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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=== | ||
Revision as of 17:24, 10 November 2011
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| 2zta, resolution 1.80Å () | |||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
GCN4 - The Leucine ZipperGCN4 - The Leucine Zipper
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 [1]. (see heptad repeat section) the Leucines are represented as red and the Valines are shown as oragne. A close up of the leucine-leucine pairing can be seen .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.[2]
StructureStructure
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 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.
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| 1ysa, resolution 2.90Å () | |||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
These two main domains are labeled the . [3] 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[4]. 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 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 DNABinding with DNA
The basic region binding domain of GCN4 inserts itself into the of the DNA. This causes a shift in bothe the AP-1 and ATF/CREB binding sites of DNA[5]. This was determined by adding fluorophores to the end of U shaped DNA segments with the specific binding sites in the centers. The shift in their positioning showed the effect of bending on the DNA. 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.[5] AP-1 refers to a group of activator proteins that bind to the same 9 base pair semi-palindromic region for transcription activation. ATF/CREB refers to a fully palendromic region. The AP-1 site sequence is 5′-ATGACTCAT-3′, and the ATF/CREB site is 5′-ATGACGTCAT-3′[6].
Heptad RepeatHeptad Repeat
GCN4 is said to have a heptad repeat, or seven unit repeated sequence. Here the heptad repeat is a leucine, every seven units. When the structure of the alpha helices is taken into account, it is clear that each leucine is being stacked on top of the last one, every seven units. This creates the zipper-like repeated projections from the two polypeptide chains. Below we see a pictorial representation of the sequence of amino acids as we look down the length of the coiled coil structure.
Image 1:A pictorial representation of the heptad repeat between the two subunits in a coiled-coil conformation. By following through the wheels alphabetically, it is clear how the leucines will stack every 7 units. The apostrophe denotes the diference between the two polypeptide subunits.(from Kgutwin in Wikipedia Commons http://commons.wikimedia.org/wiki/File:Coiledcoil-wheelcartoon.gif)
At every d and d' we have a Leucine, while at the a and a' locations we typically see valine. [4] In the opposite positions one tends to see more charged and polar residues. The Leucine and Valine repeats create a strongly hydrophobic region between the two alpha helices. This clearly shows the relationship between coils and shown below, we can see that for the two helices to be symmetrical, the Leucines must not in fact be oriented as a zipper, but on the same levels.
Image 2: The figure above comes from the paper - Secondary Structure of a Leucine Zipper Determined by NMR.[1] The caption was left for clarification.
The Leucine Zipper Nano-TweezerThe Leucine Zipper Nano-Tweezer
The X-ray structure of the 33-residue polypeptide corresponding to the leucine zipper of GCN4 was determined by Peter Kim and Thomas Alber in 1991[7]. As stated above, the leucines themselves come on every other level of the alpha helix and do not actually interchange one over the other like a zipper, but instead make side to side contact. This was noted in 1990 due to the symmetric nature of the two subunits. If the leucines showed interdigitation the subunits would be asymmetric [1].
The Leucine Zipper of GCN4, as expected of a protein, operates under a specific pH. It has been shown that at lower pH values the zipper will reversibly protenate and open up. This occurs because it loses its hydrophobic stability, protenating its polypeptide chains. Researchers are looking into this opening and closing reaction to be used purposefully as a form of nano-tweezers to grab onto and hold very-very small particles. [3] A diagram of this mechanism is shown below.
Image 3: A schematic representation of the Leucine Zipper acting as nano-tweezers under different pH conditions[3].
See AlsoSee Also
ReferenceReference
- ↑ 1.0 1.1 1.2 Oas, T. G.; McIntosh, L. P.; O'Shea, E. K.; Dahlquist, F. W.; and Kim, P. S. Biochemistry 1990 29 (12), 2891-2894
- ↑ Hope, I. A.; Struhl,K. Cell, Volume 46, Issue 6, 12 September 1986, Pages 885-894
- ↑ 3.0 3.1 3.2 Sharma, G.; Rege, K.; Budil, D. E.; Yarmush, M. L.; Mavroidis, C. Int J Nanomedicine. 2008 December; 3(4): 505–521.
- ↑ 4.0 4.1 Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008.
- ↑ 5.0 5.1 Dragan AI, Liu Y, Makeyeva EN, Privalov PL. DNA-binding domain of GCN4 induces bending of both the ATF/CREB and AP-1 binding sites of DNA. Nucleic Acids Res. 2004 Sep 30;32(17):5192-7. Print 2004. PMID:15459288 doi:10.1093/nar/gkh854
- ↑ Hockings, S. C.; Kahn, J. D.; Crothers, D. M. PNAS February 17, 1998 vol. 95 no. 4 1410-1415
- ↑ O'Shea EK, Klemm JD, Kim PS, Alber T. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science. 1991 Oct 25;254(5031):539-44. PMID:1948029