Tom Sandbox: Difference between revisions
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GCN4 (PDB [[2zta]] by itself, [[1ysa]] bound to DNA) is a eukaryotic transcription factor first isolated from Saccharomyces cerevisiae, also known as Baker's Yeast. The first 'leucine zipper' model was coined by Landshulz et al. in 1988. Today, while the name has stayed the same, we no longer view the leucine binding region in an inter-collated manner, but as | GCN4 (PDB [[2zta]] by itself, [[1ysa]] bound to DNA) is a eukaryotic transcription factor first isolated from Saccharomyces cerevisiae, also known as Baker's Yeast. The first 'leucine zipper' model was coined by Landshulz et al. in 1988. Today, while the name has stayed the same, we no longer view the leucine binding region in an inter-collated manner, but as Leucines meeting face to face <ref name="abc"> Oas, T. G.; McIntosh, L. P.; O'Shea, E. K.; Dahlquist, F. W.; and Kim, P. S. Biochemistry 1990 29 (12), 2891-2894 </ref>. (see heptad repeat section) <scene name='Tom_Sandbox/Leu_leu_and_val_val/1'>Here</scene> the Leucines are represented as red and the Valines are shown as oragne. A close up of the leucine-leucine pairing can be seen <scene name='Tom_Sandbox/Leu-leu_interaction/1'>here</scene>.GCN4 binds to promoter regions AP-1 and ATF/CREB to induce transcription via the C terminal basic residues of the two symmetric alpha helices.<ref> Hope, I. A.; Struhl,K. Cell, Volume 46, Issue 6, 12 September 1986, Pages 885-894</ref> | ||
===Structure=== | ===Structure=== | ||
GCN4 is composed of two identical 58 residue alpha helix chains that grouped together to form a parallel coiled-coil dimer. The dimer binds through interlocking leucine amino acids and <scene name='Tom_Sandbox/Hydrophobic_and_philic_regions/1'>hydrophobic residues</scene> near the C terminus, while pinching in on the major groove of DNA in the N terminal end via basic residues. It is clear from the image how the grey hydrophobic regions are between the helices, while the pink hydrophobic regions protrude outwards. | GCN4 is composed of two identical 58 residue alpha helix chains that grouped together to form a parallel coiled-coil dimer. The dimer binds through interlocking leucine amino acids and <scene name='Tom_Sandbox/Hydrophobic_and_philic_regions/1'>hydrophobic residues</scene> near the C terminus, while pinching in on the major groove of DNA in the N terminal end via basic residues. It is clear from the aforementioned image how the grey hydrophobic regions are between the helices, while the pink hydrophobic regions protrude outwards. | ||
{{STRUCTURE_1ysa| PDB=1ysa | SCENE= }} | {{STRUCTURE_1ysa| PDB=1ysa | SCENE= }} | ||
These two main domains are | These two main domains are labeled the <scene name='Tom_Sandbox/Acidic_and_basic_regions/1'>acidic leucine zipper dimerization domain and the basic DNA-binding domain</scene>. <ref name="ph"> Sharma, G.; Rege, K.; Budil, D. E.; Yarmush, M. L.; Mavroidis, C. Int J Nanomedicine. 2008 December; 3(4): 505–521. </ref> Here the acidic region is represented as Orange and the basic region in purple. The basic residues are the reason the class of binding interactions is commonly referred to as bZIP or basic region leucine zipper proteins<ref name="Voet"> Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008. </ref>. The basic region at the N-terminal of the two chains clamps in on the DNA like a pair of tweezers and makes contact with both the <scene name='Tom_Sandbox/Binding_with_dna/2'>bases and phosphate oxygens</scene> of DNA. In this example, Arginine residues of one of the helices are highlighted. The yellow Arginine binds to the oxygen of the phosphate backbone, while the light green Arginine binds to the inner nucleotide base. | ||
===Binding with DNA=== | ===Binding with DNA=== | ||
