 |
PDBsum entry 1ls1
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Protein transport
|
PDB id
|
|
|
|
1ls1
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Structural basis for mobility in the 1.1 a crystal structure of the ng domain of thermus aquaticus ffh.
|
|
|
Authors
|
|
U.D.Ramirez,
G.Minasov,
P.J.Focia,
R.M.Stroud,
P.Walter,
P.Kuhn,
D.M.Freymann.
|
|
|
Ref.
|
|
J Mol Biol, 2002,
320,
783-799.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
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
Thermus aquaticus refined at 1.10 A 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 alpha4 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.
|
|
|
|
|
|
|
|
Figure 3.
Figure 3. Anisotropic temperature factors reflect coherent
motion of the N-domain. The anisotropic ellipsoids of motion at
the 90% probability level for the a-carbon atoms of helices aN1
and aN2 highlight the mobility of the main-chain atoms of the
N-domain. The principal axes of vibration along both of the
helices are largely coherent (  vert,
similar up and down; compare with the ellipsoids near residue
1). The direction of this motion (presumably trapped substrates
in the crystal) is similar to that seen between the apo and GDP
complex crystal structures.
|
|
Figure 8.
Figure 8. Conserved residues at the NG interface contribute
to a well-packed interface. Small probe contact dots[8] are
shown at a dot density of 50 dots/Å2. The color of the
dots indicates the types of interactions, with blue dots
indicating wide contacts, greater than 0.25 Å, green
indicating close contacts between 0 Å and 0.25 Å,
yellow indicating small overlaps of less than 0.2 Å, and
purple indicating hydrogen bonds. Hydrogen atoms are included in
the analysis, but are not shown in the Figure. (a) The packing
density around Gly253 and Gly254 (at the center) is especially
tight for glycine residues and thus explains conservation of
these two residues. (b) Leu257 appears to have relatively few
interactions; however, those are with highly conserved residues,
including Leu5, Val43, Leu38, and Leu82. Note the interaction
between Leu5 and Leu257, which involves methyl hydrogen atoms of
the two residues. (c) Interactions with Ser258, which is a
completely conserved residue in the SRP GTPases. Both the
Gly253/Gly254 and Ser258 interactions serve as the "glue" across
the N/G interaction surface.
|
|
|
|
|
|
The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2002,
320,
783-799)
copyright 2002.
|
|
|
|
|
|
|
