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PDBsum entry 1o87
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Protein transport
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PDB id
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1o87
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Novel protein and mg2+ configurations in the mg2+gdp complex of the srp gtpase ffh.
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Authors
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P.J.Focia,
H.Alam,
T.Lu,
U.D.Ramirez,
D.M.Freymann.
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Ref.
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Proteins, 2004,
54,
222-230.
[DOI no: ]
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PubMed id
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Abstract
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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 Mg(2+)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 gamma-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.
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Figure 1.
Figure 1. Ribbon diagram of the nucleotide bound protein. The
ribbon diagram of monomer A of the Mg^2+GDP complex of the Ffh
NG domain is oriented to view into the active site. The  -helical
N domain is in light blue, and the G domain is in light green.
The motif I P-loop at the center of the G domain interacts with
the phosphate groups of GDP (ball-and-stick). Motif II to the
left, and motif III to the center right (indicated), interact
with the bound magnesium ion through intervening water
molecules. The hydrated magnesium ion is shown as a CPK
representation. The carboxylate group of Asp248 hydrogen-bonds
the guanine base; the carboxylate of Asp135 contributes to the
second coordination sphere of the magnesium in monomer A, but is
usually found in a different conformation (see text).
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Figure 3.
Figure 3. Difference in magnesium ion hydration in monomers A
and B. The 2Fo-Fc electron density maps of the hydrated
magnesium ions in the active sites of monomers A and B are
shown, contoured at 1.0  .
In monomer A, each of the coordinating water molecules is
clearly defined. In contrast, although three coordinating waters
are well defined in monomer B, and the temperature factors of
the magnesium ions and coordinating waters are similar, no
coordinating water at position 1 (asterisk) is visible in the
electron density map. As this position is the site of
interaction with the  -phosphate
oxygen of bound GTP, facile exchange may be functionally
significant. The magnesium omit difference map allowed for an
identical interpretation. Thr112 and the phosphate groups of the
bound GDP are shown in each figure. The map cover radius was 1.1
Å, including the missing water position.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2004,
54,
222-230)
copyright 2004.
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