3W54

Crystal structure of cyanide-insensitive alternative oxidase from Trypanosoma brucei with colletochlorin B

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structure of the trypanosome cyanide-insensitive alternative oxidase

Shiba, T., Kido, Y., Sakamoto, K., Inaoka, D.K., Tsuge, C., Tatsumi, R., Takahashi, G., Balogun, E.O., Nara, T., Aoki, T., Honma, T., Tanaka, A., Inoue, M., Matsuoka, S., Saimoto, H., Moore, A.L., Harada, S., Kita, K.

(2013) Proc.Natl.Acad.Sci.USA 110: 4580-4585

  • DOI: 10.1073/pnas.1218386110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • In addition to haem copper oxidases, all higher plants, some algae, yeasts, molds, metazoans, and pathogenic microorganisms such as Trypanosoma brucei contain an additional terminal oxidase, the cyanide-insensitive alternative oxidase (AOX). AOX is a ...

    In addition to haem copper oxidases, all higher plants, some algae, yeasts, molds, metazoans, and pathogenic microorganisms such as Trypanosoma brucei contain an additional terminal oxidase, the cyanide-insensitive alternative oxidase (AOX). AOX is a diiron carboxylate protein that catalyzes the four-electron reduction of dioxygen to water by ubiquinol. In T. brucei, a parasite that causes human African sleeping sickness, AOX plays a critical role in the survival of the parasite in its bloodstream form. Because AOX is absent from mammals, this protein represents a unique and promising therapeutic target. Despite its bioenergetic and medical importance, however, structural features of any AOX are yet to be elucidated. Here we report crystal structures of the trypanosomal alternative oxidase in the absence and presence of ascofuranone derivatives. All structures reveal that the oxidase is a homodimer with the nonhaem diiron carboxylate active site buried within a four-helix bundle. Unusually, the active site is ligated solely by four glutamate residues in its oxidized inhibitor-free state; however, inhibitor binding induces the ligation of a histidine residue. A highly conserved Tyr220 is within 4 Å of the active site and is critical for catalytic activity. All structures also reveal that there are two hydrophobic cavities per monomer. Both inhibitors bind to one cavity within 4 Å and 5 Å of the active site and Tyr220, respectively. A second cavity interacts with the inhibitor-binding cavity at the diiron center. We suggest that both cavities bind ubiquinol and along with Tyr220 are required for the catalytic cycle for O2 reduction.

    Organizational Affiliation: 

    Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alternative oxidase, mitochondrial
A, B, C, D
329Trypanosoma brucei bruceiGene Names: AOX
EC: 1.-.-.-
Membrane protein
mpstruct		Group: 
MONOTOPIC MEMBRANE PROTEINS		Sub Group: 
Oxidases		Protein: 
Alternative oxidase (AOX), cyanide-insensitive
Find proteins for Q26710 (Trypanosoma brucei brucei)
Go to UniProtKB:  Q26710
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL
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Download CCD File 
D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
RNB
Query on RNB
Download SDF File 
Download CCD File 
A, B, C, D
3-chloro-5-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-4,6-dihydroxy-2-methylbenzaldehyde
Colletochlorin B
C18 H23 Cl O3
UEUMAXMCCDEOIJ-XYOKQWHBSA-N
 Ligand Interaction
OH
Query on OH
Download SDF File 
Download CCD File 
A, B, C, D
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
 Ligand Interaction
FE
Query on FE
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Download CCD File 
A, B, C, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RNBKi: 0.2 nM BINDINGMOAD
RNBIC50: 0.2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 228.017α = 90.00
b = 137.920β = 106.08
c = 63.058γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
SPACEdata collection
REFMACrefinement
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-13
    Type: Initial release
  • Version 1.1: 2013-03-27
    Type: Database references