Chemoreceptor-based signaling is a central mechanism in bacterial signal transduction. Receptors are classified according to the size of their ligand-binding region. The well-studied cluster I proteins have a 100-to 150-residue ligand-binding region that contains a single site for chemoattractant recognition. Cluster II receptors, which contain a 220-to 300-residue ligand-binding region and which are almost as abundant as cluster I receptors, remain largely uncharacterized. Here, we report high-resolution structures of the ligand-binding region of the cluster II McpS chemotaxis receptor (McpS-LBR) of Pseudomonas putida KT2440 in complex with different chemoattractants. The structure of McpS-LBR represents a small-molecule binding domain composed of two modules, each able to bind different signal molecules. Malate and succinate were found to bind to the membrane-proximal module, whereas acetate binds to the membrane-distal module. A structural alignment of the two modules revealed that the ligand-binding sites could be superimposed and that amino acids involved in ligand recognition are conserved in both binding sites. Ligand binding to both modules was shown to trigger chemotactic responses. Further analysis showed that McpS-like receptors were found in different classes of proteobacteria, indicating that this mode of response to different carbon sources may be universally distributed. The physiological relevance of the McpS architecture may lie in its capacity to respond with high sensitivity to the preferred carbon sources malate and succinate and, at the same time, mediate lower sensitivity responses to the less preferred but very abundant carbon source acetate.sensor domain | four-helix bundle T he ability to sense and respond to extracellular signals is of crucial importance for microorganisms. Bacteria have several types of signal-transduction systems that sense environmental signals and trigger a corresponding response. Genome analyses indicate a dominant role for one-component systems, two-component systems, and chemoreceptor-based mechanisms in bacterial signal transduction (1, 2).Chemoreceptors have been initially described in the context of chemotactic signaling. However, more recent studies reveal that chemoreceptors are also involved in the regulation of different cellular processes, such as the synthesis of second messengers (3) or the control of gene expression during development (4). Typically, chemoreceptors are composed of a ligand-binding region (LBR) and a signaling domain. Signal recognition by the LBR creates a molecular stimulus that is conveyed to the signaling domain, which forms a complex with CheA and CheW. This molecular stimulus modulates CheA autophosphorylation and, subsequently, transphosphorylation toward the response regulator (5).The enterobacterial chemoreceptors, and in particular Tar and Tsr, have been studied extensively (5, 6). The Tar-LBR forms a four-helix bundle structure (7), and there are two mechanisms by which Tar-LBR recognizes chemoattractants. One mode consists o...