title: 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.
authors.affiliation: Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea.
authors.forename: Doyoun
authors.initials: D
authors.lastname: Kim
authors.affiliation: Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea.
authors.forename: Jeonghwan
authors.initials: J
authors.lastname: Hur
authors.affiliation: Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea.
authors.forename: Kwangsoo
authors.initials: K
authors.lastname: Park
authors.affiliation: Department of Physics and Astronomy, Seoul National University, Seoul 151-747, Korea National Center for Creative Research Initiatives, Seoul National University, Seoul 151-747, Korea.
authors.forename: Sangsu
authors.initials: S
authors.lastname: Bae
authors.affiliation: Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Korea.
authors.forename: Donghyuk
authors.initials: D
authors.lastname: Shin
authors.affiliation: Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Korea.
authors.forename: Sung Chul
authors.initials: SC
authors.lastname: Ha
authors.affiliation: Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea.
authors.forename: Hye-Yeon
authors.initials: HY
authors.lastname: Hwang
authors.affiliation: Department of Physics and Astronomy, Seoul National University, Seoul 151-747, Korea National Center for Creative Research Initiatives, Seoul National University, Seoul 151-747, Korea Department of Biophysics and Chemical Biology, Seoul National University, Seoul 151-747, Korea.
authors.forename: Sungchul
authors.initials: S
authors.lastname: Hohng
authors.affiliation: Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongnam 660-701, Korea.
authors.forename: Joon-Hwa
authors.initials: JH
authors.lastname: Lee
authors.affiliation: Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Korea.
authors.forename: Sangho
authors.initials: S
authors.lastname: Lee
authors.affiliation: Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea kyeongkyu@skku.edu.
authors.forename: Yang-Gyun
authors.initials: YG
authors.lastname: Kim
authors.affiliation: Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea kyeongkyu@skku.edu.
authors.forename: Kyeong Kyu
authors.initials: KK
authors.lastname: Kim
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D043542:DNA, Z-Form / Q000737:chemistry*; D029941:Fish Proteins / Q000737:chemistry*; D006054:Goldfish; D006860:Hydrogen Bonding; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D012965:Sodium Chloride / Q000737:chemistry; D019892:eIF-2 Kinase / Q000737:chemistry*
chemical_list: D043542:DNA, Z-Form; D029941:Fish Proteins; D012965:Sodium Chloride; D019892:eIF-2 Kinase