6QV9

Staphylococcus aureus superoxide dismutase SodA double mutant

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


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


Literature

An evolutionary path to altered cofactor specificity in a metalloenzyme.

Barwinska-Sendra, A., Garcia, Y.M., Sendra, K.M., Basle, A., Mackenzie, E.S., Tarrant, E., Card, P., Tabares, L.C., Bicep, C., Un, S., Kehl-Fie, T.E., Waldron, K.J.

(2020) Nat Commun 11: 2738-2738

  • DOI: 10.1038/s41467-020-16478-0
  • Primary Citation of Related Structures:  
    6QV8, 6QV9

  • PubMed Abstract: 

    • Almost half of all enzymes utilize a metal cofactor. However, the features that dictate the metal utilized by metalloenzymes are poorly understood, limiting our ability to manipulate these enzymes for industrial and health-associated applications. The ubiquitous iron/manganese superoxide dismutase (SOD) family exemplifies this deficit, as the specific metal used by any family member cannot be predicted ...

    Almost half of all enzymes utilize a metal cofactor. However, the features that dictate the metal utilized by metalloenzymes are poorly understood, limiting our ability to manipulate these enzymes for industrial and health-associated applications. The ubiquitous iron/manganese superoxide dismutase (SOD) family exemplifies this deficit, as the specific metal used by any family member cannot be predicted. Biochemical, structural and paramagnetic analysis of two evolutionarily related SODs with different metal specificity produced by the pathogenic bacterium Staphylococcus aureus identifies two positions that control metal specificity. These residues make no direct contacts with the metal-coordinating ligands but control the metal's redox properties, demonstrating that subtle architectural changes can dramatically alter metal utilization. Introducing these mutations into S. aureus alters the ability of the bacterium to resist superoxide stress when metal starved by the host, revealing that small changes in metal-dependent activity can drive the evolution of metalloenzymes with new cofactor specificity.

    Organizational Affiliation: 

    Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK. kevin.waldron@ncl.ac.uk.



Macromolecules
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(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 P0A0J3 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore P0A0J3 
Go to UniProtKB:  P0A0J3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A0J3
Protein Feature View
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  • 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: 1.80 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.25α = 90
b = 68.15β = 100.58
c = 57.29γ = 90
Software Package:
Software NamePurpose
GDAdata collection
xia2data reduction
XDSdata scaling
Aimlessdata scaling
MOLREPphasing
Cootmodel building
REFMACrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomDTP
Wellcome TrustUnited Kingdom098675/Z/12/Z

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-06-10
    Changes: Database references