Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 9.89 kDa 
• Atom Count: 705 
• Modelled Residue Count: 88 
• Deposited Residue Count: 88 
• Unique protein chains: 1

4XP8

Structure of EtgA D60N mutant

• PDB DOI: 10.2210/pdb4XP8/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-01-16 Released: 2015-02-18 
• Deposition Author(s): Burkinshaw, B.J., Worrall, L.J., Strynadka, N.C.J.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.244 
• R-Value Work: 0.207 
• R-Value Observed: 0.211 

Literature

Structural Analysis of a Specialized Type III Secretion System Peptidoglycan-cleaving Enzyme.

Burkinshaw, B.J., Deng, W., Lameignere, E., Wasney, G.A., Zhu, H., Worrall, L.J., Finlay, B.B., Strynadka, N.C.

(2015) J Biol Chem 290: 10406-10417

• PubMed: 25678709 
• DOI: 10.1074/jbc.M115.639013
• Primary Citation of Related Structures:  
  4XP8


• PubMed Abstract: 
  

The Gram-negative bacterium enteropathogenic Escherichia coli uses a syringe-like type III secretion system (T3SS) to inject virulence or "effector" proteins into the cytoplasm of host intestinal epithelial cells. To assemble, the T3SS must traverse both bacterial membranes, as well as the peptidoglycan layer. Peptidoglycan is made of repeating N-acetylmuramic acid and N-acetylglucosamine disaccharides cross-linked by pentapeptides to form a tight mesh barrier. Assembly of many macromolecular machines requires a dedicated peptidoglycan lytic enzyme (PG-lytic enzyme) to locally clear peptidoglycan. Here we have solved the first structure of a T3SS-associated PG-lytic enzyme, EtgA from enteropathogenic E. coli. Unexpectedly, the active site of EtgA has features in common with both lytic transglycosylases and hen egg white lysozyme. Most notably, the β-hairpin region resembles that of lysozyme and contains an aspartate that aligns with lysozyme Asp-52 (a residue critical for catalysis), a conservation not observed in other previously characterized lytic transglycosylase families to which the conserved T3SS enzymes had been presumed to belong. Mutation of the EtgA catalytic glutamate, Glu-42, conserved across lytic transglycosylases and hen egg white lysozyme, and this differentiating aspartate diminishes type III secretion in vivo, supporting its essential role in clearing the peptidoglycan for T3SS assembly. Finally, we show that EtgA forms a 1:1 complex with the building block of the polymerized T3SS inner rod component, EscI, and that this interaction enhances PG-lytic activity of EtgA in vitro, collectively providing the necessary strict localization and regulation of the lytic activity to prevent overall cell lysis.

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Organizational Affiliation: 

From the Department of Biochemistry and Molecular Biology and the Center for Blood Research, [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EtgA protein	A	88	Escherichia coli	Mutation(s): 1  Gene Names: etgA
UniProt
Find proteins for C7BUG6 (Escherichia coli) Explore C7BUG6  Go to UniProtKB:  C7BUG6

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.244 
• R-Value Work: 0.207 
• R-Value Observed: 0.211 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.4	α = 90
b = 31.4	β = 90
c = 149.53	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
SHARP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-01-16 
• Released Date: 2015-02-18 
Deposition Author(s): Burkinshaw, B.J., Worrall, L.J., Strynadka, N.C.J.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2015-02-18
  Type: Initial release
  
• Version 1.1: 2015-03-04
  Changes: Database references
• Version 1.2: 2015-04-29
  Changes: Database references
• Version 1.3: 2017-09-06
  Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
• Version 1.4: 2017-11-22
  Changes: Refinement description
• Version 1.5: 2020-01-08
  Changes: Author supporting evidence