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

Summary for 4MET

• Entry DOI: 10.2210/pdb4met/pdb
• Descriptor: Oxalate decarboxylase OxdC, COBALT (II) ION (3 entities in total)
• Functional Keywords: cupin fold, lyase
• Biological source: Bacillus subtilis subsp. subtilis
• Total number of polymer chains: 4
• Total formula weight: 176836.81

Authors

Campomanes, P.,Kellett, W.F.,Easthon, L.M.,Ozarowski, A.,Allen, K.N.,Angerhofer, A.,Rothlisberger, U.,Richards, N.G.J. (deposition date: 2013-08-27, release date: 2014-03-05, Last modification date: 2023-09-20)

Primary citation

Campomanes, P.,Kellett, W.F.,Easthon, L.M.,Ozarowski, A.,Allen, K.N.,Angerhofer, A.,Rothlisberger, U.,Richards, N.G.
Assigning the EPR Fine Structure Parameters of the Mn(II) Centers in Bacillus subtilis Oxalate Decarboxylase by Site-Directed Mutagenesis and DFT/MM Calculations.
J.Am.Chem.Soc., 136:2313-2323, 2014

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 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.

PubMed: 24444454
DOI: 10.1021/ja408138f

Experimental method

X-RAY DIFFRACTION (2.095 Å)