2jq7
From Proteopedia
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| - | [[Image:2jq7.png|left|200px]] | ||
| - | + | ==Model for thiostrepton binding to the ribosomal L11-RNA== | |
| + | <StructureSection load='2jq7' size='340' side='right'caption='[[2jq7]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[2jq7]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589] and [https://en.wikipedia.org/wiki/Streptomyces_azureus Streptomyces azureus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2nyo 2nyo]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JQ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JQ7 FirstGlance]. <br> | ||
| + | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BB9:(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC+ACID'>BB9</scene>, <scene name='pdbligand=DBU:(2Z)-2-AMINOBUT-2-ENOIC+ACID'>DBU</scene>, <scene name='pdbligand=DCY:D-CYSTEINE'>DCY</scene>, <scene name='pdbligand=DHA:2-AMINO-ACRYLIC+ACID'>DHA</scene>, <scene name='pdbligand=MH6:3-HYDROXY-2-IMINOPROPANOIC+ACID'>MH6</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=QUA:8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC+ACID'>QUA</scene>, <scene name='pdbligand=TS9:(2S,3S,4R)-2-AMINO-3,4-DIHYDROXY-3-METHYLPENTANOIC+ACID'>TS9</scene></td></tr> | ||
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1d8t|1d8t]], [[1e9w|1e9w]], [[1oln|1oln]], [[2c77|2c77]], [[2zjp|2zjp]], [[3cf5|3cf5]], [[1mms|1mms]]</div></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RPLK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</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=2jq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jq7 OCA], [https://pdbe.org/2jq7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jq7 RCSB], [https://www.ebi.ac.uk/pdbsum/2jq7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jq7 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [[https://www.uniprot.org/uniprot/RL11_THEMA RL11_THEMA]] This protein binds directly to 23S ribosomal RNA. [[https://www.uniprot.org/uniprot/THCL_STRAJ THCL_STRAJ]] Has bacteriocidal activity. Inhibits bacterial protein biosynthesis by acting on the elongation factor Tu (EF-Tu) (By similarity). | ||
| + | == 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/jq/2jq7_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2jq7 ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Ribosomal proteins are assumed to stabilize specific RNA structures and promote compact folding of the large rRNA. The conformational dynamics of the protein between the bound and unbound state play an important role in the binding process. We have studied those dynamical changes in detail for the highly conserved complex between the ribosomal protein L11 and the GTPase region of 23S rRNA. The RNA domain is compactly folded into a well defined tertiary structure, which is further stabilized by the association with the C-terminal domain of the L11 protein (L11(ctd)). In addition, the N-terminal domain of L11 (L11(ntd)) is implicated in the binding of the natural thiazole antibiotic thiostrepton, which disrupts the elongation factor function. We have studied the conformation of the ribosomal protein and its dynamics by NMR in the unbound state, the RNA bound state and in the ternary complex with the RNA and thiostrepton. Our data reveal a rearrangement of the L11(ntd), placing it closer to the RNA after binding of thiostrepton, which may prevent binding of elongation factors. We propose a model for the ternary L11-RNA-thiostrepton complex that is additionally based on interaction data and conformational information of the L11 protein. The model is consistent with earlier findings and provides an explanation for the role of L11(ntd) in elongation factor binding. | ||
| - | + | L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy.,Jonker HR, Ilin S, Grimm SK, Wohnert J, Schwalbe H Nucleic Acids Res. 2007;35(2):441-54. Epub 2006 Dec 14. PMID:17169991<ref>PMID:17169991</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 2jq7" style="background-color:#fffaf0;"></div> | |
| - | + | ||
==See Also== | ==See Also== | ||
*[[Ribosomal protein L11|Ribosomal protein L11]] | *[[Ribosomal protein L11|Ribosomal protein L11]] | ||
| - | + | == References == | |
| - | == | + | <references/> |
| - | < | + | __TOC__ |
| + | </StructureSection> | ||
| + | [[Category: Atcc 43589]] | ||
| + | [[Category: Large Structures]] | ||
[[Category: Streptomyces azureus]] | [[Category: Streptomyces azureus]] | ||
| - | + | [[Category: Grimm, S K]] | |
| - | [[Category: Grimm, S K | + | [[Category: Ilin, S]] |
| - | [[Category: Ilin, S | + | [[Category: Jonker, H R.A]] |
| - | [[Category: Jonker, H R.A | + | [[Category: Schwalbe, H]] |
| - | [[Category: Schwalbe, H | + | [[Category: Woehnert, J]] |
| - | [[Category: Woehnert, J | + | |
[[Category: Antibacterial]] | [[Category: Antibacterial]] | ||
[[Category: L11]] | [[Category: L11]] | ||
Current revision
Model for thiostrepton binding to the ribosomal L11-RNA
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