Crystal structure of cyclodextrin glucanotransferase from alkalophilic Bacillus sp. 1011 complexed with 1-deoxynojirimycin at 2.0 A resolution.
1-Deoxynojirimycin, a pseudo-monosaccharide, is a strong inhibitor of glucoamylase 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 molecules and each molecule binds two 1-deoxynojirimycins. One 1-deoxynojirimycin molecule is bound to the active center by hydrogen bonds with catalytic residues and water molecules, but its binding mode differs from that expected in the substrate binding. Another 1-deoxynojirimycin found at the maltose-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 molecule 2. Comparison of this structure with that of the acarbose-CGTase complex suggested that the lack of stacking interaction with the aromatic side chain of Tyr-100 is responsible for the weak inhibition by 1-deoxynojirimycin of the enzymatic action of CGTase.
Biomolecules Department, National Institute of Bioscience and Human Technology, Tsukuba, Ibaraki, 305-8566, Japan.
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D017485:1-Deoxynojirimycin / Q000737:chemistry / Q000378:metabolism*; D020909:Acarbose / Q000737:chemistry / Q000378:metabolism; D001407:Bacillus / Q000201:enzymology*; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000378:metabolism*; D005087:Glucan 1,4-alpha-Glucosidase / Q000737:chemistry / Q000378:metabolism; D005964:Glucosyltransferases / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism*; D006860:Hydrogen Bonding; D008320:Maltose / Q000378:metabolism; D008958:Models, Molecular; D011487:Protein Conformation; D014867:Water / Q000378:metabolism
D004791:Enzyme Inhibitors; D014867:Water; D017485:1-Deoxynojirimycin; D008320:Maltose; D005964:Glucosyltransferases; C019963:cyclomaltodextrin glucanotransferase; D005087:Glucan 1,4-alpha-Glucosidase; D020909:Acarbose