3lgt - Revision history

OCA at 10:20, 21 February 2024

OCA — Wed, 21 Feb 2024 10:20:32 GMT

←Older revision		Revision as of 10:20, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3lgt' size='340' side='right'caption='[[3lgt]], [[Resolution\|resolution]] 2.68Å' scene=''>		<StructureSection load='3lgt' size='340' side='right'caption='[[3lgt]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3lgt]] is a 1 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=3LGT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LGT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3lgt]] 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=3LGT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LGT FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[3lgi\|3lgi]], [[3lgu\|3lgu]], [[3lgv\|3lgv]], [[3lgw\|3lgw]], [[3lgy\|3lgy]], [[3lh1\|3lh1]], [[3lh3\|3lh3]]</div></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.68Å</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=3lgt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lgt OCA], [https://pdbe.org/3lgt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lgt RCSB], [https://www.ebi.ac.uk/pdbsum/3lgt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lgt ProSAT]</span></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=3lgt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lgt OCA], [https://pdbe.org/3lgt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lgt RCSB], [https://www.ebi.ac.uk/pdbsum/3lgt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lgt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== 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>	+	[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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 19:
	</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=3lgt ConSurf].		</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=3lgt ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	DegS is a periplasmic Escherichia coli protease, which functions as a trimer to catalyze the initial rate-limiting step in a proteolytic cascade that ultimately activates transcription of stress response genes in the cytoplasm. Each DegS subunit consists of a protease domain and a PDZ domain. During protein folding stress, DegS is allosterically activated by peptides exposed in misfolded outer membrane porins, which bind to the PDZ domain and stabilize the active protease. It is not known whether allostery is conferred by the PDZ domains or is an intrinsic feature of the trimeric protease domain. Here, we demonstrate that free DegS(DeltaPDZ) equilibrates between active and inactive trimers with the latter species predominating. Substrate binding stabilizes active DegS(DeltaPDZ) in a positively cooperative fashion. Mutations can also stabilize active DegS(DeltaPDZ) and produce an enzyme that displays hyperbolic kinetics and degrades substrate with a maximal velocity within error of that for fully activated, intact DegS. Crystal structures of multiple DegS(DeltaPDZ) variants, in functional and non-functional conformations, support a two-state model in which allosteric switching is mediated by changes in specific elements of tertiary structure in the context of an invariant trimeric base. Overall, our results indicate that protein substrates must bind sufficiently tightly and specifically to the functional conformation of DegS(DeltaPDZ) to assist their own degradation. Thus, substrate binding alone may have regulated the activities of ancestral DegS trimers with subsequent fusion of the protease domain to a PDZ domain, resulting in ligand-mediated regulation.
-
-	Allostery is an intrinsic property of the protease domain of DegS: implications for enzyme function and evolution.,Sohn J, Grant RA, Sauer RT J Biol Chem. 2010 Oct 29;285(44):34039-47. Epub 2010 Aug 24. PMID:20739286<ref>PMID:20739286</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3lgt" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Grant~~, R A~~]]	+	[[Category: Grant RA]]
-	[[Category: Sauer~~, R T~~]]	+	[[Category: Sauer RT]]
-	[[Category: Sohn, J]]	+	[[Category: Sohn J]]
-	~~[[Category: Htra]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pdz omp]]~~	+
-	~~[[Category: Protease]]~~	+
-	~~[[Category: Serine protease]]~~	+
-	~~[[Category: Stress-sensor~~]]	+

OCA at 12:34, 13 October 2021

OCA — Wed, 13 Oct 2021 12:34:12 GMT

←Older revision		Revision as of 12:34, 13 October 2021
Line 1:		Line 1:

	==Y162A/H198P double mutant of DegS-deltaPDZ protease==		==Y162A/H198P double mutant of DegS-deltaPDZ protease==
-	<StructureSection load='3lgt' size='340' side='right' caption='[[3lgt]], [[Resolution\|resolution]] 2.68Å' scene=''>	+	<StructureSection load='3lgt' size='340' side='right'caption='[[3lgt]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3lgt]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LGT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3LGT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3lgt]] is a 1 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=3LGT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LGT FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3lgi\|3lgi]], [[3lgu\|3lgu]], [[3lgv\|3lgv]], [[3lgw\|3lgw]], [[3lgy\|3lgy]], [[3lh1\|3lh1]], [[3lh3\|3lh3]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3lgi\|3lgi]], [[3lgu\|3lgu]], [[3lgv\|3lgv]], [[3lgw\|3lgw]], [[3lgy\|3lgy]], [[3lh1\|3lh1]], [[3lh3\|3lh3]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b3235, degS, hhoB, htrH, JW3204 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3lgt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lgt OCA], [~~http~~://pdbe.org/3lgt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3lgt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3lgt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3lgt ProSAT]</span></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=3lgt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lgt OCA], [https://pdbe.org/3lgt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lgt RCSB], [https://www.ebi.ac.uk/pdbsum/3lgt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lgt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://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>	+	[[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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Grant, R A]]		[[Category: Grant, R A]]
	[[Category: Sauer, R T]]		[[Category: Sauer, R T]]

OCA at 19:25, 24 January 2018

OCA — Wed, 24 Jan 2018 19:25:18 GMT

←Older revision		Revision as of 19:25, 24 January 2018
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lg/3lgt_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lg/3lgt_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 11:18, 5 August 2016

OCA — Fri, 05 Aug 2016 11:18:14 GMT

←Older revision		Revision as of 11:18, 5 August 2016
Line 1:		Line 1:
		+
	==Y162A/H198P double mutant of DegS-deltaPDZ protease==		==Y162A/H198P double mutant of DegS-deltaPDZ protease==
	<StructureSection load='3lgt' size='340' side='right' caption='[[3lgt]], [[Resolution\|resolution]] 2.68Å' scene=''>		<StructureSection load='3lgt' size='340' side='right' caption='[[3lgt]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3lgt]] is a 1 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=3LGT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LGT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3lgt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LGT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LGT FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3lgi\|3lgi]], [[3lgu\|3lgu]], [[3lgv\|3lgv]], [[3lgw\|3lgw]], [[3lgy\|3lgy]], [[3lh1\|3lh1]], [[3lh3\|3lh3]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3lgi\|3lgi]], [[3lgu\|3lgu]], [[3lgv\|3lgv]], [[3lgw\|3lgw]], [[3lgy\|3lgy]], [[3lh1\|3lh1]], [[3lh3\|3lh3]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b3235, degS, hhoB, htrH, JW3204 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~562 Escherichia coli~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b3235, degS, hhoB, htrH, JW3204 ([http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3lgt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lgt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lgt RCSB], [http://www.ebi.ac.uk/pdbsum/3lgt PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3lgt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lgt OCA], [http://pdbe.org/3lgt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lgt RCSB], [http://www.ebi.ac.uk/pdbsum/3lgt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lgt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</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=3lgt ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3lgt" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: Ecoli]]
	[[Category: Grant, R A]]		[[Category: Grant, R A]]
	[[Category: Sauer, R T]]		[[Category: Sauer, R T]]

OCA at 18:22, 25 December 2014

OCA — Thu, 25 Dec 2014 18:22:46 GMT

←Older revision		Revision as of 18:22, 25 December 2014
Line 7:		Line 7:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3lgt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lgt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lgt RCSB], [http://www.ebi.ac.uk/pdbsum/3lgt PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3lgt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lgt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lgt RCSB], [http://www.ebi.ac.uk/pdbsum/3lgt PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 17:06, 18 December 2014

OCA — Thu, 18 Dec 2014 17:06:25 GMT

←Older revision		Revision as of 17:06, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3lgt\| PDB=3lgt \| SCENE= }}~~	+	==Y162A/H198P double mutant of DegS-deltaPDZ protease==
-	===Y162A/H198P double mutant of DegS-deltaPDZ protease===	+	<StructureSection load='3lgt' size='340' side='right' caption='[[3lgt]], [[Resolution\|resolution]] 2.68Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20739286}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3lgt]] is a 1 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=3LGT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LGT FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3lgi\|3lgi]], [[3lgu\|3lgu]], [[3lgv\|3lgv]], [[3lgw\|3lgw]], [[3lgy\|3lgy]], [[3lh1\|3lh1]], [[3lh3\|3lh3]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b3235, degS, hhoB, htrH, JW3204 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3lgt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lgt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lgt RCSB], [http://www.ebi.ac.uk/pdbsum/3lgt PDBsum]</span></td></tr>
		+	</table>
		+	== 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/lg/3lgt_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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DegS is a periplasmic Escherichia coli protease, which functions as a trimer to catalyze the initial rate-limiting step in a proteolytic cascade that ultimately activates transcription of stress response genes in the cytoplasm. Each DegS subunit consists of a protease domain and a PDZ domain. During protein folding stress, DegS is allosterically activated by peptides exposed in misfolded outer membrane porins, which bind to the PDZ domain and stabilize the active protease. It is not known whether allostery is conferred by the PDZ domains or is an intrinsic feature of the trimeric protease domain. Here, we demonstrate that free DegS(DeltaPDZ) equilibrates between active and inactive trimers with the latter species predominating. Substrate binding stabilizes active DegS(DeltaPDZ) in a positively cooperative fashion. Mutations can also stabilize active DegS(DeltaPDZ) and produce an enzyme that displays hyperbolic kinetics and degrades substrate with a maximal velocity within error of that for fully activated, intact DegS. Crystal structures of multiple DegS(DeltaPDZ) variants, in functional and non-functional conformations, support a two-state model in which allosteric switching is mediated by changes in specific elements of tertiary structure in the context of an invariant trimeric base. Overall, our results indicate that protein substrates must bind sufficiently tightly and specifically to the functional conformation of DegS(DeltaPDZ) to assist their own degradation. Thus, substrate binding alone may have regulated the activities of ancestral DegS trimers with subsequent fusion of the protease domain to a PDZ domain, resulting in ligand-mediated regulation.

-	~~==Function==~~	+	Allostery is an intrinsic property of the protease domain of DegS: implications for enzyme function and evolution.,Sohn J, Grant RA, Sauer RT J Biol Chem. 2010 Oct 29;285(44):34039-47. Epub 2010 Aug 24. PMID:20739286<ref>PMID:20739286</ref>
-	~~[[http~~:~~//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>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3lgt]] is~~ a ~~1 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=3LGT OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:020739286</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Grant, R A..]]	+	[[Category: Grant, R A]]
-	[[Category: Sauer, R T.]]	+	[[Category: Sauer, R T]]
-	[[Category: Sohn, J.]]	+	[[Category: Sohn, J]]
	[[Category: Htra]]		[[Category: Htra]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA: Protected "3lgt" [edit=sysop:move=sysop]

OCA — Thu, 04 Apr 2013 20:09:31 GMT

Protected "3lgt" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:09, 4 April 2013

OCA at 20:09, 4 April 2013

OCA — Thu, 04 Apr 2013 20:09:29 GMT

←Older revision		Revision as of 20:09, 4 April 2013
Line 1:		Line 1:
-	{{Seed}}
-	[[Image:3lgt.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3lgt", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3lgt\| PDB=3lgt \| SCENE= }}		{{STRUCTURE_3lgt\| PDB=3lgt \| SCENE= }}
-
	===Y162A/H198P double mutant of DegS-deltaPDZ protease===		===Y162A/H198P double mutant of DegS-deltaPDZ protease===
		+	{{ABSTRACT_PUBMED_20739286}}

-		+	==Function==
-	~~<!--~~	+	[[http://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>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_20739286}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov)~~, ~~where 20739286 is~~ the ~~PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_20739286}}~~	+

	==About this Structure==		==About this Structure==
-	~~3LGT~~ is a 1 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=3LGT OCA].	+	[[3lgt]] is a 1 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=3LGT OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20739286~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020739286</ref><references group="xtra"/><references/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Grant, R A..]]		[[Category: Grant, R A..]]
Line 34:		Line 21:
	[[Category: Serine protease]]		[[Category: Serine protease]]
	[[Category: Stress-sensor]]		[[Category: Stress-sensor]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 10 06:55:17 2010''

OCA at 03:44, 10 November 2010

OCA — Wed, 10 Nov 2010 03:44:23 GMT

←Older revision		Revision as of 03:44, 10 November 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3lgt.~~jpg~~\|left\|200px]]	+	[[Image:3lgt.png\|left\|200px]]

	<!--		<!--
Line 12:		Line 12:
	===Y162A/H198P double mutant of DegS-deltaPDZ protease===		===Y162A/H198P double mutant of DegS-deltaPDZ protease===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20739286}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20739286 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20739286}}

	==About this Structure==		==About this Structure==
	3LGT is a 1 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=3LGT OCA].		3LGT is a 1 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=3LGT OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20739286</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Grant, R A..]]		[[Category: Grant, R A..]]
Line 26:		Line 35:
	[[Category: Stress-sensor]]		[[Category: Stress-sensor]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Aug 25 08~~:56:57 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 10 06:55:17 2010''

OCA at 04:49, 25 August 2010

OCA — Wed, 25 Aug 2010 04:49:09 GMT

←Older revision		Revision as of 04:49, 25 August 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3lgt.jpg\|left\|200px]]

-	The ~~entry 3lgt~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3lgt", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3lgt\| PDB=3lgt \| SCENE= }}

-	~~Authors: Sohn, J., Grant, R.A.., Sauer, R.T.~~	+	===Y162A/H198P double mutant of DegS-deltaPDZ protease===

-	Description: Y162A/H198P double mutant of DegS-deltaPDZ protease

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Feb 17 10~~:10:22 2010''	+	==About this Structure==
		+	3LGT is a 1 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=3LGT OCA].
		+	[[Category: Escherichia coli]]
		+	[[Category: Grant, R A..]]
		+	[[Category: Sauer, R T.]]
		+	[[Category: Sohn, J.]]
		+	[[Category: Htra]]
		+	[[Category: Hydrolase]]
		+	[[Category: Pdz omp]]
		+	[[Category: Protease]]
		+	[[Category: Serine protease]]
		+	[[Category: Stress-sensor]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 25 08:56:57 2010''