Figure 5.

The BldD CTD Contains a c-di-GMP-Binding Signature Composed of Two Contiguous Motifs

(A) Structure of the BldD dimer-(c-di-GMP) complex. Top: the location of the two c-di-GMP-binding motifs (motif 1 and motif 2) of the bridged CTD promoters. Middle: a close-up of selected residues of the BldD CTD that interact with the c-di-GMP nucleotides. Bottom: alignment of the sequences of the S. venezuelae and S. coelicolor BldD CTDs. Motif 1 is colored cyan and motif 2 is magenta. Other residues that contact c-di-GMP are colored yellow.

(B) Close-up of the top and bottom layer CTD-(c-di-GMP) contacts, including the Arg114 side chain-guanine interactions, which anchor the two intercalated dimers together.

(C) Close-up of the central or middle layers of the two intercalated c-di-GMP dimers. Shown are the hydrogen bonds from R125 and one guanine and those between the N2 and N3 atoms of two guanines from different c-di-GMP dimers that tether the intercalated dimers in these layers.

(D) Side view of the c-di-GMP layers, highlighting the multiple base-base, side chain-base, and side chain-side chain stacking interactions that stabilize the c-di-GMP tetramer structure. Base stacking is depicted by appropriately colored solid lines.

See also Figures S2B, S5, and S7 and Tables S1 and S2.