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[[Image:2o5j.gif|left|200px]]
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{{STRUCTURE_2o5j|  PDB=2o5j  |  SCENE=  }}
'''Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the NTP substrate analog'''


==Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the NTP substrate analog==
<StructureSection load='2o5j' size='340' side='right'caption='[[2o5j]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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>
<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>
</table>
== 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/o5/2o5j_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=2o5j ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


==Overview==
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>
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.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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].
</div>
<div class="pdbe-citations 2o5j" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
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]
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
[[Category: DNA-directed RNA polymerase]]
== References ==
[[Category: Protein complex]]
<references/>
[[Category: Thermus thermophilus]]
__TOC__
[[Category: Vassylyev, D G.]]
</StructureSection>
[[Category: Vassylyeva, M N.]]
[[Category: Large Structures]]
[[Category: Elongation complex]]
[[Category: Thermus thermophilus HB8]]
[[Category: Non-template dna]]
[[Category: Vassylyev DG]]
[[Category: Ntp substrate]]
[[Category: Vassylyeva MN]]
[[Category: Rna polymerase]]
[[Category: Rna transcript]]
[[Category: Template dna]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 10:21:12 2008''
Retrieved from "https://proteopedia.org/2o5j"