Fig. 6.

Interaction of σ⁷⁰ region 4 with -35 element and the β-flap versus its interaction with AsiA and MotA. Structures of (A) T. aquaticus σ region 4 (residues corresponding to E. coli σ⁷⁰ residues 546-612) with the –35 region of promoter DNA ⁸ (PDB: 1KU7) and of (B) E. coli σ⁷⁰ region 4 (residues 546-613) with AsiA (residues 2-90) ³⁰ (PDB: 1TLH). σ⁷⁰ region 4 is shown in gold, AsiA is shown in green, and the DNA is shown in magenta. Alpha helices H2, H3, H4, and H5 in σ⁷⁰ (see Fig. 1A) are labeled. Spacefill structures of σ⁷⁰ residues 551, 554, and 555 in region 4.1 and residues 584 and 587 in region 4.2, which are predicted to interact with AsiA in the structure and whose substitution impairs the σ⁷⁰/AsiA interaction, are shown in red in (B). The portion of σ⁷⁰ region 4 that interacts with the β-flap is indicated by the blue oval in (A). H5 of σ⁷⁰ that interacts with MotA is indicated by the black rectangle in (B). Note that the binding of AsiA to σ⁷⁰ region 4 converts H3-T-H4 of σ⁷⁰, which normally interacts with the –35 sequences of promoter DNA, into one continuous helix.