Fig. 9.

Structural model of the recognition of the −10 region of promoter by σ³².

A. Comparison of the recognition of the −10 region of promoters by σ⁷⁰ and σ³². Amino acid sequences of Regions 2.3, 2.4 and 3.0 of σ⁷⁰, σ^A and σ³² are shown. The −10 consensus promoter sequences for each σ is indicated above or below the amino acid sequences. Thick arrows indicate contacts suggested by the previous studies for σ⁷⁰ and in this study for σ³². Arrow with dotted line indicates contact to increase selectivity.

B. Shown is the structure of σ^A Regions 2.1–3.0 and the −10 element region of the fork-junction promoter DNA from the T. aquaticus holoenzyme/fork-junction promoter DNA complex (Murakami et al., 2002). The rest of the protein and DNA are not shown. The σ^A Region 2.4 is coloured green and Region 3.0 is magenta. Most of the 3.0 helix is transparent for clarity. The positions corresponding to residues of σ³² that make base-specific contacts with the promoter are shown as α-carbon spheres, and colour-coded along with the corresponding DNA base pair: W108 (W257 in T. aquaticus σ^A)/−11CG, blue; E112 (A261)/−11CG, blue; and K130 (M279)/−13CG/−14CG, purple. This figure was prepared using PyMol (http://pymol.sourceforge.net/).