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Multitasking in the gut: the X-ray structure of the multidomain BbgIII from Bifidobacterium bifidum offers possible explanations for its alternative functions

DOI: 10.1107/S2059798321010949 DOI Help

Authors: Olga V. Moroz (University of York) , Elena Blagova (University of York) , Andrey A. Lebedev (CCP4, STFC Rutherford Appleton Laboratory) , Filomeno Sanchez Rodriguez (University of Liverpool) , Daniel J. Rigden (University of Liverpool) , Jeppe Wegener Tams (Novozymes A/S) , Reinhard Wilting (Novozymes A/S) , Jan Kjølhede Vester (Novozymes A/S) , Emily Longhi (Novozymes A/S) , Gustav Hammerich Hansen (Novozymes A/S) , Kristian Bertel Rømer Mørkeberg Krogh (Hammerich) , Roland A. Pache (Novozymes A/S) , Gideon Davies (University of York) , Keith S. Wilson (University of York)
Co-authored by industrial partner: Yes

Type: Journal Paper
Journal: Acta Crystallographica Section D Structural Biology , VOL 77

State: Published (Approved)
Published: December 2021
Diamond Proposal Number(s): 18598

Abstract: β-Galactosidases catalyse the hydrolysis of lactose into galactose and glucose; as an alternative reaction, some β-galactosidases also catalyse the formation of galactooligosaccharides by transglycosylation. Both reactions have industrial importance: lactose hydrolysis is used to produce lactose-free milk, while galactooligosaccharides have been shown to act as prebiotics. For some multi-domain β-galactosidases, the hydrolysis/transglycosylation ratio can be modified by the truncation of carbohydrate-binding modules. Here, an analysis of BbgIII, a multidomain β-galactosidase from Bifidobacterium bifidum, is presented. The X-ray structure has been determined of an intact protein corresponding to a gene construct of eight domains. The use of evolutionary covariance-based predictions made sequence docking in low-resolution areas of the model spectacularly easy, confirming the relevance of this rapidly developing deep-learning-based technique for model building. The structure revealed two alternative orientations of the CBM32 carbohydrate-binding module relative to the GH2 catalytic domain in the six crystallographically independent chains. In one orientation the CBM32 domain covers the entrance to the active site of the enzyme, while in the other orientation the active site is open, suggesting a possible mechanism for switching between the two activities of the enzyme, namely lactose hydrolysis and transgalactosylation. The location of the carbohydrate-binding site of the CBM32 domain on the opposite site of the module to where it comes into contact with the catalytic GH2 domain is consistent with its involvement in adherence to host cells. The role of the CBM32 domain in switching between hydrolysis and transglycosylation modes offers protein-engineering opportunities for selective β-galactosidase modification for industrial purposes in the future.

Journal Keywords: β-galactosidases; hydrolysis; transgalactosylation; cell adhesion; CBM32; galactooligosacharides; Bifidobacterium bifidum; deep learning

Diamond Keywords: Bacteria; Enzymes

Subject Areas: Biology and Bio-materials, Information and Communication Technology

Instruments: I04-Macromolecular Crystallography

Added On: 19/11/2021 10:37

Discipline Tags:

Information & Communication Technologies Artificial Intelligence Life Sciences & Biotech Structural biology

Technical Tags:

Diffraction Macromolecular Crystallography (MX)