title: Identification, characterization, and structure analysis of the cyclic di-AMP-binding PII-like signal transduction protein DarA.
abstract: The cyclic dimeric AMP nucleotide c-di-AMP is an essential second messenger in Bacillus subtilis. We have identified the protein DarA as one of the prominent c-di-AMP receptors in B. subtilis. Crystal structure analysis shows that DarA is highly homologous to PII signal transducer proteins. In contrast to PII proteins, the functionally important B- and T-loops are swapped with respect to their size. DarA is a homotrimer that binds three molecules of c-di-AMP, each in a pocket located between two subunits. We demonstrate that DarA is capable to bind c-di-AMP and with lower affinity cyclic GMP-AMP (3'3'-cGAMP) but not c-di-GMP or 2'3'-cGAMP. Consistently the crystal structure shows that within the ligand-binding pocket only one adenine is highly specifically recognized, whereas the pocket for the other adenine appears to be promiscuous. Comparison with a homologous ligand-free DarA structure reveals that c-di-AMP binding is accompanied by conformational changes of both the fold and the position of the B-loop in DarA.
authors.affiliation: From the Departments of General Microbiology.
authors.forename: Jan
authors.initials: J
authors.lastname: Gundlach
authors.affiliation: Molecular Structural Biology, and.
authors.forename: Achim
authors.initials: A
authors.lastname: Dickmanns
authors.affiliation: Molecular Enzymology, Georg August University Göttingen, 37077 Göttingen, Germany.
authors.forename: Kathrin
authors.initials: K
authors.lastname: Schröder-Tittmann
authors.affiliation: Molecular Structural Biology, and.
authors.forename: Piotr
authors.initials: P
authors.lastname: Neumann
authors.affiliation: Molecular Structural Biology, and.
authors.forename: Jan
authors.initials: J
authors.lastname: Kaesler
authors.affiliation: From the Departments of General Microbiology.
authors.forename: Jan
authors.initials: J
authors.lastname: Kampf
authors.affiliation: From the Departments of General Microbiology.
authors.forename: Christina
authors.initials: C
authors.lastname: Herzberg
authors.affiliation: Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany.
authors.forename: Elke
authors.initials: E
authors.lastname: Hammer
authors.affiliation: BIOLOG Life Science Institute, 28199 Bremen, Germany, and.
authors.forename: Frank
authors.initials: F
authors.lastname: Schwede
authors.affiliation: Research Core Unit Metabolomics, Hannover Medical School, 30625 Hannover, Germany.
authors.forename: Volkhard
authors.initials: V
authors.lastname: Kaever
authors.affiliation: Molecular Enzymology, Georg August University Göttingen, 37077 Göttingen, Germany.
authors.forename: Kai
authors.initials: K
authors.lastname: Tittmann
authors.affiliation: From the Departments of General Microbiology, jstuelk@gwdg.de.
authors.forename: Jörg
authors.initials: J
authors.lastname: Stülke
authors.affiliation: Molecular Structural Biology, and rficner@uni-goettingen.de.
authors.forename: Ralf
authors.initials: R
authors.lastname: Ficner
mesh_terms: D001412:Bacillus subtilis / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D018360:Crystallography, X-Ray; D015226:Dinucleoside Phosphates / Q000378:metabolism*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D015398:Signal Transduction
chemical_list: D001426:Bacterial Proteins; D015226:Dinucleoside Phosphates; C528998:cyclic diadenosine phosphate
keywords: Bacterial Signal Transduction; Crystal Structure; Cyclic Di-GMP (c-di-GMP); Cyclic Diadenosine Monophosphate (c-di-AMP); Isothermal Titration Calorimetry (ITC)