5ZCW

Structure of the Methanosarcina mazei class II CPD-photolyase in complex with intact, phosphodiester linked, CPD-lesion

Summary for 5ZCW

• Entry DOI: 10.2210/pdb5zcw/pdb
• Descriptor: Deoxyribodipyrimidine photolyase, 5'-D(*AP*TP*CP*GP*GP*CP*(TTD)P*CP*GP*CP*GP*CP*AP*A)-3', 5'-D(*TP*GP*CP*GP*CP*GP*AP*AP*GP*CP*CP*GP*AP*T)-3', ... (7 entities in total)
• Functional Keywords: dna repair, photorepair, cpd, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Methanosarcina mazei (Methanosarcina frisia); More
• Total number of polymer chains: 6
• Total formula weight: 129724.73

Authors

Maestre-Reyna, M.,Bessho, Y. (deposition date: 2018-02-21, release date: 2018-08-22, Last modification date: 2023-11-22)

Primary citation

Maestre-Reyna, M.,Yamamoto, J.,Huang, W.C.,Tsai, M.D.,Essen, L.O.,Bessho, Y.
Twist and turn: a revised structural view on the unpaired bubble of class II CPD photolyase in complex with damaged DNA.
IUCrJ, 5:608-618, 2018

PubMed 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 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.

PubMed: 30224964
DOI: 10.1107/S205225251800996X

Experimental method

X-RAY DIFFRACTION (2.7 Å)