Insights from modeling the 3D structure of NAD(P)H-dependent d-xylose reductase of Pichia stipitis and its binding interactions with NAD and NADP

doi:10.1016/j.bbrc.2007.05.101

Biochemical and Biophysical Research Communications

Volume 359, Issue 2, 27 July 2007, Pages 323-329

https://doi.org/10.1016/j.bbrc.2007.05.101 Get rights and content

Abstract

NAD(P)H-dependent d-xylose reductase is a homodimeric oxidoreductase that belongs to the aldo–keto reductase superfamily. The enzyme has the special function to catalyze the first step in the assimilation of xylose into yeast metabolic pathways. Performing this function via reducing the open chain xylose to xylitol, the xylose reductase of Pichia stipitis is one of the most important enzymes that can be used to construct recombinant Saccharomyces cerevisiae strain for utilizing xylose and producing alcohol. To investigate into the interaction mechanism of the enzyme with its ligand NAD and NADP, the 3D structure was developed for the NAD(P)H-dependent d-xylose reductase from P. stipitis. With the 3D structure, the molecular docking operations were conducted to find the most stable bindings of the enzyme with NAD and NADP, respectively. Based on these results, the binding pockets of the enzyme for NAD and NADP have been explicitly defined. It has been found that the residues in forming the binding pockets for both NAD and NADP are almost the same and mainly hydrophilic. These findings may be used to guide mutagenesis studies, providing useful clues to modify the enzyme to improve the utilization of xylose for producing alcohol. Also, because human aldose reductases have the function to reduce the open chain form of glucose to sorbitol, a process physiologically significant for diabetic patients at the time that their blood glucose levels are elevated, the information gained through this study may also stimulate the development of new strategies for therapeutic treatment of diabetes.

Section snippets

Modeling the 3D structure of xylose reductase

To use the structural bioinformatics tools for deriving the 3D structure of XYLO (Accession No. P31867), the crystal structure of the xylose reductase AKR2B5 was chosen as a template. The rationale to do so is because the two proteins belong to the same superfamily. The crystal structure of AKR2B5 was first released in 2005 [13], with the PDB code 1YE4 and resolution 2.40 Å.

The sequence of the XYLO from P. stipitis contains 318 amino acids, while that of 1YE4 contains 322 amino acids. The

Molecular docking and MD simulations

Many useful clues for drug design can be gained through molecular docking studies (see e.g., [37], [38], [39], [42], [43], [44], [45], [46], [47], [48], [49], [50], [51], [52]). In this study, the molecular docking with the Metropolis algorithm [53], also known as Monte Carlo simulated annealing, was adopted to investigate the interactions between XYLO and NAD(P): the receptor is the 3D structure of XYLO as derived in the last section; the ligands are NAD and NADP whose structures are given in

Results and discussion

Shown in Fig. 3A and B are the close views focused on the binding sites of NAD and NADP. As we can see from the figures, the interactions of XYLO with both NAD and NADP are mainly from the hydrophilic residues (blue) while the enzyme’s hydrophobic residues (green) play a significant role in stabilizing the binding pockets.

According to [20], the binding pocket of a receptor for its ligand is defined by those residues that have at least one heavy atom (i.e., other than hydrogen) with a distance 5

Conclusions

The binding pocket of XYLO from P. stipitis for NAD is formed by 16 residues, of which Glu223 and Phe236 have each contributed more than one hydrogen bond to hold NAD, and hence they are the strong hydrogen bonding interaction contributors. The binding pocket of the enzyme for NADP is also formed by the same 16 residues, of which, however, Lys21 and Phe236 are the strong hydrogen bonding contributor that have each formed two hydrogen bonds with the enzyme. The residues in forming the binding

Acknowledgments

This work was supported by the grants from the Tianjin Educational Commission, the Tianjin Commission of Sciences and Technology under the Contract No. 033801911 and 043185111-4. Additional supports were also from the special fund for intensive computation, Virtual Laboratory for Computational Chemistry of CNIC, and the Supercomputing Center of CNIC, Chinese Academy of Sciences.

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Insights from modeling the 3D structure of NAD(P)H-dependent d-xylose reductase of Pichia stipitis and its binding interactions with NAD and NADP

Abstract

Section snippets

Modeling the 3D structure of xylose reductase

Molecular docking and MD simulations

Results and discussion

Conclusions

Acknowledgments

Chem. Biol. Interact.

J. Biol. Chem.

Biophys. Chem.

J. Biol. Chem.

Gene

FEBS Lett.

Chem. Biol. Interact.

J. Mol. Biol.

FEBS Lett.

Biochem. Biophys. Res. Commun.

FEBS Lett.

Mol. Cell

Cell

Biochem. Biophys. Res. Commun.

J. Biol. Chem.

J. Biol. Chem.

Biochem. Biophys. Res. Commun.

Biochem. Biophys. Res. Commun.

Biochem. Biophys. Res. Commun.

Biochem. Biophys. Res. Commun.

Biochem. Biophys. Res. Commun.

Biochem. Biophys. Res. Commun.

FEBS Lett.

Biochem. Biophys. Res. Commun.

Peptides

Anal. Biochem.

J. Theor. Biol.

Biochem. Biophys. Res. Commun.

Computer Math. Appl.

Comparative anatomy of the aldo–keto reductase superfamily

Biochem. J.