Analysis of periplasmic sensor domains from Anaeromyxobacter dehalogenans 2CP-C: structure of one sensor domain from a histidine kinase and another from a chemotaxis protein

Abstract

Anaeromyxobacter dehalogenans is a δ-proteobacterium found in diverse soils and sediments. It is of interest in bioremediation efforts due to its dechlorination and metal-reducing capabilities. To gain an understanding on A. dehalogenans' abilities to adapt to diverse environments we analyzed its signal transduction proteins. The A. dehalogenans genome codes for a large number of sensor histidine kinases (HK) and methyl-accepting chemotaxis proteins (MCP); among these 23 HK and 11 MCP proteins have a sensor domain in the periplasm. These proteins most likely contribute to adaptation to the organism's surroundings. We predicted their three-dimensional folds and determined the structures of two of the periplasmic sensor domains by X-ray diffraction. Most of the domains are predicted to have either PAS-like or helical bundle structures, with two predicted to have solute-binding protein fold, and another predicted to have a 6-phosphogluconolactonase like fold. Atomic structures of two sensor domains confirmed the respective fold predictions. The Adeh_2942 sensor (HK) was found to have a helical bundle structure, and the Adeh_3718 sensor (MCP) has a PAS-like structure. Interestingly, the Adeh_3718 sensor has an acetate moiety bound in a binding site typical for PAS-like domains. Future work is needed to determine whether Adeh_3718 is involved in acetate sensing by A. dehalogenans.

Keywords: Acetate; PAS-like; chemotaxis; helical bundle; periplasmic sensor domains; sensor histidine kinase.

Figure 1

Schematic drawing of a typical transmembrane signal transduction protein in a cell. The cytoplasmic output domains are shown in different colors and shapes to indicate that they vary depending upon the nature of the signal transduction protein (HK or MCP).

Figure 2

A cartoon representation of the structure of Adeh_2942 sensor domain. A head-to-tail dimer structure is observed in the crystals. The Cα tracing of monomer A is shown in green and that of monomer B is shown in cyan. The helices of monomer A are labeled.

Figure 3

(A) A cartoon representation of the overall structure of Adeh_3718 sensor domain. Note the acetate ion bound in a typical binding site similar to binding of small molecules observed in various other PAS-like domains. (B) A close up view of the acetate-binding site as observed in the crystal structure of Adeh_3718 sensor domain.

Figure 4

A Pie chart representation of the tertiary folds predicted (results from Table 1) for the periplasmic sensor domains of A. dehalogenans 2CP-C.

Figure 5

Cartoon representation of helical bundles formed by the monomer of Adeh_2942 sensor and that of Tar are shown. The aspartic acid binding site in Tar is indicated by an arrow. Please note the significant deviation from helical geometry at the binding site in the helix α₄ in Tar. Adeh_2942 is shown in cyan and Tar in pink. The two structures were overlapped by the SSM routine in Coot (Emsley et al. 2010).

Figure 6

An overlap of the Adeh_3718 sensor domain with bound acetate and the sensor domain of TlpB complexed with acetamide (PDB code, 3ub7) is shown. The two structures were overlapped with SSM routine in Coot. Adeh_3718 sensor is shown in cyan and TlpB sensor in pink. The bound small molecules acetate and acetamide are shown in ball-stick representation with atom type colors (carbon: green, oxygen: red, nitrogen: blue). Note the similarity of the two structures and the binding sites. The TlpB sensor has an additional helix at the C-terminus (residues 188–201) that is not present in Adeh_3718 sensor; this helix is not shown in the figure for clarity purposes.