In-silico smart library design to engineer a xylose- tolerant hexokinase variant

Saccharomyces cerevisiae has two hexokinases ScHxk1 and ScHxk2 that catalyze ATP-dependent phosphorylation of glucose and other hexoses. ScHxk2 plays an important role in glucose metabolism and the process of bioethanol production. The presence of xylose in the fermentation medium was found to inhibit ScHxk2. Therefore development of ScHxk2 variants that are resistant to the action of xylose is needed. In the current study, in-silico investigation was done aiming to select the amino acids in ScHxk2 that can be targeted in an engineering experiment. Using Autodock Vina, xylose binding to ScHxk2 structure (PDB 1IG8) was predicted. The information available about hexokinase family in the publicly available hexokinase 3DM database were investigated and the conservancy patterns for potential residues in the xylose-binding site were extracted. The study eventually presented 54 suggested mutants that might lead to a xylose-tolerant hexokinase. Top correlated positions in the hexokinase superfamily indicated 6 proposed double-mutants that are worth to be included in the proposed smart library.