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PDBsum entry 2eqb
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Endocytosis/exocytosis
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PDB id
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2eqb
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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 sec4p{middle dot}sec2p complex in the nucleotide exchanging intermediate state.
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Authors
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Y.Sato,
S.Fukai,
R.Ishitani,
O.Nureki.
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Ref.
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Proc Natl Acad Sci U S A, 2007,
104,
8305-8310.
[DOI no: ]
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PubMed id
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Abstract
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Vesicular transport during exocytosis is regulated by Rab GTPase (Sec4p in
yeast), which is activated by a guanine nucleotide exchange factor (GEF) called
Sec2p. Here, we report the crystal structure of the Sec2p GEF domain in a
complex with the nucleotide-free Sec4p at 2.7 A resolution. Upon complex
formation, the Sec2p helices approach each other, flipping the side chain of
Phe-109 toward Leu-104 and Leu-108 of Sec2p. These three residues provide a
hydrophobic platform to attract the side chains of Phe-49, Ile-53, and Ile-55 in
the switch I region as well as Phe-57 and Trp-74 in the interswitch region of
Sec4p. Consequently, the switch I and II regions are largely deformed, to create
a flat hydrophobic interface that snugly fits the surface of the Sec2p coiled
coil. These drastic conformational changes disrupt the interactions between
switch I and the bound guanine nucleotide, which facilitates the GDP release.
Unlike the recently reported 3.3 A structure of the Sec4p.Sec2p complex, our
structure contains a phosphate ion bound to the P-loop, which may represent an
intermediate state of the nucleotide exchange reaction.
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Figure 2.
Fig. 2. Sec4p·Sec2p binding interface. (a)
Stereoview of the detailed Sec4p·Sec2p binding interface.
The coloring scheme is the same as in Fig. 1b. Hydrogen bonds
are shown by dotted orange lines. (b) Schematic representation
of the Sec4p·Sec2p interface. The hydrogen bonds (with a
3.4 Å cutoff) are displayed as solid orange lines. The
hydrophobic contacts (with a 4.0 Å cutoff) are displayed
as dotted green lines. The labels of the switch I, interswitch,
switch II, and other regions of Sec4p are highlighted in cyan,
brown, pink, and gray, respectively. The labels of the sharply
and moderately bent helices of Sec2p are highlighted in yellow
and green, respectively.
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Figure 4.
Fig. 4. Comparison of the Sec4p·GDP and Sec2p-bound
Sec4p structures. (a) Comparison of the overall structures of
Sec4p·GDP and Sec2p-bound Sec4p. Sec4p·GDP was
superposed onto Sec4p in the Sec4p·Sec2p·phosphate
complex, except for the residues 42–47, and the switch I
(residues 48–56) and switch II (residues 76–93) regions.
Sec4p·GDP is colored yellow, and Sec4p in the
Sec4p·Sec2p·phosphate complex is colored as in
Fig. 1b. The carbon atoms of the Sec4p-bound GDP are green, and
the bound cobalt ion is yellow. (b) Comparison of the Sec2p
binding region in the Sec4p·GDP and Sec2p-bound Sec4p
structures. Coloring schemes are the same as in a. Dotted black
arrows indicate positional changes of the amino acid residues.
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