Structural insight into D-xylose utilization by xylose reductase from Scheffersomyces stipitis

Hyeoncheol Francis Son,Sun-Mi Lee,Kyung-Jin Kim

doi:10.1038/s41598-018-35703-x

Hyeoncheol Francis Son, Sun-Mi Lee + Show 1 more

Open Access

https://doi.org/10.1038/s41598-018-35703-x

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Abstract

Lignocellulosic biomass, of which D-xylose accounts for approximately 35% of the total sugar, has attracted attention as a future energy source for biofuel. To elucidate molecular mechanism of D-xylose utilization, we determined the crystal structure of D-xylose reductase from Schefferzomyces stipitis (SsXR) at a 1.95 Å resolution. We also determined the SsXR structure in complex with the NADPH cofactor and revealed that the protein undergoes an open/closed conformation change upon NADPH binding. The substrate binding pocket of SsXR is somewhat hydrophobic, which seems to result in low binding affinity to the substrate. Phylogenetic tree analysis showed that AKR enzymes annotated with bacterial/archaeal XRs belonged to uncharacterized AKR families and might have no XR function, and yeast/fungi derived enzymes, which belong to the same group with SsXR, can be candidates for XR to increase xylose consumption.

Highlights

Industrialization and population growth lead to increased energy demands, and interest in alternative energy has increased because of fossil fuel depletion and environmental problems
Various heterologous xylose isomerase (XI) enzymes have been introduced into S. cerevisiae and Y. lipolytica to assimilate D-xylose and recently, the crystal structures of XI from Piromyces sp. (PsXI) were determined[4,16,17,18,19,20,21,22]
Two enzymes, xylose reductase (XR) and xylitol dehydrogenase (XDH), are used to convert D-xylose to D-xylulose using xylitol as an intermediate (Fig. 1a), and XR/XDH enzymes derived from Scherrsomyces stipitis (SsXR, SsXDH, respectively) have been introduced into S. cerevisiae and Y. lipolytica for D-xylose intake[4,23,24]

Summary

Scheffersomyces stipitis

Lignocellulosic biomass, of which D-xylose accounts for approximately 35% of the total sugar, has attracted attention as a future energy source for biofuel. We determined the SsXR structure in complex with the NADPH cofactor and revealed that the protein undergoes an open/closed conformation change upon NADPH binding. Biofuel producing organisms, such as Saccharomyces cerevisiae and Yarrowia lipolytica, lack the pentose metabolic pathway, which limits the use of lignocellulosic biomass as a resource[4,5]. Two enzymes, xylose reductase (XR) and xylitol dehydrogenase (XDH), are used to convert D-xylose to D-xylulose using xylitol as an intermediate (Fig. 1a), and XR/XDH enzymes derived from Scherrsomyces stipitis (SsXR, SsXDH, respectively) have been introduced into S. cerevisiae and Y. lipolytica for D-xylose intake[4,23,24]. We report the crystal structures of D-xylose reductase from S. stipitis (SsXR) in its apo form and in complex with NADPH cofactor. Phylogenetic tree analysis showed that bacteria/archaea derived XR-annotated AKRs might have no XR activity, and yeast/fungi derived XRs can be candidate to increase xylose consumption

Results and Discussion

NADPH NADH xyloseNADPH xyloseNADH NADPH NADH xyloseNADPH xyloseNADH

Material and Methods

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