1ny6: Difference between revisions

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-[[Image:1ny6.gif|left|200px]]<br /><applet load="1ny6" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1ny6, resolution 3.10&Aring;" />
-'''Crystal structure of sigm54 activator (AAA+ ATPase) in the active state'''<br />
-==Overview==
+==Crystal structure of sigm54 activator (AAA+ ATPase) in the active state==
-Transcription by sigma54 RNA polymerase depends on activators that contain ATPase domains of the AAA+ class. These activators, which are often response regulators of two-component signal transduction systems, remodel the polymerase so that it can form open complexes at promoters. Here, we report the first crystal structures of the ATPase domain of an activator, the NtrC1 protein from the extreme thermophile Aquifex aeolicus. This domain alone, which is active, crystallized as a ring-shaped heptamer. The protein carrying both the ATPase and adjacent receiver domains, which is inactive, crystallized as a dimer. In the inactive dimer, one residue needed for catalysis is far from the active site, and extensive contacts among the domains prevent oligomerization of the ATPase domain. Oligomerization, which completes the active site, depends on surfaces that are buried in the dimer, and hence, on a rearrangement of the receiver domains upon phosphorylation. A motif in the ATPase domain known to be critical for coupling energy to remodeling of polymerase forms a novel loop that projects from the middle of an alpha helix. The extended, structured loops from the subunits of the heptamer localize to a pore in the center of the ring and form a surface that could contact sigma54.
+<StructureSection load='1ny6' size='340' side='right'caption='[[1ny6]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1ny6]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NY6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NY6 FirstGlance]. <br>
-NY6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] with <scene name='pdbligand=ADP:'>ADP</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NY6 OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ny6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ny6 OCA], [https://pdbe.org/1ny6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ny6 RCSB], [https://www.ebi.ac.uk/pdbsum/1ny6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ny6 ProSAT]</span></td></tr>
-Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains., Lee SY, De La Torre A, Yan D, Kustu S, Nixon BT, Wemmer DE, Genes Dev. 2003 Oct 15;17(20):2552-63. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14561776 14561776]
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/O67198_AQUAE O67198_AQUAE]
+== 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/ny/1ny6_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=1ny6 ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
 [[Category: Aquifex aeolicus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Kustu, S.]]
+[[Category: Kustu S]]
-[[Category: Lee, S Y.]]
+[[Category: Lee SY]]
-[[Category: Nixon, B T.]]
+[[Category: Nixon BT]]
-[[Category: Torre, A de la.]]
+[[Category: Wemmer DE]]
-[[Category: Wemmer, D E.]]
+[[Category: De la Torre A]]
-[[Category: ADP]]
-[[Category: aaa+ atpase]]
-[[Category: bacterial transcription]]
-[[Category: heptamer]]
-[[Category: sigma54 activator]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:11:18 2008''