5FMC: Structure Of D80a-fructofuranosidase From Xanthophyllomyces Dendrorhous Complexed With Fructose And Bis-tris Propane Buffer

Citation:
Abstract
Xanthophyllomyces dendrorhousbeta-fructofuranosidase (XdINV)is a highly glycosylated dimeric enzyme that hydrolyzes sucrose and releases fructose from various fructooligosaccharides (FOS) and fructans. It also catalyzes the synthesis of FOS, prebiotics that stimulate the growth of beneficial bacteria in human gut. In contrast to most fructosylating enzymes, XdINV produces neo-FOS, which makes it an interesting biotechnology target. We present here its three-dimensional structure, which shows the expected bimodular arrangement and also a long extension of its C terminus that together with anN-linked glycan mediate the formation of an unusual dimer. The two active sites of the dimer are connected by a long crevice, which might indicate its potential ability to accommodate branched fructans. This arrangement could be representative of a group of GH32 yeast enzymes having the traits observed in XdINV. The inactive D80A mutant was used to obtain complexes with relevant substrates and products, with their crystals structures showing at least four binding subsites at each active site. Moreover, two different positions are observed from subsite +2 depending on the substrate, and thus, a flexible loop (Glu-334-His-343) is essential in binding sucrose and beta(2-1)-linked oligosaccharides. Conversely, beta(2-6) and neo-type substrates are accommodated mainly by stacking to Trp-105, explaining the production of neokestose and the efficient fructosylating activity of XdINV on alpha-glucosides. The role of relevant residues has been investigated by mutagenesis and kinetics measurements, and a model for the transfructosylating reaction has been proposed. The plasticity of its active site makes XdINV a valuable and flexible biocatalyst to produce novel bioconjugates.
PDB ID: 5FMCDownload
MMDB ID: 136440
PDB Deposition Date: 2015/11/2
Updated in MMDB: 2016/04
Experimental Method:
x-ray diffraction
Resolution: 1.84  Å
Source Organism:
Similar Structures:
Biological Unit for 5FMC: dimeric; determined by software (PISA)
Molecular Components in 5FMC
Label Count Molecule
Proteins (2 molecules)
2
Beta-fructofuranosidase
Molecule annotation
Chemicals (54 molecules)
1
2
2
2
3
40
4
2
5
8
* Click molecule labels to explore molecular sequence information.

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