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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. It is required for the general amino acid | 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. It is required for the general control of amino acid levels in yeast and binds upstream of several amino acid bio-synthetic genes.<ref>PMID:3464968</ref> Its primary function is to act as one of the main response factors for amino acid starvation by initiating transcription, however the exact mechanism of initiation is still being debated (see Binding with DNA). | ||
GCN4 is known as a bZip protein after its basic region and leucine zipper domains. The first 'leucine zipper' model was coined by Landshulz et al. in 1988 after their initial X-Ray crystallography structure was solved. Today, while the name has stayed the same, we no longer view the leucine binding region in an inter-collated manner like the teeth of a zipper, 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 orange. A close up of the leucine-leucine pairing can be seen <scene name='Tom_Sandbox/Leu-leu_interaction/ | GCN4 is known as a bZip protein after its basic region and leucine zipper domains. The first 'leucine zipper' model was coined by Landshulz et al. in 1988 after their initial X-Ray crystallography structure was solved. Today, while the name has stayed the same, we no longer view the leucine binding region in an inter-collated manner like the teeth of a zipper, 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 orange. A close up of the leucine-leucine pairing can be seen <scene name='Tom_Sandbox/Leu-leu_interaction/2'>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> | ||
===Hydrophobic Stability=== | ===Hydrophobic Stability=== | ||
GCN4 is composed of two identical 58 residue alpha helix chains that grouped together to form a parallel coiled-coil dimer. Roughly 33 of the 58 total residues are located in the Leucine Zipper region. The dimer binds through interlocking leucine amino acids and <scene name='Tom_Sandbox/Hydrophobic_and_philic_regions/ | GCN4 is composed of two identical 58 residue alpha helix chains that grouped together to form a parallel coiled-coil dimer. Roughly 33 of the 58 total residues are located in the Leucine Zipper region. The dimer binds through interlocking leucine amino acids and <scene name='Tom_Sandbox/Hydrophobic_and_philic_regions/3'>hydrophobic residues</scene> near the C terminus, while pinching in on the major groove of DNA in the N terminal end via basic residues. The aforementioned image shows how the hydrophobic regions are between the helices, while the hydrophobic regions protrude outwards. | ||
{{STRUCTURE_1ysa| PDB=1ysa | SCENE= }} | {{STRUCTURE_1ysa| PDB=1ysa | SCENE= }} | ||
===Zipper and Binding Domains=== | ===Zipper and Binding Domains=== | ||
The two main domains are labeled the <scene name='Tom_Sandbox/Acidic_and_basic_regions/ | The two main domains are labeled the <scene name='Tom_Sandbox/Acidic_and_basic_regions/2'>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 in red and the basic region in blue. 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 in a scissor-like manner, making contact with both the <scene name='Tom_Sandbox/Binding_with_dna/3'>phosphate backbone</scene> and the <scene name='Tom_Sandbox/Binding_with_dna/4'>nucleotide bases</scene> of DNA. | ||
===Binding with DNA=== | ===Binding with DNA=== | ||
The basic region binding domain of GCN4 inserts itself into the <scene name='Tom_Sandbox/Major_groove/2'>major groove</scene> of the DNA. This causes a bend in both the AP-1 and ATF/CREB binding sites of DNA<ref name="bind">PMID:15459288</ref>. AP-1 refers to a group of activator proteins that bind to the same 9 residue semi-palindromic region for transcription activation. ATF/CREB refers to a fully palindromic region. The AP-1 site sequence is 5′-ATGACTCAT-3′, and the ATF/CREB site is 5′-ATGACGTCAT-3′<ref> Hockings, S. C.; Kahn, J. D.; Crothers, D. M. PNAS February 17, 1998 vol. 95 no. 4 1410-1415 </ref>. The bending mechanism was determined by adding fluorophores to the ends of U shaped manufactured DNA segments with the specific binding sites AP-1 or ATF/CREB inserted into the center. The shift in the fluorophore positioning showed the effect of bending on the DNA due to GCN4 binding. In total, in the complex with GCN4-bZIP, the ATF/CREB site is bent by (25 ± 2)° and the AP-1 site by (20 ± 2)° toward the minor groove.<ref name="bind"/> This is thought to be the mechanism for inducing transcription, however the actual bending of DNA is still debated.<ref>DOI: 10.1021/bi970215u</ref> | The basic region binding domain of GCN4 inserts itself into the <scene name='Tom_Sandbox/Major_groove/2'>major groove</scene> of the DNA. This causes a bend in both the AP-1 and ATF/CREB binding sites of DNA<ref name="bind">PMID:15459288</ref>. AP-1 refers to a group of activator proteins that bind to the same 9 residue semi-palindromic region for transcription activation. ATF/CREB refers to a fully palindromic region. The AP-1 site sequence is 5′-ATGACTCAT-3′, and the ATF/CREB site is 5′-ATGACGTCAT-3′<ref> Hockings, S. C.; Kahn, J. D.; Crothers, D. M. PNAS February 17, 1998 vol. 95 no. 4 1410-1415 </ref>. The bending mechanism was determined by adding fluorophores to the ends of U shaped manufactured DNA segments with the specific binding sites AP-1 or ATF/CREB inserted into the center. The shift in the fluorophore positioning showed the effect of bending on the DNA due to GCN4 binding. In total, in the complex with GCN4-bZIP, the ATF/CREB site is bent by (25 ± 2)° and the AP-1 site by (20 ± 2)° toward the minor groove.<ref name="bind"/> This is thought to be the mechanism for inducing transcription, however the actual bending of DNA is still debated.<ref>DOI: 10.1021/bi970215u</ref><ref>DOI: 10.1021/bi990053x</ref> | ||
===Heptad Repeat=== | ===Heptad Repeat=== | ||
| Line 51: | Line 51: | ||
[[2zta]] | [[2zta]] | ||
[[1ysa]] | [[1ysa]] | ||
<ref>DOI:10.1016</ref> | |||
==Reference== | ==Reference== | ||
<references/> | <references/> | ||
