6s82

From Proteopedia

Structure Of D80A-Fructofuranosidase From Xanthophyllomyces Dendrorhous Complexed With Tris-buffer molecule And hydroquinone

PDB ID 6s82

Drag the structure with the mouse to rotate

Structural highlights

6s82 is a 2 chain structure with sequence from Phaffia rhodozyma. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.85Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

J7HDY4_PHARH

Publication Abstract from PubMed

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 beta-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 A 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.

Deciphering the molecular specificity of phenolic compounds as inhibitors or glycosyl acceptors of beta-fructofuranosidase from Xanthophyllomyces dendrorhous.,Ramirez-Escudero M, Miguez N, Gimeno-Perez M, Ballesteros AO, Fernandez-Lobato M, Plou FJ, Sanz-Aparicio J Sci Rep. 2019 Nov 25;9(1):17441. doi: 10.1038/s41598-019-53948-y. PMID:31767902^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ramirez-Escudero M, Miguez N, Gimeno-Perez M, Ballesteros AO, Fernandez-Lobato M, Plou FJ, Sanz-Aparicio J. Deciphering the molecular specificity of phenolic compounds as inhibitors or glycosyl acceptors of beta-fructofuranosidase from Xanthophyllomyces dendrorhous. Sci Rep. 2019 Nov 25;9(1):17441. doi: 10.1038/s41598-019-53948-y. PMID:31767902 doi:http://dx.doi.org/10.1038/s41598-019-53948-y