An electrochemical gradient of protons (PMF) is a universal high-energy intermediate in biological systems. Two related families of proton pumps, denoted F- and V-ATPases, are among the principal generators of a PMF from ATP and can form ATP at the expense of a PMF. The enzymes of these two families share a similar structure and subunit composition; some subunits in the two families evolved from common ancestors. Other subunits having no common ancestry were added independently to the various enzymes and defined the two separate families. The general mechanism for the proton pumping activity is similar in the two families. However, whereas F-ATPases can act in both proton pumping and ATP formation, the V-ATPases of eukaryotes function exclusively as ATP-dependent proton pumps. The catalytic and membrane sectors of F-ATPases and archaebacterial V-ATPases can separately catalyze their specific partial activities of ATPase and proton conduction. The catalytic and membrane sectors of the eukaryotic V-ATPases cannot act separately. This property is correlated with the presence of a large proteolipid that traverses the membrane four times. The gene duplication of the smaller proteolipid in the formation of the large proteolipid was one of the most important events in the evolution of the V-ATPases of eukaryotic cells.

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