In silico Investigation of the PglB Active Site Reveals Transient Catalytic States and Octahedral Metal Ion Coordination. (28th July 2015)

• Record Type: Journal Article
• Authors: Pedebos, Conrado; Arantes, Pablo Ricardo; Giesel, Guilherme Menegon; Verli, Hugo
• Is Part Of: Glycobiology. Volume 25:Number 11(2015:Nov.)
• Page Start: 1183
• Page End: 1195
• Publication Date: 2015-07-28
• Subjects: computational glycobiology -- enzyme catalysis -- molecular dynamics -- oligosaccharyltransferase -- PglB; Glycoproteins -- Periodicals; Glycolipids -- Periodicals; Glycoconjugates -- Periodicals; 572.567
• DOI: 10.1093/glycob/cwv053
• Languages: English
• ISSNs: 0959-6658

Abstract

Abstract : The last step of the bacterial N-glycosylation pathway involves PglB, an oligosaccharyltransferase, which is responsible for the en bloc transfer of a fully assembled oligosaccharide chain to a protein possessing the extended motif D/E-X-N-X-S/T. Recently, this molecule had its full structure elucidated, enabling the description of its domains and the proposition of a catalytic mechanism. By employing molecular dynamics simulations, we were able to evaluate structural aspects of PglB, suggesting prevalent motions that may bring insights into the mechanism of the glycosylated peptide detachment. Additionally, we identified transient states at the catalytic site, in which the previously described carboxamide twisting mechanism was observed. Aided by quantum mechanics calculations for each different conformational states of the catalytic site, we determined the presence of an octahedral metal coordination, along with the presence of one water molecule at the catalytic site.