6FJE

Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructose and glucose

Summary for 6FJE

• Entry DOI: 10.2210/pdb6fje/pdb
• Related: 5ann 5fix 5fk7 5fk8 5fkb 5fkc 5fmb 5fmc 5fmd
• Descriptor: Beta-fructofuranosidase, alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (10 entities in total)
• Functional Keywords: hydrolase, carbohydrates, catalysis, catalytic domain, cloning, dimerization, glycoside hydrolases, fungal proteins, kinetics, substrate specificity, beta-fructofuranosidase, invertase, inhibition, glucose
• Biological source: Phaffia rhodozyma
• Total number of polymer chains: 2
• Total formula weight: 159112.20

Authors

Ramirez-Escudero, M.,Sanz-Aparicio, J. (deposition date: 2018-01-22, release date: 2019-07-24, Last modification date: 2024-01-17)

Primary citation

Ramirez-Escudero, M.,Miguez, N.,Gimeno-Perez, M.,Ballesteros, A.O.,Fernandez-Lobato, M.,Plou, F.J.,Sanz-Aparicio, J.
Deciphering the molecular specificity of phenolic compounds as inhibitors or glycosyl acceptors of beta-fructofuranosidase from Xanthophyllomyces dendrorhous.
Sci Rep, 9:17441-17441, 2019

PubMed Abstract: Enzymatic glycosylation of polyphenols is a tool to improve their physicochemical properties and bioavailability. On the other hand, glycosidic enzymes can be inhibited by phenolic compounds. In this work, we studied the specificity of various phenolics (hydroquinone, hydroxytyrosol, epigallocatechin gallate, catechol and p-nitrophenol) as fructosyl acceptors or inhibitors of the β-fructofuranosidase from Xanthophyllomyces dendrorhous (pXd-INV). Only hydroquinone and hydroxytyrosol gave rise to the formation of glycosylated products. For the rest, an inhibitory effect on both the hydrolytic (H) and transglycosylation (T) activity of pXd-INV, as well as an increase in the H/T ratio, was observed. To disclose the binding mode of each compound and elucidate the molecular features determining its acceptor or inhibitor behaviour, ternary complexes of the inactive mutant pXd-INV-D80A with fructose and the different polyphenols were analyzed by X-ray crystallography. All the compounds bind by stacking against Trp105 and locate one of their phenolic hydroxyls making a polar linkage to the fructose O2 at 3.6-3.8 Å from the C2, which could enable the ulterior nucleophilic attack leading to transfructosylation. Binding of hydroquinone was further investigated by soaking in absence of fructose, showing a flexible site that likely allows productive motion of the intermediates. Therefore, the acceptor capacity of the different polyphenols seems mediated by their ability to make flexible polar links with the protein, this flexibility being essential for the transfructosylation reaction to proceed. Finally, the binding affinity of the phenolic compounds was explained based on the two sites previously reported for pXd-INV.

PubMed: 31767902
DOI: 10.1038/s41598-019-53948-y

Experimental method

X-RAY DIFFRACTION (1.85 Å)