5KWF

Joint X-ray Neutron Structure of Cholesterol Oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.499 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.190 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.214 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.283 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An extended N-H bond, driven by a conserved second-order interaction, orients the flavin N5 orbital in cholesterol oxidase.

Golden, E.Yu, L.J.Meilleur, F.Blakeley, M.P.Duff, A.P.Karton, A.Vrielink, A.

(2017) Sci Rep 7: 40517-40517

  • DOI: 10.1038/srep40517

  • PubMed Abstract: 
  • The protein microenvironment surrounding the flavin cofactor in flavoenzymes is key to the efficiency and diversity of reactions catalysed by this class of enzymes. X-ray diffraction structures of oxidoreductase flavoenzymes have revealed recurrent f ...

    The protein microenvironment surrounding the flavin cofactor in flavoenzymes is key to the efficiency and diversity of reactions catalysed by this class of enzymes. X-ray diffraction structures of oxidoreductase flavoenzymes have revealed recurrent features which facilitate catalysis, such as a hydrogen bond between a main chain nitrogen atom and the flavin redox center (N5). A neutron diffraction study of cholesterol oxidase has revealed an unusual elongated main chain nitrogen to hydrogen bond distance positioning the hydrogen atom towards the flavin N5 reactive center. Investigation of the structural features which could cause such an unusual occurrence revealed a positively charged lysine side chain, conserved in other flavin mediated oxidoreductases, in a second shell away from the FAD cofactor acting to polarize the peptide bond through interaction with the carbonyl oxygen atom. Double-hybrid density functional theory calculations confirm that this electrostatic arrangement affects the N-H bond length in the region of the flavin reactive center. We propose a novel second-order partial-charge interaction network which enables the correct orientation of the hydride receiving orbital of N5. The implications of these observations for flavin mediated redox chemistry are discussed.


    Organizational Affiliation

    Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights NSW, 2234, Australia.,Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, United States of America.,School of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia, 6009 Australia.,Structural and Molecular Biochemistry, North Carolina State University, Raleigh, NC 27695, United States of America.,Institut Laue-Langevin, 71 Avenue des Martyrs, Grenoble, 38000, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cholesterol oxidase
A
510Streptomyces sp. (strain SA-COO)Mutation(s): 0 
Gene Names: choA
EC: 1.1.3.6
Find proteins for P12676 (Streptomyces sp. (strain SA-COO))
Go to UniProtKB:  P12676
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
DOD
Query on DOD

Download SDF File 
Download CCD File 
A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.499 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.605α = 90.00
b = 74.084β = 105.21
c = 63.828γ = 90.00
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.214 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.283 
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-3000data reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Data collection