|
Figure 4.
Figure 4. a, Model of the apo-ArgRBst−DNA interaction. The
apoArgRBst hexamer is shown superimposed on the arginine-bound
ArgRBst−C hexamer as in Fig. 2c, but with the bottom trimers
removed for clarity. DNA-binding domains are labeled a-f at the
 3
helices. The bent DNA duplex from the CAP/DNA complex^23 was
extended in both directions to give a total length of 38 base
pairs, docked with the apo-ArgRBst hexamer, then undocked for
clarity. Arrows indicate clashes between the 3
helices and the phosphate backbone of the DNA duplex. b, Model
of the arginine-bound ArgRBst−DNA interaction. The top (green)
trimer in ArgRBst was independently rotated (by ~15°) onto
the ArgRBst-C core trimer to approximate the quaternary
structure of ArgRBst in the arginine-bound state. Arrows
indicate 3-major
groove contacts when docked with the hexamer in the orientation
shown. c, Schematic representation of ArgR DNA operators. E.
coli operators contain 18 base pair 'Arg boxes' separated by a
2−3 base pair spacer^21, ^22. Arrows indicate 9 base pair
half-sites that are arranged as inverted repeats within the E.
coli consensus Arg box sequence. The B. subtilis and B.
stearothermophilus operator sequences show only limited homology
to the E. coli operators, but similar nuclease and chemical
protection patterns and the ability of B. subtilis AhrC to
complement ArgR functions in E. coli indicate that the
repressor−operator interactions are closely related^3, ^8.
|
