Crystal Structure of the Archaeal A1AO ATP Synthase Subunit B from Methanosarcina mazei Gö1: Implications of Nucleotide-binding Differences in the Major A1AO Subunits A and B

The A1AO ATP synthase from archaea represents a class of chimeric ATPases/synthases, whose function and general structural design share characteristics both with vacuolar V1VO ATPases and with F1FO ATP synthases. The primary sequences of the two large polypeptides A and B, from the catalytic part, are closely related to the eukaryotic V1VO ATPases. The chimeric nature of the A1AO ATP synthase from the archaeon Methanosarcina mazei Gö1 was investigated in terms of nucleotide interaction. Here, we demonstrate the ability of the overexpressed A and B subunits to bind ADP and ATP by photoaffinity labeling. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to map the peptide of subunit B involved in nucleotide interaction. Nucleotide affinities in both subunits were determined by fluorescence correlation spectroscopy, indicating a weaker binding of nucleotide analogues to subunit B than to A. In addition, the nucleotide-free crystal structure of subunit B is presented at 1.5 Å resolution, providing the first view of the so-called non-catalytic subunit of the A1AO ATP synthase. Superposition of the A-ATP synthase non-catalytic B subunit and the F-ATP synthase non-catalytic α subunit provides new insights into the similarities and differences of these nucleotide-binding ATPase subunits in particular, and into nucleotide binding in general. The arrangement of subunit B within the intact A1AO ATP synthase is presented.