3bm8 - Revision history

OCA at 12:10, 30 August 2023

OCA — Wed, 30 Aug 2023 12:10:55 GMT

←Older revision		Revision as of 12:10, 30 August 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3bm8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_enterocolitica Yersinia enterocolitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BM8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3bm8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_enterocolitica Yersinia enterocolitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BM8 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PSY:PHENYL+ETHENESULFONATE'>PSY</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]] 2.7Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>yopH, yop51 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~630 Yersinia enterocolitica])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PSY:PHENYL+ETHENESULFONATE'>PSY</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48]~~ </~~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=3bm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm8 OCA], [https://pdbe.org/3bm8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bm8 RCSB], [https://www.ebi.ac.uk/pdbsum/3bm8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bm8 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=3bm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm8 OCA], [https://pdbe.org/3bm8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bm8 RCSB], [https://www.ebi.ac.uk/pdbsum/3bm8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bm8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/YOPH_YEREN YOPH_YEREN]] Essential virulence determinant. This protein is a protein tyrosine phosphatase. The essential function of YopH in Yersinia pathogenesis is host-protein dephosphorylation. It contributes to the ability of the bacteria to resist phagocytosis by peritoneal macrophages.	+	[https://www.uniprot.org/uniprot/YOPH_YEREN YOPH_YEREN] Essential virulence determinant. This protein is a protein tyrosine phosphatase. The essential function of YopH in Yersinia pathogenesis is host-protein dephosphorylation. It contributes to the ability of the bacteria to resist phagocytosis by peritoneal macrophages.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Protein-tyrosine-phosphatase]]
	[[Category: Yersinia enterocolitica]]		[[Category: Yersinia enterocolitica]]
-	[[Category: Liu~~, S J~~]]	+	[[Category: Liu SJ]]
-	[[Category: Zhang~~, Z Y]]~~	+	[[Category: Zhang ZY]]
-	~~[[Category: Binding affinity]]~~	+
-	~~[[Category: Binding selectivity]]~~	+
-	~~[[Category: Co-valent binding]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Outer membrane]]~~	+
-	~~[[Category: Plasmid]]~~	+
-	~~[[Category: Protein phosphatase]]~~	+
-	~~[[Category: Pvsn]]~~	+
-	~~[[Category: Secreted]]~~	+
-	~~[[Category: Virulence~~]]	+

OCA at 18:59, 20 October 2021

OCA — Wed, 20 Oct 2021 18:59:04 GMT

←Older revision		Revision as of 18:59, 20 October 2021
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	==crystal structure of YopH mutant D356A complexed with irreversible inhibitor PVSN==		==crystal structure of YopH mutant D356A complexed with irreversible inhibitor PVSN==
-	<StructureSection load='3bm8' size='340' side='right' caption='[[3bm8]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='3bm8' size='340' side='right'caption='[[3bm8]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bm8]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Yersinia_enterocolitica Yersinia enterocolitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3BM8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bm8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_enterocolitica Yersinia enterocolitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BM8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PSY:PHENYL+ETHENESULFONATE'>PSY</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PSY:PHENYL+ETHENESULFONATE'>PSY</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopH, yop51 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=630 Yersinia enterocolitica])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopH, yop51 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=630 Yersinia enterocolitica])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </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=3bm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm8 OCA], [~~http~~://pdbe.org/3bm8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3bm8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3bm8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3bm8 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=3bm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm8 OCA], [https://pdbe.org/3bm8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bm8 RCSB], [https://www.ebi.ac.uk/pdbsum/3bm8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bm8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/YOPH_YEREN YOPH_YEREN]] Essential virulence determinant. This protein is a protein tyrosine phosphatase. The essential function of YopH in Yersinia pathogenesis is host-protein dephosphorylation. It contributes to the ability of the bacteria to resist phagocytosis by peritoneal macrophages.	+	[[https://www.uniprot.org/uniprot/YOPH_YEREN YOPH_YEREN]] Essential virulence determinant. This protein is a protein tyrosine phosphatase. The essential function of YopH in Yersinia pathogenesis is host-protein dephosphorylation. It contributes to the ability of the bacteria to resist phagocytosis by peritoneal macrophages.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Tyrosine phosphatase\|Tyrosine phosphatase]]	+	*[[Tyrosine phosphatase 3D structures\|Tyrosine phosphatase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Protein-tyrosine-phosphatase]]		[[Category: Protein-tyrosine-phosphatase]]
	[[Category: Yersinia enterocolitica]]		[[Category: Yersinia enterocolitica]]

OCA at 07:56, 31 October 2018

OCA — Wed, 31 Oct 2018 07:56:09 GMT

←Older revision		Revision as of 07:56, 31 October 2018
Line 1:		Line 1:
		+
	==crystal structure of YopH mutant D356A complexed with irreversible inhibitor PVSN==		==crystal structure of YopH mutant D356A complexed with irreversible inhibitor PVSN==
	<StructureSection load='3bm8' size='340' side='right' caption='[[3bm8]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3bm8' size='340' side='right' caption='[[3bm8]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopH, yop51 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=630 Yersinia enterocolitica])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopH, yop51 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=630 Yersinia enterocolitica])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </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=3bm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm8 OCA], [http://pdbe.org/3bm8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bm8 RCSB], [http://www.ebi.ac.uk/pdbsum/3bm8 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=3bm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm8 OCA], [http://pdbe.org/3bm8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bm8 RCSB], [http://www.ebi.ac.uk/pdbsum/3bm8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bm8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bm/3bm8_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bm/3bm8_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>
Line 46:		Line 47:
	[[Category: Membrane]]		[[Category: Membrane]]
	[[Category: Outer membrane]]		[[Category: Outer membrane]]
		+	[[Category: Plasmid]]
	[[Category: Protein phosphatase]]		[[Category: Protein phosphatase]]
	[[Category: Pvsn]]		[[Category: Pvsn]]
	[[Category: Secreted]]		[[Category: Secreted]]
	[[Category: Virulence]]		[[Category: Virulence]]

OCA at 11:00, 7 February 2016

OCA — Sun, 07 Feb 2016 11:00:54 GMT

←Older revision		Revision as of 11:00, 7 February 2016
Line 6:		Line 6:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopH, yop51 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=630 Yersinia enterocolitica])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopH, yop51 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=630 Yersinia enterocolitica])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </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=3bm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bm8 RCSB], [http://www.ebi.ac.uk/pdbsum/3bm8 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=3bm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm8 OCA], [http://pdbe.org/3bm8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bm8 RCSB], [http://www.ebi.ac.uk/pdbsum/3bm8 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<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=3bm8 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	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 3bm8" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 14:35, 24 December 2014

OCA — Wed, 24 Dec 2014 14:35:19 GMT

←Older revision		Revision as of 14:35, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3bm8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_enterocolitica Yersinia enterocolitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BM8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3bm8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_enterocolitica Yersinia enterocolitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BM8 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PSY:PHENYL+ETHENESULFONATE'>PSY</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PSY:PHENYL+ETHENESULFONATE'>PSY</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopH, yop51 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=630 Yersinia enterocolitica])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopH, yop51 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=630 Yersinia enterocolitica])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </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=3bm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bm8 RCSB], [http://www.ebi.ac.uk/pdbsum/3bm8 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=3bm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bm8 RCSB], [http://www.ebi.ac.uk/pdbsum/3bm8 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/YOPH_YEREN YOPH_YEREN]] Essential virulence determinant. This protein is a protein tyrosine phosphatase. The essential function of YopH in Yersinia pathogenesis is host-protein dephosphorylation. It contributes to the ability of the bacteria to resist phagocytosis by peritoneal macrophages.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Protein-tyrosine-phosphatase]]		[[Category: Protein-tyrosine-phosphatase]]
	[[Category: Yersinia enterocolitica]]		[[Category: Yersinia enterocolitica]]
-	[[Category: Liu, S J.]]	+	[[Category: Liu, S J]]
-	[[Category: Zhang, Z Y.]]	+	[[Category: Zhang, Z Y]]
	[[Category: Binding affinity]]		[[Category: Binding affinity]]
	[[Category: Binding selectivity]]		[[Category: Binding selectivity]]

OCA at 21:10, 2 October 2014

OCA — Thu, 02 Oct 2014 21:10:35 GMT

←Older revision		Revision as of 21:10, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~3bm8.~~png~~\|~~left~~\|200px]]	+	==crystal structure of YopH mutant D356A complexed with irreversible inhibitor PVSN==
		+	<StructureSection load='3bm8' size='340' side='right' caption='[[3bm8]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3bm8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_enterocolitica Yersinia enterocolitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BM8 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PSY:PHENYL+ETHENESULFONATE'>PSY</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopH, yop51 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=630 Yersinia enterocolitica])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </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=3bm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bm8 RCSB], [http://www.ebi.ac.uk/pdbsum/3bm8 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/bm/3bm8_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 ==
		+	Protein tyrosine phosphatases (PTPs) play key roles in the regulation of normal and pathological processes ranging from cell proliferation, differentiation, metabolism, and survival to many human diseases including cancer and diabetes. Functional studies of PTP can be greatly facilitated by small molecule probes that covalently label the active site of a PTP through an activity-dependent chemical reaction. In this article, we characterize phenyl vinyl sulfonate (PVSN) and phenyl vinyl sulfone (PVS) as a new class of mechanism-based PTP probes. PVSN and PVS inactivate a broad range of PTPs in a time- and concentration-dependent fashion. The PVSN- and PVS-mediated PTP inactivation is active site-directed and irreversible, resulting from a Michael addition of the active-site Cys Sgamma onto the terminal carbon of the vinyl group. Structural and mechanistic analyses reveal the molecular basis for the preference of PVSN/PVS toward the PTPs, which lies in the ability of PVSN and PVS to engage the conserved structural and catalytic machinery of the PTP active site. In contrast to early alpha-bromobenzyl phosphonate-based probes, PVSN and PVS are resistant to solvolysis and are cell-permeable and thus hold promise for in vivo applications. Collectively, these properties bode well for the development of aryl vinyl sulfonate/sulfone-based PTP probes to interrogate PTP activity in complex proteomes.

-	~~{{STRUCTURE_3bm8\| PDB=3bm8 \| SCENE= }}~~	+	Aryl Vinyl Sulfonates and Sulfones as Active Site-Directed and Mechanism-Based Probes for Protein Tyrosine Phosphatases.,Liu S, Zhou B, Yang H, He Y, Jiang ZX, Kumar S, Wu L, Zhang ZY J Am Chem Soc. 2008 Jun 4;. PMID:18528979<ref>PMID:18528979</ref>

-	~~===crystal structure~~ of ~~YopH mutant D356A complexed with irreversible inhibitor PVSN===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_18528979}}~~	+	==See Also==
-		+	*[[Tyrosine phosphatase\|Tyrosine phosphatase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~3bm8~~]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_enterocolitica Yersinia enterocolitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM8 OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:018528979<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Protein-tyrosine-phosphatase]]		[[Category: Protein-tyrosine-phosphatase]]
	[[Category: Yersinia enterocolitica]]		[[Category: Yersinia enterocolitica]]

OCA: Protected "3bm8" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 20:52:16 GMT

Protected "3bm8" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:52, 7 January 2013

OCA at 20:52, 7 January 2013

OCA — Mon, 07 Jan 2013 20:52:13 GMT

←Older revision		Revision as of 20:52, 7 January 2013
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-	{{Seed}}
	[[Image:3bm8.png\|left\|200px]]		[[Image:3bm8.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3bm8", 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.
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	{{STRUCTURE_3bm8\| PDB=3bm8 \| SCENE= }}		{{STRUCTURE_3bm8\| PDB=3bm8 \| SCENE= }}

	===crystal structure of YopH mutant D356A complexed with irreversible inhibitor PVSN===		===crystal structure of YopH mutant D356A complexed with irreversible inhibitor PVSN===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18528979}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18528979 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_18528979}}		{{ABSTRACT_PUBMED_18528979}}

	==About this Structure==		==About this Structure==
-	~~3BM8~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Yersinia_enterocolitica Yersinia enterocolitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM8 OCA].	+	[[3bm8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_enterocolitica Yersinia enterocolitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM8 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18528979~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018528979</ref><references group="xtra"/>
	[[Category: Protein-tyrosine-phosphatase]]		[[Category: Protein-tyrosine-phosphatase]]
	[[Category: Yersinia enterocolitica]]		[[Category: Yersinia enterocolitica]]
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	[[Category: Membrane]]		[[Category: Membrane]]
	[[Category: Outer membrane]]		[[Category: Outer membrane]]
-	[[Category: Plasmid]]
	[[Category: Protein phosphatase]]		[[Category: Protein phosphatase]]
	[[Category: Pvsn]]		[[Category: Pvsn]]
	[[Category: Secreted]]		[[Category: Secreted]]
	[[Category: Virulence]]		[[Category: Virulence]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 13:21:25 2009''

OCA at 11:21, 16 February 2009

OCA — Mon, 16 Feb 2009 11:21:26 GMT

←Older revision		Revision as of 11:21, 16 February 2009
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	==About this Structure==		==About this Structure==
-	3BM8 is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Yersinia_enterocolitica Yersinia enterocolitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM8 OCA].	+	3BM8 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Yersinia_enterocolitica Yersinia enterocolitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM8 OCA].

	==Reference==		==Reference==
-	Aryl Vinyl Sulfonates and Sulfones as Active Site-Directed and Mechanism-Based Probes for Protein Tyrosine Phosphatases., Liu S, Zhou B, Yang H, He Y, Jiang ZX, Kumar S, Wu L, Zhang ZY, J Am Chem Soc. 2008 Jun 4;. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18528979 18528979]~~	+	<ref group="xtra">PMID:18528979</ref><references group="xtra"/>
	[[Category: Protein-tyrosine-phosphatase]]		[[Category: Protein-tyrosine-phosphatase]]
-	[[Category: Single protein]]
	[[Category: Yersinia enterocolitica]]		[[Category: Yersinia enterocolitica]]
	[[Category: Liu, S J.]]		[[Category: Liu, S J.]]
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	[[Category: Virulence]]		[[Category: Virulence]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jul 9 10~~:09:~~49 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 13:21:25 2009''

OCA at 07:09, 9 July 2008

OCA — Wed, 09 Jul 2008 07:09:49 GMT

←Older revision		Revision as of 07:09, 9 July 2008
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		+	[[Image:3bm8.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_3bm8\| PDB=3bm8 \| SCENE= }}		{{STRUCTURE_3bm8\| PDB=3bm8 \| SCENE= }}

-	~~'''~~crystal structure of YopH mutant D356A complexed with irreversible inhibitor PVSN~~'''~~	+	===crystal structure of YopH mutant D356A complexed with irreversible inhibitor PVSN===


-	~~==Overview==~~	+	<!--
-	~~Protein tyrosine phosphatases (PTPs) play key roles in the regulation of normal and pathological processes ranging from cell proliferation~~, ~~differentiation~~, ~~metabolism, and survival~~ to ~~many human diseases including cancer and diabetes. Functional studies of PTP can be greatly facilitated by small molecule probes that covalently label~~ the ~~active site of a PTP through an activity-dependent chemical reaction. In this article, we characterize phenyl vinyl sulfonate~~ (~~PVSN) and phenyl vinyl sulfone (PVS)~~ as ~~a new class of mechanism-based PTP probes~~. ~~PVSN and PVS inactivate a broad range of PTPs in a time- and concentration-dependent fashion~~. ~~The PVSN- and PVS-mediated PTP inactivation~~ is ~~active site-directed and irreversible, resulting from a Michael addition of~~ the ~~active-site Cys Sgamma onto the terminal carbon of the vinyl group~~. Structural and mechanistic analyses reveal the molecular basis for the preference of PVSN/PVS toward the PTPs, which lies in the ability of PVSN and PVS to engage the conserved structural and catalytic machinery of the PTP active site. In contrast to early alpha-~~bromobenzyl phosphonate~~-based probes, PVSN and PVS are resistant to solvolysis and are cell-permeable and thus hold promise for in vivo applications. Collectively, these properties bode well for the development of aryl vinyl sulfonate/sulfone-based PTP probes to interrogate PTP activity in complex proteomes.	+	The line below this paragraph, {{ABSTRACT_PUBMED_18528979}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18528979 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18528979}}

	==About this Structure==		==About this Structure==
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	[[Category: Secreted]]		[[Category: Secreted]]
	[[Category: Virulence]]		[[Category: Virulence]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jun 18 12~~:08:24 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 9 10:09:49 2008''