2o5i

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[[Image:2o5i.gif|left|200px]]
 
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{{Structure
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==Crystal structure of the T. thermophilus RNA polymerase elongation complex==
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|PDB= 2o5i |SIZE=350|CAPTION= <scene name='initialview01'>2o5i</scene>, resolution 2.5&Aring;
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<StructureSection load='2o5i' size='340' side='right'caption='[[2o5i]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> and <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene>
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<table><tr><td colspan='2'>[[2o5i]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O5I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O5I FirstGlance]. <br>
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|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]
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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]] 2.5&#8491;</td></tr>
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|GENE=
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<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>
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}}
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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=2o5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o5i OCA], [https://pdbe.org/2o5i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o5i RCSB], [https://www.ebi.ac.uk/pdbsum/2o5i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o5i ProSAT]</span></td></tr>
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</table>
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'''Crystal structure of the T. thermophilus RNA polymerase elongation complex'''
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== Function ==
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[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.
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== Evolutionary Conservation ==
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==Overview==
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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/o5/2o5i_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=2o5i 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 ==
The RNA polymerase elongation complex (EC) is both highly stable and processive, rapidly extending RNA chains for thousands of nucleotides. Understanding the mechanisms of elongation and its regulation requires detailed information about the structural organization of the EC. Here we report the 2.5-A resolution structure of the Thermus thermophilus EC; the structure reveals the post-translocated intermediate with the DNA template in the active site available for pairing with the substrate. DNA strand separation occurs one position downstream of the active site, implying that only one substrate at a time can specifically bind to the EC. The upstream edge of the RNA/DNA hybrid stacks on the beta'-subunit 'lid' loop, whereas the first displaced RNA base is trapped within a protein pocket, suggesting a mechanism for RNA displacement. The RNA is threaded through the RNA exit channel, where it adopts a conformation mimicking that of a single strand within a double helix, providing insight into a mechanism for hairpin-dependent pausing and termination.
The RNA polymerase elongation complex (EC) is both highly stable and processive, rapidly extending RNA chains for thousands of nucleotides. Understanding the mechanisms of elongation and its regulation requires detailed information about the structural organization of the EC. Here we report the 2.5-A resolution structure of the Thermus thermophilus EC; the structure reveals the post-translocated intermediate with the DNA template in the active site available for pairing with the substrate. DNA strand separation occurs one position downstream of the active site, implying that only one substrate at a time can specifically bind to the EC. The upstream edge of the RNA/DNA hybrid stacks on the beta'-subunit 'lid' loop, whereas the first displaced RNA base is trapped within a protein pocket, suggesting a mechanism for RNA displacement. The RNA is threaded through the RNA exit channel, where it adopts a conformation mimicking that of a single strand within a double helix, providing insight into a mechanism for hairpin-dependent pausing and termination.
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==About this Structure==
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Structural basis for transcription elongation by bacterial RNA polymerase.,Vassylyev DG, Vassylyeva MN, Perederina A, Tahirov TH, Artsimovitch I Nature. 2007 Jul 12;448(7150):157-62. Epub 2007 Jun 20. PMID:17581590<ref>PMID:17581590</ref>
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2O5I 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=2O5I OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structural basis for transcription elongation by bacterial RNA polymerase., Vassylyev DG, Vassylyeva MN, Perederina A, Tahirov TH, Artsimovitch I, Nature. 2007 Jul 12;448(7150):157-62. Epub 2007 Jun 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17581590 17581590]
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</div>
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[[Category: DNA-directed RNA polymerase]]
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<div class="pdbe-citations 2o5i" style="background-color:#fffaf0;"></div>
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[[Category: Protein complex]]
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[[Category: Thermus thermophilus]]
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[[Category: Tahirov, T H.]]
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[[Category: Vassylyev, D G.]]
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[[Category: Vassylyeva, M N.]]
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[[Category: MG]]
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[[Category: ZN]]
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[[Category: elongation complex]]
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[[Category: non-template dna]]
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[[Category: rna polymerase]]
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[[Category: rna transcript]]
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[[Category: template dna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:55:21 2008''
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==See Also==
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Thermus thermophilus HB8]]
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[[Category: Tahirov TH]]
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[[Category: Vassylyev DG]]
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[[Category: Vassylyeva MN]]

Current revision

Crystal structure of the T. thermophilus RNA polymerase elongation complex

PDB ID 2o5i

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