3gdv: Difference between revisions

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-{{Seed}}
-[[Image:3gdv.jpg|left|200px]]
-<!--
+==Crystal structure of DegS H198P/D320A mutant modified by DFP and in complex with YQF peptide==
-The line below this paragraph, containing "STRUCTURE_3gdv", creates the "Structure Box" on the page.
+<StructureSection load='3gdv' size='340' side='right'caption='[[3gdv]], [[Resolution|resolution]] 2.49&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3gdv]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GDV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GDV FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MIS:MONOISOPROPYLPHOSPHORYLSERINE'>MIS</scene></td></tr>
--->
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gds|3gds]], [[3gdu|3gdu]]</div></td></tr>
-{{STRUCTURE_3gdv|  PDB=3gdv  |  SCENE=  }}
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b3235, degS, hhoB, htrH, JW3204 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3gdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gdv OCA], [https://pdbe.org/3gdv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gdv RCSB], [https://www.ebi.ac.uk/pdbsum/3gdv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gdv ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/DEGS_ECOLI DEGS_ECOLI]] When heat shock or other environmental stresses disrupt protein folding in the periplasm, DegS senses the accumulation of unassembled outer membrane porins (OMPs) and then initiates RseA (anti sigma-E factor) degradation by cleaving it in its periplasmic domain, making it an attractive substrate for subsequent cleavage by RseP. This cascade that ultimately leads to the sigma-E-driven expression of a variety of factors dealing with folding stress in the periplasm and OMP assembly.<ref>PMID:12183369</ref> <ref>PMID:19695325</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/gd/3gdv_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=3gdv ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In the E. coli periplasm, C-terminal peptides of misfolded outer-membrane porins (OMPs) bind to the PDZ domains of the trimeric DegS protease, triggering cleavage of a transmembrane regulator and transcriptional activation of stress genes. We show that an active-site DegS mutation partially bypasses the requirement for peptide activation and acts synergistically with mutations that disrupt contacts between the protease and PDZ domains. Biochemical results support an allosteric model, in which these mutations, active-site modification, and peptide/substrate binding act in concert to stabilize proteolytically active DegS. Cocrystal structures of DegS in complex with different OMP peptides reveal activation of the protease domain with varied conformations of the PDZ domain and without specific contacts from the bound OMP peptide. Taken together, these results indicate that the binding of OMP peptides activates proteolysis principally by relieving inhibitory contacts between the PDZ domain and the protease domain of DegS.
-===Crystal structure of DegS H198P/D320A mutant modified by DFP and in complex with YQF peptide===
+OMP peptides activate the DegS stress-sensor protease by a relief of inhibition mechanism.,Sohn J, Grant RA, Sauer RT Structure. 2009 Oct 14;17(10):1411-21. PMID:19836340<ref>PMID:19836340</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==About this Structure==
+</div>
-GDV is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GDV OCA].
+<div class="pdbe-citations 3gdv" style="background-color:#fffaf0;"></div>
-[[Category: Escherichia coli]]
+== References ==
-[[Category: Grant, R A.]]
+<references/>
-[[Category: Sauer, R T.]]
+__TOC__
-[[Category: Sohn, J.]]
+</StructureSection>
+[[Category: Ecoli]]
+[[Category: Large Structures]]
+[[Category: Grant, R A]]
+[[Category: Sauer, R T]]
+[[Category: Sohn, J]]
 [[Category: Htra]]
 [[Category: Hydrolase]]
-[[Category: Hydrolase/hydrolase activator complex]]
+[[Category: Hydrolase-hydrolase activator complex]]
 [[Category: Pdz omp]]
-[[Category: Periplasm]]
 [[Category: Protease]]
 [[Category: Serine protease]]
 [[Category: Stress-sensor]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr  2 16:14:07 2009''