Abstract
Ffh is the signal sequence recognition and targeting
subunit of the prokaryotic signal recognition particle (SRP). Previous structural studies of the NG
GTPase domain of Ffh demonstrated magnesium-dependent and magnesium-independent
binding conformations for GDP and GMPPNP that are believed to reflect novel
mechanisms for exchange and activation in this member of the GTPase
superfamily. The current study of
the NG GTPase bound to Mg2+GDP reveals two new binding conformations
– in the first the magnesium interactions are similar to those seen previously,
however, the protein undergoes a conformational change that brings a conserved
aspartate into its second coordination sphere. In the second, the protein conformation is similar to that
seen previously, but the magnesium coordination sphere is disrupted so that
only five oxygen ligands are present.
The loss of the coordinating water molecule, at the position that would
be occupied by the oxygen of the g-phosphate of GTP, is
consistent with that position being privileged for exchange during phosphate
release. The available structures
of the GDP-bound protein provide a series of structural snapshots that illuminate
steps along the pathway of GDP release following GTP hydrolysis.
This manuscript establishes that the catalytic configuration of conserved motif II observed in the SRP GTPase complex arises from a conformational ensemble. There is an interesting followup to the observation of a five-coordinate Mg2+ ion in one of the two active sites in the crystal structure - see: Kluge, S., & Weston, J. (2005) Can a hydroxide ligand trigger a change in the coordination number of magnesium ions in biological systems? Biochemistry 44 4877-85