User:Wayne Decatur/Gal 4: Difference between revisions
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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' > | |||
<!-- 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. | ||
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==DNA Recognition by Gal4p== | ==DNA Recognition by Gal4p== | ||
<jmol> | |||
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<script>load /wiki/scripts/70/701975/1d66_firstglance/2.spt</script> | |||
<text>Restore Default Scene</text> | |||
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<br/> | |||
The protein <scene name='70/701975/1d66_firstglance/2'>binds as a dimer to a symmetrical 17-base-pair sequence</scene>. Specifically, the consensus Gal4p-binding site is a 17-mer of sequence conforming to the motif below.<br> | <scene name='70/701975/1d66_firstglance_secondary/2'>Each monomer</scene> of the protein dimer has 3 '''<font color='#f00080'> alpha helices</font>'''. | ||
The protein <scene name='70/701975/1d66_firstglance/2'>binds as a dimer to a symmetrical 17-base-pair sequence</scene>. Specifically, the consensus Gal4p-binding site is a 17-mer of sequence conforming to the motif below, which has the key feature of CGG triplets at the 5' ends, separated by 11 bps, or 5′-CGG-N11-CCG-3′.<br> | |||
<br> | <br> | ||
<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> | |||
| <font style='background:black;color:#ffffff;'>|||||||||||||||||</font><br> | ||
<span style="background:black;color:#FFFF80">3'-CGGNNNNNNNNNNNGGC-5'</span></span> | |||
<br> | <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> | |||
<jmol> | <jmol> | ||
<jmolButton> | <jmolButton> | ||
<script>select A,ADE,DA; color [x5050FF]; color cartoon | <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 by Nucleotide</text> | <text>Color Structure by Nucleotide</text> | ||
</jmolButton> | </jmolButton> | ||
</jmol> | </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> | |||
The third large helix of each dimer subunit interacts with the other <scene name='70/701975/1d66_firstglance_slab/3'>by arranging hydrophobic residues in the contact region</scene>. Note the abundance of gray residues in the central stem protruding from a site roughly the center of the DNA binding site. The dimer interface is more fully explored in a later publication with an expanded structure, see [[3coq]]. | The third, large helix of each dimer subunit interacts with the other <scene name='70/701975/1d66_firstglance_slab/3'>by arranging hydrophobic residues in the contact region</scene>. Note the abundance of gray residues in the central stem protruding from a site roughly above the center of the DNA binding site. The dimer interface is more fully explored in a later publication with an expanded structure, see [[3coq]]. | ||
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"/> | ||
== | ==Impetus== | ||
This page accompanies a [http://fenglabwkshopmay2015.readthedocs.org/en/latest/ hands-on workshop for ChIP-Seq] being given by Wayne Decatur May 14th, 2015. | |||
==See Also== | |||
* [[Gal3-Gal80-Gal4]] | * [[Gal3-Gal80-Gal4]] | ||
