C4-Dicarboxylates Sensing Mechanism Revealed by the Crystal Structures of DctB Sensor Domain

Zhou, Yan; Nan, Beiyan; Nan, Jie; Ma, Qingjun; Panjikar, Santosh; Yu, Lian; Wang, Yi‐Ping; Su, Xiao Dong

doi:10.1016/j.jmb.2008.08.010

Cited by 75 publications

(103 citation statements)

References 57 publications

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“…In this context, it is interesting to compare the structures of the KinD-SD in complex with pyruvic acid to that of the dicarboxylic acid sensor, DctB-SD, in complex with succinic acid. 36 The sensor histidine kinase, DctB, is known to activate in response to several dicarboxylic acids, including succinate and malate. 36 Overall, the ligand-binding domains of DctB and KinD are remarkably similar and the respective ligands occupy similar binding pockets.…”

Section: Is Pyruvate the Physiological Ligand Of Kind?mentioning

confidence: 99%

“…36 The sensor histidine kinase, DctB, is known to activate in response to several dicarboxylic acids, including succinate and malate. 36 Overall, the ligand-binding domains of DctB and KinD are remarkably similar and the respective ligands occupy similar binding pockets. Strikingly, the carboxy group of pyruvate and succinate in the respective proteins is coordinated by a conserved arginine (R131 in KinD).…”

Section: Is Pyruvate the Physiological Ligand Of Kind?mentioning

confidence: 99%

“…Two ortholog sensor domains were determined from different bacteria. 36,39 Furthermore, several forms of the sensors DctB (3BY9 36 ) and LuxQ (3C30 37 ) were determined in more than one crystal form with different ligands bound to them. The structures are not altered significantly by crystal packing in different unit cells when crystallized from different precipitating agents.…”

Section: Comparison Of Periplasmic Sensors Composed Of Tandem Pas-likmentioning

confidence: 99%

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

Wilton

et al. 2013

Protein Science

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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.

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Section: Is Pyruvate the Physiological Ligand Of Kind?mentioning

confidence: 99%

Section: Is Pyruvate the Physiological Ligand Of Kind?mentioning

confidence: 99%

Section: Comparison Of Periplasmic Sensors Composed Of Tandem Pas-likmentioning

confidence: 99%

See 1 more Smart Citation

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

Wilton

et al. 2013

Protein Science

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“…Furthermore, like CqsS, many two-component sensors have complicated membrane-spanning domains, which has made structural analyses particularly difficult. For these reasons, analyses of ligandreceptor interactions using structural approaches have been limited to a few histidine kinases with well-defined periplasmic sensing domains and known ligands (13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23). Thus, despite intensive effort, it remains unclear how ligand binding affects signaling activity in this important family of receptors.…”

mentioning

confidence: 99%

Probing bacterial transmembrane histidine kinase receptor–ligand interactions with natural and synthetic molecules

Wei

Perez³

et al. 2010

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

136

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Bacterial histidine kinases transduce extracellular signals into the cytoplasm. Most stimuli are chemically undefined; therefore, despite intensive study, signal recognition mechanisms remain mysterious. We exploit the fact that quorum-sensing signals are known molecules to identify mutants in the Vibrio cholerae quorum-sensing receptor CqsS that display altered responses to natural and synthetic ligands. Using this chemical-genetics approach, we assign particular amino acids of the CqsS sensor to particular roles in recognition of the native ligand, CAI-1 (S-3 hydroxytridecan-4-one) as well as ligand analogues. Amino acids W104 and S107 dictate receptor preference for the carbon-3 moiety. Residues F162 and C170 specify ligand head size and tail length, respectively. By combining mutations, we can build CqsS receptors responsive to ligand analogues altered at both the head and tail. We suggest that rationally designed ligands can be employed to study, and ultimately to control, histidine kinase activity.agonist | antagonist | quorum-sensing | two-component protein

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“…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).…”

mentioning

confidence: 98%

Sensor Domain of Histidine Kinase KinB of Pseudomonas

Tan

Chhor

Binkowski

et al. 2014

Journal of Biological Chemistry

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Background:The sensor domain (SD) of histidine kinase (HK) KinB (KinB-SD) receives signals from the environment and induces a transduction cascade. Results: Structures of the KinB-SD were obtained in ligand-free, phosphate-bound, and mutant forms. Conclusion:The unique helix-swapped KinB-SD structure forms a ligand-binding cavity on the dimer interface. Significance: KinB-SD studies provide insights into the signal transduction and identity of potential signaling molecules.

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C4-Dicarboxylates Sensing Mechanism Revealed by the Crystal Structures of DctB Sensor Domain

Cited by 75 publications

References 57 publications

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

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

Probing bacterial transmembrane histidine kinase receptor–ligand interactions with natural and synthetic molecules

Sensor Domain of Histidine Kinase KinB of Pseudomonas

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