X-ray absorption spectroscopic evidence for a unique nickel site in Clostridium thermoaceticum carbon monoxide dehydrogenase

Abstract

Carbon monoxide dehydrogenase (COdH) in Clostridium thermoaceticum is an a3/33 protein containing six nickels per molecule, in addition to a number of Fe-S clusters. Previous electron paramagnetic resonance (ÉPR) spectroscopic work has suggested that nickel is involved in binding CO forming an EPR-detectable species, which is probably a key intermediate in the oxidation of CO to C02 and in the synthesis of acetate. In order to better define the nature of this nickel site, Ni X-ray absorption spectra have been recorded and interpreted by comparison with model compounds. The extended X-ray absorption fine structure (EXAFS) spectrum for oxidized COdH is different from that of other Ni enzymes. Both the EXAFS and the X-ray absorption edge spectra suggest a Ni site containing substantial sulfur ligation. The Ni X-ray absorption edge spectrum of rubredoxin-oxidized COdH exhibits a characteristic shoulder with an inflection point at 8336 eV. Such a feature is absent in octahedral model compounds, whereas a well-resolved peak is observed in square-planar Ni complexes. A distinct Is -3d transition at 8333 eV is observed in a tetrahedral model. The lack of correspondence suggests that square-pyramidal and distorted-square-planar geometries are plausible candidates for the COdH Ni site. Treatment of rubredoxin-oxidized COdH with hydrogenase and H2 shifts the Ni edge to lower energies, indicating Ni-based reduction.

On the structure of the nickel/iron/sulfur center of the carbon monoxide dehydrogenase from Rhodospirillum rubrum: an x-ray absorption spectroscopy study.

“…Sci. USA 89 (1992) From spectra of others (16,34,35) as well as those recorded by us, several conclusions can now be drawn about the Ni site in Rr-CODH. (i) The edge spectra for oxidized and reduced Rr-CODH (data not shown) are very nearly superimposable, thus indicating that the additional electron does not reside in primarily Ni-derived orbitals and that there is no significant structural rearrangement upon oxidation/ reduction.…”

“…Edge features indicate that a planar fourcoordinate structure is unlikely and point to a distorted noncentric tetrahedral or five-coordinate Ni environment in oxidized and reduced Rr-CODH. As for C. thermoaceticum CODH (15,16), no firm evidence is found for the presence of Ni-Fe interactions. One model consistent with our XAS results is a mononuclear Ni2+ site, bridged by S-Cys or sulfide to one or both Fe4S4 clusters with the remaining coordination sites being occupied by additional S-Cys or N/O-liganding amino acids.…”

“…Included for comparison are Ni edge spectra of several S-and N,S-coordinated Ni complexes of planar (top traces), distorted five-coordinate and tetrahedral (middle traces), and NiFe3S4-cubane (bottom traces) geometry. Ni K-edge features show systematic trends that have been interpreted to be diagnostic of certain coordination geometries (16,34,35). The relatively weak preedge feature around 8333 eV is generally accepted to derive from a ls-+ 3d transition.…”

“…Some of these enzymes effect the synthesis of acetyl coenzyme A by means of the Wood pathway (13,14). Recent extended x-ray absorption fine structure (EXAFS) and x-ray absorption spectroscopy (XAS) edge studies of the CO-free, electron paramagnetic resonance-silent form of CODH from Clostridium thermoaceticum indicate a NiS4 (15) or =NiS2(O/N)2 (16) coordination environment with distorted square-planar or pyramidal geometry (16). EXAFS further suggests that an Fe-S cluster may be nearby (15).…”

Incorporation of thiolate donation using 2,2′-dithiodibenzaldehyde: Complexes of a pentadentate N2S3 ligand with relevance to the active site of Co nitrile hydratase

“…Examples include nitrile hydratase [1][2][3][4][5][6][7][8][9][10] and the A-cluster of carbon monoxide dehydrogenase/acetyl CoA synthase [11][12][13][14][15][16][17][18][19][20][21][22][23]. Understanding the catalytic mechanisms of these enzymes can be greatly aided by the study of small-molecule analogs, or model complexes, which reproduce the active-site structure and/or the function of the enzyme.…”