1MXT

Atomic resolution structure of Cholesterol oxidase (Streptomyces sp. SA-COO)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.132 
  • R-Value Work: 0.110 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Sub-atomic resolution crystal structure of cholesterol oxidase: What atomic resolution crystallography reveals about enzyme mechanism and the role of FAD cofactor in redox activity

Lario, P.I.Sampson, N.Vrielink, A.

(2003) J.Mol.Biol. 326: 1635-1650


  • PubMed Abstract: 
  • The crystal structure of cholesterol oxidase, a 56kDa flavoenzyme was anisotropically refined to 0.95A resolution. The final crystallographic R-factor and R(free) value is 11.0% and 13.2%, respectively. The quality of the electron density maps has en ...

    The crystal structure of cholesterol oxidase, a 56kDa flavoenzyme was anisotropically refined to 0.95A resolution. The final crystallographic R-factor and R(free) value is 11.0% and 13.2%, respectively. The quality of the electron density maps has enabled modeling of alternate conformations for 83 residues in the enzyme, many of which are located in the active site. The additional observed structural features were not apparent in the previous high-resolution structure (1.5A resolution) and have enabled the identification of a narrow tunnel leading directly to the isoalloxazine portion of the FAD prosthetic group. The hydrophobic nature of this narrow tunnel suggests it is the pathway for molecular oxygen to access the isoalloxazine group for the oxidative half reaction. Resolving the alternate conformations in the active site residues provides a model for the dynamics of substrate binding and a potential oxidation triggered gating mechanism involving access to the hydrophobic tunnel. This structure reveals that the NE2 atom of the active site histidine residue, H447, critical to the redox activity of this flavin oxidase, acts as a hydrogen bond donor rather than as hydrogen acceptor. The atomic resolution structure of cholesterol oxidase has revealed the presence of hydrogen atoms, dynamic aspects of the protein and how side-chain conformations are correlated with novel structural features such as the oxygen tunnel. This new structural information has provided us with the opportunity to re-analyze the roles played by specific residues in the mechanism of the enzyme.


    Related Citations: 
    • Atomic resolution crystallography reveals how changes in pH shape the protein microenvironment
      Lyubimov, A.Y.,Lario, P.I.,Moustafa, I.,Vrielink, A.
      (2006) Nat.Chem.Biol. 2: 259


    Organizational Affiliation

    Department of Molecular, Cellular and Developmental Biology, Sinsheimer Laboratory, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHOLESTEROL OXIDASE
A
504Streptomyces 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
FAE
Query on FAE

Download SDF File 
Download CCD File 
A
FLAVIN-N7 PROTONATED-ADENINE DINUCLEOTIDE
C27 H34 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-O
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.132 
  • R-Value Work: 0.110 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.227α = 90.00
b = 72.902β = 105.10
c = 62.947γ = 90.00
Software Package:
Software NamePurpose
SHELXphasing
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance