3FIR

Crystal structure of Glycosylated K135E PEB3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Specificity of Campylobacter jejuni adhesin PEB3 for phosphates and structural differences among its ligand complexes.

Min, T.Vedadi, M.Watson, D.C.Wasney, G.A.Munger, C.Cygler, M.Matte, A.Young, N.M.

(2009) Biochemistry 48: 3057-3067

  • DOI: 10.1021/bi802195d
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • PEB3 is a glycoprotein adhesin from Campylobacter jejuni whose structure suggested a role in transport. We have investigated potential ligands for PEB3 and characterized their binding properties using biophysical methods in solution and by X-ray crys ...

    PEB3 is a glycoprotein adhesin from Campylobacter jejuni whose structure suggested a role in transport. We have investigated potential ligands for PEB3 and characterized their binding properties using biophysical methods in solution and by X-ray crystallography. A thermal aggregation assay of PEB3 with a library of physiological compounds identified three possible ligands [3-phosphoglycerate (3-PG), phosphoenolpyruvate (PEP), and aconitate], which stabilized wild-type PEB3 but did not stabilize either a PEB3 form containing two mutations at the ligand-binding site, T138A/S139A, or a second PEB3 mutant, K135E, at a site approximately 14 A away. Fluorescence titration experiments and cocrystal structures with various ligands were used to characterize the binding of 3-PG, PEP, and phosphate to PEB3. Further, a C. jejuni growth experiment in minimal medium supplemented with 3-PG showed that this molecule enhances the growth of wild-type C. jejuni, but not of the PEB3 mutants. Crystallographic analysis of PEB3 complexes revealed that the Ser171-Gln180 region in the presence of 3-PG or other phosphates is helical and similar to those of other transport proteins, but it is nonhelical when citrate is bound. The K135E mutation resulted in expression of a more highly glycosylated form of PEB3 in vivo, and its crystal structure showed the conformation of the first two residues of the glycan. On the basis of our findings, we suggest that PEB3 is a transport protein that may function in utilization of 3-PG or other phosphate-containing molecules from the host.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major antigenic peptide PEB3
A, B
251Campylobacter jejuniMutation(s): 1 
Gene Names: Cj0289cpeb3
Find proteins for Q0PBL7 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168))
Go to UniProtKB:  Q0PBL7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B6D
Query on B6D

Download CCD File 
A, B
2,4-bis(acetylamino)-2,4,6-trideoxy-beta-D-glucopyranose
C10 H18 N2 O5
NRXWTRNYICXMBF-DAJIKZSHSA-N
 Ligand Interaction
NGZ
Query on NGZ

Download CCD File 
A, B
2-(ACETYLAMINO)-2-DEOXY-ALPHA-L-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-DMHSOCPYSA-N
 Ligand Interaction
FLC
Query on FLC

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.58α = 90
b = 101.962β = 108.88
c = 56.809γ = 90
Software Package:
Software NamePurpose
SGXCATdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Advisory, Structure summary