3RCE

Bacterial oligosaccharyltransferase PglB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

X-ray structure of a bacterial oligosaccharyltransferase.

Lizak, C.Gerber, S.Numao, S.Aebi, M.Locher, K.P.

(2011) Nature 474: 350-355

  • DOI: 10.1038/nature10151

  • PubMed Abstract: 
  • Asparagine-linked glycosylation is a post-translational modification of proteins containing the conserved sequence motif Asn-X-Ser/Thr. The attachment of oligosaccharides is implicated in diverse processes such as protein folding and quality control, ...

    Asparagine-linked glycosylation is a post-translational modification of proteins containing the conserved sequence motif Asn-X-Ser/Thr. The attachment of oligosaccharides is implicated in diverse processes such as protein folding and quality control, organism development or host-pathogen interactions. The reaction is catalysed by oligosaccharyltransferase (OST), a membrane protein complex located in the endoplasmic reticulum. The central, catalytic enzyme of OST is the STT3 subunit, which has homologues in bacteria and archaea. Here we report the X-ray structure of a bacterial OST, the PglB protein of Campylobacter lari, in complex with an acceptor peptide. The structure defines the fold of STT3 proteins and provides insight into glycosylation sequon recognition and amide nitrogen activation, both of which are prerequisites for the formation of the N-glycosidic linkage. We also identified and validated catalytically important, acidic amino acid residues. Our results provide the molecular basis for understanding the mechanism of N-linked glycosylation.


    Organizational Affiliation

    Institute of Microbiology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oligosaccharide transferase to N-glycosylate proteins
A
724Campylobacter lari (strain RM2100 / D67 / ATCC BAA-1060)Gene Names: pglB
EC: 2.4.99.19
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oligosaccharyltransferases (OST)
Protein: 
PglB OST in complex with acceptor peptide
Find proteins for B9KDD4 (Campylobacter lari (strain RM2100 / D67 / ATCC BAA-1060))
Go to UniProtKB:  B9KDD4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Substrate Mimic Peptide
B
8N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PPN
Query on PPN
B
L-PEPTIDE LINKINGC9 H10 N2 O4PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 85.060α = 90.00
b = 116.100β = 90.00
c = 175.040γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
SHARPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-17
    Type: Database references
  • Version 1.3: 2013-05-22
    Type: Refinement description
  • Version 1.4: 2017-11-08
    Type: Advisory, Refinement description