Regulation of Ca2+ transport determines the duration of a Ca2+ signal, and hence, the nature of the biological response. Ca2+/H+ antiporters such as CAX1 (cation exchanger 1), play a key role in determining cytosolic Ca2+ levels. Analysis of a full-length CAX1 clone suggested that the CAX1 open reading frame contains an additional 36 amino acids at the N terminus that were not found in the original clone identified by suppression of yeast (Saccharomyces cerevisiae) vacuolar Ca2+ transport mutants. The long CAX1 (1CAX1) could not suppress the yeast Ca2+ transport defects despite localization to the yeast vacuole. Calmodulin could not stimulate 1CAX1 Ca2+/H+ transport in yeast; however, minor alterations in the 36-amino acid region restored Ca2+/H+ transport. Sequence analysis suggests that a 36-amino acid N-terminal regulatory domain may be present in all Arabidopsis CAX-like genes. Together, these results suggest a structural feature involved in regulation of Ca2+/H+ antiport.