PglD-CoA complex: An acetyl transferase from Campylobacter jejuni

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

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Structure and Active Site Residues of Pgld, an N-Acetyltransferase from the Bacillosamine Synthetic Pathway Required for N-Glycan Synthesis in Campylobacter Jejuni

Rangarajan, E.S.Ruane, K.M.Sulea, T.Watson, D.C.Proteau, A.Leclerc, S.Cygler, M.Matte, A.Young, N.M.

(2008) Biochemistry 47: 1827

  • DOI: https://doi.org/10.1021/bi702032r
  • Primary Citation of Related Structures:  
    2VHE, 3BFP

  • PubMed Abstract: 

    Campylobacter jejuni is highly unusual among bacteria in forming N-linked glycoproteins. The heptasaccharide produced by its pgl system is attached to protein Asn through its terminal 2,4-diacetamido-2,4,6-trideoxy-d-Glc (QuiNAc4NAc or N,N'-diacetylbacillosamine) moiety. The crucial, last part of this sugar's synthesis is the acetylation of UDP-2-acetamido-4-amino-2,4,6-trideoxy-d-Glc by the enzyme PglD, with acetyl-CoA as a cosubstrate. We have determined the crystal structures of PglD in CoA-bound and unbound forms, refined to 1.8 and 1.75 A resolution, respectively. PglD is a trimer of subunits each comprised of two domains, an N-terminal alpha/beta-domain and a C-terminal left-handed beta-helix. Few structural differences accompany CoA binding, except in the C-terminal region following the beta-helix (residues 189-195), which adopts an extended structure in the unbound form and folds to extend the beta-helix upon binding CoA. Computational molecular docking suggests a different mode of nucleotide-sugar binding with respect to the acetyl-CoA donor, with the molecules arranged in an "L-shape", compared with the "in-line" orientation in related enzymes. Modeling indicates that the oxyanion intermediate would be stabilized by the NH group of Gly143', with His125' the most likely residue to function as a general base, removing H+ from the amino group prior to nucleophilic attack at the carbonyl carbon of acetyl-CoA. Site-specific mutations of active site residues confirmed the importance of His125', Glu124', and Asn118. We conclude that Asn118 exerts its function by stabilizing the intricate hydrogen bonding network within the active site and that Glu124' may function to increase the pKa of the putative general base, His125'.

  • Organizational Affiliation

    Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6 Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
194Campylobacter jejuniMutation(s): 0 
Find proteins for Q0P9D1 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168))
Explore Q0P9D1 
Go to UniProtKB:  Q0P9D1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0P9D1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.25α = 90
b = 99.25β = 90
c = 143.027γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-09-28
    Changes: Atomic model, Derived calculations, Non-polymer description
  • Version 1.3: 2022-11-02
    Changes: Database references, Derived calculations, Other
  • Version 1.4: 2024-01-31
    Changes: Data collection, Refinement description