<i>Bacillus subtilis</i>
            YvrK Is an Acid-Induced Oxalate Decarboxylase

Tanner, Adam; Bornemann, Stephen

doi:10.1128/jb.182.18.5271-5273.2000

Cited by 105 publications

(148 citation statements)

References 21 publications

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“…Despite the low solubility of metal oxalates (Kps=4×10 -9 for Ca oxalate), they can be dissolved by oxalate-utilizing bacteria (Chandra and Shethna 1975;Dijkhuizen et al 1977;Friedrich et al 1979;Tamer and Aragno 1980). Generally, the metabolic role of oxalate in other bacteria remains unclear, but it is assumed to be used in pH regulation, energy production from glyoxylate and in aluminum detoxification by some bacteria (Hamel et al 1999;Tanner and Bornemann 2000). Another reason for bacterial degradation of oxalate is its detoxification, as it can easily become toxic for many strains.…”

Section: Introductionmentioning

confidence: 99%

Is the contribution of bacteria to terrestrial carbon budget greatly underestimated?

Braissant

Verrecchia

Aragno

2002

Naturwissenschaften

119

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Some commonly found species of soil bacteria use low molecular weight organic acids as their sole source of carbon and energy. This study shows that acids such as citrate and oxalate (produced in large amounts by fungi and plants) can rapidly be consumed by these bacteria. Two strains, Ralstonia eutropha and Xanthobacter autotrophicus, were cultured on acetate-and citrate-rich media. The resulting CO 2 and/or HCO 3 -reacted with calcium ions to precipitate two polymorphs of calcium carbonate (CaCO 3 ), calcite and vaterite, depending on the quantity of slime produced by the strains. This production of primary calcium carbonate crystals by oxalate-and citrate-degrading bacteria from soil organic carbon sources highlights the existence of an important and underestimated potential carbon sink.

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Section: Introductionmentioning

confidence: 99%

Is the contribution of bacteria to terrestrial carbon budget greatly underestimated?

Braissant

Verrecchia

Aragno

2002

Naturwissenschaften

119

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“…The oxalate decarboxylase (OxDC, 1 or YvrK based on the corresponding open reading frame) from Bacillus subtilis has recently garnered attention because of its mechanistically intriguing reaction (1-4) (Scheme 1). Purified OxDC crystallizes as a hexamer of 43-kDa subunits, each of which is a member of the "bicupin" structural family (5), and contains two mononuclear manganese centers with amino acid ligands that are functionally similar to those of manganese superoxide dismutase (MnSOD) (6); namely three histidine residues and one carboxylic acid residue.…”

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confidence: 99%

EPR Spectroscopic Characterization of the Manganese Center and a Free Radical in the Oxalate Decarboxylase Reaction

Chang

Svedružić

Ożarowski

et al. 2004

Journal of Biological Chemistry

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Several molecular mechanisms for cleavage of the oxalate carbon-carbon bond by manganese-dependent oxalate decarboxylase have recently been proposed involving high oxidation states of manganese. We have examined the oxalate decarboxylase from Bacillus subtilis by electron paramagnetic resonance in perpendicular and parallel polarization configurations to test for the presence of such species in the resting state and during enzymatic turnover. Simulation and the position of the half-field Mn(II) line suggest a nearly octahedral metal geometry in the resting state. No spectroscopic signature for Mn(III) or Mn(IV) is seen in parallel mode EPR for samples frozen during turnover, consistent either with a large zero-field splitting in the oxidized metal center or undetectable levels of these putative high-valent intermediates in the steady state. A narrow, featureless g ‫؍‬ 2.0 species was also observed in perpendicular mode in the presence of substrate, enzyme, and dioxygen. Additional splittings in the signal envelope became apparent when spectra were taken at higher temperatures. Isotopic editing resulted in an altered line shape only when tyrosine residues of the enzyme were specifically deuterated. Spectral processing confirmed multiple splittings with isotopically neutral enzyme that collapsed to a single prominent splitting in the deuterated enzyme. These results are consistent with formation of an enzyme-based tyrosyl radical upon oxalate exposure. Modestly enhanced relaxation relative to abiological tyrosyl radicals was observed, but site-directed mutagenesis indicated that conserved tyrosine residues in the active site do not host the unpaired spin. Potential roles for manganese and a peripheral tyrosyl radical during steady-state turnover are discussed.The oxalate decarboxylase (OxDC, 1 or YvrK based on the corresponding open reading frame) from Bacillus subtilis has recently garnered attention because of its mechanistically intriguing reaction (1-4) (Scheme 1). Purified OxDC crystallizes as a hexamer of 43-kDa subunits, each of which is a member of the "bicupin" structural family (5), and contains two mononuclear manganese centers with amino acid ligands that are functionally similar to those of manganese superoxide dismutase (MnSOD) (6); namely three histidine residues and one carboxylic acid residue. Oxalate 13 C and 18 O isotope effects on V max /K m of YvrK suggest the presence of a slow, partially rate-determining step prior to the irreversible C-C bond cleavage (4), which was proposed to be a proton-coupled electron transfer.The requirement for and substoichiometric consumption of dioxygen in the YvrK catalytic process, involvement of open shell manganese (2), and chemical precedent for oxalate decarboxylation in the Kolbe electrolysis (7,8) and the BorodinHunsdiecker reaction (9 -11) have led to various mechanistic proposals involving radical intermediates, and enzymic manganese complexes with formal oxidation states of either Mn(III) (2, 4) or Mn(IV) (3). A previously published electron paramagneti...

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“…The best-characterized enzymes are enzymes that have a fungal origin, are induced by oxalate, and appear to control excessive concentrations of oxalate (12). The first oxalate decarboxylase to be identified in a prokaryote was the acid-inducible OxdC enzyme from B. subtilis, which may have a role in proton consumption within the cytoplasm (51). OxdC belongs to the cupin superfamily, whose members contain a ␤-sandwich domain consisting of one six-strand ␤-sheet and one five-strand ␤-sheet (1,12,51).…”

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confidence: 99%

“…The first oxalate decarboxylase to be identified in a prokaryote was the acid-inducible OxdC enzyme from B. subtilis, which may have a role in proton consumption within the cytoplasm (51). OxdC belongs to the cupin superfamily, whose members contain a ␤-sandwich domain consisting of one six-strand ␤-sheet and one five-strand ␤-sheet (1,12,51). OxdC is a homohexameric enzyme in which each monomer has two cupin ␤-barrel domains, and hence it belongs to the bicupin subclass of the cupin superfamily (1,12,51).…”

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confidence: 99%

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Assembly of an Oxalate Decarboxylase Produced under σ ^K Control into the Bacillus subtilis Spore Coat

et al. 2004

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Over 30 polypeptides are synthesized at various times during sporulation in Bacillus subtilis, and they are assembled at the surface of the developing spore to form a multilayer protein structure called the coat. The coat consists of three main layers, an amorphous undercoat close to the underlying spore cortex peptidoglycan, a lamellar inner layer, and an electron-dense striated outer layer. The product of the B. subtilis oxdD gene was previously shown to have oxalate decarboxylase activity when it was produced in Escherichia coli and to be a spore constituent. In this study, we found that OxdD specifically associates with the spore coat structure, and in this paper we describe regulation of its synthesis and assembly. We found that transcription of oxdD is induced during sporulation as a monocistronic unit under the control of K and is negatively regulated by GerE. We also found that localization of a functional OxdD-green fluorescent protein (GFP) at the surface of the developing spore depends on the SafA morphogenetic protein, which localizes at the interface between the spore cortex and coat layers. OxdD-GFP localizes around the developing spore in a cotE mutant, which does not assemble the spore outer coat layer, but it does not persist in spores produced by the mutant. Together, the data suggest that OxdD-GFP is targeted to the interior layers of the coat. Additionally, we found that expression of a multicopy allele of oxdD resulted in production of spores with increased levels of OxdD that were able to degrade oxalate but were sensitive to lysozyme.

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Bacillus subtilis YvrK Is an Acid-Induced Oxalate Decarboxylase

Cited by 105 publications

References 21 publications

Is the contribution of bacteria to terrestrial carbon budget greatly underestimated?

Is the contribution of bacteria to terrestrial carbon budget greatly underestimated?

EPR Spectroscopic Characterization of the Manganese Center and a Free Radical in the Oxalate Decarboxylase Reaction

Assembly of an Oxalate Decarboxylase Produced under σ ^K Control into the Bacillus subtilis Spore Coat

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Bacillus subtilis YvrK Is an Acid-Induced Oxalate Decarboxylase

Cited by 105 publications

References 21 publications

Is the contribution of bacteria to terrestrial carbon budget greatly underestimated?

Is the contribution of bacteria to terrestrial carbon budget greatly underestimated?

EPR Spectroscopic Characterization of the Manganese Center and a Free Radical in the Oxalate Decarboxylase Reaction

Assembly of an Oxalate Decarboxylase Produced under σ K Control into the Bacillus subtilis Spore Coat

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Assembly of an Oxalate Decarboxylase Produced under σ ^K Control into the Bacillus subtilis Spore Coat