User:Christina Manner/Sandbox 810

From Proteopedia

Revision as of 21:51, 7 January 2014

Description

Shown is bound to its autoinducer 3-oxooctanoyl-homoserine lactone (OOHL) ^[1] and .

Hallo:^[2]

TraR is a quorum sensing protein in Agrobacterium tumefaciens. Shown is TraR bound to its autoinducer 3-oxooctanoyl-homoserine lactone (OOHL) ^[1], also called Agrobacterium autoinducer (AAI) [4], and its target DNA. Quorum sensing is used by bacteria to regulate gene expression depending on cell-population density ^[3]. Therefore, Bacteria use small hormone-like proteins called autoinducers ^[4]. These autoinducers increase in concentration in connection to increasing cell density ^[3]. Reaching a minimal threshold stimulatory concentration, the autoinducers activate gene regulation processes ^[3]. This quorum sensing becomes beneficial as soon as it is performed by many cells ^[4]. Quorum sensing is used by Gram-negative as well as Gram-positive bacteria and occurs within and between bacterial species ^[3]. The communication via quorum sensing may have been a first step of multi-cellularity and makes the distinction between eukaryotes and prokaryotes more complex ^{[3] [4]}.

TraR is member of the quorum-sensing transcription factor family called LuxR including the Helix-Turn-Helix motif, that is typical for transcription factors (?) [5]. In presence of its autoinducer AAI, TraR regulates genes connected to the tumor inducing (Ti) plasmid ^[1]. When a certain cell density of Agrobacterium tumefaciens is reached, the transfer of the Ti-plasmid is induced. [5] There are two proteins that influence this transfer: TraR and TraI. The TraI gene encodes AAI. The absence of AAI causes rapid proteolysis of TraR ^[1] , which implies, that AAI protects TraR from degradation [4]. TraR itself activates …

Structure

General Structure In general TraR works as a dimer, consisting of two different monomers. Each TraR monomer consists of 234 amino acids. In this structure, two TraR dimers binding the tra box are shown. A and C are the same molecule, while B is the same protein as D. Each monomer possesses its own ligand binding domain as well as a DNA binding domain. Thus, all in all four autoinducer molecules are bound to the TraR proteins at one tra box.

The dimers AB and CD interact with each other via molecular interactions between B and C. Additionally, the palindromic sequence of the tra box causes a base stacking between the beginning and the end of the sequence. 

As A and B are slightly different, there is an dimeric asymmetry that has two consequences for the function. At first, the N-terminal parts of the two monomers have different positions. The N-terminal part of A is between the ligand-binding domain and the DNA-binding domain in the center of the protein. In opposition to that, the N-terminal part of B is located externally. Moreover, there is a distribution of charge at the surface of the dimer. Because of that, the DNA-binding domain forms a long and basic region for the interaction with DNA, whereas the C-terminal residues form a positively charged patch exposed to the solvent. This region might be involved in protein-protein interaction (TraM?).

N-ter Region : Ligand binding secondary: N-ter dimer: linker: Dimer:

Ligand: Ligand Binding Site: neg charge dna binding

References

1. ↑ ^{1.0 1.1 1.2 1.3} Chai Y, Winsans SC (2005): Amino-terminal protein fusions to the TraR quorum-sensing transcription factor enhance protein stability and autoinducer-independent activity. In: J. Bacteriol. 187(4); 1219-26;
2. ↑ my mind
3. ↑ ^{3.0 3.1 3.2 3.3 3.4} Miller M.B., Bassler C. L. (2001): Quorum Sensing in Bacteria. In: Annu. Rev. Microbiol.; 55; 165-199
4. ↑ ^{4.0 4.1 4.2} Waters C. M., Bassler C. L. (2005): Quorum Sensing: Cell-to-Cell Communication in Bacteria. In: Annu. Rev. Cell Biol.; 21; 319-346