title: In silico Investigation of the PglB Active Site Reveals Transient Catalytic States and Octahedral Metal Ion Coordination.
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.
authors.affiliation: Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, CP 15005, Porto Alegre 91500-970, RS, Brazil.
authors.forename: Conrado
authors.initials: C
authors.lastname: Pedebos
authors.affiliation: Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, CP 15005, Porto Alegre 91500-970, RS, Brazil.
authors.forename: Pablo Ricardo
authors.initials: PR
authors.lastname: Arantes
authors.affiliation: Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, CP 15005, Porto Alegre 91500-970, RS, Brazil.
authors.forename: Guilherme Menegon
authors.initials: GM
authors.lastname: Giesel
authors.affiliation: Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, CP 15005, Porto Alegre 91500-970, RS, Brazil hverli@cbiot.ufrgs.br.
authors.forename: Hugo
authors.initials: H
authors.lastname: Verli
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D002167:Campylobacter / Q000201:enzymology; D020134:Catalytic Domain; D006602:Hexosyltransferases / Q000737:chemistry* / Q000378:metabolism; D008274:Magnesium / Q000737:chemistry / Q000494:pharmacology*; D008565:Membrane Proteins / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding
chemical_list: D001426:Bacterial Proteins; D008565:Membrane Proteins; D006602:Hexosyltransferases; C025620:dolichyl-diphosphooligosaccharide - protein glycotransferase; D008274:Magnesium
keywords: PglB; computational glycobiology; enzyme catalysis; molecular dynamics; oligosaccharyltransferase