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 
  • R-Value Observed: 0.200 

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:  
    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 ...

    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: 
    • 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
    • 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
    • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AcetyltransferaseA194Campylobacter jejuniMutation(s): 0 
Gene Names: pglD
EC: 2.3.1.203
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download Ideal Coordinates CCD File 
B [auth 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 
  • R-Value Observed: 0.200 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.462α = 90
b = 86.462β = 90
c = 65.547γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

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