Structure of the nucleotide-binding subunit B of the energy producer A₁A₀ ATP synthase in complex with adenosine diphosphate

A₁A₀ ATP synthases are the major energy producers in archaea. Like the related prokaryotic and eukaryotic F₁F₀ ATP synthases, they are responsible for most of the synthesis of adenosine triphosphate. The catalytic events of A₁A₀ ATP synthases take place inside the A₃B₃ hexamer of the A₁ domain. Recently, the crystallographic structure of the nucleotide-free subunit B of Methanosarcina mazei Gö1 A₁A₀ ATP synthase has been determined at 1.5 Å resolution. To understand more about the nucleotide-binding mechanism, a protocol has been developed to crystallize the subunit B–ADP complex. The crystallographic structure of this complex has been solved at 2.7 Å resolution. The ADP occupies a position between the essential phosphate-binding loop and amino-acid residue Phe149, which are involved in the binding of the antibiotic efrapeptin in the related F₁F₀ ATP synthases. This trapped ADP location is about 13 Å distant from its final binding site and is therefore called the transition ADP-binding position. In the trapped ADP position the structure of subunit B adopts a different conformation, mainly in its C-terminal domain and also in the final nucleotide-binding site of the central αβ-domain. This atomic model provides insight into how the substrate enters into the nucleotide-binding protein and thereby into the catalytic A₃B₃ domain.