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PDBsum entry 1jx2
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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 a dynamin gtpase domain in both nucleotide-Free and gdp-Bound forms.
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Authors
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H.H.Niemann,
M.L.Knetsch,
A.Scherer,
D.J.Manstein,
F.J.Kull.
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Ref.
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EMBO J, 2001,
20,
5813-5821.
[DOI no: ]
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PubMed id
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Abstract
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Dynamins form a family of multidomain GTPases involved in endocytosis, vesicle
trafficking and maintenance of mitochondrial morphology. In contrast to the
classical switch GTPases, a force-generating function has been suggested for
dynamins. Here we report the 2.3 A crystal structure of the nucleotide-free and
GDP-bound GTPase domain of Dictyostelium discoideum dynamin A. The GTPase domain
is the most highly conserved region among dynamins. The globular structure
contains the G-protein core fold, which is extended from a six-stranded
beta-sheet to an eight-stranded one by a 55 amino acid insertion. This
topologically unique insertion distinguishes dynamins from other subfamilies of
GTP-binding proteins. An additional N-terminal helix interacts with the
C-terminal helix of the GTPase domain, forming a hydrophobic groove, which could
be occupied by C-terminal parts of dynamin not present in our construct. The
lack of major conformational changes between the nucleotide-free and the
GDP-bound state suggests that mechanochemical rearrangements in dynamin occur
during GTP binding, GTP hydrolysis or phosphate release and are not linked to
loss of GDP.
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Figure 4.
Figure 4 Comparison of the nucleotide-binding site of empty and
GDP-bound dynamin A with those of empty EF-G and GDP-bound Ras.
(A) In nucleotide-free dynamin A, the side chain of Thr207 from
the TKLD motif makes a hydrogen bond (dashed lines) to the
carbonyl of Ser36 in the P-loop. Lys38 binds to residues from
switch II (Asp138 and Leu139). (B) In GDP-bound dynamin A, Lys38
preserves its interactions with residues from switch II and does
not bind to the  -phosphate.
Lys208 binds the endocyclic oxygen of the ribose and Asp210
makes two hydrogen bonds with the base, while Thr207 does not
bind the base. The coordination of the Mg2+ (magenta), which is
usually octahedral in G-proteins [see (D)], is non-standard due
to the disorder of the structural elements and water molecules
(cyan) in this region. (C) In nucleotide-free EF-G, the P-loop
Lys25 binds to residues from switch II, as in dynamin A. Asn137,
equivalent to dynamin A Thr207, interacts with the side chain of
Thr28 in the helix following the P-loop. (D) The canonical
nucleotide-binding site of Ras-GDP. Lys16 binds to the -phosphate.
The interactions of Lys117 and Asp119 with the nucleotide
correspond to those of Lys208 and Asp210 in dynamin A. Asn116 in
Ras makes two hydrogen bonds, one to the carbonyl of Val14 in
the P-loop and one to the base.
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Figure 5.
Figure 5 Comparison of dynamin A Phe50 and Ras Phe28. Dynamin A
is colored in orange and Ras in green. GDP is only shown for
Ras. Gly47 at the end of helix  1
allows the switch I loop to take off at a different angle in
dynamin A than in Ras, which has no glycine at the equivalent
position. In dynamin A, Phe50 is buried by hydrophobic residues
of the -sheet
(not shown) instead of stabilizing the base as Ras Phe28 does.
The position of the Ras G5 motif (145SAK147) and of dynamin A
Asn238 and Arg 239 is also shown.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2001,
20,
5813-5821)
copyright 2001.
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