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 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.25 kDa 
• Atom Count: 3365 
• Residue Count: 396 
• Unique protein chains: 1

5N57

Staphylococcus aureus cambialistic superoxide dismutase SodM

• DOI: 10.2210/pdb5N57/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-13 Released: 2018-03-07 
• Deposition Author(s): Barwinska-Sendra, A., Basle, A., Waldron, K.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council, Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.237 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

A charge polarization model for the metal-specific activity of superoxide dismutases.

Barwinska-Sendra, A., Basle, A., Waldron, K.J., Un, S.

(2018) Phys Chem Chem Phys 20: 2363-2372

• PubMed: 29308487 
• DOI: 10.1039/c7cp06829h
• Primary Citation of Related Structures:  
  5N57, 5N56


• PubMed Abstract: 
  

The pathogenicity of Staphylococcus aureus is enhanced by having two superoxide dismutases (SODs): a Mn-specific SOD and another that can use either Mn or Fe. Using 94 GHz electron-nuclear double resonance (ENDOR) and electron double resonance detected (ELDOR)-NMR we show that, despite their different metal-specificities, their structural and electronic similarities extend down to their active-site ¹ H- and ¹⁴ N-Mn(ii) hyperfine interactions. However these interactions, and hence the positions of these nuclei, are different in the inactive Mn-reconstituted Escherichia coli Fe-specific SOD. Density functional theory modelling attributes this to a different angular position of the E. coli H171 ligand. This likely disrupts the Mn-H171-E170' triad causing a shift in charge and in metal redox potential, leading to the loss of activity. This is supported by the correlated differences in the Mn(ii) zero-field interactions of the three SOD types and suggests that the triad is important for determining metal specific activity.

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Organizational Affiliation: 

Department of Biochemistry, Biophysics and Structural Biology, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS UMR 9198, CEA-Saclay, Gif-sur-Yvette, F-91198, France. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase	A, B	199	Staphylococcus aureus	Mutation(s): 0  Gene Names:  sodA, sodM, A4U86_04870, BN1321_40056, ERS072738_00830, ERS072840_00559, ERS073147_02394, ERS073767_02269, ERS074020_00889, ERS1058648_00955, FORC27_0128, HMPREF3211_00238, SAMEA2298760_02426 EC: 1.15.1.1
Find proteins for Q2G261 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G261  Go to UniProtKB:  Q2G261

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	A, B	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.237 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.225	α = 90
b = 142.225	β = 90
c = 46.426	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-02-13 
• Released Date: 2018-03-07 
Deposition Author(s): Barwinska-Sendra, A., Basle, A., Waldron, K.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	--
Wellcome Trust	United Kingdom	098375/Z/12/Z

Revision History 

• Version 1.0: 2018-03-07
  Type: Initial release
  
• Version 1.1: 2018-03-21
  Changes: Database references