1. Volume 14, Issue 2, Pages 237-246 (February 2006)
Ligand-Induced Domain Rearrangement of Fatty Acid β-Oxidation Multienzyme Complex 
Daisuke Tsuchiya, Nobutaka Shimizu, Momoyo Ishikawa, Yoshikazu Suzuki, Kosuke Morikawa 
Structure 
Volume 14, Issue 2, Pages (February 2006)
DOI: /j.str
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2. Figure 1 Overall Structure of the FOM Complex
(A) Two orthogonal views of the complex in the form V crystal. The α subunit comprises the three domains: αN (orange), αM (green), and αC (cyan). The yellow helix connects αN and αM. The dimeric β subunits are colored dark/faint purple. The proximal α subunit is drawn with the dark colors, while the faint coloring indicates the distal subunit. The stick models represent the bound ligands (blue, NAD+; red, acetyl-CoA).
(B) Comparison of structures among forms I (red), II (blue), and V (green). These figures are viewed as in (A). Only the β subunits were superimposed to highlight the overall 2-fold symmetry. Arrows indicate projected translations for the HACD region (dark coloring) onto the paper plane. All structural illustrations were prepared with the programs MOLSCRIPT (Kraulis, 1991) and Raster3D (Merrit and Bacon, 1997).
Structure  , DOI: ( /j.str )
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3. Figure 2 Substrate Recognition in the α Subunit
(A) Local structures around the adenine base binding site in the α 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 α 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 αC domain exhibits a significant difference. The circle with the broken line indicates the adenine base moiety in (A).
Structure  , DOI: ( /j.str )
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4. Figure 3 Experimental Solution Scattering Profiles
The solution scattering profiles for the ligand-free (red), the NAD+ bound (blue), and the 3HA(C16)-CoA bound (green) states are plotted with their error bars (±1 SD). The curves in the two regions, (I) 0.07 < Q < 0.11 (Å−1) and (II) 0.13 < Q < 0.18 (Å−1), show the significant differences among the three.
Structure  , DOI: ( /j.str )
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5. Figure 4
Rigid-Body Optimization of the Structure with the Experimental Scattering Profile
(A–F) Structural ensembles for (A) the ligand-free, (C) the NAD+ bound, and (E) the 3HA(C16)-CoA bound states are displayed by the Cα traces. Each rigid-body unit is colored differently (red, αN1; yellow, αM1; yellow-green, αC1; green, αN2; cyan, αM2; purple, αC2; magenta, β2 dimer). The scattering curves calculated from the mean structures (black lines) are overlaid onto the corresponding experimental scattering profile (red dots with error bars [±1 SD]) for (B) the ligand-free, (D) the NAD+ bound, and (F) the 3HA(C16)-CoA bound states. The upper plots represent deviations of the calculated curve from the observed intensities.
Structure  , DOI: ( /j.str )
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6. Figure 5 Structural Comparison among the Mean Structures
(A) The adenine base binding pocket observed in the crystal (red), onto which the corresponding structures for the ligand-free (yellow and yellow-green), the NAD+ bound (green and cyan), and the 3HA(C16)-CoA bound (purple and magenta) states are superimposed. The Cα positions of the four residues forming the pocket are shown with spheres. The red stick model represents the bound acetyl-CoA molecule. This figure is viewed as in Figure 2A.
(B and C) Comparison of the α subunit in the mean structure (B) between the ligand-free (red) and the NAD+ bound (cyan) and (C) between the NAD+ bound (cyan) and the 3HA(C16)-CoA bound (blue) structures when the β subunits (green) are superimposed. The regions that undergo structural changes are highlighted by the dark coloring. The numbers in parentheses refer to the order of the operation, indicated by arrows.
Structure  , DOI: ( /j.str )
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7. Figure 6
A Proposed Structural Event during the Chain Reaction Catalyzed by the FOM Complex
(A–F) The coloring is the same as in Figure 1A, except the dark colors show the subunits in the catalytic reaction. The encircled S represents the bound substrate, which is transferred between the component enzymes, as indicated by purple arrows. In (A) and (F), the FOM complex is in a dynamic equilibrium between the two structural states.
Structure  , DOI: ( /j.str )
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