3RCE

Bacterial oligosaccharyltransferase PglB

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 

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
  • Primary Citation of Related Structures:  
    3RCE

  • 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, org ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Oligosaccharide transferase to N-glycosylate proteins A724Campylobacter lariMutation(s): 1 
Gene Names: pglB, Cla_1253
EC: 2.4.99.19
Membrane protein
Mpstruc		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))
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 LengthOrganismDetailsImage
Substrate Mimic Peptide B8N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
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: 0.271 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.06α = 90
b = 116.1β = 90
c = 175.04γ = 90
Software Package:
Software NamePurpose
SHARPphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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