5kdg - Revision history

OCA at 09:58, 27 September 2023

OCA — Wed, 27 Sep 2023 09:58:33 GMT

←Older revision		Revision as of 09:58, 27 September 2023
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	<StructureSection load='5kdg' size='340' side='right'caption='[[5kdg]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='5kdg' size='340' side='right'caption='[[5kdg]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kdg]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KDG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KDG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kdg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KDG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KDG FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'>GOL</scene~~>, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.73Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>SBOV09681, DD95_21385, ERS450001_01848, SEETMRM9437_5135, TJ44_09000 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~90371~~ "~~Bacillus typhimurium~~" ~~Loeffler 1892])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Papain Papain], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.2 3.4.22.2]~~ </~~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=5kdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kdg OCA], [https://pdbe.org/5kdg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kdg RCSB], [https://www.ebi.ac.uk/pdbsum/5kdg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kdg 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=5kdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kdg OCA], [~~http~~://pdbe.org/5kdg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kdg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kdg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kdg ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9XC73_SALTM Q9XC73_SALTM]
	<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 typhimurium loeffler 1892]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Papain]]~~	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Cygler M]]
-	[[Category: Cygler, M]]	+	[[Category: Gehring K]]
-	[[Category: Gehring, K]]	+	[[Category: Kozlov G]]
-	[[Category: Kozlov, G]]	+	[[Category: Wong K]]
-	[[Category: Wong, K]]	+	[[Category: Xu C]]
-	[[Category: Xu, C]]	+
-	~~[[Category: Bsgi]]~~	+
-	~~[[Category: Cysteine protease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Papain-like fold]]~~	+
-	~~[[Category: Psi-biology]]~~	+
-	~~[[Category: Virulence factor~~]]	+

OCA at 08:09, 8 January 2020

OCA — Wed, 08 Jan 2020 08:09:08 GMT

←Older revision		Revision as of 08:09, 8 January 2020
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	==Crystal Structure of Salmonella Typhimurium Effector GtgE==		==Crystal Structure of Salmonella Typhimurium Effector GtgE==
-	<StructureSection load='5kdg' size='340' side='right' caption='[[5kdg]], [[Resolution\|resolution]] 1.73Å' scene=''>	+	<StructureSection load='5kdg' size='340' side='right'caption='[[5kdg]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kdg]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KDG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KDG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kdg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KDG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KDG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SBOV09681, DD95_21385, ERS450001_01848, SEETMRM9437_5135, TJ44_09000 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Papain Papain], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.2 3.4.22.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Papain Papain], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.2 3.4.22.2] </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=5kdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kdg OCA], [http://pdbe.org/5kdg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kdg RCSB], [http://www.ebi.ac.uk/pdbsum/5kdg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kdg 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=5kdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kdg OCA], [http://pdbe.org/5kdg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kdg RCSB], [http://www.ebi.ac.uk/pdbsum/5kdg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kdg ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus typhimurium loeffler 1892]]
		+	[[Category: Large Structures]]
	[[Category: Papain]]		[[Category: Papain]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 09:45, 4 January 2017

OCA — Wed, 04 Jan 2017 09:45:21 GMT

←Older revision		Revision as of 09:45, 4 January 2017
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	<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=5kdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kdg OCA], [http://pdbe.org/5kdg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kdg RCSB], [http://www.ebi.ac.uk/pdbsum/5kdg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kdg 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=5kdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kdg OCA], [http://pdbe.org/5kdg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kdg RCSB], [http://www.ebi.ac.uk/pdbsum/5kdg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kdg ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Salmonella Typhimurium GtgE is an effector protein contributing to the virulence of this pathogen. It was shown to possess highly selective proteolytic activity against a subset of Rab proteins that helps in evasion of Salmonella-containing vacuole (SCV) fusion with lysosomes. Cys45, His151 and Asp169 are essential for proteolytic activity. The structure of a C-terminal fragment GtgE(79-214) indicated the presence of a papain-like fold. Here, we present the structure of GtgE(17-214) containing the fully assembled active site. The design of a proteolytically active and crystallizable GtgE construct was aided by NMR spectroscopy. The protein indeed displays papain-like fold with an assembled Cys-His-Asp catalytic triad. Like the full-length GtgE, the crystallizable construct showed low activity in vitro for its known substrates, Rab32 and Rab29. NMR titration experiments showed at most very weak binding of GtgE to the peptide encompassing the Rab29 cleavage site. In view of the low in vitro activity and poor substrate binding, we postulate that the function of GtgE in vivo as a proteolytic enzyme is dependent on other factor(s), such as a protein partner or interactions with the SCV membrane, which stimulate(s) GtgE activity in vivo.
		+
		+	Crystal Structure of the Salmonella Typhimurium Effector GtgE.,Xu C, Kozlov G, Wong K, Gehring K, Cygler M PLoS One. 2016 Dec 6;11(12):e0166643. doi: 10.1371/journal.pone.0166643., eCollection 2016. PMID:27923041<ref>PMID:27923041</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5kdg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 03:28, 10 December 2016

OCA — Sat, 10 Dec 2016 03:28:53 GMT

←Older revision		Revision as of 03:28, 10 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kdg is ~~ON HOLD until Paper Publication~~	+	==Crystal Structure of Salmonella Typhimurium Effector GtgE==
-		+	<StructureSection load='5kdg' size='340' side='right' caption='[[5kdg]], [[Resolution\|resolution]] 1.73Å' scene=''>
-	~~Authors~~: ~~Kozlov~~, G.~~, Xu, C~~., ~~Wong~~, K., ~~Gehring, K~~., ~~Cygler, M~~., ~~Montreal~~-~~Kingston Bacterial Structural Genomics Initiative (BSGI)~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5kdg]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KDG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KDG FirstGlance]. <br>
-	~~Description: Crystal Structure of Salmonella Typhimurium Effector GtgE~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Papain Papain], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.2 3.4.22.2] </span></td></tr>
-	[[Category: ~~Montreal-Kingston Bacterial~~ Structural ~~Genomics Initiative (Bsgi)~~]]	+	<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=5kdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kdg OCA], [http://pdbe.org/5kdg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kdg RCSB], [http://www.ebi.ac.uk/pdbsum/5kdg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kdg ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Papain]]
		+	[[Category: Structural genomic]]
	[[Category: Cygler, M]]		[[Category: Cygler, M]]
		+	[[Category: Gehring, K]]
		+	[[Category: Kozlov, G]]
	[[Category: Wong, K]]		[[Category: Wong, K]]
	[[Category: Xu, C]]		[[Category: Xu, C]]
-	[[Category: ~~Kozlov, G~~]]	+	[[Category: Bsgi]]
-	[[Category: ~~Gehring, K~~]]	+	[[Category: Cysteine protease]]
		+	[[Category: Hydrolase]]
		+	[[Category: Papain-like fold]]
		+	[[Category: Psi-biology]]
		+	[[Category: Virulence factor]]

OCA at 21:26, 23 June 2016

OCA — Thu, 23 Jun 2016 21:26:37 GMT

←Older revision		Revision as of 21:26, 23 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Kozlov, G., Xu, C., Wong, K., Gehring, K., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)		Authors: Kozlov, G., Xu, C., Wong, K., Gehring, K., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

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

OCA — Mon, 20 Jun 2016 13:46:49 GMT

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

←Older revision

Revision as of 13:46, 20 June 2016

OCA: New page: '''Unreleased structure''' The entry 5kdg is ON HOLD Authors: Kozlov, G., Xu, C., Wong, K., Gehring, K., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) D...

OCA — Mon, 20 Jun 2016 13:46:47 GMT

New page: '''Unreleased structure''' The entry 5kdg is ON HOLD Authors: Kozlov, G., Xu, C., Wong, K., Gehring, K., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) D...

New page

'''Unreleased structure'''

The entry 5kdg is ON HOLD

Authors: Kozlov, G., Xu, C., Wong, K., Gehring, K., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

Description: Crystal Structure of Salmonella Typhimurium Effector GtgE
[[Category: Unreleased Structures]]
[[Category: Montreal-Kingston Bacterial Structural Genomics Initiative (Bsgi)]]
[[Category: Cygler, M]]
[[Category: Wong, K]]
[[Category: Xu, C]]
[[Category: Kozlov, G]]
[[Category: Gehring, K]]