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Publication Abstract from PubMed

Double-stranded ribonucleic acid-activated protein kinase (PKR) downregulates translation as a defense mechanism against viral infection. In fish species, PKZ, a PKR-like protein kinase containing left-handed deoxyribonucleic acid (Z-DNA) binding domains, performs a similar role in the antiviral response. To understand the role of PKZ in Z-DNA recognition and innate immune response, we performed structural and functional studies of the Z-DNA binding domain (Zalpha) of PKZ from Carassius auratus (caZalphaPKZ). The 1.7-A resolution crystal structure of caZalphaPKZ:Z-DNA revealed that caZalphaPKZ shares the overall fold with other Zalpha, but has discrete structural features that differentiate its DNA binding mode from others. Functional analyses of caZalphaPKZ and its mutants revealed that caZalphaPKZ mediates the fastest B-to-Z transition of DNA among Zalpha, and the minimal interaction for Z-DNA recognition is mediated by three backbone phosphates and six residues of caZalphaPKZ. Structure-based mutagenesis and B-to-Z transition assays confirmed that Lys56 located in the beta-wing contributes to its fast B-to-Z transition kinetics. Investigation of the DNA binding kinetics of caZalphaPKZ further revealed that the B-to-Z transition rate is positively correlated with the association rate constant. Taking these results together, we conclude that the positive charge in the beta-wing largely affects fast B-to-Z transition activity by enhancing the DNA binding rate.

Distinct Z-DNA binding mode of a PKR-like protein kinase containing a Z-DNA binding domain (PKZ).,Kim D, Hur J, Park K, Bae S, Shin D, Ha SC, Hwang HY, Hohng S, Lee JH, Lee S, Kim YG, Kim KK Nucleic Acids Res. 2014 May 1;42(9):5937-48. doi: 10.1093/nar/gku189. Epub 2014, Mar 20. PMID:24682817^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.