Isolation and biochemical characterization of maleic-acid hydratase, an iron-requiring hydro-lyase

Stereochemistry of enzymatic water addition to C=C bonds

Water addition to carbon-carbon double bonds using hydratases is attracting great interest in biochemistry. Most of the known hydratases are involved in primary metabolism and to a lesser extent in secondary metabolism. New hydratases have recently been added to the toolbox, both from natural sources or artificial metalloenzymes. In order to comprehensively understand how the hydratases are able to catalyse the water addition to carbon-carbon double bonds, this review will highlight the mechanistic and stereochemical studies of the enzymatic water addition to carbon-carbon double bonds, focusing on the syn/anti-addition and stereochemistry of the reaction.

The selective addition of water

Water is omnipresent and unreactive. How to speed up water addition and even make it selective are highlighted in this perspective.

Purification and Characterization of Maleate Hydratase from Pseudomonas pseudoalcaligenes

Maleate hydratase (malease) from Pseudomonas pseudoalcaligenes has been purified. The purified enzyme (98% pure) catalyzes the stereospecific addition of water to maleate and citraconate (2-methylmaleate), forming d-(+)-malate and d-(+)-citramalate, respectively. 2,3-Dimethylmaleate was also a substrate for malease. The stability of the enzyme was dependent on the protein concentration and the addition of dicarboxylic acids. The purified enzyme (89 kDa) consisted of two subunits (57 and 24 kDa). No cofactor was required for full activity of this colorless enzyme. Maximum enzyme activity was measured at pH 8 and 45 degrees C. The K(m) for maleate was 0.35 mM, and that for citraconate was 0.20 mM. Thiol reagents, such as p-chloromercuribenzoate and iodoacetamide, and sodium dodecyl sulfate completely inhibited malease activity. Malease activity was competitively inhibited by d-malate (K(i) = 0.63 mM) and d-citramalate (K(i) = 0.083 mM) and by the substrate analog 2,2-dimethylsuccinate (K(i) = 0.025 mM). The apparent equilibrium constants for the maleate, citraconate, and 2,3-dimethylmaleate hydration reactions were 2,050, 104, and 11.2, respectively.

Distribution of orphan metabolic activities

A significant fraction (30-40%) of known metabolic activities is currently orphan. Although orphan activities have been biochemically characterized, we do not know a single gene responsible for these reactions in any organism. The problem of orphan activities represents one of the major challenges of modern biochemistry. We analyze the distribution of orphans across biochemical space, through years of enzymatic characterization, and by biological organisms. We find that orphan metabolic activities have been accumulating for many decades. They are widely distributed across enzymatic functional space and metabolic network neighborhoods. Although orphans are relatively more abundant in less studied species, over half of orphan reactions have been experimentally characterized in more than one organism. Shrinking the space of orphan activities will likely require a close collaboration between computational and experimental laboratories.

Enzymology and evolution of the pyruvate pathway to 2-oxobutyrate in Methanocaldococcus jannaschii

The archaeon Methanocaldococcus jannaschii uses three different 2-oxoacid elongation pathways, which extend the chain length of precursors in leucine, isoleucine, and coenzyme B biosyntheses. In each of these pathways an aconitase-type hydrolyase catalyzes an hydroxyacid isomerization reaction. The genome sequence of M. jannaschii encodes two homologs of each large and small subunit that forms the hydrolyase, but the genes are not cotranscribed. The genes are more similar to each other than to previously characterized isopropylmalate isomerase or homoaconitase enzyme genes. To identify the functions of these homologs, the four combinations of subunits were heterologously expressed in Escherichia coli, purified, and reconstituted to generate the iron-sulfur center of the holoenzyme. Only the combination of MJ0499 and MJ1277 proteins catalyzed isopropylmalate and citramalate isomerization reactions. This pair also catalyzed hydration half-reactions using citraconate and maleate. Another broad-specificity enzyme, isopropylmalate dehydrogenase (MJ0720), catalyzed the oxidative decarboxylation of beta-isopropylmalate, beta-methylmalate, and d-malate. Combined with these results, phylogenetic analysis suggests that the pyruvate pathway to 2-oxobutyrate (an alternative to threonine dehydratase in isoleucine biosynthesis) evolved several times in bacteria and archaea. The enzymes in the isopropylmalate pathway of leucine biosynthesis facilitated the evolution of 2-oxobutyrate biosynthesis through the introduction of a citramalate synthase, either by gene recruitment or gene duplication and functional divergence.

The potential of lyases for the industrial production of optically active compounds

Lyases catalyse the cleavage of C-C, C-N, C-O and other bonds by elimination to produce double bonds or, conversely, catalyse the addition of groups to double bonds. These enzymes do not require cofactor recycling, show an absolute stereospecificity and can give a theoretical yield of 100%, compared with only 50% for enantiomeric resolutions. Lyases are therefore attracting considerable interest as biocatalysts for the production of optically active compounds, and have already found application in several large commercial processes.

Thermodynamics of the maleate and citraconate hydration reactions catalysed by malease from Pseudomonas pseudoalcaligenes

Malease from Pseudomonas pseudoalcaligenes catalyses the hydration of both maleate and citraconate to D-malate and D-citramalate, respectively. The Kapp for these hydration reactions were 2050 and 104, respectively, under standard biochemical conditions (25 degrees C, pH 7.0, I = 0.1). The influence of the pH (6.0-8.5) on Kapp was determined. The Gibbs-free-energy changes under standard biochemical conditions for the hydration of the dianionic acids were calculated to be -19.28 kJ.mol-1 and -11.65 kJ.mol-1, respectively. From the obtained data together with data from the literature, the Gibbs free energy of formation of maleate2- and citraconate2- were calculated to be -588.91 kJ.mol-1 and -600.56 kJ.mol-1, respectively. The influence of the temperature (10-40 degrees C) on Kapp was determined for both hydration reactions. The enthalpy change (delta H degrees') and entropy change (delta S degrees') under standard biochemical conditions for the maleate2- (delta H degrees' = 18.07 kJ.mol-1, delta S degrees' = 2.94 J.mol-1 x K-1) and citraconate2- (delta H degrees' = -22.55 kJ.mol-1, delta S degrees' = -35.92 kJ.mol-1 x K-1) hydration reactions were calculated. The reaction rate of malease from Ps. pseudoalcaligenes was studied for both hydration reactions as a function of temperature. From these studies, the Gibbs free energies of activation for the maleate and citraconate hydration reactions catalysed by malease from Ps. pseudoalcaligenes were calculated to be 62.21 kJ.mol-1 and 63.43 kJ.mol-1, respectively.

In Azotobacter vinelandii hydrogenase, substitution of serine for the cysteine residues at positions 62, 65, 294, and 297 in the small (HoxK) subunit affects H2 oxidation [corrected]

The essential role of the small (HoxK) subunit of hydrogenase of Azotobacter vinelandii in H2 oxidation was established. This was achieved by modification of the two Cys-X2-Cys amino acid motifs at the N and C termini of the HoxK subunit (Cys-62, -65, -294, and -297). The Cys codons were individually mutated to Ser codons. Modifications in these two motifs resulted in loss of hydrogenase activity. At the N terminus, the mutations of the codons for the motif Cys-62-Thr-Cys-64-Cys-65 decreased the activity of hydrogenase to levels no higher than 30% of those of the parental strain. H2 oxidation with the alternate electron acceptors methylene blue and benzyl viologen was decreased. H2 evolution and exchange activities were also affected. Cys-64 possibly substitutes for either Cys-62 or Cys-65, allowing for partial activity. Mutation of the codons for Cys-294 and Cys-297 to Ser codons resulted in no hydrogenase activity. The results are consistent with alterations of the ligands of FeS clusters in the HoxK subunit of hydrogenase [corrected].

Screening for microorganisms producing D-malate from maleate

More than 300 microorganisms were screened for their ability to convert maleate into D-malate as a result of the action of maleate hydratase. Accumulation of fumarate during incubation of permeabilized cells with maleate was shown to be indicative of one of the two enzymes known to transform maleate. The ratio in which fumarate and malate accumulated could be used to estimate the enantiomeric composition of the malate formed. Many strains (n = 128) were found to be capable of converting maleate to D-malate with an enantiomeric purity of more than 97%. Pseudomonas pseudoalcaligenes NCIMB 9867 was selected for more detailed studies. Although this strain was not able to grow on maleate, permeabilized cells were able to degrade maleate to undetectable levels, with a concomitant formation of D-malate. The D-malate was formed with an enantiomeric purity of more than 99.97%.

Iron-sulphur clusters with labile metal ions

A study has been carried out of the redox-linked metal ion uptake processes of the iron-sulphur cluster [3Fe-4S] in the bacterial ferredoxin, Fd III from Desulphovibrio africanus using a combination of electron paramagnetic resonance (EPR) and low-temperature magnetic circular dichroism (MCD) spectroscopy and direct, unmediated electrochemistry of the Fd in a film deposited at a pyrolytic graphite electrode. Reduction of the three-iron cluster is required before a divalent metal ion becomes bound as in the reaction sequence [formula: see text] The redox potentials of these processes and the metal binding constants have been determined. The affinities of the [3Fe-4S]0 cluster for divalent ions lie in the sequence Cd greater than Zn much greater than Fe. In addition, specific binding of a monovalent ion, Thallium(I), is detected for [3Fe-4S]1+ as well as for [3Fe-4S]0. The results provide a clear and quantitative demonstration of the capability of the open triangular tri-mu 2-sulphido face of a [3Fe-4S] cluster to bind a variety of metal ions if the protein environment permits. In each case the entering metal ion is coordinated by at least one additional ligand which may be from solvent (H2O or OH-) or from a protein side chain (e.g., carboxylate from aspartic acid). Hence the [3Fe-4S] core can be a redox-linked sensor of divalent metal ions, Fe(II) or Zn(II), that may trigger conformational change.

Disposition of [14C]furan in the male F344 rat

In a recently completed 2-yr bioassay, furan was found to induce cholangiocarcinomas at high incidence in rats. The disposition of single and multiple gavage doses of [2,5-14C]furan has been determined in male F344 rats to aid in interpretation of that study. In the 24 h after dosing about 80% of the furan-derived radioactivity was eliminated, primarily via urine and expired air. [14C]Carbon dioxide was a major metabolite, indicating that furan ring opening followed by complete oxidation of at least one of the labeled carbons was a major part of the overall metabolism of furan. Liver contained more furan-derived radioactivity by far than other tissues after 24 h. Approximately 80% of the radioactivity in liver was not extracted by organic solvents and was associated with protein. There was either no binding to DNA or the furan-DNA adduct was not stable to the isolation procedure. Repeated daily administration of [14C]furan resulted in a more or less linear increase in covalent binding through four doses; at this point the amount of nonextractable radioactivity plateaus. Urine contained at least 10 metabolites, again indicating extensive metabolism of the furan ring. From the data obtained in this study it is clear that furan is metabolized to reactive species, apparently primarily in liver, and these intermediates react with protein. The hepatotoxicity resulting from furan exposure may be due to the reaction of furan metabolites with liver macromolecules; the presence of some of these reactive metabolites following chronic exposure to furan may result in cholangiocarcinomas.

19th Sir Hans Krebs lecture. Engineering of protein bound iron-sulfur clusters. A tool for the study of protein and cluster chemistry and mechanism of iron-sulfur enzymes

An increasing number of iron-sulfur (Fe-S) proteins are found in which the Fe-S cluster is not involved in net electron transfer, as it is in the majority of Fe-S proteins. Most of the former are (de)hydratases, of which the most extensively studied is aconitase. Approaches are described and discussed by which the Fe-S cluster of this enzyme could be brought into states of different structure, ligation, oxidation and isotope composition. The species, so obtained, provided the basis for spectroscopic and chemical investigations. Results from studies by protein chemistry, EPR, Mössbauer, 1H, 2H and 57Fe electron-nuclear double resonance spectroscopy are described. Conclusions, which bear on the electronic structure of the Fe-S cluster, enzyme-substrate interaction and the enzymatic mechanism, were derived from a synopsis of the recent work described here and of previous contributions from several laboratories. These conclusions are discussed and summarized in a final section.

Two biochemically distinct classes of fumarase in Escherichia coli

Biochemical studies with strains of Escherichia coli that are amplified for the products of the three fumarase genes, fumA (FUMA), fumB (FUMB) and fumC (FUMC), have shown that there are two distinct classes of fumarase. The Class I enzymes include FUMA, FUMB, and the immunologically related fumarase of Euglena gracilis. These are characteristically thermolabile dimeric enzymes containing identical subunits of Mr 60,000. FUMA and FUMB are differentially regulated enzymes that function in the citric acid cycle (FUMA) or to provide fumarate as an anaerobic electron acceptor (FUMB), and their affinities for fumarate and L-malate are consistent with these roles. The Class II enzymes include FUMC, and the fumarases of Bacillus subtilis, Saccharomyces cerevisiae and mammalian sources. They are thermostable tetrameric enzymes containing identical subunits Mr 48,000-50,000. The Class II fumarases share a high degree of sequence identity with each other (approx. 60%) and with aspartase (approx. 38%) and argininosuccinase (approx. 15%), and it would appear that these are all members of a family of structurally related enzymes. It is also suggested that the Class I enzymes may belong to a wider family of iron-dependent carboxylic acid hydro-lyases that includes maleate dehydratase and aconitase. Apart from one region containing a Gly-Ser-X-X-Met-X-X-Lys-X-Asn consensus sequence, no significant homology was detected between the Class I and Class II fumarases.

The role of iron in the activation of mannonic and altronic acid hydratases, two Fe-requiring hydro-lyases

D-Altronate hydratase and D-mannonate hydratase belong to a class of Fe2+-requiring enzymes, but the function of iron in these enzymes is largely unknown. Methods are described for the convenient preparation of both these hydratases from Escherichia coli and studies related to metal activation are presented. The enzymes are inactive in the absence of a bivalent metal and a reducing agent such as dithiothreitol. Fe2+ at low concentrations activates the enzymes efficiently, but inhibits them over 2 mM. Furthermore Mn2+ is also capable of activating aldonic acid hydratases and appears to be a constituent of the enzyme active center. A marked synergistic activation is observed in the presence of both ions, raising the possibility that the enzyme has two binding sites for ions. Upon activation, the two aldonic acid hydratases incorporate a single Fe atom and contain no Fe-S core, in contrast to other characterized Fe-hydratases, such as aconitase or maleic acid hydratase. The incorporated iron is losely bound (with Kd about 4.5 mM and 20 mM for mannonate and altronate hydratase, respectively) and can be readily removed with EDTA. The enzymes exhibit no requirement for sulphide ions and are insensitive to thiol reagents. A first-order inhibition is observed with iron chelators and can be removed by competition with excess metal ions. No change in the absorption spectra is observed upon oxidation-reduction or activation with metals. The activated enzymes exhibit no electron paramagnetic (EPR) spectrum under anaerobic conditions; in the presence of oxygen, an intense EPR spectrum develops in Fe2+-activated samples with signal at g = 1.98, which upon reaction of the enzyme with the substrate moves into a species with signals at g = 4.15 and g = 9.07, with EPR parameters very similar to those of oxidized rubredoxins.