α-Amylases from Thermoactinomyces vulgaris R-47 (TVA I and TVA II) hydrolyze pullulan to produce panose, and isopullulanase (IPU) from Aspeygillus niger ATCC 9642 hydrolyzes Pullulan to produce isopanose. The structure/function relationships of these pullulan-hydrolyzing enzymes were studied. The crystal structure of TVA II has been determined. TVA II is composed of domain A/B, which has a (β/α) ₈ barrel structure with a small component called domain B; domain C, which contains the C-terminus; and domain N, which contains the N-terminus. Although the role of domain N for the enzyme activity has been unclear, it is unique in the structures of the α-amylase family. We modified some amino acid residues in region II, one of the four regions conserved in α-amylase family enzymes, of the TVA I by means of site-directed mutagenesis. The action pattern of the mutated enzyme for pullulan was greatly altered and it produced maltotriose from pullulan. The ipuA gene encoding IPU has been isolated. Although IPU does not hydrolyze dextran, IPU showed a high amino acid sequence similarity with dextranases. The ipuA gene was expressed in Aspeygillus oryzae, and the substrate properties of the recombinant IPU were identical with those of the native enzyme.