title: 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.
authors.affiliation: Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dundee DD1 5EH, UK. d.m.lilley@dundee.ac.uk
authors.forename: David M J
authors.initials: DM
authors.lastname: Lilley
mesh_terms: D001665:Binding Sites; D004722:Endoribonucleases / Q000235:genetics* / Q000378:metabolism; D009491:Neurospora / Q000235:genetics / Q000378:metabolism; D009690:Nucleic Acid Conformation; D012313:RNA / Q000378:metabolism*; D016337:RNA, Catalytic / Q000235:genetics* / Q000378:metabolism; D013379:Substrate Specificity
chemical_list: D016337:RNA, Catalytic; D012313:RNA; D004722:Endoribonucleases; C438195:varkud satellite ribozyme