The low-resolution structure and overall dimensions of the A(3)B(3)CDF complex of the A(1) ATPase from Methanosarcina mazei Gö1 in solution is analyzed by synchrotron X-ray small-angle scattering. The radius of gyration and the maximum size of the complex are 5.03 +/- 0.1 and 18.0 +/- 0.1 nm, respectively. The low-resolution shape of the protein determined by two independent ab initio approaches has a knob-and-stalk-like feature. Its headpiece is approximately 9.4 nm long and 9.2 nm wide. The stalk, which is known to connect the headpiece to its membrane-bound A(O) part, is approximately 8.4 nm long. Limited tryptic digestion of the A(3)B(3)CDF complex was used to probe the topology of the smaller subunits (C-F). Trypsin was found to cleave subunit C most rapidly at three sites, Lys(20), Lys(21), and Arg(209), followed by subunit F. In the A(3)B(3)CDF complex, subunit D remained protected from proteolysis.

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Recent molecular studies revealed nine to ten gene products involved in function/assembly of the methanoarchaeal ATPase and unravel a close relationship of the A1A0-ATPase and the V1V0-ATPase with respect to subunit composition and the structure of individual subunits. Most interestingly, there is an astonishing variability in the size of the proteolipids in methanoarchaeal A1A0-ATPases with six, four, or two transmembrane helices and a variable number of conserved protonizable groups per monomer. Despite the structural similarities the A1A0-ATPase differs fundamentally from the V1V0-ATPase by its ability to synthesize ATP, a feature shared with F1F0-ATPases. The discovery of duplicated and triplicated versions of the proteolipid in A1A0-ATP synthases questions older views of the structural requirements for ATP synthases versus ATP hydrolases and sheds new light on the evolution of these secondary energy converters.