2be5: Difference between revisions

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-[[Image:2be5.gif|left|200px]]
- {{Structure
+==Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with inhibitor tagetitoxin==
-|PDB= 2be5 |SIZE=350|CAPTION= <scene name='initialview01'>2be5</scene>, resolution 2.40&Aring;
+<StructureSection load='2be5' size='340' side='right'caption='[[2be5]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TGT:TAGETITOXIN'>TGT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
+<table><tr><td colspan='2'>[[2be5]] 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=2BE5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BE5 FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[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] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#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=TGT:TAGETITOXIN'>TGT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2be5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2be5 OCA], [https://pdbe.org/2be5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2be5 RCSB], [https://www.ebi.ac.uk/pdbsum/2be5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2be5 ProSAT], [https://www.topsan.org/Proteins/RSGI/2be5 TOPSAN]</span></td></tr>
-|RELATEDENTRY=[[1iw7|1IW7]], [[1smy|1SMY]], [[2a6e|2A6E]], [[2a69|2A69]], [[2a68|2A68]], [[2a6h|2A6H]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2be5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2be5 OCA], [http://www.ebi.ac.uk/pdbsum/2be5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2be5 RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/RPOZ_THET8 RPOZ_THET8] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits (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/be/2be5_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=2be5 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Tagetitoxin (Tgt) inhibits transcription by an unknown mechanism. A structure at a resolution of 2.4 A of the Thermus thermophilus RNA polymerase (RNAP)-Tgt complex revealed that the Tgt-binding site within the RNAP secondary channel overlaps that of the stringent control effector ppGpp, which partially protects RNAP from Tgt inhibition. Tgt binding is mediated exclusively through polar interactions with the beta and beta' residues whose substitutions confer resistance to Tgt in vitro. Importantly, a Tgt phosphate, together with two active site acidic residues, coordinates the third Mg(2+) ion, which is distinct from the two catalytic metal ions. We show that Tgt inhibits all RNAP catalytic reactions and propose a mechanism in which the Tgt-bound Mg(2+) ion has a key role in stabilization of an inactive transcription intermediate. Remodeling of the active site by metal ions could be a common theme in the regulation of catalysis by nucleic acid enzymes.
-'''Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with inhibitor tagetitoxin'''
+Structural basis for transcription inhibition by tagetitoxin.,Vassylyev DG, Svetlov V, Vassylyeva MN, Perederina A, Igarashi N, Matsugaki N, Wakatsuki S, Artsimovitch I Nat Struct Mol Biol. 2005 Dec;12(12):1086-93. Epub 2005 Nov 6. PMID:16273103<ref>PMID:16273103</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2be5" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Tagetitoxin (Tgt) inhibits transcription by an unknown mechanism. A structure at a resolution of 2.4 A of the Thermus thermophilus RNA polymerase (RNAP)-Tgt complex revealed that the Tgt-binding site within the RNAP secondary channel overlaps that of the stringent control effector ppGpp, which partially protects RNAP from Tgt inhibition. Tgt binding is mediated exclusively through polar interactions with the beta and beta' residues whose substitutions confer resistance to Tgt in vitro. Importantly, a Tgt phosphate, together with two active site acidic residues, coordinates the third Mg(2+) ion, which is distinct from the two catalytic metal ions. We show that Tgt inhibits all RNAP catalytic reactions and propose a mechanism in which the Tgt-bound Mg(2+) ion has a key role in stabilization of an inactive transcription intermediate. Remodeling of the active site by metal ions could be a common theme in the regulation of catalysis by nucleic acid enzymes.
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
+*[[Sigma factor 3D structures|Sigma factor 3D structures]]
-==About this Structure==
+== References ==
-BE5 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=2BE5 OCA].
+<references/>
+__TOC__
-==Reference==
+</StructureSection>
-Structural basis for transcription inhibition by tagetitoxin., Vassylyev DG, Svetlov V, Vassylyeva MN, Perederina A, Igarashi N, Matsugaki N, Wakatsuki S, Artsimovitch I, Nat Struct Mol Biol. 2005 Dec;12(12):1086-93. Epub 2005 Nov 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16273103 16273103]
+[[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 V]]
-[[Category: Svetlov, V.]]
+[[Category: Vassylyev DG]]
-[[Category: Vassylyev, D G.]]
+[[Category: Vassylyeva MN]]
-[[Category: Vassylyeva, M N.]]
+[[Category: Wakatsuki S]]
-[[Category: Wakatsuki, S.]]
-[[Category: antibiotic]]
-[[Category: riken structural genomics/proteomics initiative]]
-[[Category: rna polymerase holoenzyme]]
-[[Category: rsgi]]
-[[Category: structural genomic]]
-[[Category: tagetitoxin]]
-[[Category: transcription regulation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:05:03 2008''