Solution structure of the Z-DNA binding domain of PKR-like protein kinase from Carassius auratus and quantitative analyses of the intermediate complex during B–Z transition

Z-DNA binding proteins (ZBPs) play important roles in RNA editing, innate immune response and viral infection. Structural and biophysical studies show that ZBPs initially form an intermediate complex with B-DNA for B–Z conversion. However, a comprehensive understanding of the mechanism of Z-DNA binding and B–Z transition is still lacking, due to the absence of structural information on the intermediate complex. Here, we report the solution structure of the Zα domain of the ZBP-containing protein kinase from Carassius auratus (caZα(PKZ)). We quantitatively determined the binding affinity of caZα(PKZ) for both B-DNA and Z-DNA and characterized its B–Z transition activity, which is modulated by varying the salt concentration. Our results suggest that the intermediate complex formed by caZα(PKZ) and B-DNA can be used as molecular ruler, to measure the degree to which DNA transitions to the Z isoform.