3ikt - Revision history

OCA at 07:52, 6 September 2023

2023-09-06T07:52:31Z

←Older revision		Revision as of 07:52, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3ikt' size='340' side='right'caption='[[3ikt]], [[Resolution\|resolution]] 2.26Å' scene=''>		<StructureSection load='3ikt' size='340' side='right'caption='[[3ikt]], [[Resolution\|resolution]] 2.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ikt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Thet2 Thet2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IKT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ikt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IKT FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NAD:NICOTINAMIDE~~-~~ADENINE-DINUCLEOTIDE'>NAD</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]] 2.26Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1xcb\|1xcb]], [[3ikv\|3ikv]], [[3il2\|3il2]]~~</~~div~~>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rex, TT_C1293 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])~~</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=3ikt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikt OCA], [https://pdbe.org/3ikt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ikt RCSB], [https://www.ebi.ac.uk/pdbsum/3ikt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ikt 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=3ikt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikt OCA], [https://pdbe.org/3ikt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ikt RCSB], [https://www.ebi.ac.uk/pdbsum/3ikt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ikt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/REX_THET2 REX_THET2]] Modulates transcription in response to changes in cellular NADH/NAD(+) redox state (By similarity).	+	[https://www.uniprot.org/uniprot/REX_THET2 REX_THET2] Modulates transcription in response to changes in cellular NADH/NAD(+) redox state (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thet2~~]]	+	[[Category: Thermus thermophilus HB27]]
-	[[Category: Kielkopf~~, C L~~]]	+	[[Category: Kielkopf CL]]
-	[[Category: McLaughlin~~, K J]]~~	+	[[Category: McLaughlin KJ]]
-	~~[[Category: Cytoplasm]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Nad]]~~	+
-	~~[[Category: Nicotinamide adenine dinucleotide]]~~	+
-	~~[[Category: Redox-sensing]]~~	+
-	~~[[Category: Repressor]]~~	+
-	~~[[Category: Rex]]~~	+
-	~~[[Category: Rossmann fold]]~~	+
-	~~[[Category: Thermus aquaticus]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Winged helix~~]]	+

OCA at 03:35, 21 April 2022

2022-04-21T03:35:05Z

←Older revision		Revision as of 03:35, 21 April 2022
Line 1:		Line 1:

	==Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus==		==Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus==
-	<StructureSection load='3ikt' size='340' side='right' caption='[[3ikt]], [[Resolution\|resolution]] 2.26Å' scene=''>	+	<StructureSection load='3ikt' size='340' side='right'caption='[[3ikt]], [[Resolution\|resolution]] 2.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ikt]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Thet2 Thet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3IKT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ikt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet2 Thet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IKT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xcb\|1xcb]], [[3ikv\|3ikv]], [[3il2\|3il2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xcb\|1xcb]], [[3ikv\|3ikv]], [[3il2\|3il2]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rex, TT_C1293 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rex, TT_C1293 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</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=3ikt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikt OCA], [~~http~~://pdbe.org/3ikt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ikt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ikt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ikt 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=3ikt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikt OCA], [https://pdbe.org/3ikt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ikt RCSB], [https://www.ebi.ac.uk/pdbsum/3ikt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ikt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/REX_THET2 REX_THET2]] Modulates transcription in response to changes in cellular NADH/NAD(+) redox state (By similarity).	+	[[https://www.uniprot.org/uniprot/REX_THET2 REX_THET2]] Modulates transcription in response to changes in cellular NADH/NAD(+) redox state (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Thet2]]		[[Category: Thet2]]
	[[Category: Kielkopf, C L]]		[[Category: Kielkopf, C L]]

OCA at 10:06, 19 December 2018

2018-12-19T10:06:25Z

←Older revision		Revision as of 10:06, 19 December 2018
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ik/3ikt_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ik/3ikt_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 37:		Line 37:
	[[Category: Kielkopf, C L]]		[[Category: Kielkopf, C L]]
	[[Category: McLaughlin, K J]]		[[Category: McLaughlin, K J]]
		+	[[Category: Cytoplasm]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: Dna binding protein-dna complex]]		[[Category: Dna binding protein-dna complex]]

OCA at 06:20, 5 August 2016

2016-08-05T06:20:08Z

←Older revision		Revision as of 06:20, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus==		==Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus==
	<StructureSection load='3ikt' size='340' side='right' caption='[[3ikt]], [[Resolution\|resolution]] 2.26Å' scene=''>		<StructureSection load='3ikt' size='340' side='right' caption='[[3ikt]], [[Resolution\|resolution]] 2.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ikt]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus_hb27 Thermus thermophilus hb27~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IKT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ikt]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet2 Thet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IKT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xcb\|1xcb]], [[3ikv\|3ikv]], [[3il2\|3il2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xcb\|1xcb]], [[3ikv\|3ikv]], [[3il2\|3il2]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rex, TT_C1293 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 ~~Thermus thermophilus HB27~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rex, TT_C1293 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</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=3ikt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ikt RCSB], [http://www.ebi.ac.uk/pdbsum/3ikt 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=3ikt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikt OCA], [http://pdbe.org/3ikt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ikt RCSB], [http://www.ebi.ac.uk/pdbsum/3ikt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ikt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ikt ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 29:
	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 3ikt" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermus thermophilus hb27~~]]	+	[[Category: Thet2]]
	[[Category: Kielkopf, C L]]		[[Category: Kielkopf, C L]]
	[[Category: McLaughlin, K J]]		[[Category: McLaughlin, K J]]

OCA at 16:28, 25 December 2014

2014-12-25T16:28:12Z

←Older revision		Revision as of 16:28, 25 December 2014
Line 8:		Line 8:
	<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=3ikt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ikt RCSB], [http://www.ebi.ac.uk/pdbsum/3ikt 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=3ikt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ikt RCSB], [http://www.ebi.ac.uk/pdbsum/3ikt PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/REX_THET2 REX_THET2]] Modulates transcription in response to changes in cellular NADH/NAD(+) redox state (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:31, 18 December 2014

2014-12-18T06:31:05Z

←Older revision		Revision as of 06:31, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3ikt\| PDB=3ikt \| SCENE= }}~~	+	==Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus==
-	===Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus===	+	<StructureSection load='3ikt' size='340' side='right' caption='[[3ikt]], [[Resolution\|resolution]] 2.26Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20513431}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ikt]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb27 Thermus thermophilus hb27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IKT FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xcb\|1xcb]], [[3ikv\|3ikv]], [[3il2\|3il2]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rex, TT_C1293 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 Thermus thermophilus HB27])</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=3ikt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ikt RCSB], [http://www.ebi.ac.uk/pdbsum/3ikt PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ik/3ikt_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nicotinamide adenine dinucleotides have emerged as key signals of the cellular redox state. Yet the structural basis for allosteric gene regulation by the ratio of reduced NADH to oxidized NAD(+) is poorly understood. A key sensor among Gram-positive bacteria, Rex represses alternative respiratory gene expression until a limited oxygen supply elevates the intracellular NADH:NAD(+) ratio. Here we investigate the molecular mechanism for NADH/NAD(+) sensing among Rex family members by determining structures of Thermus aquaticus Rex bound to (1) NAD(+), (2) DNA operator, and (3) without ligand. Comparison with the Rex/NADH complex reveals that NADH releases Rex from the DNA site following a 40 degrees closure between the dimeric subunits. Complementary site-directed mutagenesis experiments implicate highly conserved residues in NAD-responsive DNA-binding activity. These rare views of a redox sensor in action establish a means for slight differences in the nicotinamide charge, pucker, and orientation to signal the redox state of the cell.

-	~~==About this Structure==~~	+	Structural basis for NADH/NAD+ redox sensing by a Rex family repressor.,McLaughlin KJ, Strain-Damerell CM, Xie K, Brekasis D, Soares AS, Paget MS, Kielkopf CL Mol Cell. 2010 May 28;38(4):563-75. PMID:20513431<ref>PMID:20513431</ref>
-	~~[[3ikt]] is~~ a 4 ~~chain structure with sequence from [http~~:~~//en~~.~~wikipedia.org/wiki/Thermus_thermophilus_hb27 Thermus thermophilus hb27]. Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3IKT OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	<~~ref group="xtra">PMID:020513431<~~/~~ref~~><~~references group="xtra"~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Thermus thermophilus hb27]]		[[Category: Thermus thermophilus hb27]]
-	[[Category: Kielkopf, C L.]]	+	[[Category: Kielkopf, C L]]
-	[[Category: McLaughlin, K J.]]	+	[[Category: McLaughlin, K J]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: Dna binding protein-dna complex]]		[[Category: Dna binding protein-dna complex]]

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

2013-03-13T11:03:10Z

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

←Older revision

Revision as of 11:03, 13 March 2013

OCA at 11:03, 13 March 2013

2013-03-13T11:03:08Z

←Older revision		Revision as of 11:03, 13 March 2013
Line 1:		Line 1:
-	{{Seed}}
-	[[Image:3ikt.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3ikt", 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_3ikt\| PDB=3ikt \| SCENE= }}		{{STRUCTURE_3ikt\| PDB=3ikt \| SCENE= }}
-
	===Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus===		===Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20513431}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20513431 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20513431}}		{{ABSTRACT_PUBMED_20513431}}

	==About this Structure==		==About this Structure==
-	~~3IKT~~ is a 4 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb27 Thermus thermophilus hb27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKT OCA].	+	[[3ikt]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb27 Thermus thermophilus hb27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKT OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20513431~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020513431</ref><references group="xtra"/>
	[[Category: Thermus thermophilus hb27]]		[[Category: Thermus thermophilus hb27]]
	[[Category: Kielkopf, C L.]]		[[Category: Kielkopf, C L.]]
	[[Category: McLaughlin, K J.]]		[[Category: McLaughlin, K J.]]
-	[[Category: Cytoplasm]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: Dna binding protein-dna complex]]		[[Category: Dna binding protein-dna complex]]
Line 41:		Line 24:
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
	[[Category: Winged helix]]		[[Category: Winged helix]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 16 08:13:52 2010''

OCA at 04:09, 16 June 2010

2010-06-16T04:09:10Z

←Older revision		Revision as of 04:09, 16 June 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3ikt.~~jpg~~\|left\|200px]]	+	[[Image:3ikt.png\|left\|200px]]

	<!--		<!--
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	===Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus===		===Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20513431}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20513431 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20513431}}

	==About this Structure==		==About this Structure==
	3IKT is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb27 Thermus thermophilus hb27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKT OCA].		3IKT is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb27 Thermus thermophilus hb27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKT OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20513431</ref><references group="xtra"/>
	[[Category: Thermus thermophilus hb27]]		[[Category: Thermus thermophilus hb27]]
	[[Category: Kielkopf, C L.]]		[[Category: Kielkopf, C L.]]
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	[[Category: Winged helix]]		[[Category: Winged helix]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Jun ~~10 11~~:14:18 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 16 08:13:52 2010''

OCA at 07:09, 10 June 2010

2010-06-10T07:09:32Z

←Older revision		Revision as of 07:09, 10 June 2010
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3ikt.jpg\|left\|200px]]

-	The ~~entry 3ikt~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3ikt", 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_3ikt\| PDB=3ikt \| SCENE= }}

-	~~Authors: McLaughlin, K.J., Kielkopf, C.L.~~	+	===Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus===

-	Description: Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu ~~Sep 3 15~~:21:~~24 2009~~''	+	==About this Structure==
		+	3IKT is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb27 Thermus thermophilus hb27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKT OCA].
		+	[[Category: Thermus thermophilus hb27]]
		+	[[Category: Kielkopf, C L.]]
		+	[[Category: McLaughlin, K J.]]
		+	[[Category: Cytoplasm]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Dna-binding]]
		+	[[Category: Nad]]
		+	[[Category: Nicotinamide adenine dinucleotide]]
		+	[[Category: Redox-sensing]]
		+	[[Category: Repressor]]
		+	[[Category: Rex]]
		+	[[Category: Rossmann fold]]
		+	[[Category: Thermus aquaticus]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription regulation]]
		+	[[Category: Winged helix]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jun 10 11:14:18 2010''