5NGL

The endo-beta1,6-glucanase BT3312

Summary for 5NGL

• Entry DOI: 10.2210/pdb5ngl/pdb
• Descriptor: Glucosylceramidase, beta-D-glucopyranose-(1-6)-1-DEOXYNOJIRIMYCIN, SODIUM ION, ... (4 entities in total)
• Functional Keywords: glycoside hydrolase; endo-beta1, 6-clucanase; beta-1, 6-glucan; bacteroides; human gut microbiota; yeast glycan, hydrolase
• Biological source: Bacteroides thetaiotaomicron
• Total number of polymer chains: 3
• Total formula weight: 166995.34

Authors

Basle, A.,Temple, M.,Cuskin, F.,Lowe, E.,Gilbert, H. (deposition date: 2017-03-17, release date: 2017-05-10, Last modification date: 2024-11-06)

Primary citation

Temple, M.J.,Cuskin, F.,Basle, A.,Hickey, N.,Speciale, G.,Williams, S.J.,Gilbert, H.J.,Lowe, E.C.
A Bacteroidetes locus dedicated to fungal 1,6-beta-glucan degradation: Unique substrate conformation drives specificity of the key endo-1,6-beta-glucanase.
J. Biol. Chem., 292:10639-10650, 2017

PubMed Abstract: Glycans are major nutrients available to the human gut microbiota. The are generalist glycan degraders, and this function is mediated largely by polysaccharide utilization loci (PULs). The genomes of several species contain a PUL, PUL, that was predicted to target mixed linked plant 1,3;1,4-β-glucans. To test this hypothesis we characterized the proteins encoded by this locus in , a member of the human gut microbiota. We show here that PUL does not orchestrate the degradation of a plant polysaccharide but targets a fungal cell wall glycan, 1,6-β-glucan, which is a growth substrate for the bacterium. The locus is up-regulated by 1,6-β-glucan and encodes two enzymes, a surface endo-1,6-β-glucanase, BT3312, and a periplasmic β-glucosidase that targets primarily 1,6-β-glucans. The non-catalytic proteins encoded by PUL target 1,6-β-glucans and comprise a surface glycan-binding protein and a SusD homologue that delivers glycans to the outer membrane transporter. We identified the central role of the endo-1,6-β-glucanase in 1,6-β-glucan depolymerization by deleting , which prevented the growth of on 1,6-β-glucan. The crystal structure of BT3312 in complex with β-glucosyl-1,6-deoxynojirimycin revealed a TIM barrel catalytic domain that contains a deep substrate-binding cleft tailored to accommodate the hook-like structure adopted by 1,6-β-glucan. Specificity is driven by the complementarity of the enzyme active site cleft and the conformation of the substrate. We also noted that PUL is syntenic to many PULs from other Bacteroidetes, suggesting that utilization of yeast and fungal cell wall 1,6-β-glucans is a widespread adaptation within the human microbiota.

PubMed: 28461332
DOI: 10.1074/jbc.M117.787606

Experimental method

X-RAY DIFFRACTION (1.85 Å)