4K19

The structure of Human Siderocalin bound to the bacterial siderophore fluvibactin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Siderocalin Outwits the Coordination Chemistry of Vibriobactin, a Siderophore of Vibrio cholerae.

Allred, B.E.Correnti, C.Clifton, M.C.Strong, R.K.Raymond, K.N.

(2013) Acs Chem.Biol. 8: 1882-1887

  • DOI: 10.1021/cb4002552

  • PubMed Abstract: 
  • The human protein siderocalin (Scn) inhibits bacterial iron acquisition by binding catechol siderophores. Several pathogenic bacteria respond by making stealth siderophores that are not recognized by Scn. Fluvibactin and vibriobactin, respectively of ...

    The human protein siderocalin (Scn) inhibits bacterial iron acquisition by binding catechol siderophores. Several pathogenic bacteria respond by making stealth siderophores that are not recognized by Scn. Fluvibactin and vibriobactin, respectively of Vibrio fluvialis and Vibrio cholerae , include an oxazoline adjacent to a catechol. This chelating unit binds iron either in a catecholate or a phenolate-oxazoline coordination mode. The latter has been suggested to make vibriobactin a stealth siderophore without directly identifying the coordination mode in relation to Scn binding. We use Scn binding assays with the two siderophores and two oxazoline-substituted analogs and the crystal structure of Fe-fluvibactin:Scn to show that the oxazoline does not prevent Scn binding; hence, vibriobactin is not a stealth siderophore. We show that the phenolate-oxazoline coordination mode is present at physiological pH and is not bound by Scn. However, Scn binding shifts the coordination to the catecholate mode and thereby inactivates this siderophore.


    Organizational Affiliation

    Department of Chemistry, University of California , Berkeley, California 94720-1460, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neutrophil gelatinase-associated lipocalin
A, B, C
180Homo sapiensMutation(s): 1 
Gene Names: LCN2 (HNL, NGAL)
Find proteins for P80188 (Homo sapiens)
Go to Gene View: LCN2
Go to UniProtKB:  P80188
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1OD
Query on 1OD

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A, B, C
(4S,5R)-N,N-bis{3-[(2,3-dihydroxybenzoyl)amino]propyl}-2-(2,3-dihydroxyphenyl)-5-methyl-4,5-dihydro-1,3-oxazole-4-carboxamide
fluvibactin
C31 H34 N4 O10
LHJFXHHBUCCXIF-OSPHWJPCSA-N
 Ligand Interaction
NA
Query on NA

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C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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A, B, C
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1ODKd: 34 nM (98) BINDINGDB
1ODKd: 4.4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.236 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 114.200α = 90.00
b = 114.200β = 90.00
c = 119.300γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
REFMACrefinement
DENZOdata reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-10-23
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description