6R3U

Endo-levanase BT1760 mutant E221A from Bacteroides thetaiotaomicron complexed with levantetraose

Summary for 6R3U

• Entry DOI: 10.2210/pdb6r3u/pdb
• Related: 6R3R
• Descriptor: Glycoside hydrolase family 32, beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose, ZINC ION, ... (5 entities in total)
• Functional Keywords: glycoside hydrolase 32, 5-fold beta-propeller, beta-sandwich, substrate complex, hydrolase
• Biological source: Bacteroides thetaiotaomicron
• Total number of polymer chains: 1
• Total formula weight: 58933.68

Authors

Eek, P.,Ernits, K.,Lukk, T.,Alamae, T. (deposition date: 2019-03-21, release date: 2019-06-19, Last modification date: 2024-01-24)

Primary citation

Ernits, K.,Eek, P.,Lukk, T.,Visnapuu, T.,Alamae, T.
First crystal structure of an endo-levanase - the BT1760 from a human gut commensal Bacteroides thetaiotaomicron.
Sci Rep, 9:8443-8443, 2019

PubMed Abstract: The endo-levanase BT1760 of a human gut commensal Bacteroides thetaiotaomicron randomly cuts a β-2,6-linked fructan, levan, into fructo-oligosaccharides providing a prebiotic substrate for gut microbiota. Here we introduce the crystal structure of BT1760 at resolution of 1.65 Å. The fold of the enzyme is typical for GH32 family proteins: a catalytic N-terminal five-bladed β-propeller connected with a C-terminal β-sandwich domain. The levantetraose-bound structure of catalytically inactive mutant E221A at 1.90-Å resolution reveals differences in substrate binding between the endo-acting fructanases. A shallow substrate-binding pocket of the endo-inulinase INU2 of Aspergillus ficuum binds at least three fructose residues at its flat bottom. In the levantetraose-soaked crystal of the endo-levanase E221A mutant the ligand was bent into the pond-like substrate pocket with its fructose residues making contacts at -3, -2, -1 and + 1 subsites residing at several pocket depths. Binding of levantetraose to the β-sandwich domain was not detected. The N- and C-terminal modules of BT1760 did not bind levan if expressed separately, the catalytic domain lost its activity and both modules tended to precipitate. We gather that endo-levanase BT1760 requires both domains for correct folding, solubility and stability of the protein.

PubMed: 31186460
DOI: 10.1038/s41598-019-44785-0

Experimental method

X-RAY DIFFRACTION (1.9 Å)