4rr1 - Revision history

OCA at 08:25, 8 March 2023

2023-03-08T08:25:04Z

←Older revision		Revision as of 08:25, 8 March 2023
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	<StructureSection load='4rr1' size='340' side='right'caption='[[4rr1]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4rr1' size='340' side='right'caption='[[4rr1]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rr1]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RR1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4RR1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rr1]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RR1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RR1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:~~NICKEL+(II)+ION~~'>NI</scene>, <scene name='pdbligand=~~PO4~~:~~PHOSPHATE~~+ION'>~~PO4~~</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</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=4rr1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rr1 OCA], [https://pdbe.org/4rr1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rr1 RCSB], [https://www.ebi.ac.uk/pdbsum/4rr1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rr1 ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sot\|1sot]]</td></tr>~~	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">degS, P12B_c3347 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=4rr1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rr1 OCA], [~~http~~://pdbe.org/4rr1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4rr1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4rr1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4rr1 ProSAT]</span></td></tr>	+
	</table>		</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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~Gram-negative bacteria respond to misfolded proteins in the cell envelope with the sigmaE-driven expression of periplasmic proteases/chaperones~~. ~~Activation of sigmaE is controlled by~~ a ~~proteolytic~~ cascade ~~that is~~ initiated by ~~the~~ DegS ~~protease~~. DegS ~~senses misfolded protein in the periplasm~~, ~~undergoes autoactivation~~, and ~~cleaves the antisigma factor RseA~~. ~~Here, we present~~ the ~~crystal structures of three distinct states of DegS from E~~. ~~coli. DegS alone exists in a catalytically inactive form. Binding~~ of ~~stress~~-~~signaling peptides~~ to ~~its~~ PDZ ~~domain induces~~ a ~~series~~ of ~~conformational changes~~ that ~~activates protease function. Backsoaking of crystals containing the DegS~~-~~activator complex revealed~~ the ~~presence of an~~ active~~/inactive hybrid structure~~ and ~~demonstrated the reversibility of activation. Taken together~~, the ~~structural data illustrate~~ in ~~molecular detail how DegS acts as a periplasmic stress sensor~~. ~~Our results suggest~~ a ~~novel regulatory role for PDZ domains and unveil a novel~~ mechanism of ~~reversible~~ protease activation.	+	In E. coli, outer-membrane stress causes a transcriptional response through a signaling cascade initiated by DegS cleavage of a transmembrane antisigma factor. Each subunit of DegS, an HtrA-family protease, contains a protease domain and a PDZ domain. The trimeric protease domain is autoinhibited by the unliganded PDZ domains. Allosteric activation requires binding of unassembled outer-membrane proteins (OMPs) to the PDZ domains and protein substrate binding. Here, we identify a set of DegS residues that cluster together at subunit-subunit interfaces in the trimer, link the active sites and substrate binding sites, and are crucial for stabilizing the active enzyme conformation in response to OMP signaling. These residues are conserved across the HtrA-protease family, including orthologs linked to human disease, supporting a common mechanism of allosteric activation. Indeed, mutation of residues at homologous positions in the DegP quality-control protease also eliminates allosteric activation.

-	~~Crystal structure of the DegS stress sensor: How a PDZ domain recognizes misfolded protein and activates a protease~~.,~~Wilken C~~, ~~Kitzing K~~, ~~Kurzbauer R~~, ~~Ehrmann M~~, ~~Clausen T Cell~~. ~~2004 May 14~~;~~117~~(4):~~483~~-94. PMID:~~15137941~~<ref>PMID:~~15137941~~</ref>	+	A Conserved Activation Cluster Is Required for Allosteric Communication in HtrA-Family Proteases.,de Regt AK, Kim S, Sohn J, Grant RA, Baker TA, Sauer RT Structure. 2015 Mar 3;23(3):517-26. doi: 10.1016/j.str.2015.01.012. Epub 2015 Feb, 19. PMID:25703375<ref>PMID:25703375</ref>

	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>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Grant~~, R A~~]]	+	[[Category: Grant RA]]
-	[[Category: Sauer~~, R T]]~~	+	[[Category: Sauer RT]]
-	~~[[Category: Htra]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pdz]]~~	+
-	~~[[Category: Protein quality control]]~~	+
-	~~[[Category: Stress response]]~~	+
-	~~[[Category: Upr~~]]	+

OCA at 10:24, 1 May 2019

2019-05-01T10:24:38Z

←Older revision		Revision as of 10:24, 1 May 2019
Line 1:		Line 1:

	==re-refinement of entry 1sot, Crystal Structure of the DegS stress sensor==		==re-refinement of entry 1sot, Crystal Structure of the DegS stress sensor==
-	<StructureSection load='4rr1' size='340' side='right' caption='[[4rr1]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='4rr1' size='340' side='right'caption='[[4rr1]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rr1]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RR1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RR1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rr1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RR1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RR1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sot\|1sot]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sot\|1sot]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">degS, P12B_c3347 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=4rr1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rr1 OCA], [http://pdbe.org/4rr1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rr1 RCSB], [http://www.ebi.ac.uk/pdbsum/4rr1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rr1 ProSAT]</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=4rr1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rr1 OCA], [http://pdbe.org/4rr1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rr1 RCSB], [http://www.ebi.ac.uk/pdbsum/4rr1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rr1 ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Grant, R A]]		[[Category: Grant, R A]]
	[[Category: Sauer, R T]]		[[Category: Sauer, R T]]

OCA at 17:26, 18 January 2017

2017-01-18T17:26:27Z

←Older revision		Revision as of 17:26, 18 January 2017
Line 1:		Line 1:
		+
	==re-refinement of entry 1sot, Crystal Structure of the DegS stress sensor==		==re-refinement of entry 1sot, Crystal Structure of the DegS stress sensor==
	<StructureSection load='4rr1' size='340' side='right' caption='[[4rr1]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4rr1' size='340' side='right' caption='[[4rr1]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sot\|1sot]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sot\|1sot]]</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=4rr1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rr1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rr1 RCSB], [http://www.ebi.ac.uk/pdbsum/4rr1 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=4rr1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rr1 OCA], [http://pdbe.org/4rr1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rr1 RCSB], [http://www.ebi.ac.uk/pdbsum/4rr1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rr1 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 4rr1" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:43, 11 March 2015

2015-03-11T11:43:46Z

←Older revision		Revision as of 11:43, 11 March 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==re-refinement of entry 1sot, Crystal Structure of the DegS stress sensor==
		+	<StructureSection load='4rr1' size='340' side='right' caption='[[4rr1]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4rr1]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RR1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RR1 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sot\|1sot]]</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=4rr1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rr1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rr1 RCSB], [http://www.ebi.ac.uk/pdbsum/4rr1 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Gram-negative bacteria respond to misfolded proteins in the cell envelope with the sigmaE-driven expression of periplasmic proteases/chaperones. Activation of sigmaE is controlled by a proteolytic cascade that is initiated by the DegS protease. DegS senses misfolded protein in the periplasm, undergoes autoactivation, and cleaves the antisigma factor RseA. Here, we present the crystal structures of three distinct states of DegS from E. coli. DegS alone exists in a catalytically inactive form. Binding of stress-signaling peptides to its PDZ domain induces a series of conformational changes that activates protease function. Backsoaking of crystals containing the DegS-activator complex revealed the presence of an active/inactive hybrid structure and demonstrated the reversibility of activation. Taken together, the structural data illustrate in molecular detail how DegS acts as a periplasmic stress sensor. Our results suggest a novel regulatory role for PDZ domains and unveil a novel mechanism of reversible protease activation.

-	~~The entry 4rr1 is ON HOLD~~	+	Crystal structure of the DegS stress sensor: How a PDZ domain recognizes misfolded protein and activates a protease.,Wilken C, Kitzing K, Kurzbauer R, Ehrmann M, Clausen T Cell. 2004 May 14;117(4):483-94. PMID:15137941<ref>PMID:15137941</ref>

-	~~Authors: Sauer~~, R.T.~~, Grant, R.A~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: re-refinement of entry 1sot, Crystal Structure of the DegS stress sensor~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
-	[[Category: Sauer, R.T]]	+	__TOC__
-	[[Category: ~~Grant, R.A~~]]	+	</StructureSection>
		+	[[Category: Grant, R A]]
		+	[[Category: Sauer, R T]]
		+	[[Category: Htra]]
		+	[[Category: Hydrolase]]
		+	[[Category: Pdz]]
		+	[[Category: Protein quality control]]
		+	[[Category: Stress response]]
		+	[[Category: Upr]]

OCA at 17:14, 24 December 2014

2014-12-24T17:14:39Z

←Older revision		Revision as of 17:14, 24 December 2014
Line 6:		Line 6:

	Description: re-refinement of entry 1sot, Crystal Structure of the DegS stress sensor		Description: re-refinement of entry 1sot, Crystal Structure of the DegS stress sensor
		+	[[Category: Unreleased Structures]]
		+	[[Category: Sauer, R.T]]
		+	[[Category: Grant, R.A]]

OCA at 06:45, 26 November 2014

2014-11-26T06:45:04Z

←Older revision		Revision as of 06:45, 26 November 2014
Line 5:		Line 5:
	Authors: Sauer, R.T., Grant, R.A.		Authors: Sauer, R.T., Grant, R.A.

-	Description: re-refinement of entry ~~1s0t~~, Crystal Structure of the DegS stress sensor	+	Description: re-refinement of entry 1sot, Crystal Structure of the DegS stress sensor

OCA: Protected "4rr1" [edit=sysop:move=sysop]

2014-11-19T11:31:02Z

Protected "4rr1" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:31, 19 November 2014

OCA: New page: '''Unreleased structure''' The entry 4rr1 is ON HOLD Authors: Sauer, R.T., Grant, R.A. Description: re-refinement of entry 1s0t, Crystal Structure of the DegS stress sensor

2014-11-19T11:31:00Z

New page: '''Unreleased structure''' The entry 4rr1 is ON HOLD Authors: Sauer, R.T., Grant, R.A. Description: re-refinement of entry 1s0t, Crystal Structure of the DegS stress sensor

New page

'''Unreleased structure'''

The entry 4rr1 is ON HOLD

Authors: Sauer, R.T., Grant, R.A.

Description: re-refinement of entry 1s0t, Crystal Structure of the DegS stress sensor