4rzs - Revision history

OCA at 12:57, 1 March 2024

OCA — Fri, 01 Mar 2024 12:57:25 GMT

←Older revision		Revision as of 12:57, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4rzs]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_DH1 Escherichia coli DH1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RZS FirstGlance]. <br>		<table><tr><td colspan='2'>[[4rzs]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_DH1 Escherichia coli DH1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RZS 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></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]] 2.71Å</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></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=4rzs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzs OCA], [https://pdbe.org/4rzs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rzs RCSB], [https://www.ebi.ac.uk/pdbsum/4rzs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzs 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=4rzs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzs OCA], [https://pdbe.org/4rzs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rzs RCSB], [https://www.ebi.ac.uk/pdbsum/4rzs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/LACI_ECOLI LACI_ECOLI] Repressor of the lactose operon. Binds allolactose as an inducer.		[https://www.uniprot.org/uniprot/LACI_ECOLI LACI_ECOLI] Repressor of the lactose operon. Binds allolactose as an inducer.
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Genetic regulatory proteins inducible by small molecules are useful synthetic biology tools as sensors and switches. Bacterial allosteric transcription factors (aTFs) are a major class of regulatory proteins, but few aTFs have been redesigned to respond to new effectors beyond natural aTF-inducer pairs. Altering inducer specificity in these proteins is difficult because substitutions that affect inducer binding may also disrupt allostery. We engineered an aTF, the Escherichia coli lac repressor, LacI, to respond to one of four new inducer molecules: fucose, gentiobiose, lactitol and sucralose. Using computational protein design, single-residue saturation mutagenesis or random mutagenesis, along with multiplex assembly, we identified new variants comparable in specificity and induction to wild-type LacI with its inducer, isopropyl beta-D-1-thiogalactopyranoside (IPTG). The ability to create designer aTFs will enable applications including dynamic control of cell metabolism, cell biology and synthetic gene circuits.
-
-	Engineering an allosteric transcription factor to respond to new ligands.,Taylor ND, Garruss AS, Moretti R, Chan S, Arbing MA, Cascio D, Rogers JK, Isaacs FJ, Kosuri S, Baker D, Fields S, Church GM, Raman S Nat Methods. 2015 Dec 21. doi: 10.1038/nmeth.3696. PMID:26689263<ref>PMID:26689263</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4rzs" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Lac repressor\|Lac repressor]]		*[[Lac repressor\|Lac repressor]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:36, 15 March 2023

OCA — Wed, 15 Mar 2023 10:36:40 GMT

←Older revision		Revision as of 10:36, 15 March 2023
Line 1:		Line 1:

	==Lac repressor engineered to bind sucralose, unliganded tetramer==		==Lac repressor engineered to bind sucralose, unliganded tetramer==
-	<StructureSection load='4rzs' size='340' side='right' caption='[[4rzs]], [[Resolution\|resolution]] 2.71Å' scene=''>	+	<StructureSection load='4rzs' size='340' side='right'caption='[[4rzs]], [[Resolution\|resolution]] 2.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rzs]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecod1 Ecod1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4RZS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rzs]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_DH1 Escherichia coli DH1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RZS 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>~~</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></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0345, ECDH1ME8569_0332, EcDH1_3261, lacI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=536056 ECOD1])</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=4rzs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzs OCA], [https://pdbe.org/4rzs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rzs RCSB], [https://www.ebi.ac.uk/pdbsum/4rzs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzs 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=4rzs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzs OCA], [~~http~~://pdbe.org/4rzs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4rzs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4rzs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzs ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/LACI_ECOLI LACI_ECOLI] Repressor of the lactose operon. Binds allolactose as an inducer.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4rzs" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4rzs" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lac repressor\|Lac repressor]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	~~[[Category: Ecod1]]~~	+	[[Category: Escherichia coli DH1]]
-	~~[[Category: Arbing, M A]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Cascio, D]]~~	+	[[Category: Arbing MA]]
-	~~[[Category: Church, G M]]~~	+	[[Category: Cascio D]]
-	~~[[Category: Kosuri, S]]~~	+	[[Category: Church GM]]
-	~~[[Category: Allostery]]~~	+	[[Category: Kosuri S]]
-	[[Category: Escherichia coli]]	+
-	[[Category: ~~Lac repressor~~]]	+
-	[[Category: ~~Laci~~]]	+
-	[[Category: ~~Lactose operon repressor~~]]	+
-	[[Category: ~~Protein design~~]]	+
-	[[Category: ~~Sucralose]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 09:13, 22 November 2017

OCA — Wed, 22 Nov 2017 09:13:05 GMT

←Older revision		Revision as of 09:13, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='4rzs' size='340' side='right' caption='[[4rzs]], [[Resolution\|resolution]] 2.71Å' scene=''>		<StructureSection load='4rzs' size='340' side='right' caption='[[4rzs]], [[Resolution\|resolution]] 2.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rzs]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RZS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rzs]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecod1 Ecod1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RZS 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></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=4rzs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzs OCA], [http://pdbe.org/4rzs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rzs RCSB], [http://www.ebi.ac.uk/pdbsum/4rzs PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0345, ECDH1ME8569_0332, EcDH1_3261, lacI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=536056 ECOD1])</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=4rzs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzs OCA], [http://pdbe.org/4rzs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rzs RCSB], [http://www.ebi.ac.uk/pdbsum/4rzs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rzs ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecod1]]
	[[Category: Arbing, M A]]		[[Category: Arbing, M A]]
	[[Category: Cascio, D]]		[[Category: Cascio, D]]

OCA at 06:49, 2 March 2016

OCA — Wed, 02 Mar 2016 06:49:07 GMT

←Older revision		Revision as of 06:49, 2 March 2016
Line 1:		Line 1:
		+
	==Lac repressor engineered to bind sucralose, unliganded tetramer==		==Lac repressor engineered to bind sucralose, unliganded tetramer==
	<StructureSection load='4rzs' size='340' side='right' caption='[[4rzs]], [[Resolution\|resolution]] 2.71Å' scene=''>		<StructureSection load='4rzs' size='340' side='right' caption='[[4rzs]], [[Resolution\|resolution]] 2.71Å' scene=''>

OCA at 04:50, 7 January 2016

OCA — Thu, 07 Jan 2016 04:50:58 GMT

←Older revision		Revision as of 04:50, 7 January 2016
Line 6:		Line 6:
	<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=4rzs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzs OCA], [http://pdbe.org/4rzs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rzs RCSB], [http://www.ebi.ac.uk/pdbsum/4rzs 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=4rzs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzs OCA], [http://pdbe.org/4rzs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rzs RCSB], [http://www.ebi.ac.uk/pdbsum/4rzs PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Genetic regulatory proteins inducible by small molecules are useful synthetic biology tools as sensors and switches. Bacterial allosteric transcription factors (aTFs) are a major class of regulatory proteins, but few aTFs have been redesigned to respond to new effectors beyond natural aTF-inducer pairs. Altering inducer specificity in these proteins is difficult because substitutions that affect inducer binding may also disrupt allostery. We engineered an aTF, the Escherichia coli lac repressor, LacI, to respond to one of four new inducer molecules: fucose, gentiobiose, lactitol and sucralose. Using computational protein design, single-residue saturation mutagenesis or random mutagenesis, along with multiplex assembly, we identified new variants comparable in specificity and induction to wild-type LacI with its inducer, isopropyl beta-D-1-thiogalactopyranoside (IPTG). The ability to create designer aTFs will enable applications including dynamic control of cell metabolism, cell biology and synthetic gene circuits.
		+
		+	Engineering an allosteric transcription factor to respond to new ligands.,Taylor ND, Garruss AS, Moretti R, Chan S, Arbing MA, Cascio D, Rogers JK, Isaacs FJ, Kosuri S, Baker D, Fields S, Church GM, Raman S Nat Methods. 2015 Dec 21. doi: 10.1038/nmeth.3696. PMID:26689263<ref>PMID:26689263</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4rzs" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 12:44, 23 December 2015

OCA — Wed, 23 Dec 2015 12:44:35 GMT

←Older revision		Revision as of 12:44, 23 December 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Lac repressor engineered to bind sucralose, unliganded tetramer==
-		+	<StructureSection load='4rzs' size='340' side='right' caption='[[4rzs]], [[Resolution\|resolution]] 2.71Å' scene=''>
-	~~The entry~~ 4rzs is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4rzs]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RZS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RZS FirstGlance]. <br>
-	~~Authors~~: ~~Arbing, M~~.A.~~, Cascio, D~~.~~, Kosuri, S~~.~~, Church, G~~.M.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=4rzs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rzs OCA], [http://pdbe.org/4rzs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rzs RCSB], [http://www.ebi.ac.uk/pdbsum/4rzs PDBsum]</span></td></tr>
-	~~Description: Lac repressor engineered to bind sucralose, unliganded tetramer~~	+	</table>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	__TOC__
-	[[~~Category~~: ~~Church~~, G.M]]	+	</StructureSection>
-	[~~[Category~~: ~~Kosuri, S~~]]	+	[[Category: Arbing, M A]]
-	[[Category: Arbing, M.A]]	+
	[[Category: Cascio, D]]		[[Category: Cascio, D]]
		+	[[Category: Church, G M]]
		+	[[Category: Kosuri, S]]
		+	[[Category: Allostery]]
		+	[[Category: Escherichia coli]]
		+	[[Category: Lac repressor]]
		+	[[Category: Laci]]
		+	[[Category: Lactose operon repressor]]
		+	[[Category: Protein design]]
		+	[[Category: Sucralose]]
		+	[[Category: Transcription]]

OCA at 22:52, 30 November 2015

OCA — Mon, 30 Nov 2015 22:52:51 GMT

←Older revision		Revision as of 22:52, 30 November 2015
Line 7:		Line 7:
	Description: Lac repressor engineered to bind sucralose, unliganded tetramer		Description: Lac repressor engineered to bind sucralose, unliganded tetramer
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kosuri, S]]
	[[Category: Church, G.M]]		[[Category: Church, G.M]]
		+	[[Category: Kosuri, S]]
	[[Category: Arbing, M.A]]		[[Category: Arbing, M.A]]
	[[Category: Cascio, D]]		[[Category: Cascio, D]]

OCA at 12:49, 7 February 2015

OCA — Sat, 07 Feb 2015 12:49:07 GMT

←Older revision		Revision as of 12:49, 7 February 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4rzs is ON HOLD	+	The entry 4rzs is ON HOLD until Paper Publication

	Authors: Arbing, M.A., Cascio, D., Kosuri, S., Church, G.M.		Authors: Arbing, M.A., Cascio, D., Kosuri, S., Church, G.M.

OCA: Protected "4rzs" [edit=sysop:move=sysop]

OCA — Wed, 31 Dec 2014 12:18:16 GMT

Protected "4rzs" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:18, 31 December 2014

OCA: New page: '''Unreleased structure''' The entry 4rzs is ON HOLD Authors: Arbing, M.A., Cascio, D., Kosuri, S., Church, G.M. Description: Lac repressor engineered to bind sucralose, unliganded tet...

OCA — Wed, 31 Dec 2014 12:18:14 GMT

New page: '''Unreleased structure''' The entry 4rzs is ON HOLD Authors: Arbing, M.A., Cascio, D., Kosuri, S., Church, G.M. Description: Lac repressor engineered to bind sucralose, unliganded tet...

New page

'''Unreleased structure'''

The entry 4rzs is ON HOLD

Authors: Arbing, M.A., Cascio, D., Kosuri, S., Church, G.M.

Description: Lac repressor engineered to bind sucralose, unliganded tetramer
[[Category: Unreleased Structures]]
[[Category: Kosuri, S]]
[[Category: Church, G.M]]
[[Category: Arbing, M.A]]
[[Category: Cascio, D]]