Aspergillus niger isopullulanase (IPU) is the only pullulanhydrolase in glycosyl hydrolase (GH) family 49 and does not hydrolyse dextran at all, while all other GH family 49 enzymes are dextran-hydrolysing enzymes. To investigate the common catalytic mechanism of GH family 49 enzymes, nine mutants were prepared to replace residues conserved among GH family 49 (four Trp, three Asp and two Glu). Homology modelling of IPU was also carried out based on the structure of Penicillium minioluteum dextranase, and the result showed that Asp353, Glu356, Asp372, Asp373 and Trp402, whose substitutions resulted in the reduction of activity for both pullulan and panose, were predicted to be located in the negatively numbered subsites. Three Aspmutated enzymes, D353N, D372N and D373N, lost their activities, indicating that these residues are candidates for the catalytic residues of IPU. The W402F enzyme significantly reduced IPU activity, and the K m value was sixfold higher and the k 0 value was 500-fold lower than those for the wildtype enzyme, suggesting that Trp402 is a residue participating in subsite )1. Trp31 and Glu273, whose substitutions caused a decrease in the activity for pullulan but not for panose, were predicted to be located in the interface between N-terminal and b-helical domains. The substrate preference of the negatively numbered subsites of IPU resembles that of GH family 49 dextranases. These findings suggest that IPU and the GH family 49 dextranases have a similar catalytic mechanism in their negatively numbered subsites in spite of the difference of their substrate specificities.Keywords: dextranase; GH family 49; isopullulanase; pullulan-hydrolase; site-directed mutagenesis.Isopullulanase (IPU, EC 3.2.1.57; pullulan 4-glucanohydrolase) from Aspergillus niger ATCC9642 hydrolyses pullulan to produce isopanose (Glc-a-(1fi4)-Glc-a-(1fi6)-Glc) and also hydrolyses substrates containing the panose (Glc-a-(1fi6)-Glc-a-(1fi4)-Glc) structure, and cleaves the a-1,4-glucosidic linkage in the panose motif [1,2]. Enzymes that hydrolyse specific sites of pullulan can be classified into the following three types (schematic action patterns of these enzymes have been illustrated previously [2]). (a) Pullulanase (EC 3.2.1.41), which hydrolyses a-1,6-glucosidic linkages to produce maltotriose [3]; (b) Thermoactinomyces vulgaris R-47 a-amylase (TVA, EC 3.2.1.1) [4] and neopullulanase (EC 3.2.1.135) [5], which hydrolyse a-1,4-glucosidic linkages to produce panose; and (c) IPU, which hydrolyses the other a-1,4-glucosidic linkages to produce isopanose. Except for IPU, these enzymes are classified into glycosyl hydrolase (GH) family 13, known as the a-amylase family (reviewed in [6][7][8]). In contrast, IPU is the sole enzyme classified into GH family 49 [2,9,10] among these pullulan-hydrolases, and no homology between IPU and a-amylase family enzymes has been found (http://afmb.cnrs-mrs.fr/cazy/CAZY/ index.html).Interestingly, IPU does not hydrolyse dextran at all, while all other GH family 49 enzymes are dextran-hydrolysing ...