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Figure 4.
Figure 4. DNA Interaction Surface of σ^70[2](A) Stereo
RIBBONS ([10]) diagram of the cluster of four helices comprising
the conserved regions. The view is 180° about a vertical
axis from the view of Figure 3. Helix 14, containing part of
conserved region 2.3 and conserved region 2.4, runs nearly
horizontally across the middle of the picture. Shown in yellow
are residues that comprise the conserved hydrophobic core
(Ile-119, Ile-123, Ala-375, Met-379, Val-380, Val-387, Ala-391,
Leu-399, Leu-404, Leu-412, Ala-415, Val-416, Phe-419, Phe-427,
Ala-431, Ile-435, Ile-439, Ile-443). Other residues are shown in
color as follows: cyan, exposed conserved aromatic residues from
region 2.3, important for promoter melting; orange, residues
known to interact with the −12 position of the −10 consensus
element; blue, conserved basic residues flanking the promoter
recognition and promoter melting residues that may be involved
in DNA phosphate backbone interactions.(B) Likely orientation of
helix 14/nontemplate DNA strand interactions. The backbone of
helix 14 is shown as a coil with the solvent-exposed face of the
helix facing down. The α-carbon positions of residues important
for promoter recognition or melting are indicated. Schematically
illustrated below is the nontemplate strand sequence of the
−10 consensus element. Interactions between specific residues
and bases determined from genetic or biochemical studies are
indicated by dashed lines. The interaction indicated between the
residue at position 441 and the −13 position is not specific
in the case of σ^70 (the −13 position is not conserved in the
−10 element recognized by σ^70) but is indicated from genetic
studies on alternative σ factors that recognize −10 elements
with a conserved −13 position ([15]).
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