6Z8A | pdb_00006z8a

Outer membrane FoxA in complex with nocardamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.270 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6Z8A

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Nocardamine-Dependent Iron Uptake in Pseudomonas aeruginosa : Exclusive Involvement of the FoxA Outer Membrane Transporter.

Normant, V.Josts, I.Kuhn, L.Perraud, Q.Fritsch, S.Hammann, P.Mislin, G.L.A.Tidow, H.Schalk, I.J.

(2020) ACS Chem Biol 15: 2741-2751

  • DOI: https://doi.org/10.1021/acschembio.0c00535
  • Primary Citation Related Structures: 
    6Z8A

  • PubMed Abstract: 

    Iron is a key nutrient for almost all living organisms. Paradoxically, it is poorly soluble and consequently poorly bioavailable. Bacteria have thus developed multiple strategies to access this metal. One of the most common consists of the use of siderophores, small compounds that chelate ferric iron with very high affinity. Many bacteria are able to produce their own siderophores or use those produced by other microorganisms (exosiderophores) in a piracy strategy. Pseudomonas aeruginosa produces two siderophores, pyoverdine and pyochelin, and is also able to use a large panel of exosiderophores. We investigated the ability of P. aeruginosa to use nocardamine (NOCA) and ferrioxamine B (DFOB) as exosiderophores under iron-limited planktonic growth conditions. Proteomic and RT-qPCR approaches showed induction of the transcription and expression of the outer membrane transporter FoxA in the presence of NOCA or DFOB in the bacterial environment. Expression of the proteins of the heme- or pyoverdine- and pyochelin-dependent iron uptake pathways was not affected by the presence of these two tris-hydroxamate siderophores. 55 Fe uptake assays using foxA mutants showed ferri-NOCA to be exclusively transported by FoxA, whereas ferri-DFOB was transported by FoxA and at least one other unidentified transporter. The crystal structure of FoxA complexed with NOCA-Fe revealed very similar siderophore binding sites between NOCA-Fe and DFOB-Fe. We discuss iron uptake by hydroxamate exosiderophores in P. aeruginosa cells in light of these results.


  • Organizational Affiliation
    • CNRS, UMR7242, ESBS, Université de Strasbourg, Bld Sébastien Brant, F-67412 Illkirch, France.

Macromolecule Content 

  • Total Structure Weight: 86.61 kDa 
  • Atom Count: 5,395 
  • Modeled Residue Count: 677 
  • Deposited Residue Count: 776 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferrioxamine receptor FoxA776Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: foxAPA2466
Membrane Entity: Yes 
UniProt
Find proteins for Q9I116 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I116 
Go to UniProtKB:  Q9I116
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I116
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6L0
(Subject of Investigation/LOI)

Query on 6L0



Download:Ideal Coordinates CCD File
E [auth A](8E)-6,17,28-trihydroxy-1,6,12,17,23,28-hexaazacyclotritriacont-8-ene-2,5,13,16,24,27-hexone
C27 H46 N6 O9
SHTNNSLDUIEFSM-LREOWRDNSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS

Query on DMS



Download:Ideal Coordinates CCD File
D [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
F [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.270 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.222α = 90
b = 95.222β = 90
c = 178.651γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary