9M0E

Enhancing the synthesis efficiency of galacto-oligosaccharides of a beta-galactosidase from Paenibacillus barengoltzii by engineering the active and distal sites

Summary for 9M0E

• Entry DOI: 10.2210/pdb9m0e/pdb
• EMDB information: 63544
• Descriptor: Beta-galactosidase (1 entity in total)
• Functional Keywords: beta-galactosidase, transglycosylation, gos synthesis, cryo-em structure, hydrolase
• Biological source: Paenibacillus barengoltzii
• Total number of polymer chains: 6
• Total formula weight: 694882.36

Authors

Yu, H.Y.,Wang, Y.L.,Yang, Z.S.,Liu, X.,Xin, F.J. (deposition date: 2025-02-24, release date: 2025-04-23)

Primary citation

Yu, H.,Wang, Y.,Yang, Z.,Ying, J.,Guan, F.,Liu, B.,Miao, M.,Mohamed, A.,Wei, X.,Yang, Y.,Liu, X.,Sun, L.,Jiang, Z.,Yang, S.,Xin, F.
Enhancing the synthesis efficiency of galacto-oligosaccharides of a beta-galactosidase from Paenibacillus barengoltzii by engineering the active and distal sites.
Food Chem, 483:144208-144208, 2025

PubMed Abstract: Previously, a glycoside hydrolase (GH) family 2 β-galactosidase (PbBGal2A) from Paenibacillus barengoltzii is characterized for its high transglycosylation capability. Here, the cryo-electron microscopy (cryo-EM) structure of PbBGal2A was determined, revealing an enlarged acidic catalytic pocket that facilitate the binding of carbohydrate substrates. Three structure-based strategies as well as machine learning MECE platform (method for enhancing the catalytic efficiency) were employed to identify active and distal mutations with enhanced galacto-oligosaccharides (GOS) synthesis and their synergistic effects were evaluated. The best H331V mutation yielded a maximum GOS production of 76.57 % at 4 h when 35 % (w/v) of lactose was used as a substrate. Molecular dynamics (MD) simulation analysis further indicated that distal mutations increase the rigidity of the loops surrounding the catalytic pocket. This research sheds light on the structural and catalytic mechanisms of PbBGal2A, highlighting the importance of both active and distal mutations in the efficient design of customized β-galactosidases.

PubMed: 40220440
DOI: 10.1016/j.foodchem.2025.144208

Experimental method

ELECTRON MICROSCOPY (2.8 Å)