The A730 loop is an important component of the active site of the VS ribozyme

The core of the VS ribozyme comprises five helices, that act either in cis or in trans on a stem-loop substrate to catalyse site-specific cleavage. Th e structure of the 2-3-6 helical junction indicates that a cleft is formed between helices II and VI that is likely to serve as a receptor for the sub strate. Detailed analysis of sequence variants suggests that the base bulge s of helices II and VI play an architectural role. By contrast, the identit y of the nucleotides in the A730 loop is very important for ribozyme activi ty. The base of A756 is particularly vital, and substitution by any other n ucleotide or ablation of the base leads to a major reduction in cleavage ra te. However, variants of A756 bind substrate efficiently, and are not defec tive in global folding. These results suggest that the A730 loop is an impo rtant component of the active site of the ribozyme, and that A756 could pla y a kev role in catalysis. (C) 2001 Academic Press.