2c96: Difference between revisions

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-[[Image:2c96.jpg|left|200px]]<br /><applet load="2c96" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2c96, resolution 1.80&Aring;" />
-'''STRUCTURAL BASIS OF THE NUCLEOTIDE DRIVEN CONFORMATIONAL CHANGES IN THE AAA DOMAIN OF TRANSCRIPTION ACTIVATOR PSPF'''<br />
-==Overview==
+==Structural basis of the nucleotide driven conformational changes in the AAA domain of transcription activator PspF==
-Bacterial enhancer-binding proteins (EBP) activate transcription by, hydrolyzing ATP to restructure the sigma(54)-RNA polymerase-promoter, complex. We compare six high resolution structures (&lt;2.1 A) of the AAA(+), domain of EBP phage shock protein F (PspF) including apo, AMPPNP, Mg(2+)-ATP, and ADP forms. These structures permit a description of the, atomic details underpinning the origins of the conformational changes, occurring during ATP hydrolysis. Conserved regions of PspF's AAA(+) domain, respond distinctively to nucleotide binding and hydrolysis, suggesting, functional roles during the hydrolysis cycle, which completely agree with, those derived from activities of PspF mutated at these positions. We, propose a putative atomic switch that is responsible for coupling, structural changes in the nucleotide-binding site to the repositioning of, the sigma(54)-interacting loops. Striking similarities in, nucleotide-specific conformational changes and atomic switch exist between, PspF and the large T antigen helicase, suggesting conservation in the, origin of those events amongst AAA(+) proteins.
+<StructureSection load='2c96' size='340' side='right'caption='[[2c96]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2c96]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C96 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C96 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]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</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=2c96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c96 OCA], [https://pdbe.org/2c96 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c96 RCSB], [https://www.ebi.ac.uk/pdbsum/2c96 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c96 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PSPF_ECOLI PSPF_ECOLI] Transcriptional activator for the phage shock protein (psp) operon (pspABCDE) and pspG gene.<ref>PMID:8606168</ref> <ref>PMID:15485810</ref> <ref>PMID:19804784</ref>
+== 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/c9/2c96_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=2c96 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Bacterial enhancer-binding proteins (EBP) activate transcription by hydrolyzing ATP to restructure the sigma(54)-RNA polymerase-promoter complex. We compare six high resolution structures (&lt;2.1 A) of the AAA(+) domain of EBP phage shock protein F (PspF) including apo, AMPPNP, Mg(2+)-ATP, and ADP forms. These structures permit a description of the atomic details underpinning the origins of the conformational changes occurring during ATP hydrolysis. Conserved regions of PspF's AAA(+) domain respond distinctively to nucleotide binding and hydrolysis, suggesting functional roles during the hydrolysis cycle, which completely agree with those derived from activities of PspF mutated at these positions. We propose a putative atomic switch that is responsible for coupling structural changes in the nucleotide-binding site to the repositioning of the sigma(54)-interacting loops. Striking similarities in nucleotide-specific conformational changes and atomic switch exist between PspF and the large T antigen helicase, suggesting conservation in the origin of those events amongst AAA(+) proteins.
-==About this Structure==
+Structural basis of the nucleotide driven conformational changes in the AAA+ domain of transcription activator PspF.,Rappas M, Schumacher J, Niwa H, Buck M, Zhang X J Mol Biol. 2006 Mar 24;357(2):481-92. Epub 2006 Jan 13. PMID:16430918<ref>PMID:16430918</ref>
-C96 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=ATP:'>ATP</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Known structural/functional Site: <scene name='pdbsite=AC1:Atp+Binding+Site+For+Chain+A'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C96 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structural basis of the nucleotide driven conformational changes in the AAA+ domain of transcription activator PspF., Rappas M, Schumacher J, Niwa H, Buck M, Zhang X, J Mol Biol. 2006 Mar 24;357(2):481-92. Epub 2006 Jan 13. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16430918 16430918]
+</div>
-[[Category: Escherichia coli]]
+<div class="pdbe-citations 2c96" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
+== References ==
-[[Category: Buck, M.]]
+<references/>
-[[Category: Niwa, H.]]
+__TOC__
-[[Category: Rappas, M.]]
+</StructureSection>
-[[Category: Schumacher, J.]]
+[[Category: Escherichia coli K-12]]
-[[Category: Zhang, X.]]
+[[Category: Large Structures]]
-[[Category: ATP]]
+[[Category: Buck M]]
-[[Category: aaa domain]]
+[[Category: Niwa H]]
-[[Category: activator]]
+[[Category: Rappas M]]
-[[Category: atp-binding]]
+[[Category: Schumacher J]]
-[[Category: atpase]]
+[[Category: Zhang X]]
-[[Category: bacterial sigma54 activator]]
-[[Category: dna-binding]]
-[[Category: nucleotide-binding]]
-[[Category: sensory transduction]]
-[[Category: transcription regulation]]
-[[Category: two-component regulatory system]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb  3 10:32:59 2008''