6GXC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 

wwPDB Validation 3D Report Full Report



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

  • DOI: 10.1038/s41598-018-34534-0
  • Structures With Same Primary Citation

  • 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 ...

    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. locher@mol.biol.ethz.ch.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Undecaprenyl-diphosphooligosaccharide--protein glycotransferaseA724Campylobacter lari RM2100Mutation(s): 24 
Gene Names: pglBCla_1253
EC: 2.4.99.19
Find proteins for B9KDD4 (Campylobacter lari (strain RM2100 / D67 / ATCC BAA-1060))
Explore B9KDD4 
Go to UniProtKB:  B9KDD4
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GLY-ASP-GLN-DAB-ALA-THR-PPN-GLYB8Campylobacter lari RM2100Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FFK
Query on FFK

Download CCD File 
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
 Ligand Interaction
MES
Query on MES

Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
DAB
Query on DAB
BL-PEPTIDE LINKINGC4 H10 N2 O2ALA
PPN
Query on PPN
BL-PEPTIDE LINKINGC9 H10 N2 O4PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.81α = 90
b = 116.54β = 90
c = 173.89γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandSNF 310030B_166672

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release