View source for 3dll


==The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning==
<StructureSection load='3dll' size='340' side='right'caption='[[3dll]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3dll]] is a 10 chain structure with sequence from [https://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 [https://proteopedia.org/fgij/fg.htm?mol=3DLL FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dll OCA], [https://pdbe.org/3dll PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dll RCSB], [https://www.ebi.ac.uk/pdbsum/3dll PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dll ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RL2_DEIRA RL2_DEIRA] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_B]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dl/3dll_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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/main_output.php?pdb_ID=3dll ConSurf].
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== Publication Abstract from PubMed ==
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.

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>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 3dll" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ribosome 3D structures|Ribosome 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Deinococcus radiodurans]]
[[Category: Large Structures]]
[[Category: Connell SR]]
[[Category: Fucini P]]
[[Category: Harms JM]]
[[Category: Schluenzen F]]
[[Category: Starosta AL]]
[[Category: Wilson DN]]