1xbp

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[[Image:1xbp.png|left|200px]]
 
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==Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin==
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The line below this paragraph, containing "STRUCTURE_1xbp", creates the "Structure Box" on the page.
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<StructureSection load='1xbp' size='340' side='right'caption='[[1xbp]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1xbp]] 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=1XBP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XBP FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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=MUL:TIAMULIN'>MUL</scene></td></tr>
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{{STRUCTURE_1xbp| PDB=1xbp | SCENE= }}
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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=1xbp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xbp OCA], [https://pdbe.org/1xbp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xbp RCSB], [https://www.ebi.ac.uk/pdbsum/1xbp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xbp ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RL5_DEIRA RL5_DEIRA] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement (By similarity). Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_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/xb/1xbp_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=1xbp 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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Tiamulin, a prominent member of the pleuromutilin class of antibiotics, is a potent inhibitor of protein synthesis in bacteria. Up to now the effect of pleuromutilins on the ribosome has not been determined on a molecular level. The 3.5 A structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin provides for the first time a detailed picture of its interactions with the 23S rRNA, thus explaining the molecular mechanism of the antimicrobial activity of the pleuromutilin class of antibiotics. Our results show that tiamulin is located within the peptidyl transferase center (PTC) of the 50S ribosomal subunit with its tricyclic mutilin core positioned in a tight pocket at the A-tRNA binding site. Also, the extension, which protrudes from its mutilin core, partially overlaps with the P-tRNA binding site. Thereby, tiamulin directly inhibits peptide bond formation. Comparison of the tiamulin binding site with other PTC targeting drugs, like chloramphenicol, clindamycin and streptogramins, may facilitate the design of modified or hybridized drugs that extend the applicability of this class of antibiotics.
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===Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin===
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Inhibition of peptide bond formation by pleuromutilins: the structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin.,Schlunzen F, Pyetan E, Fucini P, Yonath A, Harms JM Mol Microbiol. 2004 Dec;54(5):1287-94. PMID:15554968<ref>PMID:15554968</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_15554968}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1xbp" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 15554968 is the PubMed ID number.
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{{ABSTRACT_PUBMED_15554968}}
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==About this Structure==
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[[1xbp]] is a 30 chain structure of [[Ribosomal protein L2]], [[Ribosomal protein L3]], [[Ribosomal protein L4]], [[Ribosomal protein L5]] and [[Ribosomal protein L6]] 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=1XBP OCA].
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==See Also==
==See Also==
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*[[Ribosomal protein L2]]
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*[[Ribosome 3D structures|Ribosome 3D structures]]
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*[[Ribosomal protein L3]]
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== References ==
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*[[Ribosomal protein L4]]
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<references/>
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*[[Ribosomal protein L5]]
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__TOC__
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*[[Ribosomal protein L6]]
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</StructureSection>
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==Reference==
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<ref group="xtra">PMID:15554968</ref><references group="xtra"/>
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[[Category: Deinococcus radiodurans]]
[[Category: Deinococcus radiodurans]]
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[[Category: Fucini, P.]]
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[[Category: Large Structures]]
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[[Category: Harms, J M.]]
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[[Category: Fucini P]]
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[[Category: Pyetan, E.]]
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[[Category: Harms JM]]
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[[Category: Schluenzen, F.]]
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[[Category: Pyetan E]]
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[[Category: Yonath, A.]]
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[[Category: Schluenzen F]]
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[[Category: 50s ribosome]]
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[[Category: Yonath A]]
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[[Category: Pleuromutilin]]
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[[Category: Tiamulin]]
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Current revision

Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin

PDB ID 1xbp

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