Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 62.95 kDa 
• Atom Count: 5148 
• Modelled Residue Count: 536 
• Deposited Residue Count: 561 
• Unique protein chains: 1

2I0K

Cholesterol Oxidase from Brevibacterium sterolicum- His121Ala Mutant

• PDB DOI: 10.2210/pdb2I0K/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Brevibacterium sterolicum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-08-10 Released: 2007-12-11 
• Deposition Author(s): Vrielink, A., Lim, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.167 
• R-Value Work: 0.148 
• R-Value Observed: 0.149 

Literature

Structural and kinetic analyses of the H121A mutant of cholesterol oxidase.

Lim, L., Molla, G., Guinn, N., Ghisla, S., Pollegioni, L., Vrielink, A.

(2006) Biochem J 400: 13-22

• PubMed: 16856877 
• DOI: 10.1042/BJ20060664
• Primary Citation of Related Structures:  
  2I0K


• PubMed Abstract: 
  

Cholesterol oxidase is a monomeric flavoenzyme that catalyses the oxidation of cholesterol to cholest-5-en-3-one followed by isomerization to cholest-4-en-3-one. The enzyme from Brevibacterium sterolicum contains the FAD cofactor covalently bound to His121. It was previously demonstrated that the H121A substitution results in a approximately 100 mV decrease in the midpoint redox potential and a approximately 40-fold decrease in turnover number compared to wild-type enzyme [Motteran, Pilone, Molla, Ghisla and Pollegioni (2001) Journal of Biological Chemistry 276, 18024-18030]. A detailed kinetic analysis of the H121A mutant enzyme shows that the decrease in turnover number is largely due to a corresponding decrease in the rate constant of flavin reduction, whilst the re-oxidation reaction is only marginally altered and the isomerization reaction is not affected by the substitution and precedes product dissociation. The X-ray structure of the mutant protein, determined to 1.7 A resolution (1 A identical with 0.1 nm), reveals only minor changes in the overall fold of the protein, namely: two loops have slight movements and a tryptophan residue changes conformation by a rotation of 180 degrees about chi1 compared to the native enzyme. Comparison of the isoalloxazine ring moiety of the FAD cofactor between the structures of the native and mutant proteins shows a change from a non-planar to a planar geometry (resulting in a more tetrahedral-like geometry for N5). This change is proposed to be a major factor contributing to the observed alteration in redox potential. Since a similar distortion of the flavin has not been observed in other covalent flavoproteins, it is proposed to represent a specific mode to facilitate flavin reduction in covalent cholesterol oxidase.

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Related Citations: 

• Oxygen access to the active site of cholesterol oxidase through a narrow channel is gated by an Arg-Glu pair.
  Coulombe, R., Yue, K.Q., Ghisla, S., Vrielink, A.
  (2001) J Biol Chem 276: 30435

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, Sinsheimer Laboratory, University of California at Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase	A	561	Brevibacterium sterolicum	Mutation(s): 1  EC: 1.1.3.6
UniProt
Find proteins for Q7SID9 (Brevibacterium sterolicum) Explore Q7SID9  Go to UniProtKB:  Q7SID9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	F [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
CAC	C [auth A], D [auth A]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
GOL	G [auth A], H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	B [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.167 
• R-Value Work: 0.148 
• R-Value Observed: 0.149 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.635	α = 90
b = 85.851	β = 112.48
c = 78.755	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-08-10 
• Released Date: 2007-12-11 
Deposition Author(s): Vrielink, A., Lim, L.

Revision History  

• Version 1.0: 2007-12-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations