1kho - Revision history

OCA at 07:25, 14 February 2024

2024-02-14T07:25:03Z

←Older revision		Revision as of 07:25, 14 February 2024
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	<StructureSection load='1kho' size='340' side='right'caption='[[1kho]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1kho' size='340' side='right'caption='[[1kho]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kho]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus~~ perfringens~~" veillon and zuber 1898~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1KHO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kho]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KHO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.4Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[1ca1\|1ca1]], [[1qm6\|1qm6]], [[1qmd\|1qmd]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">CPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1502 "Bacillus perfringens" Veillon and Zuber 1898])~~</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=1kho FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kho OCA], [https://pdbe.org/1kho PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kho RCSB], [https://www.ebi.ac.uk/pdbsum/1kho PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kho 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=1kho FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kho OCA], [~~http~~://pdbe.org/1kho PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1kho RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1kho PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1kho ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PHLC_CLOPF PHLC_CLOPF]] Bacterial hemolysins are exotoxins that attack blood cell membranes and cause cell rupture. Constitutes an essential virulence factor in gas gangrene. Binds to eukaryotic membranes where it hydrolyzes both phosphatidylcholine and sphingomyelin, causing cell rupture. The diacylglycerol produced can activate both the arachidonic acid pathway, leading to modulation of the inflammatory response cascade and thrombosis, and protein kinase C, leading to activation of eukaryotic phospholipases and further membrane damage.	+	[https://www.uniprot.org/uniprot/PHLC_CLOPF PHLC_CLOPF] Bacterial hemolysins are exotoxins that attack blood cell membranes and cause cell rupture. Constitutes an essential virulence factor in gas gangrene. Binds to eukaryotic membranes where it hydrolyzes both phosphatidylcholine and sphingomyelin, causing cell rupture. The diacylglycerol produced can activate both the arachidonic acid pathway, leading to modulation of the inflammatory response cascade and thrombosis, and protein kinase C, leading to activation of eukaryotic phospholipases and further membrane damage.
	== 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=1kho 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=1kho ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Clostridium perfringens alpha-toxin is a 370-residue, zinc-dependent, phospholipase C that is the key virulence determinant in gas gangrene. It is also implicated in the pathogenesis of sudden death syndrome in young animals and necrotic enteritis in chickens. Previously characterized alpha-toxins from different strains of C. perfringens are almost identical in sequence and biochemical properties. We describe the cloning, nucleotide sequencing, expression, characterization, and crystal structure of alpha-toxin from an avian strain, SWan C. perfringens (SWCP), which has a large degree of sequence variation and altered substrate specificity compared to these strains. The structure of alpha-toxin from strain CER89L43 has been previously reported in open (active site accessible to substrate) and closed (active site obscured by loop movements) conformations. The SWCP structure is in an open-form conformation, with three zinc ions in the active site. This is the first example of an open form of alpha-toxin crystallizing without the addition of divalent cations to the crystallization buffer, indicating that the protein can retain three zinc ions bound in the active site. The topology of the calcium binding site formed by residues 269, 271, 336, and 337, which is essential for membrane binding, is significantly altered in comparison with both the open and closed alpha-toxin structures. We are able to relate these structural changes to the different substrate specificity and membrane binding properties of this divergent alpha-toxin. This will provide essential information when developing an effective vaccine that will protect against C. perfringens infection in a wide range of domestic livestock.
-
-	The first strain of Clostridium perfringens isolated from an avian source has an alpha-toxin with divergent structural and kinetic properties.,Justin N, Walker N, Bullifent HL, Songer G, Bueschel DM, Jost H, Naylor C, Miller J, Moss DS, Titball RW, Basak AK Biochemistry. 2002 May 21;41(20):6253-62. PMID:12009886<ref>PMID:12009886</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1kho" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Hemolysin 3D structures\|Hemolysin 3D structures]]		*[[Hemolysin 3D structures\|Hemolysin 3D structures]]
	*[[Phospholipase C\|Phospholipase C]]		*[[Phospholipase C\|Phospholipase C]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ perfringens ~~veillon and zuber 1898~~]]	+	[[Category: Clostridium perfringens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Basak~~, A K~~]]	+	[[Category: Basak AK]]
-	[[Category: Justin, N]]	+	[[Category: Justin N]]
-	[[Category: Moss~~, D S~~]]	+	[[Category: Moss DS]]
-	[[Category: Titball~~, R W]]~~	+	[[Category: Titball RW]]
-	~~[[Category: C-terminal beta-sheet]]~~	+
-	~~[[Category: N-terminal alpha-helix]]~~	+
-	~~[[Category: Toxin~~]]	+

OCA at 07:44, 25 November 2020

2020-11-25T07:44:57Z

←Older revision		Revision as of 07:44, 25 November 2020
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	==Crystal Structure Analysis of Clostridium perfringens alpha-Toxin Isolated from Avian Strain SWCP==		==Crystal Structure Analysis of Clostridium perfringens alpha-Toxin Isolated from Avian Strain SWCP==
-	<StructureSection load='1kho' size='340' side='right' caption='[[1kho]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='1kho' size='340' side='right'caption='[[1kho]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kho]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus perfringens" veillon and zuber 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1KHO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kho]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus perfringens" veillon and zuber 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1KHO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ca1\|1ca1]], [[1qm6\|1qm6]], [[1qmd\|1qmd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ca1\|1ca1]], [[1qm6\|1qm6]], [[1qmd\|1qmd]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1502 "Bacillus perfringens" Veillon and Zuber 1898])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1502 "Bacillus perfringens" Veillon and Zuber 1898])</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=1kho FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kho OCA], [http://pdbe.org/1kho PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kho RCSB], [http://www.ebi.ac.uk/pdbsum/1kho PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kho 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=1kho FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kho OCA], [http://pdbe.org/1kho PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kho RCSB], [http://www.ebi.ac.uk/pdbsum/1kho PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kho ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1kho" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kho" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Hemolysin 3D structures\|Hemolysin 3D structures]]
		+	*[[Phospholipase C\|Phospholipase C]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus perfringens veillon and zuber 1898]]		[[Category: Bacillus perfringens veillon and zuber 1898]]
		+	[[Category: Large Structures]]
	[[Category: Basak, A K]]		[[Category: Basak, A K]]
	[[Category: Justin, N]]		[[Category: Justin, N]]

OCA at 21:13, 24 January 2018

2018-01-24T21:13:49Z

←Older revision		Revision as of 21:13, 24 January 2018
Line 1:		Line 1:
		+
	==Crystal Structure Analysis of Clostridium perfringens alpha-Toxin Isolated from Avian Strain SWCP==		==Crystal Structure Analysis of Clostridium perfringens alpha-Toxin Isolated from Avian Strain SWCP==
	<StructureSection load='1kho' size='340' side='right' caption='[[1kho]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1kho' size='340' side='right' caption='[[1kho]], [[Resolution\|resolution]] 2.40Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ca1\|1ca1]], [[1qm6\|1qm6]], [[1qmd\|1qmd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ca1\|1ca1]], [[1qm6\|1qm6]], [[1qmd\|1qmd]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1502 "Bacillus perfringens" Veillon and Zuber 1898])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1502 "Bacillus perfringens" Veillon and Zuber 1898])</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=1kho FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kho OCA], [http://pdbe.org/1kho PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kho RCSB], [http://www.ebi.ac.uk/pdbsum/1kho 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=1kho FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kho OCA], [http://pdbe.org/1kho PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kho RCSB], [http://www.ebi.ac.uk/pdbsum/1kho PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kho ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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/kh/1kho_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kh/1kho_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 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1kho" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kho" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Hemolysin\|Hemolysin]]
-	*[[Phospholipase C\|Phospholipase C]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:23, 9 February 2016

2016-02-09T14:23:24Z

←Older revision		Revision as of 14:23, 9 February 2016
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=1kho ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[~~Alpha-toxin~~\|~~Alpha-toxin~~]]	+	*[[Hemolysin\|Hemolysin]]
		+	*[[Phospholipase C\|Phospholipase C]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:06, 10 September 2015

2015-09-10T23:06:56Z

←Older revision		Revision as of 23:06, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1kho' size='340' side='right' caption='[[1kho]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1kho' size='340' side='right' caption='[[1kho]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kho]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Clostridium_perfringens Clostridium~~ perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KHO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kho]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus perfringens" veillon and zuber 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KHO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ca1\|1ca1]], [[1qm6\|1qm6]], [[1qmd\|1qmd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ca1\|1ca1]], [[1qm6\|1qm6]], [[1qmd\|1qmd]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1502 ~~Clostridium~~ perfringens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1502 "Bacillus perfringens" Veillon and Zuber 1898])</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=1kho FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kho OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kho RCSB], [http://www.ebi.ac.uk/pdbsum/1kho 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=1kho FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kho OCA], [http://pdbe.org/1kho PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kho RCSB], [http://www.ebi.ac.uk/pdbsum/1kho PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 1kho" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Clostridium~~ perfringens]]	+	[[Category: Bacillus perfringens veillon and zuber 1898]]
	[[Category: Basak, A K]]		[[Category: Basak, A K]]
	[[Category: Justin, N]]		[[Category: Justin, N]]

OCA at 07:22, 25 December 2014

2014-12-25T07:22:05Z

←Older revision		Revision as of 07:22, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kho]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KHO FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kho]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KHO FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ca1\|1ca1]], [[1qm6\|1qm6]], [[1qmd\|1qmd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ca1\|1ca1]], [[1qm6\|1qm6]], [[1qmd\|1qmd]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1502 Clostridium perfringens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1502 Clostridium perfringens])</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=1kho FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kho OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kho RCSB], [http://www.ebi.ac.uk/pdbsum/1kho 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=1kho FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kho OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kho RCSB], [http://www.ebi.ac.uk/pdbsum/1kho PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PHLC_CLOPF PHLC_CLOPF]] Bacterial hemolysins are exotoxins that attack blood cell membranes and cause cell rupture. Constitutes an essential virulence factor in gas gangrene. Binds to eukaryotic membranes where it hydrolyzes both phosphatidylcholine and sphingomyelin, causing cell rupture. The diacylglycerol produced can activate both the arachidonic acid pathway, leading to modulation of the inflammatory response cascade and thrombosis, and protein kinase C, leading to activation of eukaryotic phospholipases and further membrane damage.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Clostridium perfringens]]		[[Category: Clostridium perfringens]]
-	[[Category: Basak, A K.]]	+	[[Category: Basak, A K]]
-	[[Category: Justin, N.]]	+	[[Category: Justin, N]]
-	[[Category: Moss, D S.]]	+	[[Category: Moss, D S]]
-	[[Category: Titball, R W.]]	+	[[Category: Titball, R W]]
	[[Category: C-terminal beta-sheet]]		[[Category: C-terminal beta-sheet]]
	[[Category: N-terminal alpha-helix]]		[[Category: N-terminal alpha-helix]]
	[[Category: Toxin]]		[[Category: Toxin]]

OCA at 08:47, 3 October 2014

2014-10-03T08:47:09Z

←Older revision		Revision as of 08:47, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1kho\| PDB=1kho \| SCENE= }}~~	+	==Crystal Structure Analysis of Clostridium perfringens alpha-Toxin Isolated from Avian Strain SWCP==
-	===Crystal Structure Analysis of Clostridium perfringens alpha-Toxin Isolated from Avian Strain SWCP===	+	<StructureSection load='1kho' size='340' side='right' caption='[[1kho]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~{{ABSTRACT_PUBMED_12009886}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1kho]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KHO FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ca1\|1ca1]], [[1qm6\|1qm6]], [[1qmd\|1qmd]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1502 Clostridium perfringens])</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=1kho FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kho OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kho RCSB], [http://www.ebi.ac.uk/pdbsum/1kho 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/kh/1kho_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 ==
		+	Clostridium perfringens alpha-toxin is a 370-residue, zinc-dependent, phospholipase C that is the key virulence determinant in gas gangrene. It is also implicated in the pathogenesis of sudden death syndrome in young animals and necrotic enteritis in chickens. Previously characterized alpha-toxins from different strains of C. perfringens are almost identical in sequence and biochemical properties. We describe the cloning, nucleotide sequencing, expression, characterization, and crystal structure of alpha-toxin from an avian strain, SWan C. perfringens (SWCP), which has a large degree of sequence variation and altered substrate specificity compared to these strains. The structure of alpha-toxin from strain CER89L43 has been previously reported in open (active site accessible to substrate) and closed (active site obscured by loop movements) conformations. The SWCP structure is in an open-form conformation, with three zinc ions in the active site. This is the first example of an open form of alpha-toxin crystallizing without the addition of divalent cations to the crystallization buffer, indicating that the protein can retain three zinc ions bound in the active site. The topology of the calcium binding site formed by residues 269, 271, 336, and 337, which is essential for membrane binding, is significantly altered in comparison with both the open and closed alpha-toxin structures. We are able to relate these structural changes to the different substrate specificity and membrane binding properties of this divergent alpha-toxin. This will provide essential information when developing an effective vaccine that will protect against C. perfringens infection in a wide range of domestic livestock.

-	~~==Function==~~	+	The first strain of Clostridium perfringens isolated from an avian source has an alpha-toxin with divergent structural and kinetic properties.,Justin N, Walker N, Bullifent HL, Songer G, Bueschel DM, Jost H, Naylor C, Miller J, Moss DS, Titball RW, Basak AK Biochemistry. 2002 May 21;41(20):6253-62. PMID:12009886<ref>PMID:12009886</ref>
-	~~[[http://www.uniprot.org/uniprot/PHLC_CLOPF PHLC_CLOPF]] Bacterial hemolysins are exotoxins that attack blood cell membranes and cause cell rupture. Constitutes~~ an ~~essential virulence factor in gas gangrene. Binds to eukaryotic membranes where it hydrolyzes both phosphatidylcholine~~ and ~~sphingomyelin, causing cell rupture~~. ~~The diacylglycerol produced can activate both the arachidonic acid pathway~~, ~~leading to modulation of the inflammatory response cascade and thrombosis~~, ~~and protein kinase~~ C, ~~leading to activation of eukaryotic phospholipases and further membrane damage~~.	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[1kho]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Clostridium_perfringens Clostridium perfringens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1KHO OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:012009886</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Alpha-toxin\|Alpha-toxin]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Clostridium perfringens]]		[[Category: Clostridium perfringens]]
	[[Category: Basak, A K.]]		[[Category: Basak, A K.]]

OCA: Protected "1kho" [edit=sysop:move=sysop]

2014-04-16T10:34:23Z

Protected "1kho" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:34, 16 April 2014

OCA at 10:34, 16 April 2014

2014-04-16T10:34:22Z

←Older revision		Revision as of 10:34, 16 April 2014
Line 1:		Line 1:
-	{{Seed}}
-	[[Image:1kho.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_1kho", 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_1kho\| PDB=1kho \| SCENE= }}		{{STRUCTURE_1kho\| PDB=1kho \| SCENE= }}
-
	===Crystal Structure Analysis of Clostridium perfringens alpha-Toxin Isolated from Avian Strain SWCP===		===Crystal Structure Analysis of Clostridium perfringens alpha-Toxin Isolated from Avian Strain SWCP===
		+	{{ABSTRACT_PUBMED_12009886}}

-		+	==Function==
-	~~<!--~~	+	[[http://www.uniprot.org/uniprot/PHLC_CLOPF PHLC_CLOPF]] Bacterial hemolysins are exotoxins that attack blood cell membranes and cause cell rupture. Constitutes an essential virulence factor in gas gangrene. Binds to eukaryotic membranes where it hydrolyzes both phosphatidylcholine and sphingomyelin, causing cell rupture. The diacylglycerol produced can activate both the arachidonic acid pathway, leading to modulation of the inflammatory response cascade and thrombosis, and protein kinase C, leading to activation of eukaryotic phospholipases and further membrane damage.
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_12009886}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov),~~ where ~~12009886 is~~ the ~~PubMed ID number~~.	+
-	~~-->~~	+
-	~~{{ABSTRACT_PUBMED_12009886}}~~	+

	==About this Structure==		==About this Structure==
-	~~1KHO~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHO OCA].	+	[[1kho]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHO OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12009886~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012009886</ref><references group="xtra"/><references/>
	[[Category: Clostridium perfringens]]		[[Category: Clostridium perfringens]]
	[[Category: Basak, A K.]]		[[Category: Basak, A K.]]
Line 31:		Line 18:
	[[Category: C-terminal beta-sheet]]		[[Category: C-terminal beta-sheet]]
	[[Category: N-terminal alpha-helix]]		[[Category: N-terminal alpha-helix]]
-		+	[[Category: Toxin]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 10:27:28 2009''~~	+

OCA at 08:27, 17 February 2009

2009-02-17T08:27:29Z

←Older revision		Revision as of 08:27, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1KHO is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHO OCA].	+	1KHO is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHO OCA].

	==Reference==		==Reference==
-	The first strain of Clostridium perfringens isolated from an avian source has an alpha-toxin with divergent structural and kinetic properties., Justin N, Walker N, Bullifent HL, Songer G, Bueschel DM, Jost H, Naylor C, Miller J, Moss DS, Titball RW, Basak AK, Biochemistry. 2002 May 21;41(20):6253-62. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12009886 12009886]~~	+	<ref group="xtra">PMID:12009886</ref><references group="xtra"/>
	[[Category: Clostridium perfringens]]		[[Category: Clostridium perfringens]]
-	[[Category: Single protein]]
	[[Category: Basak, A K.]]		[[Category: Basak, A K.]]
	[[Category: Justin, N.]]		[[Category: Justin, N.]]
Line 33:		Line 32:
	[[Category: N-terminal alpha-helix]]		[[Category: N-terminal alpha-helix]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jul 2~~ 10:21:~~37 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:27:28 2009''