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C4-dicarboxylates sensing mechanism revealed by the crystal structures of DctB sensor domain

Zhou, Yan-Feng; Nan, Beiyan; Nan, Jie LU ; Ma, Qingjun; Panjikar, Santosh; Liang, Yu-He; Wang, Yiping and Su, Xiao-Dong LU (2008) In Journal of Molecular Biology 383(1). p.49-61
Abstract

C(4)-dicarboxylates are the major carbon and energy sources during the symbiotic growth of rhizobia. Responses to C(4)-dicarboxylates depend on typical two-component systems (TCS) consisting of a transmembrane sensor histidine kinase and a cytoplasmic response regulator. The DctB-DctD system is the first identified TCS for C(4)-dicarboxylates sensing. Direct ligand binding to the sensor domain of DctB is believed to be the first step of the sensing events. In this report, the water-soluble periplasmic sensor domain of Sinorhizobium meliloti DctB (DctBp) was studied, and three crystal structures were solved: the apo protein, a complex with C(4) succinate, and a complex with C(3) malonate. Different from the two structurally known CitA... (More)

C(4)-dicarboxylates are the major carbon and energy sources during the symbiotic growth of rhizobia. Responses to C(4)-dicarboxylates depend on typical two-component systems (TCS) consisting of a transmembrane sensor histidine kinase and a cytoplasmic response regulator. The DctB-DctD system is the first identified TCS for C(4)-dicarboxylates sensing. Direct ligand binding to the sensor domain of DctB is believed to be the first step of the sensing events. In this report, the water-soluble periplasmic sensor domain of Sinorhizobium meliloti DctB (DctBp) was studied, and three crystal structures were solved: the apo protein, a complex with C(4) succinate, and a complex with C(3) malonate. Different from the two structurally known CitA family of carboxylate sensor proteins CitA and DcuS, the structure of DctBp consists of two tandem Per-Arnt-Sim (PAS) domains and one N-terminal helical region. Only the membrane-distal PAS domain was found to bind the ligands, whereas the proximal PAS domain was empty. Comparison of DctB, CitA, and DcuS suggests a detailed stereochemistry of C(4)-dicarboxylates ligand perception. The structures of the different ligand binding states of DctBp also revealed a series of conformational changes initiated upon ligand binding and propagated to the N-terminal domain responsible for dimerization, providing insights into understanding the detailed mechanism of the signal transduction of TCS histidine kinases.

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organization
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publication status
published
keywords
Amino Acid Sequence, Bacterial Proteins, Crystallography, X-Ray, Dicarboxylic Acid Transporters, Dicarboxylic Acids, Dimerization, Escherichia coli Proteins, Ligands, Models, Molecular, Molecular Sequence Data, Protein Conformation, Protein Kinases, Protein Structure, Quaternary, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Signal Transduction, Sinorhizobium meliloti
in
Journal of Molecular Biology
volume
383
issue
1
pages
13 pages
publisher
Elsevier
external identifiers
  • scopus:52249108909
ISSN
1089-8638
DOI
10.1016/j.jmb.2008.08.010
language
English
LU publication?
yes
id
eb25935c-2eca-44fa-afba-41ea572b2126
date added to LUP
2016-09-07 22:53:45
date last changed
2017-03-05 04:36:12
@article{eb25935c-2eca-44fa-afba-41ea572b2126,
  abstract     = {<p>C(4)-dicarboxylates are the major carbon and energy sources during the symbiotic growth of rhizobia. Responses to C(4)-dicarboxylates depend on typical two-component systems (TCS) consisting of a transmembrane sensor histidine kinase and a cytoplasmic response regulator. The DctB-DctD system is the first identified TCS for C(4)-dicarboxylates sensing. Direct ligand binding to the sensor domain of DctB is believed to be the first step of the sensing events. In this report, the water-soluble periplasmic sensor domain of Sinorhizobium meliloti DctB (DctBp) was studied, and three crystal structures were solved: the apo protein, a complex with C(4) succinate, and a complex with C(3) malonate. Different from the two structurally known CitA family of carboxylate sensor proteins CitA and DcuS, the structure of DctBp consists of two tandem Per-Arnt-Sim (PAS) domains and one N-terminal helical region. Only the membrane-distal PAS domain was found to bind the ligands, whereas the proximal PAS domain was empty. Comparison of DctB, CitA, and DcuS suggests a detailed stereochemistry of C(4)-dicarboxylates ligand perception. The structures of the different ligand binding states of DctBp also revealed a series of conformational changes initiated upon ligand binding and propagated to the N-terminal domain responsible for dimerization, providing insights into understanding the detailed mechanism of the signal transduction of TCS histidine kinases.</p>},
  author       = {Zhou, Yan-Feng and Nan, Beiyan and Nan, Jie and Ma, Qingjun and Panjikar, Santosh and Liang, Yu-He and Wang, Yiping and Su, Xiao-Dong},
  issn         = {1089-8638},
  keyword      = {Amino Acid Sequence,Bacterial Proteins,Crystallography, X-Ray,Dicarboxylic Acid Transporters,Dicarboxylic Acids,Dimerization,Escherichia coli Proteins,Ligands,Models, Molecular,Molecular Sequence Data,Protein Conformation,Protein Kinases,Protein Structure, Quaternary,Protein Structure, Tertiary,Sequence Homology, Amino Acid,Signal Transduction,Sinorhizobium meliloti},
  language     = {eng},
  month        = {10},
  number       = {1},
  pages        = {49--61},
  publisher    = {Elsevier},
  series       = {Journal of Molecular Biology},
  title        = {C4-dicarboxylates sensing mechanism revealed by the crystal structures of DctB sensor domain},
  url          = {http://dx.doi.org/10.1016/j.jmb.2008.08.010},
  volume       = {383},
  year         = {2008},
}