5f5j - Revision history

OCA at 08:48, 12 July 2023

2023-07-12T08:48:08Z

←Older revision		Revision as of 08:48, 12 July 2023
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	<StructureSection load='5f5j' size='340' side='right'caption='[[5f5j]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5f5j' size='340' side='right'caption='[[5f5j]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5f5j]] is a 2 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=5F5J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5F5J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5f5j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster] and [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5F5J FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=5XU:(2~{S})-2-AZANYLPROPANAL'>5XU</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></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]] 2.4Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5f5b\|5f5b]]~~, [[~~5f5d~~\|~~5f5d]], [[5f5g\|5f5g]], [[5f5k\|5f5k~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5XU:(2~{S})-2-AZANYLPROPANAL'>5XU</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></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=5f5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f5j OCA], [https://pdbe.org/5f5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5f5j RCSB], [https://www.ebi.ac.uk/pdbsum/5f5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5f5j 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=5f5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f5j OCA], [~~http~~://pdbe.org/5f5j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5f5j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5f5j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5f5j 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: Drosophila melanogaster]]
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Rhomboid protease]]~~	+	[[Category: Cho S]]
-	[[Category: Cho, S]]	+	[[Category: Dickey S]]
-	[[Category: Dickey, S]]	+	[[Category: Urban S]]
-	[[Category: Urban, S]]	+
-	~~[[Category: Aldehyde inhibitor]]~~	+
-	~~[[Category: Bicelle]]~~	+
-	~~[[Category: Glpg]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+
-	~~[[Category: Hydrolase-inhibitor complex]]~~	+
-	~~[[Category: Rhomboid~~]]	+

OCA at 08:00, 29 April 2020

2020-04-29T08:00:44Z

←Older revision		Revision as of 08:00, 29 April 2020
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	==E.coli GlpG Y205F mutant complexed with aldehyde inhibitor in DMPC/CHAPSO bicelle==		==E.coli GlpG Y205F mutant complexed with aldehyde inhibitor in DMPC/CHAPSO bicelle==
-	<StructureSection load='5f5j' size='340' side='right' caption='[[5f5j]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='5f5j' size='340' side='right'caption='[[5f5j]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5f5j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F5J OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5F5J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5f5j]] is a 2 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=5F5J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5F5J FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5XU:(2~{S})-2-AZANYLPROPANAL'>5XU</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5XU:(2~{S})-2-AZANYLPROPANAL'>5XU</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5f5b\|5f5b]], [[5f5d\|5f5d]], [[5f5g\|5f5g]], [[5f5k\|5f5k]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5f5b\|5f5b]], [[5f5d\|5f5d]], [[5f5g\|5f5g]], [[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=5f5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f5j OCA], [http://pdbe.org/5f5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f5j RCSB], [http://www.ebi.ac.uk/pdbsum/5f5j 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=5f5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f5j OCA], [http://pdbe.org/5f5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f5j RCSB], [http://www.ebi.ac.uk/pdbsum/5f5j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f5j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5f5j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5f5j" 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 19:06, 20 February 2016

2016-02-20T19:06:18Z

←Older revision		Revision as of 19:06, 20 February 2016
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		+
	==E.coli GlpG Y205F mutant complexed with aldehyde inhibitor in DMPC/CHAPSO bicelle==		==E.coli GlpG Y205F mutant complexed with aldehyde inhibitor in DMPC/CHAPSO bicelle==
	<StructureSection load='5f5j' size='340' side='right' caption='[[5f5j]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5f5j' size='340' side='right' caption='[[5f5j]], [[Resolution\|resolution]] 2.40Å' scene=''>

OCA at 17:12, 10 February 2016

2016-02-10T17:12:58Z

←Older revision		Revision as of 17:12, 10 February 2016
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==E.coli GlpG Y205F mutant complexed with aldehyde inhibitor in DMPC/CHAPSO bicelle==
		+	<StructureSection load='5f5j' size='340' side='right' caption='[[5f5j]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5f5j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F5J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F5J FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5XU:(2~{S})-2-AZANYLPROPANAL'>5XU</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5f5b\|5f5b]], [[5f5d\|5f5d]], [[5f5g\|5f5g]], [[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=5f5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f5j OCA], [http://pdbe.org/5f5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f5j RCSB], [http://www.ebi.ac.uk/pdbsum/5f5j 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.

-	~~The entry 5f5j is ON HOLD until Paper Publication~~	+	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>

-	~~Authors: Urban~~, S.~~, Cho,~~ S.~~, Dickey, S~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~E.coli GlpG Y205F mutant complexed with aldehyde inhibitor in DMPC~~/~~CHAPSO bicelle~~	+	<div class="pdbe-citations 5f5j" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Rhomboid protease]]
		+	[[Category: Cho, S]]
	[[Category: Dickey, S]]		[[Category: Dickey, S]]
-	[[Category: Cho, S]]
	[[Category: Urban, S]]		[[Category: Urban, S]]
		+	[[Category: Aldehyde inhibitor]]
		+	[[Category: Bicelle]]
		+	[[Category: Glpg]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Hydrolase-inhibitor complex]]
		+	[[Category: Rhomboid]]

OCA at 23:39, 27 January 2016

2016-01-27T23:39:55Z

←Older revision		Revision as of 23:39, 27 January 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5f5j is ON HOLD	+	The entry 5f5j is ON HOLD until Paper Publication

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

OCA at 10:40, 7 January 2016

2016-01-07T10:40:02Z

←Older revision		Revision as of 10:40, 7 January 2016
Line 3:		Line 3:
	The entry 5f5j is ON HOLD		The entry 5f5j is ON HOLD

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

	Description: E.coli GlpG Y205F mutant complexed with aldehyde inhibitor in DMPC/CHAPSO bicelle		Description: E.coli GlpG Y205F mutant complexed with aldehyde inhibitor in DMPC/CHAPSO bicelle
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Urban, Sinisa~~, Cho, ~~Sangwoo, Dickey~~, ~~Seth~~]]	+	[[Category: Dickey, S]]
		+	[[Category: Cho, S]]
		+	[[Category: Urban, S]]

OCA: Protected "5f5j" [edit=sysop:move=sysop]

2015-12-09T12:40:02Z

Protected "5f5j" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:40, 9 December 2015

OCA: New page: '''Unreleased structure''' The entry 5f5j is ON HOLD Authors: Urban, Sinisa, Cho, Sangwoo, Dickey, Seth Description: E.coli GlpG Y205F mutant complexed with aldehyde inhibitor in DMPC/...

2015-12-09T12:40:01Z

New page: '''Unreleased structure''' The entry 5f5j is ON HOLD Authors: Urban, Sinisa, Cho, Sangwoo, Dickey, Seth Description: E.coli GlpG Y205F mutant complexed with aldehyde inhibitor in DMPC/...

New page

'''Unreleased structure'''

The entry 5f5j is ON HOLD

Authors: Urban, Sinisa, Cho, Sangwoo, Dickey, Seth

Description: E.coli GlpG Y205F mutant complexed with aldehyde inhibitor in DMPC/CHAPSO bicelle
[[Category: Unreleased Structures]]
[[Category: Urban, Sinisa, Cho, Sangwoo, Dickey, Seth]]