Crystal structure of the archaeal A1Ao ATP synthase subunit B from Methanosarcina mazei Go1:: Implications of nucleotide-binding differences in the major A1Ao Subunits A and B

The A(1)A(O) ATP synthase from archaea represents a class of chimeric ATPases/synthases, whose function and general structural design share characteristics both with vacuolar VIVO ATPases and with F1FO ATP synthases. The primary sequences of the two large polypeptides A and 13, from the catalytic part, are closely related to the eukaryotic VIVO ATPases. The chimeric nature of the A(1)A(O) ATP synthase from the archaeon Methanosarcina mazei Go1 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 angstrom resolution, providing the first view of the so-called non-catalytic subunit of the A(1)A(O) ATP synthase. Superposition of the A-ATP synthase non-catalytic B subunit and the F-ATP synthase non-catalytic alpha 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 A(1)A(O) ATP synthase is presented. (c) 2006 Elsevier Ltd. All rights reserved.