Surface Binding Sites (SBSs), Mechanism and Regulation of Enzymes Degrading Amylopectin and α-limit Dextrins

Abstract

Certain enzymes interact with polysaccharides at surface binding sites (SBSs) situated outside of their active sites. SBSs are not easily identified and their function has been discerned in relatively few cases. Starch degradation is a concerted action involving GH13 hydrolases. New insight into barley seed α-amylase 1 (AMY1) and limit dextrinase (LD) includes i) kinetics of bi-exponential amylopectin hydrolysis by AMY1, one reaction having low K_m (8 µg/ml) and high k_cat (57 s^-1) and the other high K_m (97 µg/ml) and low k_cat (23 s^-1). β-Cyclodextrin (β-CD) inhibits the first reaction by binding to an SBS (SBS2) on domain C with K_d = 70 µM, which for the SBS2 Y380A mutant increases to 1.4 mM. SBS2 thus has a role in the fast, high-affinity component of amylopectin degradation. ii) The N-terminal domain of LD, the debranching enzyme in germinating seeds, shows distant structural similarity with domains including CBM21 present in other proteins and involved in various molecular interactions, but no binding site identity. LD is controlled by barley limit dextrinase inhibitor (LDI) which belongs to the cereal-type inhibitor family and forms a tight 1:1 complex with LD. iii) LDI in turn is regulated by disulfide reduction mediated by the barley thioredoxin h (trxh) NADPH-dependent thioredoxin reductase (NTR) system. Based on the progress monitored by released free thiol groups from LDI and its failure to inhibit LD as elicited by trxh, the LDI inactivation is proposed to stem from loss of structural integrity due to reduction of all four disulfides.