Crystallization and preliminary X-ray crystallographic studies of the Z-DNA-binding domain of a PKR-like kinase (PKZ) in complex with Z-DNA

PKZ, a PKR-like eIF2α kinase, consists of a Z-DNA-specific binding domain (Zα) and an eIF2α kinase domain. The kinase activity of PKZ is modulated by the binding of Zα to Z-DNA. The mechanisms underlying Z-DNA binding and the subsequent stimulation of PKZ raise intriguing questions. Interestingly, the Z-­DNA-binding domain of PKZ from goldfish (Carassius auratus; caZα_PKZ) shows limited sequence homology to other canonical Zα domains, suggesting that it may have a distinct Z-DNA-recognition mode. In this study, the Z-DNA-binding activity and stoichiometry of caZα_PKZ were confirmed using circular dichroism (CD). In addition, preliminary X-ray studies of the caZα_PKZ–Z-­DNA complex are reported as the first step in the determination of its three-dimensional structure. Bacterially expressed recombinant caZα_PKZ was purified and crystallized with Z-DNA at 295 K using the microbatch method. X-ray diffraction data were collected to 1.7 Å resolution with an R_merge of 7.4%. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 55.54, b = 49.93, c = 29.44 Å, β = 96.5°. Structural analysis of caZα_PKZ–Z-­DNA will reveal the binding mode of caZα_PKZ to Z-DNA and its relevance to other Z-DNA-binding proteins.