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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'''
| + | ===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.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_10425683}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 10425683 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_10425683}} |
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| | ==About this Structure== | | ==About this Structure== |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NEM OCA]. | + | Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NEM OCA]. |
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| | ==Reference== | | ==Reference== |
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| | [[Category: Antibiotic]] | | [[Category: Antibiotic]] |
| | [[Category: Rna aptamer]] | | [[Category: Rna aptamer]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 02:26:25 2008'' | + | |
| | + | ''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
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
Page seeded by OCA on Mon Jul 28 17:29:00 2008
