2o5j

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{{Seed}}
 
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[[Image:2o5j.png|left|200px]]
 
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==Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the NTP substrate analog==
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The line below this paragraph, containing "STRUCTURE_2o5j", creates the "Structure Box" on the page.
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<StructureSection load='2o5j' size='340' side='right'caption='[[2o5j]], [[Resolution|resolution]] 3.00&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'>[[2o5j]] 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=2O5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O5J 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&#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=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_2o5j| PDB=2o5j | 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=2o5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o5j OCA], [https://pdbe.org/2o5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o5j RCSB], [https://www.ebi.ac.uk/pdbsum/2o5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o5j ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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).
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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/o5/2o5j_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=2o5j 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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The mechanism of substrate loading in multisubunit RNA polymerase is crucial for understanding the general principles of transcription yet remains hotly debated. Here we report the 3.0-A resolution structures of the Thermus thermophilus elongation complex (EC) with a non-hydrolysable substrate analogue, adenosine-5'-[(alpha,beta)-methyleno]-triphosphate (AMPcPP), and with AMPcPP plus the inhibitor streptolydigin. In the EC/AMPcPP structure, the substrate binds to the active ('insertion') site closed through refolding of the trigger loop (TL) into two alpha-helices. In contrast, the EC/AMPcPP/streptolydigin structure reveals an inactive ('preinsertion') substrate configuration stabilized by streptolydigin-induced displacement of the TL. Our structural and biochemical data suggest that refolding of the TL is vital for catalysis and have three main implications. First, despite differences in the details, the two-step preinsertion/insertion mechanism of substrate loading may be universal for all RNA polymerases. Second, freezing of the preinsertion state is an attractive target for the design of novel antibiotics. Last, the TL emerges as a prominent target whose refolding can be modulated by regulatory factors.
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===Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the NTP substrate analog===
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Structural basis for substrate loading in bacterial RNA polymerase.,Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M, Artsimovitch I, Landick R Nature. 2007 Jul 12;448(7150):163-8. Epub 2007 Jun 20. PMID:17581591<ref>PMID:17581591</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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<div class="pdbe-citations 2o5j" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_17581591}}, adds the Publication Abstract to the page
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 17581591 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_17581591}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2O5J 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=2O5J OCA].
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[[Category: Thermus thermophilus HB8]]
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[[Category: Vassylyev DG]]
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==Reference==
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[[Category: Vassylyeva MN]]
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Structural basis for substrate loading in bacterial RNA polymerase., Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M, Artsimovitch I, Landick R, Nature. 2007 Jul 12;448(7150):163-8. Epub 2007 Jun 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17581591 17581591]
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[[Category: DNA-directed RNA polymerase]]
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[[Category: Protein complex]]
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[[Category: Thermus thermophilus]]
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[[Category: Vassylyev, D G.]]
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[[Category: Vassylyeva, M N.]]
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[[Category: Elongation complex]]
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[[Category: Non-template dna]]
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[[Category: Ntp substrate]]
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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 Tue Jul 29 15:07:24 2008''
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Current revision

Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the NTP substrate analog

PDB ID 2o5j

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OCA

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