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From Proteopedia

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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.

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 regulatory protein with 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. GAL4 is typically a yeast protein, 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. 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.

The GAL4 activator interacts directly with the SRB4 subunit of the RNA polymerase II holoenzyme. The GAL4 activation domain binds to two essential segments of SRB4 on the RNA polymerase II holoenzyme. It also binds to the GAL11 protein which may serve to expedite the phosphorylation of GAL4. Thus, GAL4 takes part in the biological processes of Carbohydrate metabolism, Galactose metabolism, Transcription, and Transcription regulation. It has ligands that bind to metal, especially Zinc.

We find that Gal4 dimerization on DNA is mediated by an intertwined helical bundle that deviates significantly from the solution NMR structure of the free dimerization.

GAL4 has an elongated dimer structure with C2 symmetry containing three 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. One GAL11P monomer binds to one GAL4-dd dimer rendering the dimer asymmetric and implying an extreme negative cooperativity mechanism. Alanine-scanning mutagenesis of GAL4-dd showed that the NMR-derived GAL11P-binding face is crucial for the novel transcriptional activating function of the GAL4-dd on GAL11P interaction.The binding of GAL4 to GAL11P, although an artificial interaction, represents a unique structural motif for an activating region capable of binding to a single target to effect gene expression.

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. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes. It functions as an activator and a DNA-binding protein.

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

GAL4 is a specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator. This protein binds as a dimer to a symmetrical 17 base-pair sequence. A small domain within this protein containing zinc recognizes a conserved CCG triplet at each end of the site through direct contact with the major groove. A short coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The complex's open structure allows for another protein to bind coordinately with GAL4.

Structural highlights

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/