Figure 4. WhiB7 interactions with σ^AD4 and DNA.

A. Structure-based sequence alignment of Mtb WhiB7 and WhiB1. Residues of WhiB1 that interact with σ^AD4 (Wan et al., 2020) are highlighted by the nature of interactions and compared to those of WhiB7 (this study). Residues of σ^AD4 participating in ionic interactions are indicated above or below the sequences. The DNA binding AT-hook motif of WhiB7 is boxed. The interactions between WhiB7 and σ^AD4 were determined using a 4.5 Å distance cutoff (CCP4) (Winn et al., 2011) between carbon atoms for nonpolar interactions, a 4.5 Å cutoff between basic and acidic side chains for ionic interactions, and a 3.5 Å cutoff for hydrogen bonds between donors and acceptors. Identical residues are bolded orange, homologous residues colored orange, and the conserved cysteines that chelate the 4Fe-4S cluster are in bolded purple. The secondary structure of each protein is shown in red: H indicates helices.

B. Residues of WhiB7 and σ^AD4 that interact with each other are shown in stick, and each protein’s backbone is shown in cartoon tube. Dotted lines connect residues of σ^AD4 and WhiB7 that participate in ionic or hydrogen bond interactions. The 4Fe-4S cluster is drawn as spheres.

C. Top left: WhiB7 AT-hook interactions with the AT-rich DNA are indicated. Both the AT-hook and the DNA are drawn as cartoon sticks and colored, as indicated. Bottom left: A top view showing the WhiB7 AT-hook fits intimately into the minor groove of the AT-rich motif. The DNA is rendered in surface, and backbone oxygens are colored red to highlight the ionic and hydrogen bonds between WhiB7 and the DNA. Top Right: an alignment of the AT-rich DNA of W-RPo to that of the crystal structure of the human HMGA1 AT-hook with DNA (Fonfría-Subirós et al., 2012) shows that the AT-hooks superimpose well. Bottom Right: Image in the top inset shows the W-RPo structure for reference with the region of interest boxed.