1nem: Difference between revisions
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[[ | ==Saccharide-RNA recognition in the neomycin B / RNA aptamer complex== | ||
<StructureSection load='1nem' size='340' side='right' caption='[[1nem]], [[NMR_Ensembles_of_Models | 9 NMR models]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1nem]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NEM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NEM FirstGlance]. <br> | |||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BDG:O-2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE'>BDG</scene>, <scene name='pdbligand=NEB:2-DEOXY-D-STREPTAMINE'>NEB</scene>, <scene name='pdbligand=BDR:BETA-D-RIBOFURANOSYL'>BDR</scene>, <scene name='pdbligand=IDG:O-2,6-DIAMINO-2,6-DIDEOXY-BETA-L-IDOPYRANOSE'>IDG</scene><br> | |||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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.rcsb.org/pdb/explore.do?structureId=1nem RCSB], [http://www.ebi.ac.uk/pdbsum/1nem PDBsum]</span></td></tr> | |||
<table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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<ref>PMID:10425683</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
< | |||
[[Category: Hu, W.]] | [[Category: Hu, W.]] | ||
[[Category: Jaishree, T J.]] | [[Category: Jaishree, T J.]] | ||
Revision as of 06:50, 9 June 2014
Saccharide-RNA recognition in the neomycin B / RNA aptamer complex
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