The alpha metallosubunit of carbon monoxide dehydrogenase from Clostridium thermoaceticum was isolated by subjecting native enzyme to low concentrations of the detergent sodium dodecyl sulfate, followed by anaerobic preparative native polyacrylamide gel electrophoresis. The isolated alpha subunit absorbs in the 400 nm region and contains one Ni and four Fe ions. The irons are organized into an [Fe4S4](2+/1+) cluster, the reduced form of which exhibits EPR features between g = 6 and 3, and a weak (0.1 spin/alpha) g(av) = 1.94 signal. The reduced cluster appears to exist in an S = 3/2 : S = 1/2 spin-state mixture and to be predominantly S = 3/2 at 10 K. The Ni center is EPR silent and presumably Ni(II). X-ray absorption edge and EXAFS spectra reveal that the Ni center has a distorted square-planar geometry with two S donors at 2.19 degrees and two N/O donors at 1.89 Angstrom. Comparison of the Ni edge spectrum with those of structurally characterized Ni(II)N2S2 model compounds suggests a D-2d distortion with a dihedral angle of about 20-30 degrees. The Ni center does not appear to be incorporated into the cluster, and it may or may not be bridged to the cluster. These centers may be decompositional relatives of the A-cluster, the active site for acetyl-coenzyme A synthesis.