4P7Q

Structure of Escherichia coli PgaB C-terminal domain in complex with N-acetylglucosamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.651 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Modification and periplasmic translocation of the biofilm exopolysaccharide poly-beta-1,6-N-acetyl-D-glucosamine.

Little, D.J.Li, G.Ing, C.DiFrancesco, B.R.Bamford, N.C.Robinson, H.Nitz, M.Pomes, R.Howell, P.L.

(2014) Proc.Natl.Acad.Sci.USA 111: 11013-11018

  • DOI: 10.1073/pnas.1406388111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Poly-β-1,6-N-acetyl-D-glucosamine (PNAG) is an exopolysaccharide produced by a wide variety of medically important bacteria. Polyglucosamine subunit B (PgaB) is responsible for the de-N-acetylation of PNAG, a process required for polymer export and b ...

    Poly-β-1,6-N-acetyl-D-glucosamine (PNAG) is an exopolysaccharide produced by a wide variety of medically important bacteria. Polyglucosamine subunit B (PgaB) is responsible for the de-N-acetylation of PNAG, a process required for polymer export and biofilm formation. PgaB is located in the periplasm and likely bridges the inner membrane synthesis and outer membrane export machinery. Here, we present structural, functional, and molecular simulation data that suggest PgaB associates with PNAG continuously during periplasmic transport. We show that the association of PgaB's N- and C-terminal domains forms a cleft required for the binding and de-N-acetylation of PNAG. Molecular dynamics (MD) simulations of PgaB show a binding preference for N-acetylglucosamine (GlcNAc) to the N-terminal domain and glucosammonium to the C-terminal domain. Continuous ligand binding density is observed that extends around PgaB from the N-terminal domain active site to an electronegative groove on the C-terminal domain that would allow for a processive mechanism. PgaB's C-terminal domain (PgaB310-672) directly binds PNAG oligomers with dissociation constants of ∼1-3 mM, and the structures of PgaB310-672 in complex with β-1,6-(GlcNAc)6, GlcNAc, and glucosamine reveal a unique binding mode suitable for interaction with de-N-acetylated PNAG (dPNAG). Furthermore, PgaB310-672 contains a β-hairpin loop (βHL) important for binding PNAG that was disordered in previous PgaB42-655 structures and is highly dynamic in the MD simulations. We propose that conformational changes in PgaB310-672 mediated by the βHL on binding of PNAG/dPNAG play an important role in the targeting of the polymer for export and its release.


    Organizational Affiliation

    Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada M5G 1X8;Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; howell@sickkids.ca mnitz@chem.utoronto.ca pomes@sickkids.ca.,Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000.,Department of Chemistry, University of Toronto, Toronto, ON, Canada M5S 3H6; and.,Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada M5G 1X8;Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8;,Department of Chemistry, University of Toronto, Toronto, ON, Canada M5S 3H6; and howell@sickkids.ca mnitz@chem.utoronto.ca pomes@sickkids.ca.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
A
367Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: pgaB (ycdR)
EC: 3.5.1.-
Find proteins for P75906 (Escherichia coli (strain K12))
Go to UniProtKB:  P75906
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.651 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.380α = 90.00
b = 77.958β = 90.00
c = 115.276γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data reduction
HKL-2000data collection
Cootmodel building
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanada--

Revision History 

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-07-23
    Type: Database references
  • Version 1.2: 2014-10-01
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary