8GEX | pdb_00008gex

Crystal structure of the ferric enterobactin transporter (XusB) from Bacteroides thetaiotaomicron

• PDB DOI: https://doi.org/10.2210/pdb8GEX/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Bacteroides thetaiotaomicron
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-03-07 Released: 2023-08-02 
• Deposition Author(s): Perera, Y.R., Chazin, W.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: in silico

Literature

Iron acquisition by a commensal bacterium modifies host nutritional immunity during Salmonella infection.

Spiga, L., Fansler, R.T., Perera, Y.R., Shealy, N.G., Munneke, M.J., David, H.E., Torres, T.P., Lemoff, A., Ran, X., Richardson, K.L., Pudlo, N., Martens, E.C., Folta-Stogniew, E., Yang, Z.J., Skaar, E.P., Byndloss, M.X., Chazin, W.J., Zhu, W.

(2023) Cell Host Microbe 31: 1639-1654.e10

• PubMed: 37776864 
• DOI: https://doi.org/10.1016/j.chom.2023.08.018
• Primary Citation Related Structures: 
  8GEX


• PubMed Abstract: 
  

  During intestinal inflammation, host nutritional immunity starves microbes of essential micronutrients, such as iron. Pathogens scavenge iron using siderophores, including enterobactin; however, this strategy is counteracted by host protein lipocalin-2, which sequesters iron-laden enterobactin. Although this iron competition occurs in the presence of gut bacteria, the roles of commensals in nutritional immunity involving iron remain unexplored. Here, we report that the gut commensal Bacteroides thetaiotaomicron acquires iron and sustains its resilience in the inflamed gut by utilizing siderophores produced by other bacteria, including Salmonella, via a secreted siderophore-binding lipoprotein XusB. Notably, XusB-bound enterobactin is less accessible to host sequestration by lipocalin-2 but can be "re-acquired" by Salmonella, allowing the pathogen to evade nutritional immunity. Because the host and pathogen have been the focus of studies of nutritional immunity, this work adds commensal iron metabolism as a previously unrecognized mechanism modulating the host-pathogen interactions and nutritional immunity.

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Organizational Affiliation: 
• Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
Departments of Biochemistry and Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.
Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA.
Departments of Chemistry, Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37232, USA.
Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, CT 06511, USA.
Departments of Biochemistry and Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA. Electronic address: [e-mail].
Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 278.85 kDa 
• Atom Count: 19,062 
• Modeled Residue Count: 2,419 
• Deposited Residue Count: 2,544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF4374 domain-containing protein	A, B, C, D, E, F	424	Bacteroides thetaiotaomicron	Mutation(s): 0  Gene Names: Btheta7330_00980, DW780_15885, GAN91_09105, GAO00_22735, GAO51_09325
UniProt
Find proteins for A0A0P0ENH6 (Bacteroides thetaiotaomicron) Explore A0A0P0ENH6  Go to UniProtKB:  A0A0P0ENH6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.193	α = 90
b = 174.193	β = 90
c = 294.28	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
Coot	model building
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-02 
Deposition Author(s): Perera, Y.R., Chazin, W.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM147470
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	#1R01DK134692-01

Revision History  

• Version 1.0: 2023-08-02
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection
• Version 1.2: 2024-08-14
  Changes: Database references