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

Abstract

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 Z alpha domain of the ZBP-containing protein kinase from Carassius auratus (caZ alpha(PKZ)). We quantitatively determined the binding affinity of caZ alpha(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 caZ alpha(PKZ) and B-DNA can be used as molecular ruler, to measure the degree to which DNA transitions to the Z isoform.