5N57

Staphylococcus aureus cambialistic superoxide dismutase SodM

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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


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

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

  • 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 ...

    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.

    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. sun.un@cea.fr.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Superoxide dismutaseA, B199Staphylococcus aureusMutation(s): 0 
Gene Names: 
EC: 1.15.1.1
UniProt
Find proteins for Q2G261 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G261 
Go to UniProtKB:  Q2G261
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2G261
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
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 = 142.225α = 90
b = 142.225β = 90
c = 46.426γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited Kingdom--
Wellcome TrustUnited Kingdom098375/Z/12/Z

Revision History  (Full details and data files)

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