1FFT

The structure of ubiquinol oxidase from Escherichia coli

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å

wwPDB Validation   3D Report Full Report


This is version 1.4 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 Biol 7: 910-917

  • DOI: 10.1038/82824
  • Primary Citation of Related Structures:  
    1FFT

  • 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 first structure of a ubiquinol oxidase, cytochrome bo3, from Escherichia coli ...

    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 D Biol Crystallogr 56: 1076
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL OXIDASEA,
E [auth F]		663Escherichia coliMutation(s): 0 
EC: 1.10.3 (PDB Primary Data), 7.1.1.3 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P0ABI8 (Escherichia coli (strain K12))
Explore P0ABI8 
Go to UniProtKB:  P0ABI8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABI8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL OXIDASEB,
F [auth G]		315Escherichia coliMutation(s): 0 
EC: 1.10.3
Membrane Entity: Yes 
UniProt
Find proteins for P0ABJ1 (Escherichia coli (strain K12))
Explore P0ABJ1 
Go to UniProtKB:  P0ABJ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABJ1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL OXIDASEC,
G [auth H]		204Escherichia coliMutation(s): 0 
EC: 1.10.3
Membrane Entity: Yes 
UniProt
Find proteins for P0ABJ3 (Escherichia coli (strain K12))
Explore P0ABJ3 
Go to UniProtKB:  P0ABJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABJ3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL OXIDASED,
H [auth I]		109Escherichia coliMutation(s): 0 
EC: 1.10.3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEO
Query on HEO
Download Ideal Coordinates CCD File 
K [auth A],
N [auth F]		HEME O
C49 H58 Fe N4 O5
FRKORVCRVCLRBA-BZKSIRDQSA-L		 Ligand Interaction
HEM
Query on HEM
Download Ideal Coordinates CCD File 
J [auth A],
M [auth F]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
CU
Query on CU
Download Ideal Coordinates CCD File 
I [auth A],
L [auth F]		COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.1α = 90
b = 372.5β = 90
c = 232.7γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-10-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Advisory, Experimental preparation
  • Version 1.4: 2020-06-17
    Changes: Data collection, Database references