Kinetic challenges facing oxalate, malonate, acetoacetate, and oxaloacetate decarboxylases

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.

Enhanced Yield of Methyl Ethyl Ketone through Levulinic Acid Decarboxylation in the AgNO3/K2S2O8 System: Mechanistic Insights and Characterization of Metallic Species

Methyl ethyl ketone (MEK) is among the most extensively utilized solvents in various industrial applications. In this study, we present a highly efficient synthesis route for MEK via the decarboxylation of biomass-derived levulinic acid, using potassium persulfate (K2S2O8) and silver nitrate (AgNO3) as key reagents. The specific roles of AgNO3 and K2S2O8 were thoroughly investigated. Additional silver species, such as Ag2O and AgO, were also detected during the reaction. X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD) analyses provided evidence of the evolution of solid phases throughout the reaction. Based on these findings, we propose a radical decarboxylation mechanism initiated by the generation of sulfate radicals (SO4•⁻) through the catalytic breakdown of K2S2O8 by AgNO3. This mechanistic understanding, combined with a parametric study, enabled us to achieve an unprecedented level of levulinic acid conversion (97.9%) and MEK yield (86.6%) with this system, surpassing all previously reported results in the literature.

Is the TCA cycle malate dehydrogenase-citrate synthase metabolon an illusion?

This review discusses the intriguing yet controversial concept of metabolons, focusing on the malate dehydrogenase-citrate synthase (MDH-CISY) metabolon as a model. Metabolons are multienzyme complexes composed of enzymes that catalyze sequential reactions in metabolic pathways. Metabolons have been proposed to enhance metabolic pathway efficiency by facilitating substrate channeling. However, there is skepticism about the presence of metabolons and their functionality in physiological conditions in vivo. We address the skepticism by reviewing compelling evidence supporting the existence of the MDH-CISY metabolon and highlighting its potential functions in cellular metabolism. The electrostatic interaction between MDH and CISY and the intermediate oxaloacetate, channeled within the metabolon, has been demonstrated using various experimental techniques, including protein-protein interaction assays, isotope dilution studies, and enzyme coupling assays. Regardless of the wealth of in vitro evidence, further validation is required to elucidate the functionality of MDH-CISY metabolons in living systems using advanced structural and spatial analysis techniques.

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.

One-Pot Biosynthesis of Acetone from Waste Poly(hydroxybutyrate)

The plastic waste crisis is catalyzing change across the plastics life cycle. Central to this is increased production and application of bioplastics and biodegradable plastics. In particular, poly(hydroxybutyrate) (PHB) is a biodegradable bioplastic that can be produced from various renewable and waste feedstocks and is a promising alternative to some petrochemical-derived and non-biodegradable plastics. Despite its advantages, PHB biodegradation depends on environmental conditions, and the effects of degradation into microplastics, oligomers, and the 3-hydroxybutyrate (3-HB) monomer on soil microbiomes are unknown. We hypothesized that the ease of PHB biodegradation renders this next-generation plastic an ideal feedstock for microbial recycling into platform chemicals currently produced from fossil fuels. To demonstrate this, we report the one-pot degradation and recycling of PHB into acetone using a single strain of engineered Escherichia coli. Following strain development and initial bioprocess optimization, we report maximum titers of 123 mM acetone (7 g/L) from commercial PHB granules after 24 h fermentation at 30 °C. We further report biorecycling of an authentic sample of post-consumer PHB waste at a preparative scale. This is the first demonstration of biological recycling of PHB into a second-generation chemical, and it demonstrates next-generation plastic waste as a novel feedstock for the circular bioeconomy.

Proton Transfer via π-Interactions from Pyridine Provides a Facilitated Route for Transfer of CO2 in Its Complex with a Carbanion

Aromatic π-interactions have been recognized as enhancing enzymatic catalytic processes, providing an efficient route to overcome entropic barriers. A nonenzymic analogue, a complex of protonated pyridine and a phenyl substituent in a thiamin conjugate, facilitates the departure of CO2 by protonation of a vicinal carbanion in a reactive complex. To evaluate the efficiency of the catalytic pathway from the π-associated proton donor, a system was assessed that produced measurable competition through the rates of formation of alternative products resulting from the same thiamin-derived carbanion. The barriers to competing pathways from the decarboxylation of p-(bromomethyl)-mandelylthiamin in the presence and absence of protonated pyridine were determined, establishing the efficiency of the vicinal proton transfer between π-associated species. The formation of the complex of CO2 and the co-formed carbanion also addresses the mechanism of the uncatalyzed exchange of 13CO2 into carboxyl groups discovered by Lundgren. Finally, microscopic reversibility implicates pyridine as a vicinal Brønsted base in thiamin-aldehyde adducts, producing carbanions that could incorporate dissolved CO2 into carboxyl groups.

Preventing mitochondrial reverse electron transport as a strategy for cardioprotection

In the context of myocardial infarction, the burst of superoxide generated by reverse electron transport (RET) at complex I in mitochondria is a crucial trigger for damage during ischaemia/reperfusion (I/R) injury. Here we outline the necessary conditions for superoxide production by RET at complex I and how it can occur during reperfusion. In addition, we explore various pathways that are implicated in generating the conditions for RET to occur and suggest potential therapeutic strategies to target RET, aiming to achieve cardioprotection.

Aldol Cleavage in Water and the Power of Citrate Lyase as a Catalyst

Citrate lyase allows Klebsiella aerogenes to grow anaerobically on citrate as the sole carbon source. Arrhenius analysis of experiments at high temperatures indicates that citrate is cleaved nonenzymatically to acetate and oxaloacetate with a t_1/2 of 6.9 million years in neutral solution at 25 °C, while malate cleavage occurs even more slowly (t_1/2 = 280 million years). However, t_1/2 is only 10 days for the nonenzymatic cleavage of 4-hydroxy-2-ketoglutarate, indicating that the introduction of an α-keto group enhances the rate of aldol cleavage of malate by a factor of 10¹⁰. The aldol cleavages of citrate and malate, like the decarboxylation of malonate (t_1/2 = 180 years), are associated with a near-zero entropy of activation, and their extreme differences in rate reflect differences between their heats of activation. Citrate lyase enhances the rate of substrate cleavage 6 × 10¹⁵-fold, comparable in magnitude with the rate enhancement produced by OMP decarboxylase, although these enzymes are strikingly different in their mechanisms of action.

Hydrogen Drives Part of the Reverse Krebs Cycle under Metal or Meteorite Catalysis

Hydrogen (H₂ ) is a geological source of reducing electrons that is thought to have powered the metabolism of the last universal common ancestor to all extant life, and that is still metabolized by various modern organisms. It has been suggested that H₂ drove a geochemical analogue of some or all of the reverse Krebs cycle at the emergence of the metabolic network, catalyzed by metals, but this has yet to be demonstrated experimentally. Herein, we show that three consecutive steps of the reverse Krebs cycle, converting oxaloacetate into succinate, can be driven without enzymes and in one-pot by H₂ as the reducing agent under mild conditions compatible with biological chemistry. Low catalytic amounts of nickel (10-20 mol %) or platinum group metals (0.1-1 mol %) or even small amounts of ground meteorites were found to promote the reductive chemistry at temperatures between 5 and 60 °C and over a wide pH range, including pH 7. These results lend additional support to the hypothesis that geologically produced hydrogen and metal catalysts could have initiated early metabolic networks.

Cyanide as a primordial reductant enables a protometabolic reductive glyoxylate pathway

Investigation of prebiotic metabolic pathways is predominantly based on abiotically replicating the reductive citric acid cycle. While attractive from a parsimony point of view, attempts using metal/mineral-mediated reductions have produced complex mixtures with inefficient and uncontrolled reactions. Here we show that cyanide acts as a mild and efficient reducing agent mediating abiotic transformations of tricarboxylic acid intermediates and derivatives. The hydrolysis of the cyanide adducts followed by their decarboxylation enables the reduction of oxaloacetate to malate and of fumarate to succinate, whereas pyruvate and α-ketoglutarate themselves are not reduced. In the presence of glyoxylate, malonate and malononitrile, alternative pathways emerge that bypass the challenging reductive carboxylation steps to produce metabolic intermediates and compounds found in meteorites. These results suggest a simpler prebiotic forerunner of today's metabolism, involving a reductive glyoxylate pathway without oxaloacetate and α-ketoglutarate-implying that the extant metabolic reductive carboxylation chemistries are an evolutionary invention mediated by complex metalloproteins.

Prebiotic photoredox synthesis from carbon dioxide and sulfite

Carbon dioxide (CO2) is the major carbonaceous component of many planetary atmospheres, which includes the Earth throughout its history. Carbon fixation chemistry-which reduces CO2 to organics, utilizing hydrogen as the stoichiometric reductant-usually requires high pressures and temperatures, and the yields of products of potential use to nascent biology are low. Here we demonstrate an efficient ultraviolet photoredox chemistry between CO2 and sulfite that generates organics and sulfate. The chemistry is initiated by electron photodetachment from sulfite to give sulfite radicals and hydrated electrons, which reduce CO2 to its radical anion. A network of reactions that generates citrate, malate, succinate and tartrate by irradiation of glycolate in the presence of sulfite was also revealed. The simplicity of this carboxysulfitic chemistry and the widespread occurrence and abundance of its feedstocks suggest that it could have readily taken place on the surfaces of rocky planets. The availability of the carboxylate products on early Earth could have driven the development of central carbon metabolism before the advent of biological CO2 fixation.

In Vivo Estimation of Ketogenesis Using Metabolic Flux Analysis-Technical Aspects and Model Interpretation

Ketogenesis occurs in liver mitochondria where acetyl-CoA molecules, derived from lipid oxidation, are condensed into acetoacetate (AcAc) and reduced to β-hydroxybutyrate (BHB). During carbohydrate scarcity, these two ketones are released into circulation at high rates and used as oxidative fuels in peripheral tissues. Despite their physiological relevance and emerging roles in a variety of diseases, endogenous ketone production is rarely measured in vivo using tracer approaches. Accurate determination of this flux requires a two-pool model, simultaneous BHB and AcAc tracers, and special consideration for the stability of the AcAc tracer and analyte. We describe the implementation of a two-pool model using a metabolic flux analysis (MFA) approach that simultaneously regresses liquid chromatography-tandem mass spectrometry (LC-MS/MS) ketone isotopologues and tracer infusion rates. Additionally, ¹H NMR real-time reaction monitoring was used to evaluate AcAc tracer and analyte stability during infusion and sample analysis, which were critical for accurate flux calculations. The approach quantifies AcAc and BHB pool sizes and their rates of appearance, disposal, and exchange. Regression analysis provides confidence intervals and detects potential errors in experimental data. Complications for the physiological interpretation of individual ketone fluxes are discussed.

Solvation Induction of Free Energy Barriers of Decarboxylation Reactions in Aqueous Solution from Dual-Level QM/MM Simulations

Carbon dioxide capture, corresponding to the recombination process of decarboxylation reactions of organic acids, is typically barrierless in the gas phase and has a relatively low barrier in aprotic solvents. However, these processes often encounter significant solvent-reorganization-induced barriers in aqueous solution if the decarboxylation product is not immediately protonated. Both the intrinsic stereoelectronic effects and solute-solvent interactions play critical roles in determining the overall decarboxylation equilibrium and free energy barrier. An understanding of the interplay of these factors is important for designing novel materials applied to greenhouse gas capture and storage as well as for unraveling the catalytic mechanisms of a range of carboxy lyases in biological CO₂ production. A range of decarboxylation reactions of organic acids with rates spanning nearly 30 orders of magnitude have been examined through dual-level combined quantum mechanical and molecular mechanical simulations to help elucidate the origin of solvation-induced free energy barriers for decarboxylation and the reverse carboxylation reactions in water.

Origin of Free Energy Barriers of Decarboxylation and the Reverse Process of CO2 Capture in Dimethylformamide and in Water

In aqueous solution, biological decarboxylation reactions proceed irreversibly to completion, whereas the reverse carboxylation processes are typically powered by the hydrolysis of ATP. The exchange of the carboxylate of ring-substituted arylacetates with isotope-labeled CO₂ in polar aprotic solvents reported recently suggests a dramatic change in the partition of reaction pathways. Yet, there is little experimental data pertinent to the kinetic barriers for protonation and thermodynamic data on CO₂ capture by the carbanions of decarboxylation reactions. Employing a combined quantum mechanical and molecular mechanical simulation approach, we investigated the decarboxylation reactions of a series of organic carboxylate compounds in aqueous and in dimethylformamide solutions, revealing that the reverse carboxylation barriers in solution are fully induced by solvent effects. A linear Bell-Evans-Polanyi relationship was found between the rates of decarboxylation and the Gibbs energies of reaction, indicating diminishing recombination barriers in DMF. In contrast, protonation of the carbanions by the DMF solvent has large free energy barriers, rendering the competing exchange of isotope-labeled CO₂ reversible in DMF. The finding of an intricate interplay of carbanion stability and solute-solvent interaction in decarboxylation and carboxylation could be useful to designing novel materials for CO₂ capture.

Metals likely promoted protometabolism in early ocean alkaline hydrothermal systems

One of the most plausible scenarios of the origin of life assumes the preceding prebiotic autotrophic metabolism in sulfide-rich hydrothermal vent environments. However, geochemical mechanisms to harness the reductive power provided by hydrothermal systems remain to be elucidated. Here, we show that, under a geoelectrochemical condition realizable in the early ocean hydrothermal systems, several metal sulfides (FeS, Ag2S, CuS, and PbS) undergo hour- to day-scale conversion to the corresponding metals at ≤-0.7 V (versus the standard hydrogen electrode). The electrochemically produced FeS-Fe0 assemblage promoted various reactions including certain steps in the reductive tricarboxylic acid cycle with efficiencies far superior to those due to pure FeS. The threshold potential is readily generated in the H2-rich alkaline hydrothermal systems that were probably ubiquitous on the Hadean seafloor. Thus, widespread metal production and metal-sustained primordial metabolism were likely to occur as a natural consequence of the active hydrothermal processes on the Hadean Earth.

Hyperpolarized ketone body metabolism in the rat heart

The aim of this work was to investigate the use of ¹³ C-labelled acetoacetate and β-hydroxybutyrate as novel hyperpolarized substrates in the study of cardiac metabolism. [1-¹³ C]Acetoacetate was synthesized by catalysed hydrolysis, and both it and [1-¹³ C]β-hydroxybutyrate were hyperpolarized by dissolution dynamic nuclear polarization (DNP). Their metabolism was studied in isolated, perfused rat hearts. Hyperpolarized [1-¹³ C]acetoacetate metabolism was also studied in the in vivo rat heart in the fed and fasted states. Hyperpolarization of [1-¹³ C]acetoacetate and [1-¹³ C]β-hydroxybutyrate provided liquid state polarizations of 8 ± 2% and 3 ± 1%, respectively. The hyperpolarized T₁ values for the two substrates were 28 ± 3 s (acetoacetate) and 20 ± 1 s (β-hydroxybutyrate). Multiple downstream metabolites were observed within the perfused heart, including acetylcarnitine, citrate and glutamate. In the in vivo heart, an increase in acetylcarnitine production from acetoacetate was observed in the fed state, as well as a potential reduction in glutamate. In this work, methods for the generation of hyperpolarized [1-¹³ C]acetoacetate and [1-¹³ C]β-hydroxybutyrate were investigated, and their metabolism was assessed in both isolated, perfused rat hearts and in the in vivo rat heart. These preliminary investigations show that DNP can be used as an effective in vivo probe of ketone body metabolism in the heart.

Measurement of breath acetone in patients referred for an oral glucose tolerance test

Breath acetone concentrations were measured in 141 subjects (aged 19-91 years, mean = 59.11 years, standard deviation = 12.99 years), male and female, undergoing an oral glucose tolerance test (OGTT), having been referred to clinic on suspicion of type 2 diabetes. Breath samples were measured using an ion-molecule-reaction mass spectrometer, at the commencement of the OGTT, and after 1 and 2 h. Subjects were asked to observe the normal routine before and during the OGTT, which includes an overnight fast and ingestion of 75 g glucose at the beginning of the routine. Several groups of diagnosis were identified: type 2 diabetes mellitus positive (T2DM), n = 22; impaired glucose intolerance (IGT), n = 33; impaired fasting glucose, n = 14; and reactive hypoglycaemia, n = 5. The subjects with no diagnosis (i.e. normoglycaemia) were used as a control group, n = 67. Distributions of breath acetone are presented for the different groups. There was no evidence of a direct relationship between blood glucose (BG) and acetone measurements at any time during the study (0 h: p = 0.4482; 1 h: p = 0.6854; and 2 h: p = 0.1858). Nor were there significant differences between the measurements of breath acetone for the control group and the T2DM group (0 h: p = 0.1759; 1 h: p = 0.4521; and 2 h: p = 0.7343). However, the ratio of breath acetone at 1 h to the initial breath acetone was found to be significantly different for the T2DM group compared to both the control and IGT groups (p = 0.0189 and 0.011, respectively). The T2DM group was also found to be different in terms of ratio of breath acetone after 1 h to that at 2 h during the OGTT. And was distinctive in that it showed a significant dependence upon the level of BG at 2 h (p = 0.0146). We conclude that single measurements of the concentrations of breath acetone cannot be used as a potential screening diagnostic for T2DM diabetes in this cohort, but monitoring the evolution of breath acetone could open a non-invasive window to aid in the diagnosis of metabolic conditions.

The fumarylacetoacetate hydrolase (FAH) superfamily of enzymes: multifunctional enzymes from microbes to mitochondria

Prokaryotic and eukaryotic fumarylacetoacetate hydrolase (FAH) superfamily members, sharing conserved regions that form the so-called FAH-domain, catalyze a remarkable variety of reactions. These enzymes are essential in the metabolic pathways to degrade aromatic compounds in prokaryotes and eukaryotes. It appears that prokaryotic FAH superfamily members evolved mainly to allow microbes to generate energy and useful metabolites from complex carbon sources. We review recent findings, indicating that both prokaryotic and eukaryotic members of the FAH superfamily also display oxaloacetate decarboxylase (ODx) activity. The identification of human FAH domain-containing protein 1 as mitochondrial ODx regulating mitochondrial function supports the new concept that, during evolution, eukaryotic FAH superfamily members have acquired important regulatory functions beyond catabolism of complex carbon sources. Molecular studies on the evolution and function of FAH superfamily members are expected to provide new mechanistic insights in their physiological roles.

Biodegradation of the artificial sweetener acesulfame in biological wastewater treatment and sandfilters

A considerable removal of the artificial sweetener acesulfame (ACE) was observed during activated sludge processes at 13 wastewater treatment plants (WWTPs) as well as in a full-scale sand filter of a water works. A long-term sampling campaign over a period of almost two years revealed that ACE removal in WWTPs can be highly variable over time. Nitrifying/denitrifying sequencing batch reactors (SBR) as well as aerobic batch experiments with activated sludge and filter sand from a water works confirmed that both activated sludge as well as filter sand can efficiently remove ACE and that the removal can be attributed to biologically mediated degradation processes. The lab results strongly indicated that varying ACE removal in WWTPs is not associated with nitrification processes. Neither an enhancement of the nitrification rate nor the availability of ammonium or the inhibition of ammonium monooxygenase by N-allylthiourea (ATU) affected the degradation. Moreover, ACE was found to be also degradable by activated sludge under denitrifying conditions, while being persistent in the absence of both dissolved oxygen and nitrate. Using ion chromatography coupled with high resolution mass spectrometry, sulfamic acid (SA) was identified as the predominant transformation product (TP). Quantitative analysis of ACE and SA revealed a closed mass balance during the entire test period and confirmed that ACE was quantitatively transformed to SA. Measurements of dissolved organic carbon (DOC) revealed an almost complete removal of the carbon originating from ACE, thereby further confirming that SA is the only relevant final TP in the assumed degradation pathway of ACE. A first analysis of SA in three municipal WWTP revealed similar concentrations in influents and effluents with maximum concentrations of up to 2.3 mg/L. The high concentrations of SA in wastewater are in accordance with the extensive use of SA in acid cleaners, while the degradation of ACE in WWTPs adds only a very small portion of the total load of SA discharged into surface waters. No removal of SA was observed by the biological treatment applied at these WWTPs. Moreover, SA was also stable in the aerobic batch experiments conducted with the filter sand from a water works. Hence, SA might be a more appropriate wastewater tracer than ACE due to its chemical and microbiological persistence, the negligible sorbing affinity (high negative charge density) and its elevated concentrations in WWTP effluents.

Characterization of the Vibrio fischeri Fatty Acid Chemoreceptors, VfcB and VfcB2

Bacteria use a wide variety of methyl-accepting chemotaxis proteins (MCPs) to mediate their attraction to or repulsion from different chemical signals in their environment. The bioluminescent marine bacterium Vibrio fischeri is the monospecific symbiont of the Hawaiian bobtail squid, Euprymna scolopes, and encodes a large repertoire of MCPs that are hypothesized to be used during different parts of its complex, multistage lifestyle. Here, we report the initial characterization of two such MCPs from V. fischeri that are responsible for mediating migration toward short- and medium-chain aliphatic (or fatty) acids. These receptors appear to be distributed among only members of the family Vibrionaceae and are likely descended from a receptor that has been lost by the majority of the members of this family. While chemotaxis greatly enhances the efficiency of host colonization by V. fischeri, fatty acids do not appear to be used as a chemical cue during this stage of the symbiosis. This study presents an example of straight-chain fatty acid chemoattraction and contributes to the growing body of characterized MCP-ligand interactions.

Catalyzing decarboxylation by taming carbon dioxide

Decarboxylation reactions on enzymes are consistently much faster than their nonenzymic counterparts. Examination of the potential for catalysis in the nonenzymic reactions revealed that the reaction is slowed by the failure of CO2 to be launched into solution upon C–C bond cleavage. Catalysts can facilitate the reaction by weakening the C–CO2H bond but this is not sufficient. Converting the precursor of CO2 into a precursor of bicarbonate facilitates the forward reaction as does protonation of the nascent carbanion.

Facile C(sp(2))-C(sp(2)) bond cleavage in oxalic acid-derived radicals

Oxalate decarboxylase (OxDC) catalyzes the Mn-dependent conversion of the oxalate monoanion into CO2 and formate. Many questions remain about the catalytic mechanism of OxDC although it has been proposed that the reaction proceeds via substrate-based radical intermediates. Using coupled cluster theory combined with implicit solvation models we have examined the effects of radical formation on the structure and reactivity of oxalic acid-derived radicals in aqueous solution. Our results show that the calculated solution-phase free-energy barrier for C-C bond cleavage to form CO2 is decreased from 34.2 kcal/mol for oxalic acid to only 9.3 kcal/mol and a maximum of 3.5 kcal/mol for the cationic and neutral oxalic acid-derived radicals, respectively. These studies also show that the C-C σ bonding orbital of the radical cation contains only a single electron, giving rise to an elongated C-C bond distance of 1.7 Å; a similar lengthening of the C-C bond is not observed for the neutral radical. This study provides new chemical insights into the structure and stability of plausible intermediates in the catalytic mechanism of OxDC, and suggests that removal of an electron to form a radical (with or without the concomitant loss of a proton) may be a general strategy for cleaving the unreactive C-C bonds between adjacent sp(2)-hybridized carbon atoms.

Observation of superoxide production during catalysis of Bacillus subtilis oxalate decarboxylase at pH 4

This contribution describes the trapping of the hydroperoxyl radical at a pH of 4 during turnover of wild-type oxalate decarboxylase and its T165V mutant using the spin-trap BMPO. Radicals were detected and identified by a combination of EPR and mass spectrometry. Superoxide, or its conjugate acid, the hydroperoxyl radical, is expected as an intermediate in the decarboxylation and oxidation reactions of the oxalate monoanion, both of which are promoted by oxalate decarboxylase. Another intermediate, the carbon dioxide radical anion was also observed. The quantitative yields of superoxide trapping are similar in the wild type and the mutant while it is significantly different for the trapping of the carbon dioxide radical anion. This suggests that the two radicals are released from different sites of the protein.

Identification of FAH domain-containing protein 1 (FAHD1) as oxaloacetate decarboxylase

Fumarylacetoacetate hydrolase (FAH) domain-containing proteins occur in both prokaryotes and eukaryotes, where they carry out diverse enzymatic reactions, probably related to structural differences in their respective FAH domains; however, the precise relationship between structure of the FAH domain and the associated enzyme function remains elusive. In mammals, three FAH domain-containing proteins, FAHD1, FAHD2A, and FAHD2B, are known; however, their enzymatic function, if any, remains to be demonstrated. In bacteria, oxaloacetate is subject to enzymatic decarboxylation; however, oxaloacetate decarboxylases (ODx) were so far not identified in eukaryotes. Based on molecular modeling and subsequent biochemical investigations, we identified FAHD1 as a eukaryotic ODx enzyme. The results presented here indicate that dedicated oxaloacetate decarboxylases exist in eukaryotes.

The role of biotin and oxamate in the carboxyltransferase reaction of pyruvate carboxylase

Pyruvate carboxylase (PC) is a biotin-dependent enzyme that catalyzes the MgATP-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in central metabolism. During catalysis, carboxybiotin is translocated to the carboxyltransferase domain where the carboxyl group is transferred to the acceptor substrate, pyruvate. Many studies on the carboxyltransferase domain of PC have demonstrated an enhanced oxaloacetate decarboxylation activity in the presence of oxamate and it has been shown that oxamate accepts a carboxyl group from carboxybiotin during oxaloacetate decarboxylation. The X-ray crystal structure of the carboxyltransferase domain from Rhizobium etli PC reveals that oxamate is positioned in the active site in an identical manner to the substrate, pyruvate, and kinetic data are consistent with the oxamate-stimulated decarboxylation of oxaloacetate proceeding through a simple ping-pong bi bi mechanism in the absence of the biotin carboxylase domain. Additionally, analysis of truncated PC enzymes indicates that the BCCP domain devoid of biotin does not contribute directly to the enzymatic reaction and conclusively demonstrates a biotin-independent oxaloacetate decarboxylation activity in PC. These findings advance the description of catalysis in PC and can be extended to the study of related biotin-dependent enzymes.

One-pot decarboxylative acylation of N-, O-, S-nucleophiles and peptides with 2,2-disubstituted malonic acids

Monocarbonyl activation of 2,2-disubstituted malonic acids with benzotriazole leads to decarboxylation of one of the carboxy groups and formation of a CH bond. Intermediate carbonyl benzotriazoles then readily acylate nucleophilic reagents and peptides resulting in libraries of conjugates and peptidomimetics.

An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases

Malate and lactate dehydrogenases (MDH and LDH) are homologous, core metabolic enzymes that share a fold and catalytic mechanism yet possess strict specificity for their substrates. In the Apicomplexa, convergent evolution of an unusual LDH from MDH produced a difference in specificity exceeding 12 orders of magnitude. The mechanisms responsible for this extraordinary functional shift are currently unknown. Using ancestral protein resurrection, we find that specificity evolved in apicomplexan LDHs by classic neofunctionalization characterized by long-range epistasis, a promiscuous intermediate, and few gain-of-function mutations of large effect. In canonical MDHs and LDHs, a single residue in the active-site loop governs substrate specificity: Arg102 in MDHs and Gln102 in LDHs. During the evolution of the apicomplexan LDH, however, specificity switched via an insertion that shifted the position and identity of this 'specificity residue' to Trp107f. Residues far from the active site also determine specificity, as shown by the crystal structures of three ancestral proteins bracketing the key duplication event. This work provides an unprecedented atomic-resolution view of evolutionary trajectories creating a nascent enzymatic function.

Metabolic evolution of a deep-branching hyperthermophilic chemoautotrophic bacterium

Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here we present the whole-genome metabolic network of this organism and examine in detail the driving forces that have shaped it. We make extensive use of phylometabolic analysis, a method we recently introduced that generates trees of metabolic phenotypes by integrating phylogenetic and metabolic constraints. We reconstruct the evolution of a range of metabolic sub-systems, including the reductive citric acid (rTCA) cycle, as well as the biosynthesis and functional roles of several amino acids and cofactors. We show that A. aeolicus uses the reconstructed ancestral pathways within many of these sub-systems, and highlight how the evolutionary interconnections between sub-systems facilitated several key innovations. Our analyses further highlight three general classes of driving forces in metabolic evolution. One is the duplication and divergence of genes for enzymes as these progress from lower to higher substrate specificity, improving the kinetics of certain sub-systems. A second is the kinetic optimization of established pathways through fusion of enzymes, or their organization into larger complexes. The third is the minimization of the ATP unit cost to synthesize biomass, improving thermodynamic efficiency. Quantifying the distribution of these classes of innovations across metabolic sub-systems and across the tree of life will allow us to assess how a tradeoff between maximizing growth rate and growth efficiency has shaped the long-term metabolic evolution of the biosphere.

Assigning the EPR fine structure parameters of the Mn(II) centers in Bacillus subtilis oxalate decarboxylase by site-directed mutagenesis and DFT/MM calculations

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.

Chemical and technical challenges in the analysis of central carbon metabolites by liquid-chromatography mass spectrometry

This review deals with chemical and technical challenges in the analysis of small-molecule metabolites involved in central carbon and energy metabolism via liquid-chromatography mass-spectrometry (LC-MS). The covered analytes belong to the prominent pathways in biochemical carbon oxidation such as glycolysis or the tricarboxylic acid cycle and, for the most part, share unfavorable properties such as a high polarity, chemical instability or metal-affinity. The topic is introduced by selected examples on successful applications of metabolomics in the clinic. In the core part of the paper, the structural features of important analyte classes such as nucleotides, coenzyme A thioesters or carboxylic acids are linked to "problematic hotspots" along the analytical chain (sample preparation and-storage, separation and detection). We discuss these hotspots from a chemical point of view, covering issues such as analyte degradation or interactions with metals and other matrix components. Based on this understanding we propose solutions wherever available. A major notion derived from these considerations is that comprehensive carbon metabolomics inevitably requires multiple, complementary analytical approaches covering different chemical classes of metabolites.

CO2 migration pathways in oxalate decarboxylase and clues about its active site

Oxalate decarboxylase catalyzes the decarboxylation of oxalate to formate and CO2 in the presence of molecular oxygen. This enzyme has two domains, each containing a Mn(II) ion coordinated with three histidine residues. The specific domain in which the decarboxylation process takes place is still a matter of investigation. Herein, the transport of the product, i.e., CO2, from the reaction center to the surface of the enzyme is studied using atomistic molecular dynamics simulations. The specific pathway for the migration of the molecule as well as its microscopic interactions with the amino acid residues lining the path is delineated. Further, the transport of CO2 is shown to occur in a facile manner from only domain I and not from domain II, indicating that the former is likely to be the active site of the enzyme.

A substrate-induced biotin binding pocket in the carboxyltransferase domain of pyruvate carboxylase

Biotin-dependent enzymes catalyze carboxyl transfer reactions by efficiently coordinating multiple reactions between spatially distinct active sites. Pyruvate carboxylase (PC), a multifunctional biotin-dependent enzyme, catalyzes the bicarbonate- and MgATP-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in mammalian tissues. To complete the overall reaction, the tethered biotin prosthetic group must first gain access to the biotin carboxylase domain and become carboxylated and then translocate to the carboxyltransferase domain, where the carboxyl group is transferred from biotin to pyruvate. Here, we report structural and kinetic evidence for the formation of a substrate-induced biotin binding pocket in the carboxyltransferase domain of PC from Rhizobium etli. Structures of the carboxyltransferase domain reveal that R. etli PC occupies a symmetrical conformation in the absence of the biotin carboxylase domain and that the carboxyltransferase domain active site is conformationally rearranged upon pyruvate binding. This conformational change is stabilized by the interaction of the conserved residues Asp(590) and Tyr(628) and results in the formation of the biotin binding pocket. Site-directed mutations at these residues reduce the rate of biotin-dependent reactions but have no effect on the rate of biotin-independent oxaloacetate decarboxylation. Given the conservation with carboxyltransferase domains in oxaloacetate decarboxylase and transcarboxylase, the structure-based mechanism described for PC may be applicable to the larger family of biotin-dependent enzymes.