title: NMR spectroscopic elucidation of the B-Z transition of a DNA double helix induced by the Z alpha domain of human ADAR1.
abstract: The human RNA editing enzyme ADAR1 (double-stranded RNA deaminase I) deaminates adenine in pre-mRNA to yield inosine, which codes as guanine. ADAR1 has two left-handed Z-DNA binding domains, Z alpha and Z beta, at its NH(2)-terminus and preferentially binds Z-DNA, rather than B-DNA, with high binding affinity. The cocrystal structure of Z alpha(ADAR1) complexed to Z-DNA showed that one monomeric Z alpha(ADAR1) domain binds to one strand of double-stranded DNA and a second Z alpha(ADAR1) monomer binds to the opposite strand with 2-fold symmetry with respect to DNA helical axis. It remains unclear how Z alpha(ADAR1) protein specifically recognizes Z-DNA sequence in a sea of B-DNA to produce the stable Z alpha(ADAR1)-Z-DNA complex during the B-Z transition induced by Z alpha(ADAR1). In order to characterize the molecular recognition of Z-DNA by Z alpha(ADAR1), we performed circular dichroism (CD) and NMR experiments with complexes of Zalpha(ADAR1) bound to d(CGCGCG)(2) (referred to as CG6) produced at a variety of protein-to-DNA molar ratios. From this study, we identified the intermediate states of the CG6-Z alpha(ADAR1) complex and calculated their relative populations as a function of the Z alpha(ADAR1) concentration. These findings support an active B-Z transition mechanism in which the Z alpha(ADAR1) protein first binds to B-DNA and then converts it to left-handed Z-DNA, a conformation that is then stabilized by the additional binding of a second Z alpha(ADAR1) molecule.
authors.affiliation: Department of Chemistry, RINS, and Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju, Gyeongnam 660-701, Korea.
authors.forename: Young-Min
authors.initials: YM
authors.lastname: Kang
authors.forename: Jongchul
authors.initials: J
authors.lastname: Bang
authors.forename: Eun-Hae
authors.initials: EH
authors.lastname: Lee
authors.forename: Hee-Chul
authors.initials: HC
authors.lastname: Ahn
authors.forename: Yeo-Jin
authors.initials: YJ
authors.lastname: Seo
authors.forename: Kyeong Kyu
authors.initials: KK
authors.lastname: Kim
authors.forename: Yang-Gyun
authors.initials: YG
authors.lastname: Kim
authors.forename: Byong-Seok
authors.initials: BS
authors.lastname: Choi
authors.forename: Joon-Hwa
authors.initials: JH
authors.lastname: Lee
mesh_terms: D000243:Adenosine Deaminase / Q000032:analysis / Q000378:metabolism*; D001665:Binding Sites; D004247:DNA / Q000032:analysis / Q000378:metabolism; D043542:DNA, Z-Form / Q000032:analysis / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D016601:RNA-Binding Proteins
chemical_list: D043542:DNA, Z-Form; D016601:RNA-Binding Proteins; D004247:DNA; C567955:ADARB1 protein, human; D000243:Adenosine Deaminase