Distinct Z-DNA binding mode of a PKR-like protein kinase containing a Z-DNA binding domain (PKZ)

Abstract

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 (Zα) of PKZ from Carassius auratus (caZαPKZ). The 1.7-Å resolution crystal structure of caZαPKZ:Z-DNA revealed that caZαPKZ shares the overall fold with other Zα, but has discrete structural features that differentiate its DNA binding mode from others. Functional analyses of caZαPKZ and its mutants revealed that caZαPKZ mediates the fastest B-to-Z transition of DNA among Zα, and the minimal interaction for Z-DNA recognition is mediated by three backbone phosphates and six residues of caZαPKZ. Structure-based mutagenesis and B-to-Z transition assays confirmed that Lys56 located in the β-wing contributes to its fast B-to-Z transition kinetics. Investigation of the DNA binding kinetics of caZαPKZ 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 β-wing largely affects fast B-to-Z transition activity by enhancing the DNA binding rate.

The Structure of the Cyprinid herpesvirus 3 ORF112-Zα·Z-DNA Complex Reveals a Mechanism of Nucleic Acids Recognition Conserved with E3L, a Poxvirus Inhibitor of Interferon Response

“…PKZ, which instead of dsRNA-binding domains has two Z␣ domains (11), was shown to phosphorylate eukaryotic initiation factor 2␣ similarly to PKR in response to CpG DNA, but not to poly(IC), a classic dsRNA activator of PKR (13). Previously, we and others solved the crystal structures of the PKZ-Z␣ domain (7,14) and clarified the details of the interaction of PKZ-Z␣ with Z-DNA.…”

Structural studies of RFCCtf18 reveal a novel chromatin recruitment role for Dcc1

“…The results indicated that Dcc1 contains three‐winged helix (WH) domains from residues 182–252, 253–317 and 318–380, which we have called WH1, WH2 and WH3, respectively (Fig C). These WH domains show structural homology to the WH domains from PKZ , cullin‐1 and DsrD , with Z‐scores of 5.7, 7.4 and 4.9, respectively (Fig EV1). WH domains are often involved in DNA binding or mediating protein–protein interactions , suggesting possible functions for this structural feature.…”

NMR Study on the Preferential Binding of the Zα Domain of Human ADAR1 to CG-repeat DNA Duplex

“…[1][2][3] The crystal structures of various ZBPs in complex with 6-base-paired (6-bp) CG-repeat DNA found that the interaction with Z-DNA is mediated by the α3 helix and in the β-hairpin. [4][5][6][7] When the ZBPs produce Z-DNA segments in a genomic DNA, two B-Z junctions at each end of Z-DNA should be formed. A crystal structural study of the Zα domain of human ADAR1 (Zα ADAR1 ) complexed with 15-bp DNA showed that DNA are stabilized at one end in the Z-conformation by Zα ADAR1 proteins, while the other end remains B-DNA.…”