Biological Assembly 1  

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

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

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

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 22.75 kDa 
• Atom Count: 1659 
• Modelled Residue Count: 183 
• Deposited Residue Count: 203 
• Unique protein chains: 1

6V98

Crystal structure of Type VI secretion system effector, TseH (VCA0285)

• PDB DOI: 10.2210/pdb6V98/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-13 Released: 2020-01-15 
• Deposition Author(s): Watanabe, N., Hersch, S.J., Dong, T.G., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.217 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Literature

Envelope stress responses defend against type six secretion system attacks independently of immunity proteins.

Hersch, S.J., Watanabe, N., Stietz, M.S., Manera, K., Kamal, F., Burkinshaw, B., Lam, L., Pun, A., Li, M., Savchenko, A., Dong, T.G.

(2020) Nat Microbiol 5: 706-714

• PubMed: 32094588 
• DOI: 10.1038/s41564-020-0672-6
• Primary Citation of Related Structures:  
  6V98


• PubMed Abstract: 
  

The arms race among microorganisms is a key driver in the evolution of not only the weapons but also defence mechanisms. Many Gram-negative bacteria use the type six secretion system (T6SS) to deliver toxic effectors directly into neighbouring cells. Defence against effectors requires cognate immunity proteins. However, here we show immunity-independent protection mediated by envelope stress responses in Escherichia coli and Vibrio cholerae against a V. cholerae T6SS effector, TseH. We demonstrate that TseH is a PAAR-dependent species-specific effector highly potent against Aeromonas species but not against its V. cholerae immunity mutant or E. coli. A structural analysis reveals TseH is probably a NlpC/P60-family cysteine endopeptidase. We determine that two envelope stress-response pathways, Rcs and BaeSR, protect E. coli from TseH toxicity by mechanisms including capsule synthesis. The two-component system WigKR (VxrAB) is critical for protecting V. cholerae from its own T6SS despite expressing immunity genes. WigR also regulates T6SS expression, suggesting a dual role in attack and defence. This deepens our understanding of how bacteria survive T6SS attacks and suggests that defence against the T6SS represents a major selective pressure driving the evolution of species-specific effectors and protective mechanisms mediated by envelope stress responses and capsule synthesis.

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Organizational Affiliation: 

State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine hydrolase	A	203	Vibrio cholerae	Mutation(s): 0  Gene Names: C9J66_18215, ERS013186_03768, ERS013193_04941, ERS013197_05943, ERS013198_03598, ERS013200_03989, ERS013202_03729, ERS013206_03782, FPV63_00060
UniProt
Find proteins for Q9KMN9 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KMN9  Go to UniProtKB:  Q9KMN9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAF	A	L-PEPTIDE LINKING	C5 H12 As N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.217 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.756	α = 90
b = 63.645	β = 90
c = 70.292	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
HKL-3000	data reduction
HKL-3000	data scaling
Aimless	data scaling
SHARP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-12-13 
• Released Date: 2020-01-15 
Deposition Author(s): Watanabe, N., Hersch, S.J., Dong, T.G., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2020-01-15
  Type: Initial release
  
• Version 1.1: 2020-03-11
  Changes: Database references
• Version 1.2: 2020-05-13
  Changes: Database references