4U2L

Dithionite reduced cholesterol in complex with sulfite


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.337 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.097 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

High-resolution structures of cholesterol oxidase in the reduced state provide insights into redox stabilization.

Golden, E.Karton, A.Vrielink, A.

(2014) Acta Crystallogr.,Sect.D 70: 3155-3166

  • DOI: 10.1107/S139900471402286X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cholesterol oxidase (CO) is a flavoenzyme that catalyzes the oxidation and isomerization of cholesterol to cholest-4-en-3-one. The reductive half reaction occurs via a hydride transfer from the substrate to the FAD cofactor. The structures of CO redu ...

    Cholesterol oxidase (CO) is a flavoenzyme that catalyzes the oxidation and isomerization of cholesterol to cholest-4-en-3-one. The reductive half reaction occurs via a hydride transfer from the substrate to the FAD cofactor. The structures of CO reduced with dithionite under aerobic conditions and in the presence of the substrate 2-propanol under both aerobic and anaerobic conditions are presented. The 1.32 Å resolution structure of the dithionite-reduced enzyme reveals a sulfite molecule covalently bound to the FAD cofactor. The isoalloxazine ring system displays a bent structure relative to that of the oxidized enzyme, and alternate conformations of a triad of aromatic residues near to the cofactor are evident. A 1.12 Å resolution anaerobically trapped reduced enzyme structure in the presence of 2-propanol does not show a similar bending of the flavin ring system, but does show alternate conformations of the aromatic triad. Additionally, a significant difference electron-density peak is observed within a covalent-bond distance of N5 of the flavin moiety, suggesting that a hydride-transfer event has occurred as a result of substrate oxidation trapping the flavin in the electron-rich reduced state. The hydride transfer generates a tetrahedral geometry about the flavin N5 atom. High-level density-functional theory calculations were performed to correlate the crystallographic findings with the energetics of this unusual arrangement of the flavin moiety. These calculations suggest that strong hydrogen-bond interactions between Gly120 and the flavin N5 centre may play an important role in these structural features.


    Organizational Affiliation

    School of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia.




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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SFD
Query on SFD

Download SDF File 
Download CCD File 
A
(S)-10-((2S,3S,4R)-5-((S)-((S)-(((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHOXY)(HYDROXY)PHOSPHORYLOXY)(HYDROXY)PHOSPHORYLOXY)-2,3,4-TRIHYDROXYPENTYL)-7,8-DIMETHYL-2,4-DIOXO-2,3,4,4A-TETRAHYDROBENZO[G]PTERIDINE-5(10H)-SULFONIC ACID
N5-SULFONO FLAVIN-ADENINE DINUCLEOTIDE
C27 H35 N9 O18 P2 S
WCBOBURWKHIISA-LDVRFEIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.337 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.097 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.375α = 90.00
b = 73.565β = 105.03
c = 63.431γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2014-12-24
    Type: Database references
  • Version 1.2: 2015-02-04
    Type: Derived calculations
  • Version 1.3: 2016-06-01
    Type: Data collection
  • Version 1.4: 2017-11-22
    Type: Data collection, Derived calculations, Refinement description