Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2001 Oct 9;98(21):11973-8.
doi: 10.1073/pnas.211429998. Epub 2001 Oct 2.

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

C L Drennan  1 , J Heo, M D Sintchak, E Schreiter, P W Ludden
Affiliations

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

C L Drennan et al. Proc Natl Acad Sci U S A. .

Abstract

A crystal structure of the anaerobic Ni-Fe-S carbon monoxide dehydrogenase (CODH) from Rhodospirillum rubrum has been determined to 2.8-A resolution. The CODH family, for which the R. rubrum enzyme is the prototype, catalyzes the biological oxidation of CO at an unusual Ni-Fe-S cluster called the C-cluster. The Ni-Fe-S C-cluster contains a mononuclear site and a four-metal cubane. Surprisingly, anomalous dispersion data suggest that the mononuclear site contains Fe and not Ni, and the four-metal cubane has the form [NiFe(3)S(4)] and not [Fe(4)S(4)]. The mononuclear site and the four-metal cluster are bridged by means of Cys(531) and one of the sulfides of the cube. CODH is organized as a dimer with a previously unidentified [Fe(4)S(4)] cluster bridging the two subunits. Each monomer is comprised of three domains: a helical domain at the N terminus, an alpha/beta (Rossmann-like) domain in the middle, and an alpha/beta (Rossmann-like) domain at the C terminus. The helical domain contributes ligands to the bridging [Fe(4)S(4)] cluster and another [Fe(4)S(4)] cluster, the B-cluster, which is involved in electron transfer. The two Rossmann domains contribute ligands to the active site C-cluster. This x-ray structure provides insight into the mechanism of biological CO oxidation and has broader significance for the roles of Ni and Fe in biological systems.

PubMed Disclaimer

Figures

Scheme 1
Scheme 1
Figure 1
Figure 1
(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.
Figure 2
Figure 2
(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.
Figure 3
Figure 3
Identification of the positions of Ni and Fe in the C-cluster by using data from a two-wavelength Ni-edge experiment. The (FNi-remote − FNi-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.
Figure 4
Figure 4
(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 (2Fobs − Fcalc) 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 (Fobs − Fcalc) 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.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Uffen R L. Proc Natl Acad Sci USA. 1976;73:3298–3302. - PMC - PubMed
    1. Ragsdale S W, Kumar M. Chem Rev. 1996;96:2515–2539. - PubMed
    1. Bartholomew G W, Alexander M. Appl Environ Microbiol. 1979;37:932–937. - PMC - PubMed
    1. Kasting J F. Science. 1993;259:920–926. - PubMed
    1. Seravalli J, Kumar M, Lu W-P, Ragsdale S W. Biochemistry. 1995;34:7879–7888. - PubMed

Publication types

Associated data