Structural basis of carbohydrate binding in domain C of a type I pullulanase from Paenibacillus barengoltzii

Pullulanase (EC 3.2.1.41) is a well known starch‐debranching enzyme that catalyzes the cleavage of α‐1,6‐glycosidic linkages in α‐glucans such as starch and pullulan. Crystal structures of a type I pullulanase from Paenibacillus barengoltzii (PbPulA) and of PbPulA in complex with maltopentaose (G5), maltohexaose (G6)/α‐cyclodextrin (α‐CD) and β‐cyclodextrin (β‐CD) were determined in order to better understand substrate binding to this enzyme. PbPulA belongs to glycoside hydrolase (GH) family 13 subfamily 14 and is composed of three domains (CBM48, A and C). Three carbohydrate‐binding sites identified in PbPulA were located in CBM48, near the active site and in domain C, respectively. The binding site in CBM48 was specific for β‐CD, while that in domain C has not been reported for other pullulanases. The domain C binding site had higher affinity for α‐CD than for G6; a small motif (FGGEH) seemed to be one of the major determinants for carbohydrate binding in this domain. Structure‐based mutations of several surface‐exposed aromatic residues in CBM48 and domain C had a debilitating effect on the activity of the enzyme. These results suggest that both CBM48 and domain C play a role in binding substrates. The crystal forms described contribute to the understanding of pullulanase domain–carbohydrate interactions. The crystal structures of PbPulA provide the first experimental evidence for functional carbohydrate‐binding roles of domain C and CBM48 in GH family 13 pullulanases.