Sandbox Reserved 1251
From Proteopedia
Contents |
genetics is ok
'Molecules it Interacts With and where '
The protein binds to GDP as well as the following ligands in order to promote the attachment of the protein complex to the ribosome A site.
PHOSHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
PHENYLALANINE
MAGNESIUM ION
'Origin'
It has domains that are created in yeast (phenyl-transfer RNA) , in the heat resistant Thermus aquaticus (EF-Tu elongation factor, and can be synthetically manufactured.
'Structure'
It has 3 domains. G proteins, Elongation Factors, and the EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain. It is composed of 6 chains, which combine in alignment.
Specific are highlighted here. The ligands listed above, GDP, Phe, and Mg+2 ion each attach at these locations which are still being explored.
which play a crucial role in binding to the ribosome during translation. They form positive pockets with which negative amino acids can bind to.
'Molecules it Interacts With and where '
The protein binds to GDP as well as the following ligands in order to promote the attachment of the protein complex to the ribosome A site.
PHOSHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
PHENYLALANINE
MAGNESIUM ION
'Origin'
It has domains that are created in yeast (phenyl-transfer RNA) , in the heat resistant Thermus aquaticus (EF-Tu elongation factor, and can be synthetically manufactured.
'Structure'
It has 3 domains. G proteins, Elongation Factors, and the EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain. It is composed of 6 chains, which combine in alignment.
Specific are highlighted here.
which play a crucial role in binding to the ribosome during translation.
'Function"
The protein complex participates in placing the amino acids in their correct order when messenger RNA is translated into a protein sequence on the ribosome by promoting GTP-dependent binding of tRNA to the A site of the ribosome. In other words, it is involved with elongation during polypeptide synthesis.
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GAL4
Origin
The GAL4 Protein is found mostly in Yeast cells, but have also been known to be in some Drosphilia and human cells. It is located in the nucleus of cells that create GAL4.
Function
Gal4 is a Zn2Cys6 binuclear cluster that has the transcription factor that binds DNA as a homodimer and interacts with the mutant Gal11P protein to activate transcription.GAL4 is typically a yeast protein but it can also work as a transcription activator in Drosophila and some human cells, showing that the same mechanisms for gene expression have been conserved over the course of evolution. GAL4 has a DNA-binding domain and an activation domain.
GAL4 binds to CGG-N11-CCG, which is upstream of the sequence, on a DNA strand, where N can be any base. This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose.
Gal11 is part of the RNA polymerase holoenzyme and normally does not interact with the dimerization domain of Gal4. However, a single mutation in Gal11 converts it into a transcriptional potentiator (called Gal11P) that interacts directly with the dimerization domain of Gal4.
Overall, GAL4 is involved indirectly and directly in the biological processes of Carbohydrate metabolism, Galactose metabolism, Transcription, and Transcription regulation. It has ligands that bind to metal, especially Zinc.
Relevance
The GAL4 dimerization domain is a powerful transcriptional activator when tethered to DNA in a cell bearing a mutant of the GAL11 protein and interacts with the RNA–polymerase II holoenzyme. Thus, GAL4 plays a part in the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA.
Structure
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GAL4 has an elongated dimer structure with C2 symmetry and has three alpha helices that mediate dimerization via coiled-coil contacts.The two loops between the three coiled coils form mobile bulges causing a variation of twist angles between the helix pairs. When a GAL11P monomer binds to a GAL4 dimer, the GAL4 dimer becomes asymmetric. GAL4 consists of a DNA-binding domain and an activation domain. The binding domain binds to the DNA while the activation domain can interact with other molecules, mainly transcription factors and proteins. In Gal4, the interactions between the helical bundle and the coiled-coil region effect DNA binding, protein stability and interaction with other transcription factors such as Gal11P.
Structural highlights
The and the combine to form the DNA binding region.The dimerization domain makes up the first helix and has a typical coiled coil structure. The DNA recognition elements form the other two helices and fold back in antiparallel fashions to form helical bundles. The on the helical bundles provide binding sites.
There are several apolar residues that participate in the interactions between GAL4 and DNA. The accumulation of these interactions works to create a hydrophobic core in the center of the helical bundle. This greatly stabilizes the GAL4 dimer interface. Beyond the hydrophobic core, there are two hydrogen bonds made by the side chain with the backbone oxygen atoms. These hydrogen bonds assist in the positioning of the α2 helix in order to encourage more optimal van der Waals interactions. The of GAL4 are highly acidic and can be replaced by a short peptide designed to form a negatively charged, amphipathic alpha-helix.
References
https://en.wikipedia.org/wiki/GAL4/UAS_system
http://genesdev.cshlp.org/content/15/8/1007.full.pdf
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2515386/ https://www.ncbi.nlm.nih.gov/pubmed/?term=1557122 https://www.ncbi.nlm.nih.gov/pubmed/3128741/
