Computational study of β-N-acetylhexosaminidase from Talaromyces flavus, a glycosidase with high substrate flexibility. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Kulik, Natallia; Slámová, Kristýna; Ettrich, Rüdiger; Křen, Vladimír
• Is Part Of: BMC bioinformatics. Volume 16:Issue 1(2015)
• Page Start: 1
• Page End: 15
• Publication Date: 2015-12
• Subjects: Molecular docking -- Substrate specificity -- Unnatural substrates -- Phylogenetic analysis; Bioinformatics -- Periodicals; Computational biology -- Periodicals; 570.285
• DOI: 10.1186/s12859-015-0465-8
• Languages: English
• ISSNs: 1471-2105

Abstract

Abstract Background β-N -Acetylhexosaminidase (GH20) from the filamentous fungusTalaromyces flavus, previously identified as a prominent enzyme in the biosynthesis of modified glycosides, lacks a high resolution three-dimensional structure so far. Despite of high sequence identity to previously reportedAspergillus oryzae andPenicilluim oxalicum β-N -acetylhexosaminidases, this enzyme tolerates significantly better substrate modification. Understanding of key structural features, prediction of effective mutants and potential substrate characteristics prior to their synthesis are of general interest. Results Computational methods including homology modeling and molecular dynamics simulations were applied to shad light on the structure-activity relationship in the enzyme. Primary sequence analysis revealed some variable regions able to influence difference in substrate affinity of hexosaminidases. Moreover, docking in combination with consequent molecular dynamics simulations of C-6 modified glycosides enabled us to identify the structural features required for accommodation and processing of these bulky substrates in the active site of hexosaminidase fromT. flavus . To access the reliability of predictions on basis of the reported model, all results were confronted with available experimental data that demonstrated the principal correctness of the predictions as well as the model. Conclusions The main variable regions in β-N -acetylhexosaminidases determining difference in modified substrate affinity are located close to the active site entrance and engage two loops. Differences in primary sequence and the spatial arrangement of these loops and their interplay with active site amino acids, reflected by interaction energies and dynamics, account for the different catalytic activity and substrate specificity of the various fungal and bacterial β-N -acetylhexosaminidases.