3BFP

Crystal Structure of apo-PglD from Campylobacter jejuni


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 1827-1836

  • DOI: 10.1021/bi702032r
  • Primary Citation of Related Structures:  

  • 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'-diacetylb ...

    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'.


    Related Citations: 
    • Structure of the N-linked glycan present in multiple glycoproteins in the gram-negative bacterium Campylobacter jejuni
      Young, N.M.,Brisson, J.R.,Kelly, J.,Watson, D.C.,Tessier, L.,Lanthier, P.H.,Cadotte, N.,Michael, F.St.,Aberg, E.,Szymanski, C.M.
      (2002) J.Biol.Chem. 277: 42530
    • In vitro biosynthesis of UDP-N,N'-diacetylbacillosamine by enzymes of the Campylobacter jejuni general protein glycosylation system
      Olivier, N.B.,Chen, M.M.,Behr, J.R.,Imperiali, B.
      (2006) Biochemistry 45: 13659
    • Conformational and sequence signatures in beta-helix proteins
      Lengar, P.,Joshi, N.V.,Balaram, P.
      (2006) Structure 14: 529


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acetyltransferase
A
194Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)Mutation(s): 0 
Gene Names: pglD
EC: 2.3.1.203
Find proteins for Q0P9D1 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168))
Go to UniProtKB:  Q0P9D1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download SDF File 
Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.198 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 86.462α = 90.00
b = 86.462β = 90.00
c = 65.547γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
SHARPphasing
DMphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description