1FFT

The structure of ubiquinol oxidase from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structure of the ubiquinol oxidase from Escherichia coli and its ubiquinone binding site.

Abramson, J.Riistama, S.Larsson, G.Jasaitis, A.Svensson-Ek, M.Laakkonen, L.Puustinen, A.Iwata, S.Wikstrom, M.

(2000) Nat.Struct.Mol.Biol. 7: 910-917

  • DOI: 10.1038/82824

  • PubMed Abstract: 
  • Cell respiration is catalyzed by the heme-copper oxidase superfamily of enzymes, which comprises cytochrome c and ubiquinol oxidases. These membrane proteins utilize different electron donors through dissimilar access mechanisms. We report here the f ...

    Cell respiration is catalyzed by the heme-copper oxidase superfamily of enzymes, which comprises cytochrome c and ubiquinol oxidases. These membrane proteins utilize different electron donors through dissimilar access mechanisms. We report here the first structure of a ubiquinol oxidase, cytochrome bo3, from Escherichia coli. The overall structure of the enzyme is similar to those of cytochrome c oxidases; however, the membrane-spanning region of subunit I contains a cluster of polar residues exposed to the interior of the lipid bilayer that is not present in the cytochrome c oxidase. Mutagenesis studies on these residues strongly suggest that this region forms a quinone binding site. A sequence comparison of this region with known quinone binding sites in other membrane proteins shows remarkable similarities. In light of these findings we suggest specific roles for these polar residues in electron and proton transfer in ubiquinol oxidase.


    Related Citations: 
    • Purification, crystallization and preliminary crystallographic studies on an integral membrane protein, cytochrome bo3 ubiquinol oxidase from Escherichia coli.
      Abramson, J.,Larsson, G.,Byrne, B.,Puustinen, A.,Garcia-Horsman, A.,Iwata, S.
      (2000) Acta Crystallogr.,Sect.D 56: 1076


    Organizational Affiliation

    Uppsala University, Department of Biochemistry, Biomedical Center Box 576, Uppsala S-75123, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL OXIDASE
A, F
663Escherichia coli (strain K12)Gene Names: cyoB
EC: 1.10.3.10
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Ubiquinol Oxidase, cytochrome bo3
Find proteins for P0ABI8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABI8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL OXIDASE
B, G
315Escherichia coli (strain K12)Gene Names: cyoA
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Ubiquinol Oxidase, cytochrome bo3
Find proteins for P0ABJ1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABJ1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL OXIDASE
C, H
204Escherichia coli (strain K12)Gene Names: cyoC
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Ubiquinol Oxidase, cytochrome bo3
Find proteins for P0ABJ3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABJ3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL OXIDASE
D, I
109N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, F
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, F
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
HEO
Query on HEO

Download SDF File 
Download CCD File 
A, F
HEME O
C49 H58 Fe N4 O5
FRKORVCRVCLRBA-BZKSIRDQSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
D, I
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 92.100α = 90.00
b = 372.500β = 90.00
c = 232.700γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-10-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Advisory, Experimental preparation