from crystals belonging to space group P212121, the same crystal form as that obtained for its formacetal linkage-containing equivalent (FDM; PDB entry 2xrz), but with limited isomorphism owing to changes in unit-cell parameters of up to 2 A
Both crystal structures comprise two MmCPDII–CPD DNA complexes per asymmetric unit (Supplementary Fig. S2), with that corresponding to protein chain A showing better defined DNA termini (Fig. 1)

Summary

Introduction

DNA photolyases are ancient and ubiquitous flavin adenine dinucleotide (FAD)-containing enzymes (Essen & Klar, 2006) which harness the energy of blue light to repair UV-induced DNA lesions in a sequence-independent manner. They constitute the oldest and best conserved DNA-repair pathway in any biological system (Mei & Dvornyk, 2015). DNA photolyases can be functionally divided into (6–4) and CPD photolyases (Lucas-Lledo & Lynch, 2009). Cryptochromes can function as magnetoreceptors by lightinduced formation of magnetosensitive radical pairs (Ritz et al, 2000)

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Results

Conclusion