2ddt - Revision history

OCA at 13:47, 13 March 2024

OCA — Wed, 13 Mar 2024 13:47:18 GMT

←Older revision		Revision as of 13:47, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='2ddt' size='340' side='right'caption='[[2ddt]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2ddt' size='340' side='right'caption='[[2ddt]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ddt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_14579 Atcc 14579~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DDT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ddt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DDT FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MES:2~~-~~(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2ddr\|2ddr]], [[2dds\|2dds]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12]~~ </~~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=2ddt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddt OCA], [https://pdbe.org/2ddt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ddt RCSB], [https://www.ebi.ac.uk/pdbsum/2ddt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ddt ProSAT], [https://www.topsan.org/Proteins/RSGI/2ddt TOPSAN]</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=2ddt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddt OCA], [https://pdbe.org/2ddt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ddt RCSB], [https://www.ebi.ac.uk/pdbsum/2ddt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ddt ProSAT], [https://www.topsan.org/Proteins/RSGI/2ddt TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PHL2_BACCE PHL2_BACCE]] Required, with sphingomyelinase, to effect target cell lysis (hemolysis).	+	[https://www.uniprot.org/uniprot/PHL2_BACCE PHL2_BACCE] Required, with sphingomyelinase, to effect target cell lysis (hemolysis).
	== 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=2ddt 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=2ddt ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Sphingomyelinase (SMase) from Bacillus cereus (Bc-SMase) hydrolyzes sphingomyelin to phosphocholine and ceramide in a divalent metal ion-dependent manner. Bc-SMase is a homologue of mammalian neutral SMase (nSMase) and mimics the actions of the endogenous mammalian nSMase in causing differentiation, development, aging, and apoptosis. Thus Bc-SMase may be a good model for the poorly characterized mammalian nSMase. The metal ion activation of sphingomyelinase activity of Bc-SMase was in the order Co2+ > or = Mn2+ > or = Mg2+ >> Ca2+ > or = Sr2+. The first crystal structures of Bc-SMase bound to Co2+, Mg2+, or Ca2+ were determined. The water-bridged double divalent metal ions at the center of the cleft in both the Co2+- and Mg2+-bound forms were concluded to be the catalytic architecture required for sphingomyelinase activity. In contrast, the architecture of Ca2+ binding at the site showed only one binding site. A further single metal-binding site exists at one side edge of the cleft. Based on the highly conserved nature of the residues of the binding sites, the crystal structure of Bc-SMase with bound Mg2+ or Co2+ may provide a common structural framework applicable to phosphohydrolases belonging to the DNase I-like folding superfamily. In addition, the structural features and site-directed mutagenesis suggest that the specific beta-hairpin with the aromatic amino acid residues participates in binding to the membrane-bound sphingomyelin substrate.
-
-	Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from Bacillus cereus.,Ago H, Oda M, Takahashi M, Tsuge H, Ochi S, Katunuma N, Miyano M, Sakurai J J Biol Chem. 2006 Jun 9;281(23):16157-67. Epub 2006 Apr 4. PMID:16595670<ref>PMID:16595670</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2ddt" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Sphingomyelinase\|Sphingomyelinase]]		*[[Sphingomyelinase\|Sphingomyelinase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 14579~~]]	+	[[Category: Bacillus cereus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Sphingomyelin phosphodiesterase]]~~	+	[[Category: Ago H]]
-	[[Category: Ago, H]]	+	[[Category: Katunuma N]]
-	[[Category: Katunuma, N]]	+	[[Category: Miyano M]]
-	[[Category: Miyano, M]]	+	[[Category: Oda M]]
-	[[Category: Oda, M]]	+	[[Category: Sakurai J]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Tsuge H]]
-	[[Category: Sakurai, J]]	+
-	[[Category: Tsuge, H]]	+
-	~~[[Category: Dnase i like folding]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Rsgi~~]]	+

OCA at 10:30, 8 December 2021

OCA — Wed, 08 Dec 2021 10:30:21 GMT

←Older revision		Revision as of 10:30, 8 December 2021
Line 3:		Line 3:
	<StructureSection load='2ddt' size='340' side='right'caption='[[2ddt]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2ddt' size='340' side='right'caption='[[2ddt]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ddt]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DDT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ddt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DDT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">[[2ddr\|2ddr]], [[2dds\|2dds]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ddr\|2ddr]], [[2dds\|2dds]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </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=2ddt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddt OCA], [~~http~~://pdbe.org/2ddt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ddt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ddt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ddt ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/2ddt TOPSAN]</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=2ddt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddt OCA], [https://pdbe.org/2ddt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ddt RCSB], [https://www.ebi.ac.uk/pdbsum/2ddt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ddt ProSAT], [https://www.topsan.org/Proteins/RSGI/2ddt TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PHL2_BACCE PHL2_BACCE]] Required, with sphingomyelinase, to effect target cell lysis (hemolysis).	+	[[https://www.uniprot.org/uniprot/PHL2_BACCE PHL2_BACCE]] Required, with sphingomyelinase, to effect target cell lysis (hemolysis).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:35, 4 March 2020

OCA — Wed, 04 Mar 2020 07:35:44 GMT

←Older revision		Revision as of 07:35, 4 March 2020
Line 1:		Line 1:

	==Crystal structure of sphingomyelinase from Bacillus cereus with magnesium ion==		==Crystal structure of sphingomyelinase from Bacillus cereus with magnesium ion==
-	<StructureSection load='2ddt' size='340' side='right' caption='[[2ddt]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='2ddt' size='340' side='right'caption='[[2ddt]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ddt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDT FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ddt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDT FirstGlance]. <br>
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 14579]]		[[Category: Atcc 14579]]
		+	[[Category: Large Structures]]
	[[Category: Sphingomyelin phosphodiesterase]]		[[Category: Sphingomyelin phosphodiesterase]]
	[[Category: Ago, H]]		[[Category: Ago, H]]

OCA at 06:15, 30 May 2018

OCA — Wed, 30 May 2018 06:15:03 GMT

←Older revision		Revision as of 06:15, 30 May 2018
Line 1:		Line 1:
		+
	==Crystal structure of sphingomyelinase from Bacillus cereus with magnesium ion==		==Crystal structure of sphingomyelinase from Bacillus cereus with magnesium ion==
	<StructureSection load='2ddt' size='340' side='right' caption='[[2ddt]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2ddt' size='340' side='right' caption='[[2ddt]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddr\|2ddr]], [[2dds\|2dds]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddr\|2ddr]], [[2dds\|2dds]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </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=2ddt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddt OCA], [http://pdbe.org/2ddt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ddt RCSB], [http://www.ebi.ac.uk/pdbsum/2ddt PDBsum], [http://www.topsan.org/Proteins/RSGI/2ddt TOPSAN]</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=2ddt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddt OCA], [http://pdbe.org/2ddt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ddt RCSB], [http://www.ebi.ac.uk/pdbsum/2ddt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ddt ProSAT], [http://www.topsan.org/Proteins/RSGI/2ddt TOPSAN]</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/dd/2ddt_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/2ddt_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>

OCA at 02:08, 8 February 2016

OCA — Mon, 08 Feb 2016 02:08:31 GMT

←Older revision		Revision as of 02:08, 8 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=2ddt ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:52, 10 September 2015

OCA — Thu, 10 Sep 2015 06:52:26 GMT

←Older revision		Revision as of 06:52, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2ddt' size='340' side='right' caption='[[2ddt]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2ddt' size='340' side='right' caption='[[2ddt]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ddt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_cereus Bacillus cereus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ddt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_14579 Atcc 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">[[2ddr\|2ddr]], [[2dds\|2dds]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddr\|2ddr]], [[2dds\|2dds]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </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=2ddt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ddt RCSB], [http://www.ebi.ac.uk/pdbsum/2ddt PDBsum], [http://www.topsan.org/Proteins/RSGI/2ddt TOPSAN]</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=2ddt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddt OCA], [http://pdbe.org/2ddt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ddt RCSB], [http://www.ebi.ac.uk/pdbsum/2ddt PDBsum], [http://www.topsan.org/Proteins/RSGI/2ddt TOPSAN]</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 2ddt" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus cereus~~]]	+	[[Category: Atcc 14579]]
	[[Category: Sphingomyelin phosphodiesterase]]		[[Category: Sphingomyelin phosphodiesterase]]
	[[Category: Ago, H]]		[[Category: Ago, H]]

OCA at 19:47, 24 December 2014

OCA — Wed, 24 Dec 2014 19:47:30 GMT

←Older revision		Revision as of 19:47, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ddt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDT FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ddt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDT FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddr\|2ddr]], [[2dds\|2dds]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddr\|2ddr]], [[2dds\|2dds]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </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=2ddt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ddt RCSB], [http://www.ebi.ac.uk/pdbsum/2ddt PDBsum], [http://www.topsan.org/Proteins/RSGI/2ddt TOPSAN]</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=2ddt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ddt RCSB], [http://www.ebi.ac.uk/pdbsum/2ddt PDBsum], [http://www.topsan.org/Proteins/RSGI/2ddt TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PHL2_BACCE PHL2_BACCE]] Required, with sphingomyelinase, to effect target cell lysis (hemolysis).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Bacillus cereus]]		[[Category: Bacillus cereus]]
	[[Category: Sphingomyelin phosphodiesterase]]		[[Category: Sphingomyelin phosphodiesterase]]
-	[[Category: Ago, H.]]	+	[[Category: Ago, H]]
-	[[Category: Katunuma, N.]]	+	[[Category: Katunuma, N]]
-	[[Category: Miyano, M.]]	+	[[Category: Miyano, M]]
-	[[Category: Oda, M.]]	+	[[Category: Oda, M]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Sakurai, J.]]	+	[[Category: Sakurai, J]]
-	[[Category: Tsuge, H.]]	+	[[Category: Tsuge, H]]
	[[Category: Dnase i like folding]]		[[Category: Dnase i like folding]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]

OCA at 04:29, 29 September 2014

OCA — Mon, 29 Sep 2014 04:29:12 GMT

←Older revision		Revision as of 04:29, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2ddt.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of sphingomyelinase from Bacillus cereus with magnesium ion==
		+	<StructureSection load='2ddt' size='340' side='right' caption='[[2ddt]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2ddt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDT FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddr\|2ddr]], [[2dds\|2dds]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </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=2ddt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ddt RCSB], [http://www.ebi.ac.uk/pdbsum/2ddt PDBsum], [http://www.topsan.org/Proteins/RSGI/2ddt TOPSAN]</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/dd/2ddt_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 ==
		+	Sphingomyelinase (SMase) from Bacillus cereus (Bc-SMase) hydrolyzes sphingomyelin to phosphocholine and ceramide in a divalent metal ion-dependent manner. Bc-SMase is a homologue of mammalian neutral SMase (nSMase) and mimics the actions of the endogenous mammalian nSMase in causing differentiation, development, aging, and apoptosis. Thus Bc-SMase may be a good model for the poorly characterized mammalian nSMase. The metal ion activation of sphingomyelinase activity of Bc-SMase was in the order Co2+ > or = Mn2+ > or = Mg2+ >> Ca2+ > or = Sr2+. The first crystal structures of Bc-SMase bound to Co2+, Mg2+, or Ca2+ were determined. The water-bridged double divalent metal ions at the center of the cleft in both the Co2+- and Mg2+-bound forms were concluded to be the catalytic architecture required for sphingomyelinase activity. In contrast, the architecture of Ca2+ binding at the site showed only one binding site. A further single metal-binding site exists at one side edge of the cleft. Based on the highly conserved nature of the residues of the binding sites, the crystal structure of Bc-SMase with bound Mg2+ or Co2+ may provide a common structural framework applicable to phosphohydrolases belonging to the DNase I-like folding superfamily. In addition, the structural features and site-directed mutagenesis suggest that the specific beta-hairpin with the aromatic amino acid residues participates in binding to the membrane-bound sphingomyelin substrate.

-	~~{{STRUCTURE_2ddt\| PDB=2ddt \| SCENE= }}~~	+	Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from Bacillus cereus.,Ago H, Oda M, Takahashi M, Tsuge H, Ochi S, Katunuma N, Miyano M, Sakurai J J Biol Chem. 2006 Jun 9;281(23):16157-67. Epub 2006 Apr 4. PMID:16595670<ref>PMID:16595670</ref>

-	~~===Crystal structure~~ of ~~sphingomyelinase from Bacillus cereus with magnesium ion===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16595670}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2ddt]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_cereus Bacillus cereus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2DDT OCA].~~	+

	==See Also==		==See Also==
	*[[Sphingomyelinase\|Sphingomyelinase]]		*[[Sphingomyelinase\|Sphingomyelinase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:016595670<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bacillus cereus]]		[[Category: Bacillus cereus]]
	[[Category: Sphingomyelin phosphodiesterase]]		[[Category: Sphingomyelin phosphodiesterase]]

OCA at 08:32, 20 October 2012

OCA — Sat, 20 Oct 2012 08:32:48 GMT

←Older revision		Revision as of 08:32, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2ddt]] is a 2 chain structure ~~of [[Sphingomyelinase]]~~ with sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDT OCA].	+	[[2ddt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDT OCA].

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

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

OCA — Wed, 25 Jul 2012 19:51:48 GMT

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

←Older revision

Revision as of 19:51, 25 July 2012