3GYJ

Cholesterol oxidase from Streptomyces sp. N485L mutant (0.92A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.92 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.124 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A hydrogen-bonding network is important for oxidation and isomerization in the reaction catalyzed by cholesterol oxidase.

Lyubimov, A.Y.Chen, L.Sampson, N.S.Vrielink, A.

(2009) Acta Crystallogr.,Sect.D 65: 1222-1231

  • DOI: 10.1107/S0907444909037421
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cholesterol oxidase is a flavoenzyme that catalyzes the oxidation and isomerization of 3beta-hydroxysteroids. Structural and mutagenesis studies have shown that Asn485 plays a key role in substrate oxidation. The side chain makes an NH...pi interacti ...

    Cholesterol oxidase is a flavoenzyme that catalyzes the oxidation and isomerization of 3beta-hydroxysteroids. Structural and mutagenesis studies have shown that Asn485 plays a key role in substrate oxidation. The side chain makes an NH...pi interaction with the reduced form of the flavin cofactor. A N485D mutant was constructed to further test the role of the amide group in catalysis. The mutation resulted in a 1800-fold drop in the overall k(cat). Atomic resolution structures were determined for both the N485L and N485D mutants. The structure of the N485D mutant enzyme (at 1.0 A resolution) reveals significant perturbations in the active site. As predicted, Asp485 is oriented away from the flavin moiety, such that any stabilizing interaction with the reduced flavin is abolished. Met122 and Glu361 form unusual hydrogen bonds to the functional group of Asp485 and are displaced from the positions they occupy in the wild-type active site. The overall effect is to disrupt the stabilization of the reduced FAD cofactor during catalysis. Furthermore, a narrow transient channel that is shown to form when the wild-type Asn485 forms the NH...pi interaction with FAD and that has been proposed to function as an access route of molecular oxygen, is not observed in either of the mutant structures, suggesting that the dynamics of the active site are altered.


    Organizational Affiliation

    Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Sinsheimer Laboratories, 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): 1 
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
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.92 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.124 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.289α = 90.00
b = 73.396β = 105.15
c = 63.140γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SHELXL-97refinement
REFMACphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance