2GEW

Atomic resolution structure of cholesterol oxidase @ pH 9.0 (Streptomyces sp. SA-COO)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.113 
  • R-Value Observed: 0.113 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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: 259-264

  • DOI: 10.1038/nchembio784
  • Primary Citation of Related Structures:  
    1N4V, 1N4U, 1N4W, 2GEW

  • PubMed Abstract: 
  • Hydrogen atoms are a vital component of enzyme structure and function. In recent years, atomic resolution crystallography (>or=1.2 A) has been successfully used to investigate the role of the hydrogen atom in enzymatic catalysis. Here, atomic resolution crystallography was used to study the effect of pH on cholesterol oxidase from Streptomyces sp ...

    Hydrogen atoms are a vital component of enzyme structure and function. In recent years, atomic resolution crystallography (>or=1.2 A) has been successfully used to investigate the role of the hydrogen atom in enzymatic catalysis. Here, atomic resolution crystallography was used to study the effect of pH on cholesterol oxidase from Streptomyces sp., a flavoenzyme oxidoreductase. Crystallographic observations of the anionic oxidized flavin cofactor at basic pH are consistent with the UV-visible absorption profile of the enzyme and readily explain the reversible pH-dependent loss of oxidation activity. Furthermore, a hydrogen atom, positioned at an unusually short distance from the main chain carbonyl oxygen of Met122 at high pH, was observed, suggesting a previously unknown mechanism of cofactor stabilization. This study shows how a redox active site responds to changes in the enzyme's environment and how these changes are able to influence the mechanism of enzymatic catalysis.


    Organizational Affiliation

    Department of Molecular, Cell and Developmental Biology, 1156 High Street, University of California, Santa Cruz, California 95064, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cholesterol oxidaseA504Streptomyces sp. SA-COOMutation(s): 0 
Gene Names: choA
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
OXY
Query on OXY

Download Ideal Coordinates CCD File 
D [auth A]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.113 
  • R-Value Observed: 0.113 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.11α = 90
b = 73.256β = 104.05
c = 62.432γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXLrefinement
SHELXL-97refinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-02
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Structure summary
  • Version 1.4: 2019-12-18
    Changes: Advisory, Derived calculations