Abstract
Homodimeric H+-pyrophosphatase (H+-PPase; EC 3.6.1.1) is a unique enzyme playing a pivotal physiological role in pH homeostasis of organisms. This novel enzyme supplies energy at expense of hydrolyzing metabolic byproduct, pyrophosphate (PPi), for H+ translocation across membrane. The functional unit of a monomer suffices for enzymatic reaction of H+-PPase, while that for the translocation is homodimer. Its active site on each subunit consists of PPi binding motif, Acidic I and II motifs, and several essential residues. In this investigation, structural mapping of these vital regions was primarily determined utilizing single molecule fluorescence resonance energy transfer. Distances between two C termini and also two N termini on homodimeric subunits of H+-PPase are 49.3 ± 4.0 Å and 67.2 ± 5.7 Å, respectively. Furthermore, putative PPi binding motifs on individual subunits are found to be relatively far away from each other (70.8 ± 4.8 Å), while binding of potassium and substrate analogue led them to closer proximity (56.6 ± 4.1 Å). Moreover, substrate analogue but not potassium elicits significantly distance variations between two Acidic I motifs and two H622 residues on homodimeric subunits. Taken together, this study provides the first quantitative measurements of distances between various essential motifs, residues and putative active sites on homodimeric subunits of H+-PPase. A working model is accordingly proposed elucidating the distance variations of dimeric H+-PPase upon substrate binding.