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Figure 7.
Figure 7. The Arginine-Rich, Helix-Turn-Helix Motif of the
M Domain(A) Stereo view of the HTH motif (αM3 to αM4) and a
third helix (αM2) of the M domain (green) superimposed onto the
corresponding region from the lac repressor (blue) ([9]). The
least-squares overlap of α carbons was performed using LSQMAN (
[24]). Conserved residues contributing to the compact
hydrophobic core of the lac repressor are indicated, along with
their counterparts in the M domain. Helix αM4 extends beyond
helix α2 of the lac repressor by  vert,
similar 3 additional turns and contains basic residues at an
extended C terminus; these characteristics are similar to the
recognition helix of homeodomain DNA-binding proteins ([14]).(B)
Stereo view of the conserved SRP RNA-binding motif of Ffh. This
view is rotated vert,
similar 90° about the vertical axis with respect to the
orientation in Figure 7A. Positively charged side chains located
in helix αM3 are likely to mediate the specific interaction of
the M domain with SRP RNA. Arg-387 and Arg-361 form well-ordered
salt bridges with the conserved residues Glu-373 and Glu-398,
respectively.
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