1f5e - Revision history

OCA at 08:27, 22 May 2024

2024-05-22T08:27:49Z

←Older revision		Revision as of 08:27, 22 May 2024
Line 20:		Line 20:
	</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=1f5e 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=1f5e ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: In Aspergillus nidulans, the transcription activator AlcR mediates specific induction of a number of the genes of the alc cluster. This cluster includes genes involved in the oxidation of ethanol and other alcohols to acetate. The pattern of binding and of transactivation of AlcR is unique within the Zn(2)Cys(6) family. The structural bases for these specificities have not been analyzed at the atomic level until now. RESULTS: We have used NMR spectroscopy and restrained molecular dynamics to determine a set of structures of the AlcR DNA binding domain [AlcR(1-60)] in complex with a 10-mer DNA duplex. Analysis of the structures reveals specific interactions between AlcR and DNA common to the other known zinc clusters. In addition, the involvement of the N-terminal residues upstream of the AlcR zinc cluster in DNA binding is clearly highlighted, and the pivotal role of R6 is confirmed. Totally unprecedented specific and nonspecific contacts of two additional regions of the protein with the DNA are demonstrated. The differences with the available crystallographic structures of other zinc binuclear cluster proteins-DNA complexes are analyzed. CONCLUSIONS: The structures of the AlcR(1-60)-DNA complex provide the basis for a better understanding of some of the specificities of the AlcR system: the DNA consensus recognition sequence--usually the triplet CGG--is extended to five base pairs, AlcR acts as a monomer, and additional contacts inside and outside the DNA binding domain in the major and minor groove are observed. These extensive interactions stabilize the AlcR monomer to its cognate DNA site.
		+
		+	The solution structure of an AlcR-DNA complex sheds light onto the unique tight and monomeric DNA binding of a Zn(2)Cys(6) protein.,Cahuzac B, Cerdan R, Felenbok B, Guittet E Structure. 2001 Sep;9(9):827-36. PMID:11566132<ref>PMID:11566132</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1f5e" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:10, 20 March 2024

2024-03-20T10:10:43Z

←Older revision		Revision as of 10:10, 20 March 2024
Line 1:		Line 1:

	==STRUCTURE OF TRANSCRIPTIONAL FACTOR ALCR IN COMPLEX WITH A TARGET DNA==		==STRUCTURE OF TRANSCRIPTIONAL FACTOR ALCR IN COMPLEX WITH A TARGET DNA==
-	<StructureSection load='1f5e' size='340' side='right'caption='[[1f5e~~]], [[NMR_Ensembles_of_Models \| 1 NMR models~~]]' scene=''>	+	<StructureSection load='1f5e' size='340' side='right'caption='[[1f5e]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f5e]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~A._nidulans A.~~ nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F5E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f5e]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_nidulans Aspergillus nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F5E FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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">Solution NMR</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2alc\|2alc]], [[3alc\|3alc]], [[1f4s\|1f4s]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1f5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f5e OCA], [https://pdbe.org/1f5e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f5e RCSB], [https://www.ebi.ac.uk/pdbsum/1f5e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f5e 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=1f5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f5e OCA], [https://pdbe.org/1f5e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f5e RCSB], [https://www.ebi.ac.uk/pdbsum/1f5e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f5e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ALCR_EMENI ALCR_EMENI]] Positive regulatory protein for the ethanol regulon, alcA and aldA. It control positively its own expression and possibly in a negative fashion the expression of the gene coding for ADH-II.	+	[https://www.uniprot.org/uniprot/ALCR_EMENI ALCR_EMENI] Positive regulatory protein for the ethanol regulon, alcA and aldA. It control positively its own expression and possibly in a negative fashion the expression of the gene coding for ADH-II.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</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=1f5e 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=1f5e ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	BACKGROUND: In Aspergillus nidulans, the transcription activator AlcR mediates specific induction of a number of the genes of the alc cluster. This cluster includes genes involved in the oxidation of ethanol and other alcohols to acetate. The pattern of binding and of transactivation of AlcR is unique within the Zn(2)Cys(6) family. The structural bases for these specificities have not been analyzed at the atomic level until now. RESULTS: We have used NMR spectroscopy and restrained molecular dynamics to determine a set of structures of the AlcR DNA binding domain [AlcR(1-60)] in complex with a 10-mer DNA duplex. Analysis of the structures reveals specific interactions between AlcR and DNA common to the other known zinc clusters. In addition, the involvement of the N-terminal residues upstream of the AlcR zinc cluster in DNA binding is clearly highlighted, and the pivotal role of R6 is confirmed. Totally unprecedented specific and nonspecific contacts of two additional regions of the protein with the DNA are demonstrated. The differences with the available crystallographic structures of other zinc binuclear cluster proteins-DNA complexes are analyzed. CONCLUSIONS: The structures of the AlcR(1-60)-DNA complex provide the basis for a better understanding of some of the specificities of the AlcR system: the DNA consensus recognition sequence--usually the triplet CGG--is extended to five base pairs, AlcR acts as a monomer, and additional contacts inside and outside the DNA binding domain in the major and minor groove are observed. These extensive interactions stabilize the AlcR monomer to its cognate DNA site.
-
-	The solution structure of an AlcR-DNA complex sheds light onto the unique tight and monomeric DNA binding of a Zn(2)Cys(6) protein.,Cahuzac B, Cerdan R, Felenbok B, Guittet E Structure. 2001 Sep;9(9):827-36. PMID:11566132<ref>PMID:11566132</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1f5e" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: A. nidulans]]	+	[[Category: Aspergillus nidulans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cahuzac, B]]	+	[[Category: Cahuzac B]]
-	[[Category: Cerdan, R]]	+	[[Category: Cerdan R]]
-	[[Category: Felenbok, B]]	+	[[Category: Felenbok B]]
-	[[Category: Guittet, E]]	+	[[Category: Guittet E]]
-	~~[[Category: Protein-dna complex]]~~	+
-	~~[[Category: Transcription-dna complex]]~~	+
-	~~[[Category: Zinc binuclear cluster protein~~]]	+

OCA at 15:09, 3 November 2021

2021-11-03T15:09:45Z

←Older revision		Revision as of 15:09, 3 November 2021
Line 3:		Line 3:
	<StructureSection load='1f5e' size='340' side='right'caption='[[1f5e]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1f5e' size='340' side='right'caption='[[1f5e]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f5e]] is a 3 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F5E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f5e]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/A._nidulans A. nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F5E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2alc\|2alc]], [[3alc\|3alc]], [[1f4s\|1f4s]]</div></td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2alc\|2alc]], [[3alc\|3alc]], [[1f4s\|1f4s]]</div></td></tr>
Line 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: A. nidulans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Cahuzac, B]]		[[Category: Cahuzac, B]]

OCA at 07:19, 17 March 2021

2021-03-17T07:19:16Z

←Older revision		Revision as of 07:19, 17 March 2021
Line 3:		Line 3:
	<StructureSection load='1f5e' size='340' side='right'caption='[[1f5e]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1f5e' size='340' side='right'caption='[[1f5e]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f5e]] is a 3 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1F5E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f5e]] is a 3 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F5E FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2alc\|2alc]], [[3alc\|3alc]], [[1f4s\|1f4s]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2alc\|2alc]], [[3alc\|3alc]], [[1f4s\|1f4s]]</div></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=1f5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f5e OCA], [~~http~~://pdbe.org/1f5e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1f5e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1f5e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1f5e 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=1f5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f5e OCA], [https://pdbe.org/1f5e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f5e RCSB], [https://www.ebi.ac.uk/pdbsum/1f5e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f5e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ALCR_EMENI ALCR_EMENI]] Positive regulatory protein for the ethanol regulon, alcA and aldA. It control positively its own expression and possibly in a negative fashion the expression of the gene coding for ADH-II.	+	[[https://www.uniprot.org/uniprot/ALCR_EMENI ALCR_EMENI]] Positive regulatory protein for the ethanol regulon, alcA and aldA. It control positively its own expression and possibly in a negative fashion the expression of the gene coding for ADH-II.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:59, 12 June 2019

2019-06-12T06:59:39Z

←Older revision		Revision as of 06:59, 12 June 2019
Line 1:		Line 1:

	==STRUCTURE OF TRANSCRIPTIONAL FACTOR ALCR IN COMPLEX WITH A TARGET DNA==		==STRUCTURE OF TRANSCRIPTIONAL FACTOR ALCR IN COMPLEX WITH A TARGET DNA==
-	<StructureSection load='1f5e' size='340' side='right' caption='[[1f5e]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>	+	<StructureSection load='1f5e' size='340' side='right'caption='[[1f5e]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1f5e]] is a 3 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F5E FirstGlance]. <br>		<table><tr><td colspan='2'>[[1f5e]] is a 3 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F5E FirstGlance]. <br>
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f5/1f5e_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f5/1f5e_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 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Cahuzac, B]]		[[Category: Cahuzac, B]]
	[[Category: Cerdan, R]]		[[Category: Cerdan, R]]

OCA at 03:47, 6 September 2017

2017-09-06T03:47:26Z

←Older revision		Revision as of 03:47, 6 September 2017
Line 1:		Line 1:
		+
	==STRUCTURE OF TRANSCRIPTIONAL FACTOR ALCR IN COMPLEX WITH A TARGET DNA==		==STRUCTURE OF TRANSCRIPTIONAL FACTOR ALCR IN COMPLEX WITH A TARGET DNA==
	<StructureSection load='1f5e' size='340' side='right' caption='[[1f5e]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1f5e' size='340' side='right' caption='[[1f5e]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f5e]] is a 3 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/A._nidulans A. nidulans]~~. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F5E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f5e]] is a 3 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F5E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2alc\|2alc]], [[3alc\|3alc]], [[1f4s\|1f4s]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2alc\|2alc]], [[3alc\|3alc]], [[1f4s\|1f4s]]</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=1f5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f5e OCA], [http://pdbe.org/1f5e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f5e RCSB], [http://www.ebi.ac.uk/pdbsum/1f5e 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=1f5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f5e OCA], [http://pdbe.org/1f5e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f5e RCSB], [http://www.ebi.ac.uk/pdbsum/1f5e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1f5e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	<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=1f5e ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: A. nidulans]]
	[[Category: Cahuzac, B]]		[[Category: Cahuzac, B]]
	[[Category: Cerdan, R]]		[[Category: Cerdan, R]]

OCA at 08:35, 11 September 2015

2015-09-11T08:35:41Z

←Older revision		Revision as of 08:35, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1f5e' size='340' side='right' caption='[[1f5e]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1f5e' size='340' side='right' caption='[[1f5e]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f5e]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Emericella_nidulans Emericella~~ nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F5E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f5e]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/A._nidulans A. nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F5E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2alc\|2alc]], [[3alc\|3alc]], [[1f4s\|1f4s]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2alc\|2alc]], [[3alc\|3alc]], [[1f4s\|1f4s]]</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=1f5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f5e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f5e RCSB], [http://www.ebi.ac.uk/pdbsum/1f5e 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=1f5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f5e OCA], [http://pdbe.org/1f5e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f5e RCSB], [http://www.ebi.ac.uk/pdbsum/1f5e PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 1f5e" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Emericella~~ nidulans]]	+	[[Category: A. nidulans]]
	[[Category: Cahuzac, B]]		[[Category: Cahuzac, B]]
	[[Category: Cerdan, R]]		[[Category: Cerdan, R]]

OCA at 13:56, 25 December 2014

2014-12-25T13:56:59Z

←Older revision		Revision as of 13:56, 25 December 2014
Line 7:		Line 7:
	<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=1f5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f5e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f5e RCSB], [http://www.ebi.ac.uk/pdbsum/1f5e 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=1f5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f5e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f5e RCSB], [http://www.ebi.ac.uk/pdbsum/1f5e PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ALCR_EMENI ALCR_EMENI]] Positive regulatory protein for the ethanol regulon, alcA and aldA. It control positively its own expression and possibly in a negative fashion the expression of the gene coding for ADH-II.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 22:59, 22 December 2014

2014-12-22T22:59:41Z

←Older revision		Revision as of 22:59, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1f5e]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Emericella_nidulans Emericella nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F5E FirstGlance]. <br>		<table><tr><td colspan='2'>[[1f5e]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Emericella_nidulans Emericella nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F5E FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2alc\|2alc]], [[3alc\|3alc]], [[1f4s\|1f4s]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2alc\|2alc]], [[3alc\|3alc]], [[1f4s\|1f4s]]</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=1f5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f5e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f5e RCSB], [http://www.ebi.ac.uk/pdbsum/1f5e 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=1f5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f5e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f5e RCSB], [http://www.ebi.ac.uk/pdbsum/1f5e PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Emericella nidulans]]		[[Category: Emericella nidulans]]
-	[[Category: Cahuzac, B.]]	+	[[Category: Cahuzac, B]]
-	[[Category: Cerdan, R.]]	+	[[Category: Cerdan, R]]
-	[[Category: Felenbok, B.]]	+	[[Category: Felenbok, B]]
-	[[Category: Guittet, E.]]	+	[[Category: Guittet, E]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]
	[[Category: Transcription-dna complex]]		[[Category: Transcription-dna complex]]
	[[Category: Zinc binuclear cluster protein]]		[[Category: Zinc binuclear cluster protein]]

OCA at 12:44, 28 September 2014

2014-09-28T12:44:31Z

←Older revision		Revision as of 12:44, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1f5e.~~png~~\|~~left~~\|200px]]	+	==STRUCTURE OF TRANSCRIPTIONAL FACTOR ALCR IN COMPLEX WITH A TARGET DNA==
		+	<StructureSection load='1f5e' size='340' side='right' caption='[[1f5e]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1f5e]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Emericella_nidulans Emericella nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F5E FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2alc\|2alc]], [[3alc\|3alc]], [[1f4s\|1f4s]]</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=1f5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f5e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f5e RCSB], [http://www.ebi.ac.uk/pdbsum/1f5e 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/f5/1f5e_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 ==
		+	BACKGROUND: In Aspergillus nidulans, the transcription activator AlcR mediates specific induction of a number of the genes of the alc cluster. This cluster includes genes involved in the oxidation of ethanol and other alcohols to acetate. The pattern of binding and of transactivation of AlcR is unique within the Zn(2)Cys(6) family. The structural bases for these specificities have not been analyzed at the atomic level until now. RESULTS: We have used NMR spectroscopy and restrained molecular dynamics to determine a set of structures of the AlcR DNA binding domain [AlcR(1-60)] in complex with a 10-mer DNA duplex. Analysis of the structures reveals specific interactions between AlcR and DNA common to the other known zinc clusters. In addition, the involvement of the N-terminal residues upstream of the AlcR zinc cluster in DNA binding is clearly highlighted, and the pivotal role of R6 is confirmed. Totally unprecedented specific and nonspecific contacts of two additional regions of the protein with the DNA are demonstrated. The differences with the available crystallographic structures of other zinc binuclear cluster proteins-DNA complexes are analyzed. CONCLUSIONS: The structures of the AlcR(1-60)-DNA complex provide the basis for a better understanding of some of the specificities of the AlcR system: the DNA consensus recognition sequence--usually the triplet CGG--is extended to five base pairs, AlcR acts as a monomer, and additional contacts inside and outside the DNA binding domain in the major and minor groove are observed. These extensive interactions stabilize the AlcR monomer to its cognate DNA site.

-	~~{{STRUCTURE_1f5e\| PDB=1f5e \| SCENE= }}~~	+	The solution structure of an AlcR-DNA complex sheds light onto the unique tight and monomeric DNA binding of a Zn(2)Cys(6) protein.,Cahuzac B, Cerdan R, Felenbok B, Guittet E Structure. 2001 Sep;9(9):827-36. PMID:11566132<ref>PMID:11566132</ref>

-	~~===STRUCTURE OF TRANSCRIPTIONAL FACTOR ALCR IN COMPLEX WITH A TARGET DNA===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~==About this Structure==~~	+	<references/>
-	~~[[1f5e]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Emericella_nidulans Emericella nidulans]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1F5E OCA].~~	+	__TOC__
-		+	</StructureSection>
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:011566132<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Emericella nidulans]]		[[Category: Emericella nidulans]]
	[[Category: Cahuzac, B.]]		[[Category: Cahuzac, B.]]