User:Wayne Decatur/Gal 4 - Revision history

Wayne Decatur at 01:47, 17 May 2015

2015-05-17T01:47:57Z

← Older revision		Revision as of 01:47, 17 May 2015
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	<jmol>		<jmol>
	<jmolButton>		<jmolButton>
	<script>select A,ADE,DA; color [x5050FF]; color cartoon [x5050FF]; select C, CYT,DC; color [xE00000]; color cartoon [xE00000]; select G,GUA,DG; color [x00C000]; color cartoon [x00C000] select T,THY,DT; color [xE6E600]; color cartoon [xE6E600]; select U,URA; color [xCC9900]; color cartoon [xCC9900];</script>		<script>select A,ADE,DA; color [x5050FF]; color cartoon [x5050FF]; select C, CYT,DC; color [xE00000]; color cartoon [xE00000]; select G,GUA,DG; color [x00C000]; color cartoon [x00C000]; select T,THY,DT; color [xE6E600]; color cartoon [xE6E600]; select U,URA; color [xCC9900]; color cartoon [xCC9900];</script>
	<text>Color Structure by Nucleotide</text>		<text>Color Structure by Nucleotide</text>
	</jmolButton>		</jmolButton>
	</jmol>{{ColorKey Bases DNA}}		</jmol>
			{{ColorKey Bases DNA}}

	Despite only making base-specific contacts at the ends, <scene name='70/701975/Spacefill/1'>Ga14p is mostly in contact with the DNA for its entire span of the binding site.</scene>		Despite only making base-specific contacts at the ends, <scene name='70/701975/Spacefill/1'>Ga14p is mostly in contact with the DNA for its entire span of the binding site.</scene>

Wayne Decatur at 01:39, 17 May 2015

2015-05-17T01:39:11Z

← Older revision		Revision as of 01:39, 17 May 2015
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	The DNA binding domain <scene name='70/701975/1d66_firstglance_zn_binding/2'>uses six Cys residues to coordinate the binding of two ions of zinc (Zn(II))</scene>. (In the crystal structure [[1d66]], the zinc ions are actually represented by other members of the same group on the periodic table, the heavier cadmium ions.) The Zn-binding motif lets the structure accomplish more with fewer amino acids, the metals lending an "economy of structure", arranging two small helices to recognize a specific DNA site. <scene name='70/701975/1d66_base_conctacts/2'>Two lysines (17 and 18) make direct base contacts in the DNA major groove with the specified CGG triplets</scene>.<br>		The DNA binding domain <scene name='70/701975/1d66_firstglance_zn_binding/2'>uses six Cys residues to coordinate the binding of two ions of zinc (Zn(II))</scene>. (In the crystal structure [[1d66]], the zinc ions are actually represented by other members of the same group on the periodic table, the heavier cadmium ions.) The Zn-binding motif lets the structure accomplish more with fewer amino acids, the metals lending an "economy of structure", arranging two small helices to recognize a specific DNA site. <scene name='70/701975/1d66_base_conctacts/2'>Two lysines (17 and 18) make direct base contacts in the DNA major groove with the specified CGG triplets</scene>.<br>
	~~{{Button Toggle NucleicDrumsColorSchemeWcartoon}}~~ {{ColorKey Bases DNA}}		<jmol>
			<jmolButton>
			<script>select A,ADE,DA; color [x5050FF]; color cartoon [x5050FF]; select C, CYT,DC; color [xE00000]; color cartoon [xE00000]; select G,GUA,DG; color [x00C000]; color cartoon [x00C000] select T,THY,DT; color [xE6E600]; color cartoon [xE6E600]; select U,URA; color [xCC9900]; color cartoon [xCC9900];</script>
			<text>Color Structure by Nucleotide</text>
			</jmolButton>
			</jmol>{{ColorKey Bases DNA}}

	Despite only making base-specific contacts at the ends, <scene name='70/701975/Spacefill/1'>Ga14p is mostly in contact with the DNA for its entire span of the binding site.</scene>		Despite only making base-specific contacts at the ends, <scene name='70/701975/Spacefill/1'>Ga14p is mostly in contact with the DNA for its entire span of the binding site.</scene>

Wayne Decatur at 20:34, 16 May 2015

2015-05-16T20:34:14Z

← Older revision		Revision as of 20:34, 16 May 2015
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	Gal4p is a transcriptional activator in ''Saccharomyces cerevisiae'' that regulates the expression of genes to coordinate the response to the carbon source galactose.		Gal4p is a transcriptional activator in ''Saccharomyces cerevisiae'' that regulates the expression of genes to coordinate the response to the carbon source galactose.

	<StructureSection load='1d66' size='500' frame='true' side='right' caption='The N-terminal amino acids of Gal4p bound to DNA ([[1d66]])' scene='70/701975/1d66_firstglance/2' >		<StructureSection load='1d66' size='500' frame='true' side='right' caption='The N-terminal amino acids of Gal4p bound to DNA ([[1d66]])' scene='70/701975/1d66_firstglance/2' >
	<!-- important to note you need to use 'side' in a StructureSEction instead of 'align'. If you leave 'align' it doesn't work.-->		<!-- important to note you need to use 'side' in a StructureSEction instead of 'align'. If you leave 'align' it doesn't work.-->

	==Background==		==Background==
	Gal4p is a transcriptional activator in ''Saccharomyces cerevisiae'' that regulates the expression of genes to coordinate the response to the carbon source galactose.		Gal4p is a transcriptional activator in ''Saccharomyces cerevisiae'' that regulates the expression of genes to coordinate the response to the carbon source galactose.

Wayne Decatur at 20:33, 16 May 2015

2015-05-16T20:33:34Z

← Older revision		Revision as of 20:33, 16 May 2015
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			Gal4p is a transcriptional activator in ''Saccharomyces cerevisiae'' that regulates the expression of genes to coordinate the response to the carbon source galactose.

	<StructureSection load='1d66' size='500' frame='true' side='right' caption='The N-terminal amino acids of Gal4p bound to DNA ([[1d66]])' scene='70/701975/1d66_firstglance/2' >		<StructureSection load='1d66' size='500' frame='true' side='right' caption='The N-terminal amino acids of Gal4p bound to DNA ([[1d66]])' scene='70/701975/1d66_firstglance/2' >
	<!-- important to note you need to use 'side' in a StructureSEction instead of 'align'. If you leave 'align' it doesn't work.-->		<!-- important to note you need to use 'side' in a StructureSEction instead of 'align'. If you leave 'align' it doesn't work.-->
	~~Gal4p is a transcriptional activator in ''Saccharomyces cerevisiae'' that regulates the expression of genes to coordinate the response to the carbon source galactose.~~

	==Background==		==Background==

Wayne Decatur: fixing binding site text so fits next to added structuresection

2015-05-16T20:33:04Z

fixing binding site text so fits next to added structuresection

← Older revision		Revision as of 20:33, 16 May 2015
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	<StructureSection load='1d66' size='500' frame='true' side='right' caption='The N-terminal amino acids of Gal4p bound to DNA ([[1d66]])' scene='70/701975/1d66_firstglance/2' >		<StructureSection load='1d66' size='500' frame='true' side='right' caption='The N-terminal amino acids of Gal4p bound to DNA ([[1d66]])' scene='70/701975/1d66_firstglance/2' >
			<!-- important to note you need to use 'side' in a StructureSEction instead of 'align'. If you leave 'align' it doesn't work.-->
	Gal4p is a transcriptional activator in ''Saccharomyces cerevisiae'' that regulates the expression of genes to coordinate the response to the carbon source galactose.		Gal4p is a transcriptional activator in ''Saccharomyces cerevisiae'' that regulates the expression of genes to coordinate the response to the carbon source galactose.

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	<span style="background:black;color:#FFC0C8">5'-CGGNNNNNNNNNNNCCG-3'</span><br>		<span style="background:black;color:#FFC0C8">5'-CGGNNNNNNNNNNNCCG-3'</span><br>
	<font style='background:black;color:#ffffff;'>\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|</font><br>		<font style='background:black;color:#ffffff;'>\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|</font><br>
	;  <span style="background:black;color:#FFFF80">3'-CGGNNNNNNNNNNNGGC-5'</span></span>		<span style="background:black;color:#FFFF80">3'-CGGNNNNNNNNNNNGGC-5'</span></span>
	<br>		<br>

Wayne Decatur at 20:30, 16 May 2015

2015-05-16T20:30:54Z

← Older revision		Revision as of 20:30, 16 May 2015
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	<StructureSection load='1d66' size='~~400~~' frame='true' side='right' caption='The N-terminal amino acids of Gal4p bound to DNA ([[1d66]])' scene='70/701975/1d66_firstglance/2' >		<StructureSection load='1d66' size='500' frame='true' side='right' caption='The N-terminal amino acids of Gal4p bound to DNA ([[1d66]])' scene='70/701975/1d66_firstglance/2' >
	Gal4p is a transcriptional activator in ''Saccharomyces cerevisiae'' that regulates the expression of genes to coordinate the response to the carbon source galactose.		Gal4p is a transcriptional activator in ''Saccharomyces cerevisiae'' that regulates the expression of genes to coordinate the response to the carbon source galactose.

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	<span style="font-weight: bold;font-family: Courier New; font-size: 14pt">		<span style="font-weight: bold;font-family: Courier New; font-size: 14pt">
	<!-- By setting font to courier, I can use non-proportional font. Whereas by default, rest of Proteopedia is proportional -->		<!-- By setting font to courier, I can use non-proportional font. Whereas by default, rest of Proteopedia is proportional -->
	~~      ~~  <span style="background:black;color:#FFC0C8">5'-CGGNNNNNNNNNNNCCG-3'</span><br>		<span style="background:black;color:#FFC0C8">5'-CGGNNNNNNNNNNNCCG-3'</span><br>
	~~      ~~  <font style='background:black;color:#ffffff;'>\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|</font><br>		<font style='background:black;color:#ffffff;'>\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|</font><br>
	~~     &nbsp~~;  <span style="background:black;color:#FFFF80">3'-CGGNNNNNNNNNNNGGC-5'</span></span>		;  <span style="background:black;color:#FFFF80">3'-CGGNNNNNNNNNNNGGC-5'</span></span>
	<br>		<br>

Wayne Decatur at 20:29, 16 May 2015

2015-05-16T20:29:31Z

← Older revision		Revision as of 20:29, 16 May 2015
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	<StructureSection load='1d66' size='~~600~~' frame='true' side='right' caption='The N-terminal amino acids of Gal4p bound to DNA ([[1d66]])' scene='70/701975/1d66_firstglance/2' >		<StructureSection load='1d66' size='400' frame='true' side='right' caption='The N-terminal amino acids of Gal4p bound to DNA ([[1d66]])' scene='70/701975/1d66_firstglance/2' >
	Gal4p is a transcriptional activator in ''Saccharomyces cerevisiae'' that regulates the expression of genes to coordinate the response to the carbon source galactose.		Gal4p is a transcriptional activator in ''Saccharomyces cerevisiae'' that regulates the expression of genes to coordinate the response to the carbon source galactose.

Wayne Decatur: still trying to add structure section

2015-05-16T20:28:04Z

still trying to add structure section

← Older revision		Revision as of 20:28, 16 May 2015
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	<StructureSection load='1d66' size='600' frame='true' ~~align~~='right' caption='The N-terminal amino acids of Gal4p bound to DNA ([[1d66]])' scene='70/701975/1d66_firstglance/2' />		<StructureSection load='1d66' size='600' frame='true' side='right' caption='The N-terminal amino acids of Gal4p bound to DNA ([[1d66]])' scene='70/701975/1d66_firstglance/2' >
	Gal4p is a transcriptional activator in ''Saccharomyces cerevisiae'' that regulates the expression of genes to coordinate the response to the carbon source galactose.		Gal4p is a transcriptional activator in ''Saccharomyces cerevisiae'' that regulates the expression of genes to coordinate the response to the carbon source galactose.

Wayne Decatur: still trying to add structure section

2015-05-16T20:24:50Z

still trying to add structure section

← Older revision		Revision as of 20:24, 16 May 2015
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			<StructureSection load='1d66' size='600' frame='true' align='right' caption='The N-terminal amino acids of Gal4p bound to DNA ([[1d66]])' scene='70/701975/1d66_firstglance/2' />
	Gal4p is a transcriptional activator in ''Saccharomyces cerevisiae'' that regulates the expression of genes to coordinate the response to the carbon source galactose.		Gal4p is a transcriptional activator in ''Saccharomyces cerevisiae'' that regulates the expression of genes to coordinate the response to the carbon source galactose.


	<StructureSection load='Insert PDB code or filename here' size='600' frame='true' align='right' caption='The N-terminal amino acids of Gal4p bound to DNA ([[1d66]])' scene='70/701975/1d66_firstglance/2' />

	==Background==		==Background==

Wayne Decatur at 20:21, 16 May 2015

2015-05-16T20:21:58Z

← Older revision		Revision as of 20:21, 16 May 2015
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	The conformation of the linker connecting each dimerization helix and the metal-binding domains determines the preferred total number of bases between the triplets.		The conformation of the linker connecting each dimerization helix and the metal-binding domains determines the preferred total number of bases between the triplets.
			</StructureSection>
	==Reference==		==Reference==
	<ref group="xtra">PMID:1557122</ref><references group="xtra"/>		<ref group="xtra">PMID:1557122</ref><references group="xtra"/>