title: 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 Zα domain of the ZBP-containing protein kinase from Carassius auratus(caZαPKZ). We quantitatively determined the binding affinity of caZαPKZ 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 caZαPKZ and B-DNA can be used as molecular ruler, to measure the degree to which DNA transitions to the Z isoform.
authors.affiliation: Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Republic of Korea.
authors.forename: Ae-Ree
authors.initials: AR
authors.lastname: Lee
authors.affiliation: Division of Liberal Arts and Sciences and Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea.
authors.forename: Chin-Ju
authors.initials: CJ
authors.lastname: Park
authors.affiliation: Division of Magnetic Resonance, KBSI, Chungbuk 28119, Republic of Korea.
authors.forename: Hae-Kap
authors.initials: HK
authors.lastname: Cheong
authors.affiliation: Division of Magnetic Resonance, KBSI, Chungbuk 28119, Republic of Korea.
authors.forename: Kyoung-Seok
authors.initials: KS
authors.lastname: Ryu
authors.affiliation: Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Republic of Korea Division of Magnetic Resonance, KBSI, Chungbuk 28119, Republic of Korea.
authors.forename: Jin-Wan
authors.initials: JW
authors.lastname: Park
authors.affiliation: Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Republic of Korea.
authors.forename: Mun-Young
authors.initials: MY
authors.lastname: Kwon
authors.affiliation: Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.
authors.forename: Janghyun
authors.initials: J
authors.lastname: Lee
authors.affiliation: Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Gyeonggi 16419, Republic of Korea.
authors.forename: Kyeong Kyu
authors.initials: KK
authors.lastname: Kim
authors.affiliation: Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.
authors.forename: Byong-Seok
authors.initials: BS
authors.lastname: Choi
authors.affiliation: Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Republic of Korea joonhwa@gnu.ac.kr.
authors.forename: Joon-Hwa
authors.initials: JH
authors.lastname: Lee
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D003001:Cloning, Molecular; D059371:DNA, B-Form / Q000737:chemistry* / Q000378:metabolism; D043542:DNA, Z-Form / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029941:Fish Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D006054:Goldfish / Q000378:metabolism*; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D011494:Protein Kinases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D012965:Sodium Chloride / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D059371:DNA, B-Form; D043542:DNA, Z-Form; D004268:DNA-Binding Proteins; D029941:Fish Proteins; D011994:Recombinant Proteins; D012965:Sodium Chloride; D011494:Protein Kinases