1nem
From Proteopedia
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|PDB= 1nem |SIZE=350|CAPTION= <scene name='initialview01'>1nem</scene> | |PDB= 1nem |SIZE=350|CAPTION= <scene name='initialview01'>1nem</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=BDG:O-2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE'>BDG</scene> | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-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'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-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'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |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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[[Category: Patel, D J.]] | [[Category: Patel, D J.]] | ||
[[Category: Xu, W.]] | [[Category: Xu, W.]] | ||
| - | [[Category: BDG]] | ||
| - | [[Category: NEB]] | ||
[[Category: aminoglycoside]] | [[Category: aminoglycoside]] | ||
[[Category: antibiotic]] | [[Category: antibiotic]] | ||
[[Category: rna aptamer]] | [[Category: rna aptamer]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:29:23 2008'' |
Revision as of 19:29, 30 March 2008
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| Ligands: | , , , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| 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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