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2o9l

From Proteopedia

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[[Image:2o9l.jpg|left|200px]]
 
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{{Structure
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==AMBER refined NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element==
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|PDB= 2o9l |SIZE=350|CAPTION= <scene name='initialview01'>2o9l</scene>
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<StructureSection load='2o9l' size='340' side='right'caption='[[2o9l]]' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
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<table><tr><td colspan='2'>[[2o9l]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O9L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O9L FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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|GENE= rpoN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])
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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=2o9l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o9l OCA], [https://pdbe.org/2o9l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o9l RCSB], [https://www.ebi.ac.uk/pdbsum/2o9l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o9l ProSAT]</span></td></tr>
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|DOMAIN=
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</table>
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|RELATEDENTRY=[[2o8k|2O8K]]
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== Function ==
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2o9l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o9l OCA], [http://www.ebi.ac.uk/pdbsum/2o9l PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2o9l RCSB]</span>
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[https://www.uniprot.org/uniprot/O66858_AQUAE O66858_AQUAE]
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}}
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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/o9/2o9l_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=2o9l 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 sigma subunit of bacterial RNA polymerase (RNAP) regulates gene expression by directing RNAP to specific promoters. Unlike sigma(70)-type proteins, the alternative sigma factor, sigma(54), requires interaction with an ATPase to open DNA. We present the solution structure of the C-terminal domain of sigma(54) bound to the -24 promoter element, in which the conserved RpoN box motif inserts into the major groove of the DNA. This structure elucidates the basis for sequence specific recognition of the -24 element, orients sigma(54) on the promoter, and suggests how the C-terminal domain of sigma(54) interacts with RNAP.
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'''AMBER refined NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element'''
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Structural basis of DNA recognition by the alternative sigma-factor, sigma54.,Doucleff M, Pelton JG, Lee PS, Nixon BT, Wemmer DE J Mol Biol. 2007 Jun 15;369(4):1070-8. Epub 2007 Apr 12. PMID:17481658<ref>PMID:17481658</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 2o9l" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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The sigma subunit of bacterial RNA polymerase (RNAP) regulates gene expression by directing RNAP to specific promoters. Unlike sigma(70)-type proteins, the alternative sigma factor, sigma(54), requires interaction with an ATPase to open DNA. We present the solution structure of the C-terminal domain of sigma(54) bound to the -24 promoter element, in which the conserved RpoN box motif inserts into the major groove of the DNA. This structure elucidates the basis for sequence specific recognition of the -24 element, orients sigma(54) on the promoter, and suggests how the C-terminal domain of sigma(54) interacts with RNAP.
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*[[Sigma factor 3D structures|Sigma factor 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2O9L is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O9L OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Structural basis of DNA recognition by the alternative sigma-factor, sigma54., Doucleff M, Pelton JG, Lee PS, Nixon BT, Wemmer DE, J Mol Biol. 2007 Jun 15;369(4):1070-8. Epub 2007 Apr 12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17481658 17481658]
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[[Category: Aquifex aeolicus]]
[[Category: Aquifex aeolicus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Doucleff, M.]]
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[[Category: Doucleff M]]
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[[Category: Lee, P S.]]
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[[Category: Lee PS]]
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[[Category: Pelton, J G.]]
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[[Category: Pelton JG]]
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[[Category: Wemmer, D E.]]
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[[Category: Wemmer DE]]
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[[Category: amber]]
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[[Category: generalized born solvent model]]
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[[Category: helix-turn-helix]]
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[[Category: protein-dna complex]]
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[[Category: rna polymerase]]
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[[Category: sigma-54]]
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[[Category: transcription factor]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:14:41 2008''
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Current revision

AMBER refined NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element

PDB ID 2o9l

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