The crystal structure of DMP12 presents a DNA-like surface. (A) The secondary structural elements are shown above the amino acid sequence, with blue cylinders representing α-helices and green arrows representing β-sheets. (B) A ribbon diagram of two DMP12 monomers in an asymmetric unit. The α-helices and β-sheets were colored red and yellow, respectively, in one DMP12 monomer, and cyan and purple in the other, respectively. Two magnesium ions (orange) were found on the protein surface. (C) Comparison of the surface charge distribution of DMP12 and HU-bound dsDNA. DMP12 electrostatic potential surface is colored by Pymol, with red to blue representing the electrostatic potential from −77 to +77 kBT. The DNA surface is colored according to atomic charge by the same program. The distances between the β-carbons of neighboring acidic residues on DMP12 and the phosphate groups on HU-bound dsDNA were measured, and similar distances between the negative spots on DMP12 and HU-bound dsDNA were found. The pseudo 2-fold symmetries of the Hu-interacting surface of the HU/DNA complex and our proposed HU-DMP12-binding model are indicated by a green rhombus. (D) DMP12's β-carbons were used to indicate the location of the negatively charged side chains of ASP and GLU on the DMP12 monomer. β-Carbons that were matched in the DNA of the HU-bound dsDNA are labeled as red spheres; non-matched carbons are white. This diagram is shown in stereo. (E) Proposed HU-DMP12–binding model. This model was produced by the alignment of the negatively charged spots and shapes of the DMP12 monomer and the phosphate backbone of HU-bound dsDNA in Figure 2C and D. In this model, the HU-bound dsDNA in the HU/DNA complex (PDB code: 1P78) is overlaid by DMP12.
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