Structure of E. coli superoxide oxidase

Experimental Data Snapshot

  • Resolution: 1.97 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Scavenging of superoxide by a membrane-bound superoxide oxidase.

Lundgren, C.A.K.Sjostrand, D.Biner, O.Bennett, M.Rudling, A.Johansson, A.L.Brzezinski, P.Carlsson, J.von Ballmoos, C.Hogbom, M.

(2018) Nat Chem Biol 14: 788-793

  • DOI: https://doi.org/10.1038/s41589-018-0072-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Superoxide is a reactive oxygen species produced during aerobic metabolism in mitochondria and prokaryotes. It causes damage to lipids, proteins and DNA and is implicated in cancer, cardiovascular disease, neurodegenerative disorders and aging. As protection, cells express soluble superoxide dismutases, disproportionating superoxide to oxygen and hydrogen peroxide. Here, we describe a membrane-bound enzyme that directly oxidizes superoxide and funnels the sequestered electrons to ubiquinone in a diffusion-limited reaction. Experiments in proteoliposomes and inverted membranes show that the protein is capable of efficiently quenching superoxide generated at the membrane in vitro. The 2.0 Å crystal structure shows an integral membrane di-heme cytochrome b poised for electron transfer from the P-side and proton uptake from the N-side. This suggests that the reaction is electrogenic and contributes to the membrane potential while also conserving energy by reducing the quinone pool. Based on this enzymatic activity, we propose that the enzyme family be denoted superoxide oxidase (SOO).

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b561189Escherichia coli K-12Mutation(s): 0 
Gene Names: cybBb1418JW5224
Membrane Entity: Yes 
Find proteins for P0ABE5 (Escherichia coli (strain K12))
Explore P0ABE5 
Go to UniProtKB:  P0ABE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABE5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.97 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.046α = 90
b = 91.102β = 90
c = 97.923γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-07-04
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-07
    Changes: Data collection, Database references