4UNI

beta-(1,6)-galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 in complex with galactose

Summary for 4UNI

• Entry DOI: 10.2210/pdb4uni/pdb
• Descriptor: BETA-GALACTOSIDASE, beta-D-galactopyranose, TRIETHYLENE GLYCOL, ... (7 entities in total)
• Functional Keywords: hydrolase, gh42
• Biological source: BIFIDOBACTERIUM ANIMALIS SUBSP. LACTIS
• Total number of polymer chains: 3
• Total formula weight: 237220.57

Authors

Viborg, A.H.,Fredslund, F.,Katayama, T.,Nielsen, S.K.,Svensson, B.,Kitaoka, M.,Lo Leggio, L.,Abou Hachem, M. (deposition date: 2014-05-28, release date: 2014-10-15, Last modification date: 2024-01-10)

Primary citation

Viborg, A.H.,Fredslund, F.,Katayama, T.,Nielsen, S.K.,Svensson, B.,Kitaoka, M.,Lo Leggio, L.,Abou Hachem, M.
A beta 1-6/ beta 1-3 galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 gives insight into sub-specificities of beta-galactoside catabolism within Bifidobacterium.
Mol. Microbiol., 2014

PubMed Abstract: The Bifidobacterium genus harbours several health promoting members of the gut microbiota. Bifidobacteria display metabolic specialization by preferentially utilizing dietary or host-derived β-galactosides. This study investigates the biochemistry and structure of a glycoside hydrolase family 42 (GH42) β-galactosidase from the probiotic Bifidobacterium animalis subsp. lactis Bl-04 (BlGal42A). BlGal42A displays a preference for undecorated β1-6 and β1-3 linked galactosides and populates a phylogenetic cluster with close bifidobacterial homologues implicated in the utilization of N-acetyl substituted β1-3 galactosides from human milk and mucin. A long loop containing an invariant tryptophan in GH42, proposed to bind substrate at subsite + 1, is identified here as specificity signature within this clade of bifidobacterial enzymes. Galactose binding at the subsite - 1 of the active site induced conformational changes resulting in an extra polar interaction and the ordering of a flexible loop that narrows the active site. The amino acid sequence of this loop provides an additional specificity signature within this GH42 clade. The phylogenetic relatedness of enzymes targeting β1-6 and β1-3 galactosides likely reflects structural differences between these substrates and β1-4 galactosides, containing an axial galactosidic bond. These data advance our molecular understanding of the evolution of sub-specificities that support metabolic specialization in the gut niche.

PubMed: 25287704
DOI: 10.1111/mmi.12815

Experimental method

X-RAY DIFFRACTION (2.6 Å)