5eht - Revision history

OCA at 06:28, 5 July 2023

OCA — Wed, 05 Jul 2023 06:28:37 GMT

←Older revision		Revision as of 06:28, 5 July 2023
Line 3:		Line 3:
	<StructureSection load='5eht' size='340' side='right'caption='[[5eht]], [[Resolution\|resolution]] 1.29Å' scene=''>		<StructureSection load='5eht' size='340' side='right'caption='[[5eht]], [[Resolution\|resolution]] 1.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5eht]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_cereus_var._thuringiensis"_smith_et_al._1952 "bacillus cereus var.~~ thuringiensis~~" smith et al. 1952~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EHT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5EHT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5eht]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_thuringiensis Bacillus thuringiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EHT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EHT FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<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]] 1.29Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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">[[5eh9\|5eh9]]</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=5eht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eht OCA], [https://pdbe.org/5eht PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5eht RCSB], [https://www.ebi.ac.uk/pdbsum/5eht PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5eht ProSAT]</span></td></tr>
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b><~~/td><td class="sblockDat">aiiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1428 "Bacillus cereus var. thuringiensis" Smith et al. 1952])</td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[http://en.wikipedia.org/wiki/Quorum-quenching_N-acyl-homoserine_lactonase Quorum-quenching N-acyl-homoserine lactonase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.81 3.1.1.81] </~~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=5eht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eht OCA], [~~http~~://pdbe.org/5eht PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5eht RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5eht PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5eht ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/AHLL_BACTU AHLL_BACTU]] Catalyzes hydrolysis of N-hexanoyl-(S)-homoserine lactone, but not the R-enantiomer. Hydrolyzes short- and long-chain N-acyl homoserine lactones with or without 3-oxo substitution at C3, has maximum activity on C10-AHL.<ref>PMID:15895999</ref>	+	[https://www.uniprot.org/uniprot/AHLL_BACTU AHLL_BACTU] Catalyzes hydrolysis of N-hexanoyl-(S)-homoserine lactone, but not the R-enantiomer. Hydrolyzes short- and long-chain N-acyl homoserine lactones with or without 3-oxo substitution at C3, has maximum activity on C10-AHL.<ref>PMID:15895999</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~cereus var.~~ thuringiensis ~~smith et al. 1952~~]]	+	[[Category: Bacillus thuringiensis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Quorum-quenching~~ N-~~acyl-homoserine lactonase]]~~	+	[[Category: Hong N-S]]
-	~~[[Category: Hong, N~~ S]]	+	[[Category: Jackson CJ]]
-	[[Category: Jackson~~, C J]]~~	+
-	~~[[Category: Aiia]]~~	+
-	~~[[Category: Directed evolution]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Lactonase]]~~	+
-	~~[[Category: N-acyl-homoserine lactonase]]~~	+
-	~~[[Category: Paraoxonase]]~~	+
-	~~[[Category: Phosphatase]]~~	+
-	~~[[Category: Qql~~]]	+

OCA at 06:58, 22 April 2020

OCA — Wed, 22 Apr 2020 06:58:50 GMT

←Older revision		Revision as of 06:58, 22 April 2020
Line 1:		Line 1:

	==Indirect contributions of mutations underlie optimization of new enzyme function==		==Indirect contributions of mutations underlie optimization of new enzyme function==
-	<StructureSection load='5eht' size='340' side='right' caption='[[5eht]], [[Resolution\|resolution]] 1.29Å' scene=''>	+	<StructureSection load='5eht' size='340' side='right'caption='[[5eht]], [[Resolution\|resolution]] 1.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5eht]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EHT OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5EHT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5eht]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cereus_var._thuringiensis"_smith_et_al._1952 "bacillus cereus var. thuringiensis" smith et al. 1952]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EHT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EHT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5eh9\|5eh9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5eh9\|5eh9]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aiiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1428 "Bacillus cereus var. thuringiensis" Smith et al. 1952])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Quorum-quenching_N-acyl-homoserine_lactonase Quorum-quenching N-acyl-homoserine lactonase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.81 3.1.1.81] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Quorum-quenching_N-acyl-homoserine_lactonase Quorum-quenching N-acyl-homoserine lactonase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.81 3.1.1.81] </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=5eht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eht OCA], [http://pdbe.org/5eht PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eht RCSB], [http://www.ebi.ac.uk/pdbsum/5eht PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5eht 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=5eht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eht OCA], [http://pdbe.org/5eht PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eht RCSB], [http://www.ebi.ac.uk/pdbsum/5eht PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5eht ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus cereus var. thuringiensis smith et al. 1952]]
		+	[[Category: Large Structures]]
	[[Category: Quorum-quenching N-acyl-homoserine lactonase]]		[[Category: Quorum-quenching N-acyl-homoserine lactonase]]
	[[Category: Hong, N S]]		[[Category: Hong, N S]]

OCA at 21:03, 10 September 2016

OCA — Sat, 10 Sep 2016 21:03:54 GMT

←Older revision		Revision as of 21:03, 10 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5eht is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Indirect contributions of mutations underlie optimization of new enzyme function==
		+	<StructureSection load='5eht' size='340' side='right' caption='[[5eht]], [[Resolution\|resolution]] 1.29Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5eht]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EHT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EHT FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5eh9\|5eh9]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Quorum-quenching_N-acyl-homoserine_lactonase Quorum-quenching N-acyl-homoserine lactonase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.81 3.1.1.81] </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=5eht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eht OCA], [http://pdbe.org/5eht PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eht RCSB], [http://www.ebi.ac.uk/pdbsum/5eht PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5eht ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AHLL_BACTU AHLL_BACTU]] Catalyzes hydrolysis of N-hexanoyl-(S)-homoserine lactone, but not the R-enantiomer. Hydrolyzes short- and long-chain N-acyl homoserine lactones with or without 3-oxo substitution at C3, has maximum activity on C10-AHL.<ref>PMID:15895999</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	How remote mutations can lead to changes in enzyme function at a molecular level is a central question in evolutionary biochemistry and biophysics. Here, we combine laboratory evolution with biochemical, structural, genetic, and computational analysis to dissect the molecular basis for the functional optimization of phosphotriesterase activity in a bacterial lactonase (AiiA) from the metallo-beta-lactamase (MBL) superfamily. We show that a 1000-fold increase in phosphotriesterase activity is caused by a more favorable catalytic binding position of the paraoxon substrate in the evolved enzyme that resulted from conformational tinkering of the active site through peripheral mutations. A nonmutated active site residue, Phe68, was displaced by approximately 3 A through the indirect effects of two second-shell trajectory mutations, allowing molecular interactions between the residue and paraoxon. Comparative mutational scanning, i.e., examining the effects of alanine mutagenesis on different genetic backgrounds, revealed significant changes in the functional roles of Phe68 and other nonmutated active site residues caused by the indirect effects of trajectory mutations. Our work provides a quantitative measurement of the impact of second-shell mutations on the catalytic contributions of nonmutated residues and unveils the underlying intramolecular network of strong epistatic mutational relationships between active site residues and more remote residues. Defining these long-range conformational and functional epistatic relationships has allowed us to better understand the subtle, but cumulatively significant, role of second- and third-shell mutations in evolution.

-	~~Authors: Jackson, C.J~~., Hong, N.-S.	+	Conformational Tinkering Drives Evolution of a Promiscuous Activity through Indirect Mutational Effects.,Yang G, Hong N, Baier F, Jackson CJ, Tokuriki N Biochemistry. 2016 Aug 16;55(32):4583-93. doi: 10.1021/acs.biochem.6b00561. Epub , 2016 Aug 2. PMID:27444875<ref>PMID:27444875</ref>

-	~~Description: Indirect contributions~~ of ~~mutations underlie optimization~~ of ~~new enzyme function~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Jackson, C.J]]	+	<div class="pdbe-citations 5eht" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Hong,~~ N.-S]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Quorum-quenching N-acyl-homoserine lactonase]]
		+	[[Category: Hong, N S]]
		+	[[Category: Jackson, C J]]
		+	[[Category: Aiia]]
		+	[[Category: Directed evolution]]
		+	[[Category: Hydrolase]]
		+	[[Category: Lactonase]]
		+	[[Category: N-acyl-homoserine lactonase]]
		+	[[Category: Paraoxonase]]
		+	[[Category: Phosphatase]]
		+	[[Category: Qql]]

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

OCA — Tue, 01 Dec 2015 02:51:41 GMT

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

←Older revision

Revision as of 02:51, 1 December 2015

OCA: New page: '''Unreleased structure''' The entry 5eht is ON HOLD until Paper Publication Authors: Jackson, C.J., Hong, N.-S. Description: Indirect contributions of mutations underlie optimization ...

OCA — Tue, 01 Dec 2015 02:51:40 GMT

New page: '''Unreleased structure''' The entry 5eht is ON HOLD until Paper Publication Authors: Jackson, C.J., Hong, N.-S. Description: Indirect contributions of mutations underlie optimization ...

New page

'''Unreleased structure'''

The entry 5eht is ON HOLD until Paper Publication

Authors: Jackson, C.J., Hong, N.-S.

Description: Indirect contributions of mutations underlie optimization of new enzyme function
[[Category: Unreleased Structures]]
[[Category: Jackson, C.J]]
[[Category: Hong, N.-S]]