3d2c - Revision history

OCA at 19:20, 29 May 2024

2024-05-29T19:20:22Z

←Older revision		Revision as of 19:20, 29 May 2024
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	<StructureSection load='3d2c' size='340' side='right'caption='[[3d2c]], [[Resolution\|resolution]] 2.18Å' scene=''>		<StructureSection load='3d2c' size='340' side='right'caption='[[3d2c]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3d2c]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"vibrio_subtilis"_ehrenberg_1835 "vibrio~~ subtilis~~" ehrenberg 1835~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D2C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3d2c]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D2C FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1t2n\|1t2n]], [[1t4m\|1t4m]], [[3d2a\|3d2a]], [[3d2b\|3d2b]]</div></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]] 2.18Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">lipA, lip, BSU02700 ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Triacylglycerol_lipase Triacylglycerol lipase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.3 3.1.1.3] </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=3d2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d2c OCA], [https://pdbe.org/3d2c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d2c RCSB], [https://www.ebi.ac.uk/pdbsum/3d2c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d2c 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=3d2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d2c OCA], [https://pdbe.org/3d2c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d2c RCSB], [https://www.ebi.ac.uk/pdbsum/3d2c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d2c ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ESTA_BACSU ESTA_BACSU]] Active toward p-nitrophenyl esters and triacylglycerides with a marked preference for esters with C8 acyl groups.<ref>PMID:8396026</ref>	+	[https://www.uniprot.org/uniprot/ESTA_BACSU ESTA_BACSU] Active toward p-nitrophenyl esters and triacylglycerides with a marked preference for esters with C8 acyl groups.<ref>PMID:8396026</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Vibrio~~ subtilis ~~ehrenberg 1835~~]]	+	[[Category: Bacillus subtilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Triacylglycerol lipase]]~~	+	[[Category: Kamal MZ]]
-	[[Category: Kamal~~, M Z~~]]	+	[[Category: Sankaranarayanan R]]
-	[[Category: Sankaranarayanan, R]]	+
-	~~[[Category: Alpha/beta hydrolase]]~~	+
-	~~[[Category: Directed evolution]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Lipase]]~~	+
-	~~[[Category: Lipid degradation]]~~	+
-	~~[[Category: Secreted]]~~	+
-	~~[[Category: Stability~~]]	+

OCA at 07:31, 10 November 2021

2021-11-10T07:31:00Z

←Older revision		Revision as of 07:31, 10 November 2021
Line 1:		Line 1:

	==Structure of 4D3, a thermostable mutant of Bacillus subtilis lipase obtained through directed evolution==		==Structure of 4D3, a thermostable mutant of Bacillus subtilis lipase obtained through directed evolution==
-	<StructureSection load='3d2c' size='340' side='right' caption='[[3d2c]], [[Resolution\|resolution]] 2.18Å' scene=''>	+	<StructureSection load='3d2c' size='340' side='right'caption='[[3d2c]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3d2c]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"~~bacillus_globigii~~"~~_migula_1900~~ "~~bacillus globigii~~" ~~migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2C OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3D2C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3d2c]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D2C FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t2n\|1t2n]], [[1t4m\|1t4m]], [[3d2a\|3d2a]], [[3d2b\|3d2b]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1t2n\|1t2n]], [[1t4m\|1t4m]], [[3d2a\|3d2a]], [[3d2b\|3d2b]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lipA, lip, BSU02700 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "~~Bacillus globigii~~" ~~Migula 1900~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lipA, lip, BSU02700 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Triacylglycerol_lipase Triacylglycerol lipase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.3 3.1.1.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Triacylglycerol_lipase Triacylglycerol lipase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.3 3.1.1.3] </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=3d2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d2c OCA], [~~http~~://pdbe.org/3d2c PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3d2c RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3d2c PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3d2c 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=3d2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d2c OCA], [https://pdbe.org/3d2c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d2c RCSB], [https://www.ebi.ac.uk/pdbsum/3d2c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d2c ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ESTA_BACSU ESTA_BACSU]] Active toward p-nitrophenyl esters and triacylglycerides with a marked preference for esters with C8 acyl groups.<ref>PMID:8396026</ref>	+	[[https://www.uniprot.org/uniprot/ESTA_BACSU ESTA_BACSU]] Active toward p-nitrophenyl esters and triacylglycerides with a marked preference for esters with C8 acyl groups.<ref>PMID:8396026</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d2/3d2c_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d2/3d2c_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 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 3d2c" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3d2c" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lipase 3D Structures\|Lipase 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus globigii migula 1900~~]]	+	[[Category: Vibrio subtilis ehrenberg 1835]]
		+	[[Category: Large Structures]]
	[[Category: Triacylglycerol lipase]]		[[Category: Triacylglycerol lipase]]
	[[Category: Kamal, M Z]]		[[Category: Kamal, M Z]]

OCA at 08:41, 25 October 2017

2017-10-25T08:41:17Z

←Older revision		Revision as of 08:41, 25 October 2017
Line 1:		Line 1:
		+
	==Structure of 4D3, a thermostable mutant of Bacillus subtilis lipase obtained through directed evolution==		==Structure of 4D3, a thermostable mutant of Bacillus subtilis lipase obtained through directed evolution==
	<StructureSection load='3d2c' size='340' side='right' caption='[[3d2c]], [[Resolution\|resolution]] 2.18Å' scene=''>		<StructureSection load='3d2c' size='340' side='right' caption='[[3d2c]], [[Resolution\|resolution]] 2.18Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lipA, lip, BSU02700 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lipA, lip, BSU02700 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triacylglycerol_lipase Triacylglycerol lipase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.3 3.1.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triacylglycerol_lipase Triacylglycerol lipase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.3 3.1.1.3] </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=3d2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d2c OCA], [http://pdbe.org/3d2c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d2c RCSB], [http://www.ebi.ac.uk/pdbsum/3d2c 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=3d2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d2c OCA], [http://pdbe.org/3d2c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d2c RCSB], [http://www.ebi.ac.uk/pdbsum/3d2c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3d2c ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 3d2c" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3d2c" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Lipase\|Lipase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:24, 9 February 2016

2016-02-09T13:24:24Z

←Older revision		Revision as of 13:24, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3d2c' size='340' side='right' caption='[[3d2c]], [[Resolution\|resolution]] 2.18Å' scene=''>		<StructureSection load='3d2c' size='340' side='right' caption='[[3d2c]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3d2c]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_subtilis Bacillus subtilis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D2C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3d2c]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D2C FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t2n\|1t2n]], [[1t4m\|1t4m]], [[3d2a\|3d2a]], [[3d2b\|3d2b]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t2n\|1t2n]], [[1t4m\|1t4m]], [[3d2a\|3d2a]], [[3d2b\|3d2b]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lipA, lip, BSU02700 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus ~~subtilis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lipA, lip, BSU02700 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triacylglycerol_lipase Triacylglycerol lipase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.3 3.1.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triacylglycerol_lipase Triacylglycerol lipase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.3 3.1.1.3] </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=3d2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d2c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d2c RCSB], [http://www.ebi.ac.uk/pdbsum/3d2c 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=3d2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d2c OCA], [http://pdbe.org/3d2c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d2c RCSB], [http://www.ebi.ac.uk/pdbsum/3d2c PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~LIP_BACSU LIP_BACSU~~]] Active toward p-nitrophenyl esters and triacylglycerides with a marked preference for esters with C8 acyl groups.<ref>PMID:8396026</ref>	+	[[http://www.uniprot.org/uniprot/ESTA_BACSU ESTA_BACSU]] Active toward p-nitrophenyl esters and triacylglycerides with a marked preference for esters with C8 acyl groups.<ref>PMID:8396026</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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=3d2c ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3d2c" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~subtilis~~]]	+	[[Category: Bacillus globigii migula 1900]]
	[[Category: Triacylglycerol lipase]]		[[Category: Triacylglycerol lipase]]
	[[Category: Kamal, M Z]]		[[Category: Kamal, M Z]]

OCA at 07:04, 25 December 2014

2014-12-25T07:04:51Z

←Older revision		Revision as of 07:04, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3d2c]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D2C FirstGlance]. <br>		<table><tr><td colspan='2'>[[3d2c]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D2C FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t2n\|1t2n]], [[1t4m\|1t4m]], [[3d2a\|3d2a]], [[3d2b\|3d2b]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t2n\|1t2n]], [[1t4m\|1t4m]], [[3d2a\|3d2a]], [[3d2b\|3d2b]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lipA, lip, BSU02700 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lipA, lip, BSU02700 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triacylglycerol_lipase Triacylglycerol lipase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.3 3.1.1.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triacylglycerol_lipase Triacylglycerol lipase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.3 3.1.1.3] </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=3d2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d2c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d2c RCSB], [http://www.ebi.ac.uk/pdbsum/3d2c 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=3d2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d2c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d2c RCSB], [http://www.ebi.ac.uk/pdbsum/3d2c PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LIP_BACSU LIP_BACSU]] Active toward p-nitrophenyl esters and triacylglycerides with a marked preference for esters with C8 acyl groups.<ref>PMID:8396026</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Triacylglycerol lipase]]		[[Category: Triacylglycerol lipase]]
-	[[Category: Kamal, M Z.]]	+	[[Category: Kamal, M Z]]
-	[[Category: Sankaranarayanan, R.]]	+	[[Category: Sankaranarayanan, R]]
	[[Category: Alpha/beta hydrolase]]		[[Category: Alpha/beta hydrolase]]
	[[Category: Directed evolution]]		[[Category: Directed evolution]]

OCA at 06:48, 29 September 2014

2014-09-29T06:48:48Z

←Older revision		Revision as of 06:48, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3d2c.~~png~~\|~~left~~\|200px]]	+	==Structure of 4D3, a thermostable mutant of Bacillus subtilis lipase obtained through directed evolution==
		+	<StructureSection load='3d2c' size='340' side='right' caption='[[3d2c]], [[Resolution\|resolution]] 2.18Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3d2c]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D2C FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t2n\|1t2n]], [[1t4m\|1t4m]], [[3d2a\|3d2a]], [[3d2b\|3d2b]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lipA, lip, BSU02700 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triacylglycerol_lipase Triacylglycerol lipase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.3 3.1.1.3] </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=3d2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d2c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d2c RCSB], [http://www.ebi.ac.uk/pdbsum/3d2c 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/d2/3d2c_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 ==
		+	In vitro evolution methods are now being routinely used to identify protein variants with novel and enhanced properties that are difficult to achieve using rational design. However, one of the limitations is in screening for beneficial mutants through several generations due to the occurrence of neutral/negative mutations occurring in the background of positive ones. While evolving a lipase in vitro from mesophilic Bacillus subtilis to generate thermostable variants, we have designed protocols that combine stringent three-tier testing, sequencing and stability assessments on the protein at the end of each generation. This strategy resulted in a total of six stabilizing mutations in just two generations with three mutations per generation. Each of the six mutants when evaluated individually contributed additively to thermostability. A combination of all of them resulted in the best variant that shows a remarkable 15 degrees C shift in melting temperature and a millionfold decrease in the thermal inactivation rate with only a marginal increase of 3 kcal mol(-1) in free energy of stabilization. Notably, in addition to the dramatic shift in optimum temperature by 20 degrees C, the activity has increased two- to fivefold in the temperature range 25-65 degrees C. High-resolution crystal structures of three of the mutants, each with 5 degrees increments in melting temperature, reveal the structural basis of these mutations in attaining higher thermostability. The structures highlight the importance of water-mediated ionic networks on the protein surface in imparting thermostability. Saturation mutagenesis at each of the six positions did not result in enhanced thermostability in almost all the cases, confirming the crucial role played by each mutation as revealed through the structural study. Overall, our study presents an efficient strategy that can be employed in directed evolution approaches employed for obtaining improved properties of proteins.

-	~~{{STRUCTURE_3d2c\| PDB=3d2c \| SCENE= }}~~	+	Thermostable Bacillus subtilis lipases: in vitro evolution and structural insight.,Ahmad S, Kamal MZ, Sankaranarayanan R, Rao NM J Mol Biol. 2008 Aug 29;381(2):324-40. Epub 2008 Jul 2. PMID:18599073<ref>PMID:18599073</ref>

-	~~===Structure of 4D3~~, a ~~thermostable mutant~~ of ~~Bacillus subtilis lipase obtained through directed evolution===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18599073}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3d2c]] is a 12 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_subtilis Bacillus subtilis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3D2C OCA].~~	+

	==See Also==		==See Also==
	*[[Lipase\|Lipase]]		*[[Lipase\|Lipase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018599073<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Triacylglycerol lipase]]		[[Category: Triacylglycerol lipase]]

OCA at 13:58, 20 October 2012

2012-10-20T13:58:58Z

←Older revision		Revision as of 13:58, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[3d2c]] is a 12 chain structure ~~of [[Lipase]]~~ with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2C OCA].	+	[[3d2c]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2C OCA].

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

OCA at 13:41, 26 July 2012

2012-07-26T13:41:50Z

←Older revision		Revision as of 13:41, 26 July 2012
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	[[Image:3d2c.png\|left\|200px]]		[[Image:3d2c.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3d2c", 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_3d2c\| PDB=3d2c \| SCENE= }}		{{STRUCTURE_3d2c\| PDB=3d2c \| SCENE= }}

	===Structure of 4D3, a thermostable mutant of Bacillus subtilis lipase obtained through directed evolution===		===Structure of 4D3, a thermostable mutant of Bacillus subtilis lipase obtained through directed evolution===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18599073}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18599073 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18599073}}		{{ABSTRACT_PUBMED_18599073}}

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	==See Also==		==See Also==
-	*[[Lipase]]	+	*[[Lipase\|Lipase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18599073~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018599073</ref><references group="xtra"/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Triacylglycerol lipase]]		[[Category: Triacylglycerol lipase]]

OCA: Protected "3d2c" [edit=sysop:move=sysop]

2010-12-26T08:51:32Z

Protected "3d2c" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:51, 26 December 2010

OCA at 08:51, 26 December 2010

2010-12-26T08:51:31Z

←Older revision		Revision as of 08:51, 26 December 2010
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-	{{Seed}}
	[[Image:3d2c.png\|left\|200px]]		[[Image:3d2c.png\|left\|200px]]

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	==About this Structure==		==About this Structure==
-	~~3D2C~~ is a 12 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2C OCA].	+	[[3d2c]] is a 12 chain structure of [[Lipase]] with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2C OCA].
		+
		+	==See Also==
		+	*[[Lipase]]

	==Reference==		==Reference==
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	[[Category: Secreted]]		[[Category: Secreted]]
	[[Category: Stability]]		[[Category: Stability]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:06:13 2009''