6UFI

W96Y Oxalate Decarboxylase (Bacillus subtilis)

Summary for 6UFI

• Entry DOI: 10.2210/pdb6ufi/pdb
• Descriptor: Cupin domain-containing protein, MANGANESE (II) ION, GLYCEROL, ... (6 entities in total)
• Functional Keywords: hexamer, oxdc, mn, lyase
• Biological source: Bacillus subtilis
• Total number of polymer chains: 1
• Total formula weight: 43893.73

Authors

Pastore, A.J.,Burg, M.J.,Twahir, U.T.,Bruner, S.D.,Angerhofer, A. (deposition date: 2019-09-24, release date: 2020-09-30, Last modification date: 2023-10-11)

Primary citation

Pastore, A.J.,Teo, R.D.,Montoya, A.,Burg, M.J.,Twahir, U.T.,Bruner, S.D.,Beratan, D.N.,Angerhofer, A.
Oxalate decarboxylase uses electron hole hopping for catalysis.
J.Biol.Chem., 297:100857-100857, 2021

PubMed Abstract: The hexameric low-pH stress response enzyme oxalate decarboxylase catalyzes the decarboxylation of the oxalate mono-anion in the soil bacterium Bacillus subtilis. A single protein subunit contains two Mn-binding cupin domains, and catalysis depends on Mn(III) at the N-terminal site. The present study suggests a mechanistic function for the C-terminal Mn as an electron hole donor for the N-terminal Mn. The resulting spatial separation of the radical intermediates directs the chemistry toward decarboxylation of the substrate. A π-stacked tryptophan pair (W96/W274) links two neighboring protein subunits together, thus reducing the Mn-to-Mn distance from 25.9 Å (intrasubunit) to 21.5 Å (intersubunit). Here, we used theoretical analysis of electron hole-hopping paths through redox-active sites in the enzyme combined with site-directed mutagenesis and X-ray crystallography to demonstrate that this tryptophan pair supports effective electron hole hopping between the C-terminal Mn of one subunit and the N-terminal Mn of the other subunit through two short hops of ∼8.5 Å. Replacement of W96, W274, or both with phenylalanine led to a large reduction in catalytic efficiency, whereas replacement with tyrosine led to recovery of most of this activity. W96F and W96Y mutants share the wildtype tertiary structure. Two additional hole-hopping networks were identified leading from the Mn ions to the protein surface, potentially protecting the enzyme from high Mn oxidation states during turnover. Our findings strongly suggest that multistep hole-hopping transport between the two Mn ions is required for enzymatic function, adding to the growing examples of proteins that employ aromatic residues as hopping stations.

PubMed: 34097877
DOI: 10.1016/j.jbc.2021.100857

Experimental method

X-RAY DIFFRACTION (1.72 Å)