Cleavage reaction of HDV ribozymes in the presence of Mg2+ is accompanied by a conformational change.
BACKGROUND
Hepatitis delta virus (HDV) ribozymes cleave RNA in the presence of divalent metal ions. We have previously elucidated the solution conformation of a minimized trans-acting HDV ribozyme and obtained evidence by NMR study that an Mg2+ ion binds to a site close to the cleavage site.


RESULTS
We examined two ribozyme systems: a pre-cleavage complex with a non-cleavable substrate analogue (mS8) and a post-cleavage complex with a 3' cleavage product (P7). Upon titration with MgCl2, the complex with P7 showed a profound spectral change, while that with mS8 showed broadening of the signals. Analysis of the NOESY spectra of the P7 complex at high Mg2+ concentration revealed that a G:U pair is formed within the L3 loop, and the P1 and P4 stems are stabilized with respect to those of the pre-cleavage complex.


CONCLUSIONS
The present analysis indicates that the cleavage reaction of the HDV ribozyme produces a big conformational change. Furthermore, presence of the 5'-terminal cytidine residue prevents this conformational change and its absence stabilizes the product-ribozyme complex in the presence of Mg2+. The structure of the Mg2+-bound P7 complex is similar to the crystal structure found for a product-ribozyme complex but is different from the pre-cleavage structure.
Tanaka
Yoichiro
Y
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.
Tagaya
Mitsuhiro
M
Hori
Tamaki
T
Sakamoto
Taiichi
T
Kurihara
Yasuyuki
Y
Katahira
Masato
M
Uesugi
Seiichi
S
D003698:Hepatitis Delta Virus / Q000235:genetics* / Q000378:metabolism; D008274:Magnesium / Q000378:metabolism*; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry / Q000378:metabolism*
D016337:RNA, Catalytic; D008274:Magnesium