Chapter 1 : Two-Component Systems

Two commonly encountered organizational schemes of two-component signaling modules. (A) The “paradigmatic” two-component system that undergoes phosphotransfer from the sensor kinase protein to the response regulator protein is pictured. (B) A “hybrid” or “unorthodox” sensor kinase, which participates in a phosphorelay mechanism, involves two additional modules but ultimately leads to the same result, phosphorylation of the receiver domain of the response regulator. Symbols: TM, transmembrane region; H, catalytic histidine; D, catalytic aspartic acid; P, phosphate. The path of phosphate transfer is shown by curved arrows. Rectangles represent conserved domains, and ellipses represent divergent domains. The extents of different domains that are discussed in the text are delineated below each example. The vertical gray bar represents the inner membrane of gram-negative organisms or the cytoplasmic membrane of gram-positive organisms. Nomenclature for the proteins and modules of two-component systems continues to evolve. The nomenclature presented here is used throughout this chapter.

Highly conserved residues among the conserved domains of twocomponent systems. For the histidine kinase, these residues are represented by the H, N, G1, F, and G2 boxes indicated, with consensus sequences shown. For the receiver domain, important residues are shown, numbered as for the CheY protein of E. coli. The actual residue numbers of different receiver domains vary slightly, although the overall linear relationship is highly conserved. For positions where at least 70% of the sequences show the same residue, letters indicate that residue. For positions where 50% of aligned sequences have an amino acid of the same chemical family, symbols indicate that family. Positions with less than 50% conservation are indicated by black dots. Symbols: open circles, nonpolar (I, L, M, V); filled circles, polar (A, G, P, S, T); circles with plus signs, basic (H, K, R); circles with minus signs, acidic or amidic (D, E, N, Q). Residues directly participating in phosphotransfer are starred. Adapted from reference 6 with permission.

NMR solution structure of the dimeric core domain of EnvZ. The protein structure is depicted in ribbon format showing the four-helix bundle formed from two identical monomers. The catalytic histidine at position 243 is shown in ball-and-stick format. Based on structural coordinates deposited in the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB), as described in reference 10. (See Color Plates following p. 256.)

NMR solution structure of the catalytic kinase domain of EnvZ. The protein structure is depicted in ribbon format. The segments corresponding to the conserved N, G1, F, and G2 boxes are colored blue, and key residues from these are shown in ball-and-stick format. This structure was determined in the presence of the nonhydrolyzable ATP analog AMP-PNP, which is shown in green ball-and-stick format. Based on structural coordinates deposited in the RCSB PDB, as described in reference 8. (See Color Plates p. 256.)

CheY structure determined by X-ray crystallography. The structure of CheY is presented as representative of the common structure of receiver domains from many sources. The protein structure is shown in ribbon format, and the α-helical and β-strand segments are numbered. Key residues introduced in Fig. 2 are shown in blue ball-and-stick format. Two views are shown for clarity. Based on structural coordinates deposited in the RCSB PDB, as described in reference 7. (See Color Plates following p. 256.)

Structure of the monomeric HPt domain from the ArcB sensor kinase of E. coli determined by X-ray crystallography. Protein structure is shown in ribbon format, with the catalytic histidine at position 717 shown in blue ball-and-stick format. Based on structural coordinates deposited in the RCSB PDB, as described in reference 3. (See Color Plates following p. 256.)

Structure of Spo0B (A) and a complex between Spo0F and Spo0B (B) determined by X-ray crystallography. (A) The structure of a Spo0B dimer is presented as representative of the overall structure of histidine kinase domains. Protein structure is shown in ribbon format while catalytic histidines are shown in blue ball-and-stick format. Based on structural coordinates deposited in the RCSB PDB, as described in reference 11. (B) The structure of a complex between a Spo0B dimer and two cognate receiver domains of Spo0F. Based on structural coordinates deposited in the RCSB PDB, as described in reference 13. (See Color Plates p. 256.)