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PDBsum entry 2bcg
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Protein transport
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PDB id
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2bcg
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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 doubly prenylated ypt1:gdi complex and the mechanism of gdi-Mediated rab recycling.
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Authors
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O.Pylypenko,
A.Rak,
T.Durek,
S.Kushnir,
B.E.Dursina,
N.H.Thomae,
A.T.Constantinescu,
L.Brunsveld,
A.Watzke,
H.Waldmann,
R.S.Goody,
K.Alexandrov.
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Ref.
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EMBO J, 2006,
25,
13-23.
[DOI no: ]
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PubMed id
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Abstract
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In eukaryotic cells Rab/Ypt GTPases represent a family of key membrane traffic
controllers that associate with their targeted membranes via C-terminally
conjugated geranylgeranyl groups. GDP dissociation inhibitor (GDI) is a general
and essential regulator of Rab recycling that extracts prenylated Rab proteins
from membranes at the end of their cycle of activity and facilitates their
delivery to the donor membranes. Here, we present the structure of a complex
between GDI and a doubly prenylated Rab protein. We show that one geranylgeranyl
residue is deeply buried in a hydrophobic pocket formed by domain II of GDI,
whereas the other lipid is more exposed to solvent and is skewed across several
atoms of the first moiety. Based on structural information and biophysical
measurements, we propose mechanistic and thermodynamic models for GDI and Rab
escort protein-mediated interaction of RabGTPase with intracellular membranes.
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Figure 1.
Figure 1 Structure of the doubly prenylated Ypt1:GDI complex.
(A) Ribbon representation of GDI (blue) bound to Ypt1 (yellow).
Domain I (dark blue), domain II (light blue), the Rab-binding
platform (red), the C-terminus-binding region (CBR gold) and the
mobile effector loop (MEL green) of GDI are highlighted. The
Switch I and II regions of Ypt1 are highlighted in green and
grey, respectively. The helices composing domain II of GDI are
marked by letters. The isoprenoid moieties 1 (red) and 2 (dark
yellow) are displayed in ball-and-stick representation. The GDP
(atomic colours) and Mg2+ (magenta) ion are shown in the
nucleotide-binding pocket in ball-and-stick and space filling
representations, respectively. Unless otherwise indicated, this
and other figures were prepared using ICM (Molsoft LLC). (B)
Plot of a sigma A-weighted F[o]-F[c] map contoured at 2  (red)
or at 0.6 (black)
in the region of the geranylgeranyl. The maps were generated
after several refinement rounds omitting the GG groups. The
picture was generated with BobScript and RASTER3D (Merritt and
Murphy, 1994; Esnouf, 1997). (C) Domain II of GDI from
Ypt1GG:GDI complex displayed in ribbon representation (grey);
the secondary structure elements are denoted as in (A). The last
visible residues of the Ypt1 C-terminus and of the MEL of GDI
are coloured blue and green, respectively. The geranylgeranyl
moieties 1 (red) and 2 (blue) filling the lipid binding site are
displayed in ball-and-stick representation.
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Figure 3.
Figure 3 Model for the GDI-mediated Rab/Ypt interaction with the
putative Rab receptors and membranes. (A) GDI-mediated delivery
of prenylated RabGTPases to the membrane is proposed to involve
docking of the Rab:GDI complex with a putative membrane Rab
recruitment/GDF via a protein:protein interaction (2). The
docked complex undergoes a conformational change, which leads to
the transfer of the first and then the second geranylgeranyl
moiety into the membrane and subsequently to the release of the
Rab C-terminus from the CBR (3 and 4). Finally, GDI is released
into the cytosol and the Rab protein enters its functional
cycle. (B) GDI-mediated extraction of prenylated RabGTPases from
the membrane. Initial recognition is mediated by the
low-affinity interaction of the Rab-binding platform with the
CBR of GDI (7). This leads to the positioning of GDI domain II
on the lipid bilayer over the buried geranylgeranyl moieties of
the Rab protein (8). The geranylgeranyl lipids are transferred
from the membrane to the lipid binding sites on GDI in two
consecutive steps (9 and 10), leading to dissociation of the
complex from membrane (11).
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
EMBO J
(2006,
25,
13-23)
copyright 2006.
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