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 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1126/science.aaf2477
  • Primary Citation of Related Structures:  
    5IR6, 5DOQ

  • 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 fo ...

    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. hartmut.michel@biophys.mpg.de.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bd-type quinol oxidase subunit IA448Geobacillus thermodenitrificans NG80-2Mutation(s): 0 
Gene Names: GTNG_0518
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)		Protein: 
Cytochrome bd-type oxidase (anisotropy corrected)
Find proteins for A4IKP6 (Geobacillus thermodenitrificans (strain NG80-2))
Explore A4IKP6 
Go to UniProtKB:  A4IKP6
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Bd-type quinol oxidase subunit IIB342Geobacillus thermodenitrificans NG80-2Mutation(s): 0 
Gene Names: GTNG_0519
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)		Protein: 
Cytochrome bd-type oxidase (anisotropy corrected)
Find proteins for A4IKP7 (Geobacillus thermodenitrificans (strain NG80-2))
Explore A4IKP7 
Go to UniProtKB:  A4IKP7
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Putative membrane proteinC33Geobacillus sp. PA-3Mutation(s): 0 
Gene Names: GEPA3_0587
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)		Protein: 
Cytochrome bd-type oxidase (anisotropy corrected)
Find proteins for A0A0Q0UXS2 (Geobacillus sp. PA-3)
Explore A0A0Q0UXS2 
Go to UniProtKB:  A0A0Q0UXS2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HDD
Query on HDD
Download Ideal Coordinates CCD File 
A
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
C34 H32 Fe N4 O5
UMGOPAWIGKFTRK-QQDQPIDJSA-N		 Ligand Interaction
HEB
Query on HEB
Download Ideal Coordinates CCD File 
A
HEME B/C
C34 H34 Fe N4 O4
NEGHHAJBRZGUAY-ICENSXKYDL		 Ligand Interaction
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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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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