4r22 - Revision history

OCA at 12:49, 1 March 2024

OCA — Fri, 01 Mar 2024 12:49:45 GMT

←Older revision		Revision as of 12:49, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4r22]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Priestia_megaterium_WSH-002 Priestia megaterium WSH-002] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R22 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4R22 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4r22]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Priestia_megaterium_WSH-002 Priestia megaterium WSH-002] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R22 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4R22 FirstGlance]. <br>
-	</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=4r22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r22 OCA], [https://pdbe.org/4r22 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4r22 RCSB], [https://www.ebi.ac.uk/pdbsum/4r22 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4r22 ProSAT]</span></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]] 2.6Å</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=4r22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r22 OCA], [https://pdbe.org/4r22 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4r22 RCSB], [https://www.ebi.ac.uk/pdbsum/4r22 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4r22 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/TNRA_PRIMW TNRA_PRIMW] Transcription regulator that actives the transcription of genes required for nitrogen assimilation during nitrogen limitation. On the contrary of the MerR members, which require longer DNA sites for high-affinity binding, TnrA requires a DNA sequence of 17 nucleotides as minimal binding site.[UniProtKB:Q45666]		[https://www.uniprot.org/uniprot/TNRA_PRIMW TNRA_PRIMW] Transcription regulator that actives the transcription of genes required for nitrogen assimilation during nitrogen limitation. On the contrary of the MerR members, which require longer DNA sites for high-affinity binding, TnrA requires a DNA sequence of 17 nucleotides as minimal binding site.[UniProtKB:Q45666]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	All cells must sense and adapt to changing nutrient availability. However, detailed molecular mechanisms coordinating such regulatory pathways remain poorly understood. In Bacillus subtilis, nitrogen homeostasis is controlled by a unique circuitry composed of the regulator TnrA, which is deactivated by feedback-inhibited glutamine synthetase (GS) during nitrogen excess and stabilized by GlnK upon nitrogen depletion, and the repressor GlnR. Here we describe a complete molecular dissection of this network. TnrA and GlnR, the global nitrogen homeostatic transcription regulators, are revealed as founders of a new structural family of dimeric DNA-binding proteins with C-terminal, flexible, effector-binding sensors that modulate their dimerization. Remarkably, the TnrA sensor domains insert into GS intersubunit catalytic pores, destabilizing the TnrA dimer and causing an unprecedented GS dodecamer-to-tetradecamer conversion, which concomitantly deactivates GS. In contrast, each subunit of the GlnK trimer "templates" active TnrA dimers. Unlike TnrA, GlnR sensors mediate an autoinhibitory dimer-destabilizing interaction alleviated by GS, which acts as a GlnR chaperone. Thus, these studies unveil heretofore unseen mechanisms by which inducible sensor domains drive metabolic reprograming in the model Gram-positive bacterium B. subtilis.
-
-	Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis.,Schumacher MA, Chinnam NB, Cuthbert B, Tonthat NK, Whitfill T Genes Dev. 2015 Feb 15;29(4):451-64. doi: 10.1101/gad.254714.114. PMID:25691471<ref>PMID:25691471</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4r22" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 14:06, 22 February 2023

OCA — Wed, 22 Feb 2023 14:06:39 GMT

←Older revision		Revision as of 14:06, 22 February 2023
Line 3:		Line 3:
	<StructureSection load='4r22' size='340' side='right'caption='[[4r22]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='4r22' size='340' side='right'caption='[[4r22]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4r22]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacmw Bacmw~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R22 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4R22 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4r22]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Priestia_megaterium_WSH-002 Priestia megaterium WSH-002] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R22 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4R22 FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4r24\|4r24]], [[4r25\|4r25]]</td></tr>~~	+	</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=4r22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r22 OCA], [https://pdbe.org/4r22 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4r22 RCSB], [https://www.ebi.ac.uk/pdbsum/4r22 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4r22 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tnrA, BMWSH_3277 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1006007 BACMW])</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=4r22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r22 OCA], [~~http~~://pdbe.org/4r22 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4r22 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4r22 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4r22 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TNRA_PRIMW TNRA_PRIMW] Transcription regulator that actives the transcription of genes required for nitrogen assimilation during nitrogen limitation. On the contrary of the MerR members, which require longer DNA sites for high-affinity binding, TnrA requires a DNA sequence of 17 nucleotides as minimal binding site.[UniProtKB:Q45666]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacmw]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Schumacher, M A~~]]	+	[[Category: Priestia megaterium WSH-002]]
-	[[Category: ~~New family of transcription regulator~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Transcription]]~~	+	[[Category: Schumacher MA]]
-	~~[[Category: Transcription-dna complex~~]]	+

OCA at 08:37, 24 April 2019

OCA — Wed, 24 Apr 2019 08:37:12 GMT

←Older revision		Revision as of 08:37, 24 April 2019
Line 1:		Line 1:

	==TnrA-DNA complex==		==TnrA-DNA complex==
-	<StructureSection load='4r22' size='340' side='right' caption='[[4r22]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='4r22' size='340' side='right'caption='[[4r22]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4r22]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R22 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4R22 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4r22]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacmw Bacmw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R22 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4R22 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4r24\|4r24]], [[4r25\|4r25]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4r24\|4r24]], [[4r25\|4r25]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tnrA, BMWSH_3277 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1006007 BACMW])</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=4r22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r22 OCA], [http://pdbe.org/4r22 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4r22 RCSB], [http://www.ebi.ac.uk/pdbsum/4r22 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4r22 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=4r22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r22 OCA], [http://pdbe.org/4r22 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4r22 RCSB], [http://www.ebi.ac.uk/pdbsum/4r22 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4r22 ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacmw]]
		+	[[Category: Large Structures]]
	[[Category: Schumacher, M A]]		[[Category: Schumacher, M A]]
-	[[Category: G]]
	[[Category: New family of transcription regulator]]		[[Category: New family of transcription regulator]]
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transcription-dna complex]]		[[Category: Transcription-dna complex]]

OCA at 17:17, 18 January 2017

OCA — Wed, 18 Jan 2017 17:17:50 GMT

←Older revision		Revision as of 17:17, 18 January 2017
Line 1:		Line 1:
		+
	==TnrA-DNA complex==		==TnrA-DNA complex==
	<StructureSection load='4r22' size='340' side='right' caption='[[4r22]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='4r22' size='340' side='right' caption='[[4r22]], [[Resolution\|resolution]] 2.60Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4r22]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R22 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4R22 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4r22]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R22 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4R22 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4r24\|4r24]], [[4r25\|4r25]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4r24\|4r24]], [[4r25\|4r25]]</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=4r22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r22 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4r22 RCSB], [http://www.ebi.ac.uk/pdbsum/4r22 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=4r22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r22 OCA], [http://pdbe.org/4r22 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4r22 RCSB], [http://www.ebi.ac.uk/pdbsum/4r22 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4r22 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 15:
	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 4r22" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:21, 4 March 2015

OCA — Wed, 04 Mar 2015 11:21:44 GMT

←Older revision		Revision as of 11:21, 4 March 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==TnrA-DNA complex==
		+	<StructureSection load='4r22' size='340' side='right' caption='[[4r22]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4r22]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R22 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4R22 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4r24\|4r24]], [[4r25\|4r25]]</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=4r22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r22 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4r22 RCSB], [http://www.ebi.ac.uk/pdbsum/4r22 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	All cells must sense and adapt to changing nutrient availability. However, detailed molecular mechanisms coordinating such regulatory pathways remain poorly understood. In Bacillus subtilis, nitrogen homeostasis is controlled by a unique circuitry composed of the regulator TnrA, which is deactivated by feedback-inhibited glutamine synthetase (GS) during nitrogen excess and stabilized by GlnK upon nitrogen depletion, and the repressor GlnR. Here we describe a complete molecular dissection of this network. TnrA and GlnR, the global nitrogen homeostatic transcription regulators, are revealed as founders of a new structural family of dimeric DNA-binding proteins with C-terminal, flexible, effector-binding sensors that modulate their dimerization. Remarkably, the TnrA sensor domains insert into GS intersubunit catalytic pores, destabilizing the TnrA dimer and causing an unprecedented GS dodecamer-to-tetradecamer conversion, which concomitantly deactivates GS. In contrast, each subunit of the GlnK trimer "templates" active TnrA dimers. Unlike TnrA, GlnR sensors mediate an autoinhibitory dimer-destabilizing interaction alleviated by GS, which acts as a GlnR chaperone. Thus, these studies unveil heretofore unseen mechanisms by which inducible sensor domains drive metabolic reprograming in the model Gram-positive bacterium B. subtilis.

-	~~The entry 4r22 is ON HOLD until Paper Publication~~	+	Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis.,Schumacher MA, Chinnam NB, Cuthbert B, Tonthat NK, Whitfill T Genes Dev. 2015 Feb 15;29(4):451-64. doi: 10.1101/gad.254714.114. PMID:25691471<ref>PMID:25691471</ref>

-	~~Authors~~: Schumacher, M.A.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~TnrA-DNA complex~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
-	[[Category: ~~Schumacher, M.A~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Schumacher, M A]]
		+	[[Category: G]]
		+	[[Category: New family of transcription regulator]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription-dna complex]]

OCA at 16:24, 24 December 2014

OCA — Wed, 24 Dec 2014 16:24:04 GMT

←Older revision		Revision as of 16:24, 24 December 2014
Line 6:		Line 6:

	Description: TnrA-DNA complex		Description: TnrA-DNA complex
		+	[[Category: Unreleased Structures]]
		+	[[Category: Schumacher, M.A]]

OCA at 11:22, 19 November 2014

OCA — Wed, 19 Nov 2014 11:22:50 GMT

←Older revision		Revision as of 11:22, 19 November 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4r22 is ON HOLD	+	The entry 4r22 is ON HOLD until Paper Publication

	Authors: Schumacher, M.A.		Authors: Schumacher, M.A.

	Description: TnrA-DNA complex		Description: TnrA-DNA complex

OCA: Protected "4r22" [edit=sysop:move=sysop]

OCA — Wed, 20 Aug 2014 14:45:37 GMT

Protected "4r22" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:45, 20 August 2014

OCA: New page: '''Unreleased structure''' The entry 4r22 is ON HOLD Authors: Schumacher, M.A. Description: TnrA-DNA complex

OCA — Wed, 20 Aug 2014 14:45:35 GMT

New page: '''Unreleased structure''' The entry 4r22 is ON HOLD Authors: Schumacher, M.A. Description: TnrA-DNA complex

New page

'''Unreleased structure'''

The entry 4r22 is ON HOLD

Authors: Schumacher, M.A.

Description: TnrA-DNA complex