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| | <StructureSection load='1i9v' size='340' side='right'caption='[[1i9v]], [[Resolution|resolution]] 2.60Å' scene=''> | | <StructureSection load='1i9v' size='340' side='right'caption='[[1i9v]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1i9v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I9V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1I9V FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1i9v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I9V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I9V FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NMY:NEOMYCIN'>NMY</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NMY:NEOMYCIN'>NMY</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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://pdbe.org/1i9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1i9v RCSB], [http://www.ebi.ac.uk/pdbsum/1i9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1i9v ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1i9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i9v OCA], [https://pdbe.org/1i9v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i9v RCSB], [https://www.ebi.ac.uk/pdbsum/1i9v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i9v ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| | [[Category: Saccharomyces cerevisiae]] | | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Johansson, K]] | + | [[Category: Johansson K]] |
| - | [[Category: Kirsebom, L A]] | + | [[Category: Kirsebom LA]] |
| - | [[Category: Mikkelsen, N E]] | + | [[Category: Mikkelsen NE]] |
| - | [[Category: Virtanen, A]] | + | [[Category: Virtanen A]] |
| - | [[Category: Amino-acid transport]]
| + | |
| - | [[Category: Aminoglycoside]]
| + | |
| - | [[Category: Neomycin b]]
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| - | [[Category: Phe-trna]]
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| - | [[Category: Phenylalanine]]
| + | |
| - | [[Category: Rna]]
| + | |
| - | [[Category: Transfer rna]]
| + | |
| - | [[Category: Yeast]]
| + | |
| Structural highlights
Publication Abstract from PubMed
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'.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Mikkelsen NE, Johansson K, Virtanen A, Kirsebom LA. Aminoglycoside binding displaces a divalent metal ion in a tRNA-neomycin B complex. Nat Struct Biol. 2001 Jun;8(6):510-4. PMID:11373618 doi:10.1038/88569
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