Understanding the Positional Binding and Substrate Interaction of a Highly Thermostable GH10 Xylanase from Thermotoga maritima by Molecular Docking.

Jiangke Yang,Zhenggang Han

doi:10.3390/biom8030064

Abstract

Glycoside hydrolase family 10 (GH10) xylanases are responsible for enzymatic cleavage of the internal glycosidic linkages of the xylan backbone, to generate xylooligosaccharides (XOS) and xyloses. The topologies of active-site cleft determine the substrate preferences and product profiles of xylanases. In this study, positional bindings and substrate interactions of TmxB, one of the most thermostable xylanases characterized from Thermotoga maritima to date, was investigated by docking simulations. XOS with backbone lengths of two to five (X2–X5) were docked into the active-site cleft of TmxB by AutoDock The modeled complex structures provided a series of snapshots of the interactions between XOS and TmxB. Changes in binding energy with the length of the XOS backbone indicated the existence of four effective subsites in TmxB. The interaction patterns at subsites −2 to +1 in TmxB were conserved among GH10 xylanases whereas those at distal aglycone subsite +2, consisting of the hydrogen bond network, was unique for TmxB. This work helps in obtaining an in-depth understanding of the substrate-binding property of TmxB and provides a basis for rational design of mutants with desired product profiles.

Highlights

Glycoside hydrolase family 10 (GH10) xylanases are responsible for enzymatic cleavage of the internal glycosidic linkages of the xylan backbone, to generate xylooligosaccharides (XOS) and xyloses
According to the Carbohydrate-Active Enzyme (CAZy) database [8], xylanases mainly belong to glycoside hydrolase families 10 and 11 (GH10 and GH11, respectively) [9]
We showed that snapshots of GH10 xylanases and XOS interaction can be rapidly obtained by in silico study

Summary

Introduction

Glycoside hydrolase family 10 (GH10) xylanases are responsible for enzymatic cleavage of the internal glycosidic linkages of the xylan backbone, to generate xylooligosaccharides (XOS) and xyloses. XOS with backbone lengths of two to five (X2–X5) were docked into the active-site cleft of TmxB by AutoDock The modeled complex structures provided a series of snapshots of the interactions between XOS and TmxB. Amino acids on the inner wall of the cleft compose the so-called subsites, which are responsible for binding of xylose residues [12]. Structural data combined with kinetic activity toward XOS generally indicated that approximately four to seven xylose binding sites exist in the active-site cleft of GH10 xylanases [12]. The subsites in the glycone and aglycone regions interact with xylose residues in distinct patterns. The glycone subsites bind to xylose residues through abundant hydrogen bonds, whereas the aglycone subsites anchor xylose residues mainly through hydrophobic stacking interactions [17,18]

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Conclusion