1nem

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[[Image:1nem.gif|left|200px]]
[[Image:1nem.gif|left|200px]]
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{{Structure
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<!--
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|PDB= 1nem |SIZE=350|CAPTION= <scene name='initialview01'>1nem</scene>
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The line below this paragraph, containing "STRUCTURE_1nem", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=BDG:O-2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE'>BDG</scene>, <scene name='pdbligand=BDR:BETA-D-RIBOFURANOSYL'>BDR</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=IDG:O-2,6-DIAMINO-2,6-DIDEOXY-BETA-L-IDOPYRANOSE'>IDG</scene>, <scene name='pdbligand=NEB:2-DEOXY-D-STREPTAMINE'>NEB</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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|ACTIVITY=
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or leave the SCENE parameter empty for the default display.
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|GENE=
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|DOMAIN=
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{{STRUCTURE_1nem| PDB=1nem | SCENE= }}
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|RELATEDENTRY=
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nem OCA], [http://www.ebi.ac.uk/pdbsum/1nem PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nem RCSB]</span>
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}}
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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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==About this Structure==
==About this Structure==
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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].
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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://www.ncbi.nlm.nih.gov/pubmed/10425683 10425683]
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]
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[[Category: Protein complex]]
 
[[Category: Hu, W.]]
[[Category: Hu, W.]]
[[Category: Jaishree, T J.]]
[[Category: Jaishree, T J.]]
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[[Category: Patel, D J.]]
[[Category: Patel, D J.]]
[[Category: Xu, W.]]
[[Category: Xu, W.]]
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[[Category: aminoglycoside]]
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[[Category: Aminoglycoside]]
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[[Category: antibiotic]]
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[[Category: Antibiotic]]
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[[Category: rna aptamer]]
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[[Category: Rna aptamer]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 02:26:25 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:29:23 2008''
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Revision as of 23:26, 2 May 2008

Image:1nem.gif

Template:STRUCTURE 1nem

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

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 Sat May 3 02:26:25 2008

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