6Q5E | pdb_00006q5e

Crystal structure of the ferric enterobactin receptor from Pseudomonas aeruginosa (PfeA) in complex with enterobactin

• PDB DOI: https://doi.org/10.2210/pdb6Q5E/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2018-12-07 Released: 2019-01-16 
• Deposition Author(s): Moynie, L., Naismith, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.249 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

The complex of ferric-enterobactin with its transporter from Pseudomonas aeruginosa suggests a two-site model.

Moynie, L., Milenkovic, S., Mislin, G.L.A., Gasser, V., Malloci, G., Baco, E., McCaughan, R.P., Page, M.G.P., Schalk, I.J., Ceccarelli, M., Naismith, J.H.

(2019) Nat Commun 10: 3673-3673

• PubMed: 31413254 
• DOI: https://doi.org/10.1038/s41467-019-11508-y
• Primary Citation Related Structures: 
  5M9B, 5MZS, 5NC4, 5NR2, 5OUT, 6I2J, 6Q5E, 6R1F


• PubMed Abstract: 
  

  Bacteria use small molecules called siderophores to scavenge iron. Siderophore-Fe ³⁺ complexes are recognised by outer-membrane transporters and imported into the periplasm in a process dependent on the inner-membrane protein TonB. The siderophore enterobactin is secreted by members of the family Enterobacteriaceae, but many other bacteria including Pseudomonas species can use it. Here, we show that the Pseudomonas transporter PfeA recognises enterobactin using extracellular loops distant from the pore. The relevance of this site is supported by in vivo and in vitro analyses. We suggest there is a second binding site deeper inside the structure and propose that correlated changes in hydrogen bonds link binding-induced structural re-arrangements to the structural adjustment of the periplasmic TonB-binding motif.

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Organizational Affiliation: 
• Division of Structural Biology, Wellcome Trust Centre of Human Genomics, 7 Roosevelt Drive, Oxford, OX3 7BN, UK.
The Research Complex at Harwell, Harwell Campus, Oxfordshire, OX11 0FA, UK.
The Rosalind Franklin Institute, Didcot, OX11 0FA, UK.
Department of Physics, University of Cagliari, Cittadella Universitaria, SP Monserrato-Sestu Km 0.700, Monserrato, 09042, Italy.
Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67413, Strasbourg, France.
CNRS, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67413, Strasbourg, France.
BSRC, The University of St Andrews, St Andrews, KY16 9ST, UK.
Department of Life Sciences & Chemistry, Campus Ring 1, Bremen, 28759, Germany.
Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67413, Strasbourg, France. [e-mail].
Istituto Officina dei Materiali-CNR, Cittadella Universitaria, Monserrato, 09042, Italy. [e-mail].
Department of Physics, University of Cagliari, Cittadella Universitaria, SP Monserrato-Sestu Km 0.700, Monserrato, 09042, Italy. [e-mail].
Istituto Officina dei Materiali-CNR, Cittadella Universitaria, Monserrato, 09042, Italy. [e-mail].
Division of Structural Biology, Wellcome Trust Centre of Human Genomics, 7 Roosevelt Drive, Oxford, OX3 7BN, UK. [e-mail].
The Research Complex at Harwell, Harwell Campus, Oxfordshire, OX11 0FA, UK. [e-mail].
The Rosalind Franklin Institute, Didcot, OX11 0FA, UK. [e-mail].

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: 79.92 kDa 
• Atom Count: 5,486 
• Modeled Residue Count: 698 
• Deposited Residue Count: 721 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferric enterobactin receptor	A	721	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: pfeA, PA2688 Membrane Entity: Yes
UniProt
Find proteins for Q05098 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q05098  Go to UniProtKB:  Q05098

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LP5	D [auth A]	(R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE C34 H66 N O12 P HEHQDWUWJVPREQ-XQJZMFRCSA-N
EB4	C [auth A]	N,N',N''-[(3S,7S,11S)-2,6,10-trioxo-1,5,9-trioxacyclododecane-3,7,11-triyl]tris(2,3-dihydroxybenzamide) C30 H27 N3 O15 SERBHKJMVBATSJ-BZSNNMDCSA-N
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.249 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.63	α = 90
b = 159.26	β = 90
c = 78.61	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Moynie, L., Naismith, J.H.

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Funding Organization	Location	Grant Number
	United Kingdom	--

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2019-08-28
  Changes: Data collection, Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary