5i3d - Revision history

OCA at 08:21, 23 August 2023

2023-08-23T08:21:49Z

←Older revision		Revision as of 08:21, 23 August 2023
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	<StructureSection load='5i3d' size='340' side='right'caption='[[5i3d]], [[Resolution\|resolution]] 2.16Å' scene=''>		<StructureSection load='5i3d' size='340' side='right'caption='[[5i3d]], [[Resolution\|resolution]] 2.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i3d]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Sacs2 Sacs2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I3D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5I3D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i3d]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I3D FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ACT:ACETATE+ION'~~>~~ACT</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21~~-~~HEPTAOXATRICOSANE-1~~,~~23-DIOL'>PE8</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.16Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>lacS, SSO3019 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~273057 SACS2])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL'>PE8</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Beta~~-~~galactosidase Beta~~-~~galactosidase]~~, ~~with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23]~~ </~~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=5i3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i3d OCA], [https://pdbe.org/5i3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i3d RCSB], [https://www.ebi.ac.uk/pdbsum/5i3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i3d 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=5i3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i3d OCA], [~~http~~://pdbe.org/5i3d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5i3d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5i3d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5i3d ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/BGAL_SACS2 BGAL_SACS2]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Beta-galactosidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sacs2~~]]	+	[[Category: Saccharolobus solfataricus P2]]
-	[[Category: Davis~~, B D~~]]	+	[[Category: Davis BD]]
-	[[Category: Fordham-Skelton, A]]	+	[[Category: Fordham-Skelton A]]
-	[[Category: Hancock~~, S M~~]]	+	[[Category: Hancock SM]]
-	[[Category: Iglesias-Fernandez, J]]	+	[[Category: Iglesias-Fernandez J]]
-	[[Category: Lee~~, S S~~]]	+	[[Category: Lee SS]]
-	[[Category: McAuley~~, K E~~]]	+	[[Category: McAuley KE]]
-	[[Category: Rovira, C]]	+	[[Category: Rovira C]]
-	~~[[Category: Glycosidase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 10:27, 27 March 2020

2020-03-27T10:27:48Z

←Older revision		Revision as of 10:27, 27 March 2020
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	==Sulfolobus solfataricus beta-glycosidase - E387Y mutant==		==Sulfolobus solfataricus beta-glycosidase - E387Y mutant==
-	<StructureSection load='5i3d' size='340' side='right' caption='[[5i3d]], [[Resolution\|resolution]] 2.16Å' scene=''>	+	<StructureSection load='5i3d' size='340' side='right'caption='[[5i3d]], [[Resolution\|resolution]] 2.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i3d]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I3D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I3D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i3d]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Sacs2 Sacs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I3D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I3D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL'>PE8</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL'>PE8</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lacS, SSO3019 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SACS2])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </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=5i3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i3d OCA], [http://pdbe.org/5i3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i3d RCSB], [http://www.ebi.ac.uk/pdbsum/5i3d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i3d 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=5i3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i3d OCA], [http://pdbe.org/5i3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i3d RCSB], [http://www.ebi.ac.uk/pdbsum/5i3d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i3d ProSAT]</span></td></tr>
Line 17:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5i3d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5i3d" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Galactosidase 3D structures\|Galactosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Beta-galactosidase]]		[[Category: Beta-galactosidase]]
		+	[[Category: Large Structures]]
		+	[[Category: Sacs2]]
	[[Category: Davis, B D]]		[[Category: Davis, B D]]
	[[Category: Fordham-Skelton, A]]		[[Category: Fordham-Skelton, A]]

OCA at 12:41, 6 November 2017

2017-11-06T12:41:03Z

←Older revision		Revision as of 12:41, 6 November 2017
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5i3d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5i3d" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Galactosidase\|Galactosidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:00, 3 August 2017

2017-08-03T11:00:00Z

←Older revision		Revision as of 11:00, 3 August 2017
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	<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=5i3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i3d OCA], [http://pdbe.org/5i3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i3d RCSB], [http://www.ebi.ac.uk/pdbsum/5i3d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i3d 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=5i3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i3d OCA], [http://pdbe.org/5i3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i3d RCSB], [http://www.ebi.ac.uk/pdbsum/5i3d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i3d ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	SNi-like mechanisms, which involve front-face leaving group departure and nucleophile approach, have been observed experimentally and computationally in chemical and enzymatic substitution at alpha-glycosyl electrophiles. Since SNi-like, SN1 and SN2 substitution pathways can be energetically comparable, engineered switching could be feasible. Here, engineering of Sulfolobus solfataricus beta-glycosidase, which originally catalyzed double SN2 substitution, changed its mode to SNi-like. Destruction of the first SN2 nucleophile through E387Y mutation created a beta-stereoselective catalyst for glycoside synthesis from activated substrates, despite lacking a nucleophile. The pH profile, kinetic and mutational analyses, mechanism-based inactivators, X-ray structure and subsequent metadynamics simulations together suggest recruitment of substrates by pi-sugar interaction and reveal a quantum mechanics-molecular mechanics (QM/MM) free-energy landscape for the substitution reaction that is similar to those of natural, SNi-like glycosyltransferases. This observation of a front-face mechanism in a beta-glycosyltransfer enzyme highlights that SNi-like pathways may be engineered in catalysts with suitable environments and suggests that 'beta-SNi' mechanisms may be feasible for natural glycosyltransfer enzymes.
		+
		+	A front-face 'SNi synthase' engineered from a retaining 'double-SN2' hydrolase.,Iglesias-Fernandez J, Hancock SM, Lee SS, Khan M, Kirkpatrick J, Oldham NJ, McAuley K, Fordham-Skelton A, Rovira C, Davis BG Nat Chem Biol. 2017 Jun 12. doi: 10.1038/nchembio.2394. PMID:28604696<ref>PMID:28604696</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5i3d" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Galactosidase\|Galactosidase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 18:06, 1 February 2017

2017-02-01T18:06:45Z

←Older revision		Revision as of 18:06, 1 February 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5i3d ~~is ON HOLD until Paper Publication~~	+	==Sulfolobus solfataricus beta-glycosidase - E387Y mutant==
-		+	<StructureSection load='5i3d' size='340' side='right' caption='[[5i3d]], [[Resolution\|resolution]] 2.16Å' scene=''>
-	~~Authors~~: ~~Iglesias~~-~~Fernandez, J~~.~~, Hancock, S~~.M., ~~Lee~~, S.S., ~~McAuley, K~~.E., ~~Fordham~~-~~Skelton~~, A., ~~Rovira, C~~., ~~Davis~~, B.D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5i3d]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I3D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I3D FirstGlance]. <br>
-	~~Description: Sulfolobus solfataricus beta-glycosidase -E387Y mutant~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL'>PE8</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </span></td></tr>
-	[[Category: Davis, B.D]]	+	<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=5i3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i3d OCA], [http://pdbe.org/5i3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i3d RCSB], [http://www.ebi.ac.uk/pdbsum/5i3d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i3d ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-galactosidase]]
		+	[[Category: Davis, B D]]
	[[Category: Fordham-Skelton, A]]		[[Category: Fordham-Skelton, A]]
-	[[Category: ~~Mcauley~~, K.E]]	+	[[Category: Hancock, S M]]
		+	[[Category: Iglesias-Fernandez, J]]
		+	[[Category: Lee, S S]]
		+	[[Category: McAuley, K E]]
	[[Category: Rovira, C]]		[[Category: Rovira, C]]
-	[[Category: ~~Iglesias-Fernandez, J~~]]	+	[[Category: Glycosidase]]
-	[[Category: ~~Lee, S.S]]~~	+	[[Category: Hydrolase]]
-	~~[[Category: Hancock, S.M~~]]	+

OCA at 12:28, 19 October 2016

2016-10-19T12:28:57Z

←Older revision		Revision as of 12:28, 19 October 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5i3d is ON HOLD	+	The entry 5i3d is ON HOLD until Paper Publication

	Authors: Iglesias-Fernandez, J., Hancock, S.M., Lee, S.S., McAuley, K.E., Fordham-Skelton, A., Rovira, C., Davis, B.D.		Authors: Iglesias-Fernandez, J., Hancock, S.M., Lee, S.S., McAuley, K.E., Fordham-Skelton, A., Rovira, C., Davis, B.D.

OCA: Protected "5i3d" [edit=sysop:move=sysop]

2016-02-21T01:32:19Z

Protected "5i3d" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:32, 21 February 2016

OCA: New page: '''Unreleased structure''' The entry 5i3d is ON HOLD Authors: Iglesias-Fernandez, J., Hancock, S.M., Lee, S.S., McAuley, K.E., Fordham-Skelton, A., Rovira, C., Davis, B.D. Description:...

2016-02-21T01:32:18Z

New page: '''Unreleased structure''' The entry 5i3d is ON HOLD Authors: Iglesias-Fernandez, J., Hancock, S.M., Lee, S.S., McAuley, K.E., Fordham-Skelton, A., Rovira, C., Davis, B.D. Description:...

New page

'''Unreleased structure'''

The entry 5i3d is ON HOLD

Authors: Iglesias-Fernandez, J., Hancock, S.M., Lee, S.S., McAuley, K.E., Fordham-Skelton, A., Rovira, C., Davis, B.D.

Description: Sulfolobus solfataricus beta-glycosidase -E387Y mutant
[[Category: Unreleased Structures]]
[[Category: Davis, B.D]]
[[Category: Fordham-Skelton, A]]
[[Category: Mcauley, K.E]]
[[Category: Rovira, C]]
[[Category: Iglesias-Fernandez, J]]
[[Category: Lee, S.S]]
[[Category: Hancock, S.M]]