5vlm - Revision history

OCA at 14:11, 13 March 2024

2024-03-13T14:11:06Z

←Older revision		Revision as of 14:11, 13 March 2024
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	<StructureSection load='5vlm' size='340' side='right'caption='[[5vlm]], [[Resolution\|resolution]] 3.40Å' scene=''>		<StructureSection load='5vlm' size='340' side='right'caption='[[5vlm]], [[Resolution\|resolution]] 3.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vlm]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"enterobacter_lignolyticus"_deangelis_et_al._2011 "enterobacter~~ lignolyticus~~" deangelis et al. 2011~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VLM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VLM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vlm]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacter_lignolyticus Enterobacter lignolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VLM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VLM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=CVI:CRYSTAL+VIOLET'>CVI</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]] 3.403Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vlg\|5vlg]]~~, [[~~5vl9~~\|~~5vl9~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CVI:CRYSTAL+VIOLET'>CVI</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>Entcl_2353 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1334193~~ "~~Enterobacter lignolyticus~~" ~~Deangelis et al. 2011])~~</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=5vlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vlm OCA], [https://pdbe.org/5vlm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vlm RCSB], [https://www.ebi.ac.uk/pdbsum/5vlm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vlm 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=5vlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vlm OCA], [~~http~~://pdbe.org/5vlm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vlm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vlm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vlm ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/E3G817_ENTLS E3G817_ENTLS]
-	Tightly regulated promoters are essential for numerous biological applications, where strong inducibility, portability, and scalability are desirable. Current systems are often incompatible with large-scale fermentations due to high inducer costs and strict media requirements. Here, we describe the bottom-up engineering of 'Jungle Express', an expression system that enables efficient gene regulation in diverse proteobacteria. This system is guided by EilR, a multidrug-binding repressor with high affinity to its optimized operator and cationic dyes that act as powerful inducers at negligible costs. In E. coli, the engineered promoters exhibit minimal basal transcription and are inducible over four orders of magnitude by 1 microM crystal violet, reaching expression levels exceeding those of the strongest current bacterial systems. Further, we provide molecular insights into specific interactions of EilR with its operator and with two inducers. ~~The versatility of Jungle Express opens the way for tightly controlled and efficient gene expression that is not restricted to host organism, substrate, or scale~~.	+

-	Jungle Express is a versatile repressor system for tight transcriptional control.,Ruegg TL, Pereira JH, Chen JC, DeGiovanni A, Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson NJ, Simmons BA, Adams PD, Thelen MP Nat Commun. 2018 Sep 6;9(1):3617. doi: 10.1038/s41467-018-05857-3. PMID:30190458<ref>PMID:30190458</ref>	+	==See Also==
-		+	*[[Tetracycline repressor protein 3D structures\|Tetracycline repressor protein 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 5vlm" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Enterobacter lignolyticus deangelis et al. 2011]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Adams~~, P D~~]]	+	[[Category: Adams PD]]
-	[[Category: Chen, J]]	+	[[Category: Chen J]]
-	[[Category: DeGiovani, A]]	+	[[Category: DeGiovani A]]
-	[[Category: Novichkov, P]]	+	[[Category: Novichkov P]]
-	[[Category: Pereira~~, J H~~]]	+	[[Category: Pereira JH]]
-	[[Category: Ruegg~~, T L~~]]	+	[[Category: Ruegg TL]]
-	[[Category: Simmons, B]]	+	[[Category: Simmons B]]
-	[[Category: Singer, S]]	+	[[Category: Singer S]]
-	[[Category: Thelen, M]]	+	[[Category: Thelen M]]
-	[[Category: Tomaleri~~, G P]]~~	+	[[Category: Tomaleri GP]]
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription factor~~]]	+

OCA at 09:37, 4 December 2019

2019-12-04T09:37:13Z

←Older revision		Revision as of 09:37, 4 December 2019
Line 1:		Line 1:

	==Crystal structure of EilR in complex with crystal violet==		==Crystal structure of EilR in complex with crystal violet==
-	<StructureSection load='5vlm' size='340' side='right' caption='[[5vlm]], [[Resolution\|resolution]] 3.40Å' scene=''>	+	<StructureSection load='5vlm' size='340' side='right'caption='[[5vlm]], [[Resolution\|resolution]] 3.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5vlm]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"enterobacter_lignolyticus"_deangelis_et_al._2011 "enterobacter lignolyticus" deangelis et al. 2011]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VLM FirstGlance]. <br>		<table><tr><td colspan='2'>[[5vlm]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"enterobacter_lignolyticus"_deangelis_et_al._2011 "enterobacter lignolyticus" deangelis et al. 2011]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VLM FirstGlance]. <br>
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Enterobacter lignolyticus deangelis et al. 2011]]		[[Category: Enterobacter lignolyticus deangelis et al. 2011]]
		+	[[Category: Large Structures]]
	[[Category: Adams, P D]]		[[Category: Adams, P D]]
	[[Category: Chen, J]]		[[Category: Chen, J]]

OCA at 20:47, 2 December 2018

2018-12-02T20:47:24Z

←Older revision		Revision as of 20:47, 2 December 2018
Line 3:		Line 3:
	<StructureSection load='5vlm' size='340' side='right' caption='[[5vlm]], [[Resolution\|resolution]] 3.40Å' scene=''>		<StructureSection load='5vlm' size='340' side='right' caption='[[5vlm]], [[Resolution\|resolution]] 3.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vlm]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VLM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vlm]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"enterobacter_lignolyticus"_deangelis_et_al._2011 "enterobacter lignolyticus" deangelis et al. 2011]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VLM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CVI:CRYSTAL+VIOLET'>CVI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CVI:CRYSTAL+VIOLET'>CVI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vlg\|5vlg]], [[5vl9\|5vl9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vlg\|5vlg]], [[5vl9\|5vl9]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Entcl_2353 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1334193 "Enterobacter lignolyticus" Deangelis et al. 2011])</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=5vlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vlm OCA], [http://pdbe.org/5vlm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vlm RCSB], [http://www.ebi.ac.uk/pdbsum/5vlm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vlm 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=5vlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vlm OCA], [http://pdbe.org/5vlm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vlm RCSB], [http://www.ebi.ac.uk/pdbsum/5vlm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vlm ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tightly regulated promoters are essential for numerous biological applications, where strong inducibility, portability, and scalability are desirable. Current systems are often incompatible with large-scale fermentations due to high inducer costs and strict media requirements. Here, we describe the bottom-up engineering of 'Jungle Express', an expression system that enables efficient gene regulation in diverse proteobacteria. This system is guided by EilR, a multidrug-binding repressor with high affinity to its optimized operator and cationic dyes that act as powerful inducers at negligible costs. In E. coli, the engineered promoters exhibit minimal basal transcription and are inducible over four orders of magnitude by 1 microM crystal violet, reaching expression levels exceeding those of the strongest current bacterial systems. Further, we provide molecular insights into specific interactions of EilR with its operator and with two inducers. The versatility of Jungle Express opens the way for tightly controlled and efficient gene expression that is not restricted to host organism, substrate, or scale.
		+
		+	Jungle Express is a versatile repressor system for tight transcriptional control.,Ruegg TL, Pereira JH, Chen JC, DeGiovanni A, Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson NJ, Simmons BA, Adams PD, Thelen MP Nat Commun. 2018 Sep 6;9(1):3617. doi: 10.1038/s41467-018-05857-3. PMID:30190458<ref>PMID:30190458</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5vlm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Enterobacter lignolyticus deangelis et al. 2011]]
	[[Category: Adams, P D]]		[[Category: Adams, P D]]
	[[Category: Chen, J]]		[[Category: Chen, J]]

OCA at 05:26, 27 June 2018

2018-06-27T05:26:33Z

←Older revision		Revision as of 05:26, 27 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vlm is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of EilR in complex with crystal violet==
-		+	<StructureSection load='5vlm' size='340' side='right' caption='[[5vlm]], [[Resolution\|resolution]] 3.40Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5vlm]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VLM FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CVI:CRYSTAL+VIOLET'>CVI</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vlg\|5vlg]], [[5vl9\|5vl9]]</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=5vlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vlm OCA], [http://pdbe.org/5vlm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vlm RCSB], [http://www.ebi.ac.uk/pdbsum/5vlm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vlm ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Adams, P D]]
		+	[[Category: Chen, J]]
		+	[[Category: DeGiovani, A]]
		+	[[Category: Novichkov, P]]
		+	[[Category: Pereira, J H]]
		+	[[Category: Ruegg, T L]]
		+	[[Category: Simmons, B]]
		+	[[Category: Singer, S]]
		+	[[Category: Thelen, M]]
		+	[[Category: Tomaleri, G P]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription factor]]

OCA at 14:06, 27 September 2017

2017-09-27T14:06:36Z

←Older revision		Revision as of 14:06, 27 September 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2017-05-04T11:27:05Z

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

←Older revision

Revision as of 11:27, 4 May 2017

OCA: New page: '''Unreleased structure''' The entry 5vlm is ON HOLD Authors: Description: Category: Unreleased Structures

2017-05-04T11:27:03Z

New page: '''Unreleased structure''' The entry 5vlm is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5vlm is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]