Engineered Socket Study of Signaling through a Four-Helix Bundle: Evidence for a Yin−Yang Mechanism in the Kinase Control Module of the Aspartate Receptor

Swain, Kalin; González, Miguel Ángel Conde; Falke, Joseph J.

doi:10.1021/bi901020d

Cited by 96 publications

(156 citation statements)

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“…signal output (47)(48)(49)(50)(51) to determine the structural basis of those emergent properties. The mechanism of signal transduction through a highly cooperative network of chemoreceptors and other chemotaxis proteins (2) continues to be a fascinating topic to explore.…”

Section: Resultsmentioning

confidence: 99%

Molecular architecture of chemoreceptor arrays revealed by cryoelectron tomography of Escherichia coli minicells

Li¹,

Morado

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

187

339

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The chemoreceptors of Escherichia coli localize to the cell poles and form a highly ordered array in concert with the CheA kinase and the CheW coupling factor. However, a high-resolution structure of the array has been lacking, and the molecular basis of array assembly has thus remained elusive. Here, we use cryoelectron tomography of flagellated E. coli minicells to derive a 3D map of the intact array. Docking of high-resolution structures into the 3D map provides a model of the core signaling complex, in which a CheA/CheW dimer bridges two adjacent receptor trimers via multiple hydrophobic interactions. A further, hitherto unknown, hydrophobic interaction between CheW and the homologous P5 domain of CheA in an adjacent core complex connects the complexes into an extended array. This architecture provides a structural basis for array formation and could explain the high sensitivity and cooperativity of chemotaxis signaling in E. coli.

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Section: Resultsmentioning

confidence: 99%

Molecular architecture of chemoreceptor arrays revealed by cryoelectron tomography of Escherichia coli minicells

Li¹,

Morado

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

187

339

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“…membrane (13). HAMP is then proposed to undergo a change in both structure and dynamics (7,14). Mutagenesis studies suggest that HAMP in kinase-off states is less dynamic than in kinase-on states (7,15,16).…”

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confidence: 99%

“…Dynamical changes in HAMP may be mirrored by dynamical changes in the KCM: mutations that destabilize packing in the PIR lock in kinase-on states, whereas destabilization of the adaptation region produces kinase-off states (17). Rates of disulfide cross-linking indicate that kinase-off mutations are, indeed, more dynamic (14,17). This socalled yin-yang model (14) represents the cytoplasmic regions of the receptor as two units-the adaptation and PIRs-that alternate their degree of conformational fluctuation depending on signaling state (14).…”

mentioning

confidence: 99%

“…Rates of disulfide cross-linking indicate that kinase-off mutations are, indeed, more dynamic (14,17). This socalled yin-yang model (14) represents the cytoplasmic regions of the receptor as two units-the adaptation and PIRs-that alternate their degree of conformational fluctuation depending on signaling state (14). Between these modules, a flexible bundle region facilitates conformational coupling (18).…”

mentioning

confidence: 99%

“…The HAMP AS2 helices may undergo a scissoropening motion when transitioning from kinase off to kinase on (14,19). Attractant-sensitive disulfide bond formation between CheA and receptor suggests that the N-terminal CD1 helices rotate in the PIR on ligand binding (20).…”

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confidence: 99%

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Bacterial chemoreceptor dynamics correlate with activity state and are coupled over long distances

Samanta

Borbat

Dzikovski

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Dynamics are hypothesized to play an important role in the transmission of signals across membranes by receptors. Bacterial chemoreceptors are long helical proteins that consist of a periplasmic ligand-binding domain; a transmembrane region; a cytoplasmic HAMP (histidine kinase, adenylyl cyclases, methyl-accepting chemotaxis proteins, and phosphatases) domain; and a kinase-control module (KCM). The KCM is further composed of adaptation, hinge, and protein interaction regions (PIRs), the latter of which binds the histidine kinase CheA and adaptor CheW. Fusions of the Escherichia coli aspartate receptor KCM to HAMP domains of defined structure (H1-Tar vs. H1-2-Tar) give opposite responses in phosphotransfer and cellular assays, despite similar binding to CheA and CheW. Pulsed dipolar ESR spectroscopy (PDS) of these isolated on and off dimeric effectors reveals that, in the kinase-on state, the HAMP is more conformationally destabilized compared with the PIR, whereas in the kinase-off state, the HAMP is more compact, and the PIR samples a greater breadth of conformations. On and off HAMP states produce different conformational effects at the KCM junction, but these differences decrease through the adaptation region and into the hinge only to return with the inverted relationship in the PIR. Continuous wave-ESR of the spin-labeled proteins confirms that broader PDS distance distributions correlate with increased rates of dynamics. Conformational breadth in the adaptation region changes with charge alterations caused by modification enzymes. Activating modifications broaden the HAMP conformational ensemble but correspondingly, compact the PIR. Thus, chemoreceptors behave as coupled units, in which dynamics in regions proximal and distal to the membrane change coherently but with opposite sign.chemotaxis | transmembrane signaling receptor | allostery | dynamics | adaptation T he ability of localized dynamics to modulate the function of transmembrane receptors is an emerging theme in signal transduction (1-4). These ideas have been largely supported by computational studies (2), although direct measurements also correlate dynamics with activity (1-4). Nonetheless, we are only beginning to address the link between conformational heterogeneity and signal propagation in complex proteins. Bacterial chemotaxis, the process by which cells modulate their motility in response to the chemical environment, provides an important model system to explore receptor dynamics experimentally (5, 6). During chemotaxis, attractant-bound chemoreceptors cause counterclockwise (CCW) flagella rotation and smooth swimming, whereas repellant-bound receptors cause clockwise flagella rotation and cell tumbling. Chemoreceptors, also termed methyl-accepting chemotaxis proteins, form extended arrays in the cytoplasmic membrane to communicate ligand binding (6) to the histidine kinase CheA and the coupling protein CheW. Great progress has been made in understanding how receptors communicate ligand-binding events across the cytoplasmic membrane, but h...

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Regulatory Systems: Two‐Component

Raivio

2019

Encyclopedia of Life Sciences

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Two‐component signal transduction (TCST) systems constitute a large class of regulatory proteins that function as signal transducers. Each system comprises a sensor or histidine kinase (HK) and an effector or response regulator (RR), which communicate through a conserved set of phosphotransfer reactions to effect adaptive changes in response to specific environmental signals. HKs and RRs are modular in nature, with variable sensory and output structures appended to the conserved domains that facilitate phosphotransfer mediated signal transduction. Input signals trigger successive conformational changes in domains and protein:protein interactions that alter phosphotransfer, and ultimately an output response mediated by the phosphorylated RR. TCST systems are abundant in bacteria and many microbes utilise multiple TCST pathways to sense and respond to a plethora of environmental and physiological changes. Specificity between cognate HKs and RRs is largely maintained through co‐evolving residues at a conserved interface where the RR docks on the HK. TCST systems are integrated into cellular signalling networks and interact with macromolecules and proteins that connect them to salient regulatory pathways and cellular functions. The current state of knowledge around TCST systems will be summarised, emphasising findings published since the first version of this article in 2006. Key Concepts A prototypical two‐component system is made up of a membrane‐bound sensory histidine kinase that senses a unique environmental or cellular parameter and a cytoplasmic response regulator that controls an adaptive response. HKs and RRs communicate through phosphotransfer reactions that are mediated by conserved domains; signal sensing alters the ratio of HK kinase to phosphatase activity to change the function of the RR by altering its phosphorylation status. HKs and RRs are organised in a modular fashion; a variety of sensing domains can be appended to the HK enzymatic module while diverse output domains with DNA binding, RNA binding, enzymatic activity or protein binding functions are often fused to the C‐terminal end of the response regulator phosphorylated receiver (REC) domain. The HK is a dimer containing a catalytic domain composed of two DHp and CA domains. The DHp domain consists of a d imer of two alpha helices connected by a flexible linker that makes a four‐helical bundle and contains the conserved h istidine that is the site of auto p hosphorylation. The CA domain resembles other ATP‐binding folds and is the enzymatic portion of the HK. The RR consists at its N‐terminus of the conserved receiver (REC) domain, which consists of a five‐stranded beta sheet surrounded by alpha helices and contains the conserved aspartate that is the site of phosphorylation. Signals are detected through conformational changes in a sensory domain that are propagated through some combination of rotational, piston and order to disorder transitions by alpha‐helical transduction elements to the cytoplasmic enzymatic domain of the HK. These movements lead to alterations in HK dimer symmetry that dictate kinase or phosphatase activity. In the inactive state, the cytoplasmic DHp and CA domains of the HK are organised in a symmetrical fashion with the CA domain juxtaposed against the membrane‐proximal end of the DHp four‐helical bundle. The RR REC domain can interact with the inactive HK DHp four‐helical bundle at a more membrane‐distal location in an orientation that would facilitate dephosphorylation of the aspartate. The active, kinase state of the HK is asymmetrical due to a bend or kink in the DHp domain that leads to one CA domain adopting a looser association that positions it well for phosphorylation of a histidine residue. A single RR REC domain can bind near the other CA domain, which is more closely associated with the DHp domain, in a conformation supporting phosphorylation of the aspartate residue utilising the phosphorylated histidine as a substrate. Repeated cycles of DHp domain bending and RR REC domain binding are hypothesised to support successive rounds of HK autophosphorylation and RR phosphorylation in response to signal inputs received from the sensory domain. HKs and RRs regulate and interact with other macromolecules and proteins to connect signalling pathways, coordinate their activities and sense environmental parameters and changes to cellular physiology.

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Engineered Socket Study of Signaling through a Four-Helix Bundle: Evidence for a Yin−Yang Mechanism in the Kinase Control Module of the Aspartate Receptor

Cited by 96 publications

References 51 publications

Molecular architecture of chemoreceptor arrays revealed by cryoelectron tomography of Escherichia coli minicells

Molecular architecture of chemoreceptor arrays revealed by cryoelectron tomography of Escherichia coli minicells

Bacterial chemoreceptor dynamics correlate with activity state and are coupled over long distances

Regulatory Systems: Two‐Component

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