1nem

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Saccharide-RNA recognition in the neomycin B / RNA aptamer complex

Overview

BACKGROUND: Aminoglycoside antibiotics can target RNA folds with, micromolar affinity and inhibit biological processes ranging from protein, biosynthesis to ribozyme action and viral replication. Specific features, of aminoglycoside antibiotic-RNA recognition have been probed using, chemical, biochemical, spectroscopic and computational approaches on both, natural RNA targets and RNA aptamers identified through in vitro, selection. Our previous studies on tobramycin-RNA aptamer complexes are, extended to neomycin B bound to its selected RNA aptamer with 100 nM, affinity. RESULTS: The neamine moiety (rings I and II) of neomycin B is, sandwiched between the major groove floor of a 'zippered-up' G.U mismatch, aligned segment and a looped-out purine base that flaps over the bound, antibiotic. Specific intermolecular hydrogen bonds are observed between, the charged amines of neomycin B and base mismatch edges and backbone, phosphates. These interactions anchor 2-deoxystreptamine ring I and, pyranose ring II within the RNA-binding pocket. CONCLUSIONS: The RNA, aptamer complexes with tobramycin and neomycin B utilize common, architectural principles to generate RNA-binding pockets for the bound, aminoglycoside antibiotics. In each case, the 2-deoxystreptamine ring I, and an attached pyranose ring are encapsulated within the major groove, binding pocket, which is lined with mismatch pairs. The bound antibiotic, within the pocket is capped over by a looped-out base and anchored in, place through intermolecular hydrogen bonds involving charged amine groups, of the antibiotic.

About this Structure

1NEM is a Protein complex structure of sequences from [1] with BDG and NEB as ligands. Full crystallographic information is available from OCA.

Reference

Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer., Jiang L, Majumdar A, Hu W, Jaishree TJ, Xu W, Patel DJ, Structure. 1999 Jul 15;7(7):817-27. PMID:10425683

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