6EJI

Structure of a glycosyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase.

Ramirez, A.S.Boilevin, J.Mehdipour, A.R.Hummer, G.Darbre, T.Reymond, J.L.Locher, K.P.

(2018) Nat Commun 9: 445-445

  • DOI: 10.1038/s41467-018-02880-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The membrane-associated, processive and retaining glycosyltransferase PglH from Campylobacter jejuni is part of the biosynthetic pathway of the lipid-linked oligosaccharide (LLO) that serves as the glycan donor in bacterial protein N-glycosylation. U ...

    The membrane-associated, processive and retaining glycosyltransferase PglH from Campylobacter jejuni is part of the biosynthetic pathway of the lipid-linked oligosaccharide (LLO) that serves as the glycan donor in bacterial protein N-glycosylation. Using an unknown counting mechanism, PglH catalyzes the transfer of exactly three α1,4 N-acetylgalactosamine (GalNAc) units to the growing LLO precursor, GalNAc-α1,4-GalNAc-α1,3-Bac-α1-PP-undecaprenyl. Here, we present crystal structures of PglH in three distinct states, including a binary complex with UDP-GalNAc and two ternary complexes containing a chemo-enzymatically generated LLO analog and either UDP or synthetic, nonhydrolyzable UDP-CH 2 -GalNAc. PglH contains an amphipathic helix ("ruler helix") that has a dual role of facilitating membrane attachment and glycan counting. The ruler helix contains three positively charged side chains that can bind the pyrophosphate group of the LLO substrate and thus limit the addition of GalNAc units to three. These results, combined with molecular dynamics simulations, provide the mechanism of glycan counting by PglH.


    Organizational Affiliation

    Institute of Biophysics, Goethe University, DE-60438, Frankfurt, Germany.,Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), CH-8093, Zürich, Switzerland. locher@mol.biol.ethz.ch.,Department of Chemistry and Biochemistry, University of Berne, CH-3012, Berne, Switzerland.,Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), CH-8093, Zürich, Switzerland.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, DE-60438, Frankfurt, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
WlaC protein
A, B
373Campylobacter jejuniMutation(s): 0 
Gene Names: wlaC
Membrane protein
mpstruct
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Glycosyltransferases
Protein: 
PglH glycosyltransferase in complex with UDP-galNAc
Find proteins for O86151 (Campylobacter jejuni)
Go to UniProtKB:  O86151
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
UD2
Query on UD2

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Download CCD File 
A, B
URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE
(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate
C17 H27 N3 O17 P2
LFTYTUAZOPRMMI-NESSUJCYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.620α = 90.00
b = 127.030β = 90.13
c = 71.580γ = 90.00
Software Package:
Software NamePurpose
CRANK2phasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Switzerland--

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-14
    Type: Database references