Ligand Induced Folding of the First Identified CBM69 Starch Binding Domain AmyP-SBD

AmyP is an α-amylase which shows preferential degradation to soluble starch. In this substrate preference its Starch Binding Domain (SBD), which was recently assigned to a new Carbohydrate Binding Module (CBM) family 69, plays an important role. In the present study, the SBD of AmyP (AmyP-SBD) was recombinantly expressed, purified, and structurally characterized. Using Circular Dichroism (CD), intrinsic fluorescence, and nuclear magnetic resonance (NMR) spectroscopy, the structures of AmyP-SBD in the absence and presence of substrate analogue β-cyclodextrin were measured. The results intriguingly showed that free form AmyP-SBD is partially unfolded, like a compact molten globule, and could be induced by the ligand to fold into a relatively rigid state. Further structure determination for folded AmyP-SBD revealed a topology distinctive from those of SBDs from other CBM families. Our data indicate AmyP-SBD is a structurally novel SBD, and this may be helpful for understanding the properties of AmyP-SBD and CBM69 and elucidation of functioning mechanism of AmyP.