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PDBsum entry 1fkm
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Endocytosis/exocytosis
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PDB id
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1fkm
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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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Crystal structure of the gap domain of gyp1p: first insights into interaction with ypt/rab proteins.
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Authors
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A.Rak,
R.Fedorov,
K.Alexandrov,
S.Albert,
R.S.Goody,
D.Gallwitz,
A.J.Scheidig.
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Ref.
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EMBO J, 2000,
19,
5105-5113.
[DOI no: ]
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PubMed id
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Abstract
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We present the 1.9 A resolution crystal structure of the catalytic domain of
Gyp1p, a specific GTPase activating protein (GAP) for Ypt proteins, the yeast
homologues of Rab proteins, which are involved in vesicular transport. Gyp1p is
a member of a large family of eukaryotic proteins with shared sequence motifs.
Previously, no structural information was available for any member of this class
of proteins. The GAP domain of Gyp1p was found to be fully alpha-helical.
However, the observed fold does not superimpose with other alpha-helical GAPs
(e.g. Ras- and Cdc42/Rho-GAP). The conserved and catalytically crucial arginine
residue, identified by mutational analysis, is in a comparable position to the
arginine finger in the Ras- and Cdc42-GAPs, suggesting that Gyp1p utilizes an
arginine finger in the GAP reaction, in analogy to Ras- and Cdc42-GAPs. A model
for the interaction between Gyp1p and the Ypt protein satisfying biochemical
data is given.
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Figure 4.
Figure 4 The putative Ypt binding cleft. (A) Electrostatic
surface representations viewed into the concave side of the
molecule. The figure was generated using the program GRASP
(Nicholls et al., 1993) and rendered with the program raster3D
(Merritt and Murphy, 1994). Red indicates negatively charged (-7
kT) and blue positively charged regions (+7 kT). (B) Surface CPK
representation of the Gyp1p Ypt-GAP domain shown in the same
orientation as in (A). Residues that are highly conserved in the
different Gyp Ypt-GAP domains are coloured pink; well conserved
residues are coloured yellow (see sequence alignment, Figure 2).
Residues that are solvent accessible and form the surface of the
cleft are labelled.
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Figure 5.
Figure 5 Docking approach for the complex between Gyp1p and
Ypt51p-GTP, modelled manually on the basis of known GAP–GTPase
structures. (A) Active site of the complex formed between
p120-GAP and H-Ras p21(GDP-AlF[3]). The hydrogen bonds between
GAP residues Arg789 and Arg903 and H-Ras p21 residues Gln61 and
Glu63 as well as with AlF[3] are indicated. This specific
hydrogen bond network and the orientation of the side chains
were used as a model for manual docking of Ypt51-GTP to
Gyp1-46p. (B) Close-up view of the active site in the putative
Gyp1-46p–Ypt51-GTP complex. For the interaction between the
side chain of Arg343 and the  -phosphate
group, the salt bridge formed between Arg343 and Asp340 has to
be broken. Gln66 of Ypt51p is well oriented to become positioned
closer to the -phosphate
by forming a hydrogen bond between its side chain and the main
chain carbonyl group of Arg343 of Gyp1p. (C) Ribbon
representation of the putative complex. The orientation of
Gyp1-46p is the same as in Figure 1. The essential arginine
Arg343 of Gyp1p, the active site glutamine Gln66 of Ypt51p and
the bound nucleotide GTP are shown in ball-and-stick
representation. This figure was generated using the programs
BOBSCRIPT (Esnouf, 1997) and raster3D (Merritt and Murphy, 1994).
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2000,
19,
5105-5113)
copyright 2000.
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Secondary reference #1
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Title
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Identification of the catalytic domains and their functionally critical arginine residues of two yeast gtpase-Activating proteins specific for ypt/rab transport gtpases.
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Authors
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S.Albert,
E.Will,
D.Gallwitz.
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Ref.
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EMBO J, 1999,
18,
5216-5225.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1 Schematic representation of N- and C-terminal
truncations of Gyp1p and Gyp7p. The amino acids contained in the
GAP fragments tested for activity are shown to the left.
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Figure 4.
Figure 4 Sequence alignment of the catalytically active domains
of Gyp1p and Gyp7p. Shared motifs (A -F) according to Neuwald
(1997) were aligned manually, intermediate regions using the
CLUSTAL V program (Higgins et al., 1992). Identical residues are
highlighted on a black, invariant arginines on a blue and the
essential arginine on a red background. Conservative
substitutions are shaded. Arrows indicate the start of the
shortest active fragments identified.
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by Macmillan Publishers Ltd
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