2JBV

Crystal structure of choline oxidase reveals insights into the catalytic mechanism


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Role of Glu312 in Binding and Positioning of the Substrate for the Hydride Transfer Reaction in Choline Oxidase.

Quaye, O.Lountos, G.T.Fan, F.Orville, A.M.Gadda, G.

(2008) Biochemistry 47: 243

  • DOI: 10.1021/bi7017943

  • PubMed Abstract: 
  • Choline oxidase catalyzes the oxidation of choline to glycine betaine, a compatible solute that accumulates in pathogenic bacteria and plants so they can withstand osmotic and temperature stresses. The crystal structure of choline oxidase was determi ...

    Choline oxidase catalyzes the oxidation of choline to glycine betaine, a compatible solute that accumulates in pathogenic bacteria and plants so they can withstand osmotic and temperature stresses. The crystal structure of choline oxidase was determined and refined to a resolution of 1.86 A with data collected at 100 K using synchrotron X-ray radiation. The structure reveals a covalent linkage between His99 Nepsilon2 and FAD C8M atoms, and a 123 A3 solvent-excluded cavity adjacent to the re face of the flavin. A hypothetical model for choline docked into the cavity suggests that several aromatic residues and Glu312 may orient the cationic substrate for efficient catalysis. The role of the negative charge on Glu312 was investigated by engineering variant enzymes in which Glu312 was replaced with alanine, glutamine, or aspartate. The Glu312Ala enzyme was inactive. The Glu312Gln enzyme exhibited a Kd value for choline at least 500 times larger than that of the wild-type enzyme. The Glu312Asp enzyme had a kcat/KO2 value similar to that of the wild-type enzyme but kcat and kcat/Km values that were 230 and 35 times lower, respectively, than in the wild-type enzyme. These data are consistent with the spatial location of the negative charge on residue 312 being important for the oxidation of the alcohol substrate. Solvent viscosity and substrate kinetic isotope effects suggest the presence of an internal equilibrium in the Glu312Asp enzyme prior to the hydride transfer reaction. Altogether, the crystallographic and mechanistic data suggest that Glu312 is important for binding and positioning of the substrate in the active site of choline oxidase.


    Related Citations: 
    • Cloning, Sequence Analysis, and Purification of Choline Oxidase from Arthrobacter Globiformis: A Bacterial Enzyme Involved in Osmotic Stress Tolerance
      Fan, F.,Ghanem, M.,Gadda, G.
      (2004) Arch.Biochem.Biophys. 421: 149
    • On the Catalytic Mechanism of Choline Oxidase
      Fan, F.,Gadda, G.
      (2005) J.Am.Chem.Soc. 127: 2067
    • The Trimethylammonium Headgroup of Choline is a Major Determinant for Substrate Binding and Specificity in Choline Oxidase
      Gadda, G.,Powell, N.L.,Menon, P.
      (2004) Arch.Biochem.Biophys. 430: 264
    • On the Catalytic Role of the Conserved Active Site Residue His466 of Choline Oxidase
      Ghanem, M.,Gadda, G.
      (2005) Biochemistry 44: 893
    • Effects of Reversing the Protein Positive Charge in the Proximity of the Flavin N(1) Locus of Choline Oxidase
      Ghanem, M.,Gadda, G.
      (2006) Biochemistry 45: 1979
    • Kinetic Mechanism of Choline Oxidase from Arthrobacter Globiformis
      Gadda, G.
      (2003) Biochim.Biophys.Acta 1646: 112


    Organizational Affiliation

    Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHOLINE OXIDASE
A, B
546Arthrobacter globiformisGene Names: codA
EC: 1.1.3.17
Find proteins for Q7X2H8 (Arthrobacter globiformis)
Go to UniProtKB:  Q7X2H8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download SDF File 
Download CCD File 
A, B
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
FAO
Query on FAO

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Download CCD File 
A, B
[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(4aS,10aR)-7,8-dimethyl-2,4-dioxo-1,3,4,4a,5,10a-hexahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate
C27 H37 N9 O15 P2
VSWYNLHGQAGAHX-AWYOOINRSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FAOKd: 290000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.169 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 84.355α = 90.00
b = 84.355β = 90.00
c = 343.450γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata scaling
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance