5IR6 | pdb_00005ir6

The structure of bd oxidase from Geobacillus thermodenitrificans

• PDB DOI: https://doi.org/10.2210/pdb5IR6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Geobacillus stearothermophilus, Geobacillus sp. PA-3
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2016-03-12 Released: 2016-05-04 
• Deposition Author(s): Safarian, S., Mueller, H., Rajendran, C., Preu, J., Ovchinnikov, S., Kusumoto, T., Hirose, T., Langer, J., Sakamoto, J., Michel, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 
  0.325 (Depositor), 0.330 (DCC) 
• R-Value Work: 
  0.303 (Depositor), 0.301 (DCC) 
• R-Value Observed: 
  0.304 (Depositor) 

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

• PubMed: 27126043 
• DOI: https://doi.org/10.1126/science.aaf2477
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt/Main, Germany.
Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt/Main, Germany. Present address: Faculty of Biology and Preclinical Medicine, University of Regensburg, Universitätsstrasse 31, D-93051 Regensburg, Germany.
Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt/Main, Germany. Present address: Department of Molecular Membrane Biology, Max Planck Institute for Brain Research, Max-von-Laue-Straße 4, D-60438 Frankfurt/Main, Germany.
Department of Biochemistry, University of Washington, Seattle, WA, USA.
Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kawazu 680-4, Iizuka, Fukuoka-ken 820-8502, Japan.
Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt/Main, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.81 kDa 
• Atom Count: 6,471 
• Modeled Residue Count: 792 
• Deposited Residue Count: 823 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bd-type quinol oxidase subunit I	A	448	Geobacillus stearothermophilus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q9Z9N1 (Geobacillus stearothermophilus) Explore Q9Z9N1  Go to UniProtKB:  Q9Z9N1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bd-type quinol oxidase subunit II	B	342	Geobacillus stearothermophilus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q9Z9N0 (Geobacillus stearothermophilus) Explore Q9Z9N0  Go to UniProtKB:  Q9Z9N0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative membrane protein	C	33	Geobacillus sp. PA-3	Mutation(s): 0
UniProt
Find proteins for A0ACD6B9X7 (Geobacillus sp. PA-3) Explore A0ACD6B9X7  Go to UniProtKB:  A0ACD6B9X7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HDD	F [auth A]	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE C34 H32 Fe N4 O5 UMGOPAWIGKFTRK-QQDQPIDJSA-N
HEB	D [auth A], E [auth A]	HEME B/C C34 H34 Fe N4 O4 NEGHHAJBRZGUAY-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free:  0.325 (Depositor), 0.330 (DCC) 
• R-Value Work:  0.303 (Depositor), 0.301 (DCC) 
• R-Value Observed: 0.304 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.06	α = 90
b = 120.86	β = 90
c = 122.72	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SHELX	phasing
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Safarian, S., Mueller, H., Rajendran, C., Preu, J., Ovchinnikov, S., Kusumoto, T., Hirose, T., Langer, J., Sakamoto, J., Michel, H.

Revision History  

• 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