6EJI | pdb_00006eji

Structure of a glycosyltransferase

• PDB DOI: https://doi.org/10.2210/pdb6EJI/pdb

• Classification: TRANSFERASE
• Organism(s): Campylobacter jejuni
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-21 Released: 2018-02-07 
• Deposition Author(s): Ramirez, A.S., Boilevin, J., Mehdipour, A.R., Hummer, G., Darbre, T., Reymond, J.L., Locher, K.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

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

• PubMed: 29386647 
• DOI: https://doi.org/10.1038/s41467-018-02880-2
• Primary Citation Related Structures: 
  6EJI, 6EJJ, 6EJK


• 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. 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.

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Organizational Affiliation: 
• Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), CH-8093, Zürich, Switzerland.
Department of Chemistry and Biochemistry, University of Berne, CH-3012, Berne, Switzerland.
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, DE-60438, Frankfurt, Germany.
Institute of Biophysics, Goethe University, DE-60438, Frankfurt, Germany.
Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), CH-8093, Zürich, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 88.19 kDa 
• Atom Count: 6,130 
• Modeled Residue Count: 720 
• Deposited Residue Count: 746 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WlaC protein	A, B	373	Campylobacter jejuni	Mutation(s): 0  Gene Names: wlaC
UniProt
Find proteins for O86151 (Campylobacter jejuni) Explore O86151  Go to UniProtKB:  O86151

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UD2	C [auth A], J [auth B]	URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE C17 H27 N3 O17 P2 LFTYTUAZOPRMMI-NESSUJCYSA-N
GOL	E [auth A], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	D [auth A], K [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	H [auth A], I [auth A], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	F [auth A], G [auth A], M [auth B], N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.62	α = 90
b = 127.03	β = 90.13
c = 71.58	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
CRANK2	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-02-07 
Deposition Author(s): Ramirez, A.S., Boilevin, J., Mehdipour, A.R., Hummer, G., Darbre, T., Reymond, J.L., Locher, K.P.

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Funding Organization	Location	Grant Number
	Switzerland	--

Revision History  

• Version 1.0: 2018-02-07
  Type: Initial release
  
• Version 1.1: 2018-02-14
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary