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Figure 1
Overall fold of MmCPDII in complex with double-stranded DNA containing a native cyclobutane pyrimidine dimer (CPD). (a) View of the overall complex, with the two subdomains in blue (N-terminal) and green (C-terminal). The DNA is shown as a double-stranded cartoon, while the oxidized FAD cofactor (yellow) and the CPD damage (green) are shown as stick models. (b) Differences in the domain-linker region (grey) in the PDM structure (PDB entry 5zcw) versus the FDM structure (PDB entry 2xrz). (c) DNA geometry distortions as a result of photolyase binding. Double strands are shown in green (PDM), pale blue (FDM) and black (A. nidulans class I CPD photolyase; AnCPDI). For orientation purposes, the outline of the MmCPDII structure is shown in pale green in the background. The side view (left) shows the kink angle, i.e. the sharp bend in the DNA resulting from CPD flipping and partial unstacking of the complementary adenines. Here, kink angles were calculated from the vector products of the 5′ versus 3′ arms of each chain. The top view (right) shows the dislocation of the 3′ arm in class II CPD photolyase (green, PDM; pale blue, FDM) when compared with class I (black, AnCPDI). Dislocation angles were calculated by superposing the 5′ arms of all three molecules, followed by determining the vector products between either the PDM or FDM 3′ arm and the AnCPDI 3′ arm.

IUCrJ
Volume 5| Part 5| September 2018| Pages 608-618
ISSN: 2052-2525
https://doi.org/10.1107/S205225251800996X