Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 5 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.61 kDa 
• Atom Count: 4813 
• Modelled Residue Count: 486 
• Deposited Residue Count: 508 
• Unique protein chains: 1

2ITF

Crystal structure IsdA NEAT domain from Staphylococcus aureus with heme bound

• PDB DOI: 10.2210/pdb2ITF/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2006-10-19 Released: 2006-12-26 
• Deposition Author(s): Grigg, J.C., Vermeiren, C.L., Heinrichs, D.E., Murphy, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.213 
• R-Value Work: 0.171 

Literature

Haem recognition by a Staphylococcus aureus NEAT domain.

Grigg, J.C., Vermeiren, C.L., Heinrichs, D.E., Murphy, M.E.

(2007) Mol Microbiol 63: 139-149

• PubMed: 17229211 
• DOI: 10.1111/j.1365-2958.2006.05502.x
• Primary Citation of Related Structures:  
  2ITE, 2ITF


• PubMed Abstract: 
  

Successful pathogenic organisms have developed mechanisms to thrive under extreme levels of iron restriction. Haem-iron represents the largest iron reservoir in the human body and is a significant source of iron for some bacterial pathogens. NEAT (NEAr Transporter) domains are found exclusively in a family of cell surface proteins in Gram-positive bacteria. Many NEAT domain-containing proteins, including IsdA in Staphylococcus aureus, are implicated in haem binding. Here, we show that overexpression of IsdA in S. aureus enhances growth and an inactivation mutant of IsdA has a growth defect, compared with wild type, when grown in media containing haem as the sole iron source. Furthermore, the haem-binding property of IsdA is contained within the NEAT domain. Crystal structures of the apo-IsdA NEAT domain and in complex with haem were solved and reveal a clathrin adapter-like beta-sandwich fold with a large hydrophobic haem-binding pocket. Haem is bound with the propionate groups directed at the molecular surface and the iron is co-ordinated solely by Tyr(166). The phenol groups of Tyr(166) and Tyr(170) form an H-bond that may function in regulating haem binding and release. An analysis of IsdA structure-sequence alignments indicate that conservation of Tyr(166) is a predictor of haem binding by NEAT domains.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-regulated surface determinant protein A	A, B, C, D	127	Staphylococcus aureus	Mutation(s): 2  Gene Names: isdA, frpA, stbA
UniProt
Find proteins for Q2FZE9 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FZE9  Go to UniProtKB:  Q2FZE9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], F [auth B], G [auth C], H [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.213 
• R-Value Work: 0.171 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.089	α = 90
b = 58.533	β = 93.28
c = 95.584	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
O	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-10-19 
• Released Date: 2006-12-26 
Deposition Author(s): Grigg, J.C., Vermeiren, C.L., Heinrichs, D.E., Murphy, M.E.

Revision History  

• Version 1.0: 2006-12-26
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description