4oqp - Revision history

OCA at 17:18, 20 September 2023

2023-09-20T17:18:03Z

←Older revision		Revision as of 17:18, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4oqp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OQP FirstGlance]. <br>		<table><tr><td colspan='2'>[[4oqp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OQP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</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]] 1.6Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></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=4oqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqp OCA], [https://pdbe.org/4oqp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oqp RCSB], [https://www.ebi.ac.uk/pdbsum/4oqp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqp 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=4oqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqp OCA], [https://pdbe.org/4oqp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oqp RCSB], [https://www.ebi.ac.uk/pdbsum/4oqp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqp ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:40, 25 January 2023

2023-01-25T07:40:22Z

←Older revision		Revision as of 07:40, 25 January 2023
Line 3:		Line 3:
	<StructureSection load='4oqp' size='340' side='right'caption='[[4oqp]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='4oqp' size='340' side='right'caption='[[4oqp]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4oqp]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacsu Bacsu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4OQP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4oqp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OQP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oqq\|4oqq]]</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=4oqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqp OCA], [https://pdbe.org/4oqp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oqp RCSB], [https://www.ebi.ac.uk/pdbsum/4oqp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqp ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">deoR, yxxC, BSU39430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=4oqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqp OCA], [~~http~~://pdbe.org/4oqp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4oqp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4oqp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqp ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DEOR_BACSU DEOR_BACSU]] Negative regulator of the dra-nupC-pdp operon. DeoR binds cooperatively to the operator DNA, which consists of a palindrome and a direct repeat sequence located 3' to the palindrome.	+	[https://www.uniprot.org/uniprot/DEOR_BACSU DEOR_BACSU] Negative regulator of the dra-nupC-pdp operon. DeoR binds cooperatively to the operator DNA, which consists of a palindrome and a direct repeat sequence located 3' to the palindrome.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacsu~~]]	+	[[Category: Bacillus subtilis subsp. subtilis str. 168]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Rezacova, P]]	+	[[Category: Rezacova P]]
-	[[Category: Skerlova, J]]	+	[[Category: Skerlova J]]
-	~~[[Category: Rossmann fold]]~~	+
-	~~[[Category: Schiff base]]~~	+
-	~~[[Category: Sugar-binding transcriptional regulator]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 08:00, 17 April 2019

2019-04-17T08:00:28Z

←Older revision		Revision as of 08:00, 17 April 2019
Line 1:		Line 1:

	==Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis in complex with deoxyribose-5-phosphate==		==Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis in complex with deoxyribose-5-phosphate==
-	<StructureSection load='4oqp' size='340' side='right' caption='[[4oqp]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='4oqp' size='340' side='right'caption='[[4oqp]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4oqp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OQP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4oqp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OQP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oqq\|4oqq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oqq\|4oqq]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">deoR, yxxC, BSU39430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=4oqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqp OCA], [http://pdbe.org/4oqp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oqp RCSB], [http://www.ebi.ac.uk/pdbsum/4oqp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqp 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=4oqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqp OCA], [http://pdbe.org/4oqp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oqp RCSB], [http://www.ebi.ac.uk/pdbsum/4oqp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqp ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacsu]]
		+	[[Category: Large Structures]]
	[[Category: Rezacova, P]]		[[Category: Rezacova, P]]
	[[Category: Skerlova, J]]		[[Category: Skerlova, J]]

OCA at 22:09, 4 August 2016

2016-08-04T22:09:44Z

←Older revision		Revision as of 22:09, 4 August 2016
Line 1:		Line 1:
		+
	==Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis in complex with deoxyribose-5-phosphate==		==Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis in complex with deoxyribose-5-phosphate==
	<StructureSection load='4oqp' size='340' side='right' caption='[[4oqp]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='4oqp' size='340' side='right' caption='[[4oqp]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oqq\|4oqq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oqq\|4oqq]]</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=4oqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oqp RCSB], [http://www.ebi.ac.uk/pdbsum/4oqp 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=4oqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqp OCA], [http://pdbe.org/4oqp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oqp RCSB], [http://www.ebi.ac.uk/pdbsum/4oqp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oqp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 4oqp" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:33, 25 December 2014

2014-12-25T13:33:41Z

←Older revision		Revision as of 13:33, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4oqp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OQP FirstGlance]. <br>		<table><tr><td colspan='2'>[[4oqp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OQP FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oqq\|4oqq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oqq\|4oqq]]</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=4oqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oqp RCSB], [http://www.ebi.ac.uk/pdbsum/4oqp 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=4oqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oqp RCSB], [http://www.ebi.ac.uk/pdbsum/4oqp PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DEOR_BACSU DEOR_BACSU]] Negative regulator of the dra-nupC-pdp operon. DeoR binds cooperatively to the operator DNA, which consists of a palindrome and a direct repeat sequence located 3' to the palindrome.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Rezacova, P.]]	+	[[Category: Rezacova, P]]
-	[[Category: Skerlova, J.]]	+	[[Category: Skerlova, J]]
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]
	[[Category: Schiff base]]		[[Category: Schiff base]]
	[[Category: Sugar-binding transcriptional regulator]]		[[Category: Sugar-binding transcriptional regulator]]
	[[Category: Transcription]]		[[Category: Transcription]]

OCA at 05:42, 18 June 2014

2014-06-18T05:42:50Z

←Older revision		Revision as of 05:42, 18 June 2014
Line 9:		Line 9:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~Expression~~ of ~~genes in the gapA operon encoding five~~ enzymes ~~for triose phosphate interconversion~~ in ~~Bacillus subtilis is negatively regulated by~~ the ~~Central glycolytic genes Regulator (CggR)~~. ~~CggR belongs~~ to the ~~large SorC/DeoR~~ family of ~~prokaryotic transcriptional~~ regulators~~, characterized by~~ an N-terminal DNA-binding domain and a ~~large~~ C-terminal effector-binding domain. When no glucose is present in growth media, CggR binds to its target DNA sequence and blocks the transcription of genes in the gapA operon. In the presence of glucose, binding of the known effector molecule fructose-1,6-bisphosphate abolishes this interaction. We have ~~identified dihydroxyacetone phosphate, glucose-6-phosphate, and fructose-6-phosphate as additional CggR ligands that can bind to~~ the ~~effector-binding site. Crystal structures~~ of ~~C-CggR,~~ the ~~C-terminal~~ effector-binding domain of ~~CggR, both unliganded as well as~~ in complex with the ~~four ligands at resolutions between 1.65 and 1.80 A reveal unique ligand-specific structural changes~~ in the ~~binding site that affect the dimer interface. Binding affinities~~ of ~~these ligands were determined by isothermal titration calorimetry~~. ~~Chemical cross-linking shows that CggR oligomerization~~ is ~~mediated~~ through ~~its~~ effector-binding ~~domain~~ and ~~that binding~~ of ~~the different ligands differentially affects the distribution of oligomers~~. ~~Electrophoretic mobility shift assays (EMSAs) confirmed a destabilizing effect~~ of ~~FBP on~~ the ~~CggR/DNA complex~~ and ~~also showed similar effects~~ for ~~dihydroxyacetone phosphate. Our results suggest that CggR stability and~~ function ~~may be modulated by various effectors in~~ a ~~complex fashion~~.	+	Deoxyribonucleoside regulator DeoR from Bacillus subtilis negatively regulates expression of enzymes involved in the catabolism of deoxyribonucleosides and deoxyribose. The DeoR protein is homologous to the sorbitol operon regulator family of metabolic regulators and comprises an N-terminal DNA-binding domain and a C-terminal effector-binding domain. We have determined the crystal structure of the effector-binding domain of DeoR (C-DeoR) in free form and in covalent complex with its effector deoxyribose-5-phosphate (dR5P). This is the first case of a covalently attached effector molecule captured in the structure of a bacterial transcriptional regulator. The dR5P molecule is attached through a Schiff base linkage to residue Lys141. The crucial role of Lys141 in effector binding was confirmed by mutational analysis and mass spectrometry of Schiff base adducts formed in solution. Structural analyses of the free and effector-bound C-DeoR structures provided a structural explanation for mechanism of DeoR function as a molecular switch. This article is protected by copyright. All rights reserved.

-	~~Crystal structures~~ of the effector-binding domain of ~~repressor CggR~~ from Bacillus subtilis ~~reveal ligand-induced structural changes upon binding of several glycolytic intermediates~~.,~~Rezacova P~~, ~~Kozisek~~ M, ~~Moy SF, Sieglova I, Joachimiak A, Machius~~ M, Otwinowski Z ~~Mol Microbiol~~. ~~2008 Jun~~ 10;. PMID:~~18554327~~<ref>PMID:~~18554327~~</ref>	+	Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis.,Skerlova J, Fabry M, Hubalek M, Otwinowski Z, Rezacova P FEBS J. 2014 May 23. doi: 10.1111/febs.12856. PMID:24863636<ref>PMID:24863636</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==

OCA at 05:08, 4 June 2014

2014-06-04T05:08:06Z

←Older revision		Revision as of 05:08, 4 June 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis in complex with deoxyribose-5-phosphate==
		+	<StructureSection load='4oqp' size='340' side='right' caption='[[4oqp]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4oqp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OQP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OQP FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4oqq\|4oqq]]</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=4oqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oqp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oqp RCSB], [http://www.ebi.ac.uk/pdbsum/4oqp PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Expression of genes in the gapA operon encoding five enzymes for triose phosphate interconversion in Bacillus subtilis is negatively regulated by the Central glycolytic genes Regulator (CggR). CggR belongs to the large SorC/DeoR family of prokaryotic transcriptional regulators, characterized by an N-terminal DNA-binding domain and a large C-terminal effector-binding domain. When no glucose is present in growth media, CggR binds to its target DNA sequence and blocks the transcription of genes in the gapA operon. In the presence of glucose, binding of the known effector molecule fructose-1,6-bisphosphate abolishes this interaction. We have identified dihydroxyacetone phosphate, glucose-6-phosphate, and fructose-6-phosphate as additional CggR ligands that can bind to the effector-binding site. Crystal structures of C-CggR, the C-terminal effector-binding domain of CggR, both unliganded as well as in complex with the four ligands at resolutions between 1.65 and 1.80 A reveal unique ligand-specific structural changes in the binding site that affect the dimer interface. Binding affinities of these ligands were determined by isothermal titration calorimetry. Chemical cross-linking shows that CggR oligomerization is mediated through its effector-binding domain and that binding of the different ligands differentially affects the distribution of oligomers. Electrophoretic mobility shift assays (EMSAs) confirmed a destabilizing effect of FBP on the CggR/DNA complex and also showed similar effects for dihydroxyacetone phosphate. Our results suggest that CggR stability and function may be modulated by various effectors in a complex fashion.

-	~~The entry 4oqp is ON HOLD until Paper Publication~~	+	Crystal structures of the effector-binding domain of repressor CggR from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates.,Rezacova P, Kozisek M, Moy SF, Sieglova I, Joachimiak A, Machius M, Otwinowski Z Mol Microbiol. 2008 Jun 10;. PMID:18554327<ref>PMID:18554327</ref>

-	~~Authors~~: Rezacova, P.~~, Pisackova~~, J.	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Structure of the effector~~-binding ~~domain of deoxyribonucleoside~~ regulator ~~DeoR from Bacillus subtilis in complex with deoxyribose-5-phosphate~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Rezacova, P.]]
		+	[[Category: Skerlova, J.]]
		+	[[Category: Rossmann fold]]
		+	[[Category: Schiff base]]
		+	[[Category: Sugar-binding transcriptional regulator]]
		+	[[Category: Transcription]]

OCA at 16:49, 3 March 2014

2014-03-03T16:49:09Z

←Older revision		Revision as of 16:49, 3 March 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Rezacova, P., Pisackova, J.		Authors: Rezacova, P., Pisackova, J.

	Description: Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis in complex with deoxyribose-5-phosphate		Description: Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis in complex with deoxyribose-5-phosphate

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

2014-02-19T16:19:45Z

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

←Older revision

Revision as of 16:19, 19 February 2014

OCA: New page: '''Unreleased structure''' The entry 4oqp is ON HOLD Authors: Rezacova, P., Pisackova, J. Description: Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR fr...

2014-02-19T16:19:43Z

New page: '''Unreleased structure''' The entry 4oqp is ON HOLD Authors: Rezacova, P., Pisackova, J. Description: Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR fr...

New page

'''Unreleased structure'''

The entry 4oqp is ON HOLD

Authors: Rezacova, P., Pisackova, J.

Description: Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis in complex with deoxyribose-5-phosphate