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The structural basis for the GTP-dependent co-translational targeting complex
between the signal recognition particle (SRP) and its receptor is unknown. The
complex has been shown to have unusual kinetics of formation, and association in
vivo is likely to be dependent on catalysis by the SRP RNA. We have determined
conditions for RNA-independent association of the 'NG' GTPase domains of the
prokaryotic homologs of the SRP components, Ffh and FtsY, from Thermus
aquaticus. Consistent with previous studies of the Escherichia coli proteins,
the kinetics of association and dissociation are slow. The T. aquaticus FtsY is
sensitive to an endogenous proteolytic activity that cleaves at two sites--the
first in a lengthy linker peptide that spans the interface between the N and G
domains, and the second near the N-terminus of the N domain of FtsY. Remarkably,
this second cleavage occurs only on formation of the Ffh/FtsY complex. The
change in protease sensitivity of this region, which is relatively unstructured
in the FtsY but not in the Ffh NG domain, implies that it undergoes
conformational change on formation of the complex between the two proteins. The
N domain, therefore, participates in the interactions that mediate the
GTP-dependent formation of the targeting complex.
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