3gdu: Difference between revisions

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-[[Image:3gdu.png|left|200px]]
-{{STRUCTURE_3gdu|  PDB=3gdu  |  SCENE=  }}
+==Crystal structure of DegS H198P/D320A mutant modified by DFP and in complex with YRF peptide==
+<StructureSection load='3gdu' size='340' side='right'caption='[[3gdu]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3gdu]] 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=3GDU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GDU FirstGlance]. <br>
+</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]], [[3gdv|3gdv]]</div></td></tr>
+<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=3gdu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gdu OCA], [https://pdbe.org/3gdu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gdu RCSB], [https://www.ebi.ac.uk/pdbsum/3gdu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gdu 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/3gdu_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=3gdu 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 YRF 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>
-{{ABSTRACT_PUBMED_19836340}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3gdu" style="background-color:#fffaf0;"></div>
-[[3gdu]] is a 6 chain structure with sequence 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=3GDU OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:019836340</ref><references group="xtra"/>
+</StructureSection>
-[[Category: Escherichia coli]]
+[[Category: Ecoli]]
-[[Category: Grant, R A.]]
+[[Category: Large Structures]]
-[[Category: Sauer, R T.]]
+[[Category: Grant, R A]]
-[[Category: Sohn, J.]]
+[[Category: Sauer, R T]]
+[[Category: Sohn, J]]
 [[Category: Htra]]
 [[Category: Hydrolase]]
 [[Category: Hydrolase-hydrolase activator complex]]
 [[Category: Pdz omp]]
+[[Category: Periplasm]]
 [[Category: Protease]]
 [[Category: Serine protease]]
 [[Category: Stress-sensor]]