Purification and characterization of the respiratory nitrate reductase of Bacillus stearothermophilus

The reduced methylviolegen-nitrate reductase of the obligate thermophile, Bacillus stearothermophilus NCA strain 2184 (ATCC 12016), has been purified to electrophoretic homogeneity, 53-fold with a yield of 12,5%. The purification procedure involved solubilization with octyl glucoside, ammonium sulfate precipitation, ion-exchange, and molecular sieve chromatography. The molecular weight of the enzyme was estimated by polyacrylamide gel electrophoresis to be about 210,000. The enzyme possesses two subunits of 150,000 and 44,000 daltons in equimolar ratio, and no cytochrome. There are 6 atoms of nonheme iron and 12 mol of labile sulfide in 1 mol of the purified enzyme. The 44,000-dalton β subunit is the smallest of all the characterized bacterial nitrate reductases and is very close to the size of the β¹ subunit of Escherichia coli. The various β components of other bacterial nitrate reductases are probably derived from this 44,000-dalton subunit.     

EPR spectroscopy and electrospray ionization mass spectrometry reveal distinctive features of the iron site in leukocyte 12-lipoxygenase

The procedure for the expression and purification of recombinant porcine leukocyte 12-lipoxygenase using Escherichia coli [K.M. Richards, L.J. Marnett, Biochemistry 36 (1997) 6692-6699] was updated to make it possible to produce enough protein for physical measurements. Electrospray ionization tandem mass spectrometry confirmed the amino acid sequence. The redox properties of the cofactor iron site were examined by EPR spectroscopy at 25 K following treatment with a variety of fatty acid hydroperoxides. Combination of the enzyme in a stoichiometric ratio with the hydroperoxides led to a g4.3 signal in EPR spectra instead of the g6 signal characteristic of similarly treated soybean lipoxygenase-1. Native 12-lipoxygenase was also subjected to electrospray ionization mass spectrometry. There was evidence for loss of the mass of an iron atom from the protein as the pH was lowered from 5 to 4. Native ions in these samples indicated that iron was lost without the protein completely unfolding.     

Large scale isolation,purification, and partial characterization of the intermediate filament-specific,Ca2+-activated proteinase from porcine kidney and Ehrlich ascites tumor cells: A comparative study

The Ca²⁺-activated, neutral thiol proteinase specific for intermediate filament subunit proteins was isolated at large scale from the postribosomal supernatant of a low-ionic-strength extract of porcine kidney and Ehrlich ascites tumor (EAT) cells, respectively. The purification procedure encompassed DEAE-Sephacel ion exchange chromatography of the material precipitating between 23 and 55% (NH₄)₂SO₄ saturation, followed by hyroxylapatite chromatography and activated thiol Sepharose 4B covalent chromatography. On the average, 25 mg of 62% pure enzyme was obtained from 500 g frozen kidney and 55 mg of 51% pure enzyme from 500 g EAT cells within a week. Both enzyme preparations were free of Ca²⁺-independent proteolytic activities and indistinguishable with respect to their physicochemical and functional properties; their catalytic properties were indistinguishable from those of enzyme purified to homogeneity on arginine methylester Sepharose 4B. Because of this identity, porcine kidney proves to be an inexpensive source for the Ca²⁺-activated proteinase which had previously been isolated and purified at small scale from EAT cells (W. J. Nelson and P. Traub, (1983) J. Biol. Chem.257, 5544–5553). Despite a 38% protein contamination, the partially purified enzyme from porcine kidney is useful for the in vitro study of structure-function relationships of intermediate filaments and their subunit proteins. During affinity chromatography of the partially purified proteinase from EAT cells on arginine methylester Sepharose 4B, a 100-kDa protein was purified which has a high affinity for arginine residues. It also occurs in porcine kidney, although at a considerably lower concentration. Its cellular localization and function remain to be determined.     

L-(+)-Tartrate dehydratase from Pseudomonas putida is an iron-sulphur enzyme

The enzyme L-(+)-tartrate dehydratase has been isolated from extracts of Pseudomonas putida by a one-step procedure involving dye-ligand chromatography. The enzyme loses activity rapidly in the absence of Fe²⁺; concentrated solutions have a brown colour typical of iron-sulphur proteins. Analysis of iron and acid-labile sulphide indicated 3–5 atoms of each per molecule of 100 kDa. The enzyme's structure consists of four subunits, two each of 23 and 27 kDa.     

Purification and Properties of Glyoxysomal Cuprozinc Superoxide Dismutase from Watermelon Cotyledons (Citrullus vulgaris Schrad)

A glyoxysomal copper,zinc-containing superoxide dismutase (EC 1.15.1.1) was purified to homogeneity, for the first time, from watermelon cotyledons (Citrullus vulgaris Schrad.). The stepwise purification procedure consisted of acetone precipitation, batch anion-exchange chromatography, anion-exchange Fast Protein Liquid Chromatography and gel-filtration column chromatography. Pure copper,zinc-superoxide dismutase (Cu,Zn-SOD II) had a specific activity of 1211 units per milligram protein and was purified 400-fold, with a yield of 8 micrograms enzyme per gram cotyledon. The glyoxysomal Cu,Zn-SOD had a relative molecular weight of about 33,000 and was composed of two equal subunits of 16,500 Daltons. Metal analysis showed that the enzyme, unlike other Cu,Zn-SODs, contained 1 gram-atom Cu and 1 gram-atom Zn per mole dimer. No iron and manganese were detected. Ultraviolet and visible absorption spectra were reminiscent of other copper,zinc-superoxide dismutases.     

Characterization of the ω-hydroxylase of Pseudomonas oleovorans as a nonheme iron protein

The ω-hydroxylase of Pseudomonas oleovorans, which catalyzes the hydroxylation of fatty acids and alkanes and the epoxidation of alkenes in the presence of a reduced pyridine nucleotide, a reductase, rubredoxin, and molecular oxygen, has been purified to electrophoretic homogeneity. Octane hydroxylation and octadiene epoxidation activities appear to remain at a constant ratio during the purification procedure. The hydroxylase has been characterized as a nonheme iron protein containing one iron atom and one cysteine residue per polypeptide chain of molecular weight 40,800. The enzyme is inhibited by cyanide, and activity is restored upon removal of the cyanide by dialysis. Iron is removed from the enzyme by dialysis against EDTA provided that a reducing agent such as dithionite or ascorbate is also added, and enzyme activity is restored by the addition of ferrous ions to the apohydroxylase.     

Nonidentical subunits of pyrocatechase from Pseudomonas arvilla C-1.

Pyrocatechase [catechol:oxygen, 1,2-oxidoreductase (decyclizing), EC 1.13.11.1] from Pseudomonas arvilla C-1 has been reported to contain 2 g atoms of iron/mol of enzyme, based on a molecular weight of 90,000, determined by sedimentation and diffusion constants (Y. Kojima, H. Fujisawa, A. Nakazawa, T. Nakazawa, F. Kanetsuna, H. Taniuchi, M. Nozaki, and O. Hayaishi, 1967, J. Biol. Chem., 242, 3270–3278). The molecular weight was estimated again by sedimentation equilibrium and Sephadex G-200 gel filtration and found to be 63,000 and 60,000, respectively. The enzyme was also found to contain 1 g atom of iron/mol of enzyme, based on a molecular weight of 63,000. The enzyme was dissociated into two bands on polyarcylamide gel electrophoresis in the presence of either sodium dodecyl sulfate or 8 m urea, and was separated into two subunits, α and β, by CM-cellulose chromatography using a buffer solution containing 8 m urea. The molecular weights of the α and β subunits were determined to be 30,000 and 32,000, respectively, by sodium dodecyl sulfate-gel electrophoresis. The NH₂-terminal sequences of these subunits determined by Edman degradation were as follows: α subunit, Thr-Val-Asn-Ile-Ser-His-Thr-Ala-Gln-Ile-Gln-Gln-Phe-Phe-Gln-Gln-(X)-(X)-Gly -Phe-Gly; β subunit, Thr-Val-Lys-Ile-Ser-His-Thr-Ala-Asp-Ile-Gln-Ala-Phe-Phe-Asn-Gln-Val-(X)-Gly-Leu-Asx. The COOH-terminal amino acid residues were determined to be alanine for the α subunit and glycine for the β subunit by three different methods: carboxypeptidase digestion, tritium labeling, and hydrazinolysis. These results indicate that the enzyme consists of two nonidentical subunits, α and β.     

Properties of pig heart aconitase

Comparison of pig heart aconitase (Kennedy et al., 1972) with yeast (Candida lipolytica) aconitase (Suzuki et al., 1973) reveals similarities in molecular weight and iron content but not in sulphide content. Comparison with the Mildvan & Villafranca (1971) pig heart aconitase preparation reveals differences in iron ligands, specific activity and other properties; these differences possibly arise from protein association as pig heart protein associates under a variety of conditions. The electron spin resonance spectrum, g 4.25, and the low molar relaxivity, 473m⁻¹·s⁻¹, of water H⁺ suggest the presence of high-spin Fe(III) unco-ordinated to water in the enzyme. The iron chromophore on acid titration at 320nm gives a curve with an inflexion at pH4.2. Ten of 16 expected thiol equivalents are titrated with p-hydroxymercuribenzoate suggesting the presence of cystine as well as cysteine residues. Inhibition of the activation of inactive (activatable) enzyme is sigmoidally related to the molar ratio, p-hydroxymercuribenzoate/enzyme with 10–11mol of mercurial compound causing complete inhibition. Active enzyme, free from activating reagents, requires high molar ratios of mercurial compound for rapid inhibition. In terms of p-hydroxymercuribenzoate the enzyme then lacks an essential thiol group.     

Biochemical and Genetic Evidence for meta-Ring Cleavage of 2,4,5-Trihydroxytoluene in Burkholderia sp. Strain DNT

2,4,5-Trihydroxytoluene (THT) oxygenase from Burkholderia sp. strain DNT catalyzes the conversion of THT to an unstable ring fission product. Biochemical and genetic studies of THT oxygenase were undertaken to elucidate the mechanism of the ring fission reaction. The THT oxygenase gene (dntD) was previously localized to the 1.2-kb DNA insert subcloned in the recombinant plasmid designated pJS76 (W. C. Suen and J. C. Spain, J. Bacteriol. 175:1831–1837, 1993). Analysis of the deduced amino acid sequence of DntD revealed the presence of the highly conserved residues characteristic of the catechol 2,3-dioxygenase gene family I. The deduced amino acid sequence of DntD corresponded to a molecular mass of 35 kDa. The native molecular masses for the THT oxygenase estimated by using gel filtration chromatography and nondenaturing gel electrophoresis were 67.4 and 77.8 kDa, respectively. The results suggested that the native protein consists of two identical subunits. The colorless protein contained 2 mol of iron per mol of protein. Stimulation of activity in the presence of ferrous iron and ascorbate suggested a requirement for ferrous iron in the active site. The properties of the enzyme are similar to those of the catechol 2,3-dioxygenases (meta-cleavage dioxygenases). In addition to THT, the enzyme exhibited activity towards 1,2,4-benzenetriol, catechol, 3- and 4-methylcatechol, and 3- and 4-chlorocatechol. The chemical analysis of the THT ring cleavage product showed that the product was 2,4-dihydroxy-5-methyl-6-oxo-2,4-hexadienoic acid, consistent with extradiol ring fission of THT.     

Molecular and kinetic properties of purified γ-glutamyl transpeptidase from yeast (Saccharomyces cerevisiae)

The enzyme γ-glutamyl transpeptidase was purified from the yeast Saccharomyces cerevisiae by a procedure involving protamine sulfate treatment, chromatography on DEAE-Sephadex A 50, salt fractionation, successive chromatography on Sephadex G 150 and lentil lectin sepharose 6B. The procedure achieves 25 % yield and 4200-fold purification. The final preparation is a glycoprotein (M, 90 000) containing 31.4 % carbohydrates and composed of two non-identical subunits (M, 64 000 and 23 000). The specificity patterns of the yeast enzyme are rather similar to those of mammalian and higher plant transpeptidases. The enzyme mechanism might be of the double displacement (ping-pong) type.     

Improved method for rapid purification of protein kinase from streptomycetes

Protein kinase from Streptomyces lincolnensis was purified nearly to homogeneity using a high performance liquid chromatography (HPLC) and a Pharmacia FPLC system. The procedure used employed column chromatography on DE-53, followed by FPLC affinity chromatography with serine- or threonine-Sepharose (prepared as described in this paper) and gel filtration using a Superose 12 or TSK G3000SW column. Starting with 3.5 g of mycelial proteins, ∼ 1 mg of pure enzyme was obtained. The procedure is simple and highly reproducible. The protein kinase thus obtained was nearly pure by silver staining after sodium dodecyl sulfate-polyacrylaminde gel electrophoresis. The purified protein kinase phosphorylated substrate proteins at the seryl residues.     

A facile method of isolation for the iron molybdenum cofactor of nitrogenase and bacterial ferritin from extracts of azotobacter vinelandii

An alternative method has been developed for the isolation of both the iron molybdenum cofactor of nitrogenase (FeMoco), a small molecular weight FeMoS cluster which is the putative nitrogen- reducing site of the enzyme, and bacterioferritin, an iron storage protein similar to other ferritins, but containing heme prosthetic groups. Previously the isolation of these two species, the characterization of which is of significant current interest, has been dependent on the purification of the nitrogenase enzyme from Azotobacter vinelandii. Out new procedure eliminates the use of the anaerobic column chromatography necessary to obtain pure nitrogenase components, involving instead the heat and RNAase/ DNAase treatment of crude extracts of ruptured cells followed by sedimentation (150000 × g for 18 h) of both the 'nitrogenase complex' and bacterioferritin. The redissolved pellet from this centrifugation yields the pure crystalline bacterioferritin on addition of Mg²⁺. and cooling, the iron content of the protein being higher by this method than in previous reports. Likewise, denaturation by acid/base treatment of this protein mixture yields a precipitate which can be extracted with either N-methylformamide or N,N-dimethylformamide containing dithionite ion to yield solutions of FeMoco, as evidenced by UW 45 reconstitution and EPR spectral criteria. Unfortunately, preparations of FeMoco obtained by this method have a variable, but consistently low, Fe/Mo ratio and additional visible spectral features, indicating that they are significantly less pure than that those generated from purified nitrogenase. The aqueous supernatant from the denaturation also yields bacterioferritin, but with a lower iron content than that from the direct crystallization method.     

Purification and properties of D-3-hydroxybutyrate dehydrogenase from Paracoccus denitrificans

D-3-Hydroxybutyrate dehydrogenase from Paracoccus denitrificans has been purified to near homogeneity. The enzyme was prepared using DEAE-cellulose chromatography, affinity chromatography on immobilized Cibacron blue (Matrex Gel Blue A) and gel permeation chromatography. The pure enzyme was obtained by chromatofocusing as the final isolation step. The purification procedure yielded the enzyme with a specific activity of about 100 units/mg protein. The enzyme is specific for D-3-hydroxybutyrate and NAD and it exhibits anomalous kinetics (hysteresis) at low enzyme and coenzyme concentrations. It is relatively stable in the presence of EDTA at pH 7–8 higer salt concentrations. D-3-Hydroxybutyrate dehydrogenase is a tetramer with a molecular weight of 130 000 ± 10 000, its isoelectric point equals 5.10 ± 0.05. The enzyme is applicable to the determination of acetoacetate and D-3-hydroxybutyrate concentrations.     

l-Myoinositol-1-phosphate synthase from Neurospora crassa: Purification to homogeneity and partial characterization

The purification procedure of milligram quantities of stable myoinositol-1-phosphate synthase (EC 5.5.1.4) from Neurospora crassa is reported. The procedure includes: (a) (NH₄)₂SO₄ and protamine sulfate precipitations, (b) gel filtration in Ultrogel AcA-34 (LKB), (c) DEAE-cellulose chromatography, (d) AH-Sepharose 4B chromatography, and (e) calcium phosphate gel chromatography. The enzyme is considered pure according to the following criteria: (a) gel filtration, (b) sucrose density gradient centrifugation, (c) polyacrylamide gel electrophoresis, and (d) isoelectric focusing technique. The molecular weight estimated by gel filtration chromatography and sucrose density gradient centrifugation is 345,000. The subunit molecular weight is 59,000. The active enzyme seems to posses an hexameric structure. The isoelectric point estimated for the pure enzyme is 5.2. The enzyme was optimally stimulated by 10 mm (NH₄)₂SO₄ and by 50 mm KCl, while NaCl had a minor inhibitory effect at higher concentrations. The divalent cations Mg²⁺ and Mn²⁺ were inhibitory only at nonphysiological concentrations. The enzymatic activity after the salt fractionation steps was about 33% NAD⁺ independent; but with purification the resulting homogeneous enzyme showed less than 5% NAD⁺-independent activity.     

Random mutagenesis of the arylacetonitrilase from Pseudomonas fluorescens EBC191 and identification of variants,which form increased amounts of mandeloamide from mandelonitrile

The nitrilase from Pseudomonas fluorescens EBC191 was modified by introducing random mutations via error-prone PCR techniques in order to obtain nitrilase variants, which form increased amounts of mandeloamide from racemic mandelonitrile. A screening system was established and experimentally optimized, which allowed the screening of nitrilase variants with the intended phenotype. This system was based on the simultaneous expression of nitrilase variants and the mandeloamide converting amidase from Rhodococcus rhodochrous MP50 in recombinant Escherichia coli cells. The formation of increased amounts of mandeloamide from mandelonitrile by the nitrilase variants was detected after the addition of hydroxylamine and ferric iron ions by taking advantage of the acyltransferase activity of the amidase, which resulted in the formation of coloured iron(III)–hydroxamate complexes from mandeloamide. The system was applied for the screening of libraries of nitrilase variants and 30 enzyme variants identified, which formed increased amounts of mandeloamide from racemic mandelonitrile. The increase in amide formation was quantified by high-performance liquid chromatography and the genes encoding the relevant nitrilase variants sequenced. Thus, different types of mutations were identified. One group of mutants carried different deletions at the carboxy-terminus. The other types of variants carried amino acid exchanges in positions that had not been related previously to an increased amide formation. Finally, a nitrilase variant was created by combining two independently obtained point mutations. This enzyme variant demonstrated a true nitrile hydratase activity as it formed mandeloamide and mandelic acid in a ratio of about 19:1 from racemic mandelonitrile.     

Isolation of β-N-acetyl-d-hexosaminidases from lupin seed

A rapid procedure for the isolation of β-N-acetyl-d -hexosaminidase from lupin seed meal is described. This involves affinity chromatography of a seed extract on concanavalin A, followed by chromatography on DEAE-Sepharose. The purified enzyme was obtained in three forms, hexosaminidases A, B and B₁, capable of hydrolysing both p-nitrophenyl β-2-acetamido-2-deoxy-d-glucopyranoside and p-nitrophenyl β-2-acetamido-2-deoxy-d-galactopyranoside. Enzyme A was relatively less active towards the galactosaminide substrate, than were the B forms of the enzyme.     

Purification of rat chondrosarcoma xylosyltransferase

The chondroitin sulfate chain-initiating enzyme, UDP-d-xylose:core protein β-d-xylosyltransferase has been purified over 600-fold from the high-speed supernatant fraction of a rat chondrosarcoma. The purification procedure involved differential centrifugation, gel chromatography on Sephadex G-200, and affinity chromatography on a matrix consisting of core protein bound to Sepharose. The purified enzyme was homogenous by electrophoretic and immunological criteria, had a molecular weight between 95,000 and 100,000 and contained approximately 10% carbohydrate. The K_m value for UDP-xylose was 1 × 10^?5, m and for the core-protein acceptor was 330 mg/liter.     

Purification and characterization of acetate kinase from veillonella alcalescens ATCC 17748.

Acetate kinase was isolated in highly purified form from Veillonella alcalescens through a combination of ammonium sulfate fractionation, DEAE-Sephadex column chromatography, and gel filtration. It had a specific activity about 60-fold that of crude extracts. Purity of the enzyme preparation was estimated to be 90% as judged by polyacrylamide gel electrophoresis. The molecular weights of the enzyme as determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis and by gel filtration were 43,000 and 66,000, respectively. Succinate was unnecessary for the activity of this enzyme. This result is markedly different from that reported previously (Bowman, C. M. et al., 1976, J. Biol. Chem. 251, 3117–3121). This may, however, be due to the difference in bacterial strains used. The enzyme reaction with propionate was equal to about two-thirds that of its reaction with acetate. Apparent K_m values for ATP, acetate, ADP, and acetylphosphate were about 2, 30,0.3, and 1.2 mm, respectively. Phosphate donors, ATP, and acetylphosphate exhibited cooperativity while phosphate acceptors, ADP, acetate, and propionate did not. The enzyme had a broad pH optimum from 7.2 to 10, and required magnesium ions, whose optimal molar ratio to ATP was 1:1. The activity was inhibited by several SH-inhibitors, but not stimulated by free SH groups.     

Partial purification and further characterization of the novel endoglucosaminidase from human serum that hydrolyses 4-methylumbelliferyl-N-acetyl-β-d-chitotetraoside (MU-TACT hydrolase)

A novel endoglucosaminidase, originally described by Den Tandt et al. [Int. J. Biochem.20 (1988), 713–719] and bearing the provisional name MU-TACT hydrolase, was purified from human serum 56,000-fold by means of ammonium sulphate precipitation, anion-exchange chromatography, Con A-Sepharose chromatography and gel filtration on Sepharose CL-6B followed by Superose 12HR. Based on the latter technique the native apparent molecular weight of the enzyme appeared to be equal to that of myoglobin, being approx. 17 kD. The enzyme eluted clearly at a different volume than lysozyme. MU-TACT is a commercially available substrate for lysozyme. For unknown reasons two major peptides co-purify that give bands on SDS-PAGE of 55–60 and 31 kD, respectively.     

The molecular properties of the copper enzyme galactose oxidase

Galactose oxidase (EC 1.1.3.9) has been purified 140-fold by DEAE- and CM-cellulose chromatography from cultures of Polyporus circinatus. The enzyme has a molecular weight of 68,000 ± 3,000 as determined by sedimentation equilibrium, sodium dodecyl sulfate-acrylamide gel electrophoresis, Sephadex G-150 chromatography, and osmometry. Galactose oxidase is a single-chain protein which does not self-associate. Charge isozymes of the enzyme are detected by ion-exchange chromatography and gel electrophoresis. The amino acid composition determined herein is significantly different from that previously reported (Kelly-Falcoz, F., Greenberg, H., And Horecker, B. L. (1965) J. Biol. Chem.240, 2966–2970). The enzyme contains 1% by weight of neutral carbohydrate.Galactose oxidase contains 1 g-atom of copper per 70,000 g of protein. The metal does not contribute to the electrophoretic or isozymic properties of the protein. However, the sedimentation coefficients of the holo- and apoenzymes, 4.76S and 4.83S, respectively, do suggest that small differences in protein conformation accompany the removal of the copper from the holoenzyme.Attempted sulfhydryl group titration of galactose oxidase shows that the holoenzyme is resistant to denaturation. However, in β-mercaptoethanol-guanidine HCl 5 half-cystine residues are titrated in the apoenzyme. On a dry-weight basis, the E_1cm^1% value for galactose oxidase at 280 nm is 15.4. Galactose oxidase has an isoelectric point above pH 10 which is a probable source of some of its anomalous behavior in physical measurements and enzyme-activity determinations.