Refined structure for the complex of D-gluco-dihydroacarbose with glucoamylase from Aspergillus awamori var. X100 to 2.2 A resolution: dual conformations for extended inhibitors bound to the active site of glucoamylase.
The crystal structure at pH 4 of the complex of glucoamylase II(471) from Aspergillus awamori var. X100 with the pseudotetrasaccharide D-gluco-dihydroacarbose has been refined to an R-factor of 0.125 against data to 2.2 A resolution. The first two residues of the inhibitor bind at a position nearly identical to those of the closely related inhibitor acarbose in its complex with glucoamylase at pH 6. However, the electron density bifurcates beyond the second residue of the D-gluco-dihydroacarbose molecule, placing the third and fourth residues together at two positions in the active site. The position of relatively low density (estimated occupancy of 35%) corresponds to the location of the third and fourth residues of acarbose in its complex with glucoamylase at pH 6. The position of high density (65% occupancy) corresponds to a new binding mode of an extended inhibitor to the active site of glucoamylase. Presented are possible causes for the binding of D-gluco-dihydroacarbose in two conformations at the active site of glucoamylase at pH 4.
Stoffer
B
B
Department of Chemistry, Carlsberg Laboratory, Copenhagen Valby, Denmark.
Aleshin
A E
AE
Firsov
L M
LM
Svensson
B
B
Honzatko
R B
RB
D001230:Aspergillus / Q000201:enzymology*; D001665:Binding Sites; D003198:Computer Simulation; D003460:Crystallization; D018360:Crystallography, X-Ray; D005087:Glucan 1,4-alpha-Glucosidase / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism; D015394:Molecular Structure; D011487:Protein Conformation; D014312:Trisaccharides / Q000737:chemistry* / Q000378:metabolism
D014312:Trisaccharides; C052108:dihydroacarbose; D005087:Glucan 1,4-alpha-Glucosidase