4R75 | pdb_00004r75

Structure of the periplasmic binding protein AfuA from Actinobacillus pleuropneumoniae (exogenous sedoheptulose-7-phosphate bound)

• PDB DOI: https://doi.org/10.2210/pdb4R75/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Actinobacillus pleuropneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-26 Released: 2015-08-12 
• Deposition Author(s): Sit, B., Calmettes, C., Moraes, T.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 
  0.190 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

Active Transport of Phosphorylated Carbohydrates Promotes Intestinal Colonization and Transmission of a Bacterial Pathogen.

Sit, B., Crowley, S.M., Bhullar, K., Lai, C.C., Tang, C., Hooda, Y., Calmettes, C., Khambati, H., Ma, C., Brumell, J.H., Schryvers, A.B., Vallance, B.A., Moraes, T.F.

(2015) PLoS Pathog 11: e1005107-e1005107

• PubMed: 26295949 
• DOI: https://doi.org/10.1371/journal.ppat.1005107
• Primary Citation Related Structures: 
  4R72, 4R73, 4R74, 4R75


• PubMed Abstract: 
  

  Efficient acquisition of extracellular nutrients is essential for bacterial pathogenesis, however the identities and mechanisms for transport of many of these substrates remain unclear. Here, we investigate the predicted iron-binding transporter AfuABC and its role in bacterial pathogenesis in vivo. By crystallographic, biophysical and in vivo approaches, we show that AfuABC is in fact a cyclic hexose/heptose-phosphate transporter with high selectivity and specificity for a set of ubiquitous metabolites (glucose-6-phosphate, fructose-6-phosphate and sedoheptulose-7-phosphate). AfuABC is conserved across a wide range of bacterial genera, including the enteric pathogens EHEC O157:H7 and its murine-specific relative Citrobacter rodentium, where it lies adjacent to genes implicated in sugar sensing and acquisition. C. rodentium ΔafuA was significantly impaired in an in vivo murine competitive assay as well as its ability to transmit infection from an afflicted to a naïve murine host. Sugar-phosphates were present in normal and infected intestinal mucus and stool samples, indicating that these metabolites are available within the intestinal lumen for enteric bacteria to import during infection. Our study shows that AfuABC-dependent uptake of sugar-phosphates plays a critical role during enteric bacterial infection and uncovers previously unrecognized roles for these metabolites as important contributors to successful pathogenesis.

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Organizational Affiliation: 
• Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
Department of Pediatrics and the Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.
Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada; Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada.
Department of Molecular Genetics and Institute of Medical Science, University of Toronto, Ontario, Canada; Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada; SickKids Inflammatory Bowel Disease Centre, Toronto, Ontario, Canada.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 36.11 kDa 
• Atom Count: 3,128 
• Modeled Residue Count: 318 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC-type Fe3+ transport system, periplasmic component	A	321	Actinobacillus pleuropneumoniae	Mutation(s): 0  Gene Names: afuA, APL_1446
UniProt
Find proteins for A3N294 (Actinobacillus pleuropneumoniae serotype 5b (strain L20)) Explore A3N294  Go to UniProtKB:  A3N294

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S7P	B [auth A]	1-C-(hydroxymethyl)-6-O-phosphono-beta-D-altrofuranose C7 H15 O10 P RKCHIPUTSFLEHR-BNWJMWRWSA-N
PGE	F [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free:  0.190 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.405	α = 90
b = 59.895	β = 90
c = 106.014	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-12 
Deposition Author(s): Sit, B., Calmettes, C., Moraes, T.F.

Revision History  

• Version 1.0: 2015-08-12
  Type: Initial release
  
• Version 1.1: 2015-09-02
  Changes: Database references
• Version 2.0: 2020-05-13
  Changes: Atomic model, Database references
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations
• Version 2.2: 2024-11-20
  Changes: Data collection, Database references, Structure summary