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Figure 4.
Fig. 4. Structure of the proposed signal peptide binding
site. (A) Closed conformation of the hydrophobic groove in the
S. solfataricus SRP54/RNA complex. The finger loop is folded
into the groove. Helix  ML is not shown for
clarity. Elements involved in signal peptide binding are named.
(B) Superposition of the M domain of S. solfataricus (red) and
T. aquaticus (blue) to visualize the different conformations of
the signal peptide binding groove including the finger loop and
helix M1b. Movements between
structures are indicated by black arrows. The position of the
conserved motifs GP (green) and PG (pink) differ significantly,
the two "anchor" points (Leu-329 and Ile-374) are marked as
spheres. (C) Structure of the M domain of T. aquaticus Ffh with
the finger loop in an open conformation. A putative signal
peptide (gray cylinder) is modeled into the binding site. (D)
Model for the conformational changes in the SRP core. SRP54 is
shown in a ribbon diagram; color code is as in Fig. 1 A.
Rearrangements in SRP54 upon interaction with a signal peptide
at the ribosome (see text) are indicated by arrows, the linker
region LGMGD is indicated by a blue sphere, the anchor points
Leu-329 and the N terminus of helix M2 (Ile-374) as well as
the GP and PG motifs are shown as pink spheres. The M[N] domain
is adjusted at the four pink spheres to adopt a conformation
competent for signal peptide binding as shown in C. The GTP
(space-filling model) and the signal peptide (gray cylinder) are
placed in their respective binding sites.
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