Mechanism of transmembrane signaling by sensor histidine kinases

Abstract

One of the major and essential classes of transmembrane (TM) receptors, present in all domains of life, is sensor histidine kinases, parts of two-component signaling systems (TCSs). The structural mechanisms of TM signaling by these sensors are poorly understood. We present crystal structures of the periplasmic sensor domain, the TM domain, and the cytoplasmic HAMP domain of the nitrate/nitrite sensor histidine kinase NarQ in the ligand-bound and mutated ligand-free states. The structures reveal that the ligand binding induces rearrangements and pistonlike shifts of TM helices. The HAMP domain protomers undergo leverlike motions and convert these pistonlike motions into helical rotations. Our findings provide the structural framework for complete understanding of TM TCS signaling and for development of antimicrobial treatments targeting TCSs.

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

“…In fact, mixing of different motions is almost guaranteed, because α‐helices are not ideal gears, and the protein backbones, being restricted to energetically allowed conformations, are not fully flexible joints. Second, and very important, is that (as we discuss below) the TM α‐helices are far from being rigid: helical elements are interspersed with flexible (proline, glycine, or other) joints . Thus, the amount of the available conformational changes is much greater than presented in Figure , and the TM bundle is in fact a series of subdomains passing the signal downstream.…”

“…Analysis of crystallographic structures of all‐α sensor domain of Salmonella typhimurium aspartate chemoreceptor Tar revealed piston‐like displacement of one of the output helices . Piston‐like motion, accompanied by helical rotations, were also identified later in α‐helical sensors of histidine kinases NarQ, NarX, and TorS; the latter binds its ligand via an accessory protein (TorT) . Contractions, which could cause piston‐like motions, were observed in single Cache sensor of histidine kinase CitA or double Cache sensor of Campylobacter jejuni chemoreceptor Tlp3 …”

“…The full‐length proteins are usually too large to be studied using NMR, too small for conventional electron microscopy (which however may change soon), and too dynamic for X‐ray crystallography. Still, NMR was used to study fragments of HKs, such as transmembrane regions; electron microscopy was used to reveal the low resolution structure and conformational changes in chemoreceptor arrays; and X‐ray crystallography was used to obtain many static structures of truncated fragments of increasing length, including some with transmembrane domains . Full‐length crystallographic structure of an engineered soluble histidine kinase has also been determined .…”

“…However, the results of crystallization are sometimes ambiguous: For example, many sensor domains are crystallized as monomers or as unphysiological dimers . Even physiological dimers may be affected by unphysiological contacts within a crystal . Also, when the proteins are truncated for structural studies, they can adopt unusual, sometimes partially unfolded or disordered conformations.…”

“…Then, structures of truncated monomeric transmembrane regions of three HKs, ArcB, QseC, and KdpD, have been determined using NMR . Finally, crystallographic apo and holo state structures of a NarQ fragment, comprising the periplasmic sensor domain, TM domain and HAMP domain, have been determined recently . All of the crystallographic structures were obtained using crystals grown from lipidic mesophases, where proteins reside in native membrane‐like conditions .…”