The variable structural flexibility of the Bacillus circulans β-galactosidase isoforms determines their unique functionalities

• DOI: 10.1016/j.str.2024.09.005
• Publication Date: 2024-09-30T14:36:02Z
• Authors: Michaela Hovorková; Barbora Kaščáková; Lucie Petrásková; Petra Havlíčková; Jiří Nováček; Daniel Pinkas; Zdenko Gardian; Vladimír Křen; Pavla Bojarová; Ivana Kutá Smatanová

β-Galactosidase from Bacillus circulans ATCC 31382 (BgaD) is a biotechnologically important enzyme for the synthesis of β-galactooligosaccharides (GOS). Among its four isoforms, isoform A (BgaD-A) has distinct synthetic properties. Here, we present cryoelectron microscopy (cryo-EM) structures of BgaD-A and compare them with the known X-ray crystal structure of isoform D (BgaD-D), revealing substantial structural divergences between the two isoforms. In contrast to BgaD-D, BgaD-A features a flexible Big-4 domain and another enigmatic domain. The newly identified flexible region in BgaD-A is termed as "barrier domain 8," and serves as a barricade, obstructing the access of longer oligosaccharide substrates into the active site of BgaD-A. The transgalactosylation reactions catalyzed by both isoforms revealed that BgaD-A has a higher selectivity than BgaD-D in the earlier stages of the reaction and is prevailingly directed to shorter galactooligosaccharides. This study improves our understanding of the structural determinants governing β-galactosidase catalysis, with implications for tailored GOS production.