Structure of the Ni/Fe-S protein subcomponent of the acetyl-CoA decarbonylase/synthase complex from Methanosarcina thermophila at 26-Å resolution

The acetyl-CoA decarbonylase/synthase (ACDS) complex is responsible for synthesis and cleavage of acetyl-CoA in methanogens. The complex is composed of five different subunits, with a probable stoichiometry of α₈β₈γ₈δ₈ε₈. The native molecular mass of a subcomponent of the ACDS complex from Methanosarcina thermophila, the Ni/Fe-S protein containing the 90-kDa α and 19-kDa ε subunits, was determined by scanning transmission electron microscopy. A value of 218.6 ± 19.6 kDa (n = 566) was obtained, thus establishing that the oligomeric structure of this subcomponent is α₂ε₂. The three-dimensional structure of α₂ε₂ was determined at 26-Å resolution by analysis of a large number of electron microscopic images of negatively strained, randomly oriented particles. The α₂ε₂ subcomponent has a globular appearance, 110 Å in diameter, and consists of two large, hemisphere-like masses that surround a hollow internal cavity. The two large masses are connected along one face by a bridge-like structure and have relatively less protein density joining them at other positions. The internal cavity has four main openings to the outside, one of which is directly adjacent to the bridge. The results are consistent with a structure in which the large hemispheric masses are assigned to the two α subunits, with ε₂ as the bridge forming a structural link between them. The structure of the α₂ε₂ subcomponent is discussed in connection with biochemical data from gel filtration, crosslinking, and dissociation experiments and in the context of its function as a major component of the ACDS complex.