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PDBsum entry 2cnw
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Signal recognition
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PDB id
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2cnw
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Contents |
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290 a.a.
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281 a.a.
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260 a.a.
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References listed in PDB file
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Key reference
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Title
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Structure of a gdp:alf4 complex of the srp gtpases ffh and ftsy, And identification of a peripheral nucleotide interaction site.
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Authors
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P.J.Focia,
J.Gawronski-Salerno,
J.S.Coon,
D.M.Freymann.
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Ref.
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J Mol Biol, 2006,
360,
631-643.
[DOI no: ]
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PubMed id
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Abstract
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The signal recognition particle (SRP) GTPases Ffh and FtsY play a central role
in co-translational targeting of proteins, assembling in a GTP-dependent manner
to generate the SRP targeting complex at the membrane. A suite of residues in
FtsY have been identified that are essential for the hydrolysis of GTP that
accompanies disengagement. We have argued previously on structural grounds that
this region mediates interactions that serve to activate the complex for
disengagement and term it the activation region. We report here the structure of
a complex of the SRP GTPases formed in the presence of GDP:AlF4. This complex
accommodates the putative transition-state analog without undergoing significant
change from the structure of the ground-state complex formed in the presence of
the GTP analog GMPPCP. However, small shifts that do occur within the shared
catalytic chamber may be functionally important. Remarkably, an external
nucleotide interaction site was identified at the activation region, revealed by
an unexpected contaminating GMP molecule bound adjacent to the catalytic
chamber. This site exhibits conserved sequence and structural features that
suggest a direct interaction with RNA plays a role in regulating the activity of
the SRP targeting complex.
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Figure 4.
Figure 4. The external nucleotide-binding site. (a) Omit
F[o]–F[c] electron density at the external nucleotide-binding
site, contoured at 3 σ (blue) and 7.5 σ (black). The density,
located between motifs II and III of FtsY (below, purple) and
the closing loop of Ffh (above), enters the water-filled channel
that abuts the shared active site chamber,^13 and is close to
both active site nucleotides (shown ”ghosted”). (b) Stereo
view of the hydrogen bonding interactions between the external
GMP molecule and residues and water molecules at the complex
interface are shown in an orientation similar to that in (a).
Key water molecules are shown as larger spheres and labeled as
in Figure 2(c). Ffh residues are highlighted in grey, FtsY
residues in purple, and motifs I, II and III are labeled. Phe141
participates in π-π stacking interactions with the purine
ring of the GMP molecule (front, center). Figure 4. The
external nucleotide-binding site. (a) Omit F[o]–F[c] electron
density at the external nucleotide-binding site, contoured at 3
σ (blue) and 7.5 σ (black). The density, located between
motifs II and III of FtsY (below, purple) and the closing loop
of Ffh (above), enters the water-filled channel that abuts the
shared active site chamber,[3]^13 and is close to both active
site nucleotides (shown ”ghosted”). (b) Stereo view of the
hydrogen bonding interactions between the external GMP molecule
and residues and water molecules at the complex interface are
shown in an orientation similar to that in (a). Key water
molecules are shown as larger spheres and labeled as in
[4]Figure 2(c). Ffh residues are highlighted in grey, FtsY
residues in purple, and motifs I, II and III are labeled. Phe141
participates in π-π stacking interactions with the purine ring
of the GMP molecule (front, center).
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Figure 5.
Figure 5. Features of the complex surface. Mutations of FtsY
interface residues that affect assembly of the complex, and
those that do not affect assembly but affect the subsequent
GTPase hydrolysis step,^15 are mapped onto the surface of FtsY
(gold, assembly defect; magenta, activity defect). The
orientation is looking into the GTPase binding site where bound
GTP is drawn as sticks. Activity defect mutations cluster (at
the bottom) near the FtsY active center, locating residues that
likely contribute to the activation region of the complex. The
relative position of the external nucleotide site is indicated
with an asterisk (*); however, formation of that binding site
requires assembly of the heterodimer. Figure 5. Features of
the complex surface. Mutations of FtsY interface residues that
affect assembly of the complex, and those that do not affect
assembly but affect the subsequent GTPase hydrolysis step,[3]^15
are mapped onto the surface of FtsY (gold, assembly defect;
magenta, activity defect). The orientation is looking into the
GTPase binding site where bound GTP is drawn as sticks. Activity
defect mutations cluster (at the bottom) near the FtsY active
center, locating residues that likely contribute to the
activation region of the complex. The relative position of the
external nucleotide site is indicated with an asterisk (*);
however, formation of that binding site requires assembly of the
heterodimer.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2006,
360,
631-643)
copyright 2006.
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