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

IUCrJ

Huang, W.-C.¹  Yamamoto, J.²  Maestre-Reyna, M.³  Tsai, M.-D.⁴ 

[1] Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany;Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan;Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan;LOEWE Center for Synthetic Microbiology, Philipps University Marburg, Hans-Meerwein Strasse 6, Marburg 35032, Germany

关键词: CLASS II CPD PHOTOLYASES;    DNA REPAIR;    DNA DISTORTION;    CYCLOBUTANE PYRIMIDINE DIMER;    CRYSTAL STRUCTURE;   

DOI  :  10.1107/S205225251800996X

学科分类：数学（综合）

来源: International Union of Crystallography

【 摘 要 】

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.

【 授权许可】

CC BY