Structural dynamics of the two-component response regulator RstA in recognition of promoter DNA element

Yi Chuan Li; Chung Ke Chang; Chi Fon Chang; Ya Hsin Cheng; Pei Ju Fang; Tsunai Yu; Sheng Chia Chen; Yi Ching Li; Chwan Deng Hsiao; Tai Huang Huang

doi:10.1093/nar/gku572

Structural dynamics of the two-component response regulator RstA in recognition of promoter DNA element

Yi Chuan Li, Chung Ke Chang, Chi Fon Chang, Ya Hsin Cheng, Pei Ju Fang, Tsunai Yu, Sheng Chia Chen, Yi Ching Li, Chwan Deng Hsiao^*, Tai Huang Huang

^*Corresponding author for this work

Department of Physics

Research output: Contribution to journal › Article › peer-review

21 Citations (Scopus)

Abstract

The RstA/RstB system is a bacterial two-component regulatory system consisting of the membrane sensor, RstB and its cognate response regulator (RR) RstA. The RstA of Klebsiella pneumoniae (kpRstA) consists of an N-terminal receiver domain (RD, residues 1-119) and a C-terminal DNA-binding domain (DBD, residues 130-236). Phosphorylation of kpRstA induces dimerization, which allows two kpRstA DBDs to bind to a tandem repeat, called the RstA box, and regulate the expression of downstream genes. Here we report the solution and crystal structures of the free kpRstA RD, DBD and DBD/RstA box DNA complex. The structure of the kpRstA DBD/RstA box complex suggests that the two protomers interact with the RstA box in an asymmetric fashion. Equilibrium binding studies further reveal that the two protomers within the kpRstA dimer bind to the RstA box in a sequential manner. Taken together, our results suggest a binding model where dimerization of the kpRstA RDs provides the platform to allow the first kpRstA DBD protomer to anchor protein-DNA interaction, whereas the second protomer plays a key role in ensuring correct recognition of the RstA box.

Original language	English
Pages (from-to)	8777-8788
Number of pages	12
Journal	Nucleic Acids Research
Volume	42
Issue number	13
DOIs	https://doi.org/10.1093/nar/gku572
Publication status	Published - 2014 Jul 29

ASJC Scopus subject areas

Genetics

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10.1093/nar/gku572

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@article{adb53e6f8532406d931cce8dcc41c4e6,

title = "Structural dynamics of the two-component response regulator RstA in recognition of promoter DNA element",

abstract = "The RstA/RstB system is a bacterial two-component regulatory system consisting of the membrane sensor, RstB and its cognate response regulator (RR) RstA. The RstA of Klebsiella pneumoniae (kpRstA) consists of an N-terminal receiver domain (RD, residues 1-119) and a C-terminal DNA-binding domain (DBD, residues 130-236). Phosphorylation of kpRstA induces dimerization, which allows two kpRstA DBDs to bind to a tandem repeat, called the RstA box, and regulate the expression of downstream genes. Here we report the solution and crystal structures of the free kpRstA RD, DBD and DBD/RstA box DNA complex. The structure of the kpRstA DBD/RstA box complex suggests that the two protomers interact with the RstA box in an asymmetric fashion. Equilibrium binding studies further reveal that the two protomers within the kpRstA dimer bind to the RstA box in a sequential manner. Taken together, our results suggest a binding model where dimerization of the kpRstA RDs provides the platform to allow the first kpRstA DBD protomer to anchor protein-DNA interaction, whereas the second protomer plays a key role in ensuring correct recognition of the RstA box.",

author = "Li, {Yi Chuan} and Chang, {Chung Ke} and Chang, {Chi Fon} and Cheng, {Ya Hsin} and Fang, {Pei Ju} and Tsunai Yu and Chen, {Sheng Chia} and Li, {Yi Ching} and Hsiao, {Chwan Deng} and Huang, {Tai Huang}",

note = "Funding Information: Ministry of Science and Technology of the Republic of China [NSC 100-2311-B-001-023 to T.H.H. and NSC101- 2311-B-001-023-MY3 to C.-D.H.]. Funding for open access charge: Academia Sinica and Ministry of Science and Technology of the Republic of China [NSC 100-2311-B-001-023 to T.H.H. and NSC101-2311-B-001-023-MY3 to C.-D.H.]. Conflict of interest statement. None declared. Funding Information: We thank Dr Shu-Chuan Jao of the Biophysics Core Facility, Scientific Instrument Center at Academia Sinica for providing technical assistance on ITC experiments. NMR experiments were carried out at the High-Field Nuclear Magnetic Resonance Center, supported by Core Facility for Protein Structural Analysis, National Core Facility Program for Biotechnology, the Ministry of Science and Technology of the Republic of China. We are grateful for access to the synchrotron radiation beamline 13C1 at the National Synchrotron Radiation Research Center, Hsinchu, Republic of China.",

year = "2014",

month = jul,

day = "29",

doi = "10.1093/nar/gku572",

language = "English",

volume = "42",

pages = "8777--8788",

journal = "Nucleic Acids Research",

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T1 - Structural dynamics of the two-component response regulator RstA in recognition of promoter DNA element

AU - Li, Yi Chuan

AU - Chang, Chung Ke

AU - Chang, Chi Fon

AU - Cheng, Ya Hsin

AU - Fang, Pei Ju

AU - Yu, Tsunai

AU - Chen, Sheng Chia

AU - Li, Yi Ching

AU - Hsiao, Chwan Deng

AU - Huang, Tai Huang

N1 - Funding Information: Ministry of Science and Technology of the Republic of China [NSC 100-2311-B-001-023 to T.H.H. and NSC101- 2311-B-001-023-MY3 to C.-D.H.]. Funding for open access charge: Academia Sinica and Ministry of Science and Technology of the Republic of China [NSC 100-2311-B-001-023 to T.H.H. and NSC101-2311-B-001-023-MY3 to C.-D.H.]. Conflict of interest statement. None declared. Funding Information: We thank Dr Shu-Chuan Jao of the Biophysics Core Facility, Scientific Instrument Center at Academia Sinica for providing technical assistance on ITC experiments. NMR experiments were carried out at the High-Field Nuclear Magnetic Resonance Center, supported by Core Facility for Protein Structural Analysis, National Core Facility Program for Biotechnology, the Ministry of Science and Technology of the Republic of China. We are grateful for access to the synchrotron radiation beamline 13C1 at the National Synchrotron Radiation Research Center, Hsinchu, Republic of China.

PY - 2014/7/29

Y1 - 2014/7/29

N2 - The RstA/RstB system is a bacterial two-component regulatory system consisting of the membrane sensor, RstB and its cognate response regulator (RR) RstA. The RstA of Klebsiella pneumoniae (kpRstA) consists of an N-terminal receiver domain (RD, residues 1-119) and a C-terminal DNA-binding domain (DBD, residues 130-236). Phosphorylation of kpRstA induces dimerization, which allows two kpRstA DBDs to bind to a tandem repeat, called the RstA box, and regulate the expression of downstream genes. Here we report the solution and crystal structures of the free kpRstA RD, DBD and DBD/RstA box DNA complex. The structure of the kpRstA DBD/RstA box complex suggests that the two protomers interact with the RstA box in an asymmetric fashion. Equilibrium binding studies further reveal that the two protomers within the kpRstA dimer bind to the RstA box in a sequential manner. Taken together, our results suggest a binding model where dimerization of the kpRstA RDs provides the platform to allow the first kpRstA DBD protomer to anchor protein-DNA interaction, whereas the second protomer plays a key role in ensuring correct recognition of the RstA box.

AB - The RstA/RstB system is a bacterial two-component regulatory system consisting of the membrane sensor, RstB and its cognate response regulator (RR) RstA. The RstA of Klebsiella pneumoniae (kpRstA) consists of an N-terminal receiver domain (RD, residues 1-119) and a C-terminal DNA-binding domain (DBD, residues 130-236). Phosphorylation of kpRstA induces dimerization, which allows two kpRstA DBDs to bind to a tandem repeat, called the RstA box, and regulate the expression of downstream genes. Here we report the solution and crystal structures of the free kpRstA RD, DBD and DBD/RstA box DNA complex. The structure of the kpRstA DBD/RstA box complex suggests that the two protomers interact with the RstA box in an asymmetric fashion. Equilibrium binding studies further reveal that the two protomers within the kpRstA dimer bind to the RstA box in a sequential manner. Taken together, our results suggest a binding model where dimerization of the kpRstA RDs provides the platform to allow the first kpRstA DBD protomer to anchor protein-DNA interaction, whereas the second protomer plays a key role in ensuring correct recognition of the RstA box.

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Structural dynamics of the two-component response regulator RstA in recognition of promoter DNA element

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Crystal structure of Klebsiella pneumoniae RstA BeF3-activated N-terminal receiver domain

Crystal structure of Klebsiella pneumoniae RstA DNA-binding domain in complex with RstA box

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Structural dynamics of the two-component response regulator RstA in recognition of promoter DNA element

Abstract

ASJC Scopus subject areas

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Datasets

Crystal structure of Klebsiella pneumoniae RstA BeF3-activated N-terminal receiver domain

Crystal structure of Klebsiella pneumoniae RstA DNA-binding domain in complex with RstA box

Cite this