5JM8

The structure of ATP-bound aerobactin synthetase IucA from a hypervirulent pathotype of Klebsiella pneumoniae

  • Classification: LIGASE
  • Expression System: Escherichia coli

  • Deposited: 2016-04-28 Released: 2016-06-15 
  • Deposition Author(s): Bailey, D.C., Drake, E.J., Gulick, A.M.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases; National Institutes of Health/National Center for Advancing Translational Sciences 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural and Functional Characterization of Aerobactin Synthetase IucA from a Hypervirulent Pathotype of Klebsiella pneumoniae.

Bailey, D.C.Drake, E.J.Grant, T.D.Gulick, A.M.

(2016) Biochemistry 55: 3559-3570

  • DOI: 10.1021/acs.biochem.6b00409
  • Primary Citation of Related Structures:  5JM7

  • PubMed Abstract: 
  • Iron is a vital mineral nutrient required by virtually all life forms to prosper; pathogenic bacteria are no exception. Despite the abundance of iron within the human host, highly regulated iron physiology can result in exceedingly low levels of iron ...

    Iron is a vital mineral nutrient required by virtually all life forms to prosper; pathogenic bacteria are no exception. Despite the abundance of iron within the human host, highly regulated iron physiology can result in exceedingly low levels of iron bioavailable to prospective invading bacteria. To combat this scarcity of iron, many pathogenic bacteria have acquired specific and efficient iron acquisition systems, which allow them to thrive in iron-deficient host environments. One of the more prominent bacterial iron acquisition systems involves the synthesis, secretion, and reuptake of small-molecule iron chelators known as siderophores. Aerobactin, a citrate-hydroxamate siderophore originally isolated nearly 50 years ago, is produced by a number of pathogenic Gram-negative bacteria. Aerobactin has recently been demonstrated to play a pivotal role in mediating the enhanced virulence of a particularly invasive pathotype of Klebsiella pneumoniae (hvKP). Toward further understanding of this key virulence factor, we report the structural and functional characterization of aerobactin synthetase IucA from a strain of hvKP. The X-ray crystal structures of unliganded and ATP-bound forms of IucA were solved, forming the foundation of our structural analysis. Small angle X-ray scattering (SAXS) data suggest that, unlike its closest structurally characterized homologues, IucA adopts a tetrameric assembly in solution. Finally, we employed activity assays to investigate the substrate specificity and determine the apparent steady-state kinetic parameters of IucA.


    Organizational Affiliation

    The Hauptman-Woodward Medical Research Institute , Buffalo, New York, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aerobactin synthase IucA
A, B, C, D, E, F, G, H
576N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 170.850α = 90.00
b = 96.630β = 90.02
c = 173.230γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI116998
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI007614
National Institutes of Health/National Center for Advancing Translational SciencesUnited StatesUL1TR001412

Revision History 

  • Version 1.0: 2016-06-15
    Type: Initial release
  • Version 1.1: 2016-07-06
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence
  • Version 1.4: 2017-11-01
    Type: Author supporting evidence