Insight into the sporulation phosphorelay: Crystal structure of the sensor domain of Bacillus subtilis histidine kinase, KinD

Abstract

The Bacillus subtilis KinD signal-transducing histidine kinase is a part of the sporulation phosphorelay known to regulate important developmental decisions such as sporulation and biofilm formation. We have determined crystal structures of the extracytoplasmic sensing domain of KinD, which was copurified and crystallized with a pyruvate ligand. The structure of a ligandbinding site mutant was also determined; it was copurified and crystallized with an acetate ligand. The structure of the KinD extracytoplasmic segment is similar to that of several other sensing domains of signal transduction proteins and is composed of tandem Per-Arnt-Sim (PAS)-like domains. The KinD ligand-binding site is located on the membrane distal PAS-like domain and appears to be highly selective; a single mutation, R131A, abolishes pyruvate binding and the mutant binds acetate instead. Differential scanning fluorimetry, using a variety of monocarboxylic and dicarboxylic acids, identified pyruvate, propionate, and butyrate but not lactate, acetate, or malate as KinD ligands. A recent report found that malate induces biofilm formation in a KinDdependent manner. It was suggested that malate might induce a metabolic shift and increased secretion of the KinD ligand of unknown identity. The structure and binding assays now suggests that this ligand is pyruvate and/or other small monocarboxylic acids. In summary, this study gives a first insight into the identity of a molecular ligand for one of the five phosphorelay kinases of B. subtilis.

Crystal structure and redox properties of a novel cyanobacterial heme protein with a His/Cys heme axial ligation and a Per-Arnt-Sim (PAS)-like domain

“…Previous studies have suggested that the sensor domain of KinD has an extra ligand between the ␣-helix and ␤-strands, and the ligand binding site may accommodate small molecules related to metabolism such as pyruvate or propionate (48). In the electron density map of Tll0287, we indeed found an extra density at the similar position between the ␣-helix and ␤-strands (Fig.…”

“…The results (supplemental Table S1) showed that the structure of Tll0287 is similar to that of a sensor domain contained in some kinases or sensor proteins possibly involved in cellular signal transduction, such as the sporulation kinase d domain from Bacillus subtilis (KinD, PDB code 4JGO) (48) (Fig. 6b) and a methyl-accepting chemotaxis protein (Mcp, PDB code 3C8C) (Fig.…”

“…The colors for the Tll0287 protein and its heme are green and red, respectively, and those for the PsbV2 protein are as follows: heme, yellow; others, orange. b, superposition of Tll0287 and the sporulation kinase D sensor domain from B. subtilis (blue, A chain of PDB code 4JGO; pink, the ligand of this protein, pyruvate) (48). c, superimposition of Tll0287 and a methyl-accepting chemotaxis protein (Mcp) (purple, A chain of PDB code 3C8C; cyan, the ligand of this protein, alanine).…”

Sensor Domain of Histidine Kinase KinB of Pseudomonas

“…The impact of signal molecule binding on the structure and stability of the SD has been rarely studied (23). To produce a conformational change, the binding of a signal molecule may induce the formation of an energetically favorable SD dimer or stabilize a weak SD dimer.…”

“…A PASlike (16) or "PDC" fold (17) is represented by the structures of PhoQ (17,18), DcuS (19), and CitA (16). The double PAS-like domain has also been observed in LuxQ (20), DctB (21,22), and in recently reported KinD (23). PAS-like SDs are believed to serve as ligand recognition units in extracytoplasmic signal transduction proteins (24).…”