1nem: Difference between revisions
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[[Image:1nem.gif|left|200px]]< | [[Image:1nem.gif|left|200px]] | ||
'''Saccharide-RNA recognition in the neomycin B / RNA aptamer complex''' | {{Structure | ||
|PDB= 1nem |SIZE=350|CAPTION= <scene name='initialview01'>1nem</scene> | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=BDG:O-2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE'>BDG</scene> and <scene name='pdbligand=NEB:2-DEOXY-D-STREPTAMINE'>NEB</scene> | |||
|ACTIVITY= | |||
|GENE= | |||
}} | |||
'''Saccharide-RNA recognition in the neomycin B / RNA aptamer complex''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1NEM is a [ | 1NEM is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NEM OCA]. | ||
==Reference== | ==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:[http:// | 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:[http://www.ncbi.nlm.nih.gov/pubmed/10425683 10425683] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Hu, W.]] | [[Category: Hu, W.]] | ||
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[[Category: rna aptamer]] | [[Category: rna aptamer]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:55:50 2008'' | ||
Revision as of 10:55, 20 March 2008
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| Ligands: | BDG and NEB | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
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]. 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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