5h63 - Revision history

OCA at 09:15, 20 March 2024

2024-03-20T09:15:10Z

←Older revision		Revision as of 09:15, 20 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/SSEK2_SALTY SSEK2_SALTY] Protein-arginine N-acetylglucosaminyltransferase effector that catalyzes the transfer of a single N-acetylglucosamine (GlcNAc) to a conserved arginine residue in the death domain of host proteins such as FADD: arginine GlcNAcylation prevents homotypic/heterotypic death domain interactions (PubMed:28522607). Also acts on host proteins without a death domain: catalyzes arginine GlcNAcylation of host small Rab1 GTPase, thereby preventing GTPase activity and leading to impaired host vesicular protein transport (By similarity). In contrast to Ssek1, not able to disrupt TNF signaling in infected cells (PubMed:28522607).[UniProtKB:P0DUJ8]<ref>PMID:28522607</ref>		[https://www.uniprot.org/uniprot/SSEK2_SALTY SSEK2_SALTY] Protein-arginine N-acetylglucosaminyltransferase effector that catalyzes the transfer of a single N-acetylglucosamine (GlcNAc) to a conserved arginine residue in the death domain of host proteins such as FADD: arginine GlcNAcylation prevents homotypic/heterotypic death domain interactions (PubMed:28522607). Also acts on host proteins without a death domain: catalyzes arginine GlcNAcylation of host small Rab1 GTPase, thereby preventing GTPase activity and leading to impaired host vesicular protein transport (By similarity). In contrast to Ssek1, not able to disrupt TNF signaling in infected cells (PubMed:28522607).[UniProtKB:P0DUJ8]<ref>PMID:28522607</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The bacterial effector proteins SseK and NleB glycosylate host proteins on arginine residues, leading to reduced NF-kappaB-dependent responses to infection. Salmonella SseK1 and SseK2 are E. coli NleB1 orthologs that behave as NleB1-like GTs, although they differ in protein substrate specificity. Here we report that these enzymes are retaining glycosyltransferases composed of a helix-loop-helix (HLH) domain, a lid domain, and a catalytic domain. A conserved HEN motif (His-Glu-Asn) in the active site is important for enzyme catalysis and bacterial virulence. We observe differences between SseK1 and SseK2 in interactions with substrates and identify substrate residues that are critical for enzyme recognition. Long Molecular Dynamics simulations suggest that the HLH domain determines substrate specificity and the lid-domain regulates the opening of the active site. Overall, our data suggest a front-face SNi mechanism, explain differences in activities among these effectors, and have implications for future drug development against enteric pathogens.
-
-	Structural basis for arginine glycosylation of host substrates by bacterial effector proteins.,Park JB, Kim YH, Yoo Y, Kim J, Jun SH, Cho JW, El Qaidi S, Walpole S, Monaco S, Garcia-Garcia AA, Wu M, Hays MP, Hurtado-Guerrero R, Angulo J, Hardwidge PR, Shin JS, Cho HS Nat Commun. 2018 Oct 16;9(1):4283. doi: 10.1038/s41467-018-06680-6. PMID:30327479<ref>PMID:30327479</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5h63" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:24, 9 August 2023

2023-08-09T07:24:43Z

←Older revision		Revision as of 07:24, 9 August 2023
Line 3:		Line 3:
	<StructureSection load='5h63' size='340' side='right'caption='[[5h63]], [[Resolution\|resolution]] 1.92Å' scene=''>		<StructureSection load='5h63' size='340' side='right'caption='[[5h63]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h63]] is a 4 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=5H63 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5H63 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h63]] is a 4 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=5H63 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H63 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</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]] 1.92Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h5y\|5h5y]], [[5h60\|5h60]], [[5h61\|5h61]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</scene></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=5h63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h63 OCA], [~~http~~://pdbe.org/5h63 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5h63 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5h63 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5h63 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=5h63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h63 OCA], [https://pdbe.org/5h63 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h63 RCSB], [https://www.ebi.ac.uk/pdbsum/5h63 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h63 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SSEK2_SALTY SSEK2_SALTY] Protein-arginine N-acetylglucosaminyltransferase effector that catalyzes the transfer of a single N-acetylglucosamine (GlcNAc) to a conserved arginine residue in the death domain of host proteins such as FADD: arginine GlcNAcylation prevents homotypic/heterotypic death domain interactions (PubMed:28522607). Also acts on host proteins without a death domain: catalyzes arginine GlcNAcylation of host small Rab1 GTPase, thereby preventing GTPase activity and leading to impaired host vesicular protein transport (By similarity). In contrast to Ssek1, not able to disrupt TNF signaling in infected cells (PubMed:28522607).[UniProtKB:P0DUJ8]<ref>PMID:28522607</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim, J]]	+	[[Category: Kim J]]
-	[[Category: Park~~, J B~~]]	+	[[Category: Park JB]]
-	[[Category: Yoo, Y]]	+	[[Category: Yoo Y]]
-	~~[[Category: Transferase~~]]	+

OCA at 06:26, 5 August 2020

2020-08-05T06:26:46Z

←Older revision		Revision as of 06:26, 5 August 2020
Line 1:		Line 1:

	==Structure of Transferase mutant-C23S,C199S==		==Structure of Transferase mutant-C23S,C199S==
-	<StructureSection load='5h63' size='340' side='right' caption='[[5h63]], [[Resolution\|resolution]] 1.92Å' scene=''>	+	<StructureSection load='5h63' size='340' side='right'caption='[[5h63]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h63]] is a 4 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=5H63 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5H63 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h63]] is a 4 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=5H63 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5H63 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h5y\|5h5y]], [[5h60\|5h60]], [[5h61\|5h61]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h5y\|5h5y]], [[5h60\|5h60]], [[5h61\|5h61]]</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=5h63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h63 OCA], [http://pdbe.org/5h63 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h63 RCSB], [http://www.ebi.ac.uk/pdbsum/5h63 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h63 ProSAT]</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=5h63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h63 OCA], [http://pdbe.org/5h63 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h63 RCSB], [http://www.ebi.ac.uk/pdbsum/5h63 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h63 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Kim, J]]		[[Category: Kim, J]]
	[[Category: Park, J B]]		[[Category: Park, J B]]
	[[Category: Yoo, Y]]		[[Category: Yoo, Y]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 07:05, 31 October 2018

2018-10-31T07:05:29Z

←Older revision		Revision as of 07:05, 31 October 2018
Line 8:		Line 8:
	<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=5h63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h63 OCA], [http://pdbe.org/5h63 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h63 RCSB], [http://www.ebi.ac.uk/pdbsum/5h63 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h63 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=5h63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h63 OCA], [http://pdbe.org/5h63 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h63 RCSB], [http://www.ebi.ac.uk/pdbsum/5h63 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h63 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The bacterial effector proteins SseK and NleB glycosylate host proteins on arginine residues, leading to reduced NF-kappaB-dependent responses to infection. Salmonella SseK1 and SseK2 are E. coli NleB1 orthologs that behave as NleB1-like GTs, although they differ in protein substrate specificity. Here we report that these enzymes are retaining glycosyltransferases composed of a helix-loop-helix (HLH) domain, a lid domain, and a catalytic domain. A conserved HEN motif (His-Glu-Asn) in the active site is important for enzyme catalysis and bacterial virulence. We observe differences between SseK1 and SseK2 in interactions with substrates and identify substrate residues that are critical for enzyme recognition. Long Molecular Dynamics simulations suggest that the HLH domain determines substrate specificity and the lid-domain regulates the opening of the active site. Overall, our data suggest a front-face SNi mechanism, explain differences in activities among these effectors, and have implications for future drug development against enteric pathogens.
		+
		+	Structural basis for arginine glycosylation of host substrates by bacterial effector proteins.,Park JB, Kim YH, Yoo Y, Kim J, Jun SH, Cho JW, El Qaidi S, Walpole S, Monaco S, Garcia-Garcia AA, Wu M, Hays MP, Hurtado-Guerrero R, Angulo J, Hardwidge PR, Shin JS, Cho HS Nat Commun. 2018 Oct 16;9(1):4283. doi: 10.1038/s41467-018-06680-6. PMID:30327479<ref>PMID:30327479</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5h63" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 20:04, 19 September 2018

2018-09-19T20:04:29Z

←Older revision		Revision as of 20:04, 19 September 2018
Line 3:		Line 3:
	<StructureSection load='5h63' size='340' side='right' caption='[[5h63]], [[Resolution\|resolution]] 1.92Å' scene=''>		<StructureSection load='5h63' size='340' side='right' caption='[[5h63]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h63]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H63 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h63]] is a 4 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=5H63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H63 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h5y\|5h5y]], [[5h60\|5h60]], [[5h61\|5h61]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h5y\|5h5y]], [[5h60\|5h60]], [[5h61\|5h61]]</td></tr>
Line 10:		Line 10:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Kim, J]]		[[Category: Kim, J]]
	[[Category: Park, J B]]		[[Category: Park, J B]]
	[[Category: Yoo, Y]]		[[Category: Yoo, Y]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 06:03, 20 December 2017

2017-12-20T06:03:19Z

←Older revision		Revision as of 06:03, 20 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5h63 ~~is ON HOLD until Paper Publication~~	+	==Structure of Transferase mutant-C23S,C199S==
-		+	<StructureSection load='5h63' size='340' side='right' caption='[[5h63]], [[Resolution\|resolution]] 1.92Å' scene=''>
-	~~Authors~~: ~~Park, J~~.B.~~, Yoo, Y~~.~~, Kim, J~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5h63]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H63 FirstGlance]. <br>
-	~~Description~~: ~~Structure of Transferase mutant~~-~~C23S~~,~~C199S~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h5y\|5h5y]], [[5h60\|5h60]], [[5h61\|5h61]]</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=5h63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h63 OCA], [http://pdbe.org/5h63 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h63 RCSB], [http://www.ebi.ac.uk/pdbsum/5h63 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h63 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Kim, J]]		[[Category: Kim, J]]
		+	[[Category: Park, J B]]
	[[Category: Yoo, Y]]		[[Category: Yoo, Y]]
-	[[Category: ~~Park, J.B~~]]	+	[[Category: Transferase]]

OCA at 06:20, 8 November 2017

2017-11-08T06:20:54Z

←Older revision		Revision as of 06:20, 8 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5h63 is ON HOLD	+	The entry 5h63 is ON HOLD until Paper Publication

	Authors: Park, J.B., Yoo, Y., Kim, J.		Authors: Park, J.B., Yoo, Y., Kim, J.
Line 7:		Line 7:
	Description: Structure of Transferase mutant-C23S,C199S		Description: Structure of Transferase mutant-C23S,C199S
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Yoo, Y]]
	[[Category: Kim, J]]		[[Category: Kim, J]]
		+	[[Category: Yoo, Y]]
	[[Category: Park, J.B]]		[[Category: Park, J.B]]

OCA: Protected "5h63" [edit=sysop:move=sysop]

2016-12-09T13:47:12Z

Protected "5h63" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:47, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5h63 is ON HOLD Authors: Park, J.B., Yoo, Y., Kim, J. Description: Structure of Transferase mutant-C23S,C199S Category: Unreleased Structures [...

2016-12-09T13:47:11Z

New page: '''Unreleased structure''' The entry 5h63 is ON HOLD Authors: Park, J.B., Yoo, Y., Kim, J. Description: Structure of Transferase mutant-C23S,C199S Category: Unreleased Structures [...

New page

'''Unreleased structure'''

The entry 5h63 is ON HOLD

Authors: Park, J.B., Yoo, Y., Kim, J.

Description: Structure of Transferase mutant-C23S,C199S
[[Category: Unreleased Structures]]
[[Category: Yoo, Y]]
[[Category: Kim, J]]
[[Category: Park, J.B]]