The hydrolysis of rac-glycerol 1-monodecanoate by serum butyryl cholinesterase

Butyryl cholinesterase from horse and human sera catalyzed the hydrolysis of monoacylglycerols containing fatty acids varying in chain length from 8 to 12 carbons; maximum activity was obtained with rac-glycerol 1-monodecanoate as substrate. Neither the triacylglycerols of these fatty acids nor the monoacylglycerols of longer chain length fatty acids were hydrolyzed at measurable rates in the system used. The enzyme was eserine sensitive and indistinguishable from butyryl cholinesterase as judged by purification, response to the several inhibitors tested, and heat inactivation. Data from mixed substrate experiments suggest a possible effector role for butyryl choline in accelerating the rate of rac-glycerol 1-monodecanoate hydrolysis. Fatty acid released during the course of rac-glycerol 1-monodecanoate hydrolysis may irreversibly inactivate the enzyme.     

Phosphohistidine as a stoichiometric intermediate in reactions catalyzed by isoenzymes of wheat germ acid phosphatase.

Burst titration experiments conducted on a highly purified isoenzyme of wheat germ acid phosphatase under conditions where [S]_o > K_m indicate that there is one titratable active site per molecule of enzyme of molecular weight 59,000. The enzyme is labeled to only a small extent with inorganic [³²P]phosphate ion. Incubation of wheat germ acid phosphatase with ³²P-labeled substrates such as p-nitrophenyl phosphate or inorganic pyrophosphate followed by quenching in alkali results in the stoichiometric trapping of a base-stable, acid-labile phosphorylated protein. The extent of ³²P incorporation parallels the degree of purity of the enzyme and corresponds to the incorporation of 1 mol of phosphate per mole of enzyme. The incorporation is eliminated by the simultaneous presence of excess unlabeled phosphate ion (a competitive inhibitor) and is not observed when a noncatalytic protein (such as bovine serum albumin) is substituted for the enzyme. Complete alkaline hydrolysis of the labeled protein results in the recovery of an 85% yield of τ-phosphohistidine, identified by ion-exchange chromatography, high-voltage paper electrophoresis, and comparison with a synthetic sample. A ³²P-labeled tryptic tetradecapeptide was isolated following hydrolysis of the labeled, reduced, and carboxymethylated protein with trypsin at pH 8.3, separation of the labeled peptide, and purification by two methods including a novel variant of a diagonal electrophoresis technique. The end groups and composition of the peptide are reported. The data are consistent with the interpretation that a phosphohistidine-enzyme intermediate is formed as an obligatory intermediate in the catalytic reaction involving this enzyme.     

Proton inventory of the water-catalyzed hydrolysis of p-nitrotrifluoroacetanilide

A proton inventory study was made of the water-catalyzed hydrolysis of p-nitrotrifluoro-acetanilide at pH 4.0, 70°C. Multiple protons in the transition state were demonstrated; although two or three protons were shown to be involved, they were not distinguishable. Neither imidazolyl cation nor acetic acid catalyzed the water-catalyzed hydrolysis. The water-catalyzed hydrolysis proceeds through acid catalysis by a water molecule of the breakdown of the tetrahedral intermediate between the anilide and another water molecule. Acid catalysis by the first water molecule is probably assisted by proton transfer from the second water molecule.     

Structural basis of cyclic oligoadenylate degradation by ancillary Type III CRISPR-Cas ring nucleases

Type III CRISPR-Cas effector systems detect foreign RNA triggering DNA and RNA cleavage and synthesizing cyclic oligoadenylate molecules (cA) in their Cas10 subunit. cAs act as a second messenger activating auxiliary nucleases, leading to an indiscriminate RNA degradation that can end in cell dormancy or death. Standalone ring nucleases are CRISPR ancillary proteins which downregulate the strong immune response of Type III systems by degrading cA. These enzymes contain a CRISPR-associated Rossman-fold (CARF) domain, which binds and cleaves the cA molecule. Here, we present the structures of the standalone ring nuclease from Sulfolobus islandicus (Sis) 0811 in its apo and post-catalytic states. This enzyme is composed by a N-terminal CARF and a C-terminal wHTH domain. Sis0811 presents a phosphodiester hydrolysis metal-independent mechanism, which cleaves cA₄ rings to generate linear adenylate species, thus reducing the levels of the second messenger and switching off the cell antiviral state. The structural and biochemical analysis revealed the coupling of a cork-screw conformational change with the positioning of key catalytic residues to proceed with cA₄ phosphodiester hydrolysis in a non-concerted manner.     

Bacteriolytic enzymes from Staphylococcus aureus. Specificity of action of endo-β-N-acetylglucosaminidase

The bacteriolytic enzyme with an isoelectric point of 9.5 that is produced by all strains of Staphylococcus aureus investigated was purified from strain M18 (Wadström & Hisatsune, 1970). This enzyme released reducing groups from cell walls of Micrococcus lysodeikticus and was thus shown to be a bacteriolytic hexosaminidase. Although dinitrophenylation and acid hydrolysis of cell walls hydrolysed by a partially purified enzyme gave DNP-alanine and DNP-glycine from staphylococcal peptidoglycan, which indicated the presence of a peptidase and probably also an N-acetylmuramyl-l-alanine amidase, hydrolysis of cell walls by the extensively purified enzyme did not give any DNP-amino acids. The enzyme digest was purified by Amberlite CG-120 and Sephadex G-10 chromatography. Reduction by sodium borohydride of the disaccharide obtained was followed by acid hydrolysis and paper chromatography. Glucosamine completely disappeared after this treatment and a new spot identical with glucosaminitol appeared. The muramic acid spot remained unchanged. The purified enzyme was found to be devoid of exo-β-N-acetylglucosaminidase activity. These results are compatible with the action of a bacteriolytic endo-β-N-acetylglucosaminidase. It is also proposed that this enzyme is probably identical with the staphylococcal lysozyme. The mode of action of this has not previously been investigated.     

Catalytic and ligand-binding properties of rat intestinal alkaline phosphatase.

Rat intestinal alkaline phosphatase is a dimeric enzyme with identical subunits and thus possesses two presumably identical active sites. Binding studies with P_i and l-phenylalanine and pre-steady-state “burst” titrations confirm the existence of two active sites per molecule of enzyme. The sites appear to be nonequivalent with respect to P_i binding, both at low pH, where an enzyme (E)-P_i covalent complex is formed, and at high P_i, where an E-P_i noncovalent complex predominates. The binding affinity of the first site is 100-fold greater than that of the second, i.e., there is negative cooperativity. The K_i value for competitive inhibition of substrate hydrolysis by P_i corresponds to the higher affinity site. The negative cooperativity appears not to be an artifact resulting from contaminating P_i in the purified enzyme preparation. l-Phenylalanine does not bind to the enzyme unless P_i is present, as expected from the previously proposed mechanism of uncompetitive inhibition by the amino acid. No negative cooperativity is seen in l-phenylalanine binding, but the number of moles of amino acid bound at saturation depends on the degree of saturation by P_i The enzyme is also inhibited uncompetitively by NADH, which can compete with l-phenylalanine for the same site on alkaline phosphatase.     

Interactions of five- and six-membered cyclic esters with α-chymotrypsin: Kinetic evidence for covalent enzyme intermediates

Interactions of α-chymotrypsin with 2-coumaranone (I), 3,4-dihydrocoumarin (II), o-hydroxy-α-toluenesulfonic acid sultone (III), and β-o-hydroxyphenylethanesulfonic acid sultone (IV) were studied in the presence of 14% acetonitrile at pH 7.0 by means of the proflavin displacement technique and by inhibition of N-acetyl-l-tryptophan ethyl ester (ATrEE) hydrolysis. Under saturating conditions of either I, II, or III, an enzyme intermediate was shown to accumulate using either the proflavin displacement technique or the ATrEE activity assay. The intermediates have characteristics of covalent enzyme-substrate compounds and are believed to decompose simultaneously by two pathways, one to give free enzyme and hydrolyzed cyclic ester, and the other to give the original cyclic ester and free enzyme. With α-chymotrypsin and III the observed first-order rate constant for decomposition of the intermediate by the two pathways was 0.19 ± 0.04 min^?1, while the rate constant for the hydrolytic pathway alone was 0.013 ± 0.0009 min^?1. These results indicate that the covalent-like intermediate with this sultone is not only capable of reverting to starting cyclic ester but prefers this pathway over hydrolysis. Sultone IV was found to bind to enzyme; but in contrast to the behavior of esters I–III, the binding did not result in accumulation of a covalent-like intermediate.     

Biosynthesis of salicylic acid in plants

Salicylic acid (SA) is an important signal molecule in plants. Two pathways of SA biosynthesis have been proposed in plants. Biochemical studies using isotope feeding have suggested that plants synthesize SA from cinnamate produced by the activity of phenylalanine ammonia lyase (PAL). Silencing of PAL genes in tobacco or chemical inhibition of PAL activity in Arabidopsis, cucumber and potato reduces pathogen-induced SA accumulation. Genetic studies, on the other hand, indicate that the bulk of SA is produced from isochorismate. In bacteria, SA is synthesized from chorismate through two reactions catalyzed by isochorismate synthase (ICS) and isochorismate pyruvate lyase (IPL). Arabidopsis contains two ICS genes but has no gene encoding proteins similar to the bacterial IPL. Thus, how SA is synthesized in plants is not fully elucidated. Two recently identified Arabidopsis genes, PBS3 and EPS1, are important for pathogen-induced SA accumulation. PBS3 encodes a member of the acyl-adenylate/thioester-forming enzyme family and EPS1 encodes a member of the BAHD acyltransferase superfamily. PBS3 and EPS1 may be directly involved in the synthesis of an important precursor or regulatory molecule for SA biosynthesis. The pathways and regulation of SA biosynthesis in plants may be more complicated than previously thought.Key words: salicylic acid biosynthesis, isochorismate synthase, phenylalanine ammonia lyase     

The role of effector molecules in regulating ribulosebisphosphate carboxylase activity

Ribulosebisphosphate carboxylase can exist in two forms having different kinetic properties. The fraction of enzyme present in each of the two forms is determined by both the absolute and the relative amounts of substrates and other effector molecules in solution with the enzyme. High CO₂ levels induce formation of an active CO₂ form of the enzyme while high ribulosebisphosphate (RuBP) levels cause formation of a much less active form. The CO₂ form is characterized by a high K_m(RuBP), low K_m(CO2), and relatively high V. The ribulosebisphosphate form has comparatively lower K_m(RuBP) and V and higher K_m(CO2). CO₂ appears to bind before RuBP in the reaction sequence catalyzed by the CO₂ form; this catalytic binding order is apparently reversed in the RuBP form. Steady state rates of enzyme reaction reflect the contributions of both these forms. A brief model, based on the cooperative effects of binding at a small number of catalytic or activator sites in the multimeric enzyme, is presented to account for the changes in enzyme activity with varying substrate and effector molecule concentrations.     

A kinetic study of Trichoderma reesei Cel7B catalyzed cellulose hydrolysis

One prominent feature of Trichoderma reesei (Tr) endoglucanases catalyzed cellulose hydrolysis is that the reaction slows down quickly after it starts (within minutes). But the mechanism of the slowdown is not well understood. A structural model of Tr- Cel7B catalytic domain bound to cellulose was built computationally and the potentially important binding residues were identified and tested experimentally. The 13 tested mutants show different binding properties in the adsorption to phosphoric acid swollen cellulose and filter paper. Though the partitioning parameter to filter paper is about 10 times smaller than that to phosphoric acid swollen cellulose, a positive correlation is shown for two substrates. The kinetic studies show that the reactions slow down quickly for both substrates. This slowdown is not correlated to the binding constant but anticorrelated to the enzyme initial activity. The amount of reducing sugars released after 24 h by Cel7B in phosphoric acid swollen cellulose, Avicel and filter paper cellulose hydrolysis is correlated with the enzyme activity against a soluble substrate p-nitrophenyl lactoside. Six of the 13 tested mutants, including N47A, N52D, S99A, N323D, S324A, and S346A, yield ∼15–35% more reducing sugars than the wild type (WT) Cel7B in phosphoric acid swollen cellulose and filter paper hydrolysis. This study reveals that the slowdown of the reaction is not due to the binding of the enzyme to cellulose. The activity of Tr- Cel7B against the insoluble substrate cellulose is determined by the enzyme’s capability in hydrolyzing the soluble substrate.     

Novel Penicillium cellulases for total hydrolysis of lignocellulosics

The (hemi)cellulolytic systems of two novel lignocellulolytic Penicillium strains (Penicillium pulvillorum TUB F-2220 and P. cf. simplicissimum TUB F-2378) have been studied. The cultures of the Penicillium strains were characterized by high cellulase and β-glucosidase as well moderate xylanase activities compared to the Trichoderma reesei reference strains QM 6a and RUTC30 (volumetric or per secreted protein, respectively). Comparison of the novel Penicillium and T. reesei secreted enzyme mixtures in the hydrolysis of (ligno)cellulose substrates showed that the F-2220 enzyme mixture gave higher yields in the hydrolysis of crystalline cellulose (Avicel) and similar yields in hydrolysis of pre-treated spruce and wheat straw than enzyme mixture secreted by the T. reesei reference strain. The sensitivity of the Penicillium cellulase complexes to softwood (spruce) and grass (wheat straw) lignins was lignin and temperature dependent: inhibition of cellulose hydrolysis in the presence of wheat straw lignin was minor at 35 °C while at 45 °C by spruce lignin a clear inhibition was observed. The two main proteins in the F-2220 (hemi)cellulase complex were partially purified and identified by peptide sequence similarity as glycosyl hydrolases (cellobiohydrolases) of families 7 and 6. Adsorption of the GH7 enzyme PpCBH1 on cellulose and lignins was studied showing that the lignin adsorption of the enzyme is temperature and pH dependent. The ppcbh1 coding sequence was obtained using PCR cloning and the translated amino acid sequence of PpCBH1 showed up to 82% amino acid sequence identity to known Penicillium cellobiohydrolases.     

Influence of Lipid Heterogeneity and Phase Behavior on Phospholipase A2 Action at the Single Molecule Level

We monitored the action of phospholipase A₂ (PLA₂) on L- and D-dipalmitoyl-phosphatidylcholine (DPPC) Langmuir monolayers by mounting a Langmuir-trough on a wide-field fluorescence microscope with single molecule sensitivity. This made it possible to directly visualize the activity and diffusion behavior of single PLA₂ molecules in a heterogeneous lipid environment during active hydrolysis. The experiments showed that enzyme molecules adsorbed and interacted almost exclusively with the fluid region of the DPPC monolayers. Domains of gel state L-DPPC were degraded exclusively from the gel-fluid interface where the buildup of negatively charged hydrolysis products, fatty acid salts, led to changes in the mobility of PLA₂. The mobility of individual enzymes on the monolayers was characterized by single particle tracking. Diffusion coefficients of enzymes adsorbed to the fluid interface were between 3.2 μm²/s on the L-DPPC and 4.9 μm²/s on the D-DPPC monolayers. In regions enriched with hydrolysis products, the diffusion dropped to ≈0.2 μm²/s. In addition, slower normal and anomalous diffusion modes were seen at the L-DPPC gel domain boundaries where hydrolysis took place. The average residence times of the enzyme in the fluid regions of the monolayer and on the product domain were between ≈30 and 220 ms. At the gel domains it was below the experimental time resolution, i.e., enzymes were simply reflected from the gel domains back into solution.     

The purification and study of a honey bee abdominal sucrase exhibiting unusual solubility and kinetic properties.

A sucrase from honey bee abdomens was purified to a high state of homogeneity. It was unusual in that it was completely soluble in high concentrations of ammonium sulfate and because curved rather than rectilinear lines were obtained when initial velocity data for at least two substrates were plotted. The action of the enzyme towards a large number of glycosides showed that the enzyme was able to hydrolyze all α-glucosides tested except trehalose and starch. pH Optima of sucrose and p-nitrophenyl-α-d-glucopyranoside differed by 1.0 pH unit. The unusual kinetic patterns which were found seem to be unique to this disaccharidase and were shown to be the result of a combination of hydrolytic and transferolytic activity in which the initial substrate is also a very good acceptor molecule for the transferolytic process. The K_m value for hydrolysis was found to be about an order of magnitude lower than for other insect sucrases with the more usual type of kinetic action. Amino acid and amino sugar analyses showed that the sucrase was a glycoprotein which contained glucosamine and either mannosamine or galactosamine. The molecular weight of the enzyme was estimated to be 70,000 or higher and there was no evidence that the enzyme had subunit structure. An s⁰_20,w value of 5.3S was determined. The enzyme was quite stable to a series of denaturing conditions and sulfhydryl reacting agents had little effect on the activity.     

Penicillinamidohydrolase inEscherichia coli

Substrate specificity of the bacterial penicillinamidohydrolase (penicillinacylase, EC 3.5.1.11) fromEscherichia coli was determined by measuring initial rates of enzyme hydrolysis of different substrates within zero order kinetics. SomeN-phenylacetyl derivatives of amino acids and amides of phenylacetic acid and phenoxyacetic acid of different substituted amides of these acids or amides, structurally and chemically similar to these compounds, served as substrates. Significant differences in ratios of initial Tates of the enzyme hydrolysis of different substrates were found when using a toluenized suspension of bacterial cells or a crude enzyme preparation, in spite of the fact that the enzyme is localized between the cell wall and cytoplasmic membrane, in the so-called periplasmic space.N-phenylacetyl derivatives are the most rapidly hydrolyzed substrates. Beta-phenylpropionamide and 4-phenylbutyramide were not utilized as substrates. The substrate specificity of the enzyme is discussed with respect to a possible use of certain colourless compounds as substrates, hydrolysis of which yields chromophor products suitable for a simple and rapid assay of the enzyme activity.     

On the physical properties and mechanism of action of arylsulfate sulfohydrolase II from Aspergillus oryzae.

Sedimentation equilibrium studies on arylsulfate sulfohydrolase II (EC 3.1.6.1) from Aspergillus oryzae under nondissociating conditions have resulted in a revised molecular weight of 94,900 ± 7100. Sedimentation equilibrium and gel electrophoresis data collected in the presence of the dissociating agents, urea and sodium dodecylsulfate demonstrate that the native enzyme is composed of two identical subunits as suggested by previous studies employing an irreversible inhibitor.The pH dependencies of the kinetic parameters V and $\text{V}\text{K}{}_{\mathrm{m}}$ for the enzymic hydrolysis of 4-nitrophenyl sulfate indicate that two groups of pK_a 4.7 and 6.0 control the activity of the enzyme. The product inorganic sulfate was shown to be a linear competitive inhibitor of the enzyme at pH 4.0, implying that it is a last released product along the reaction pathway. Inhibition by the phenol product was not observed. Enzymic hydrolysis of 4-nitrophenyl sulfate in ¹⁸O enriched water revealed that one atom of solvent oxygen is incorporated per molecule of inorganic sulfate, which is consistent with a mechanism featuring sulfur-oxygen bond cleavage. Evidence is presented based on stopped-flow kinetics, partitioning experiments in the presence of amine nucleophiles, and ¹⁸O exchange studies that collectively suggest that the breakdown of a covalent sulfuryl enzyme intermediate probably is not the rate-limiting step along the reaction pathway.The substrate specificity of the enzyme was examined by testing a variety of sulfate and phosphate esters as inhibitors of the hydrolysis of 4-nitrophenyl sulfate. The Cbz-l-Phe-l-Tyrosine-O-sulfate methyl ester serves as a substrate for the enzyme. Apparently substrate activity requires an aromatic sulfate ester whose binding is enhanced by incorporating the aromatic moiety in a hydrophobic matrix.     

Human liver acid phosphatases: Purification and properties of a low-molecular-weight isoenzyme

A low-molecular-weight human liver acid phosphatase was purified 2580-fold to homogenity by a procedure involving ammonium sulfate fractionation, acid treatment, and SP-Sephadex ion-exchange chromatography with ion-affinity elution. The purified enzyme contains a single polypeptide chain and has a molecular weight of 14,400 as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The amino acid composition of this enzyme (E) is reported. A pH dependence study using p-nitrophenyl phosphate as a substrate (S) revealed the effect of substrate ionization (pK_a 5.2) and the participation of a group in the ES complex having a pK_a value of 7.8. The enzyme is readily inactivated by sulfhydryl reagents such as heavy metal ions. Alkylation of the enzyme with iodoacetic acid and iodoacetamide causes complete inactivation of the enzyme and this inactivation is prevented by the presence of phosphate ion. The enzyme is also inactivated by treatment with diethyl pyrocarbonate; protection against this reagent is afforded by phosphate ion. The substrate specificity of this enzyme is unusual for an acid phosphatase. Of the many alkyl and aryl phosphomonoesters tested, the only possibly physiological substrate hydrolyzed by this enzyme was flavin mononucleotide, which exhibits a V which is 3-fold larger at pH 5.0 and 6-fold larger at pH 7.0 than that for p-nitrophenyl phosphate. However, the enzyme also catalyzes the hydrolysis of acetyl phosphate at pH 5.0 with a velocity eight times larger than that reported for an acyl phosphatase from human erythrocytes.     

Study of the mode of action of endopolygalacturonase from Fusarium moniliforme

One endopolygalacturonase from Fusarium moniliforme was purified from the culture broth of a transformed strain of Saccharomyces cerevisiae. Its kinetic parameters and mode of action were studied on galacturonic acid oligomers and homogalacturonan. The dimer was not a substrate for the enzyme. The enzyme was shown to follow Michaelis–Menten behaviour towards the other substrates tested. Affinity and maximum rate of hydrolysis increased with increasing chain length, up to the hexamer or heptamer, for which V_max was in the same range as with homogalacturonan. The enzyme was demonstrated to have a multi-chain attack mode of action and its active site included five subsites ranging from −3 to +2. The final products of hydrolysis of homogalacturonan were the monomer and the dimer of galacturonic acid.     

Acid phosphatase from maize scutellum: Negative cooperativity suppression by glucose

Acid phosphatase purified from maize scutellum, upon acylation with succinic anhydride, still shows negative co-operativity for the hydrolysis of glucose-6-phosphate at pH 5.4. This phenomenon is abolished by glucose, for both native and succinylated enzymes, through stimulation of the initial velocities at sub-optimal substrate concentrations. However, negative co-operativity for the enzymatic hydrolysis of p-nitrophenylphosphate at pH 5.4 is suppressed only at high concentrations of glucose. Furthermore, the hydrolysis of p-nitrophenylphosphate is noncompetitively inhibited (low affinity form of the enzyme molecule) by glucose, which suggests the existence of different substrate binding sites.     

Enzyme inhibitor modeling with TpZn complexes of functional hydroxamates and oximates

Salicylhydroxamic acid reacts with the enzyme model Tp^Ph,MeZn-OH to form the O,O-chelating hydroxamate complex 1. The hydrogen bonding capacity of zinc enzyme bound hydroxamates is reproduced by cocrystallization of two molecules if 1 with two molecules of methanol and by cocrystallization of one molecule of Tp^Ph,MeZn-acetohydroxamate with one molecule of 3-phenyl-5-methylpyrazole. The complex formed from Tp^Ph,MeZn-OH and N-tosylproline hydroxamic acid, according to its spectra, contains the hydroxamate as an N,N-chelating ligand. In contrast, the oximate derived from pyruvic aldehyde does not act as a chelating ligand, but is monodentate via the oximate oxygen.     

Crystal Structure of Cryptosporidium parvum Pyruvate Kinase

Pyruvate kinase plays a critical role in cellular metabolism of glucose by serving as a major regulator of glycolysis. This tetrameric enzyme is allosterically regulated by different effector molecules, mainly phosphosugars. In response to binding of effector molecules and substrates, significant structural changes have been identified in various pyruvate kinase structures. Pyruvate kinase of Cryptosporidium parvum is exceptional among known enzymes of protozoan origin in that it exhibits no allosteric property in the presence of commonly known effector molecules. The crystal structure of pyruvate kinase from C. parvum has been solved by molecular replacement techniques and refined to 2.5 Å resolution. In the active site a glycerol molecule is located near the γ-phosphate site of ATP, and the protein structure displays a partially closed active site. However, unlike other structures where the active site is closed, the α6'' helix in C. parvum pyruvate kinase unwinds and assumes an extended conformation. In the crystal structure a sulfate ion is found at a site that is occupied by a phosphate of the effector molecule in many pyruvate kinase structures. A new feature of the C. parvum pyruvate kinase structure is the presence of a disulfide bond cross-linking the two monomers in the asymmetric unit. The disulfide bond is formed between cysteine residue 26 in the short N-helix of one monomer with cysteine residue 312 in a long helix (residues 303–320) of the second monomer at the interface of these monomers. Both cysteine residues are unique to C. parvum, and the disulfide bond remained intact in a reduced environment. However, the significance of this bond, if any, remains unknown at this time.