2YNK

Wzi, an Outer Membrane Protein Involved in Group 1 Capsule Assembly in Escherichia coli, is a Carbohydrate Binding Beta-Barrel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Wzi is an Outer Membrane Lectin that Underpins Group 1 Capsule Assembly in Escherichia Coli.

Bushell, S.R.Mainprize, I.L.Wear, M.A.Lou, H.Whitfield, C.Naismith, J.H.

(2013) Structure 21: 844

  • DOI: https://doi.org/10.1016/j.str.2013.03.010
  • Primary Citation of Related Structures:  
    2YNK

  • PubMed Abstract: 

    Many pathogenic bacteria encase themselves in a polysaccharide capsule that provides a barrier to the physical and immunological challenges of the host. The mechanism by which the capsule assembles around the bacterial cell is unknown. Wzi, an integral outer-membrane protein from Escherichia coli, has been implicated in the formation of group 1 capsules. The 2.6 Å resolution structure of Wzi reveals an 18-stranded β-barrel fold with a novel arrangement of long extracellular loops that blocks the extracellular entrance and a helical bundle that plugs the periplasmic end. Mutagenesis shows that specific extracellular loops are required for in vivo capsule assembly. The data show that Wzi binds the K30 carbohydrate polymer and, crucially, that mutants functionally deficient in vivo show no binding to K30 polymer in vitro. We conclude that Wzi is a novel outer-membrane lectin that assists in the formation of the bacterial capsule via direct interaction with capsular polysaccharides.


  • Organizational Affiliation

    Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
WZI456Escherichia coliMutation(s): 0 
UniProt
Find proteins for Q8GNN6 (Escherichia coli)
Explore Q8GNN6 
Go to UniProtKB:  Q8GNN6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GNN6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D12
Query on D12

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
OCT
Query on OCT

Download Ideal Coordinates CCD File 
B [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
B [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
O [auth A]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
HEX
Query on HEX

Download Ideal Coordinates CCD File 
N [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.66α = 90
b = 152.08β = 90
c = 95.04γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHELXCDEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2013-05-29
    Changes: Database references