3coq - Revision history

OCA at 09:37, 21 February 2024

OCA — Wed, 21 Feb 2024 09:37:15 GMT

←Older revision		Revision as of 09:37, 21 February 2024
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	<StructureSection load='3coq' size='340' side='right'caption='[[3coq]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3coq' size='340' side='right'caption='[[3coq]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3coq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3COQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3coq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3COQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MPD:(4S)~~-2~~-METHYL-2,~~4~~-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.4Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~GAL4 ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=559292 Baker~~'~~s yeast])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <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=3coq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3coq OCA], [https://pdbe.org/3coq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3coq RCSB], [https://www.ebi.ac.uk/pdbsum/3coq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3coq 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=3coq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3coq OCA], [https://pdbe.org/3coq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3coq RCSB], [https://www.ebi.ac.uk/pdbsum/3coq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3coq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes.	+	[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes.
	== 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=3coq 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=3coq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Gal4 is a Zn2Cys6 binuclear cluster containing transcription factor that binds DNA as a homodimer and can activate transcription by interacting with the mutant Gal11P protein. Although structures have been reported of the Gal4 dimerization domain and the binuclear cluster domain bound to DNA as a dimer, the structure of the "complete" Gal4 dimer bound to DNA has not previously been described. Here we report the structure of a complete Gal4 dimer bound to DNA and additional biochemical studies to address the molecular basis for Gal4 dimerization in DNA binding. We find that Gal4 dimerization on DNA is mediated by an intertwined helical bundle that deviates significantly from the solution NMR structure of the free dimerization domain. Associated biochemical studies show that the dimerization domain of Gal4 is important for DNA binding and protein thermostability. We also map the interaction surface of the Gal4 dimerization domain with Gal11P.
-
-	Structural basis for dimerization in DNA recognition by Gal4.,Hong M, Fitzgerald MX, Harper S, Luo C, Speicher DW, Marmorstein R Structure. 2008 Jul;16(7):1019-26. PMID:18611375<ref>PMID:18611375</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3coq" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Gal3-Gal80-Gal4\|Gal3-Gal80-Gal4]]		*[[Gal3-Gal80-Gal4\|Gal3-Gal80-Gal4]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Fitzgerald, M X~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: ~~Harper, S~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Hong, M~~]]	+	[[Category: Fitzgerald MX]]
-	[[Category: ~~Luo, C~~]]	+	[[Category: Harper S]]
-	[[Category: ~~Speicher, D W~~]]	+	[[Category: Hong M]]
-	[[Category: ~~Activator~~]]	+	[[Category: Luo C]]
-	[[Category: ~~Carbohydrate metabolism]]~~	+	[[Category: Speicher DW]]
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Galactose metabolism]]~~	+
-	~~[[Category: Helix bundle]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Protein-dna complex]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Transcription-dna complex]]~~	+
-	~~[[Category: Zinc binuclear cluster~~]]	+

OCA at 07:40, 2 February 2022

OCA — Wed, 02 Feb 2022 07:40:45 GMT

←Older revision		Revision as of 07:40, 2 February 2022
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	<StructureSection load='3coq' size='340' side='right'caption='[[3coq]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3coq' size='340' side='right'caption='[[3coq]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3coq]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3COQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3coq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3COQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GAL4 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GAL4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=3coq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3coq OCA], [~~http~~://pdbe.org/3coq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3coq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3coq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3coq 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=3coq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3coq OCA], [https://pdbe.org/3coq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3coq RCSB], [https://www.ebi.ac.uk/pdbsum/3coq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3coq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes.	+	[[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	==See Also==		==See Also==
	*[[Gal3-Gal80-Gal4\|Gal3-Gal80-Gal4]]		*[[Gal3-Gal80-Gal4\|Gal3-Gal80-Gal4]]
-	*[[User:Wayne Decatur/Gal 4\|User:Wayne Decatur/Gal 4]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:54, 24 July 2019

OCA — Wed, 24 Jul 2019 07:54:01 GMT

←Older revision		Revision as of 07:54, 24 July 2019
Line 1:		Line 1:

	==Structural Basis for Dimerization in DNA Recognition by Gal4==		==Structural Basis for Dimerization in DNA Recognition by Gal4==
-	<StructureSection load='3coq' size='340' side='right' caption='[[3coq]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='3coq' size='340' side='right'caption='[[3coq]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3coq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3COQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3coq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3COQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GAL4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~4932 Saccharomyces cerevisiae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GAL4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=3coq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3coq OCA], [http://pdbe.org/3coq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3coq RCSB], [http://www.ebi.ac.uk/pdbsum/3coq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3coq 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=3coq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3coq OCA], [http://pdbe.org/3coq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3coq RCSB], [http://www.ebi.ac.uk/pdbsum/3coq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3coq ProSAT]</span></td></tr>
	</table>		</table>
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/co/3coq_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/co/3coq_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 31:		Line 31:

	==See Also==		==See Also==
		+	*[[Gal3-Gal80-Gal4\|Gal3-Gal80-Gal4]]
	*[[User:Wayne Decatur/Gal 4\|User:Wayne Decatur/Gal 4]]		*[[User:Wayne Decatur/Gal 4\|User:Wayne Decatur/Gal 4]]
	== References ==		== References ==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae~~]]	+	[[Category: Baker's yeast]]
		+	[[Category: Large Structures]]
	[[Category: Fitzgerald, M X]]		[[Category: Fitzgerald, M X]]
	[[Category: Harper, S]]		[[Category: Harper, S]]

OCA at 08:32, 25 October 2017

OCA — Wed, 25 Oct 2017 08:32:15 GMT

←Older revision		Revision as of 08:32, 25 October 2017
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Gal3-Gal80-Gal4\|Gal3-Gal80-Gal4]]
	*[[User:Wayne Decatur/Gal 4\|User:Wayne Decatur/Gal 4]]		*[[User:Wayne Decatur/Gal 4\|User:Wayne Decatur/Gal 4]]
	== References ==		== References ==

OCA at 03:26, 5 August 2016

OCA — Fri, 05 Aug 2016 03:26:34 GMT

←Older revision		Revision as of 03:26, 5 August 2016
Line 1:		Line 1:
		+
	==Structural Basis for Dimerization in DNA Recognition by Gal4==		==Structural Basis for Dimerization in DNA Recognition by Gal4==
	<StructureSection load='3coq' size='340' side='right' caption='[[3coq]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3coq' size='340' side='right' caption='[[3coq]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GAL4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GAL4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=3coq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3coq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3coq RCSB], [http://www.ebi.ac.uk/pdbsum/3coq 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=3coq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3coq OCA], [http://pdbe.org/3coq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3coq RCSB], [http://www.ebi.ac.uk/pdbsum/3coq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3coq 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=3coq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 28:
	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 3coq" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Gal3-Gal80-Gal4\|Gal3-Gal80-Gal4]]		*[[Gal3-Gal80-Gal4\|Gal3-Gal80-Gal4]]
		+	*[[User:Wayne Decatur/Gal 4\|User:Wayne Decatur/Gal 4]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:29, 25 December 2014

OCA — Thu, 25 Dec 2014 15:29:32 GMT

←Older revision		Revision as of 15:29, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3coq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3COQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[3coq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3COQ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GAL4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GAL4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=3coq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3coq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3coq RCSB], [http://www.ebi.ac.uk/pdbsum/3coq 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=3coq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3coq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3coq RCSB], [http://www.ebi.ac.uk/pdbsum/3coq PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Fitzgerald, M X.]]	+	[[Category: Fitzgerald, M X]]
-	[[Category: Harper, S.]]	+	[[Category: Harper, S]]
-	[[Category: Hong, M.]]	+	[[Category: Hong, M]]
-	[[Category: Luo, C.]]	+	[[Category: Luo, C]]
-	[[Category: Speicher, D W.]]	+	[[Category: Speicher, D W]]
	[[Category: Activator]]		[[Category: Activator]]
	[[Category: Carbohydrate metabolism]]		[[Category: Carbohydrate metabolism]]

OCA at 06:59, 29 September 2014

OCA — Mon, 29 Sep 2014 06:59:41 GMT

←Older revision		Revision as of 06:59, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3coq.~~png~~\|~~left~~\|200px]]	+	==Structural Basis for Dimerization in DNA Recognition by Gal4==
		+	<StructureSection load='3coq' size='340' side='right' caption='[[3coq]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3coq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3COQ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GAL4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=3coq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3coq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3coq RCSB], [http://www.ebi.ac.uk/pdbsum/3coq 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/co/3coq_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 ==
		+	Gal4 is a Zn2Cys6 binuclear cluster containing transcription factor that binds DNA as a homodimer and can activate transcription by interacting with the mutant Gal11P protein. Although structures have been reported of the Gal4 dimerization domain and the binuclear cluster domain bound to DNA as a dimer, the structure of the "complete" Gal4 dimer bound to DNA has not previously been described. Here we report the structure of a complete Gal4 dimer bound to DNA and additional biochemical studies to address the molecular basis for Gal4 dimerization in DNA binding. We find that Gal4 dimerization on DNA is mediated by an intertwined helical bundle that deviates significantly from the solution NMR structure of the free dimerization domain. Associated biochemical studies show that the dimerization domain of Gal4 is important for DNA binding and protein thermostability. We also map the interaction surface of the Gal4 dimerization domain with Gal11P.

-	~~{{STRUCTURE_3coq\| PDB=3coq \| SCENE= }}~~	+	Structural basis for dimerization in DNA recognition by Gal4.,Hong M, Fitzgerald MX, Harper S, Luo C, Speicher DW, Marmorstein R Structure. 2008 Jul;16(7):1019-26. PMID:18611375<ref>PMID:18611375</ref>

-	~~===Structural Basis for Dimerization in DNA Recognition by Gal4===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18611375}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3coq]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3COQ OCA].~~	+

	==See Also==		==See Also==
-	*[[Gal4\|Gal4]]	+	*[[Gal3-Gal80-Gal4\|Gal3-Gal80-Gal4]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018611375<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Fitzgerald, M X.]]		[[Category: Fitzgerald, M X.]]

OCA at 18:20, 20 October 2012

OCA — Sat, 20 Oct 2012 18:20:30 GMT

←Older revision		Revision as of 18:20, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3coq]] is a 4 chain structure ~~of [[Gal4]]~~ with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COQ OCA].	+	[[3coq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COQ OCA].

	==See Also==		==See Also==

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

OCA — Fri, 27 Jul 2012 03:48:32 GMT

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

←Older revision

Revision as of 03:48, 27 July 2012

OCA at 03:48, 27 July 2012

OCA — Fri, 27 Jul 2012 03:48:31 GMT

←Older revision		Revision as of 03:48, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3coq.png\|left\|200px]]		[[Image:3coq.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3coq", 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.
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	{{STRUCTURE_3coq\| PDB=3coq \| SCENE= }}		{{STRUCTURE_3coq\| PDB=3coq \| SCENE= }}

	===Structural Basis for Dimerization in DNA Recognition by Gal4===		===Structural Basis for Dimerization in DNA Recognition by Gal4===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18611375}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18611375 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_18611375}}		{{ABSTRACT_PUBMED_18611375}}

	==About this Structure==		==About this Structure==
-	~~3COQ~~ is a 4 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COQ OCA].	+	[[3coq]] is a 4 chain structure of [[Gal4]] with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3COQ OCA].
		+
		+	==See Also==
		+	*[[Gal4\|Gal4]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18611375~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018611375</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Fitzgerald, M X.]]		[[Category: Fitzgerald, M X.]]
Line 41:		Line 32:
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
-	[[Category: Transcription/dna complex]]	+	[[Category: Transcription-dna complex]]
	[[Category: Zinc binuclear cluster]]		[[Category: Zinc binuclear cluster]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 20:23:05 2009''