Structural bioinformatiocs of RmXyn10A
Hydrolysis of arabinoxylan (AX) by glycoside hydrolase family 10 (GH10) xylanases produces xylo- and arabinoxylo-oligosaccharides ((A)XOS) which have shown prebiotic effects. A modular GH10 xylanase with valuable properties, RmXyn10A, has been cloned from the thermophilic bacterium Rhodothermus marinus, which was isolated from a hot spring in Iceland. Characterisation of the catalytic module revealed thermostability, activity remained for 24 hours in 70 °C, which makes it suitable for industrial applications. RmXyn10A has shown great potential to produce (A)XOS and has been used for such production from various xylan-containing sources, e.g. rye bran, wheat bran, birchwood and quinoa stalks. Efforts have been made to determine the three-dimensional structure of the catalytic module in order to study substrate binding but several attempts have failed, showing that the module is difficult to crystallise. In this project we use a different approach by applying computational methods to provide deeper insight into substrate specificity and binding. The structure of the catalytic module of RmXyn10A is studied through a homology model. Subsite affinities and substrate preferences are explored by molecular dynamics and docking techniques.