2a6e: Difference between revisions

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-[[Image:2a6e.gif|left|200px]]
- {{Structure
+==Crystal structure of the T. Thermophilus RNA polymerase holoenzyme==
-|PDB= 2a6e |SIZE=350|CAPTION= <scene name='initialview01'>2a6e</scene>, resolution 2.80&Aring;
+<StructureSection load='2a6e' size='340' side='right'caption='[[2a6e]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> and <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene>
+<table><tr><td colspan='2'>[[2a6e]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A6E FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
-|GENE=
+<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=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=2a6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6e OCA], [https://pdbe.org/2a6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a6e RCSB], [https://www.ebi.ac.uk/pdbsum/2a6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a6e ProSAT], [https://www.topsan.org/Proteins/RSGI/2a6e TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RPOA_THET8 RPOA_THET8] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
+== 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/a6/2a6e_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=2a6e ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Rifamycins, the clinically important antibiotics, target bacterial RNA polymerase (RNAP). A proposed mechanism in which rifamycins sterically block the extension of nascent RNA beyond three nucleotides does not alone explain why certain RNAP mutations confer resistance to some but not other rifamycins. Here we show that unlike rifampicin and rifapentin, and contradictory to the steric model, rifabutin inhibits formation of the first and second phosphodiester bonds. We report 2.5 A resolution structures of rifabutin and rifapentin complexed with the Thermus thermophilus RNAP holoenzyme. The structures reveal functionally important distinct interactions of antibiotics with the initiation sigma factor. Strikingly, both complexes lack the catalytic Mg2+ ion observed in the apo-holoenzyme, whereas an increase in Mg2+ concentration confers resistance to rifamycins. We propose that a rifamycin-induced signal is transmitted over approximately 19 A to the RNAP active site to slow down catalysis. Based on structural predictions, we designed enzyme substitutions that apparently interrupt this allosteric signal.
-'''Crystal structure of the T. Thermophilus RNA polymerase holoenzyme'''
+Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins.,Artsimovitch I, Vassylyeva MN, Svetlov D, Svetlov V, Perederina A, Igarashi N, Matsugaki N, Wakatsuki S, Tahirov TH, Vassylyev DG Cell. 2005 Aug 12;122(3):351-63. PMID:16096056<ref>PMID:16096056</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2a6e" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Rifamycins, the clinically important antibiotics, target bacterial RNA polymerase (RNAP). A proposed mechanism in which rifamycins sterically block the extension of nascent RNA beyond three nucleotides does not alone explain why certain RNAP mutations confer resistance to some but not other rifamycins. Here we show that unlike rifampicin and rifapentin, and contradictory to the steric model, rifabutin inhibits formation of the first and second phosphodiester bonds. We report 2.5 A resolution structures of rifabutin and rifapentin complexed with the Thermus thermophilus RNAP holoenzyme. The structures reveal functionally important distinct interactions of antibiotics with the initiation sigma factor. Strikingly, both complexes lack the catalytic Mg2+ ion observed in the apo-holoenzyme, whereas an increase in Mg2+ concentration confers resistance to rifamycins. We propose that a rifamycin-induced signal is transmitted over approximately 19 A to the RNAP active site to slow down catalysis. Based on structural predictions, we designed enzyme substitutions that apparently interrupt this allosteric signal.
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
+*[[Sigma factor 3D structures|Sigma factor 3D structures]]
-==About this Structure==
+== References ==
-A6E is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A6E OCA].
+<references/>
+__TOC__
-==Reference==
+</StructureSection>
-Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins., Artsimovitch I, Vassylyeva MN, Svetlov D, Svetlov V, Perederina A, Igarashi N, Matsugaki N, Wakatsuki S, Tahirov TH, Vassylyev DG, Cell. 2005 Aug 12;122(3):351-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16096056 16096056]
+[[Category: Large Structures]]
-[[Category: DNA-directed RNA polymerase]]
-[[Category: Protein complex]]
 [[Category: Thermus thermophilus]]
-[[Category: Artsimovitch, I.]]
+[[Category: Artsimovitch I]]
-[[Category: Igarashi, N.]]
+[[Category: Igarashi N]]
-[[Category: Matsugaki, N.]]
+[[Category: Matsugaki N]]
-[[Category: Perederina, A.]]
+[[Category: Perederina A]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Svetlov D]]
-[[Category: Svetlov, D.]]
+[[Category: Svetlov V]]
-[[Category: Svetlov, V.]]
+[[Category: Tahirov TH]]
-[[Category: Tahirov, T H.]]
+[[Category: Vassylyev DG]]
-[[Category: Vassylyev, D G.]]
+[[Category: Vassylyeva MN]]
-[[Category: Vassylyeva, M N.]]
+[[Category: Wakatsuki S]]
-[[Category: Wakatsuki, S.]]
-[[Category: MG]]
-[[Category: ZN]]
-[[Category: bridge helix]]
-[[Category: riken structural genomics/proteomics initiative]]
-[[Category: rna polymerase holoenzyme]]
-[[Category: rsgi]]
-[[Category: structural genomic]]
-[[Category: transcription regulation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:45:56 2008''