5DOQ

The structure of bd oxidase from Geobacillus thermodenitrificans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.319 
  • R-Value Observed: 0.320 

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This is version 1.2 of the entry. See complete history


Literature

Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases.

Safarian, S.Rajendran, C.Muller, H.Preu, J.Langer, J.D.Ovchinnikov, S.Hirose, T.Kusumoto, T.Sakamoto, J.Michel, H.

(2016) Science 352: 583-586

  • DOI: https://doi.org/10.1126/science.aaf2477
  • Primary Citation of Related Structures:  
    5DOQ, 5IR6

  • PubMed Abstract: 

    The cytochrome bd oxidases are terminal oxidases that are present in bacteria and archaea. They reduce molecular oxygen (dioxygen) to water, avoiding the production of reactive oxygen species. In addition to their contribution to the proton motive force, they mediate viability under oxygen-related stress conditions and confer tolerance to nitric oxide, thus contributing to the virulence of pathogenic bacteria. Here we present the atomic structure of the bd oxidase from Geobacillus thermodenitrificans, revealing a pseudosymmetrical subunit fold. The arrangement and order of the heme cofactors support the conclusions from spectroscopic measurements that the cleavage of the dioxygen bond may be mechanistically similar to that in the heme-copper-containing oxidases, even though the structures are completely different.


  • Organizational Affiliation

    Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt/Main, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bd-type quinol oxidase subunit I448Geobacillus thermodenitrificans NG80-2Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A4IKP6 (Geobacillus thermodenitrificans (strain NG80-2))
Explore A4IKP6 
Go to UniProtKB:  A4IKP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4IKP6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Bd-type quinol oxidase subunit II342Geobacillus thermodenitrificans NG80-2Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A4IKP7 (Geobacillus thermodenitrificans (strain NG80-2))
Explore A4IKP7 
Go to UniProtKB:  A4IKP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4IKP7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Putative membrane protein33Geobacillus sp. PA-3Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0Q0UXS2 (Geobacillus sp. PA-3)
Explore A0A0Q0UXS2 
Go to UniProtKB:  A0A0Q0UXS2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0Q0UXS2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.319 
  • R-Value Observed: 0.320 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.06α = 90
b = 120.86β = 90
c = 122.72γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references