4fth - Revision history

OCA at 15:33, 14 March 2024

2024-03-14T15:33:56Z

← Older revision		Revision as of 15:33, 14 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4fth]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FTH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FTH FirstGlance]. <br>		<table><tr><td colspan='2'>[[4fth]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FTH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FTH 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=4fth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fth OCA], [https://pdbe.org/4fth PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fth RCSB], [https://www.ebi.ac.uk/pdbsum/4fth PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fth 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]] 3.004Å</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=4fth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fth OCA], [https://pdbe.org/4fth PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fth RCSB], [https://www.ebi.ac.uk/pdbsum/4fth PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fth ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/O66551_AQUAE O66551_AQUAE]		[https://www.uniprot.org/uniprot/O66551_AQUAE O66551_AQUAE]
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Transcription initiation by bacterial sigma(54)-polymerase requires the action of a transcriptional activator protein. Activators bind sequence-specifically upstream of the transcription initiation site via a DNA-binding domain (DBD). The structurally characterized DBDs from activators all belong to the Fis (factor for inversion stimulation) family of helix-turn-helix DNA-binding proteins. We report here structures of the free and DNA-bound forms of the DBD of NtrC4 (4DBD) from Aquifex aeolicus, a member of the NtrC family of sigma(54) activators. Two NtrC4-binding sites were identified upstream (-145 and -85bp) from the start of the lpxC gene, which is responsible for the first committed step in lipid A biosynthesis. This is the first experimental evidence for sigma(54) regulation in lpxC expression. 4DBD was crystallized both without DNA and in complex with the -145-binding site. The structures, together with biochemical data, indicate that NtrC4 binds to DNA in a manner that is similar to that of its close homolog, Fis. The greater sequence specificity for the binding of 4DBD relative to Fis seems to arise from a larger number of base-specific contacts contributing to affinity than for Fis.

	DNA Recognition by a sigma(54) Transcriptional Activator from Aquifex aeolicus.,Vidangos NK, Heideker J, Lyubimov A, Lamers M, Huo Y, Pelton JG, Ton J, Gralla J, Berger J, Wemmer DE J Mol Biol. 2014 Oct 23;426(21):3553-68. doi: 10.1016/j.jmb.2014.08.009. Epub, 2014 Aug 23. PMID:25158097<ref>PMID:25158097</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4fth" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 20:09, 19 October 2022

2022-10-19T20:09:50Z

← Older revision		Revision as of 20:09, 19 October 2022
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	==Crystal Structure of NtrC4 DNA-binding domain bound to double-stranded DNA==		==Crystal Structure of NtrC4 DNA-binding domain bound to double-stranded DNA==
	<StructureSection load='4fth' size='340' side='right' caption='[[4fth]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='4fth' size='340' side='right'caption='[[4fth]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4fth]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex~~ aeolicus~~" huber and stetter 2001~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FTH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4FTH FirstGlance]. <br>		<table><tr><td colspan='2'>[[4fth]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FTH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FTH FirstGlance]. <br>
	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e7l\|3e7l]]</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=4fth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fth OCA], [https://pdbe.org/4fth PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fth RCSB], [https://www.ebi.ac.uk/pdbsum/4fth PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fth ProSAT]</span></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aq_164, ntrC4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</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=4fth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fth OCA], [~~http~~://pdbe.org/4fth PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4fth RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4fth PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4fth ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/O66551_AQUAE O66551_AQUAE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Aquifex aeolicus ~~huber and stetter 2001~~]]		[[Category: Aquifex aeolicus]]
	[[Category: Berger~~, J M~~]]		[[Category: Large Structures]]
	[[Category: Gralla~~, J D~~]]		[[Category: Berger JM]]
	[[Category: Heideker, J]]		[[Category: Gralla JD]]
	[[Category: Huo, Y]]		[[Category: Heideker J]]
	[[Category: Kuriyan, J]]		[[Category: Huo Y]]
	[[Category: Lamers, M]]		[[Category: Kuriyan J]]
	[[Category: Lyubimov~~, A Y~~]]		[[Category: Lamers M]]
	[[Category: Pelton~~, J G~~]]		[[Category: Lyubimov AY]]
	[[Category: Ton, J]]		[[Category: Pelton JG]]
	[[Category: Vidangos~~, N K~~]]		[[Category: Ton J]]
	[[Category: Wemmer~~, D E]]~~		[[Category: Vidangos NK]]
	~~[[Category: Dna-binding]]~~		[[Category: Wemmer DE]]
	~~[[Category: Dna-binding domain]]~~
	~~[[Category: Fi]]~~
	~~[[Category: Helix-turn-helix]]~~
	~~[[Category: Ntrc]]~~
	~~[[Category: Sigma-54]]~~
	~~[[Category: Transcription regulator-dna complex]]~~
	~~[[Category: Transcriptional activator~~]]

OCA at 16:25, 11 August 2016

2016-08-11T16:25:08Z

← Older revision		Revision as of 16:25, 11 August 2016
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	==Crystal Structure of NtrC4 DNA-binding domain bound to double-stranded DNA==		==Crystal Structure of NtrC4 DNA-binding domain bound to double-stranded DNA==
	<StructureSection load='4fth' size='340' side='right' caption='[[4fth]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='4fth' size='340' side='right' caption='[[4fth]], [[Resolution\|resolution]] 3.00Å' scene=''>
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	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e7l\|3e7l]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e7l\|3e7l]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aq_164, ntrC4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aq_164, ntrC4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</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=4fth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fth OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fth RCSB], [http://www.ebi.ac.uk/pdbsum/4fth 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=4fth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fth OCA], [http://pdbe.org/4fth PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fth RCSB], [http://www.ebi.ac.uk/pdbsum/4fth PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fth ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4fth" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:33, 25 January 2015

2015-01-25T10:33:00Z

← Older revision		Revision as of 10:33, 25 January 2015
Line 2:		Line 2:
	<StructureSection load='4fth' size='340' side='right' caption='[[4fth]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='4fth' size='340' side='right' caption='[[4fth]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4fth]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FTH FirstGlance]. <br>		<table><tr><td colspan='2'>[[4fth]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FTH FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e7l\|3e7l]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e7l\|3e7l]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aq_164, ntrC4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</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=4fth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fth OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fth RCSB], [http://www.ebi.ac.uk/pdbsum/4fth 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=4fth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fth OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fth RCSB], [http://www.ebi.ac.uk/pdbsum/4fth PDBsum]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Aquifex aeolicus huber and stetter 2001]]
	[[Category: Berger, J M]]		[[Category: Berger, J M]]
	[[Category: Gralla, J D]]		[[Category: Gralla, J D]]

OCA at 07:34, 12 November 2014

2014-11-12T07:34:47Z

← Older revision		Revision as of 07:34, 12 November 2014
Line 2:		Line 2:
	<StructureSection load='4fth' size='340' side='right' caption='[[4fth]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='4fth' size='340' side='right' caption='[[4fth]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4fth]] is a 4 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FTH FirstGlance]. <br>		<table><tr><td colspan='2'>[[4fth]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FTH FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e7l\|3e7l]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e7l\|3e7l]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aq_164, ntrC4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</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=4fth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fth OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fth RCSB], [http://www.ebi.ac.uk/pdbsum/4fth 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=4fth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fth OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fth RCSB], [http://www.ebi.ac.uk/pdbsum/4fth PDBsum]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Aquifex aeolicus huber and stetter 2001]]~~		[[Category: Berger, J M]]
	[[Category: Berger, J M.]]		[[Category: Gralla, J D]]
	[[Category: Gralla, J D.]]		[[Category: Heideker, J]]
	[[Category: Heideker, J.]]		[[Category: Huo, Y]]
	[[Category: Huo, Y.]]		[[Category: Kuriyan, J]]
	[[Category: Kuriyan, J.]]		[[Category: Lamers, M]]
	[[Category: Lamers, M.]]		[[Category: Lyubimov, A Y]]
	[[Category: Lyubimov, A Y.]]		[[Category: Pelton, J G]]
	[[Category: Pelton, J G.]]		[[Category: Ton, J]]
	[[Category: Ton, J.]]		[[Category: Vidangos, N K]]
	[[Category: Vidangos, N K.]]		[[Category: Wemmer, D E]]
	[[Category: Wemmer, D E.]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]
	[[Category: Dna-binding domain]]		[[Category: Dna-binding domain]]

OCA at 05:40, 8 October 2014

2014-10-08T05:40:50Z

← Older revision		Revision as of 05:40, 8 October 2014
Line 2:		Line 2:
	<StructureSection load='4fth' size='340' side='right' caption='[[4fth]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='4fth' size='340' side='right' caption='[[4fth]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4fth]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Aquifex_aeolicus Aquifex~~ aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FTH FirstGlance]. <br>		<table><tr><td colspan='2'>[[4fth]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FTH FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e7l\|3e7l]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e7l\|3e7l]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aq_164, ntrC4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aq_164, ntrC4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4fth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fth OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fth RCSB], [http://www.ebi.ac.uk/pdbsum/4fth 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=4fth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fth OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fth RCSB], [http://www.ebi.ac.uk/pdbsum/4fth PDBsum]</span></td></tr>
	<table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Transcription initiation by bacterial sigma(54)-polymerase requires the action of a transcriptional activator protein. Activators bind sequence-specifically upstream of the transcription initiation site via a DNA-binding domain (DBD). The structurally characterized DBDs from activators all belong to the Fis (factor for inversion stimulation) family of helix-turn-helix DNA-binding proteins. We report here structures of the free and DNA-bound forms of the DBD of NtrC4 (4DBD) from Aquifex aeolicus, a member of the NtrC family of sigma(54) activators. Two NtrC4-binding sites were identified upstream (-145 and -85bp) from the start of the lpxC gene, which is responsible for the first committed step in lipid A biosynthesis. This is the first experimental evidence for sigma(54) regulation in lpxC expression. 4DBD was crystallized both without DNA and in complex with the -145-binding site. The structures, together with biochemical data, indicate that NtrC4 binds to DNA in a manner that is similar to that of its close homolog, Fis. The greater sequence specificity for the binding of 4DBD relative to Fis seems to arise from a larger number of base-specific contacts contributing to affinity than for Fis.

			DNA Recognition by a sigma(54) Transcriptional Activator from Aquifex aeolicus.,Vidangos NK, Heideker J, Lyubimov A, Lamers M, Huo Y, Pelton JG, Ton J, Gralla J, Berger J, Wemmer DE J Mol Biol. 2014 Oct 23;426(21):3553-68. doi: 10.1016/j.jmb.2014.08.009. Epub, 2014 Aug 23. PMID:25158097<ref>PMID:25158097</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus huber and stetter 2001]]
	[[Category: Berger, J M.]]		[[Category: Berger, J M.]]
	[[Category: Gralla, J D.]]		[[Category: Gralla, J D.]]

OCA at 09:11, 11 June 2014

2014-06-11T09:11:59Z

← Older revision		Revision as of 09:11, 11 June 2014
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	~~[[Image:4fth.jpg\|left\|200px]]~~		==Crystal Structure of NtrC4 DNA-binding domain bound to double-stranded DNA==
			<StructureSection load='4fth' size='340' side='right' caption='[[4fth]], [[Resolution\|resolution]] 3.00Å' scene=''>
	~~{{STRUCTURE_4fth\| PDB=4fth \| SCENE= }}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[4fth]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FTH FirstGlance]. <br>
	===Crystal Structure of NtrC4 DNA-binding domain bound to double-stranded DNA===		</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e7l\|3e7l]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aq_164, ntrC4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4fth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fth OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fth RCSB], [http://www.ebi.ac.uk/pdbsum/4fth PDBsum]</span></td></tr>
	==~~About this Structure~~==		<table>
	[[4fth]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FTH OCA].		__TOC__
			</StructureSection>
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
	[[Category: Berger, J M.]]		[[Category: Berger, J M.]]

OCA at 05:27, 29 August 2012

2012-08-29T05:27:53Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+[[Image:4fth.jpg|left|200px]]
-The entry 4fth is ON HOLD
+{{STRUCTURE_4fth|  PDB=4fth  |  SCENE=  }}
-Authors: Vidangos, N.K., Heideker, J., Lyubimov, A.Y., Lamers, M., Huo, Y., Pelton, J.G., Ton, J., Gralla, J.D., Kuriyan, J., Berger, J.M., Wemmer, D.E.
+===Crystal Structure of NtrC4 DNA-binding domain bound to double-stranded DNA===
-Description: Crystal Structure of NtrC4 DNA-binding domain bound to double-stranded DNA

OCA at 05:25, 1 August 2012

2012-08-01T05:25:54Z

← Older revision		Revision as of 05:25, 1 August 2012
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4fth is ON HOLD ~~until sometime in the future~~		The entry 4fth is ON HOLD

	Authors: Vidangos, N.K., Heideker, J., Lyubimov, A.Y., Lamers, M., Huo, Y., Pelton, J.G., Ton, J., Gralla, J.D., Kuriyan, J., Berger, J.M., Wemmer, D.E.		Authors: Vidangos, N.K., Heideker, J., Lyubimov, A.Y., Lamers, M., Huo, Y., Pelton, J.G., Ton, J., Gralla, J.D., Kuriyan, J., Berger, J.M., Wemmer, D.E.

	Description: Crystal Structure of NtrC4 DNA-binding domain bound to double-stranded DNA		Description: Crystal Structure of NtrC4 DNA-binding domain bound to double-stranded DNA

OCA at 05:03, 18 July 2012

2012-07-18T05:03:37Z

← Older revision		Revision as of 05:03, 18 July 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4fth is ON HOLD		The entry 4fth is ON HOLD until sometime in the future

	Authors: Vidangos, N.K., Heideker, J., Lyubimov, A.Y., Lamers, M., Huo, Y., Pelton, J.G., Ton, J., Gralla, J.D., Kuriyan, J., Berger, J.M., Wemmer, D.E.		Authors: Vidangos, N.K., Heideker, J., Lyubimov, A.Y., Lamers, M., Huo, Y., Pelton, J.G., Ton, J., Gralla, J.D., Kuriyan, J., Berger, J.M., Wemmer, D.E.

	Description: Crystal Structure of NtrC4 DNA-binding domain bound to double-stranded DNA		Description: Crystal Structure of NtrC4 DNA-binding domain bound to double-stranded DNA