3dll

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{{Large structure}}
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==The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning==
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{{STRUCTURE_3dll| PDB=3dll | SCENE= }}
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<StructureSection load='3dll' size='340' side='right' caption='[[3dll]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
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===The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning===
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== Structural highlights ==
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{{ABSTRACT_PUBMED_18757750}}
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<table><tr><td colspan='2'>[[3dll]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DLL FirstGlance]. <br>
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</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=ZLD:N-{[(5S)-3-(3-FLUORO-4-MORPHOLIN-4-YLPHENYL)-2-OXO-1,3-OXAZOLIDIN-5-YL]METHYL}ACETAMIDE'>ZLD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<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=3dll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dll OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dll RCSB], [http://www.ebi.ac.uk/pdbsum/3dll PDBsum]</span></td></tr>
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</table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dl/3dll_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The oxazolidinones represent the first new class of antibiotics to enter into clinical usage within the past 30 years, but their binding site and mechanism of action has not been fully characterized. We have determined the crystal structure of the oxazolidinone linezolid bound to the Deinococcus radiodurans 50S ribosomal subunit. Linezolid binds in the A site pocket at the peptidyltransferase center of the ribosome overlapping the aminoacyl moiety of an A-site bound tRNA as well as many clinically important antibiotics. Binding of linezolid stabilizes a distinct conformation of the universally conserved 23S rRNA nucleotide U2585 that would be nonproductive for peptide bond formation. In conjunction with available biochemical data, we present a model whereby oxazolidinones impart their inhibitory effect by perturbing the correct positioning of tRNAs on the ribosome.
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==About this Structure==
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The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning.,Wilson DN, Schluenzen F, Harms JM, Starosta AL, Connell SR, Fucini P Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13339-44. Epub 2008 Aug 29. PMID:18757750<ref>PMID:18757750</ref>
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[[3dll]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLL OCA].
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==See Also==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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*[[Ribosomal protein L11|Ribosomal protein L11]]
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</div>
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*[[Ribosomal protein L13|Ribosomal protein L13]]
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*[[Ribosomal protein L14|Ribosomal protein L14]]
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*[[Ribosomal protein L15|Ribosomal protein L15]]
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*[[Ribosomal protein L16|Ribosomal protein L16]]
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*[[Ribosomal protein L17|Ribosomal protein L17]]
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*[[Ribosomal protein L18|Ribosomal protein L18]]
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*[[Ribosomal protein L19|Ribosomal protein L19]]
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*[[Ribosomal protein L2|Ribosomal protein L2]]
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*[[Ribosomal protein L20|Ribosomal protein L20]]
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*[[Ribosomal protein L21|Ribosomal protein L21]]
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*[[Ribosomal protein L22|Ribosomal protein L22]]
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*[[Ribosomal protein L23|Ribosomal protein L23]]
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*[[Ribosomal protein L24|Ribosomal protein L24]]
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*[[Ribosomal protein L25|Ribosomal protein L25]]
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*[[Ribosomal protein L27|Ribosomal protein L27]]
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*[[Ribosomal protein L28|Ribosomal protein L28]]
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*[[Ribosomal protein L29|Ribosomal protein L29]]
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*[[Ribosomal protein L3|Ribosomal protein L3]]
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*[[Ribosomal protein L30|Ribosomal protein L30]]
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*[[Ribosomal protein L32|Ribosomal protein L32]]
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*[[Ribosomal protein L33|Ribosomal protein L33]]
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*[[Ribosomal protein L34|Ribosomal protein L34]]
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*[[Ribosomal protein L35|Ribosomal protein L35]]
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*[[Ribosomal protein L36|Ribosomal protein L36]]
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*[[Ribosomal protein L4|Ribosomal protein L4]]
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*[[Ribosomal protein L5|Ribosomal protein L5]]
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*[[Ribosomal protein L6|Ribosomal protein L6]]
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*[[Ribosome|Ribosome]]
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==Reference==
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==See Also==
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<ref group="xtra">PMID:018757750</ref><references group="xtra"/>
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*[[Ribosome 3D structures|Ribosome 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Deinococcus radiodurans]]
[[Category: Deinococcus radiodurans]]
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[[Category: Connell, S R.]]
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[[Category: Connell, S R]]
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[[Category: Fucini, P.]]
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[[Category: Fucini, P]]
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[[Category: Harms, J M.]]
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[[Category: Harms, J M]]
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[[Category: Schluenzen, F.]]
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[[Category: Schluenzen, F]]
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[[Category: Starosta, A L.]]
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[[Category: Starosta, A L]]
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[[Category: Wilson, D N.]]
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[[Category: Wilson, D N]]
[[Category: Antibiotic]]
[[Category: Antibiotic]]
[[Category: Linezolid]]
[[Category: Linezolid]]

Revision as of 14:06, 17 December 2014

The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning

3dll, resolution 3.50Å

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