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1nem

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{{STRUCTURE_1nem| PDB=1nem | SCENE= }}
{{STRUCTURE_1nem| PDB=1nem | SCENE= }}
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'''Saccharide-RNA recognition in the neomycin B / RNA aptamer complex'''
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===Saccharide-RNA recognition in the neomycin B / RNA aptamer complex===
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==Overview==
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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.
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(as it appears on PubMed at http://www.pubmed.gov), where 10425683 is the PubMed ID number.
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{{ABSTRACT_PUBMED_10425683}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NEM OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NEM OCA].
==Reference==
==Reference==
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[[Category: Antibiotic]]
[[Category: Antibiotic]]
[[Category: Rna aptamer]]
[[Category: Rna aptamer]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 17:29:00 2008''

Revision as of 14:29, 28 July 2008

Image:1nem.png

Template:STRUCTURE 1nem

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

Template:ABSTRACT PUBMED 10425683

About this Structure

Full experimental 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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