Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.17 kDa 
• Atom Count: 3042 
• Modelled Residue Count: 344 
• Deposited Residue Count: 344 
• Unique protein chains: 1

5TWB

Oxidoreductase IruO in the reduced form

• DOI: 10.2210/pdb5TWB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Staphylococcus aureus subsp. aureus USA300
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-11-12 Released: 2017-10-04 
• Deposition Author(s): Kobylarz, M.J., Heieis, G.A., Loutet, S.A., Murphy, M.E.P.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.227 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

Iron Uptake Oxidoreductase (IruO) Uses a Flavin Adenine Dinucleotide Semiquinone Intermediate for Iron-Siderophore Reduction.

Kobylarz, M.J., Heieis, G.A., Loutet, S.A., Murphy, M.E.P.

(2017) ACS Chem Biol 12: 1778-1786

• PubMed: 28463500 
• DOI: 10.1021/acschembio.7b00203
• Primary Citation of Related Structures:  
  5TWC, 5TWB


• PubMed Abstract: 
  

Many pathogenic bacteria including Staphylococcus aureus use iron-chelating siderophores to acquire iron. Iron uptake oxidoreductase (IruO), a flavin adenine dinucleotide (FAD)-containing nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reductase from S. aureus, functions as a reductase for IsdG and IsdI, two paralogous heme degrading enzymes. Also, the gene encoding for IruO was shown to be required for growth of S. aureus on hydroxamate siderophores as a sole iron source. Here, we show that IruO binds the hydroxamate-type siderophores desferrioxamine B and ferrichrome A with low micromolar affinity and in the presence of NADPH, Fe(II) was released. Steady-state kinetics of Fe(II) release provides k _cat /K _m values in the range of 600 to 7000 M ^-1 s ^-1 for these siderophores supporting a role for IruO as a siderophore reductase in iron utilization. Crystal structures of IruO were solved in two distinct conformational states mediated by the formation of an intramolecular disulfide bond. A putative siderophore binding site was identified adjacent to the FAD cofactor. This site is partly occluded in the oxidized IruO structure consistent with this form being less active than reduced IruO. This reduction in activity could have a physiological role to limit iron release under oxidative stress conditions. Visible spectroscopy of anaerobically reduced IruO showed that the reaction proceeds by a single electron transfer mechanism through an FAD semiquinone intermediate. From the data, a model for single electron siderophore reduction by IruO using NADPH is described.

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Organizational Affiliation: 

The Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia , Vancouver, British Columbia V6T 1Z3; Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferredoxin--NADP reductase	A	344	Staphylococcus aureus subsp. aureus USA300	Mutation(s): 0  Gene Names: SAUSA300_2319 EC: 1.18.1.2
Find proteins for Q2FEC4 (Staphylococcus aureus (strain USA300)) Explore Q2FEC4  Go to UniProtKB:  Q2FEC4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	A	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.227 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.17	α = 90
b = 43.6	β = 93.44
c = 51.24	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-11-12 
• Released Date: 2017-10-04 
Deposition Author(s): Kobylarz, M.J., Heieis, G.A., Loutet, S.A., Murphy, M.E.P.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP-102596

Revision History  

• Version 1.0: 2017-10-04
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence