The Varkud satellite ribozyme

Abstract

The VS ribozyme is the largest nucleolytic ribozyme, for which there is no crystal structure to date. The ribozyme consists of five helical sections, organized by two three-way junctions. The global structure has been determined by solution methods, particularly FRET. The substrate stem–loop binds into a cleft formed between two helices, while making a loop–loop contact with another section of the ribozyme. The scissile phosphate makes a close contact with an internal loop (the A730 loop), the probable active site of the ribozyme. This loop contains a particularly critical nucleotide A756. Most changes to this nucleotide lead to three-orders of magnitude slower cleavage, and the Watson-Crick edge is especially important. NAIM experiments indicate that a protonated base is required at this position for the ligation reaction. A756 is thus a strong candidate for nucleobase participation in the catalytic chemistry.

Keywords

• VS ribozyme
• RNA catalysis
• RNA structure
• VS, Varkud Satellite
• HDV, Hepatitis delta virus
• NMR, nuclear magnetic resonance
• FRET, fluorescence resonance energy transfer
• NAIM, nucleotide analog interference mapping
• SN2, bimolecular nucleophilic substitution reaction
• pKa, -log10(acid dissociation constant)