The NG domain of the prokaryotic signal recognition
protein Ffh is a two-domain GTPase that comprises part of the prokaryotic
signal recognition particle (SRP) that functions in co-translational targeting
of proteins to the membrane. The
interface between the N and G domains includes two highly conserved sequence
motifs and is adjacent in sequence and structure to one of the conserved GTPase
signature motifs. Previous
structural studies have shown that the relative orientation of the two domains
is dynamic. The N domain of Ffh
has been proposed to function in regulating the nucleotide binding interactions
of the G domain. However,
biochemical studies suggest a more complex role for the domain in integrating
communication between signal sequence recognition and interaction with receptor. Here, we report the structure of the
apo NG GTPase of Ffh from T. aquaticus refined at 1.10
Å resolution. Although the G
domain is very well ordered in this structure, the N domain is less well
ordered, reflecting the dynamic relationship between the two domains previously
inferred. We demonstrate that the
anisotropic displacement parameters directly visualize the underlying mobility
between the two domains, and present a detailed structural analysis of the
packing of the residues, including the critical a4 helix ,
that comprise the interface. Our
data allows us to propose a structural explanation for the functional
significance of sequence elements conserved at the N/G interface.
PDB: 1LS1
Comment
Here we took advantage of ultra high resolution diffraction from crystals of the Ffh NG domain to carefully examine the anisotropic temperature factor distribution, which revealed underlying domain motion in the crystal consistent with that observed in the comparison of lower resolution structures of the apo and nucleotide bound protein. We were able to show that there were characteristics of the hydrogen atom packing in the interior of the protein that provided the structural basis for this mobility. Much of the analysis was carried out using computational tools developed at in the Richardson Lab at Duke.