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PDBsum entry 2d3t
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Lyase, oxidoreductase/transferase
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PDB id
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2d3t
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References listed in PDB file
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Key reference
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Title
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Ligand-Induced domain rearrangement of fatty acid beta-Oxidation multienzyme complex.
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Authors
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D.Tsuchiya,
N.Shimizu,
M.Ishikawa,
Y.Suzuki,
K.Morikawa.
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Ref.
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Structure, 2006,
14,
237-246.
[DOI no: ]
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PubMed id
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Abstract
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The quaternary structure of a fatty acid beta-oxidation multienzyme complex,
catalyzing three sequential reactions, was investigated by X-ray
crystallographic and small-angle X-ray solution scattering analyses. X-ray
crystallography revealed an intermediate structure of the complex among the
previously reported structures. However, the theoretical scattering curves
calculated from the crystal structures remarkably disagree with the experimental
profiles. Instead, an ensemble of the atomic models, which were all calculated
by rigid-body optimization, reasonably explained the experimental data. These
structures significantly differ from those in the crystals, but they maintain
the substrate binding pocket at the domain boundary. Comparisons among these
structures indicated that binding of 3-hydroxyhexadecanoyl-CoA or nicotinamide
adenine dinucleotide induces domain rearrangements in the complex. The
conformational changes suggest the structural events occurring during the chain
reaction catalyzed by the multienzyme complex.
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Figure 2.
Figure 2. Substrate Recognition in the a Subunit
(A)
Local structures around the adenine base binding site in the a
subunit, observed in forms I (red) and V (orange, green). The
bound ligand is acetyl-CoA, which is an analog of
3-hydroxyacyl-CoA.
(B and C) The corresponding structures
of the (B) proximal and (C) distal subunits in form II.
(D)
Superimposition of the two a subunits in the apparently
symmetric form I, in which the acetyl-CoA (the red space-filling
model) was observed. The ligand bound subunit (red) is more open
than the unliganded one (blue). As a consequence, only the aC
domain exhibits a significant difference. The circle with the
broken line indicates the adenine base moiety in (A).
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2006,
14,
237-246)
copyright 2006.
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Secondary reference #1
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Title
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Structural basis for channelling mechanism of a fatty acid beta-Oxidation multienzyme complex.
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Authors
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M.Ishikawa,
D.Tsuchiya,
T.Oyama,
Y.Tsunaka,
K.Morikawa.
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Ref.
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EMBO J, 2004,
23,
2745-2754.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2 Active sites of three FOM components. Stereo diagrams
show catalytic and hydrophobic residues around ligands in Form
I. (A) Two C[8]E[5] molecules bound to each ECH of the dimer (
 1
and 2)
in different modes, 'inside' (clear gray) and 'outside' (faint
gray). The alkyl groups of two C[8]E[5] molecules are trapped
with hydrophobic residues. Some parts of main chains (light
brown) represent identical portions to rECH (Engel et al, 1996).
(B) Ac-CoA and NAD^+ molecules bound to HACD in the Native3
crystal. The acetyl group of Ac-CoA points into the hydrophobic
tunnel. (C) Ac-CoA molecules bound to the two KACT subunits. In
Form II, the interaction of Arg369 with Val134 causes the 1 Å
elevation (arrow) of the loop containing Val134 and Pro136
(cyan), and the subsequent rotation of the Trp70:  2
side chain (cyan).
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Figure 5.
Figure 5 Homology model of the human TFE complex. (A) The
symmetric TFE architecture, with the mutation sites (red
spheres) relevant to various genetic diseases (Ibdah et al,
1998; Eaton et al, 2000). The arrowheads denote the HACD active
sites. The inset indicates Val282, located in the interface
between ECH in the -subunit
and KACT in the -subunit.
The insertion specific for TFE is depicted by dotted lines with
asterisks. (B) Electrostatic surface representation showing the
biased distribution of positive charges around the central
solvent region.
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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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