6H7F | pdb_00006h7f

Crystal structure of BauA, the Ferric preacinetobactin receptor from Acinetobacter baumannii in complex with Fe3+-Preacinetobactin-acinetobactin

• PDB DOI: https://doi.org/10.2210/pdb6H7F/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2018-07-31 Released: 2018-10-10 
• Deposition Author(s): Moynie, L., Naismith, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.217 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Preacinetobactin not acinetobactin is essential for iron uptake by the BauA transporter of the pathogenAcinetobacter baumannii.

Moynie, L., Serra, I., Scorciapino, M.A., Oueis, E., Page, M.G., Ceccarelli, M., Naismith, J.H.

(2018) Elife 7

• PubMed: 30558715 
• DOI: https://doi.org/10.7554/eLife.42270
• Primary Citation Related Structures: 
  6H7F, 6H7V, 6HCP


• PubMed Abstract: 
  

  New strategies are urgently required to develop antibiotics. The siderophore uptake system has attracted considerable attention, but rational design of siderophore antibiotic conjugates requires knowledge of recognition by the cognate outer-membrane transporter. Acinetobacter baumannii is a serious pathogen, which utilizes (pre)acinetobactin to scavenge iron from the host. We report the structure of the (pre)acinetobactin transporter BauA bound to the siderophore, identifying the structural determinants of recognition. Detailed biophysical analysis confirms that BauA recognises preacinetobactin. We show that acinetobactin is not recognised by the protein, thus preacinetobactin is essential for iron uptake. The structure shows and NMR confirms that under physiological conditions, a molecule of acinetobactin will bind to two free coordination sites on the iron preacinetobactin complex. The ability to recognise a heterotrimeric iron-preacinetobactin-acinetobactin complex may rationalize contradictory reports in the literature. These results open new avenues for the design of novel antibiotic conjugates (trojan horse) antibiotics.

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Organizational Affiliation: 
• Division of Structural Biology, Wellcome Trust Centre of Human Genomics, Oxford, England.
Research Complex at Harwell, Rutherford Laboratory, Didcot, England.
Department of Physics, University of Cagliari, Cagliari, Italy.
Department of Chemical and Geological Sciences, University of Cagliari, Cagliari, Italy.
Biomedical Sciences Research Complex, The University of St Andrews, Scotland, United Kingdom.
Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany.
The Rosalind Franklin Institute, Didcot, England.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 242.88 kDa 
• Atom Count: 17,122 
• Modeled Residue Count: 2,013 
• Deposited Residue Count: 2,118 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BauA	A, B, C	706	Acinetobacter baumannii	Mutation(s): 0  Gene Names: bauA Membrane Entity: Yes
UniProt
Find proteins for Q76HJ9 (Acinetobacter baumannii) Explore Q76HJ9  Go to UniProtKB:  Q76HJ9

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FV8	BA [auth B], DB [auth C], E [auth A]	(4~{S},5~{R})-2-[2,3-bis(oxidanyl)phenyl]-~{N}-[2-(1~{H}-imidazol-4-yl)ethyl]-5-methyl-~{N}-oxidanyl-4,5-dihydro-1,3-oxazole-4-carboxamide C16 H18 N4 O5 FCWIGDCVHNNXFS-RNCFNFMXSA-N
OPZ	CA [auth B], EB [auth C], G [auth A]	~{N}-[(4~{S},5~{R})-2-[2-(1~{H}-imidazol-4-yl)ethyl]-5-methyl-3-oxidanylidene-1,2-oxazolidin-4-yl]-2,3-bis(oxidanyl)benzamide C16 H18 N4 O5 YQXURFXJBIFMOA-RNCFNFMXSA-N
OPV	F [auth A]	~{N}-[(4~{S},5~{S})-2-[2-(1~{H}-imidazol-4-yl)ethyl]-5-methyl-3-oxidanylidene-1,2-oxazolidin-4-yl]-2,3-bis(oxidanyl)benzamide C16 H18 N4 O5 YQXURFXJBIFMOA-ZANVPECISA-N
C8E	DA [auth B], EA [auth B], FA [auth B], FB [auth C], GA [auth B], GB [auth C], H [auth A], HA [auth B], HB [auth C], I [auth A], IA [auth B], IB [auth C], J [auth A], JA [auth B], JB [auth C], K [auth A], KA [auth B], KB [auth C], L [auth A], LA [auth B], LB [auth C], M [auth A], MA [auth B], MB [auth C], NA [auth B], NB [auth C], OA [auth B], OB [auth C]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C16 H34 O5 FEOZZFHAVXYAMB-UHFFFAOYSA-N
EDO	AB [auth B], AC [auth C], BB [auth B], BC [auth C], CC [auth C], DC [auth C], EC [auth C], FC [auth C], N [auth A], O [auth A], P [auth A], PA [auth B], PB [auth C], Q [auth A], QA [auth B], QB [auth C], R [auth A], RA [auth B], RB [auth C], S [auth A], SA [auth B], SB [auth C], T [auth A], TA [auth B], TB [auth C], U [auth A], UA [auth B], UB [auth C], V [auth A], VA [auth B], VB [auth C], W [auth A], WA [auth B], WB [auth C], X [auth A], XA [auth B], XB [auth C], Y [auth A], YA [auth B], YB [auth C], Z [auth A], ZA [auth B], ZB [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE	AA [auth B], CB [auth C], D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.217 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.64	α = 90
b = 220.65	β = 99.09
c = 101.14	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: 2018-10-10 
Deposition Author(s): Moynie, L., Naismith, J.H.

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Funding Organization	Location	Grant Number
	United Kingdom	--

Revision History  

• Version 1.0: 2018-10-10
  Type: Initial release
  
• Version 1.1: 2019-01-16
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description