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Gottfried Unden - One of the best experts on this subject based on the ideXlab platform.
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Sensory Domain contraction in histidine kinase cita triggers transmembrane signaling in the membrane bound sensor
Proceedings of the National Academy of Sciences of the United States of America, 2017Co-Authors: Michele Salvi, Gottfried Unden, Benjamin Schomburg, Karin Giller, Sabrina Graf, Stefan Becker, Adam Lange, Christian GriesingerAbstract:Bacteria use membrane-integral sensor histidine kinases (HK) to perceive stimuli and transduce signals from the environment to the cytosol. Information on how the signal is transmitted across the membrane by HKs is still scarce. Combining both liquid- and solid-state NMR, we demonstrate that structural rearrangements in the extracytoplasmic, citrate-sensing Per-Arnt-Sim (PAS) Domain of HK CitA are identical for the isolated Domain in solution and in a longer construct containing the membrane-embedded HK and lacking only the kinase core. We show that upon citrate binding, the PAS Domain contracts, resulting in a shortening of the C-terminal β-strand. We demonstrate that this contraction of the PAS Domain, which is well characterized for the isolated Domain, is the signal transmitted to the transmembrane (TM) helices in a CitA construct in liposomes. Putting the extracytoplasmic PAS Domain into context of the membrane-embedded CitA construct slows down citrate-binding kinetics by at least a factor of 60, confirming that TM helix motions are linked to the citrate-binding event. Our results are confirmation of a hallmark of the HK signal transduction mechanism with atomic resolution on a full-length construct lacking only the kinase core Domain.
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A PAS Domain with an oxygen labile [4Fe-4S](2+) cluster in the oxygen sensor kinase NreB of Staphylococcus carnosus.
Biochemistry, 2008Co-Authors: Martin Müllner, Oliver Hammel, Bernd Mienert, Steffen Schlag, Eckhard Bill, Gottfried UndenAbstract:The cytoplasmic histidine sensor kinase NreB of Staphylococcus carnosus responds to O(2) and controls together with the response regulator NreC the expression of genes of nitrate/nitrite respiration. nreBC homologous genes were found in Staphylococcus strains and Bacillus clausii, and a modified form was found in some Lactobacillus strains. NreB contains a Sensory Domain with similarity to heme B binding PAS Domains. Anaerobically prepared NreB of S. carnosus exhibited a (diamagnetic) [4Fe-4S](2+) cluster when assessed by Mossbauer spectroscopy. Upon reaction with air, the cluster was degraded with a half-life of approximately 2.5 min. No significant amounts of Mossbauer or EPR detectable intermediates were found during the decay, but magnetic Mossbauer spectra revealed formation of diamagnetic [2Fe-2S](2+) clusters. After extended exposure to air, NreB was devoid of a FeS cluster. Photoreduction with deazaflavin produced small amounts of [4Fe-4S](+), which were degraded subsequently. The magnetically perturbed Mossbauer spectrum of the [4Fe-4S](2+) cluster corroborated the S = 0 spin state and revealed uniform electric field gradient tensors of the iron sites, suggesting full delocalization of the valence electrons and binding of each of the Fe ions by four S ligands, including the ligand to the protein. Mutation of each of the four Cys residues inactivated NreB function in vivo in accordance with their role as ligands. [4Fe-4S](2+) cluster-containing NreB had high kinase activity. Exposure to air decreased the kinase activity and content of the [4Fe-4S](2+) cluster with similar half-lives. We conclude that the Sensory Domain of NreB represents a new type of PAS Domain containing a [4Fe-4S](2+) cluster for sensing and function.
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a pas Domain with an oxygen labile 4fe 4s 2 cluster in the oxygen sensor kinase nreb of staphylococcus carnosus
Biochemistry, 2008Co-Authors: Martin Müllner, Oliver Hammel, Bernd Mienert, Steffen Schlag, Eckhard Bill, Gottfried UndenAbstract:The cytoplasmic histidine sensor kinase NreB of Staphylococcus carnosus responds to O2 and controls together with the response regulator NreC the expression of genes of nitrate/nitrite respiration. nreBC homologous genes were found in Staphylococcus strains and Bacillus clausii, and a modified form was found in some Lactobacillus strains. NreB contains a Sensory Domain with similarity to heme B binding PAS Domains. Anaerobically prepared NreB of S. carnosus exhibited a (diamagnetic) [4Fe-4S]2+ cluster when assessed by Mossbauer spectroscopy. Upon reaction with air, the cluster was degraded with a half-life of ∼2.5 min. No significant amounts of Mossbauer or EPR detectable intermediates were found during the decay, but magnetic Mossbauer spectra revealed formation of diamagnetic [2Fe-2S]2+ clusters. After extended exposure to air, NreB was devoid of a FeS cluster. Photoreduction with deazaflavin produced small amounts of [4Fe-4S]+, which were degraded subsequently. The magnetically perturbed Mossbauer spec...
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The NMR structure of the Sensory Domain of the membranous two-component fumarate sensor (histidine protein kinase) DcuS of Escherichia coli
The Journal of biological chemistry, 2003Co-Authors: Lucia Pappalardo, Ingo G. Janausch, Vinesh Vijayan, Eva Zientz, Jochen Junker, Wolfgang Peti, Markus Zweckstetter, Gottfried Unden, Christian GriesingerAbstract:Abstract The structure of the water-soluble, periplasmic Domain of the fumarate sensor DcuS (DcuS-pd) has been determined by NMR spectroscopy in solution. DcuS is a prototype for a Sensory histidine kinase with transmembrane signal transfer. DcuS belongs to the CitA family of sensors that are specific for sensing di- and tricarboxylates. The periplasmic Domain is folded autonomously and shows helices at the N and the C terminus, suggesting direct linking or connection to helices in the two transmembrane regions. The structure constitutes a novel fold. The nearest structural neighbor is the Per-Arnt-Sim Domain of the photoactive yellow protein that binds small molecules covalently. Residues Arg107, His110, and Arg147 are essential for fumarate sensing and are found clustered together. The structure constitutes the first periplasmic Domain of a two component Sensory system and is distinctly different from the aspartate Sensory Domain of the Tar chemotaxis sensor.
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assignment of 1h 13c and 15n resonances to the Sensory Domain of the membraneous two component fumarate sensor histidine protein kinase dcus of escherichia coli
Journal of Biomolecular NMR, 2001Co-Authors: T N Parac, Eva Zientz, Wolfgang Peti, Gottfried Unden, B Coligaev, Christian GriesingerAbstract:In bacteria various types of signal transduction proteins are used for the perception of environmental signals (Aizawa et al., 2000). Most of the sensors receive the signal at the periplasmic side of the membrane. By transferring the signal across the membrane, it is converted into a cellular signal, which is used for regulation of transcription, enzyme activity, or flagellar rotation. Two-component regulatory systems represent the most frequent systems of this type for transmembrane signalling in bacteria. They consist of a membraneous Sensory histidine protein kinase and a cytoplasmic response regulator. Signal transfer between the sensor and the response regulator is effected by protein phosphorylation. In the facultative anaerobic bacterium Escherichia coli the switch from aerobic to anaerobic metabolism is regulated at the transcriptional level in response to the electron acceptors O2, nitrate, and fumarate. The expression of the genes of anaerobic fumarate respiration, including fumarate reductase, an anaerobic C4-dicarboxylate (fumarate) carrier, and of fumarase B, is regulated by C4-dicarboxylates and the twocomponent regulatory system DcuSR (dicarboxylate uptake) (Zientz et al., 1998; Golby et al., 1999). The DcuSR system consists of the sensor DcuS located in the cytoplasmic membrane, and of the cytoplasmic response regulator DcuR. DcuS contains two transmembrane helices, one periplasmic Domain, and the
Stefan C. Müller - One of the best experts on this subject based on the ideXlab platform.
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Spiral wave dynamics under feedback via an equilateral triangular Sensory Domain.
Physical review. E Statistical nonlinear and soft matter physics, 2006Co-Authors: Somprasong Naknaimueang, Michael A Allen, Stefan C. MüllerAbstract:We perform a numerical study of the trajectories of spiral wave cores in excitable systems whose excitability is modulated in proportion to the integral of the activity in a Sensory Domain in the shape of an equilateral triangle. As a result of this Domain shape having vertices opposite sides, unusual forms of lobed limit cycles occur, which are destroyed and then re-form as the Domain size is varied. Some key results are also demonstrated experimentally using the light-sensitive Belousov-Zhabotinsky reaction. To characterize the observed behavior, we introduce the concept of express and stagnation zones, which are regions where the trajectory moves particularly rapidly or slowly. The location and strength of the zones far from the Domain are accounted for by approximating the parts of the spiral wave crossing the Domain by a series of plane waves.
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Spiral wave dynamics under feedback control derived from a variety of Sensory Domains.
Physical Review E, 2004Co-Authors: On-uma Kheowan, Supichai Kantrasiri, Prapin Wilairat, Ulrich Storb, Stefan C. MüllerAbstract:The dynamics of rigidly rotating spiral waves in a reaction layer with light-dependent excitability is studied by numerical integration of a reaction-diffusion equation system with a feedback control. The feedback signal is derived from Sensory Domains with different geometries by introducing an algorithm that computes the illumination intensity to be proportional to the average wave activity in these Domains. It is shown that the shape and size of the trajectories of the spiral wave tip as well as the stability of the spiral rotation depend sensitively on the choice of the geometry of the Sensory Domain. The numerically observed effects are complemented by constructing a flow map based on an analysis of the feedback signal.
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Spiral wave dynamics controlled by a square-shaped Sensory Domain
Chemical Physics Letters, 2004Co-Authors: On-uma Kheowan, Supichai Kantrasiri, Chananate Uthaisar, Vilmos Gáspár, Stefan C. MüllerAbstract:Abstract Spiral waves rotating rigidly in a thin layer of the light-sensitive Belousov–Zhabotinsky (BZ) reaction are subjected to a time-dependent uniform illumination. A non-local feedback algorithm computes the illumination intensity to be proportional to the average wave activity within a square-shaped Sensory Domain. The investigations show a broad spectrum of dynamical responses which results in square- and cross-shaped trajectories of the spiral tip, including reflections at the virtual walls. The geometry of the Sensory Domain is crucial in determining size and shape of the tip trajectories. A theoretical approach is proposed to explain the observed phenomena.
Christian Griesinger - One of the best experts on this subject based on the ideXlab platform.
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Sensory Domain contraction in histidine kinase cita triggers transmembrane signaling in the membrane bound sensor
Proceedings of the National Academy of Sciences of the United States of America, 2017Co-Authors: Michele Salvi, Gottfried Unden, Benjamin Schomburg, Karin Giller, Sabrina Graf, Stefan Becker, Adam Lange, Christian GriesingerAbstract:Bacteria use membrane-integral sensor histidine kinases (HK) to perceive stimuli and transduce signals from the environment to the cytosol. Information on how the signal is transmitted across the membrane by HKs is still scarce. Combining both liquid- and solid-state NMR, we demonstrate that structural rearrangements in the extracytoplasmic, citrate-sensing Per-Arnt-Sim (PAS) Domain of HK CitA are identical for the isolated Domain in solution and in a longer construct containing the membrane-embedded HK and lacking only the kinase core. We show that upon citrate binding, the PAS Domain contracts, resulting in a shortening of the C-terminal β-strand. We demonstrate that this contraction of the PAS Domain, which is well characterized for the isolated Domain, is the signal transmitted to the transmembrane (TM) helices in a CitA construct in liposomes. Putting the extracytoplasmic PAS Domain into context of the membrane-embedded CitA construct slows down citrate-binding kinetics by at least a factor of 60, confirming that TM helix motions are linked to the citrate-binding event. Our results are confirmation of a hallmark of the HK signal transduction mechanism with atomic resolution on a full-length construct lacking only the kinase core Domain.
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The NMR structure of the Sensory Domain of the membranous two-component fumarate sensor (histidine protein kinase) DcuS of Escherichia coli
The Journal of biological chemistry, 2003Co-Authors: Lucia Pappalardo, Ingo G. Janausch, Vinesh Vijayan, Eva Zientz, Jochen Junker, Wolfgang Peti, Markus Zweckstetter, Gottfried Unden, Christian GriesingerAbstract:Abstract The structure of the water-soluble, periplasmic Domain of the fumarate sensor DcuS (DcuS-pd) has been determined by NMR spectroscopy in solution. DcuS is a prototype for a Sensory histidine kinase with transmembrane signal transfer. DcuS belongs to the CitA family of sensors that are specific for sensing di- and tricarboxylates. The periplasmic Domain is folded autonomously and shows helices at the N and the C terminus, suggesting direct linking or connection to helices in the two transmembrane regions. The structure constitutes a novel fold. The nearest structural neighbor is the Per-Arnt-Sim Domain of the photoactive yellow protein that binds small molecules covalently. Residues Arg107, His110, and Arg147 are essential for fumarate sensing and are found clustered together. The structure constitutes the first periplasmic Domain of a two component Sensory system and is distinctly different from the aspartate Sensory Domain of the Tar chemotaxis sensor.
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assignment of 1h 13c and 15n resonances to the Sensory Domain of the membraneous two component fumarate sensor histidine protein kinase dcus of escherichia coli
Journal of Biomolecular NMR, 2001Co-Authors: T N Parac, Eva Zientz, Wolfgang Peti, Gottfried Unden, B Coligaev, Christian GriesingerAbstract:In bacteria various types of signal transduction proteins are used for the perception of environmental signals (Aizawa et al., 2000). Most of the sensors receive the signal at the periplasmic side of the membrane. By transferring the signal across the membrane, it is converted into a cellular signal, which is used for regulation of transcription, enzyme activity, or flagellar rotation. Two-component regulatory systems represent the most frequent systems of this type for transmembrane signalling in bacteria. They consist of a membraneous Sensory histidine protein kinase and a cytoplasmic response regulator. Signal transfer between the sensor and the response regulator is effected by protein phosphorylation. In the facultative anaerobic bacterium Escherichia coli the switch from aerobic to anaerobic metabolism is regulated at the transcriptional level in response to the electron acceptors O2, nitrate, and fumarate. The expression of the genes of anaerobic fumarate respiration, including fumarate reductase, an anaerobic C4-dicarboxylate (fumarate) carrier, and of fumarase B, is regulated by C4-dicarboxylates and the twocomponent regulatory system DcuSR (dicarboxylate uptake) (Zientz et al., 1998; Golby et al., 1999). The DcuSR system consists of the sensor DcuS located in the cytoplasmic membrane, and of the cytoplasmic response regulator DcuR. DcuS contains two transmembrane helices, one periplasmic Domain, and the
Igor B. Zhulin - One of the best experts on this subject based on the ideXlab platform.
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a direct sensing galactose chemoreceptor recently evolved in invasive strains of campylobacter jejuni
Nature Communications, 2016Co-Authors: Rebecca M King, Igor B. Zhulin, Aaron D Fleetwood, Lucy K Shewell, Greg Tram, Tahria Najnin, Lauren E Hartleytassell, Jennifer C Wilson, Victoria KorolikAbstract:A rare chemotaxis receptor, Tlp11, has been previously identified in invasive strains of Campylobacter jejuni, the most prevalent cause of bacterial gastroenteritis worldwide. Here we use glycan and small-molecule arrays, as well as surface plasmon resonance, to show that Tlp11 specifically interacts with galactose. Tlp11 is required for the chemotactic response of C. jejuni to galactose, as shown using wild type, allelic inactivation and addition mutants. The inactivated mutant displays reduced virulence in vivo, in a model of chicken colonization. The Tlp11 Sensory Domain represents the first known sugar-binding dCache_1 Domain, which is the most abundant family of extracellular sensors in bacteria. The Tlp11 signalling Domain interacts with the chemotaxis scaffolding proteins CheV and CheW, and comparative genomic analysis indicates a likely recent evolutionary origin for Tlp11. We propose to rename Tlp11 as CcrG, Campylobacter ChemoReceptor for Galactose. Some virulent strains of Campylobacter jejuni possess a putative chemotaxis receptor, Tlp11, of unknown function. Here the authors show that Tlp11 specifically interacts with galactose and is required for the chemotaxis response of C. jejunito galactose.
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cache Domains that are homologous to but different from pas Domains comprise the largest superfamily of extracellular sensors in prokaryotes
PLOS Computational Biology, 2016Co-Authors: Igor B. Zhulin, Amit A Upadhyay, Aaron D Fleetwood, Ogun Adebali, Robert D FinnAbstract:Cellular receptors usually contain a designated Sensory Domain that recognizes the signal. Per/Arnt/Sim (PAS) Domains are ubiquitous sensors in thousands of species ranging from bacteria to humans. Although PAS Domains were described as intracellular sensors, recent structural studies revealed PAS-like Domains in extracytoplasmic regions in several transmembrane receptors. However, these structurally defined extracellular PAS-like Domains do not match sequence-derived PAS Domain models, and thus their distribution across the genomic landscape remains largely unknown. Here we show that structurally defined extracellular PAS-like Domains belong to the Cache superfamily, which is homologous to, but distinct from the PAS superfamily. Our newly built computational models enabled identification of Cache Domains in tens of thousands of signal transduction proteins including those from important pathogens and model organisms. Furthermore, we show that Cache Domains comprise the dominant mode of extracellular sensing in prokaryotes.
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FIST: a Sensory Domain for diverse signal transduction pathways in prokaryotes and ubiquitin signaling in eukaryotes.
Bioinformatics (Oxford England), 2007Co-Authors: Kirill Borziak, Igor B. ZhulinAbstract:Motivation: Sensory Domains that are conserved among Bacteria, Archaea and Eucarya are important detectors of common signals detected by living cells. Due to their high sequence divergence, Sensory Domains are difficult to identify. We systematically look for novel Sensory Domains using sensitive profile-based searches initiated with regions of signal transduction proteins where no known Domains can be identified by current Domain models. Results: Using profile searches followed by multiple sequence alignment, structure prediction and Domain architecture analysis, we have identified a novel Sensory Domain termed FIST, which is present in signal transduction proteins from Bacteria, Archaea and Eucarya. Chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST Domains bind small ligands, such as amino acids. Contact: joulineib@ornl.gov Supplementary information: http://genomics.ornl.gov/research/ pubs/fist
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Common Extracellular Sensory Domains in Transmembrane Receptors for Diverse Signal Transduction Pathways in Bacteria and Archaea
Journal of bacteriology, 2003Co-Authors: Igor B. Zhulin, Anastasia N. Nikolskaya, Michael Y. GalperinAbstract:Transmembrane receptors in microorganisms, such as Sensory histidine kinases and methyl-accepting chemotaxis proteins, are molecular devices for monitoring environmental changes. We report here that Sensory Domain sharing is widespread among different classes of transmembrane receptors. We have identified two novel conserved extracellular Sensory Domains, named CHASE2 and CHASE3, that are found in at least four classes of transmembrane receptors: histidine kinases, adenylate cyclases, predicted diguanylate cyclases, and either serine/threonine protein kinases (CHASE2) or methyl-accepting chemotaxis proteins (CHASE3). Three other extracellular Sensory Domains were shared by at least two different classes of transmembrane receptors: histidine kinases and either diguanylate cyclases, adenylate cyclases, or phosphodiesterases. These observations suggest that microorganisms use similar conserved Domains to sense similar environmental signals and transmit this information via different signal transduction pathways to different regulatory circuits: transcriptional regulation (histidine kinases), chemotaxis (methyl-accepting proteins), catabolite repression (adenylate cyclases), and modulation of enzyme activity (diguanylate cyclases and phosphodiesterases). The variety of signaling pathways using the CHASE-type Domains indicates that these Domains sense some critically important extracellular signals.
Hae-kap Cheong - One of the best experts on this subject based on the ideXlab platform.
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Mg2+-induced folding of the Sensory Domain of QseC histidine kinase from enterohemorrhagic Escherichia coli (EHEC) O157:H7
Process Biochemistry, 2014Co-Authors: Kwon Joo Yeo, Jin-wan Park, Eun-hee Kim, Eunha Hwang, Hae-kap CheongAbstract:Abstract The QseBC two-component system is one of the quorum-sensing systems in bacteria, which are involved in the regulation of flagella, motility, and transcription factors related to bacterial virulence. The Sensory Domain of QseC in enterohemorrhagic Escherichia coli (EHEC) O157:H7 has important roles in quorum sensing via the detection of autoinducer-3 and the regulation of pathogenesis through the recognition of host hormones, such as epinephrine and norepinephrine. Therefore, structural studies of the Sensory Domain of QseC could be important to understand not only quorum sensing mechanism in bacteria but also pathogenic mechanisms in host cells. Herein, the structural properties of the Sensory Domain of QseC from EHEC O157:H7 in solution states are described. The findings suggest that its folding state is highly dependent on Mg2+: the protein is less structured in the absence of Mg2+ though is well structured in the presence of 120 mM Mg2+. According to multi-angle light scattering combined with size-exclusion chromatography, the protein exists as a monomer in the presence of 120 mM Mg2+. Moreover, we observed the same behavior for the Sensory Domain of QseC from E. coli K12. We suggest that our results may provide useful information for the determination of the structure of the Sensory Domain of QseC.
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Expression, purification, crystallization and preliminary X-ray analysis of the extracellular Sensory Domain of DraK histidine kinase from Streptomyces coelicolor
Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2013Co-Authors: Kwon Joo Yeo, Young-hyun Han, Hae-kap CheongAbstract:The bacterium Streptomyces coelicolor produces useful antibiotics from its secondary metabolites. DraK is a Sensory histidine kinase involved in the differential regulation of antibiotics in S. coelicolor through the DraR/DraK two-component system. Here, the extracellular Sensory Domain of DraK was overexpressed in Escherichia coli, purified and crystallized using the sitting-drop vapour-diffusion method. The crystal diffracted to 2.2 A resolution and belonged to space group C2221, with unit-cell parameters a = 41.91, b = 174.50, c = 145.25 A, α = β = γ = 90°.
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pH-dependent structural change of the extracellular sensor Domain of the DraK histidine kinase from Streptomyces coelicolor.
Biochemical and biophysical research communications, 2013Co-Authors: Kwon Joo Yeo, Eunha Hwang, Young-hyun Han, Eun Hye Kim, Hyun Jung Kim, Ohsuk Kwon, Young-soo Hong, Chaejoon Cheong, Hae-kap CheongAbstract:Recently, the DraR/DraK (Sco3063/Sco3062) two-component system (TCS) of Streptomycescoelicolor has been reported to be involved in the differential regulation of antibiotic biosynthesis. However, it has not been shown that under which conditions and how the DraR/DraK TCS is activated to initiate the signal transduction process. Therefore, to understand the sensing mechanism, structural study of the Sensory Domain of DraK is highly required. Here, we report the biochemical and biophysical properties of the extracellular Sensory Domain (ESD) of DraK. We observed a reversible pH-dependent conformational change of the ESD in a pH range of 2.5–10. Size-exclusion chromatography and AUC (analytical ultracentrifugation) data indicated that the ESD is predominantly monomeric in solution and exists in equilibrium between monomer and dimer states in acidic condition. Using NMR (nuclear magnetic resonance) and CD (circular dichroism) spectroscopy, our findings suggest that the structure of the ESD at low pH is more structured than that at high pH. In particular, the glutamate at position 83 is an important residue for the pH-dependent conformational change. These results suggest that this pH-dependent conformational change of ESD may be involved in signal transduction process of DraR/DraK TCS.
