Regulation of signaling directionality revealed by 3D snapshots of a kinase:regulator complex in action

Abstract

Two-component systems (TCS) are protein machineries that enable cells to respond to input signals. Histidine kinases (HK) are the sensory component, transferring information toward downstream response regulators (RR). HKs transfer phosphoryl groups to their specific RRs, but also dephosphorylate them, overall ensuring proper signaling. The mechanisms by which HKs discriminate between such disparate directions, are yet unknown. We now disclose crystal structures of the HK:RR complex DesK:DesR from Bacillus subtilis, comprising snapshots of the phosphotransfer and the dephosphorylation reactions. The HK dictates the reactional outcome through conformational rearrangements that include the reactive histidine. The phosphotransfer center is asymmetric, poised for dissociative nucleophilic substitution. The structural bases of HK phosphatase/phosphotransferase control are uncovered, and the unexpected discovery of a dissociative reactional center, sheds light on the evolution of TCS phosphotransfer reversibility. Our findings should be applicable to a broad range of signaling systems and instrumental in synthetic TCS rewiring.DOI: http://dx.doi.org/10.7554/eLife.21422.001

Signal transduction in photoreceptor histidine kinases

“…The arrows denote the helical rearrangements that interconvert the K and P states. The molecular graphics are based on the structures of DesK in its autophosphorylated and phosphatase states, respectively (PDB 5IUM and 5IUN)…”

“…Atomically resolved information on the linker and its signal‐induced conformational changes is scarce because the vast majority of structural data have been obtained on SHK fragments that entirely lack the linker. Even where resolved in the structure, the linker is often compromised by truncation of the sensor or effector modules, potentially causing fraying of the linker termini . In addition, the assignment of a given truncated structure to a specific functional state of the SHK can be challenging, thus further complicating the analysis.…”

“…The structural data are best developed for DesK, and hence the following discussion will be primarily based on this SHK. For an authoritative description of these processes in DesK, the reader is referred to Figure of Trajtenberg et al Independent of the functional state, the DHp domain consists of two long helices, denoted α1 and α2, that within the homodimeric receptor form an antiparallel heterotetrameric coiled coil of the type . The helices α1 and α2 are connected by short hairpin loops in right‐handed or left‐handed topology .…”

Non‐canonical activation of histidine kinase KdpD by phosphotransferase protein PtsN through interaction with the transmitter domain

“…The bound ATP and the histidine are in phosphotransfer distance in only one of the two subunits leading to accumulation of hemi‐phosphorylated kinase dimers. This arrangement leaves only one binding site available for the response regulator, resulting in a 2:1 stoichiometry of the histidine kinase/response regulator complex (Trajtenberg et al ., ). The same stoichiometry is also observed here, supporting our model of a kinase‐competent ternary PtsN/KdpD 2 /KdpE complex.…”

Transmembrane Signal Transduction in Two‐Component Systems: Piston, Scissoring, or Helical Rotation?

“…Equally useful to the analysis of the output signals of periplasmic sensor domains is the analysis of the input signals of cytoplasmic TCS receptor domains, for which many atomistic structures in different signaling states are available, reviewed recently in Refs [14] and [17]. The major common theme in the signal transduction to KC, DHp, and CA domains is symmetry‐asymmetry transitions and stabilization‐destabilization of α‐helical linkers caused by helical rotations .…”