The Dps Protein Protects Escherichia coli DNA in the Form of the Trimer

The Dps protein is the major DNA-binding protein of prokaryotes, which protects DNA during starvation by forming a crystalline complex. The structure of such an intracellular DNA-Dps complex is still unknown. However, the phenomenon of a decrease in the size of the Dps protein from 90 Å to 69-75 Å during the formation of a complex with DNA has been repeatedly observed, and no explanation has been given. In this work, we show that during the formation of intracellular DNA-Dps crystals, the protein transitions to another oligomeric form: from a dodecameric (of 12 monomers), which has an almost spherical shape with a diameter of 90 Å, to a trimeric (of three monomers), which has a shape close to a torus-like structure with a diameter of 70 Å and a height of 40 Å. The trimer model was obtained through the molecular dynamic modeling of the interaction of the three monomers of the Dps protein. Placement of the obtained trimer in the electron density of in vitro DNA-Dps crystal allowed for the determination of the lattice parameters of the studied crystal. This crystal model was in good agreement with the SAXS data obtained from intracellular crystals of 2-day-old Escherichia coli cells. The final crystal structure contains a DNA molecule in the through channel of the crystal structure between the Dps trimers. It was discussed that the mechanism of protein transition from one oligomeric form to another in the cell cytoplasm could be regulated by intracellular metabolites and is a simple and flexible mechanism of prokaryotic cell transition from one metabolic state to another.