title: Imino proton NMR analysis of HDV ribozymes: nested double pseudoknot structure and Mg2+ ion-binding site close to the catalytic core in solution.
abstract: Minimized trans-acting HDV ribozyme systems consisting of three (Rz-3) and two (Rz-2) RNA strands were prepared and their folding conformations were analyzed by NMR spectroscopy. The guanosine residues in one of the enzyme components of Rz-3 were labeled with 13C and 15N. Imino proton signals were assigned by analysis of NOESY and HSQC spectra. The results are consistent with the nested double pseudoknot model, which contains novel base pairs (P1.1), as observed in the crystal structure of a genomic HDV ribozyme. The NOE connectivities suggest an additional G:G pair at the bottom of P1.1 and at the top of P4. The effects of temperature and Mg2+ ions on base pairs for Rz-3 were examined. The temperature variation experiment on Rz-3 showed that P3 is the most stable and that P1.1 is as stable as P1 and P2. The imino proton signals of the G:U pair at the bottom of P1 and the top of P1.1, which are close to the cleavage site, showed the largest changes upon Mg2+ titration of Rz-3. The results suggest that the catalytic Mg2+ ion binds to the pocket formed by P1 and L3.
authors.affiliation: Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan.
authors.forename: Yoichiro
authors.initials: Y
authors.lastname: Tanaka
authors.forename: Tamaki
authors.initials: T
authors.lastname: Hori
authors.forename: Mitsuhiro
authors.initials: M
authors.lastname: Tagaya
authors.forename: Taiichi
authors.initials: T
authors.lastname: Sakamoto
authors.forename: Yasuyuki
authors.initials: Y
authors.lastname: Kurihara
authors.forename: Masato
authors.initials: M
authors.lastname: Katahira
authors.forename: Seiichi
authors.initials: S
authors.lastname: Uesugi
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D020134:Catalytic Domain; D003698:Hepatitis Delta Virus / Q000201:enzymology* / Q000235:genetics*; D008274:Magnesium / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D011522:Protons; D016337:RNA, Catalytic / Q000138:chemical synthesis / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012996:Solutions; D013696:Temperature; D017186:Titrimetry
chemical_list: D011522:Protons; D016337:RNA, Catalytic; D012996:Solutions; D008274:Magnesium