3E4O

Crystal structure of succinate bound state DctB

Summary for 3E4O

• Entry DOI: 10.2210/pdb3e4o/pdb
• Related: 3E4P 3E4Q
• Descriptor: C4-dicarboxylate transport sensor protein dctB, MAGNESIUM ION, SUCCINIC ACID, ... (4 entities in total)
• Functional Keywords: pas domain, n-term helical dimerization domain, transferase
• Biological source: Sinorhizobium meliloti
• Cellular location: Cell inner membrane; Multi-pass membrane protein: P13633
• Total number of polymer chains: 2
• Total formula weight: 66990.54

Authors

Zhou, Y.F.,Nan, J.,Nan, B.Y.,Liang, Y.H.,Panjikar, S.,Su, X.D. (deposition date: 2008-08-12, release date: 2008-10-21, Last modification date: 2024-11-20)

Primary citation

Zhou, Y.F.,Nan, B.Y.,Nan, J.,Ma, Q.J.,Panjikar, S.,Liang, Y.H.,Wang, Y.P.,Su, X.D.
C4-dicarboxylates sensing mechanism revealed by the crystal structures of DctB sensor domain.
J.Mol.Biol., 383:49-61, 2008

PubMed 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 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.

PubMed: 18725229
DOI: 10.1016/j.jmb.2008.08.010

Experimental method

X-RAY DIFFRACTION (2.3 Å)