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The Varkud satellite ribozyme Lilley DMRNA 2004[Feb]; 10 (2): 151-8The 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.|*Nucleic Acid Conformation[MESH]|Binding Sites[MESH]|Endoribonucleases/*genetics/metabolism[MESH]|Neurospora/genetics/metabolism[MESH]|RNA, Catalytic/*genetics/metabolism[MESH]|RNA/*metabolism[MESH]|Substrate Specificity[MESH] |
