Crystal structure of cyclodextrin glucanotransferase from alkalophilic Bacillus sp 1011 complexed with 1-deoxynojirimycin at 2.0 angstrom resolution

1-Deoxynojirimycin, a pseudo-monosaccharide, is a strong inhibitor of gluco amylase but a relatively weak inhibitor of cyclodextrin glucanotransferase (CGTase), To elucidate this difference, the crystal structure of the CGTase from alkalophilic Bacillus sp. 1011 complexed with 1-deoxynojirimycin was determined at 2.0 A resolution with the crystallographic R value of 0.154 ( R-free = 0.214), The asymmetric unit of the crystal contains two CGTase mol ecules and each molecule binds two 1-deoxynojirimycins, One 1-deoxynojirimy cin molecule is bound to the active center by hydrogen bonds with catalytic residues and water molecules, but its binding mode differs from that expec ted in the substrate binding. Another 1-deoxynojirimycin found at the malto se-binding site 1 is bound to Asn-667 with a hydrogen bond and by stacking interaction with the indole moiety of Trp-662 of molecule 1 or Trp-616 of m olecule 2. Comparison of this structure with that of the acarbose-CGTase co mplex suggested that the lack of stacking interaction with the aromatic sid e chain of Tyr-100 is responsible for the weak inhibition by 1-deoxynojirim ycin of the enzymatic action of CGTase.