Abstract:[Objective] Isomaltases IMA1 play key roles in full utilization of oligosaccharides containing α-1,6-O-glucosidic bonds. [Methods] We cloned, overexpressed, purified and characterized four isomaltases IMA1 from four strains of S. cerevisiae including three acidophilic ones. [Results] They showed similar pH and temperature dependence, but different kinetic parameters and thermostability. IMA1-A exhibited the highest binding affinity for α-MG (α-methylglucoside), turnover number, catalytic efficiency, and thermostability. Structure and sequence analysis revealed that even variation in two remote amino acids from the active residues and the substrate binding site could also lead to significantly different kinetic behavior and thermostability of isomaltases IMA1. [Conclusion] Our results will be useful for further investigation into the structure-function relationship of isomaltases IMA1.