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Results: 6

1.
Figure 1

Figure 1. From: Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site.

The quality of the electron density. Section of the electron-density map of cyanase calculated (a) using phases based on 30 selenium sites and (b) after density modification and phase extension to 1.65 Å resolution (see Materials and methods section for details). Atoms are shown in standard colors. (The figure was generated with Bobscript [61].)

Martin A Walsh, et al. Structure. ;8(5):505-514.
2.
Figure 3

Figure 3. From: Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site.

Cartoon representation of the cyanase decamer. (a) View looking down the fivefold axis of the decamer. (b) View perpendicular to the fivefold axis and looking down the twofold axis. One cyanase dimer is highlighted using the same colors and labeling scheme as described in Figure 2. Ten chloride ions, which bind at the five active sites of the decamer (see text), are shown. The chloride ions shown in black are situated at the active sites to which the highlighted cyanase dimer contributes; the remaining bound chloride ions are colored purple. All other dimers are colored uniformly with α helices in cyan and β strands in yellow. (The figure was generated with Molscript [62] and rendered with Raster 3D [63].)

Martin A Walsh, et al. Structure. ;8(5):505-514.
3.
Figure 5

Figure 5. From: Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site.

Ball-and-stick diagram showing orthogonal views of the five Arg87 cavity-bound sulfate ions in the cyanase decamer. (a) Looking down the fivefold axis. (b) Perpendicular to the fivefold axis. Residues are labeled by their sequence number and respective monomer chain, as described in Figure 4. The bound sulfate ions are labeled as K111–K115, which follows the assignment in the coordinate file 1DW9 deposited in the PDB. The arginine residues are colored blue and yellow to highlight the delineation of the monomers as above and below the equatorial β-sheet belt formed by the dimer interface domain (see Figure 3). The sulfate ions are colored by atom type (sulfur, orange; oxygen, red). (The figure was generated with Molscript [62] and rendered with Raster 3D [63].)

Martin A Walsh, et al. Structure. ;8(5):505-514.
4.
Figure 6

Figure 6. From: Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site.

Alignment of the amino acid sequences for the five known cyanases. Accession numbers are given in parentheses. Residues conserved in all cyanases are in boldface and labeled with an asterisk, less conserved residues are labeled with colons and full stops. Arg96, Glu99, Ser122 (proposed active-site residues) are shown in red. Secondary structure assignments were derived using the Kabsch and Sander DSSP algorithm [64]: h/H, α helix; t/T, turn; eE, β strand; and S, bend. The aligned sequences are Synechocystis PCC6803 (GenBank accession number Q55367) [29]; Synechococcus PCC7942 (BAA19515) [28]; Aquifex aeolicus (AACO6548) [25]; E. coli (AAA23629) [8]; and Arabidopsis thaliana (BAA21660) [32].

Martin A Walsh, et al. Structure. ;8(5):505-514.
5.
Figure 4

Figure 4. From: Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site.

Decamer stabilization and catalytic site of cyanase. (a) Location of the four pairs of salt bridges (indicated by dashed lines) that stabilize the cyanase decamer. The dimer pairs are color coded: green (subunit A)/red (subunit D) and orange (subunit B)/yellow (subunit F). The labeling scheme is as described in Figure 2. The catalytic site of cyanase showing (b) bound chloride and (c) bound oxalate ions. The proposed catalytic residues are drawn in ball-and-stick representation using the same color scheme as in (a). Chloride and oxalate ions are in ball-and-stick representation colored in black and blue, respectively. Hydrogen-bond interactions are represented by dashed lines. The cyanase monomers are labeled by their chain (A, B, D, F), and secondary structure elements are labeled as described in Figure 2. (The figure was generated with Molscript [62] and rendered with Raster 3D [63].)

Martin A Walsh, et al. Structure. ;8(5):505-514.
6.
Figure 2

Figure 2. From: Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site.

The cyanase dimer. (a) Ribbon diagram of the cyanase dimer. The cyanase monomers are colored red and green. Secondary structure elements are labeled H for an α helix and S for a β strand: helix 1 (H1) consists of residues 8–24; helix 2 (H2), 29–33; helix 3 (H3), 40–47; helix 4 (H4), 55–64; helix 5 (H5), 69–76; helix 6 (H6), 92–115; strand 1 (S1), 119–134; strand 2 (S2), 140–152. A prime symbol distinguishes the two monomers. (b) Stereoview Cα trace of the cyanase dimer. The colors are as described in (a) with every 20th residue labeled. (The figure was generated with Molscript [62] and rendered with Raster 3D [63].)

Martin A Walsh, et al. Structure. ;8(5):505-514.

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