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

Research output: Contribution to journalArticle


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.


  • Yan-Feng Zhou
  • Beiyan Nan
  • Jie Nan
  • Qingjun Ma
  • Santosh Panjikar
  • Yu-He Liang
  • Yiping Wang
  • Xiao-Dong Su
Research areas and 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
Original languageEnglish
Pages (from-to)49-61
Number of pages13
JournalJournal of Molecular Biology
Issue number1
Publication statusPublished - 2008 Oct 31
Publication categoryResearch