Second-Shell Hydrogen Bond Impacts Transition-State Structure in Bacillus subtilis Oxalate Decarboxylase

Enzymatic and structural properties of a novel oxalate decarboxylase BsOxdC from Bacillus safensis and its potential pH-dependent catalytic mechanism

Oxalate decarboxylase converts oxalate to formate and CO2 without requiring organic cofactors, making it biotechnologically relevant for applications in food, agriculture, and diagnostics. Its activity is highly dependent on pH; however, the pH-dependent catalytic mechanism remains poorly understood. This study identified a novel oxalate decarboxylase, BsOxdC, from Bacillus safensis and investigated its catalytic properties through heterologous expression and enzymatic assays. The purified BsOxdC efficiently degrades oxalate at an optimum temperature of 50 °C and a pH of 4.0, achieving a Vmax of 8.54 μmol/(min·mg). The apparent values of kcat, Km, and kcat/Km were 85.35 s-1, 4.67 μM, and 18.28 μM/s, respectively. The predicted structure of BsOxdC features two conserved cupin barrel folds at the N-terminal and C-terminal. Additionally, the docking model of the oxalate-BsOxdC complex is more stable than those of the formate-BsOxdC or acetate-BsOxdC complexes due to its lowest binding energy. In the open conformation of BsOxdC, the carboxyl group of the catalytic residue E181, located in the active loop S180E181N182S183T184, points away from both the oxalate and the active-site Mn ion. Simulations suggest that S180 and E181 interact with the substrate via ionic bonds and/or water bridges only at low pH (4.0), not at pH 8.0. Additionally, THR184 forms more molecular interactions with oxalate at pH 4.0 than at pH 8.0.

Bidentate Substrate Binding Mode in Oxalate Decarboxylase

Oxalate decarboxylase is an Mn- and O2-dependent enzyme in the bicupin superfamily that catalyzes the redox-neutral disproportionation of the oxalate monoanion to form carbon dioxide and formate. Its best-studied isozyme is from Bacillus subtilis where it is stress-induced under low pH conditions. Current mechanistic schemes assume a monodentate binding mode of the substrate to the N-terminal active site Mn ion to make space for a presumed O2 molecule, despite the fact that oxalate generally prefers to bind bidentate to Mn. We report on X-band 13C-electron nuclear double resonance (ENDOR) experiments on 13C-labeled oxalate bound to the active-site Mn(II) in wild-type oxalate decarboxylase at high pH, the catalytically impaired W96F mutant enzyme at low pH, and Mn(II) in aqueous solution. The ENDOR spectra of these samples are practically identical, which shows that the substrate binds bidentate (κO, κO') to the active site Mn(II) ion. Domain-based local pair natural orbital coupled cluster singles and doubles (DLPNO-CCSD) calculations of the expected 13C hyperfine coupling constants for bidentate bound oxalate predict ENDOR spectra in good agreement with the experiment, supporting bidentate bound substrate. Geometry optimization of a substrate-bound minimal active site model by density functional theory shows two possible substrate coordination geometries, bidentate and monodentate. The bidentate structure is energetically preferred by ~4.7 kcal/mol. Our results revise a long-standing hypothesis regarding substrate binding in the enzyme and suggest that dioxygen does not bind to the active site Mn ion after substrate binds. The results are in agreement with our recent mechanistic hypothesis of substrate activation via a long-range electron transfer process involving the C-terminal Mn ion.

Recent Advances of Oxalate Decarboxylase: Biochemical Characteristics, Catalysis Mechanisms, and Gene Expression and Regulation

Oxalate decarboxylase (OXDC) is a typical Mn2+/Mn3+ dependent metal enzyme and splits oxalate to formate and CO2 without any organic cofactors. Fungi and bacteria are the main organisms expressing the OXDC gene, but with a significantly different mechanism of gene expression and regulation. Many articles reported its potential applications in the clinical treatment of hyperoxaluria, low-oxalate food processing, degradation of oxalate salt deposits, oxalate acid diagnostics, biocontrol, biodemulsifier, and electrochemical oxidation. However, some questions still remain to be clarified about the role of substrate binding and/or protein environment in modulating the redox properties of enzyme-bound Mn(II)/Mn(III), the nature of dioxygen involved in the catalytic mechanism, and how OXDC acquires Mn(II) /Mn(III). This review mainly summarizes its biochemical and structure characteristics, gene expression and regulation, and catalysis mechanism. We also deep-mined oxalate decarboxylase gene data from National Center for Biotechnology Information to give some insights to explore new OXDC with diverse biochemical properties.

Molecular characterization and in silico analysis of oxalate decarboxylase of Pseudomonas sp. OXDC12

Oxalate decarboxylase (OxDC) is a Mn-dependent hexameric enzyme that is highly important in management of calcium oxalate mediated nephrolithiasis. The present study reported the production and purification of OxDC from Pseudomonas sp. OXDC12 up to 45.3-fold with an overall yield of 7%. The purified OxDC displayed a single band of approximately 40 kDa on SDS-PAGE and 240 kDa on Native-PAGE suggesting it to be a hexameric enzyme. The purified OxDC displayed an optimum activity at 26 °C and pH 4.5 in the presence of substrate sodium oxalate (30 mg/mL) with a K_m and V_max value of 43.9 mM and 8.9 µmol/min, respectively and an activation energy of 52.49 kJ/mol. The enzyme activity was significantly enhanced by adding o-phenylenediamine to the reaction mixture. OxDC exhibited a very low 17 haemolytic activity which suggested a relatively safer therapeutic aspect of the tested OxDC. The structure prediction studies of the OxDC revealed a tertiary structure with α/β chains that formed the β barrel structure, typical of all cupin domains. The Ramachandran plot produced by PROCHECK shows that 90.5% of the residues are in the most favoured region and hence the OxDC model produced was a good one. Docking studies revealed the binding of the metal ions and ligands to cluster of three histidine residues in the N terminal domain that formed the active site pocket of the enzyme. It was suggested that the histidine coordinated Mn2+ ion was critical for substrate recognition and binding and was also directly involved in OxDC catalyses.highlightsOxalate decarboxylase (OxDC) was successfully purified from Pseudomonas sp. OXDC12 up-to 45.3-fold.The K_m and V_max values of the purified OxDC were calculated as 43.9 mM and 8.9 µmol/min, respectively.Genre analysis and structure prediction studies revealed the presence of β barrel structure typical of all cupin domains. The model exhibited a bi-cupin domain that forms the dimer of the homo-hexameric OxDC.Docking experiments revealed that the cluster of three HIS residues in the N terminal domain of the tested enzyme formed the active site pocket for binding of Mn as well as the ligands.Communicated by Ramaswamy H. Sarma.

A metal ion-dependent conformational switch modulates activity of the Plasmodium M17 aminopeptidase

The metal-dependent M17 aminopeptidases are conserved throughout all kingdoms of life. This large enzyme family is characterized by a conserved binuclear metal center and a distinctive homohexameric arrangement. Recently, we showed that hexamer formation in Plasmodium M17 aminopeptidases was controlled by the metal ion environment, although the functional necessity for hexamer formation is still unclear. To further understand the mechanistic role of the hexameric assembly, here we undertook an investigation of the structure and dynamics of the M17 aminopeptidase from Plasmodium falciparum, PfA-M17. We describe a novel structure of PfA-M17, which shows that the active sites of each trimer are linked by a dynamic loop, and loop movement is coupled with a drastic rearrangement of the binuclear metal center and substrate-binding pocket, rendering the protein inactive. Molecular dynamics simulations and biochemical analyses of PfA-M17 variants demonstrated that this rearrangement is inherent to PfA-M17, and that the transition between the active and inactive states is metal dependent and part of a dynamic regulatory mechanism. Key to the mechanism is a remodeling of the binuclear metal center, which occurs in response to a signal from the neighboring active site and serves to moderate the rate of proteolysis under different environmental conditions. In conclusion, this work identifies a precise mechanism by which oligomerization contributes to PfA-M17 function. Furthermore, it describes a novel role for metal cofactors in the regulation of enzymes, with implications for the wide range of metalloenzymes that operate via a two-metal ion catalytic center, including DNA processing enzymes and metalloproteases.

Second-Shell Amino Acid R266 Helps Determine N-Succinylamino Acid Racemase Reaction Specificity in Promiscuous N-Succinylamino Acid Racemase/o-Succinylbenzoate Synthase Enzymes

Catalytic promiscuity is the coincidental ability to catalyze nonbiological reactions in the same active site as the native biological reaction. Several lines of evidence show that catalytic promiscuity plays a role in the evolution of new enzyme functions. Thus, studying catalytic promiscuity can help identify structural features that predispose an enzyme to evolve new functions. This study identifies a potentially preadaptive residue in a promiscuous N-succinylamino acid racemase/o-succinylbenzoate synthase (NSAR/OSBS) enzyme from Amycolatopsis sp. T-1-60. This enzyme belongs to a branch of the OSBS family which includes many catalytically promiscuous NSAR/OSBS enzymes. R266 is conserved in all members of the NSAR/OSBS subfamily. However, the homologous position is usually hydrophobic in other OSBS subfamilies, whose enzymes lack NSAR activity. The second-shell amino acid R266 is close to the catalytic acid/base K263, but it does not contact the substrate, suggesting that R266 could affect the catalytic mechanism. Mutating R266 to glutamine in Amycolatopsis NSAR/OSBS profoundly reduces NSAR activity but moderately reduces OSBS activity. This is due to a 1000-fold decrease in the rate of proton exchange between the substrate and the general acid/base catalyst K263. This mutation is less deleterious for the OSBS reaction because K263 forms a cation-π interaction with the OSBS substrate and/or the intermediate, rather than acting as a general acid/base catalyst. Together, the data explain how R266 contributes to NSAR reaction specificity and was likely an essential preadaptation for the evolution of NSAR activity.

Oxalate decarboxylase uses electron hole hopping for catalysis

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.