1i9v
From Proteopedia
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|PDB= 1i9v |SIZE=350|CAPTION= <scene name='initialview01'>1i9v</scene>, resolution 2.6Å | |PDB= 1i9v |SIZE=350|CAPTION= <scene name='initialview01'>1i9v</scene>, resolution 2.6Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> | + | |LIGAND= <scene name='pdbligand=5MU:5-METHYLURIDINE+5'-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NMY:NEOMYCIN'>NMY</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1i9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i9v OCA], [http://www.ebi.ac.uk/pdbsum/1i9v PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1i9v RCSB]</span> | ||
}} | }} | ||
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[[Category: Mikkelsen, N E.]] | [[Category: Mikkelsen, N E.]] | ||
[[Category: Virtanen, A.]] | [[Category: Virtanen, A.]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: NMY]] | ||
[[Category: amino-acid transport]] | [[Category: amino-acid transport]] | ||
[[Category: aminoglycoside]] | [[Category: aminoglycoside]] | ||
[[Category: neomycin b]] | [[Category: neomycin b]] | ||
| - | [[Category: phe-trna | + | [[Category: phe-trna,phenylalanine]] |
| - | + | ||
[[Category: transfer rna]] | [[Category: transfer rna]] | ||
[[Category: yeast]] | [[Category: yeast]] | ||
| - | ''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 21:16:40 2008'' |
Revision as of 18:16, 30 March 2008
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| , resolution 2.6Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEX
Overview
Aminoglycosides bind to RNA and interfere with its function, and it has been suggested that aminoglycoside binding to RNA displaces essential divalent metal ions. Here we demonstrate that addition of various aminoglycosides inhibited Pb2+-induced cleavage of yeast tRNA(Phe). Cocrystallization of yeast tRNA(Phe) and an aminoglycoside, neomycin B, resulted in crystals that diffracted to 2.6 A and the structure of the complex was solved by molecular replacement. The structure shows that the neomycin B binding site overlaps with known divalent metal ion binding sites in yeast tRNA(Phe), providing direct evidence for the hypothesis that aminoglycosides displace metal ions. Additionally, the neomycin B binding site overlaps with major determinants for Escherichia coli phenylalanyl-tRNA-synthetase. Here we present data demonstrating that addition of neomycin B inhibited aminoacylation of E. coli tRNA(Phe) in the mid microM range. Given that aminoglycoside and metal ion binding sites overlap, we discuss that aminoglycosides can be considered as 'metal mimics'.
About this Structure
1I9V is a Single protein structure of sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA.
Reference
Aminoglycoside binding displaces a divalent metal ion in a tRNA-neomycin B complex., Mikkelsen NE, Johansson K, Virtanen A, Kirsebom LA, Nat Struct Biol. 2001 Jun;8(6):510-4. PMID:11373618
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