5y28 - Revision history

OCA at 10:21, 27 March 2024

OCA — Wed, 27 Mar 2024 10:21:20 GMT

←Older revision		Revision as of 10:21, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5y28' size='340' side='right'caption='[[5y28]], [[Resolution\|resolution]] 3.09Å' scene=''>		<StructureSection load='5y28' size='340' side='right'caption='[[5y28]], [[Resolution\|resolution]] 3.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y28]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Campylobacter_pylori Campylobacter~~ pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y28 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y28 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y28]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y28 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y28 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 3.0860682Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">hp1018/19 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=85962 Campylobacter pylori])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Peptidase_Do Peptidase Do]~~, ~~with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=3.4.21.107 3.4.21.107]~~ </~~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=5y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y28 OCA], [https://pdbe.org/5y28 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y28 RCSB], [https://www.ebi.ac.uk/pdbsum/5y28 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y28 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=5y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y28 OCA], [~~http~~://pdbe.org/5y28 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y28 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y28 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y28 ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/G2J5T2_HELPY G2J5T2_HELPY]
-	Knowledge of the molecular mechanisms of specific bacterial virulence factors can significantly contribute to antibacterial drug discovery. Helicobacter pylori is a Gram-negative microaerophilic bacterium that infects almost half of the world's population, leading to gastric disorders and even gastric cancer. H. pylori expresses a series of virulence factors in the host, among which high-temperature requirement A (HpHtrA) is a newly identified serine protease secreted by H. pylori. HpHtrA cleaves the extracellular domain of the epithelial cell surface adhesion protein E-cadherin and disrupts gastric epithelial cell junctions, allowing H. pylori to access the intercellular space. Here we report the first crystal structure of HpHtrA at 3.0 A resolution. The structure revealed a new type of HtrA protease trimer stabilized by unique N-terminal domain swapping distinct from other known HtrA homologs. We further observed that truncation of the N terminus completely abrogates HpHtrA trimer formation as well as protease activity. In the presence of unfolded substrate, HpHtrA assembled into cage-like 12-mers or 24-mers. Combining crystallographic, biochemical, and mutagenic data, we propose a mechanistic model of how HpHtrA recognizes and cleaves the well-folded E-cadherin substrate. Our study provides a fundamental basis for the development of anti-H. pylori agents by using a previously uncharacterized HtrA protease as a target.	+
-		+
-	The unique trimeric assembly of the virulence factor HtrA from Helicobacter pylori occurs via N-terminal domain swapping.,Zhang Z, Huang Q, Tao X, Song G, Zheng P, Li H, Sun H, Xia W J Biol Chem. 2019 May 17;294(20):~~7990-8000. doi: 10.1074~~/~~jbc.RA119.007387. Epub, 2019 Apr 1. PMID:30936204<ref>PMID:30936204<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5y28" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Campylobacter~~ pylori]]	+	[[Category: Helicobacter pylori 26695]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Peptidase Do]]~~	+	[[Category: Huang Q]]
-	[[Category: Huang, Q]]	+	[[Category: Tao X]]
-	[[Category: Tao, X]]	+	[[Category: Zhang Z]]
-	[[Category: Zhang, Z]]	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Serine protease~~]]	+

OCA at 15:49, 28 August 2019

OCA — Wed, 28 Aug 2019 15:49:13 GMT

←Older revision		Revision as of 15:49, 28 August 2019
Line 1:		Line 1:

	==Crystal structure of H. pylori HtrA with PDZ2 deletion==		==Crystal structure of H. pylori HtrA with PDZ2 deletion==
-	<StructureSection load='5y28' size='340' side='right' caption='[[5y28]], [[Resolution\|resolution]] 3.09Å' scene=''>	+	<StructureSection load='5y28' size='340' side='right'caption='[[5y28]], [[Resolution\|resolution]] 3.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y28]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y28 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y28 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y28]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y28 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y28 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hp1018/19 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidase_Do Peptidase Do], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.107 3.4.21.107] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidase_Do Peptidase Do], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.107 3.4.21.107] </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=5y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y28 OCA], [http://pdbe.org/5y28 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y28 RCSB], [http://www.ebi.ac.uk/pdbsum/5y28 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y28 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=5y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y28 OCA], [http://pdbe.org/5y28 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y28 RCSB], [http://www.ebi.ac.uk/pdbsum/5y28 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y28 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Knowledge of the molecular mechanisms of specific bacterial virulence factors can significantly contribute to antibacterial drug discovery. Helicobacter pylori is a Gram-negative microaerophilic bacterium that infects almost half of the world's population, leading to gastric disorders and even gastric cancer. H. pylori expresses a series of virulence factors in the host, among which high-temperature requirement A (HpHtrA) is a newly identified serine protease secreted by H. pylori. HpHtrA cleaves the extracellular domain of the epithelial cell surface adhesion protein E-cadherin and disrupts gastric epithelial cell junctions, allowing H. pylori to access the intercellular space. Here we report the first crystal structure of HpHtrA at 3.0 A resolution. The structure revealed a new type of HtrA protease trimer stabilized by unique N-terminal domain swapping distinct from other known HtrA homologs. We further observed that truncation of the N terminus completely abrogates HpHtrA trimer formation as well as protease activity. In the presence of unfolded substrate, HpHtrA assembled into cage-like 12-mers or 24-mers. Combining crystallographic, biochemical, and mutagenic data, we propose a mechanistic model of how HpHtrA recognizes and cleaves the well-folded E-cadherin substrate. Our study provides a fundamental basis for the development of anti-H. pylori agents by using a previously uncharacterized HtrA protease as a target.
		+
		+	The unique trimeric assembly of the virulence factor HtrA from Helicobacter pylori occurs via N-terminal domain swapping.,Zhang Z, Huang Q, Tao X, Song G, Zheng P, Li H, Sun H, Xia W J Biol Chem. 2019 May 17;294(20):7990-8000. doi: 10.1074/jbc.RA119.007387. Epub, 2019 Apr 1. PMID:30936204<ref>PMID:30936204</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5y28" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Campylobacter pylori]]
		+	[[Category: Large Structures]]
	[[Category: Peptidase Do]]		[[Category: Peptidase Do]]
	[[Category: Huang, Q]]		[[Category: Huang, Q]]

OCA at 16:07, 15 August 2018

OCA — Wed, 15 Aug 2018 16:07:20 GMT

←Older revision		Revision as of 16:07, 15 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5y28 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of H. pylori HtrA with PDZ2 deletion==
-		+	<StructureSection load='5y28' size='340' side='right' caption='[[5y28]], [[Resolution\|resolution]] 3.09Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5y28]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y28 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y28 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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/Peptidase_Do Peptidase Do], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.107 3.4.21.107] </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=5y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y28 OCA], [http://pdbe.org/5y28 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y28 RCSB], [http://www.ebi.ac.uk/pdbsum/5y28 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y28 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Peptidase Do]]
		+	[[Category: Huang, Q]]
		+	[[Category: Tao, X]]
		+	[[Category: Zhang, Z]]
		+	[[Category: Hydrolase]]
		+	[[Category: Serine protease]]

OCA at 16:49, 1 August 2018

OCA — Wed, 01 Aug 2018 16:49:36 GMT

←Older revision		Revision as of 16:49, 1 August 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5y28 is ON HOLD	+	The entry 5y28 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 03:47, 16 May 2018

OCA — Wed, 16 May 2018 03:47:39 GMT

←Older revision		Revision as of 03:47, 16 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5y28 is ON HOLD ~~until Paper Publication~~	+	The entry 5y28 is ON HOLD

	Authors:		Authors:

OCA: Protected "5y28" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:03:18 GMT

Protected "5y28" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:03, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5y28 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 16:03:17 GMT

New page: '''Unreleased structure''' The entry 5y28 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5y28 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]