3o9x - Revision history

OCA at 09:32, 6 September 2023

OCA — Wed, 06 Sep 2023 09:32:13 GMT

←Older revision		Revision as of 09:32, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3o9x' size='340' side='right'caption='[[3o9x]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3o9x' size='340' side='right'caption='[[3o9x]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3o9x]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O9X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O9X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3o9x]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O9X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O9X 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>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.0999Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3hi2\|3hi2]], [[3gn5\|3gn5]], [[3ga8\|3ga8]], [[3fmy\|3fmy]]~~</~~div~~><~~/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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">b3021, JW2989, ygiT ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])~~</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=3o9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o9x OCA], [https://pdbe.org/3o9x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o9x RCSB], [https://www.ebi.ac.uk/pdbsum/3o9x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o9x 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=3o9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o9x OCA], [https://pdbe.org/3o9x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o9x RCSB], [https://www.ebi.ac.uk/pdbsum/3o9x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o9x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/MQSA_ECOLI MQSA_ECOLI]] Antitoxin component of a type II toxin-antitoxin (TA) module. Labile antitoxin that binds to the MqsR mRNA interferase toxin and neutralizes its endoribonuclease activity. Overexpression prevents MqsR-mediated cessation of cell growth and inhibition of cell proliferation. Initially reported to act as a cotranscription factor with MqsA (PubMed:19690171, PubMed:20105222). Following further experiments, the MqsR-MqsA complex does not bind DNA and all reported data are actually due to a small fraction of free MqsA alone binding DNA. Addition of MqsR to a preformed MqsA-promoter DNA complex causes dissociation of the MqsA-DNA complex, probably causing derepression of MqsA-repressed transcripts (PubMed:23172222). MqsA binds to 2 palindromes in the promoter region of the mqsRA operon activating its transcription. Binds to other promoters, inducing mcbR and spy and repressing cspD among others (PubMed:20105222). Binds to and represses the rpoS promoter, the master stress regulator, resulting in decreased cyclic-di-GMP, reduced stress resistance, increased cell motility and decreased biofilm formation; in these experiments 5 TA modules are missing (lacks MazEF, RelEB, ChpB, YoeB-YefM, YafQ-DinJ) (PubMed:21516113). An earlier study showed overexpression alone increases biofilm formation, perhaps by repressing cspD; in these experiments the 5 TA modules are present (PubMed:20105222). Represses the csgD promoter. In the presence of stress, when this protein is degraded, the promoters it represses are derepressed, leading to biofilm formation (Probable). This TA system mediates cell growth during bile acid deoxycholate stress by degrading mRNA for probable deoxycholate-binding protein YgiS; bile acid detergents such as deoxycholate are important for host defense against bacterial growth in the gall bladder and duodenum (PubMed:25534751).<ref>PMID:19690171</ref> <ref>PMID:19943910</ref> <ref>PMID:20105222</ref> <ref>PMID:21516113</ref> <ref>PMID:23172222</ref> <ref>PMID:25534751</ref> <ref>PMID:24212724</ref>	+	[https://www.uniprot.org/uniprot/MQSA_ECOLI MQSA_ECOLI] Antitoxin component of a type II toxin-antitoxin (TA) module. Labile antitoxin that binds to the MqsR mRNA interferase toxin and neutralizes its endoribonuclease activity. Overexpression prevents MqsR-mediated cessation of cell growth and inhibition of cell proliferation. Initially reported to act as a cotranscription factor with MqsA (PubMed:19690171, PubMed:20105222). Following further experiments, the MqsR-MqsA complex does not bind DNA and all reported data are actually due to a small fraction of free MqsA alone binding DNA. Addition of MqsR to a preformed MqsA-promoter DNA complex causes dissociation of the MqsA-DNA complex, probably causing derepression of MqsA-repressed transcripts (PubMed:23172222). MqsA binds to 2 palindromes in the promoter region of the mqsRA operon activating its transcription. Binds to other promoters, inducing mcbR and spy and repressing cspD among others (PubMed:20105222). Binds to and represses the rpoS promoter, the master stress regulator, resulting in decreased cyclic-di-GMP, reduced stress resistance, increased cell motility and decreased biofilm formation; in these experiments 5 TA modules are missing (lacks MazEF, RelEB, ChpB, YoeB-YefM, YafQ-DinJ) (PubMed:21516113). An earlier study showed overexpression alone increases biofilm formation, perhaps by repressing cspD; in these experiments the 5 TA modules are present (PubMed:20105222). Represses the csgD promoter. In the presence of stress, when this protein is degraded, the promoters it represses are derepressed, leading to biofilm formation (Probable). This TA system mediates cell growth during bile acid deoxycholate stress by degrading mRNA for probable deoxycholate-binding protein YgiS; bile acid detergents such as deoxycholate are important for host defense against bacterial growth in the gall bladder and duodenum (PubMed:25534751).<ref>PMID:19690171</ref> <ref>PMID:19943910</ref> <ref>PMID:20105222</ref> <ref>PMID:21516113</ref> <ref>PMID:23172222</ref> <ref>PMID:25534751</ref> <ref>PMID:24212724</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brown~~, B L~~]]	+	[[Category: Brown BL]]
-	[[Category: Page, R]]	+	[[Category: Page R]]
-	[[Category: Peti, W]]	+	[[Category: Peti W]]
-	~~[[Category: Bacterial antitoxin]]~~	+
-	~~[[Category: Hth-xre dna binding motif]]~~	+
-	~~[[Category: Transcription regulator-dna complex]]~~	+
-	~~[[Category: Transcriptional regulator]]~~	+
-	~~[[Category: Zn binding protein~~]]	+

OCA at 07:19, 12 May 2022

OCA — Thu, 12 May 2022 07:19:28 GMT

←Older revision		Revision as of 07:19, 12 May 2022
Line 1:		Line 1:

	==Structure of the E. coli antitoxin MqsA (YgiT/b3021) in complex with its gene promoter==		==Structure of the E. coli antitoxin MqsA (YgiT/b3021) in complex with its gene promoter==
-	<StructureSection load='3o9x' size='340' side='right' caption='[[3o9x]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3o9x' size='340' side='right'caption='[[3o9x]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3o9x]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O9X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3O9X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3o9x]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O9X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O9X 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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hi2\|3hi2]], [[3gn5\|3gn5]], [[3ga8\|3ga8]], [[3fmy\|3fmy]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3hi2\|3hi2]], [[3gn5\|3gn5]], [[3ga8\|3ga8]], [[3fmy\|3fmy]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b3021, JW2989, ygiT ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b3021, JW2989, ygiT ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3o9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o9x OCA], [~~http~~://pdbe.org/3o9x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3o9x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3o9x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3o9x 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=3o9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o9x OCA], [https://pdbe.org/3o9x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o9x RCSB], [https://www.ebi.ac.uk/pdbsum/3o9x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o9x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/MQSA_ECOLI MQSA_ECOLI]] Antitoxin component of a type II toxin-antitoxin (TA) module. Labile antitoxin that binds to the MqsR mRNA interferase toxin and neutralizes its endoribonuclease activity. Overexpression prevents MqsR-mediated cessation of cell growth and inhibition of cell proliferation. Initially reported to act as a cotranscription factor with MqsA (PubMed:19690171, PubMed:20105222). Following further experiments, the MqsR-MqsA complex does not bind DNA and all reported data are actually due to a small fraction of free MqsA alone binding DNA. Addition of MqsR to a preformed MqsA-promoter DNA complex causes dissociation of the MqsA-DNA complex, probably causing derepression of MqsA-repressed transcripts (PubMed:23172222). MqsA binds to 2 palindromes in the promoter region of the mqsRA operon activating its transcription. Binds to other promoters, inducing mcbR and spy and repressing cspD among others (PubMed:20105222). Binds to and represses the rpoS promoter, the master stress regulator, resulting in decreased cyclic-di-GMP, reduced stress resistance, increased cell motility and decreased biofilm formation; in these experiments 5 TA modules are missing (lacks MazEF, RelEB, ChpB, YoeB-YefM, YafQ-DinJ) (PubMed:21516113). An earlier study showed overexpression alone increases biofilm formation, perhaps by repressing cspD; in these experiments the 5 TA modules are present (PubMed:20105222). Represses the csgD promoter. In the presence of stress, when this protein is degraded, the promoters it represses are derepressed, leading to biofilm formation (Probable). This TA system mediates cell growth during bile acid deoxycholate stress by degrading mRNA for probable deoxycholate-binding protein YgiS; bile acid detergents such as deoxycholate are important for host defense against bacterial growth in the gall bladder and duodenum (PubMed:25534751).<ref>PMID:19690171</ref> <ref>PMID:19943910</ref> <ref>PMID:20105222</ref> <ref>PMID:21516113</ref> <ref>PMID:23172222</ref> <ref>PMID:25534751</ref> <ref>PMID:24212724</ref>	+	[[https://www.uniprot.org/uniprot/MQSA_ECOLI MQSA_ECOLI]] Antitoxin component of a type II toxin-antitoxin (TA) module. Labile antitoxin that binds to the MqsR mRNA interferase toxin and neutralizes its endoribonuclease activity. Overexpression prevents MqsR-mediated cessation of cell growth and inhibition of cell proliferation. Initially reported to act as a cotranscription factor with MqsA (PubMed:19690171, PubMed:20105222). Following further experiments, the MqsR-MqsA complex does not bind DNA and all reported data are actually due to a small fraction of free MqsA alone binding DNA. Addition of MqsR to a preformed MqsA-promoter DNA complex causes dissociation of the MqsA-DNA complex, probably causing derepression of MqsA-repressed transcripts (PubMed:23172222). MqsA binds to 2 palindromes in the promoter region of the mqsRA operon activating its transcription. Binds to other promoters, inducing mcbR and spy and repressing cspD among others (PubMed:20105222). Binds to and represses the rpoS promoter, the master stress regulator, resulting in decreased cyclic-di-GMP, reduced stress resistance, increased cell motility and decreased biofilm formation; in these experiments 5 TA modules are missing (lacks MazEF, RelEB, ChpB, YoeB-YefM, YafQ-DinJ) (PubMed:21516113). An earlier study showed overexpression alone increases biofilm formation, perhaps by repressing cspD; in these experiments the 5 TA modules are present (PubMed:20105222). Represses the csgD promoter. In the presence of stress, when this protein is degraded, the promoters it represses are derepressed, leading to biofilm formation (Probable). This TA system mediates cell growth during bile acid deoxycholate stress by degrading mRNA for probable deoxycholate-binding protein YgiS; bile acid detergents such as deoxycholate are important for host defense against bacterial growth in the gall bladder and duodenum (PubMed:25534751).<ref>PMID:19690171</ref> <ref>PMID:19943910</ref> <ref>PMID:20105222</ref> <ref>PMID:21516113</ref> <ref>PMID:23172222</ref> <ref>PMID:25534751</ref> <ref>PMID:24212724</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Brown, B L]]		[[Category: Brown, B L]]
	[[Category: Page, R]]		[[Category: Page, R]]

OCA at 10:17, 4 August 2016

OCA — Thu, 04 Aug 2016 10:17:42 GMT

←Older revision		Revision as of 10:17, 4 August 2016
Line 1:		Line 1:
		+
	==Structure of the E. coli antitoxin MqsA (YgiT/b3021) in complex with its gene promoter==		==Structure of the E. coli antitoxin MqsA (YgiT/b3021) in complex with its gene promoter==
	<StructureSection load='3o9x' size='340' side='right' caption='[[3o9x]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3o9x' size='340' side='right' caption='[[3o9x]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3o9x]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia coli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3O9X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3o9x]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3O9X 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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hi2\|3hi2]], [[3gn5\|3gn5]], [[3ga8\|3ga8]], [[3fmy\|3fmy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hi2\|3hi2]], [[3gn5\|3gn5]], [[3ga8\|3ga8]], [[3fmy\|3fmy]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b3021, JW2989, ygiT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~562 Escherichia coli~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b3021, JW2989, ygiT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3o9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o9x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3o9x RCSB], [http://www.ebi.ac.uk/pdbsum/3o9x 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=3o9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o9x OCA], [http://pdbe.org/3o9x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3o9x RCSB], [http://www.ebi.ac.uk/pdbsum/3o9x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3o9x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~YGIT_ECOLI YGIT_ECOLI~~]] Antitoxin component of a toxin-antitoxin (TA) module. Labile antitoxin that binds to the MqsR mRNA interferase toxin and neutralizes its endoribonuclease activity. Overexpression prevents MqsR-mediated cessation of cell growth and inhibition of cell proliferation. ~~Overexpression also~~ increases biofilm formation, perhaps by repressing cspD.<ref>PMID:19690171</ref> <ref>PMID:~~20105222~~</ref> <ref>PMID:~~19943910~~</ref> ~~Also acts as a transcription factor. Both MqsA and MqsRA bind to the promoter region of the mqsRA operon, inactivating (PubMed~~:~~19943910) or activating (PubMed:20105222) transcription. Alone or in complex with MqsR binds to other promoters, inducing mcbR and spy and repressing cspD among others.~~<ref>PMID:~~19690171~~</ref> <ref>PMID:~~20105222~~</ref> <ref>PMID:~~19943910~~</ref>	+	[[http://www.uniprot.org/uniprot/MQSA_ECOLI MQSA_ECOLI]] Antitoxin component of a type II toxin-antitoxin (TA) module. Labile antitoxin that binds to the MqsR mRNA interferase toxin and neutralizes its endoribonuclease activity. Overexpression prevents MqsR-mediated cessation of cell growth and inhibition of cell proliferation. Initially reported to act as a cotranscription factor with MqsA (PubMed:19690171, PubMed:20105222). Following further experiments, the MqsR-MqsA complex does not bind DNA and all reported data are actually due to a small fraction of free MqsA alone binding DNA. Addition of MqsR to a preformed MqsA-promoter DNA complex causes dissociation of the MqsA-DNA complex, probably causing derepression of MqsA-repressed transcripts (PubMed:23172222). MqsA binds to 2 palindromes in the promoter region of the mqsRA operon activating its transcription. Binds to other promoters, inducing mcbR and spy and repressing cspD among others (PubMed:20105222). Binds to and represses the rpoS promoter, the master stress regulator, resulting in decreased cyclic-di-GMP, reduced stress resistance, increased cell motility and decreased biofilm formation; in these experiments 5 TA modules are missing (lacks MazEF, RelEB, ChpB, YoeB-YefM, YafQ-DinJ) (PubMed:21516113). An earlier study showed overexpression alone increases biofilm formation, perhaps by repressing cspD; in these experiments the 5 TA modules are present (PubMed:20105222). Represses the csgD promoter. In the presence of stress, when this protein is degraded, the promoters it represses are derepressed, leading to biofilm formation (Probable). This TA system mediates cell growth during bile acid deoxycholate stress by degrading mRNA for probable deoxycholate-binding protein YgiS; bile acid detergents such as deoxycholate are important for host defense against bacterial growth in the gall bladder and duodenum (PubMed:25534751).<ref>PMID:19690171</ref> <ref>PMID:19943910</ref> <ref>PMID:20105222</ref> <ref>PMID:21516113</ref> <ref>PMID:23172222</ref> <ref>PMID:25534751</ref> <ref>PMID:24212724</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:
	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 3o9x" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: Ecoli]]
	[[Category: Brown, B L]]		[[Category: Brown, B L]]
	[[Category: Page, R]]		[[Category: Page, R]]

OCA at 08:50, 24 December 2014

OCA — Wed, 24 Dec 2014 08:50:10 GMT

←Older revision		Revision as of 08:50, 24 December 2014
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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=3o9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o9x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3o9x RCSB], [http://www.ebi.ac.uk/pdbsum/3o9x 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=3o9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o9x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3o9x RCSB], [http://www.ebi.ac.uk/pdbsum/3o9x PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/YGIT_ECOLI YGIT_ECOLI]] Antitoxin component of a toxin-antitoxin (TA) module. Labile antitoxin that binds to the MqsR mRNA interferase toxin and neutralizes its endoribonuclease activity. Overexpression prevents MqsR-mediated cessation of cell growth and inhibition of cell proliferation. Overexpression also increases biofilm formation, perhaps by repressing cspD.<ref>PMID:19690171</ref> <ref>PMID:20105222</ref> <ref>PMID:19943910</ref> Also acts as a transcription factor. Both MqsA and MqsRA bind to the promoter region of the mqsRA operon, inactivating (PubMed:19943910) or activating (PubMed:20105222) transcription. Alone or in complex with MqsR binds to other promoters, inducing mcbR and spy and repressing cspD among others.<ref>PMID:19690171</ref> <ref>PMID:20105222</ref> <ref>PMID:19943910</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 07:00, 19 December 2014

OCA — Fri, 19 Dec 2014 07:00:53 GMT

←Older revision		Revision as of 07:00, 19 December 2014
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-	~~{{STRUCTURE_3o9x\| PDB=3o9x \| SCENE= }}~~	+	==Structure of the E. coli antitoxin MqsA (YgiT/b3021) in complex with its gene promoter==
-	===Structure of the E. coli antitoxin MqsA (YgiT/b3021) in complex with its gene promoter===	+	<StructureSection load='3o9x' size='340' side='right' caption='[[3o9x]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21068382}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3o9x]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3O9X 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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hi2\|3hi2]], [[3gn5\|3gn5]], [[3ga8\|3ga8]], [[3fmy\|3fmy]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b3021, JW2989, ygiT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=3o9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o9x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3o9x RCSB], [http://www.ebi.ac.uk/pdbsum/3o9x PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial cultures, especially biofilms produce a small number of persister cells, a genetically identical sub-population of wild type cells that are metabolically dormant, exhibit multidrug tolerance, and are highly enriched in bacterial toxins. The gene most highly upregulated in E. coli persisters is mqsR, a ribonuclease toxin that, along with mqsA, forms a novel toxin:antitoxin (TA) system. Like all known TA systems, both the MqsR:MqsA complex and MqsA alone regulate their own transcription. Despite the importance of TA systems in persistence and biofilms, very little is known about how TA modules, and antitoxins in particular, bind and recognize DNA at a molecular level. Here, we report the crystal structure of MqsA bound to a 26-bp fragment from the mqsRA promoter. We show that MqsA binds DNA predominantly via its C-terminal helix-turn-helix (HTH) domain, with direct binding of recognition helix residues Asn97 and Arg101 to the DNA major groove. Unexpectedly, the structure also revealed that the MqsA N-terminal domain interacts with the DNA phosphate backbone. This results in a more than 105 degrees rotation of the N-terminal domains between the free and complexed states, an unprecedented rearrangement for an antitoxin. The structure also shows that MqsA bends the DNA by more than 55 degrees in order to achieve symmetrical binding. Finally, using a combination of biochemical and NMR studies, we show that the DNA sequence specificity of MqsA is mediated by direct readout.

-	~~==About this~~ Structure==	+	Structure of the E. coli antitoxin MQSA (YGIT/B3021) bound to its gene promoter reveals extensive domain rearrangements and the specificity of transcriptional regulation.,Brown BL, Wood TK, Peti W, Page R J Biol Chem. 2010 Nov 9. PMID:21068382<ref>PMID:21068382</ref>
-	~~[[3o9x]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia.org/wiki/Escherichia_coli Escherichia~~ coli~~]. Full crystallographic information is available from [http:~~/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3O9X OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:021068382</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Brown, B L.]]	+	[[Category: Brown, B L]]
-	[[Category: Page, R.]]	+	[[Category: Page, R]]
-	[[Category: Peti, W.]]	+	[[Category: Peti, W]]
	[[Category: Bacterial antitoxin]]		[[Category: Bacterial antitoxin]]
	[[Category: Hth-xre dna binding motif]]		[[Category: Hth-xre dna binding motif]]

OCA at 11:40, 24 April 2013

OCA — Wed, 24 Apr 2013 11:40:09 GMT

←Older revision		Revision as of 11:40, 24 April 2013
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-	[[Image:3o9x.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3o9x", creates the "Structure Box" on the page.
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-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3o9x\| PDB=3o9x \| SCENE= }}		{{STRUCTURE_3o9x\| PDB=3o9x \| SCENE= }}
-
	===Structure of the E. coli antitoxin MqsA (YgiT/b3021) in complex with its gene promoter===		===Structure of the E. coli antitoxin MqsA (YgiT/b3021) in complex with its gene promoter===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21068382}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21068382 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_21068382}}		{{ABSTRACT_PUBMED_21068382}}

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	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~21068382~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021068382</ref><references group="xtra"/><references/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Brown, B L.]]		[[Category: Brown, B L.]]
	[[Category: Page, R.]]		[[Category: Page, R.]]
	[[Category: Peti, W.]]		[[Category: Peti, W.]]
		+	[[Category: Bacterial antitoxin]]
		+	[[Category: Hth-xre dna binding motif]]
		+	[[Category: Transcription regulator-dna complex]]
		+	[[Category: Transcriptional regulator]]
		+	[[Category: Zn binding protein]]

OCA: Protected "3o9x" [edit=sysop:move=sysop]

OCA — Wed, 02 Feb 2011 05:51:47 GMT

Protected "3o9x" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:51, 2 February 2011

OCA at 05:51, 2 February 2011

OCA — Wed, 02 Feb 2011 05:51:46 GMT

←Older revision		Revision as of 05:51, 2 February 2011
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-	{{Seed}}
	[[Image:3o9x.png\|left\|200px]]		[[Image:3o9x.png\|left\|200px]]

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	==About this Structure==		==About this Structure==
-	~~3O9X~~ is a 4 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O9X OCA].	+	[[3o9x]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O9X OCA].

	==Reference==		==Reference==
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	[[Category: Page, R.]]		[[Category: Page, R.]]
	[[Category: Peti, W.]]		[[Category: Peti, W.]]
-	[[Category: Bacterial antitoxin]]
-	[[Category: Hth-xre dna binding motif]]
-	[[Category: Transcription regulator-dna complex]]
-	[[Category: Transcriptional regulator]]
-	[[Category: Zn binding protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 24 12:43:58 2010''

OCA at 09:32, 24 November 2010

OCA — Wed, 24 Nov 2010 09:32:47 GMT

←Older revision		Revision as of 09:32, 24 November 2010
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	{{Seed}}		{{Seed}}
-	[[Image:3o9x.~~jpg~~\|left\|200px]]	+	[[Image:3o9x.png\|left\|200px]]

	<!--		<!--
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	===Structure of the E. coli antitoxin MqsA (YgiT/b3021) in complex with its gene promoter===		===Structure of the E. coli antitoxin MqsA (YgiT/b3021) in complex with its gene promoter===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21068382}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21068382 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21068382}}

	==About this Structure==		==About this Structure==
	3O9X is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O9X OCA].		3O9X is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O9X OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:21068382</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Brown, B L.]]		[[Category: Brown, B L.]]
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	[[Category: Zn binding protein]]		[[Category: Zn binding protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov ~~10 06~~:51:05 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 24 12:43:58 2010''

OCA at 03:40, 10 November 2010

OCA — Wed, 10 Nov 2010 03:40:10 GMT

←Older revision		Revision as of 03:40, 10 November 2010
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3o9x.jpg\|left\|200px]]

-	The ~~entry 3o9x~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3o9x", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3o9x\| PDB=3o9x \| SCENE= }}

-	~~Authors: Brown, B.L., Peti, W., Page, R~~.	+	===Structure of the E. coli antitoxin MqsA (YgiT/b3021) in complex with its gene promoter===

-	Description: Structure of the E. coli antitoxin MqsA (YgiT/b3021) in complex with its gene promoter

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Sep 15~~ 10:35:41 2010''	+	==About this Structure==
		+	3O9X is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O9X OCA].
		+	[[Category: Escherichia coli]]
		+	[[Category: Brown, B L.]]
		+	[[Category: Page, R.]]
		+	[[Category: Peti, W.]]
		+	[[Category: Bacterial antitoxin]]
		+	[[Category: Hth-xre dna binding motif]]
		+	[[Category: Transcription regulator-dna complex]]
		+	[[Category: Transcriptional regulator]]
		+	[[Category: Zn binding protein]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 10 06:51:05 2010''