3BSY

PglD from Campylobacter jejuni, NCTC 11168, in complex with acetyl coenzyme A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure and catalytic mechanism of PglD from Campylobacter jejuni.

Olivier, N.B.Imperiali, B.

(2008) J.Biol.Chem. 283: 27937-27946

  • DOI: 10.1074/jbc.M801207200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The carbohydrate 2, 4-diacetamido-2, 4, 6-trideoxy-alpha-D-glucopyranose (BacAc(2)) is found in a variety of eubacterial pathogens. In Campylobacter jejuni, PglD acetylates the C4 amino group on UDP-2-acetamido-4-amino-2, 4, 6-trideoxy-alpha-D-glucop ...

    The carbohydrate 2, 4-diacetamido-2, 4, 6-trideoxy-alpha-D-glucopyranose (BacAc(2)) is found in a variety of eubacterial pathogens. In Campylobacter jejuni, PglD acetylates the C4 amino group on UDP-2-acetamido-4-amino-2, 4, 6-trideoxy-alpha-D-glucopyranose (UDP-4-amino-sugar) to form UDP-BacAc(2). Sequence analysis predicts PglD to be a member of the left-handed beta helix family of enzymes. However, poor sequence homology between PglD and left-handed beta helix enzymes with existing structural data precludes unambiguous identification of the active site. The co-crystal structures of PglD in the presence of citrate, acetyl coenzyme A, or the UDP-4-amino-sugar were solved. The biological assembly is a trimer with one active site formed between two protomers. Residues lining the active site were identified, and results from functional assays on alanine mutants suggest His-125 is critical for catalysis, whereas His-15 and His-134 are involved in substrate binding. These results are discussed in the context of implications for proteins homologous to PglD in other pathogens.


    Organizational Affiliation

    Department of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acetyltransferase
A, B, C
198Campylobacter 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
ACO
Query on ACO

Download SDF File 
Download CCD File 
A, B, C
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.871α = 90.00
b = 91.862β = 90.00
c = 125.195γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
PHASERphasing
HKL-2000data scaling
HKL-2000data collection
DMphasing
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-11-12
    Type: Structure summary
  • Version 1.3: 2017-10-25
    Type: Refinement description