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 

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:  

  • 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-Stra├če 3, D-60438 Frankfurt/Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bd-type quinol oxidase subunit I
A
448Geobacillus thermodenitrificans (strain NG80-2)Mutation(s): 0 
Membrane protein
mpstruct
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))
Go to UniProtKB:  A4IKP6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Bd-type quinol oxidase subunit II
B
342Geobacillus thermodenitrificans (strain NG80-2)Mutation(s): 0 
Membrane protein
mpstruct
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))
Go to UniProtKB:  A4IKP7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Putative membrane protein
C
33Geobacillus sp. PA-3Mutation(s): 0 
Membrane protein
mpstruct
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)
Go to UniProtKB:  A0A0Q0UXS2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HDD
Query on HDD

Download SDF File 
Download CCD File 
A
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
HEME
C34 H32 Fe N4 O5
UMGOPAWIGKFTRK-QQDQPIDJSA-N
 Ligand Interaction
HEB
Query on HEB

Download SDF File 
Download CCD File 
A
HEME B/C
HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)
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 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 110.060α = 90.00
b = 120.860β = 90.00
c = 122.720γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
SHELXphasing
XDSdata reduction
REFMACrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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