Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia)

Royal palm tree peroxidase (RPTP) is a very stable enzyme in regards to acidity, temperature, H₂O₂, and organic solvents. Thus, RPTP is a promising candidate for developing H₂O₂-sensitive biosensors for diverse applications in industry and analytical chemistry. RPTP belongs to the family of class III secretory plant peroxidases, which include horseradish peroxidase isozyme C, soybean and peanut peroxidases. Here we report the X-ray structure of native RPTP isolated from royal palm tree (Roystonea regia) refined to a resolution of 1.85 Å. RPTP has the same overall folding pattern of the plant peroxidase superfamily, and it contains one heme group and two calcium-binding sites in similar locations. The three-dimensional structure of RPTP was solved for a hydroperoxide complex state, and it revealed a bound 2-(N-morpholino) ethanesulfonic acid molecule (MES) positioned at a putative substrate-binding secondary site. Nine N-glycosylation sites are clearly defined in the RPTP electron-density maps, revealing for the first time conformations of the glycan chains of this highly glycosylated enzyme. Furthermore, statistical coupling analysis (SCA) of the plant peroxidase superfamily was performed. This sequence-based method identified a set of evolutionarily conserved sites that mapped to regions surrounding the heme prosthetic group. The SCA matrix also predicted a set of energetically coupled residues that are involved in the maintenance of the structural folding of plant peroxidases. The combination of crystallographic data and SCA analysis provides information about the key structural elements that could contribute to explaining the unique stability of RPTP.     

Thermodynamic characterization of the palm tree Roystonea regia peroxidase stability

The structural stability of a peroxidase, a dimeric protein from royal palm tree (Roystonea regia) leaves, has been characterized by high-sensitivity differential scanning calorimetry, circular dichroism, steady-state tryptophan fluorescence and analytical ultracentifugation under different solvent conditions. It is shown that the thermal and chemical (using guanidine hydrochloride (Gdn-HCl)) folding/unfolding of royal palm tree peroxidase (RPTP) at pH 7 is a reversible process involving a highly cooperative transition between the folded dimer and unfolded monomers, with a free stabilization energy of about 23 kcal per mol of monomer at 25 degrees C. The structural stability of RPTP is pH-dependent. At pH 3, where ion pairs have disappeared due to protonation, the thermally induced denaturation of RPTP is irreversible and strongly dependent upon the scan rate, suggesting that this process is under kinetic control. Moreover, thermally induced transitions at this pH value are dependent on the protein concentration, allowing it to be concluded that in solution RPTP behaves as dimer, which undergoes thermal denaturation coupled with dissociation. Analysis of the kinetic parameters of RPTP denaturation at pH 3 was accomplished on the basis of the simple kinetic scheme N-->kD, where k is a first-order kinetic constant that changes with temperature, as given by the Arrhenius equation; N is the native state, and D is the denatured state, and thermodynamic information was obtained by extrapolation of the kinetic transition parameters to an infinite heating rate. Obtained in this way, the value of RPTP stability at 25 degrees C is ca. 8 kcal per mole of monomer lower than at pH 7. In all probability, this quantity reflects the contribution of ion pair interactions to the structural stability of RPTP. From a comparison of the stability of RPTP with other plant peroxidases it is proposed that one of the main factors responsible for the unusually high stability of RPTP which enhances its potential use for biotechnological purposes, is its dimerization.     

Oxidation of luminol with peroxidase from royal palm leaves

We optimized the conditions for luminol oxidation by hydrogen peroxide in the presence of peroxidase (EC 1.11.1.7) from royal palm leaves (Roystonea regia). The pH range (8.3-8.6) corresponding to maximum chemiluminescence was similar for palm tree peroxidase and horseradish peroxidase. Variations in the concentration of the Tris buffer were accompanied by changes in chemiluminescence. Note that maximum chemiluminescence was observed in the 30 mM solution. The detection limit of the enzyme assay during luminol oxidation by hydrogen peroxide was 1 pM. The specific feature of palm tree peroxidase was the generation of a long-term chemiluminescent signal. In combination with the data on the high stability of palm tree peroxidase, our results indicate that this enzyme is promising for its use in analytical studies.     

Peroxidase from Astragalus maritimus: purification and properties

A peroxidase has been purified to homogeneity from Astragalus maritimus seeds using ammonium sulfate precipitation and chromatography on DEAE-cellulose and hydroxylapatite. The purification obtained was 255 fold. The enzyme preparations were homogenous by the criteria of SDS-PAGE and analytical gel electrofocusing. The protein contained 0.11% of iron that corresponds to a minimum molecular size of 50,700. Determinations of molecular size by SDS-PAGE gave values of 48,000 +/- 1,000 while the one obtained by Sephadex gel filtration was 49,000. The pH optimum of the enzyme was 6.0. The activation energy was estimated to be 6 Kcal/mol. The prosthetic group was shown to be ferriprotoporphyrin IX. The presence of 13% neutral sugars was found. The spectrophotometric analysis showed the presence, in the visible region, of absorption maxima at 403, 490 and 633 nm. The Rz value (A403/A275) was 2.7.     

Suicide inactivation of peroxidase from Chamaerops excelsa palm tree leaves

The concentration and time-dependences and the mechanism of the inactivation of Chamaerops excelsa peroxidase (CEP) by hydrogen peroxide were studied kinetically with four co-substrates (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), guaiacol, o-dianisidine and o-phenylenediamine). The turnover number (r) of H₂O₂ required to complete the inactivation of the enzyme varied for the different substrates, the enzyme most resistant to inactivation (r = 4844) with ABTS being the most useful substrate for biotechnological applications, opening a new avenue of enquiry with this peroxidase.     

Peroxidase from euphorbia characias latex: purification and properties

A peroxidase has been purified to homogeneity from Euphorbia characias latex using ammonium sulfate precipitation and chromatography on DEAE-cellulose, hydroxylapatite and SP-Sephadex columns. The substrate specificity of the enzyme is typical of a plant peroxidase except that it shows no activity with indole-3-acetic acid. The pH optimum of the enzyme was 5.75 and the isoelectric point 7.4. The activation energy was 14 kcal/mol. The prosthetic group was shown to be ferriprotoporphyrin IX. Gel chromatography and PAGE indicate that the purified protein is composed of a single polypeptide chain having a MW of ca 48 000.     

Nucleoside diphosphatase from pig liver: purification and some properties

A procedure is described for purification of nucleoside diphosphatase from pig liver microsomes which avoids exposure of the enzyme to potentially denaturing conditions. The purest fractions obtained have specific activities of approximately 100 units/mg and appear to contain approximately 35% NDPase on a protein basis. Pig liver nucleoside diphosphatase resembles the enzyme obtained from other mammalian tissues in its substrate specificity and in its interaction with MgATP^2? as an allosteric modifier. However the molecular weight of the pig liver enzyme appears higher than that reported for other nucleoside diphosphatases, and activation by MgATP^2? is attributable to an increase in the maximal rate of nucleoside diphosphate hydrolysis rather than to a decrease in K_m. These differences in properties seem to be due to a species difference since similar properties were found with pig liver enzyme prepared by a different extraction procedure. The kinetic parameters which describe the reaction catalyzed by pig liver nucleoside diphosphatase are insensitive to changes in [H⁺]over the range pH 6.5–8.6. The intracellular location of nucleoside diphosphatase is microsomal in both pig and chicken liver.     

Folylpolyglutamate synthetase from beef liver: purification and some properties.

The polypeptide chain of folylpolyglutamate synthetase from beef liver has been isolated and partially characterized. This polypeptide has an apparent molecular weight of 73,000. Its amino-terminal residue is blocked. Amino acid analysis agrees with the hydrophobic properties and the pI (6.0) of this cytosolic enzyme. Polyclonal antibodies to the denatured enzyme have been prepared.     

One-step purification and properties of catalase from leaves of Zantedeschia aethiopica

Catalase (E.C 1.11.1.6) was purified from leaves of Zandedeschia aethiopica to apparent homogeneity by a one-step hydrophobic interaction chromatography on a phenyl Sepharose CL-4B column. The purified enzyme preparation was obtained with a final recovery of enzyme activity of about 61% and a specific activity of 146 U/mg protein. The purified enzyme ran as a single protein band when analyzed both by native PAGE and SDS-PAGE corresponding to an Mr of 220,000 Da, which consists of 4 subunits with identical Mr of 54,000 Da. The pI of purified enzyme was found to be 5.2 by isoelectric focusing on ultrathin polyacrylamide gels. The purified catalase has an optimum temperature of activity at 40 degrees C, whereas it is stable between 0 degrees and 50 degrees C. As regards pH, the enzyme has an optimum activity at pH 7.0 and it is stable in the range pH 6-8. The absorption spectrum of the purified enzyme exhibited 2 peaks at 280 nm and 405 nm.     

Characterising sclerophylly: some mechanical properties of leaves from heath and forest

Although sclerophylly is widespread through the world and is often the dominant leaf-form in mediterranean climates, the mechanical properties of sclerophyllous leaves are poorly understood. The term ”sclerophyllous” means hard-leaved, but biologists also use terms such as tough, stiff and leathery to describe sclerophyllous leaves. The latter term has no precise definition that allows quantification. However, each of the former terms is well-defined in materials engineering, although they may be difficult or sometimes inappropriate to measure in leaves because of their size, shape or composite and anisotropic nature. Two of the most appropriate and practically applicable mechanical properties of sclerophyllous leaves are ”strength” and ”toughness”, which in this study were applied using punching, tearing and shearing tests to 19 species of tree and shrub at Wilson’s Promontory, Australia. The results of these tests were compared with leaf specific mass (LSM) and a sclerophylly index derived from botanists’ ranks. Principal components analysis was used to reduce the set of mechanical properties to major axes of variation. Component 1 correlated strongly with the botanists’ ranks. Overall, leaves ranked as sclerophyllous by botanists were both tough and strong in terms of punching and tearing tests. In addition, tough and strong leaves typically had high toughness and strength per unit leaf thickness. There was also a significant correlation between component 1 and LSM. Although more detailed surveys are required, we argue that sclerophylly should be defined in terms of properties that have precise meanings and are measurable, such as toughness and strength, and that relate directly to mechanical properties as implicit in the term. Received: 4 March 1999 / Accepted: 22 November 1999     

Peroxidase from cultured carrot cells: affinity purification and characteristics

Peroxidase, from cultured carrot cells, has been isolated and purified over Concanavalin-A-Sepharose by lectin affinity chromatography. The enzyme protein registers a gradual enhancement in activity concomitant with the growth of callus. Extracellular (ECP) & intracellular (ICP) peroxidases have been demonstrated in suspension cultures of carrot.     

Purification and some catalytic properties of phosphoglucomutase from maize leaves

Phosphoglucomutase (EC 2.7.5.1, PGM) was purified to homogeneity from maize (Zea mays L.) leaves. The enzyme had specific activity 11. 7 U/mg protein and molecular mass (determined by gel-chromatography) of 133 +/- 4 kD. The molecular mass of PGM subunits determined by SDS-electrophoresis was 66 +/- 3 kD. The enzyme had Km for glucose-1-phosphate and glucose-1,6-diphosphate of 20.0 +/- 0.9 and 16.0 +/- 0.8 &mgr;M, respectively. Concentrations of glucose-1-phosphate and glucose-1,6-diphosphate above 3 and 0.4 mM, respectively, cause substrate inhibition. The enzyme activity was maximal at pH 8.0 and temperature 35 degreesC. Magnesium ions activate the enzyme and manganese ions inhibit it. 3-Phosphoglycerate is an uncompetitive inhibitor of the enzyme (Ki = 1.22 +/- 0.05 mM). Fructose-6-phosphate, 6-phosphogluconate, and ADP activate PGM, whereas ATP, UTP, and AMP inhibit the enzyme. Citrate was also a potent inhibitor, inhibitory effects of isocitrate and cis-aconitate being less pronounced.     

Chicken ornithine transcarbamylase: purification and some properties

Ornithine transcarbamylase [EC 2.1.3.3] has been purified from chick kidney to homogeneity. The molecular weight is 110,000 as determined by gel filtration. Sodium dodecylsulfate polyacrylamide gel electrophoresis of the enzyme showed that the enzyme exists as a trimer of identical subunits of 36,000 daltons like other mammalian species ornithine transcarbamylases. In 0.1 M triethanolamine/HCl, the apparent optimum pH of the purified enzyme was 7.5 in the presence of 5 mM ornithine. The curve shifted toward a more alkaline region with a decrease in ornithine concentration. The specific activity of the purified enzyme as 77 units at pH 7.5. The Km for carbamyl phosphate was 0.11 mM and the Km for ornithine was 1.21 mM. With an increase in pH, a decrease in Km values for ornithine and an increase in the extent of inhibition by ornithine were observed. On using antibody against bovine liver ornithine transcarbamylase, the precipitin lines for the chick and bovine enzymes showed a spur pattern. Even when excess amounts of the antibody were added, the chick enzyme did not lose the activity while the bovine enzyme activity was inhibited completely.     

Partial purification and some properties of beta-phosphoglucomutase from Lactobacillus brevis

A phosphoglucomutase (beta-phosphoglucomutase) specific for beta-glucose 1-phosphate, which catalyzes the beta-glucose 1-phosphate:glucose 6-phosphate interconversion, was 560-fold purified from Lactobacillus brevis strain L6. The isoelectric point of beta-phosphoglucomutase was 3.8 and it had an apparent molecular weight of 29,000 estimated by gel chromatography. The enzyme required a divalent cation (Mn2+ greater than Mg2+ greater than Ni2+ greater than Co2+) and beta-glucose 1,6-bisphosphate for activity. The equilibrium constant Ke for the reaction beta-D-glucose 1-phosphate in equilibrium D-glucose 6-phosphate at 30 degrees C and pH 6.7 is 18.5. beta-phosphoglucomutase had a pH optimum between 6.3 and 6.8 and appeared to be quite specific: alpha-glucose 1-phosphate, alpha- or beta-galactose 1-phosphate and alpha- or beta-N-acetylglucosamine 1-phosphate did not substitute for beta-glucose 1-phosphate. Double reciprocal plots of the data from initial velocity studies at five beta-glucose 1-phosphate concentrations (10 to 100 microM) and four beta-glucose 1,6-bisphosphate concentrations (0.125 to 1.0 microM) showed that the apparent Michaelis constants for beta-glucose 1-phosphate and beta-glucose 1,6-bisphosphate were related to the concentrations of beta-glucose 1,6-bisphosphate and beta-glucose 1-phosphate, respectively, in such a way as to suggest a ping-pong mechanism. The same conclusion was obtained when substrate-velocity relationships were investigated at fixed ratio of both substrates: the Lineweaver-Burk plots showed linear lines and no parabolic ones. The "true" Km for beta-glucose 1-phosphate and beta-glucose 1,6-bisphosphate were found to be about 12 and 0.8 microM, respectively.     

Partial purification and some properties of shikimate dehydrogenase from tomatoes

The partial purification of shikimate dehydrogenase (SDH) from tomato fruit was achieved by precipitation with ammonium sulphate, and chromatography on DEAE-cellulose and hydroxyapatite. The enzyme has a MW of 73000, shows an optimum at pH 9.1 and K_m values of 3.8 × 10^?5 M and 1.0 × 10^?5 M with shikimic acid and NADP as substrates. NADP could not be replaced by NAD. The tomato enzyme is competitively inhibited by protocatechuic acid with a K_i value of 7.7 × 10^?5 M. On the other hand, cinnamic acid derivatives and 2-hydroxybenzoic acid were ineffective. At 50° for 5 min the SDH is inactivated by 85%. The activity was inhibited by pCMB and N-ethylmaleimide, suggesting a requirement for SH groups. The inactivation plot of oxidation by pCMB was biphasic, and NADP decreased the reactivity of sulphydryl groups to the reagent. The activation energy was found to be 14.2kcal/mol. The properties of the SDH are discussed in relation to the enzymes from other sources.     

The purification and some properties of H-lysin from Aeromonas salmonicida

H-lysin from Aeromonas salmonicida has been purified 1770-fold by freeze fractionation, ammonium sulphate precipitation, ion exchange chromatography and gel filtration chromatography. The purified material was predominantly H-lysin, devoid of detectable T-lysin, caseinase or gelatinase activity, although glycerophospholipid: cholesterol acyltransferase (GCAT) activity was present. The results suggested that H-lysin and GCAT activities were due to different extracellular products. Studies of the kinetics of haemolysis indicated that the H-lysin had an enzymic mode of action, and that initial erythrocyte damage appeared to precede lysis of the cell. The H-lysin was lethal to cultured rainbow trout gonad cells and leucocytes, but when it was injected intravenously in rainbow trout no pathological effects were observed.     

Partial purification and some properties of lipoxygenase from Saccharomyces cerevisiae

A partially purified lipoxygenase extract was obtained from the yeast Saccharomyces cerevisiae by precipitation with solid (NH₄)SO₄ at 20% to 80% saturation. The enzyme had two pH optima, at pH 8.0 and 10.0, with respective apparent K _m values of 13 and 9.5 m. At both pH optima, the lipoxygenase demonstrated highest substrate specificity towards linoleic acid, followed by linolenic acid; although the enzyme had less specificity towards mono-linolein than di-linolein at pH 8.0, the reverse was true at pH 10.0.