9WFH

Carbohydrate-binding module 32 of LnbB from Bifidobacterium bifidum, ligand free form, multiple small-wedge data set

Summary for 9WFH

• Entry DOI: 10.2210/pdb9wfh/pdb
• Descriptor: Lacto-N-biosidase, CALCIUM ION (3 entities in total)
• Functional Keywords: carbohydrate binding module family 32 domain, sugar binding protein
• Biological source: Bifidobacterium bifidum JCM 1254
• Total number of polymer chains: 2
• Total formula weight: 38970.80

Authors

Zhang, X.,Kashima, T.,Fushinobu, S. (deposition date: 2025-08-21, release date: 2025-11-19)

Primary citation

Zhang, X.,Sunagawa, N.,Kashima, T.,Igarashi, K.,Miyanaga, A.,Fushinobu, S.
Structural insights into lacto-N-biose I recognition by a family 32 carbohydrate-binding module from Bifidobacterium bifidum.
Febs Lett., 2025

PubMed Abstract: Bifidobacterium bifidum, a predominant colonizer of the infant gut, utilizes lacto-N-biose I (LNB), a prominent component of human milk oligosaccharides (HMOs), through a dedicated metabolic pathway. Among a diverse set of extracellular glycosidases involved in HMO degradation, lacto-N-biosidase (LnbB) plays a pivotal role by releasing LNB. We investigated the structure and function of the carbohydrate-binding module family 32 (CBM32) domain located at the C-terminus of the glycoside hydrolase family 20 catalytic domain in LnbB. Isothermal titration calorimetry showed that CBM32 binds LNB with a dissociation constant (K) of 98 μm. The crystal structure of the CBM32 complexed with LNB reveals the molecular basis for its specific recognition. Impact statement Bifidobacteria are beneficial gut microbes, and infant-associated strains establish symbiosis by degrading human milk oligosaccharides. This study uncovers the molecular mechanism by which Bifidobacterium bifidum captures lacto-N-biose I, a key disaccharide, functioning as a cross-feeder that promotes the growth of other bifidobacteria and supports the infant gut ecosystem.

PubMed: 41204437
DOI: 10.1002/1873-3468.70217

Experimental method

X-RAY DIFFRACTION (2 Å)