6GXC | pdb_00006gxc

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

• PDB DOI: https://doi.org/10.2210/pdb6GXC/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Campylobacter lari RM2100
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2018-06-27 Released: 2018-11-14 
• Deposition Author(s): Napiorkowska, M., Locher, K.P., Boilevin, J., Darbre, T., Reymond, J.-L.
• Funding Organization(s): Swiss National Science Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.283 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.249 (Depositor), 0.256 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Literature

Structure of bacterial oligosaccharyltransferase PglB bound to a reactive LLO and an inhibitory peptide.

Napiorkowska, M., Boilevin, J., Darbre, T., Reymond, J.L., Locher, K.P.

(2018) Sci Rep 8: 16297-16297

• PubMed: 30389987 
• DOI: https://doi.org/10.1038/s41598-018-34534-0
• Primary Citation Related Structures: 
  6GXC


• 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 ₂ 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.

---

Organizational Affiliation: 
• Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland.
Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 86.49 kDa 
• Atom Count: 5,931 
• Modeled Residue Count: 714 
• Deposited Residue Count: 732 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Undecaprenyl-diphosphooligosaccharide--protein glycotransferase	A	724	Campylobacter lari RM2100	Mutation(s): 24  Gene Names: pglB, Cla_1253 EC: 2.4.99.19 Membrane Entity: Yes
UniProt
Find proteins for B9KDD4 (Campylobacter lari (strain RM2100 / D67 / ATCC BAA-1060)) Explore B9KDD4  Go to UniProtKB:  B9KDD4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLY-ASP-GLN-DAB-ALA-THR-PPN-GLY	B	8	Campylobacter lari RM2100	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FFK	H [auth A]	[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl] [oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl] hydrogen phosphate C28 H49 N O12 P2 MCKZOQNLWLVDRX-ADLZVGHSSA-N
MES	F [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
PEG	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MN	C [auth A], D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAB	B	L-PEPTIDE LINKING	C4 H10 N2 O2		ALA
PPN	B	L-PEPTIDE LINKING	C9 H10 N2 O4		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.283 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.249 (Depositor), 0.256 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.81	α = 90
b = 116.54	β = 90
c = 173.89	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-11-14 
Deposition Author(s): Napiorkowska, M., Locher, K.P., Boilevin, J., Darbre, T., Reymond, J.-L.

---

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	SNF 310030B_166672

Revision History  

• Version 1.0: 2018-11-14
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary