The global structure of the VS ribozyme.
The VS ribozyme comprises five helical segments (II-VI) in a formal H shape, organized by two three-way junctions. It interacts with its stem-loop substrate (I) by tertiary interactions. We have determined the global shape of the 3-4-5 junction (relating helices III-V) by electrophoresis and FRET. Estimation of the dihedral angle between helices II and V electrophoretically has allowed us to build a model for the global structure of the complete ribozyme. We propose that the substrate is docked into a cleft between helices II and VI, with its loop making a tertiary interaction with that of helix V. This is consistent with the dependence of activity on the length of helix III. The scissile phosphate is well placed to interact with the probable active site of the ribozyme, the loop containing A730.
Lafontaine
Daniel A
DA
Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI/WTB Complex, The University of Dundee, DD1 5EH, UK.
Norman
David G
DG
Lilley
David M J
DM
D001483:Base Sequence; D001665:Binding Sites; D004722:Endoribonucleases / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000138:chemical synthesis / Q000737:chemistry; D016337:RNA, Catalytic / Q000737:chemistry*
D009843:Oligoribonucleotides; D016337:RNA, Catalytic; D004722:Endoribonucleases; C438195:varkud satellite ribozyme