4MET

Assigning the EPR Fine Structure Parameters of the Mn(II) Centers in Bacillus subtilis Oxalate Decarboxylase by Site-Directed Mutagenesis and DFT/MM Calculations


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.095 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


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Literature

Assigning the EPR Fine Structure Parameters of the Mn(II) Centers in Bacillus subtilis Oxalate Decarboxylase by Site-Directed Mutagenesis and DFT/MM Calculations.

Campomanes, P.Kellett, W.F.Easthon, L.M.Ozarowski, A.Allen, K.N.Angerhofer, A.Rothlisberger, U.Richards, N.G.

(2014) J.Am.Chem.Soc. 136: 2313-2323

  • DOI: 10.1021/ja408138f

  • PubMed Abstract: 
  • Oxalate decarboxylase (OxDC) catalyzes the Mn-dependent conversion of the oxalate monoanion into CO2 and formate. EPR-based strategies for investigating the catalytic mechanism of decarboxylation are complicated by the difficulty of assigning the sig ...

    Oxalate decarboxylase (OxDC) catalyzes the Mn-dependent conversion of the oxalate monoanion into CO2 and formate. EPR-based strategies for investigating the catalytic mechanism of decarboxylation are complicated by the difficulty of assigning the signals associated with the two Mn(II) centers located in the N- and C-terminal cupin domains of the enzyme. We now report a mutational strategy that has established the assignment of EPR fine structure parameters to each of these Mn(II) centers at pH 8.5. These experimental findings are also used to assess the performance of a multistep strategy for calculating the zero-field splitting parameters of protein-bound Mn(II) ions. Despite the known sensitivity of calculated D and E values to the computational approach, we demonstrate that good estimates of these parameters can be obtained using cluster models taken from carefully optimized DFT/MM structures. Overall, our results provide new insights into the strengths and limitations of theoretical methods for understanding electronic properties of protein-bound Mn(II) ions, thereby setting the stage for future EPR studies on the electronic properties of the Mn(II) centers in OxDC and site-specific variants.


    Organizational Affiliation

    Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oxalate decarboxylase OxdC
A, B, C, D
388Bacillus subtilis (strain 168)Mutation(s): 1 
Gene Names: oxdC (yvrK)
EC: 4.1.1.2
Find proteins for O34714 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34714
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO

Download SDF File 
Download CCD File 
A, B, C, D
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.095 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.196 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 156.973α = 90.00
b = 156.973β = 90.00
c = 330.473γ = 120.00
Software Package:
Software NamePurpose
SHELXSphasing
HKL-2000data reduction
HKL-2000data collection
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2019-11-20
    Type: Database references, Derived calculations