Molecular dynamics simulations of a branched tetradecasaccharide substrate in the active site of a xyloglucan endo-transglycosylase

• Published in: Molecular simulation 2011-10, Vol.37 (12), p.1001-1013
• Main Authors: Mark, Pekka, Zhang, Qiong, Czjzek, Mirjam, Brumer, Harry, Ågren, Hans
• Format: Article
• Language: English
• Subjects: glycam force field; molecular dynamics simulation; xyloglucan; xyloglucan endo-transglycosylase (XET); xyloglucan endo-transglycosylase/hydrolase (XTH)
• ISSN: 0892-7022; 1029-0435; 1029-0435
• DOI: 10.1080/08927022.2011.566605

Molecular dynamics simulations of the tetradecasaccharide XXXGXXXG in complex with the hybrid aspen xyloglucan endo-transglycosylase PttXET16-34 have been performed and analysed with respect to structure, dynamics, flexibility and ligand interactions. Notably, the charge state of the so-called 'helper residue' aspartate 87 (Asp87), which lies between the catalytic nucleophile [glutamate 85 (Glu85)] and general acid/base (Glu89) residues on the same beta strand, had a significant effect on PttXET16-34 active site structure. When Asp87 was deprotonated, electrostatic repulsion forced the nucleophile away from C1 of the sugar ring in subsite − 1 and the proton-donating ability of Glu89 was also weakened due to the formation of a hydrogen bond with Asp87, whereas the protonation of Asp87 resulted in the formation of a hydrogen bond with the catalytic nucleophile and correct positioning of the catalytic machinery. The results suggest that catalysis in glycoside hydrolase family 16, and by extension clan GH-B enzymes, is optimal when the catalytic nucleophile is deprotonated for nucleophilic attack on the substrate, whereas the 'helper residue' and general acid/base residue are both in their conjugate acid forms to align the nucleophile and deliver a proton to the departing sugar, respectively.