6rbm - Revision history

OCA at 12:18, 24 January 2024

OCA — Wed, 24 Jan 2024 12:18:39 GMT

←Older revision		Revision as of 12:18, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6rbm' size='340' side='right'caption='[[6rbm]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='6rbm' size='340' side='right'caption='[[6rbm]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rbm]] 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=6RBM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6RBM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rbm]] 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=6RBM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RBM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MIY:(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE'>MIY</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]] 2.05Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6fpl\|6fpl]], [[2tct\|2tct]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MIY:(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE'>MIY</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tetR ([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=6rbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rbm OCA], [https://pdbe.org/6rbm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rbm RCSB], [https://www.ebi.ac.uk/pdbsum/6rbm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rbm 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=6rbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rbm OCA], [~~http~~://pdbe.org/6rbm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6rbm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6rbm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6rbm ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TETR4_ECOLX TETR4_ECOLX]] TetR is the repressor of the tetracycline resistance element; its N-terminal region forms a helix-turn-helix structure and binds DNA. Binding of tetracycline to TetR reduces the repressor affinity for the tetracycline resistance gene (tetA) promoter operator sites.	+	[https://www.uniprot.org/uniprot/TETR4_ECOLX TETR4_ECOLX] TetR is the repressor of the tetracycline resistance element; its N-terminal region forms a helix-turn-helix structure and binds DNA. Binding of tetracycline to TetR reduces the repressor affinity for the tetracycline resistance gene (tetA) promoter operator sites.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Berndt, L]]	+	[[Category: Berndt L]]
-	[[Category: Girbardt, B]]	+	[[Category: Girbardt B]]
-	[[Category: Hinrichs, W]]	+	[[Category: Hinrichs W]]
-	[[Category: Palm~~, G J]]~~	+	[[Category: Palm GJ]]
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulation~~]]	+

OCA at 10:26, 18 March 2020

OCA — Wed, 18 Mar 2020 10:26:01 GMT

←Older revision		Revision as of 10:26, 18 March 2020
Line 3:		Line 3:
	<StructureSection load='6rbm' size='340' side='right'caption='[[6rbm]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='6rbm' size='340' side='right'caption='[[6rbm]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rbm]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RBM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rbm]] 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=6RBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RBM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MIY:(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE'>MIY</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MIY:(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE'>MIY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6fpl\|6fpl]], [[2tct\|2tct]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6fpl\|6fpl]], [[2tct\|2tct]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tetR ([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=6rbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rbm OCA], [http://pdbe.org/6rbm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rbm RCSB], [http://www.ebi.ac.uk/pdbsum/6rbm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rbm 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=6rbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rbm OCA], [http://pdbe.org/6rbm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rbm RCSB], [http://www.ebi.ac.uk/pdbsum/6rbm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rbm ProSAT]</span></td></tr>
	</table>		</table>
Line 12:		Line 13:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~Induction~~ of the ~~tetracycline~~ repressor (TetR) ~~results from antibiotic-dependent changes in~~ the ~~relative positioning~~ of the DNA-binding domains ~~within the promoter~~-~~associated repressor dimer, but the key determinants~~ of this ~~allosteric effect remain poorly characterised~~. ~~Intriguingly~~, ~~previous mutational~~ analyses of ~~the tetracycline~~-~~interacting site revealed a lack~~ of ~~correlation between residual affinity and induction propensity, suggesting that some~~ of ~~the residues in contact with the antibiotic primarily act in ligand recognition~~ and ~~retention~~, ~~whereas others are required to transmit the allosteric signal. Here~~, ~~we provide a structural basis for these observations via crystallographic analysis of the point mutants N82A~~, ~~H100A, T103A~~ and ~~E147A in complex with the inducer 5a,6-anhydrotetracycline~~. ~~In conjunction with the available functional data, the four~~ structures ~~demonstrate~~ that a trigger-like movement of the region between helices alpha6 and alpha7 towards and into the binding site plays a decisive role in the intramolecular communication process. In sharp contrast, residues lining the binding cavity proper have little or no influence on the allosteric ~~mechanism as such. This nearly complete physical separation~~ of ~~ligand recognition and allostery will have allowed diverging TetR-like repressors to bind novel effectors while~~ the ~~existing~~ induction ~~mechanism remained intact~~. ~~Consequently~~, ~~the modularity described here may have been~~ a ~~key factor in the evolutionary success~~ of the ~~widespread~~ and ~~highly diversified repressor class~~. ~~DATABASE: Structural data are available in~~ the ~~Protein Data Bank under~~ the ~~accession numbers 5FKK, 5FKL, 5FKM, 5FKN and 5FKO~~.	+	Allosteric regulation of the Tet repressor (TetR) homodimer relies on tetracycline binding that abolishes the affinity for the DNA operator. Previously, interpretation of circular dichroism data called for unfolding of the alpha-helical DNA-binding domains in absence of binding to DNA or tetracycline. Our small angle X-ray scattering of TetR(D) in solution contradicts this unfolding as a physiological process. Instead, in the core domain crystal structures analyses show increased immobilisation of helix alpha9 and two C-terminal turns of helix alpha8 upon tetracycline binding. Tetracycline complexes of TetR(D) and four single-site alanine variants were characterised by isothermal titration calorimetry, fluorescence titration, X-ray crystal structures, and melting curves. Five crystal structures confirm that Thr103 is a key residue for the allosteric events of induction, with the T103A variant lacking induction by any tetracycline. The T103A variant shows anti-cooperative inducer binding, and a melting curve of the tetracycline complex different to TetR(D) and other variants. For the N82A variant inducer binding is clearly anti-cooperative but triggers the induced conformation.

-	~~Modular organisation of inducer recognition~~ and ~~allostery in~~ the tetracycline repressor.,Werten S, ~~Schneider J~~, ~~Palm GJ~~, Hinrichs W ~~FEBS J~~. ~~2016 Mar 30~~. doi: 10.~~1111~~/~~febs~~.~~13723~~. PMID:~~27028290~~<ref>PMID:~~27028290~~</ref>	+	Thermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding.,Palm GJ, Buchholz I, Werten S, Girbardt B, Berndt L, Delcea M, Hinrichs W Biochim Biophys Acta Proteins Proteom. 2020 Feb 27;1868(6):140404. doi:, 10.1016/j.bbapap.2020.140404. PMID:32114262<ref>PMID:32114262</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	<div class="pdbe-citations 6rbm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6rbm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Tetracycline repressor protein 3D structures\|Tetracycline repressor protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Berndt, L]]		[[Category: Berndt, L]]

OCA at 06:11, 21 August 2019

OCA — Wed, 21 Aug 2019 06:11:15 GMT

←Older revision		Revision as of 06:11, 21 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6rbm is ~~ON HOLD until Oct~~ 11 ~~2020~~	+	==TETR(D) E147A MUTANT IN COMPLEX WITH MINOCYCLINE AND MAGNESIUM==
		+	<StructureSection load='6rbm' size='340' side='right'caption='[[6rbm]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6rbm]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RBM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MIY:(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE'>MIY</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6fpl\|6fpl]], [[2tct\|2tct]]</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=6rbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rbm OCA], [http://pdbe.org/6rbm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rbm RCSB], [http://www.ebi.ac.uk/pdbsum/6rbm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rbm ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TETR4_ECOLX TETR4_ECOLX]] TetR is the repressor of the tetracycline resistance element; its N-terminal region forms a helix-turn-helix structure and binds DNA. Binding of tetracycline to TetR reduces the repressor affinity for the tetracycline resistance gene (tetA) promoter operator sites.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Induction of the tetracycline repressor (TetR) results from antibiotic-dependent changes in the relative positioning of the DNA-binding domains within the promoter-associated repressor dimer, but the key determinants of this allosteric effect remain poorly characterised. Intriguingly, previous mutational analyses of the tetracycline-interacting site revealed a lack of correlation between residual affinity and induction propensity, suggesting that some of the residues in contact with the antibiotic primarily act in ligand recognition and retention, whereas others are required to transmit the allosteric signal. Here, we provide a structural basis for these observations via crystallographic analysis of the point mutants N82A, H100A, T103A and E147A in complex with the inducer 5a,6-anhydrotetracycline. In conjunction with the available functional data, the four structures demonstrate that a trigger-like movement of the region between helices alpha6 and alpha7 towards and into the binding site plays a decisive role in the intramolecular communication process. In sharp contrast, residues lining the binding cavity proper have little or no influence on the allosteric mechanism as such. This nearly complete physical separation of ligand recognition and allostery will have allowed diverging TetR-like repressors to bind novel effectors while the existing induction mechanism remained intact. Consequently, the modularity described here may have been a key factor in the evolutionary success of the widespread and highly diversified repressor class. DATABASE: Structural data are available in the Protein Data Bank under the accession numbers 5FKK, 5FKL, 5FKM, 5FKN and 5FKO.

-	~~Authors: Hinrichs, W~~., ~~Palm~~, G.J., ~~Berndt~~, L.~~, Girbardt, B~~.	+	Modular organisation of inducer recognition and allostery in the tetracycline repressor.,Werten S, Schneider J, Palm GJ, Hinrichs W FEBS J. 2016 Mar 30. doi: 10.1111/febs.13723. PMID:27028290<ref>PMID:27028290</ref>

-	~~Description~~: ~~TETR(D) E147A MUTANT IN COMPLEX WITH MINOCYCLINE AND MAGNESIUM~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6rbm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Berndt, L]]
	[[Category: Girbardt, B]]		[[Category: Girbardt, B]]
	[[Category: Hinrichs, W]]		[[Category: Hinrichs, W]]
-	[[Category: Palm, G.J]]	+	[[Category: Palm, G J]]
-	[[Category: ~~Berndt, L~~]]	+	[[Category: Transcription]]
		+	[[Category: Transcription regulation]]

OCA: Protected "6rbm" [edit=sysop:move=sysop]

OCA — Wed, 17 Apr 2019 04:25:19 GMT

Protected "6rbm" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:25, 17 April 2019

OCA: New page: '''Unreleased structure''' The entry 6rbm is ON HOLD until Oct 11 2020 Authors: Hinrichs, W., Palm, G.J., Berndt, L., Girbardt, B. Description: TETR(D) E147A MUTANT IN COMPLEX WITH MIN...

OCA — Wed, 17 Apr 2019 04:25:18 GMT

New page: '''Unreleased structure''' The entry 6rbm is ON HOLD until Oct 11 2020 Authors: Hinrichs, W., Palm, G.J., Berndt, L., Girbardt, B. Description: TETR(D) E147A MUTANT IN COMPLEX WITH MIN...

New page

'''Unreleased structure'''

The entry 6rbm is ON HOLD until Oct 11 2020

Authors: Hinrichs, W., Palm, G.J., Berndt, L., Girbardt, B.

Description: TETR(D) E147A MUTANT IN COMPLEX WITH MINOCYCLINE AND MAGNESIUM
[[Category: Unreleased Structures]]
[[Category: Girbardt, B]]
[[Category: Hinrichs, W]]
[[Category: Palm, G.J]]
[[Category: Berndt, L]]