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1l9z

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[[Image:1l9z.jpg|left|200px]]<br /><applet load="1l9z" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1l9z, resolution 6.5&Aring;" />
 
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'''Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution'''<br />
 
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==Overview==
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==Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution==
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The crystal structure of Thermus aquaticus RNA polymerase holoenzyme (alpha2betabeta'omegasigmaA) complexed with a fork-junction promoter DNA fragment has been determined by fitting high-resolution x-ray structures of individual components into a 6.5-angstrom resolution map. The DNA lies across one face of the holoenzyme, completely outside the RNA polymerase active site channel. All sequence-specific contacts with core promoter elements are mediated by the sigma subunit. A universally conserved tryptophan is ideally positioned to stack on the exposed face of the base pair at the upstream edge of the transcription bubble. Universally conserved basic residues of the sigma subunit provide critical contacts with the DNA phosphate backbone and play a role in directing the melted DNA template strand into the RNA polymerase active site. The structure explains how holoenzyme recognizes promoters containing variably spaced -10 and -35 elements and provides the basis for models of the closed and open promoter complexes.
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<StructureSection load='1l9z' size='340' side='right'caption='[[1l9z]], [[Resolution|resolution]] 6.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1l9z]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L9Z FirstGlance]. <br>
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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]] 6.5&#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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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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=1l9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l9z OCA], [https://pdbe.org/1l9z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l9z RCSB], [https://www.ebi.ac.uk/pdbsum/1l9z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l9z ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RPOA_THEAQ RPOA_THEAQ]
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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/l9/1l9z_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=1l9z ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1L9Z is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9Z OCA].
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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*[[Sigma factor 3D structures|Sigma factor 3D structures]]
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==Reference==
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__TOC__
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Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex., Murakami KS, Masuda S, Campbell EA, Muzzin O, Darst SA, Science. 2002 May 17;296(5571):1285-90. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12016307 12016307]
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</StructureSection>
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[[Category: DNA-directed RNA polymerase]]
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[[Category: Large Structures]]
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[[Category: Protein complex]]
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[[Category: Thermus aquaticus]]
[[Category: Thermus aquaticus]]
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[[Category: Campbell, E A.]]
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[[Category: Campbell EA]]
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[[Category: Darst, S A.]]
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[[Category: Darst SA]]
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[[Category: Masuda, S.]]
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[[Category: Masuda S]]
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[[Category: Murakami, K S.]]
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[[Category: Murakami KS]]
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[[Category: Muzzin, O.]]
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[[Category: Muzzin O]]
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[[Category: MG]]
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[[Category: ZN]]
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[[Category: coiled-coil]]
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[[Category: helix-turn-helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:42:58 2008''
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Current revision

Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution

PDB ID 1l9z

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