DSSR-PyMOL cartoon-block schematics: PDB entry 3i2r

PDB-id

3i2r; DSSR-derived features in text and JSON formats

Class

RNA

Method

X-ray (2.8 Å)

Summary

Crystal structure of the hairpin ribozyme with a 2',5'-linked substrate with n1-deazaadenosine at position a9

Reference

Spitale RC, Volpini R, Mungillo MV, Krucinska J, Cristalli G, Wedekind JE (2009): "Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core." Biochemistry, 48, 7777-7779. doi: 10.1021/bi9011622.

Abstract

The hairpin ribozyme cleaves a phosphodiester bond within a cognate substrate. Structural and biochemical data indicate the conserved A9 and A10 bases reside close to the scissile bond but make distinct contributions to catalysis. To investigate these residues, we replaced the imino moiety of each base with N1-deazaadenosine. This single-atom change resulted in an 8-fold loss in k(obs) for A9 and displacement of the base from the active site; no effects were observed for A10. We propose that the imino moiety of A9 promotes a key water-mediated contact that favors transition-state formation, which suggests an enhanced chemical repertoire for RNA.