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Results: 5

1.
Figure 1

Figure 1. From: Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase.

(A) Ribbon drawing of R. rubrum CODH monomer. The N-terminal helical domain is in red and the α/β Rossmann domains are in green and blue. The C-, B-, and D-clusters are in space-filling representations with Fe atoms in white, S in yellow, and the Mb site in orange (see Scheme S1). It should be noted that although the entire bridging D-cluster is shown, only half of the cluster is coordinated by each monomer. All figures were made by using RIBBONS (34). (B) Topology diagram of CODH with same domain coloring as shown in A. The positions of the metalloclusters are shown as yellow circles.

Catherine L. Drennan, et al. Proc Natl Acad Sci U S A. 2001 October 9;98(21):11973-11978.
2.
Figure 3

Figure 3. From: Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase.

Identification of the positions of Ni and Fe in the C-cluster by using data from a two-wavelength Ni-edge experiment. The (FNi-remoteFNi-edge) dispersive Fourier map (magenta) indicates the position of Ni. This map is calculated at 3.5-Å resolution and contoured at 6 sigma. A 3.5-Å resolution anomalous difference Fourier map (cyan) calculated at the Ni-edge wavelength, and contoured at 4 sigma, indicates the position of Fe. See text for discussion. For both Fourier maps, atoms of the clusters are omitted in the phase calculation. Color scheme: C atoms, green; N, blue; Fe of cube, white; S, yellow; Ma site, cyan; Mb site, orange.

Catherine L. Drennan, et al. Proc Natl Acad Sci U S A. 2001 October 9;98(21):11973-11978.
3.
Figure 2

Figure 2. From: Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase.

(A) Ribbon drawing of the top view of the R. rubrum CODH dimer with molecule 1 in blue and molecule 2 in green. The C-, B-, and D-clusters are in space-filling representations with Fe atoms in white, S in yellow, the Mb site in orange, and the Ma site in blue. Note the B-cluster of molecule 2 (B′) is adjacent to the C-cluster of molecule 1 (C), and that the B-cluster of molecule 1 (B) is adjacent to the C-cluster of molecule 2 (C′). Distances between the centers of the clusters are indicated. (B) Ribbon drawing of the side view of the R. rubrum CODH dimer. The D-cluster provides a path for electrons from the buried B- and C-clusters to the surface. The D-cluster may interact with CooF, the iron-sulfur membrane-anchor protein.

Catherine L. Drennan, et al. Proc Natl Acad Sci U S A. 2001 October 9;98(21):11973-11978.
4.
Figure 4

Figure 4. From: Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase.

(A) Stereoview of the C-cluster. The identity of the ligand to Ni (Ma site) is unknown (position marked with an *). Same color scheme as Fig. 3. (B) A 2.8-Å resolution (2FobsFcalc) electron density map (pink) for the C-cluster. The electron density is spread out near Cys531, and the exact position of the side chain is difficult to determine. Positive difference (FobsFcalc) electron density maps (blue) suggest the presence of an additional ligand to Ni. (C) Model of metal–COOH intermediate. If COOH is placed in the general area of the open coordination sites on Ni and FCII, it can interact with His95 and Lys568. His95, which is part of a hydrogen-bonding network with Asp223 and Trp575 and is ≈2.6 Å away from the modeled intermediate, could act as the catalytic base. Lys568, which is within hydrogen-bonding distance (≈2.5 Å), could stabilize the intermediate. (D) Putative tunnel (shown as a cylinder), identified by visual inspection of electron density maps, leading from the active site to solvent in R. rubrum CODH. His95 and Lys568 (red ball-and-stick) sit at the top of the tunnel. Histidine residues 98, 101, and 108 (red ball-and-stick), conserved among CODH sequences, line the putative tunnel.

Catherine L. Drennan, et al. Proc Natl Acad Sci U S A. 2001 October 9;98(21):11973-11978.
5.
Scheme 1

Scheme 1. From: Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase.

The Ni-Fe-S cluster responsible for CO oxidation to CO2 has been studied extensively by spectroscopic methods (reviewed in refs. 2 and 7–13). Issues addressed include whether the Ni is part of the cubane (site Ma, Scheme S1) or in a mononuclear site (site Mb, Scheme S1). Extended x-ray absorption fine structure (EXAFS) spectroscopy comparing the R. rubrum CODH (EC 1.2.99.2) with model [NiFe3S4] cubanes (10) and Mössbauer spectroscopy (7) favor a model for the C-cluster that contains one Ni atom in the Mb site bridged to an Fe with usual coordination in the Ma site (Ni-X-[Fe4S4]). This unusual Fe is typically denoted as FCII. It is therefore surprising that the results of anomalous dispersion experiments presented here suggest that Ni is located in the cube (Ma site) and that Fe is located in the Mb site. The presence of an Fe atom in a site coordinated by a histidine residue is consistent with electron nuclear double resonance (ENDOR) spectroscopy on Clostridium thermoaceticum CODH/ACS enzyme (12) and electron paramagnetic resonance (EPR) spectroscopy on the R. rubrum CODH (13). The R. rubrum CODH structure reveals that the only histidine ligand coordinates the Mb site (Scheme I), suggesting that the Mb site contains Fe. It has also been suggested that the Mb site is a [NiFe] binuclear cluster rather than a mononuclear site (11, 13). This possibility is ruled out by the current x-ray analysis.

Catherine L. Drennan, et al. Proc Natl Acad Sci U S A. 2001 October 9;98(21):11973-11978.

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