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1k01

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(New page: 200px<br /><applet load="1k01" size="450" color="white" frame="true" align="right" spinBox="true" caption="1k01, resolution 3.5&Aring;" /> '''Structural Basis for ...)
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[[Image:1k01.jpg|left|200px]]<br /><applet load="1k01" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1k01, resolution 3.5&Aring;" />
 
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'''Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria'''<br />
 
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==Overview==
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==Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria==
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Ribosomes, the site of protein synthesis, are a major target for natural, and synthetic antibiotics. Detailed knowledge of antibiotic binding sites, is central to understanding the mechanisms of drug action. Conversely, drugs are excellent tools for studying the ribosome function. To elucidate, the structural basis of ribosome-antibiotic interactions, we determined, the high-resolution X-ray structures of the 50S ribosomal subunit of the, eubacterium Deinococcus radiodurans, complexed with the clinically, relevant antibiotics chloramphenicol, clindamycin and the three macrolides, erythromycin, clarithromycin and roxithromycin. We found that antibiotic, binding sites are composed exclusively of segments of 23S ribosomal RNA at, the peptidyl transferase cavity and do not involve any interaction of the, drugs with ribosomal proteins. Here we report the details of antibiotic, interactions with the components of their binding sites. Our results also, show the importance of putative Mg+2 ions for the binding of some drugs., This structural analysis should facilitate rational drug design.
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<StructureSection load='1k01' size='340' side='right'caption='[[1k01]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1k01]] is a 4 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=1K01 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K01 FirstGlance]. <br>
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</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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CLM:CHLORAMPHENICOL'>CLM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1k01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k01 OCA], [https://pdbe.org/1k01 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k01 RCSB], [https://www.ebi.ac.uk/pdbsum/1k01 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k01 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RL4_DEIRA RL4_DEIRA] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01328_B] Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.[HAMAP-Rule:MF_01328_B] This protein is located close to the polypeptide exit tunnel, and interacts with the modified macrolide azithromycin, which blocks the tunnel.[HAMAP-Rule:MF_01328_B]
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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/k0/1k01_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/main_output.php?pdb_ID=1k01 ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1K01 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans] with MG and CLM as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1K01 OCA].
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*[[Ribosomal protein L22|Ribosomal protein L22]]
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*[[Ribosomal protein L32|Ribosomal protein L32]]
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==Reference==
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*[[Ribosomal protein L4|Ribosomal protein L4]]
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Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria., Schlunzen F, Zarivach R, Harms J, Bashan A, Tocilj A, Albrecht R, Yonath A, Franceschi F, Nature. 2001 Oct 25;413(6858):814-21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11677599 11677599]
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__TOC__
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</StructureSection>
[[Category: Deinococcus radiodurans]]
[[Category: Deinococcus radiodurans]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Albrecht, R.]]
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[[Category: Albrecht R]]
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[[Category: Bashan, A.]]
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[[Category: Bashan A]]
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[[Category: Franceschi, F.]]
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[[Category: Franceschi F]]
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[[Category: Harms, J.]]
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[[Category: Harms J]]
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[[Category: Schluenzen, F.]]
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[[Category: Schluenzen F]]
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[[Category: Tocilj, A.]]
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[[Category: Tocilj A]]
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[[Category: Yonath, A.]]
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[[Category: Yonath A]]
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[[Category: Zarivach, R.]]
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[[Category: Zarivach R]]
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[[Category: CLM]]
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[[Category: MG]]
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[[Category: 23s]]
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[[Category: 50s]]
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[[Category: 5s]]
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[[Category: antibiotics]]
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[[Category: chloramphenicol]]
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[[Category: peptidyl transferase center]]
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[[Category: ribosome]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:44:12 2007''
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Current revision

Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria

PDB ID 1k01

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