5tie - Revision history

OCA at 13:02, 4 October 2023

2023-10-04T13:02:11Z

←Older revision		Revision as of 13:02, 4 October 2023
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	<StructureSection load='5tie' size='340' side='right'caption='[[5tie]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='5tie' size='340' side='right'caption='[[5tie]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tie]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TIE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tie]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TIE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=OCA:OCTANOIC+ACID+(CAPRYLIC+ACID)'>OCA</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]] 1.15Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tic\|5tic]]~~, [[~~5tid~~\|~~5tid]], [[5tif\|5tif~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OCA:OCTANOIC+ACID+(CAPRYLIC+ACID)'>OCA</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>tesA, apeA, pldC, b0494, JW0483 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895]~~)</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=5tie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tie OCA], [https://pdbe.org/5tie PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tie RCSB], [https://www.ebi.ac.uk/pdbsum/5tie PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tie ProSAT]</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=5tie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tie OCA], [~~http~~://pdbe.org/5tie PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tie RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tie PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tie ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TESA_ECOLI TESA_ECOLI]] Hydrolyzes only long chain acyl thioesters (C12-C18). Specificity similar to chymotrypsin.	+	[https://www.uniprot.org/uniprot/TESA_ECOLI TESA_ECOLI] Hydrolyzes only long chain acyl thioesters (C12-C18). Specificity similar to chymotrypsin.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Thioesterase\|Thioesterase]]	+	*[[Thioesterase 3D structures\|Thioesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Allan~~, M F~~]]	+	[[Category: Allan MF]]
-	[[Category: Gifford~~, N P~~]]	+	[[Category: Gifford NP]]
-	[[Category: Grisewood~~, M J~~]]	+	[[Category: Grisewood MJ]]
-	[[Category: ~~Holden, H M~~]]	+	[[Category: Hernandez Lozada NJ]]
-	[[Category: ~~Lozada, N J.Hernandez~~]]	+	[[Category: Holden HM]]
-	[[Category: Marines~~, C D~~]]	+	[[Category: Marines CD]]
-	[[Category: Mendez-Perez, D]]	+	[[Category: Mendez-Perez D]]
-	[[Category: Pfleger~~, B F~~]]	+	[[Category: Pfleger BF]]
-	[[Category: Schoenberger~~, H A~~]]	+	[[Category: Schoenberger HA]]
-	[[Category: Thoden~~, J B]]~~	+	[[Category: Thoden JB]]
-	~~[[Category: Fatty acid]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Octanoic acid]]~~	+
-	~~[[Category: Tesa]]~~	+
-	~~[[Category: Thioesterase~~]]	+

OCA at 12:32, 25 December 2019

2019-12-25T12:32:31Z

←Older revision		Revision as of 12:32, 25 December 2019
Line 1:		Line 1:

	==x-ray structure of acyl-CoA thioesterase I, TesA, mutant M141L/Y145K/L146K at pH 7.5 in complex with octanoic acid==		==x-ray structure of acyl-CoA thioesterase I, TesA, mutant M141L/Y145K/L146K at pH 7.5 in complex with octanoic acid==
-	<StructureSection load='5tie' size='340' side='right' caption='[[5tie]], [[Resolution\|resolution]] 1.15Å' scene=''>	+	<StructureSection load='5tie' size='340' side='right'caption='[[5tie]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5tie]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TIE FirstGlance]. <br>		<table><tr><td colspan='2'>[[5tie]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TIE FirstGlance]. <br>
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5tie" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5tie" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thioesterase\|Thioesterase]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Allan, M F]]		[[Category: Allan, M F]]
	[[Category: Gifford, N P]]		[[Category: Gifford, N P]]

OCA at 06:57, 15 February 2018

2018-02-15T06:57:58Z

←Older revision		Revision as of 06:57, 15 February 2018
Line 11:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/TESA_ECOLI TESA_ECOLI]] Hydrolyzes only long chain acyl thioesters (C12-C18). Specificity similar to chymotrypsin.		[[http://www.uniprot.org/uniprot/TESA_ECOLI TESA_ECOLI]] Hydrolyzes only long chain acyl thioesters (C12-C18). Specificity similar to chymotrypsin.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Enzyme and metabolic engineering offer the potential to develop biocatalysts for converting natural resources into a wide range of chemicals. To broaden the scope of potential products beyond natural metabolites, methods of engineering enzymes to accept alternative substrates and/or perform novel chemistries must be developed. DNA synthesis can create large libraries of enzyme-coding sequences, but most biochemistries lack a simple assay to screen for promising enzyme variants. Our solution to this challenge is structure-guided mutagenesis in which optimization algorithms select the best sequences from libraries based on specified criteria (i.e. binding selectivity). Here, we demonstrate this approach by identifying medium-chain (C6-C12) acyl-ACP thioesterases through structure-guided mutagenesis. Medium-chain fatty acids, products of thioesterase-catalyzed hydrolysis, are limited in natural abundance compared to long-chain fatty acids; the limited supply leads to high costs of C6-C10 oleochemicals such as fatty alcohols, amines, and esters. Here, we applied computational tools to tune substrate binding to the highly-active 'TesA thioesterase in Escherichia coli. We used the IPRO algorithm to design thioesterase variants with enhanced C12- or C8-specificity while maintaining high activity. After four rounds of structure-guided mutagenesis, we identified three thioesterases with enhanced production of dodecanoic acid (C12) and twenty-seven thioesterases with enhanced production of octanoic acid (C8). The top variants reached up to 49% C12 and 50% C8 while exceeding native levels of total free fatty acids. A comparably sized library created by random mutagenesis failed to identify promising mutants. The chain length-preference of 'TesA and the best mutant were confirmed in vitro using acyl-CoA substrates. Molecular dynamics simulations, confirmed by resolved crystal structures, of 'TesA variants suggest that hydrophobic forces govern 'TesA substrate specificity. We expect that the design rules we uncovered and the thioesterase variants identified will be useful to metabolic engineering projects aimed at sustainable production of medium-chain oleochemicals.
		+
		+	Computational Redesign of Acyl-ACP Thioesterase with Improved Selectivity toward Medium-Chain-Length Fatty Acids.,Grisewood MJ, Hernandez Lozada NJ, Thoden JB, Gifford NP, Mendez-Perez D, Schoenberger HA, Allan MF, Floy ME, Lai RY, Holden HM, Pfleger BF, Maranas CD ACS Catal. 2017 Jun 2;7(6):3837-3849. doi: 10.1021/acscatal.7b00408. Epub 2017, Apr 20. PMID:29375928<ref>PMID:29375928</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5tie" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 14:24, 6 November 2017

2017-11-06T14:24:24Z

←Older revision		Revision as of 14:24, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5tie' size='340' side='right' caption='[[5tie]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='5tie' size='340' side='right' caption='[[5tie]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tie]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TIE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tie]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TIE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCA:OCTANOIC+ACID+(CAPRYLIC+ACID)'>OCA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCA:OCTANOIC+ACID+(CAPRYLIC+ACID)'>OCA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tic\|5tic]], [[5tid\|5tid]], [[5tif\|5tif]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tic\|5tic]], [[5tid\|5tid]], [[5tif\|5tif]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tesA, apeA, pldC, b0494, JW0483 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=5tie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tie OCA], [http://pdbe.org/5tie PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tie RCSB], [http://www.ebi.ac.uk/pdbsum/5tie PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tie ProSAT]</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=5tie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tie OCA], [http://pdbe.org/5tie PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tie RCSB], [http://www.ebi.ac.uk/pdbsum/5tie PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tie ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Allan, M F]]		[[Category: Allan, M F]]
	[[Category: Gifford, N P]]		[[Category: Gifford, N P]]

OCA at 14:01, 27 April 2017

2017-04-27T14:01:03Z

←Older revision		Revision as of 14:01, 27 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5tie ~~is ON HOLD until Paper Publication~~	+	==x-ray structure of acyl-CoA thioesterase I, TesA, mutant M141L/Y145K/L146K at pH 7.5 in complex with octanoic acid==
-		+	<StructureSection load='5tie' size='340' side='right' caption='[[5tie]], [[Resolution\|resolution]] 1.15Å' scene=''>
-	~~Authors~~: ~~Thoden, J~~.B.~~, Holden, H~~.M.~~, Grisewood, M~~.J.~~, Hernandez Lozada, N~~.J., ~~Gifford~~, N.P.~~, Mendez~~-~~Perez, D~~., ~~Schoenberger, H~~.A., ~~Allan~~, M.F., ~~Pfleger, B~~.F., ~~Marines, C~~.D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5tie]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TIE FirstGlance]. <br>
-	~~Description~~: ~~x-ray structure of~~ acyl-~~CoA thioesterase I~~, ~~TesA~~, ~~mutant M141L/Y145K/L146K at pH 7.5 in complex with octanoic acid~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCA:OCTANOIC+ACID+(CAPRYLIC+ACID)'>OCA</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tic\|5tic]], [[5tid\|5tid]], [[5tif\|5tif]]</td></tr>
-	[[Category: ~~Allan~~, M.F]]	+	<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=5tie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tie OCA], [http://pdbe.org/5tie PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tie RCSB], [http://www.ebi.ac.uk/pdbsum/5tie PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tie ProSAT]</span></td></tr>
-	[[Category: ~~Thoden~~, J.B]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TESA_ECOLI TESA_ECOLI]] Hydrolyzes only long chain acyl thioesters (C12-C18). Specificity similar to chymotrypsin.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Allan, M F]]
		+	[[Category: Gifford, N P]]
		+	[[Category: Grisewood, M J]]
		+	[[Category: Holden, H M]]
		+	[[Category: Lozada, N J.Hernandez]]
		+	[[Category: Marines, C D]]
	[[Category: Mendez-Perez, D]]		[[Category: Mendez-Perez, D]]
-	[[Category: ~~Grisewood~~, ~~M.J~~]]	+	[[Category: Pfleger, B F]]
-	[[Category: ~~Marines~~, ~~C.D~~]]	+	[[Category: Schoenberger, H A]]
-	[[Category: ~~Gifford~~, ~~N.P~~]]	+	[[Category: Thoden, J B]]
-	[[Category: ~~Schoenberger, H.A~~]]	+	[[Category: Fatty acid]]
-	[[Category: ~~Holden, H.M~~]]	+	[[Category: Hydrolase]]
-	[[Category: ~~Hernandez Lozada, N.J~~]]	+	[[Category: Octanoic acid]]
-	[[Category: ~~Pfleger, B.F~~]]	+	[[Category: Tesa]]
		+	[[Category: Thioesterase]]

OCA at 13:34, 9 March 2017

2017-03-09T13:34:20Z

←Older revision		Revision as of 13:34, 9 March 2017
Line 12:		Line 12:
	[[Category: Grisewood, M.J]]		[[Category: Grisewood, M.J]]
	[[Category: Marines, C.D]]		[[Category: Marines, C.D]]
		+	[[Category: Gifford, N.P]]
	[[Category: Schoenberger, H.A]]		[[Category: Schoenberger, H.A]]
	[[Category: Holden, H.M]]		[[Category: Holden, H.M]]
	[[Category: Hernandez Lozada, N.J]]		[[Category: Hernandez Lozada, N.J]]
	[[Category: Pfleger, B.F]]		[[Category: Pfleger, B.F]]
-	[[Category: Gifford, N.P]]

OCA at 17:32, 9 December 2016

2016-12-09T17:32:16Z

←Older revision		Revision as of 17:32, 9 December 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5tie is ON HOLD	+	The entry 5tie is ON HOLD until Paper Publication

	Authors: Thoden, J.B., Holden, H.M., Grisewood, M.J., Hernandez Lozada, N.J., Gifford, N.P., Mendez-Perez, D., Schoenberger, H.A., Allan, M.F., Pfleger, B.F., Marines, C.D.		Authors: Thoden, J.B., Holden, H.M., Grisewood, M.J., Hernandez Lozada, N.J., Gifford, N.P., Mendez-Perez, D., Schoenberger, H.A., Allan, M.F., Pfleger, B.F., Marines, C.D.

OCA: Protected "5tie" [edit=sysop:move=sysop]

2016-10-19T15:51:34Z

Protected "5tie" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:51, 19 October 2016

OCA: New page: '''Unreleased structure''' The entry 5tie is ON HOLD Authors: Thoden, J.B., Holden, H.M., Grisewood, M.J., Hernandez Lozada, N.J., Gifford, N.P., Mendez-Perez, D., Schoenberger, H.A., A...

2016-10-19T15:51:32Z

New page: '''Unreleased structure''' The entry 5tie is ON HOLD Authors: Thoden, J.B., Holden, H.M., Grisewood, M.J., Hernandez Lozada, N.J., Gifford, N.P., Mendez-Perez, D., Schoenberger, H.A., A...

New page

'''Unreleased structure'''

The entry 5tie is ON HOLD

Authors: Thoden, J.B., Holden, H.M., Grisewood, M.J., Hernandez Lozada, N.J., Gifford, N.P., Mendez-Perez, D., Schoenberger, H.A., Allan, M.F., Pfleger, B.F., Marines, C.D.

Description: x-ray structure of acyl-CoA thioesterase I, TesA, mutant M141L/Y145K/L146K at pH 7.5 in complex with octanoic acid
[[Category: Unreleased Structures]]
[[Category: Allan, M.F]]
[[Category: Thoden, J.B]]
[[Category: Mendez-Perez, D]]
[[Category: Grisewood, M.J]]
[[Category: Marines, C.D]]
[[Category: Schoenberger, H.A]]
[[Category: Holden, H.M]]
[[Category: Hernandez Lozada, N.J]]
[[Category: Pfleger, B.F]]
[[Category: Gifford, N.P]]