6GXC

Bacterial oligosaccharyltransferase PglB in complex with an inhibitory peptide and a reactive lipid-linked oligosaccharide analog

Summary for 6GXC

• Entry DOI: 10.2210/pdb6gxc/pdb
• Descriptor: Undecaprenyl-diphosphooligosaccharide--protein glycotransferase, GLY-ASP-GLN-DAB-ALA-THR-PPN-GLY, MANGANESE (II) ION, ... (7 entities in total)
• Functional Keywords: glycosyltransferase, lipid-linked oligosaccharide, ternary complex, membrane protein
• Biological source: Campylobacter lari (strain RM2100 / D67 / ATCC BAA-1060); More
• Total number of polymer chains: 2
• Total formula weight: 86493.64

Authors

Napiorkowska, M.,Locher, K.P.,Boilevin, J.,Darbre, T.,Reymond, J.-L. (deposition date: 2018-06-27, release date: 2018-11-14, Last modification date: 2025-04-09)

Primary citation

Napiorkowska, M.,Boilevin, J.,Darbre, T.,Reymond, J.L.,Locher, K.P.
Structure of bacterial oligosaccharyltransferase PglB bound to a reactive LLO and an inhibitory peptide.
Sci Rep, 8:16297-16297, 2018

PubMed Abstract: Oligosaccharyltransferase (OST) is a key enzyme of the N-glycosylation pathway, where it catalyzes the transfer of a glycan from a lipid-linked oligosaccharide (LLO) to an acceptor asparagine within the conserved sequon N-X-T/S. A previous structure of a ternary complex of bacterial single subunit OST, PglB, bound to a non-hydrolyzable LLO analog and a wild type acceptor peptide showed how both substrates bind and how an external loop (EL5) of the enzyme provided specific substrate-binding contacts. However, there was a relatively large separation of the substrates at the active site. Here we present the X-ray structure of PglB bound to a reactive LLO analog and an inhibitory peptide, revealing previously unobserved interactions in the active site. We found that the atoms forming the N-glycosidic bond (C-1 of the GlcNAc moiety of LLO and the -NH group of the peptide) are closer than in the previous structure, suggesting that we have captured a conformation closer to the transition state of the reaction. We find that the distance between the divalent metal ion and the glycosidic oxygen of LLO is now 4 Å, suggesting that the metal stabilizes the leaving group of the nucleophilic substitution reaction. Further, the carboxylate group of a conserved aspartate of PglB mediates an interaction network between the reducing-end sugar of the LLO, the asparagine side chain of the acceptor peptide, and a bound divalent metal ion. The interactions identified in this novel state are likely to be relevant in the catalytic mechanisms of all OSTs.

PubMed: 30389987
DOI: 10.1038/s41598-018-34534-0

Experimental method

X-RAY DIFFRACTION (3.401 Å)