How can a pinwheel-shaped protein domain bend DNA back on itself?

Details

DNA gyrase is unique among enzymes in its ability to actively introduce negative supercoils into DNA. This function is mediated in part by the C-terminal domain of its A subunit, called the GyrA CTD.

In this structural and biochemical study, the researchers determined the crystal structure of this approximately 35-kDa domain at 1.75-Å resolution. Unexpectedly, it has an unusual fold that they named a beta-pinwheel. Its overall shape resembles a beta-propeller, but its blades have a previously unobserved topology.

A large, conserved basic patch on the domain’s outer edge suggests a likely site for binding and bending DNA. Fluorescence resonance energy transfer-based assays showed that the GyrA CTD can bend DNA by at least 180 degrees over a 40-bp region.

The researchers also found, unexpectedly, that the C-terminal domain of the topoisomerase IV A subunit bends DNA, despite sharing only limited sequence homology with the GyrA CTD.

Together, these findings provide a physical explanation for DNA gyrase’s ability to constrain a positive superhelical DNA wrap. They also suggest that the particular substrate preferences of topoisomerase IV might be dictated in part by the function of this domain.