2XLL

The crystal structure of bilirubin oxidase from Myrothecium verrucaria


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.305 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Bilirubin Oxidase from Myrothecium Verrucaria: X- Ray Determination of the Complete Crystal Structure and a Rational Surface Modification for Enhanced Electrocatalytic O(2) Reduction.

Cracknell, J.A.Mcnamara, T.P.Lowe, E.D.Blanford, C.F.

(2011) Dalton Trans 40: 6668

  • DOI: 10.1039/c0dt01403f

  • PubMed Abstract: 
  • The blue multi-copper oxidase bilirubin oxidase (BOx) from the ascomycete plant pathogen Myrothecium verrucaria (Mv) efficiently catalyses the oxidation of bilirubin to biliverdin, with the concomitant reduction of O(2) to water, a reaction of consid ...

    The blue multi-copper oxidase bilirubin oxidase (BOx) from the ascomycete plant pathogen Myrothecium verrucaria (Mv) efficiently catalyses the oxidation of bilirubin to biliverdin, with the concomitant reduction of O(2) to water, a reaction of considerable interest for low-temperature bio-fuel cell applications. We have solved the complete X-ray determined structure of Mv BOx at 2.4 Å resolution, using molecular replacement with the Spore Coat Protein A (CotA) enzyme from Bacillus subtilis (PDB code 1GSK) as a template. The structure reveals an unusual environment around the blue type 1 copper (T1 Cu) that includes two non-coordinating hydrophilic amino acids, asparagine and threonine. The presence of a long, narrow and hydrophilic pocket near the T1 Cu suggests that structure of the substrate-binding site is dynamically determined in vivo. We show that the interaction between the binding pocket of Mv BOx and its highly conjugated natural organic substrate, bilirubin, can be used to stabilise the enzyme on a pyrolytic graphite electrode, more than doubling its electrocatalytic activity relative to the current obtained by simple adsorption of the protein to the carbon surface.


    Organizational Affiliation

    Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, UK OX1 3QR.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BILIRUBIN OXIDASE
A, B, C, D
534Myrothecium verrucariaMutation(s): 0 
EC: 1.3.3.5
Find proteins for Q12737 (Myrothecium verrucaria)
Go to UniProtKB:  Q12737
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download SDF File 
Download CCD File 
A, B, C, D
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.305 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.170 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 52.793α = 89.98
b = 83.602β = 89.89
c = 143.148γ = 89.90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-06-23
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance