5f5d - Revision history

OCA at 08:47, 12 July 2023

OCA — Wed, 12 Jul 2023 08:47:49 GMT

←Older revision		Revision as of 08:47, 12 July 2023
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	<StructureSection load='5f5d' size='340' side='right'caption='[[5f5d]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5f5d' size='340' side='right'caption='[[5f5d]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5f5d]] is a 1 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=5F5D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5F5D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5f5d]] is a 1 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=5F5D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5F5D FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5f5b\|5f5b]], [[5f5g\|5f5g]], [[5f5j\|5f5j]], [[5f5k\|5f5k]]</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]] 2.5Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">glpG, SK83_00858 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=5f5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f5d OCA], [https://pdbe.org/5f5d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5f5d RCSB], [https://www.ebi.ac.uk/pdbsum/5f5d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5f5d ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Rhomboid_protease Rhomboid protease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.105 3.4.21.105] </span></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5f5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f5d OCA], [~~http~~://pdbe.org/5f5d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5f5d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5f5d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5f5d ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~A0A0J2E248_ECOLX A0A0J2E248_ECOLX]~~] Rhomboid-type serine protease that catalyzes intramembrane proteolysis.~~[HAMAP-Rule~~:~~MF_01594]~~	+	[https://www.uniprot.org/uniprot/GLPG_ECOLI GLPG_ECOLI] Rhomboid-type serine protease that catalyzes intramembrane proteolysis.<ref>PMID:17099694</ref> <ref>PMID:16216077</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Rhomboid protease]]~~	+	[[Category: Cho S]]
-	[[Category: Cho, S]]	+	[[Category: Dickey SW]]
-	[[Category: Dickey~~, S W~~]]	+	[[Category: Urban S]]
-	[[Category: Urban, S]]	+
-	~~[[Category: Bicelle]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Intramembrane protease]]~~	+
-	~~[[Category: Rhomboid~~]]	+

OCA at 08:00, 29 April 2020

OCA — Wed, 29 Apr 2020 08:00:21 GMT

←Older revision		Revision as of 08:00, 29 April 2020
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	==Crystal structures and Inhibition kinetics reveal a two-state catalytic mechanism with drug design implications for rhomboid proteolysis==		==Crystal structures and Inhibition kinetics reveal a two-state catalytic mechanism with drug design implications for rhomboid proteolysis==
-	<StructureSection load='5f5d' size='340' side='right' caption='[[5f5d]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5f5d' size='340' side='right'caption='[[5f5d]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5f5d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F5D OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5F5D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5f5d]] is a 1 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=5F5D OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5F5D FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5f5b\|5f5b]], [[5f5g\|5f5g]], [[5f5j\|5f5j]], [[5f5k\|5f5k]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5f5b\|5f5b]], [[5f5g\|5f5g]], [[5f5j\|5f5j]], [[5f5k\|5f5k]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glpG, SK83_00858 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Rhomboid_protease Rhomboid protease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.105 3.4.21.105] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Rhomboid_protease Rhomboid protease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.105 3.4.21.105] </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=5f5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f5d OCA], [http://pdbe.org/5f5d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f5d RCSB], [http://www.ebi.ac.uk/pdbsum/5f5d PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5f5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f5d OCA], [http://pdbe.org/5f5d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f5d RCSB], [http://www.ebi.ac.uk/pdbsum/5f5d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f5d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5f5d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5f5d" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Rhomboid protease\|Rhomboid protease]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Rhomboid protease]]		[[Category: Rhomboid protease]]
	[[Category: Cho, S]]		[[Category: Cho, S]]

OCA at 18:08, 26 February 2016

OCA — Fri, 26 Feb 2016 18:08:57 GMT

←Older revision		Revision as of 18:08, 26 February 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5f5d is ~~ON HOLD~~	+	==Crystal structures and Inhibition kinetics reveal a two-state catalytic mechanism with drug design implications for rhomboid proteolysis==
		+	<StructureSection load='5f5d' size='340' side='right' caption='[[5f5d]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5f5d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F5D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F5D FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5f5b\|5f5b]], [[5f5g\|5f5g]], [[5f5j\|5f5j]], [[5f5k\|5f5k]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Rhomboid_protease Rhomboid protease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.105 3.4.21.105] </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=5f5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f5d OCA], [http://pdbe.org/5f5d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f5d RCSB], [http://www.ebi.ac.uk/pdbsum/5f5d PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A0J2E248_ECOLX A0A0J2E248_ECOLX]] Rhomboid-type serine protease that catalyzes intramembrane proteolysis.[HAMAP-Rule:MF_01594]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Intramembrane proteases signal by releasing proteins from the membrane, but despite their importance, their enzymatic mechanisms remain obscure. We probed rhomboid proteases with reversible, mechanism-based inhibitors that allow precise kinetic analysis and faithfully mimic the transition state structurally. Unexpectedly, inhibition by peptide aldehydes is non-competitive, revealing that in the Michaelis complex, substrate does not contact the catalytic center. Structural analysis in a membrane revealed that all extracellular loops of rhomboid make stabilizing interactions with substrate, but mainly through backbone interactions, explaining rhomboid's broad sequence selectivity. At the catalytic site, the tetrahedral intermediate lies covalently attached to the catalytic serine alone, with the oxyanion stabilized by unusual tripartite interactions with the side chains of H150, N154, and the backbone of S201. We also visualized unexpected substrate-enzyme interactions at the non-essential P2/P3 residues. These "extra" interactions foster potent rhomboid inhibition in living cells, thereby opening avenues for rational design of selective rhomboid inhibitors.

-	~~Authors: Urban, S~~., Cho, S., Dickey, S.W.	+	Crystal Structures and Inhibition Kinetics Reveal a Two-Stage Catalytic Mechanism with Drug Design Implications for Rhomboid Proteolysis.,Cho S, Dickey SW, Urban S Mol Cell. 2016 Feb 4;61(3):329-40. doi: 10.1016/j.molcel.2015.12.022. Epub 2016, Jan 21. PMID:26805573<ref>PMID:26805573</ref>

-	~~Description: Structure~~ of ~~E.Coli GlpG Y205F mutant in~~ the ~~DMPC~~/~~CHAPSO bicelle~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Dickey, S.W~~]]	+	<div class="pdbe-citations 5f5d" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Rhomboid protease]]
	[[Category: Cho, S]]		[[Category: Cho, S]]
		+	[[Category: Dickey, S W]]
	[[Category: Urban, S]]		[[Category: Urban, S]]
		+	[[Category: Bicelle]]
		+	[[Category: Hydrolase]]
		+	[[Category: Intramembrane protease]]
		+	[[Category: Rhomboid]]

OCA at 14:12, 10 February 2016

OCA — Wed, 10 Feb 2016 14:12:22 GMT

←Older revision		Revision as of 14:12, 10 February 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5f5d is ON HOLD ~~until Paper Publication~~	+	The entry 5f5d is ON HOLD

	Authors: Urban, S., Cho, S., Dickey, S.W.		Authors: Urban, S., Cho, S., Dickey, S.W.

OCA at 10:39, 7 January 2016

OCA — Thu, 07 Jan 2016 10:39:46 GMT

←Older revision		Revision as of 10:39, 7 January 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5f5d is ON HOLD	+	The entry 5f5d is ON HOLD until Paper Publication

	Authors: Urban, S., Cho, S., Dickey, S.W.		Authors: Urban, S., Cho, S., Dickey, S.W.

OCA at 11:12, 23 December 2015

OCA — Wed, 23 Dec 2015 11:12:41 GMT

←Older revision		Revision as of 11:12, 23 December 2015
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	The entry 5f5d is ON HOLD		The entry 5f5d is ON HOLD

-	Authors: ~~Sinisa~~ Urban, ~~SangWoo~~ Cho, ~~Seth W~~ Dickey	+	Authors: Urban, S., Cho, S., Dickey, S.W.

	Description: Structure of E.Coli GlpG Y205F mutant in the DMPC/CHAPSO bicelle		Description: Structure of E.Coli GlpG Y205F mutant in the DMPC/CHAPSO bicelle
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Sinisa Urban~~, ~~Sangwoo~~ Cho, ~~Seth W Dickey~~]]	+	[[Category: Dickey, S.W]]
		+	[[Category: Cho, S]]
		+	[[Category: Urban, S]]

OCA: Protected "5f5d" [edit=sysop:move=sysop]

OCA — Wed, 09 Dec 2015 12:39:43 GMT

Protected "5f5d" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:39, 9 December 2015

OCA: New page: '''Unreleased structure''' The entry 5f5d is ON HOLD Authors: Sinisa Urban, SangWoo Cho, Seth W Dickey Description: Structure of E.Coli GlpG Y205F mutant in the DMPC/CHAPSO bicelle [[C...

OCA — Wed, 09 Dec 2015 12:39:42 GMT

New page: '''Unreleased structure''' The entry 5f5d is ON HOLD Authors: Sinisa Urban, SangWoo Cho, Seth W Dickey Description: Structure of E.Coli GlpG Y205F mutant in the DMPC/CHAPSO bicelle [[C...

New page

'''Unreleased structure'''

The entry 5f5d is ON HOLD

Authors: Sinisa Urban, SangWoo Cho, Seth W Dickey

Description: Structure of E.Coli GlpG Y205F mutant in the DMPC/CHAPSO bicelle
[[Category: Unreleased Structures]]
[[Category: Sinisa Urban, Sangwoo Cho, Seth W Dickey]]