5GQC

Crystal structure of lacto-N-biosidase LnbX from Bifidobacterium longum subsp. longum, ligand-free form

Summary for 5GQC

• Entry DOI: 10.2210/pdb5gqc/pdb
• Related: 5GQF 5GQG
• Descriptor: Lacto-N-biosidase, SODIUM ION, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: hydrolase, beta-helix
• Biological source: Bifidobacterium longum subsp. longum
• Total number of polymer chains: 8
• Total formula weight: 529307.08

Authors

Yamada, C.,Arakawa, T.,Katayama, T.,Fushinobu, S. (deposition date: 2016-08-07, release date: 2017-04-19, Last modification date: 2024-03-20)

Primary citation

Yamada, C.,Gotoh, A.,Sakanaka, M.,Hattie, M.,Stubbs, K.A.,Katayama-Ikegami, A.,Hirose, J.,Kurihara, S.,Arakawa, T.,Kitaoka, M.,Okuda, S.,Katayama, T.,Fushinobu, S.
Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum
Cell Chem Biol, 24:515-524.e5, 2017

PubMed Abstract: Breast-fed infants generally have a bifidobacteria-rich microbiota with recent studies indicating that human milk oligosaccharides (HMOs) selectively promote bifidobacterial growth. Bifidobacterium bifidum possesses a glycoside hydrolase family 20 lacto-N-biosidase for liberating lacto-N-biose I from lacto-N-tetraose, an abundant HMO unique to human milk, while Bifidobacterium longum subsp. longum has a non-classified enzyme (LnbX). Here, we determined the crystal structure of the catalytic domain of LnbX and provide evidence for creation of a novel glycoside hydrolase family, GH136. The structure, in combination with inhibition and mutation studies, provides insight into the molecular mechanism and broader substrate specificity of this enzyme. Moreover, through genetic studies, we show that lnbX is indispensable for B. longum growth on lacto-N-tetraose and is a key genetic factor for persistence in the gut of breast-fed infants. Overall, this study reveals possible evolutionary routes for the emergence of symbiosis between humans and bifidobacterial species in the infant gut.

PubMed: 28392148
DOI: 10.1016/j.chembiol.2017.03.012

Experimental method

X-RAY DIFFRACTION (2.36 Å)