7B5U

RCK_C domain dimer of S.agalactiae BusR in complex with c-di-AMP

Summary for 7B5U

• Entry DOI: 10.2210/pdb7b5u/pdb
• Related: 7B5T
• Descriptor: GntR family transcriptional regulator, (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide (3 entities in total)
• Functional Keywords: effector binding domain, rck_c, dna binding protein
• Biological source: Streptococcus agalactiae
• Total number of polymer chains: 2
• Total formula weight: 18686.71

Authors

Bandera, A.M.,Witte, G. (deposition date: 2020-12-07, release date: 2021-08-11, Last modification date: 2024-01-31)

Primary citation

Bandera, A.M.,Bartho, J.,Lammens, K.,Drexler, D.J.,Kleinschwarzer, J.,Hopfner, K.P.,Witte, G.
BusR senses bipartite DNA binding motifs by a unique molecular ruler architecture.
Nucleic Acids Res., 49:10166-10177, 2021

PubMed Abstract: The cyclic dinucleotide second messenger c-di-AMP is a major player in regulation of potassium homeostasis and osmolyte transport in a variety of bacteria. Along with various direct interactions with proteins such as potassium channels, the second messenger also specifically binds to transcription factors, thereby altering the processes in the cell on the transcriptional level. We here describe the structural and biochemical characterization of BusR from the human pathogen Streptococcus agalactiae. BusR is a member of a yet structurally uncharacterized subfamily of the GntR family of transcription factors that downregulates transcription of the genes for the BusA (OpuA) glycine-betaine transporter upon c-di-AMP binding. We report crystal structures of full-length BusR, its apo and c-di-AMP bound effector domain, as well as cryo-EM structures of BusR bound to its operator DNA. Our structural data, supported by biochemical and biophysical data, reveal that BusR utilizes a unique domain assembly with a tetrameric coiled-coil in between the binding platforms, serving as a molecular ruler to specifically recognize a 22 bp separated bipartite binding motif. Binding of c-di-AMP to BusR induces a shift in equilibrium from an inactivated towards an activated state that allows BusR to bind the target DNA, leading to transcriptional repression.

PubMed: 34432045
DOI: 10.1093/nar/gkab736

Experimental method

X-RAY DIFFRACTION (1.2 Å)