1nem
From Proteopedia
(New page: 200px<br /><applet load="1nem" size="450" color="white" frame="true" align="right" spinBox="true" caption="1nem" /> '''Saccharide-RNA recognition in the neomycin B...) |
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| - | [[Image:1nem.gif|left|200px]]<br /><applet load="1nem" size=" | + | [[Image:1nem.gif|left|200px]]<br /><applet load="1nem" size="350" color="white" frame="true" align="right" spinBox="true" |
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'''Saccharide-RNA recognition in the neomycin B / RNA aptamer complex'''<br /> | '''Saccharide-RNA recognition in the neomycin B / RNA aptamer complex'''<br /> | ||
==Overview== | ==Overview== | ||
| - | BACKGROUND: Aminoglycoside antibiotics can target RNA folds with | + | 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== | ==About this Structure== | ||
| - | 1NEM is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with BDG and NEB as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1NEM is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=BDG:'>BDG</scene> and <scene name='pdbligand=NEB:'>NEB</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NEM OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Hu, W.]] | [[Category: Hu, W.]] | ||
| - | [[Category: Jaishree, T | + | [[Category: Jaishree, T J.]] |
[[Category: Jiang, L.]] | [[Category: Jiang, L.]] | ||
[[Category: Majumdar, A.]] | [[Category: Majumdar, A.]] | ||
| - | [[Category: Patel, D | + | [[Category: Patel, D J.]] |
[[Category: Xu, W.]] | [[Category: Xu, W.]] | ||
[[Category: BDG]] | [[Category: BDG]] | ||
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[[Category: rna aptamer]] | [[Category: rna aptamer]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:05:15 2008'' |
Revision as of 12:05, 21 February 2008
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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 and 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
Page seeded by OCA on Thu Feb 21 14:05:15 2008
Categories: Protein complex | Hu, W. | Jaishree, T J. | Jiang, L. | Majumdar, A. | Patel, D J. | Xu, W. | BDG | NEB | Aminoglycoside | Antibiotic | Rna aptamer
