Investigations of the metal ion-binding sites of yeast inorganic pyrophosphatase

Abstract

Yeast inorganic pyrophosphatase was found to bind two Mn2+ per subunit in the absence of phosphate and three Mn2+ per subunit in the presence of phosphate. Kinetic studies of the pyrophosphatase-catalyzed hydrolysis of Cr(NH3)4PP and Cr(H2O)4PP were carried out with Mn2+ and with Mg2+ as activators. The results from these studies suggest that three divalent cations per pyrophosphatase active site are required for catalysis. NMR and EPR studies were conducted to evaluate the relative location of the metal ion binding sites on the enzyme. The two Mn2+ ions bound to the free enzyme are in close enough proximity to magnetically interact. Analysis of the NMR and EPR data in terms of a dipolar relaxation mechanism between Mn2+ ions provides an estimate of the distance between them of 10-14 A. When the diamagnetic substrate analog [Co(NH3)4PNP]- or intermediate analog [Co(NH3)4 (P)2]- are bound to pyrophosphatase, two Mn2+ ions still bind to the enzyme and their magnetic interaction increases. In the presence of these Co3+ complexes, the Mn2+--Mn2+ separation decreases to 7-9 A. Several NMR and EPR experiments were conducted at low Mn2+ to pyrophosphatase ratios (approximately 0.3), where only one Mn2+ ion binds per subunit, in the presence of Cr3+ or Co3+ complexes of PNP or PP. Analysis of the Mn2+--Cr3+ dipolar relaxation evident in proton NMR and EPR data provided for the calculation of Mn2+--Cr3+ distances. When the substrate analog CrPNP was present, the Mn2+--Cr3+ distance was congruent to 7 A whereas, when Cr(P)2 was bound to pyrophosphatase, the Mn2+--Cr3+ distance was congruent to 5 A. These results strongly support a model for the catalytic site of pyrophosphatase that involves three metal ion cofactors.