Extracellular proteases are often produced as pre-pro-enzyme and then undergo multiple processing steps to mature into the active form. The protease Epp, a virulent factor of Vibrio anguillarum, belongs to this family. Its maturation might be regulated by Ca2+ via its polycystic kidney disease (PKD) domain, but the molecular mechanism is unknown. Herein, we report the crystal structure of the first PKD domain from V. anguillarum Epp (Epp-PKD1) and its specific Ca2+ -binding capacity. Epp-PKD1 exists as a monomer, consisting of seven beta-strands which form two beta-sheets stacking with each other. One Ca2+ is bound by the residues Asn3, Gln4, Asp27, Asp29, Asp68 and a water molecule with a pentagonal bipyramidal geometry. Incubating the apo Epp-PKD1 with Ca2+ but not Mg2+, Mn2+, or Zn2+, enhances the thermal and chemical stability of Epp-PKD1, indicating its specific binding to Ca2+. Epp-PKD1 shares high similarity in both sequence and overall structure with that of Vibrio cholerae PrtV, a homologous protease of Epp, however, they differ in the oligomeric state and local structure at the Ca2+-binding site, suggesting maturation of PrtV and Epp might be differently regulated by Ca2+. Likely, proteases may take advantage of the structural diversity in PKD domains to tune their Ca2+-regulated maturation process. (C) 2018 Elsevier Inc. All rights reserved.