C4-dicarboxylates sensing mechanism revealed by the crystal structures of DctB sensor domain |
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Authors: | Zhou Yan-Feng Nan Beiyan Nan Jie Ma Qingjun Panjikar Santosh Liang Yu-He Wang Yiping Su Xiao-Dong |
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Affiliation: | 1 National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China 2 EMBL Hamburg Outstation, c/o Deutsches Elektronen Synchrotron, Notkestrasse 85, D-22603 Hamburg, Germany |
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Abstract: | C4-dicarboxylates are the major carbon and energy sources during the symbiotic growth of rhizobia. Responses to C4-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 C4-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 C4 succinate, and a complex with C3 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 C4-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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Keywords: | TCS, two-component system(s) DctBp, periplasmic sensor domain of Sinorhizobium meliloti DctB PAS, Per-Arnt-Sim SIN, succinate Dct, dicarboxylate transport MLA, malonate DctBpp, membrane-proximal domain of DctBp DctBpd, membrane-distal domain of DctBp SeMet, selenomethionine NCS, noncrystallographic symmetry PDB, Protein Data Bank |
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