Molecular dynamics simulations of a branched tetradecasaccharide substrate in the active site of a xyloglucan endo-transglycosylase
2011 (English)In: Molecular Simulation, ISSN 0892-7022, Vol. 37, no 12, 1001-1013 p.Article in journal (Refereed) Published
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.
Place, publisher, year, edition, pages
2011. Vol. 37, no 12, 1001-1013 p.
xyloglucan, xyloglucan endo-transglycosylase (XET), xyloglucan endo-transglycosylase/hydrolase (XTH), molecular dynamics simulation, glycam force field
IdentifiersURN: urn:nbn:se:kth:diva-41806DOI: 10.1080/08927022.2011.566605ISI: 000294892400005OAI: oai:DiVA.org:kth-41806DiVA: diva2:445122
FunderSwedish e‐Science Research Center
QC 201010032011-10-032011-10-032012-05-23Bibliographically approved