6UUE

The Se-Met Structure of the Vibrio vulnificus ToxR periplasmic domain

• PDB DOI: https://doi.org/10.2210/pdb6UUE/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Vibrio vulnificus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-10-30 Released: 2020-06-17 
• Deposition Author(s): Kull, F.J., Midgett, C.R., Swindell, R.A.
• 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: 1.39 Å
• R-Value Free: 0.229 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 

Literature

A disulfide constrains the ToxR periplasmic domain structure, altering its interactions with ToxS and bile-salts.

Midgett, C.R., Swindell, R.A., Pellegrini, M., Jon Kull, F.

(2020) Sci Rep 10: 9002-9002

• PubMed: 32488093 
• DOI: https://doi.org/10.1038/s41598-020-66050-5
• Primary Citation of Related Structures:  
  6UTC, 6UUE


• PubMed Abstract: 
  

  ToxR is a transmembrane transcription factor that, together with its integral membrane periplasmic binding partner ToxS, is conserved across the Vibrionaceae family. In some pathogenic Vibrios, including V. parahaemolyticus and V. cholerae, ToxR is required for bile resistance and virulence, and ToxR is fully activated and protected from degradation by ToxS. ToxS achieves this in part by ensuring formation of an intra-chain disulfide bond in the C-terminal periplasmic domain of ToxR (dbToxRp). In this study, biochemical analysis showed dbToxRp to have a higher affinity for the ToxS periplasmic domain than the non-disulfide bonded conformation. Analysis of our dbToxRp crystal structure showed this is due to disulfide bond stabilization. Furthermore, dbToxRp is structurally homologous to the V. parahaemolyticus VtrA periplasmic domain. These results highlight the critical structural role of disulfide bond in ToxR and along with VtrA define a domain fold involved in environmental sensing conserved across the Vibrionaceae family.

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Organizational Affiliation: 

Department of Chemistry, Dartmouth College, Hanover, NH, USA. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 11.84 kDa 
• Atom Count: 770 
• Modelled Residue Count: 91 
• Deposited Residue Count: 104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional activator ToxR	A	104	Vibrio vulnificus	Mutation(s): 0  Gene Names: toxR, CRN46_04050, D8T65_08455, FORC36_0761
UniProt
Find proteins for Q9RP86 (Vibrio vulnificus) Explore Q9RP86  Go to UniProtKB:  Q9RP86

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 1.39 Å
• R-Value Free: 0.229 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.96	α = 90
b = 40.53	β = 90
c = 49.57	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-17 
Deposition Author(s): Kull, F.J., Midgett, C.R., Swindell, R.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21AI140740

Revision History  

• Version 1.0: 2020-06-17
  Type: Initial release