Rational construction of a 2-hydroxyacid dehydrogenase with new substrate specificity

Using site-directed mutagenesis on the lactate dehydrogenase gene from Bacillus stearothermophilus, three amino acid substitutions have been made at sites in the enzyme which we suggest in part determine specificity toward different hydroxyacids (R-CHOH-COOH). To change the preferred substrates from the pyruvate/lactate pair (R = -CH3) to the oxaloacetate/malate pair (R = -CH2-COO-), the volume of the active site was increased (thr 246----gly), an acid was neutralized (asp-197----asn) and a base was introduced (gln-102 - greater than arg). The wild type enzyme has a catalytic specificity for pyruvate over oxaloacetate of 1000 whereas the triple mutant has a specificity for oxaloacetate over pyruvate of 500. Despite the severity and extent of these active site alterations, the malate dehydrogenase so produced retains a reasonably fast catalytic rate constant (20 s-1 for oxaloacetate reduction) and is still allosterically controlled by fructose-1,6-bisphosphate.     

The use of fluoro- and deoxy-substrate analogs to examine binding specificity and catalysis in the enzymes of the sorbitol pathway

The carbohydrate specificity of the two enzymes that catalyze the metabolic interconversions in the sorbitol pathway, aldose reductase and sorbitol dehydrogenase, has been examined through the use of fluoro- and deoxy-substrate analogs. Hydrogen bonding has been shown to be the primary mode of interaction by which these enzymes specifically recognize and bind their respective polyol substrates. Aldose reductase has broad substrate specificity, and all of the fluoro- and deoxysugars that were examined are substrates for this enzyme. Unexpectedly, both 3-fluoro- and 4-fluoro-D-glucose were found to be better substrates, with significantly lower K(m) and higher Kcat/K(m) values than those of D-glucose. A more discriminating pattern of substrate specificity is observed for sorbitol dehydrogenase. Neither the 2-fluoro nor the 2-deoxy analogs of D-glucitol were found to be substrates or inhibitors, suggesting that the 2-hydroxyl group of sorbitol is a hydrogen bond donor. The 4-fluoro and 4-deoxy analogs are poorer substrates than sorbitol, also implying a binding role for this hydroxyl group. In contrast, both 6-fluoro- and 6-deoxy-D-glucitol are very good substrates for sorbitol dehydrogenase, indicating that the primary hydroxyl group at this position is not involved in substrate recognition by this enzyme.     

Mild, solvent-free omega-hydroxy acid polycondensations catalyzed by candida antarctica lipase B

Immobilized Candida antarctica Lipase B (Novozyme-435) was studied for bulk polyesterifications of linear aliphatic hydroxyacids of variable chain length. The products formed were not fractionated by precipitation. The relative reactivity of the hydroxyacids was l6-hydroxyhexadecanoic acid approximately 12-hydroxydodecanoic acid approximately 10-hydroxydecanoic acid (DPavg congruent with 120, Mw/Mn 6-hydroxyhexanoic acid (DPavg congruent with 80, Mw/Mn < or = 1.5, 48 h, 90 degrees C). Remarkable improvements in molecular-weight buildup resulted from leaving water in the reaction. By 4 h, without application of vacuum, the DPavg for 12- and 16-carbon hydroxyacids was about 90. In contrast, with identical substrates and water removal, the DPavg at 4 h was about 23. Large differences in the molecular-weight build up of 12-hydroxydodecanoic acid were observed for catalyst concentrations (%-by-wt relative to monomer) of 0.1, 0.5, 1, and 10. Nevertheless, by 24 h, with 1% catalyst containing 0.1% lipase, poly(12-hydroxydodecanoic acid) with Mn 17 600 was formed. For 12-hydroxydodecanoic acid polymerization at 90 degrees C, the catalyst activity decreased by 7, 18, and 25% at reaction times of 4, 24, and 48 h, respectively. Furthermore, the retention of catalyst activity was invariable as a function of the substrates used.     

Comparison of the subsite specificity of the mammalian neutral endopeptidase 24.11 (enkephalinase) to the bacterial neutral endopeptidase thermolysin

A comparison has been made of the specificity of the mammalian neutral metalloendopeptidase, endopeptidase 24.11, with that of the bacterial neutral metalloendopeptidase thermolysin. A series of synthetic oligopeptides which have previously been studied as substrates for thermolysin and used in computer modeling were examined as substrates for the mammalian enzyme. It was found that P1, P2, and P'3 subsite interactions in the mammalian enzyme, although similar to those found in thermolysin, are less restrictive spatially and are considerably less dependent on hydrophobic interactions. This difference was maximally expressed with the synthetic substrate dansyl-D-alanylglycylnitrophenylalanylglycine which is a substrate for the mammalian enzyme, but not for the bacterial enzyme. A comparison of substrates in the free acid form with their corresponding amides showed that binding to the mammalian enzyme is dependent in part on an ionic interaction between the substrate carboxylate group and the enzyme. Such an ionic interaction was not observed with the bacterial enzyme.     

The role of NAD(P)H oxidoreductase (DT-Diaphorase) in the bioactivation of quinone-containing antitumor agents: a review

Bioactivation of quinone-containing anticancer agents has been studied extensively within the context of the chemistry and structure of the individual quinones which may result in various mechanisms of bioactivation and activity. In this review we focus on the two electron enzymatic reduction/activation of quinone-containing anticancer agents by DT Diaphorase (DTD). This enzyme has become important in oncopharmacology because its activity varies with tissues and it has been found to be elevated in tumors. Thus, a selective tumor cell kill can exist for agents that are good substrates for this enzyme. In addition, the enzyme can be induced by a variety of agents, a fact that can be used in chemotherapy. That is induction by a nontoxic agent followed by treatment with a good DT-Diaphorase substrate. A wide variety of anticancer drugs are discussed some of which are not good substrates such as Adriamycin, and some of which are excellent substrates. The latter category includes a variety of quinone containing alkylating agents.     

Reversal of enzyme regiospecificity with alternative substrates for aspartokinase I from Escherichia coli.

The substrate specificity of aspartokinase I has been examined by using both steady-state kinetic analyses and phosphorus-31 NMR spectroscopic studies. Analogues in which the alpha-amino group is either derivatized or replaced are not substrates or inhibitors for the enzyme, indicating the importance of the alpha-amino group as a binding determinant. The alpha-carboxyl group is not required for substrate recognition, and the alpha-amide or alpha-esters are competent alternative substrates. In addition, beta-derivatized structural analogues, such as the beta-hydroxamate, the beta-amide, or beta-esters, were found to be viable substrates. This was unexpected since the beta-carboxyl group is the usual site of phosphorylation. The nature of the acyl phosphate products obtained from these beta-derivatized alternative substrates has been characterized by coupled enzyme assays, oxygen-18-labeling studies, and phosphorus-31 NMR spectroscopy. These beta-derivatized analogues are capable of productive binding to aspartokinase through a reversal of regiospecificity to make the alpha-carboxyl group available as a phosphoryl acceptor. Many, but not all, of these alpha-acyl phosphates have also been shown to be viable substrates for the next two enzyme-catalyzed steps in this metabolic pathway. This raises the possibility of producing enzyme-generated alternative substrates that can serve as antimetabolites for the downstream reactions in this biosynthetic pathway.     

Characterization of a cellodextrin glucohydrolase with soluble oligomeric substrates: experimental results and modeling of concentration-time-course data

A previously isolated cellodextrin glucohydrolase (beta-glucosidase) from Trichoderma reesei QM 9414 is characterized using beta-1,4-glucose oligomers with defined degrees of polymerization as soluble substrates. The enzyme splits off glucose units from the nonreducing chain ends of cellooligomers. Besides this hydrolytic activity there is also evidence for transfer activity depending on the concentration and degree of polymerization of substrates. Concentration-time-course data have been gathered for the degradation of cellobiose, cellotriose, cellotetraose, cellopentaose, and cellohexaose covering a wide range of enzyme and substrate concentrations. A Michaelis-Menten type kinetic model has been developed, which is able to satisfactorily describe the complex system of parallel and series reactions during the conversion of oligomers to glucose. The only kind of inhibition considered is competitive inhibition by the final product glucose. The model takes into account the formation of multiple enzyme-substrate complexes and is limited to those conditions, in which no transglucosylation products are observed. Cellodextrins with higher degrees of polymerization are found to be better substrates for this enzyme than is the dimer cellobiose.     

Bicelles in structure-function studies of membrane-associated proteins

Bicelles are a novel form of long-chain/short-chain phospholipid aggregates, which are useful for biophysical and biochemical studies of membrane-associated biomolecules. In this work, we review the development of bicelles and their uses in structural characterization (primarily via NMR, circular dichroism, and fluorescence) of membrane-associated peptides. We also show that bicellar phospholipids are substrates for lipolytic enzymes. For this latter work, we employed a 31P NMR enzymatic assay system to examine the kinetic behavior of cobra venom phospholipase A(2) toward a variety of bicellar substrates. This enzyme hydrolyzed all bicelle lipids at rates comparable to those found for the enzyme action on traditional micellar substrates, which are the best substrates for this enzyme. In addition, we found that this PLA(2) showed no significant preference for long-chain or short-chain phospholipids when they were presented as mixtures in bicelles.     

Binding of substrates and other anions to yeast phosphoglycerate kinase.

1. The binding of all four substrates to yeast phosphoglycerate kinase has been studied using a gel filtration technique. The binding of phosphate and sulphate anions has also been investigated. 2. Two sites for each adenine nucleotide were found, one site being weaker than the other by between 30 and 50-fold. Only one binding site for the phosphoglycerate substrates was found. 3. 1,3-Bisphosphoglycerate (1,3-P2-glycerate) bound to the enzyme approximately 1000 times tighter than the other three substrates, its dissociation constant being 0.06 micrometer at ionic strength 0.15 M. 4. Sulphate and phosphate were mutually competitive and sulphate competed with the binding of all substrates except MgADP. MgADP bound to the enzyme more weakly in the presence of sulphate. The dissociation constant for sulphate binding was 1.6 mM at ionic strength of 0.15 M, and 0.05 mM at ionic strength 0.015 M. 5. These results are consistent with sulphate acting as a competitive inhibitor, as found by kinetic studies at high sulphate concentrations. The activatory effect of sulphate at lower concentrations and the substrate activation phenomea displayed by this enzyme, are interpreted in terms of a two-step dissociation of 1, 3-P2-glycerate. The presence of moderate concentrations of MgATP, 3-phosphoglycerate or sulphate causes acceleration of the rate of dissociation of the product, 1, 3-P2-glycerate, this being the rate-limiting step in the overall enzyme reaction.     

Enzyme kinetic and molecular modelling studies of sulphur-containing substrates of phenylalanine 4-monooxygenase

Previous investigations into the binding of substrates/cofactors to the PAH active site have only concentrated on Phe, thienylalanine and BH(4). This is the first reported investigation to model aliphatic thioether amino acid substrates to PAH. The clearance of the thioether substrates (4.82-79.09% of Phe) in the rat and human (1.19-37.41% of Phe) showed species differences. The xenobiotic thioether substrates (SMC and SCMC) were predicted to be poor substrates for PAH by the molecular modelling investigation and this has now been confirmed by the in vitro enzyme kinetic data. However, reaction phenotyping investigations have found that PAH was the major enzyme involved in the metabolism of SCMC in vitro and in vivo.     

Purification and characterization of proline-beta-naphthylamidase, a novel enzyme from pig intestinal mucosa

An enzyme hydrolyzing proline-beta-naphthylamide was purified to apparent homogeneity from porcine intestinal mucosa. The purified enzyme appears to consist of three identical subunit polypeptides with a molecular weight of about 58,000 each, associated noncovalently. The enzyme is a glycoprotein, and the subunit polypeptide contains 3 residues each of mannose and N-acetylglucosamine. A wide variety of peptidase substrates were tested for the enzyme, and the results showed that it hydrolyzes only aminopeptidase substrates, such as proline-beta-naphthylamide, glycine-beta-naphthylamide, leucine-beta-naphthylamide, and alanine-beta-naphthylamide. Among these substrates, proline-beta-naphthylamide is most efficiently hydrolyzed as judged by the kcat/Km value. The optimum pH for this substrate is around 9. The enzyme also hydrolyzes efficiently the ester substrates of these amino acids. No hydrolytic activity was observed for the peptide and protein substrates tested. The proline-beta-naphthylamidase activity was drastically inhibited by diisopropylfluorophosphate, phenylmethanesulfonyl fluoride, and L-1-tosylamido-2-phenylethyl chloromethyl ketone, indicating that the enzyme is a serine hydrolase, whereas it was slightly inhibited by aminopeptidase inhibitors, such as amastatin, bestatin, and puromycin. No significant homology was found for the NH2-terminal sequence of 27 amino acid residues with any known protein sequences. From these results we conclude that the enzyme is a protein which has not been described before.     

Covalent protein modification with ISG15 via a conserved cysteine in the hinge region

The ubiquitin-like protein ISG15 (interferon-stimulated gene of 15 kDa) is strongly induced by type I interferons and displays antiviral activity. As other ubiquitin-like proteins (Ubls), ISG15 is post-translationally conjugated to substrate proteins by an isopeptide bond between the C-terminal glycine of ISG15 and the side chains of lysine residues in the substrates (ISGylation). ISG15 consists of two ubiquitin-like domains that are separated by a hinge region. In many orthologs, this region contains a single highly reactive cysteine residue. Several hundred potential substrates for ISGylation have been identified but only a few of them have been rigorously verified. In order to investigate the modification of several ISG15 substrates, we have purified ISG15 conjugates from cell extracts by metal-chelate affinity purification and immunoprecipitations. We found that the levels of proteins modified by human ISG15 can be decreased by the addition of reducing agents. With the help of thiol blocking reagents, a mutational analysis and miRNA mediated knock-down of ISG15 expression, we revealed that this modification occurs in living cells via a disulphide bridge between the substrates and Cys78 in the hinge region of ISG15. While the ISG15 activating enzyme UBE1L is conjugated by ISG15 in the classical way, we show that the ubiquitin conjugating enzyme Ubc13 can either be classically conjugated by ISG15 or can form a disulphide bridge with ISG15 at the active site cysteine 87. The latter modification would interfere with its function as ubiquitin conjugating enzyme. However, we found no evidence for an ISG15 modification of the dynamin-like GTPases MxA and hGBP1. These findings indicate that the analysis of potential substrates for ISG15 conjugation must be performed with great care to distinguish between the two types of modification since many assays such as immunoprecipitation or metal-chelate affinity purification are performed with little or no reducing agent present.     

Effect of environmental temperature on the kinetic properties of goldfish brain choline acetyltransferase

1. Michaelis constants of goldfish brain choline acetyltransferase were found to depend on the concentration of the second substrate present and on the temperature to which the fish had been adapted. 2. Primary plots constructed from results obtained with enzyme prepared from cold-adapted or warm-adapted fish indicated that synthesis of acetylcholine took place by a sequential mechanism. 3. The affinity of choline acetyltransferase for acetyl-CoA was about 100 times that for choline irrespective of whether the enzyme had been prepared from warm-adapted or cold-adapted fish. 4. The maximum rate at which choline acetyltransferase synthesized acetylcholine and the energy of activation for this synthesis remained independent of the previous environmental temperature of the fish. 5. The affinity of choline acetyltransferase for choline and acetyl-CoA showed a complex dependence on temperature. The affinity of the enzyme from cold-adapted fish for substrates increased as the incubation temperature was lowered, whereas that of the enzyme from warm-adapted fish first increased and then decreased. 6. The maximum affinity of choline acetyltransferase for both substrates, from both cold-adapted and warm-adapted fish, occurred at temperatures that corresponded approximately to the respective environmental temperatures of the fish. 7. These changes in enzyme affinity for substrates are not thought to be due to the presence of isoenzymes. Their adaptive significance is unknown, but it could be connected with the maintenance of the enzyme in a stable form.     

N-acetylphenylalanyl-tRNA hydrolase from yeast. Purification and properties.

This paper describes the purification and properties of an enzyme present in yeast which splits N-acetylphenylalanyl-tRNA to N-acetylphenylalanine and tRNA. The enzyme has been 35000 as estimated by filtration on Sephadex G-150, is maximally active in the presence of a divalent cation (Mg2+ , Mn2+ or Ca2+) and has a pH optimum at around neutrality. The enzyme is highly specific in hydrolyzing N-acetylphenylalanyl-tRNA (Km = 0.4 micron). Phenylalanyl-tRNA is hydrolyzed with a similar apparent affinity but with an efficiency of 40% of that found for N-acetylphenylalanyl-tRNA. Other free or N-substituted aminoacyl-tRNAs are not substrates of this hydrolase. Neither of the two reaction products are effective inhibitors of this enzyme. Based on its substrate specificity, the trivial name of N-acetylphenylalanyl-tRNA hydrolase is proposed for this enzyme.     

Elementary steps in the reaction mechanism of chicken liver fatty acid synthase. pH dependence of NADPH binding and isotope rate effect for beta-ketoacyl reductase

The stopped flow method has been used to determine the pH dependence of the kinetics of the binding of NADPH to chicken liver fatty acid synthase over the pH range 6.0-8.5. The kinetics is consistent with a one-step binding mechanism, and the pH dependence of the second order rate constant indicates that an ionizable group either on the enzyme or on NADPH with a pK alpha of 6.1 is of importance in the binding process. The isotope rate effects have been determined for the steady state reaction with (S)- and (R)-[4-2H] NADPH as substrates and are very small. The pH dependence of the rate constant characterizing the reduction of acetoacetyl by NADPH on the enzyme (beta-ketoacyl reductase) and the isotope rate effects on this constant with (S)-[4-2H]NADPH as substrate also have been measured with the stopped flow method. A small pH-dependent isotope rate effect is found; these results suggest hydride transfer is not rate limiting for the beta-ketoacyl reductase reaction on the enzyme surface. The pH dependence of this rate constant is bell shaped and is very similar to that of the turnover number for the overall reaction; this suggests that the beta-ketoacyl reductase reaction may be partially rate limiting for the overall reaction when the enzyme is saturated with substrates.     

Asymmetric transesterification of secondary alcohols catalyzed by feruloyl esterase from Humicola insolens

A new asymmetric transesterification of secondary alcohols catalyzed by feruloyl esterase from Humicola insolens has been found. Although alcohols are not the natural substrates for this enzyme, a high R enantioselectivity was observed. Stereochemical studies showed that variations in substrate structure lead to strong variations in enantioselectivity. The highest enantioselectivities are obtained when the beta-carbon of the secondary alcohol is tertiary or quaternary.     

Purification and characterization of 3-phosphoglycerate kinase from Ehrlich ascites carcinoma cells

3-Phosphoglycerate kinase (3-PGK) has been purified to apparent homogeneity from Ehrlich ascites carcinoma (EAC) cells by (NH4)2SO4 precipitation, gel filtration and ion-exchange chromatography. The enzyme has been partially characterized and compared with the characteristics of this enzyme of other normal and malignant cells. The EAC cell 3-PGK is composed of a single subunit of 47 kDa. It has a broad pH optimum (pH 6.0-7.5) for its enzymatic activity. The apparent Km values of 3-phosphoglycerate (3-PGA) and ATP for 3-PGK have been found out to be 0.25 mM and 0.1 mM respectively. Similar to 3-PGK of other cells, the EAC enzyme requires either Mg2+ or Mn2+ for full activity; the optimum concentrations of Mg2+ and Mn2+ are 0.8 mM and 0.5 mM respectively. When ATP and 3-PGA act as substrates, ADP, the reaction product of 3-PGK-catalyzed reaction has been found to inhibit this enzyme. Kinetic studies were made on the inhibition of ADP in presence of the substrates ATP and 3-PGA. Attempts to hybridize 3-PGK and glyceraldehyde-3-phosphate dehydrogenase of EAC cells by NAD or glutaraldehyde were unsuccessful.     

Carbohydrate structures of the third component of rat complement. Presence of both high-mannose and complex type oligosaccharide chains.

The kinetics of pyruvate kinase from Saccharomyces cerevisiae were studied in assays at pH 6.2 at 25 degrees C as a function of the concentrations of the substrates ADP, phosphoenolpyruvate and Mg2+ and the concentration of the effector fructose 1,6-bisphosphate. The enzyme was activated by 100 mM-K+ and 32 mM-NH4+ throughout. It was found that an increase in the fructose bisphosphate concentration from 24 microM to 1.2 mM brings about a transition from a sigmoidal to a non-inflected form in the relationships v = f([phosphoenolpyruvate]) and v = f([Mg2+]) together with a large increase in the affinity of these substrates for the enzyme. The binding behaviour of ADP is barely affected by the same change in effector concentration. By contrast, increase in fructose bisphosphate concentration below 24 microM increases the affinity of the enzyme for all its substrates and the sigmoidicity of the corresponding velocity-substrate-concentration relationships. As a result of this change in behaviour it has been found impossible to represent all the data by the exponential model for a regulatory enzyme, and it is suggested (supported by comparisons with previous work) that the failure may reflect a secondary action of the effector upon the enzyme.     

Mismatch uracil glycosylase from Escherichia coli: a general mismatch or a specific DNA glycosylase?

The gene for the mismatch-specific uracil glycosylase (MUG) was identified in the Escherichia coli genome as a sequence homolog of the mammalian thymine DNA glycosylase, with activity against uracil in U.G mismatches. Subsequently, 3,N4-ethenocytosine (epsilonC), thymine, 5-hydroxymethyluracil, and 8-(hydroxymethyl)-3,N4-ethenocytosine have been proposed as possible substrates for this enzyme. The evaluation of various DNA adducts as substrates is complicated by the biphasic nature of the kinetics of this enzyme. Our results demonstrate that product release by the enzyme is very slow and hence comparing the "steady-state" parameters of the enzyme for different substrates is of limited use. Consequently, the ability of the enzyme to excise a variety of damage products of purines and pyrimidines was studied under single turnover conditions. Although the enzyme excised both epsilonC and U from DNA, the former adduct was significantly better as a substrate in terms of binding and hydrolysis. Some products of oxidative and alkylation damage are also moderately good substrates for the enzyme, but thymine is a poor substrate. This comparison of different substrates under single turnover conditions provides a rational basis for comparing substrates of MUG and we relate these conclusions to the known crystal structures of the enzyme and its catalytic mechanism.