Bacillus stearothermophilus neopullulanase (NPL) structure was modeled based on Aspergillus oryzae alpha-amylase (TAA) to understand the structure-function relationships of this pullulan hydrolyzing enzyme. The NPL structure seems to consist of a central (alpha/beta)8 barrel to which the other domains are attached. The immediate surroundings of the NPL catalytic site were found to have very similar structure to TAA. The more distant sites are different due to the stereochemical requirements of accommodating in the substrate alpha-1,6-linkages at every third position instead of alpha-1,4-linkages. The substrate binding cleft is wider than in alpha-amylases. The NPL structure, function, substrate binding and the consequences of mutations were discussed based on the modeled structure.