2x55 - Revision history

OCA at 07:10, 1 May 2024

OCA — Wed, 01 May 2024 07:10:36 GMT

←Older revision		Revision as of 07:10, 1 May 2024
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	<StructureSection load='2x55' size='340' side='right'caption='[[2x55]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='2x55' size='340' side='right'caption='[[2x55]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2x55]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus~~ pestis~~" (lehmann and neumann 1896) migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X55 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2X55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2x55]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X55 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2X55 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</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]] 1.85Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2x56\|2x56]], [[2x4m\|2x4m]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</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~~'>~~[https://en.wikipedia.org/wiki/Plasminogen_activator_Pla Plasminogen activator Pla], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.48 3.4.23.48]~~ </~~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=2x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x55 OCA], [https://pdbe.org/2x55 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2x55 RCSB], [https://www.ebi.ac.uk/pdbsum/2x55 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2x55 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=2x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x55 OCA], [https://pdbe.org/2x55 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2x55 RCSB], [https://www.ebi.ac.uk/pdbsum/2x55 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2x55 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/COLY_YERPE COLY_YERPE]] Seems to play an essential role in plague transmission by mediating flea blockage in a temperature-dependent fashion. Fibrinolytic activity prevails at 37 degrees Celsius whereas coagulase expression predominates at lower temperatures (<30 degrees Celsius). Activates plasminogen by cleaving it.	+	[https://www.uniprot.org/uniprot/COLY_YERPE COLY_YERPE] Seems to play an essential role in plague transmission by mediating flea blockage in a temperature-dependent fashion. Fibrinolytic activity prevails at 37 degrees Celsius whereas coagulase expression predominates at lower temperatures (<30 degrees Celsius). Activates plasminogen by cleaving it.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2x55 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2x55 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 A. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changes of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.
-
-	An active site water network in the plasminogen activator pla from Yersinia pestis.,Eren E, Murphy M, Goguen J, van den Berg B Structure. 2010 Jul 14;18(7):809-18. PMID:20637417<ref>PMID:20637417</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2x55" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Plasminogen activator\|Plasminogen activator]]		*[[Plasminogen activator\|Plasminogen activator]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Plasminogen activator Pla]]~~	+	[[Category: Yersinia pestis]]
-	~~[[Category: Berg, B van den~~]]	+	[[Category: Eren E]]
-	[[Category: Eren, E]]	+	[[Category: Goguen J]]
-	[[Category: Goguen, J]]	+	[[Category: Murphy M]]
-	[[Category: Murphy, M]]	+	[[Category: Van den Berg B]]
-	[[Category: ~~Aspartyl protease]]~~	+
-	~~[[Category: Cell outer membrane]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Omptin]]~~	+
-	~~[[Category: Protease]]~~	+
-	~~[[Category: Transmembrane~~]]	+

OCA at 08:35, 10 November 2021

OCA — Wed, 10 Nov 2021 08:35:37 GMT

←Older revision		Revision as of 08:35, 10 November 2021
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	<StructureSection load='2x55' size='340' side='right'caption='[[2x55]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='2x55' size='340' side='right'caption='[[2x55]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2x55]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X55 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2X55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2x55]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X55 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2X55 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</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" id="ligandDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2x56\|2x56]], [[2x4m\|2x4m]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2x56\|2x56]], [[2x4m\|2x4m]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Plasminogen_activator_Pla Plasminogen activator Pla], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.48 3.4.23.48] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Plasminogen_activator_Pla Plasminogen activator Pla], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.48 3.4.23.48] </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=2x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x55 OCA], [~~http~~://pdbe.org/2x55 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2x55 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2x55 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2x55 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=2x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x55 OCA], [https://pdbe.org/2x55 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2x55 RCSB], [https://www.ebi.ac.uk/pdbsum/2x55 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2x55 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/COLY_YERPE COLY_YERPE]] Seems to play an essential role in plague transmission by mediating flea blockage in a temperature-dependent fashion. Fibrinolytic activity prevails at 37 degrees Celsius whereas coagulase expression predominates at lower temperatures (<30 degrees Celsius). Activates plasminogen by cleaving it.	+	[[https://www.uniprot.org/uniprot/COLY_YERPE COLY_YERPE]] Seems to play an essential role in plague transmission by mediating flea blockage in a temperature-dependent fashion. Fibrinolytic activity prevails at 37 degrees Celsius whereas coagulase expression predominates at lower temperatures (<30 degrees Celsius). Activates plasminogen by cleaving it.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 14:05, 25 December 2019

OCA — Wed, 25 Dec 2019 14:05:46 GMT

←Older revision		Revision as of 14:05, 25 December 2019
Line 1:		Line 1:

	==Yersinia Pestis Plasminogen Activator Pla (Native)==		==Yersinia Pestis Plasminogen Activator Pla (Native)==
-	<StructureSection load='2x55' size='340' side='right' caption='[[2x55]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='2x55' size='340' side='right'caption='[[2x55]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2x55]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2X55 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2x55]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2X55 FirstGlance]. <br>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 2x55" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2x55" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Plasminogen activator\|Plasminogen activator]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Plasminogen activator Pla]]		[[Category: Plasminogen activator Pla]]
	[[Category: Berg, B van den]]		[[Category: Berg, B van den]]

OCA at 19:07, 24 January 2018

OCA — Wed, 24 Jan 2018 19:07:25 GMT

←Older revision		Revision as of 19:07, 24 January 2018
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/x5/2x55_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/x5/2x55_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	</div>		</div>
	<div class="pdbe-citations 2x55" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2x55" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Plasminogen activator\|Plasminogen activator]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Plasminogen activator Pla]]		[[Category: Plasminogen activator Pla]]
-	[[Category: Berg, B ~~Van Den~~]]	+	[[Category: Berg, B van den]]
	[[Category: Eren, E]]		[[Category: Eren, E]]
	[[Category: Goguen, J]]		[[Category: Goguen, J]]

OCA at 20:40, 5 August 2016

OCA — Fri, 05 Aug 2016 20:40:04 GMT

←Older revision		Revision as of 20:40, 5 August 2016
Line 1:		Line 1:
		+
	==Yersinia Pestis Plasminogen Activator Pla (Native)==		==Yersinia Pestis Plasminogen Activator Pla (Native)==
	<StructureSection load='2x55' size='340' side='right' caption='[[2x55]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='2x55' size='340' side='right' caption='[[2x55]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2x55]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Yersinia_pestis Yersinia~~ pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2X55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2x55]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2X55 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</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=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2x56\|2x56]], [[2x4m\|2x4m]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2x56\|2x56]], [[2x4m\|2x4m]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Plasminogen_activator_Pla Plasminogen activator Pla], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.48 3.4.23.48] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Plasminogen_activator_Pla Plasminogen activator Pla], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.48 3.4.23.48] </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=2x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x55 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2x55 RCSB], [http://www.ebi.ac.uk/pdbsum/2x55 PDBsum]</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=2x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x55 OCA], [http://pdbe.org/2x55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2x55 RCSB], [http://www.ebi.ac.uk/pdbsum/2x55 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2x55 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2x55 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2x55" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Plasminogen activator\|Plasminogen activator]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Plasminogen activator Pla]]		[[Category: Plasminogen activator Pla]]
-	[[Category: Yersinia pestis]]
	[[Category: Berg, B Van Den]]		[[Category: Berg, B Van Den]]
	[[Category: Eren, E]]		[[Category: Eren, E]]

OCA at 05:41, 25 December 2014

OCA — Thu, 25 Dec 2014 05:41:38 GMT

←Older revision		Revision as of 05:41, 25 December 2014
Line 2:		Line 2:
	<StructureSection load='2x55' size='340' side='right' caption='[[2x55]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='2x55' size='340' side='right' caption='[[2x55]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2x55]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X55 OCA]. <br>	+	<table><tr><td colspan='2'>[[2x55]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2X55 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2x56\|2x56]], [[2x4m\|2x4m]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2x56\|2x56]], [[2x4m\|2x4m]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Glucokinase Glucokinase~~], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.~~2 2~~.7.1.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Plasminogen_activator_Pla Plasminogen activator Pla], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.48 3.4.23.48] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x55 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2x55 RCSB], [http://www.ebi.ac.uk/pdbsum/2x55 PDBsum]</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=2x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x55 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2x55 RCSB], [http://www.ebi.ac.uk/pdbsum/2x55 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/COLY_YERPE COLY_YERPE]] Seems to play an essential role in plague transmission by mediating flea blockage in a temperature-dependent fashion. Fibrinolytic activity prevails at 37 degrees Celsius whereas coagulase expression predominates at lower temperatures (<30 degrees Celsius). Activates plasminogen by cleaving it.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 24:		Line 26:
	An active site water network in the plasminogen activator pla from Yersinia pestis.,Eren E, Murphy M, Goguen J, van den Berg B Structure. 2010 Jul 14;18(7):809-18. PMID:20637417<ref>PMID:20637417</ref>		An active site water network in the plasminogen activator pla from Yersinia pestis.,Eren E, Murphy M, Goguen J, van den Berg B Structure. 2010 Jul 14;18(7):809-18. PMID:20637417<ref>PMID:20637417</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 32:		Line 34:
	[[Category: Plasminogen activator Pla]]		[[Category: Plasminogen activator Pla]]
	[[Category: Yersinia pestis]]		[[Category: Yersinia pestis]]
-	[[Category: Berg, B Van Den.]]	+	[[Category: Berg, B Van Den]]
-	[[Category: Eren, E.]]	+	[[Category: Eren, E]]
-	[[Category: Goguen, J.]]	+	[[Category: Goguen, J]]
-	[[Category: Murphy, M.]]	+	[[Category: Murphy, M]]
	[[Category: Aspartyl protease]]		[[Category: Aspartyl protease]]
	[[Category: Cell outer membrane]]		[[Category: Cell outer membrane]]

OCA at 07:47, 14 May 2014

OCA — Wed, 14 May 2014 07:47:07 GMT

←Older revision		Revision as of 07:47, 14 May 2014
Line 1:		Line 1:
-	[[~~Image:~~2x55.~~png~~\|~~left~~\|200px]]	+	==Yersinia Pestis Plasminogen Activator Pla (Native)==
		+	<StructureSection load='2x55' size='340' side='right' caption='[[2x55]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2x55]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X55 OCA]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2x56\|2x56]], [[2x4m\|2x4m]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x55 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2x55 RCSB], [http://www.ebi.ac.uk/pdbsum/2x55 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/x5/2x55_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 A. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changes of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.

-	~~<!--~~	+	An active site water network in the plasminogen activator pla from Yersinia pestis.,Eren E, Murphy M, Goguen J, van den Berg B Structure. 2010 Jul 14;18(7):809-18. PMID:20637417<ref>PMID:20637417</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_2x55"~~, ~~creates the "~~Structure ~~Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display~~.	+
-	-->	+
-	~~{{STRUCTURE_2x55\| PDB=2x55 \| SCENE= }}~~	+

-	~~===Yersinia Pestis Plasminogen Activator Pla (Native)===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_20637417}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 20637417 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_20637417}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2x55]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X55 OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:020637417<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Plasminogen activator Pla]]		[[Category: Plasminogen activator Pla]]
	[[Category: Yersinia pestis]]		[[Category: Yersinia pestis]]

OCA: Protected "2x55" [edit=sysop:move=sysop]

OCA — Wed, 28 Mar 2012 06:44:40 GMT

Protected "2x55" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:44, 28 March 2012

OCA at 06:44, 28 March 2012

OCA — Wed, 28 Mar 2012 06:44:37 GMT

←Older revision		Revision as of 06:44, 28 March 2012
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:2x55.png\|left\|200px]]
-	[[Image:2x55.~~jpg~~\|left\|200px]]	+

	<!--		<!--
Line 10:		Line 9:
	{{STRUCTURE_2x55\| PDB=2x55 \| SCENE= }}		{{STRUCTURE_2x55\| PDB=2x55 \| SCENE= }}

-	===~~YERSINIA PESTIS PLASMINOGEN ACTIVATOR PLA~~ (~~NATIVE~~)===	+	===Yersinia Pestis Plasminogen Activator Pla (Native)===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20637417}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20637417 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20637417}}

	==About this Structure==		==About this Structure==
-	~~2X55~~ is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X55 OCA].	+	[[2x55]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X55 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:020637417</ref><references group="xtra"/>
	[[Category: Plasminogen activator Pla]]		[[Category: Plasminogen activator Pla]]
	[[Category: Yersinia pestis]]		[[Category: Yersinia pestis]]
Line 25:		Line 33:
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Omptin]]		[[Category: Omptin]]
-	[[Category: Plasminogen activator]]
	[[Category: Protease]]		[[Category: Protease]]
	[[Category: Transmembrane]]		[[Category: Transmembrane]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 28 12:34:15 2010''

OCA at 08:27, 28 July 2010

OCA — Wed, 28 Jul 2010 08:27:33 GMT

←Older revision		Revision as of 08:27, 28 July 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:2x55.jpg\|left\|200px]]

-	The ~~entry 2x55~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_2x55", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_2x55\| PDB=2x55 \| SCENE= }}

-	~~Authors: Eren, E., Murphy, M., Goguen, J., van den Berg, B.~~	+	===YERSINIA PESTIS PLASMINOGEN ACTIVATOR PLA (NATIVE)===

-	Description: Yersinia Pestis Plasminogen Activator Pla (Native)

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Apr 14 09~~:16:21 2010''	+	==About this Structure==
		+	2X55 is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X55 OCA].
		+	[[Category: Plasminogen activator Pla]]
		+	[[Category: Yersinia pestis]]
		+	[[Category: Berg, B Van Den.]]
		+	[[Category: Eren, E.]]
		+	[[Category: Goguen, J.]]
		+	[[Category: Murphy, M.]]
		+	[[Category: Aspartyl protease]]
		+	[[Category: Cell outer membrane]]
		+	[[Category: Hydrolase]]
		+	[[Category: Omptin]]
		+	[[Category: Plasminogen activator]]
		+	[[Category: Protease]]
		+	[[Category: Transmembrane]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 28 12:34:15 2010''