3B3R | pdb_00003b3r

Crystal structure of Streptomyces cholesterol oxidase H447Q/E361Q mutant bound to glycerol (0.98A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 
    0.159 (Depositor), 0.148 (DCC) 
  • R-Value Work: 
    0.121 (DCC) 
  • R-Value Observed: 
    0.129 (Depositor) 

Starting Model: experimental
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Literature

Distortion of flavin geometry is linked to ligand binding in cholesterol oxidase

Lyubimov, A.Y.Heard, K.Tang, H.Sampson, N.S.Vrielink, A.

(2007) Protein Sci 16: 2647-2656

  • DOI: https://doi.org/10.1110/ps.073168207
  • Primary Citation Related Structures: 
    3B3R, 3B6D

  • PubMed Abstract: 

    Two high-resolution structures of a double mutant of bacterial cholesterol oxidase in the presence or absence of a ligand, glycerol, are presented, showing the trajectory of glycerol as it binds in a Michaelis complex-like position in the active site. A group of three aromatic residues forces the oxidized isoalloxazine moiety to bend along the N5-N10 axis as a response to the binding of glycerol in the active site. Movement of these aromatic residues is only observed in the glycerol-bound structure, indicating that some tuning of the FAD redox potential is caused by the formation of the Michaelis complex during regular catalysis. This structural study suggests a possible mechanism of substrate-assisted flavin activation, improves our understanding of the interplay between the enzyme, its flavin cofactor and its substrate, and is of use to the future design of effective cholesterol oxidase inhibitors.


  • Organizational Affiliation
    • Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, California 95064, USA.

Macromolecule Content 

  • Total Structure Weight: 56.37 kDa 
  • Atom Count: 5,343 
  • Modeled Residue Count: 503 
  • Deposited Residue Count: 506 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cholesterol oxidase506Streptomyces sp. SA-COOMutation(s): 2 
EC: 1.1.3.6 (PDB Primary Data), 5.3.3.1 (UniProt)
UniProt
Find proteins for P12676 (Streptomyces sp. (strain SA-COO))
Explore P12676 
Go to UniProtKB:  P12676
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12676
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free:  0.159 (Depositor), 0.148 (DCC) 
  • R-Value Work:  0.121 (DCC) 
  • R-Value Observed: 0.129 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.314α = 90
b = 73.643β = 104.98
c = 63.275γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
SHELXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
d*TREKdata reduction
REFMACphasing
SHELXL-97refinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description