Kinetic aspects of regulation of pyruvic decarboxylase

The decarboxylation of pyruvate catalysed by pyruvic decarboxylase (EC 4.1.1.1) from wheat germ is shown to be autocatalytic. Evidence is presented which suggests that the enzyme exists in an active and an inactive form—the latter being converted into the active form in the presence of pyruvate and by low pH. It is suggested that the relatively slow interconversion of the two forms of the enzyme may represent a time buffering system to prevent the decarboxylation of pyruvate in response to transient changes in pH.     

Human hepatic 3-hydroxy-3-methylglutaryl coenzyme A reductase: evidence for the regulation of enzymic activity by a bicyclic phosphorylation cascade

Microsomal human liver HMG-CoA reductase has been shown to exist in active (dephosphorylated) and inactive (phosphorylated) forms. Microsomal HMG-CoA reductase was inactivated in vitro by ATP-Mg in a time dependent manner; this inactivation was mediated by reductase kinase. Incubation of inactivated enzyme with phosphatase resulted in a time dependent reactivation (dephosphorylation). Polyacrylamide gel electrophoresis of purified HMG-CoA reductase incubated with reductase kinase and radiolabeled ATP revealed that the 32P radioactivity and HMG-CoA reductase enzymic activity were localized in a single electrophoretic position. Partial dephosphorylation of the phosphorylated enzyme was associated with loss of 32P and increase in HMG-CoA reductase activity. Human reductase kinase also exists in active and inactive forms. The active (phosphorylated) form of reductase kinase can be inactivated by incubation with phosphatase. Phosphorylation of inactive reductase kinase with ATP-Mg and a second kinase, reductase kinase kinase, was associated with a parallel increase in the enzymic activity of reductase kinase and the ability to inactivate HMG-CoA reductase. The combined results present initial evidence for the presence of human HMG-CoA reductase and reductase kinase in active and inactive forms, and the in vitro modulation of its enzymic activity by a bicyclic phosphorylation cascade. This bicyclic cascade system may provide a mechanism for short-term regulation of the pathway for cholesterol biosynthesis in man.     

Thermal effects on an enzymatically latent conformation of coagulation factor VIIa.

Activation of the zymogen factor VII yields an enzyme form, factor VIIa, with only modest activity. The thermal effect on this low activity of factor VIIa and its enhancement by the cofactor tissue factor was investigated. Factor VIIa activity measured with a chromogenic peptide substrate is characterized by an unusual temperature dependency which indicates that the activated protease exists in an equilibrium between a latent (enzymatically inactive) and an active conformation. As shown by calorimetry and activity measurements the thermal effects on factor VIIa are fully reversible below the denaturation temperature of 58.1 degrees C. A model for factor VIIa has been proposed [Higashi, S., Nishimura, H., Aita, K. & Iwanaga, S. (1994) J. Biol. Chem. 269, 18891-18898] in which the protease is supposed to exist primarily as a latent enzyme form because of the poor incorporation into the protease structure of the N-terminal Ile153 released by proteolytic cleavage during activation of factor VII. Binding of tissue factor to factor VIIa is assumed to shift the equilibrium towards an active conformation in which the N-terminal Ile153 forms a salt bridge with Asp343. We corroborate the validity of this model by: (a) chemical modification of factor VIIa; this suggests that the thermal effect on the equilibrium between the active and inactive conformation is reflected in the relative accessibility of the active site and the N-terminal Ile153; (b) measurements of factor VIIa binding to tissue factor indicating that complex formation is favoured by stabilization of the active conformation; and (c) activity measurements of a cross-linked factor VIIa-tissue factor complex; this showed that cross-linking stabilized the active conformation of factor VIIa and essentially prevented its thermally-induced transformation into the inactive state.     

Structural and catalytic properties of oxidized and reduced chloroplast NADP-malate dehydrogenase upon denaturation and renaturation

Chloroplast NADP-dependent malate dehydrogenase exists in two interconvertible forms: the inactive disulfide-containing form and the active dithiol form. No major difference in secondary structure or conformation was found between the oxidized and the reduced enzyme as determined by circular dichroism and intrinsic protein fluorescence. The guanidine/HCl-dependent unfolding of the enzyme is characterized by two transition midpoints: those of the reduced enzyme are lower by about 0.2 M guanidine/HCl compared to the oxidized enzyme. As shown by analytical ultracentrifugation, there was no effect of guanidine/HCl concentrations up to 0.25 M on the quaternary structure of the enzyme in its oxidized and reduced forms: both sedimentation coefficient (S20,w = 4.9 +/- 0.1 S) and sedimentation equilibrium (75 +/- 3 kDa) yield the dimer. In the oxidized state the enzyme undergoes guanidine-dependent dissociation to the monomer with a midpoint of transition at 0.5 M. The kinetics of unfolding were found to be significantly faster for the reduced than for the oxidized enzyme. Renaturation and reactivation of reduced enzyme was more rapid and occurred with higher yields (100%) than for the oxidized enzyme (60-80% yield). Furthermore, the effect of denaturants on catalytic activity, and reductive activation of the oxidized form, were studied. Both increase in protein fluorescence and a stimulatory effect on the activities at low guanidine/HCl concentrations were observed for the oxidized and the reduced form of the enzyme. Denaturants increase the rate of reductive activation of NADP-malate dehydrogenase.     

The relationship between the two forms of glycogen phosphorylase in Dictyostelium discoideum

The cellular slime mold, Dictyostelium disoideum, provides an ideal model system to study eukaryotic cell differentiation. In D. discoideum, glycogen degradation provides precursors for the synthesis of developmentally regulated structural products. The enzyme responsible for glycogen degradation, glycogen phosphorylase, exists in active and inactive forms. The active, or 'a' form, is independent of 5'adenosine monophosphate (5'AMP) while the inactive, or 'b' form, is 5'AMP-dependent. The activity of the 'b' form predominates early in development, while the activity of the 'a' form peaks in mid-late development; their combined specific activities remain constant at any point. Polyclonal antibodies raised to the purified forms of this enzyme showed low cross-reactivity. The anti-'a' serum reacted with a 104-kDa protein that was associated with phosphorylase 'a' activity; the anti-'b' serum reacted with a 92-kDa protein that was associated with phosphorylase 'b' activity and weakly cross-reacted with the 104-kDa protein. Immunoblots of peptide maps of the purified enzyme forms showed that each antibody was specific for the proteolytic fragments of its respective antigen. We also demonstrated in vitro phosphorylation of the 'b' form by an endogenous protein kinase. Cyclic AMP perturbation of intact cells caused induction of both phosphorylase-'a' activity and the 104-kDa protein. Immunotitration data suggested that the 'a' form accumulates due to de novo protein synthesis, although this result must be interpreted with caution.     

Activation and inactivation of an enzyme catalyzed by a single, bifunctional protein: a new example and why

Recent studies have shown that the light-dark mediated regulation of the leaf photosynthetic enzyme pyruvate, Pi dikinase results from interconversion between an active nonphosphorylated form of the enzyme and an inactive form phosphorylated on a threonine residue. These phosphorylation and dephosphorylation reactions are apparently catalyzed by a single protein termed the pyruvate, Pi dikinase regulatory protein and, notably, both reactions are mechanistically unique. We consider the evidence that this regulatory protein belongs to a group of unusual bifunctional enzymes that catalyze opposing reactions, apparently at separate catalytic sites on the same polypeptide. In three of the four known cases these bifunctional enzymes interconvert the active and inactive forms of another enzyme. The possible advantages of such opposing reactions being catalyzed by the same protein are considered.     

The nature of the multiple forms of D-erythrodihydroneopterin triphosphate synthetase.

1. Three forms of the Lactobacillus plantarum enzyme D-erythro-dihydroneopterin triphosphate synthetase, the first enzyme in folate biosynthesis, have been demonstrated by polyacrylamide gel electrophoresis. The enzyme forms designated the alpha prime, alpha and beta forms have been shown to be conformers with molecular weights of approx. 200 000. Study of the subunit structure of the beta enzyme species by sodium dodecylsulfate-polyacrylamide gel electrophoresis revealed a single protein with an estimated molecular weight of 20 000 which suggests that the enzyme molecule may be composed of ten polypeptide chains. 2. Of the three conformers only one form, the beta form, appears to be enzymatically active. The two other conformers must undergo conformational changes to the beta species before enzymatic activity can be demonstrated in reaction mixtures containing these enzyme forms. 3. The three enzyme species are interconvertible. The removal of phosphate ions from the enzymatically active beta form results in the formation of two inactive species which suggests that the conformation of the active enzyme is stabilized by non-covalently bound phosphate ions. Conversion of the inactive species to the beta enzyme form may be effected by the readdition of phosphate, substrate or certain nucleotides.     

A simple model for studies on the regulation of cholesterol synthesis using freshly isolated hepatocytes

Rat hepatocytes isolated by the procedure described here showed 3-hydroxy-3-methylglutaryl-CoA reductase activity in the range of that reported for rat liver at the maximum of the circadian cycle, even if they were taken from rats at the time of the minimum. The enzyme was present in cells as both its active dephosphorylated (20 +/- 8%) and the inactive phosphorylated forms. The enzyme activity and the ratio between the two forms were unaltered during 3 h of cell incubation. 25-Hydroxycholesterol (50 microM) induced about 50% inhibition of 3-hydroxy-3-methylglutaryl-CoA reductase activity during 1 h incubation but the relative amount of the two forms was not modified by the sterol. Cells isolated by the described procedure may therefore be a useful tool in studies on the regulation of cholesterol neogenesis, both through the synthesis of the enzyme, which can be shown by measuring the activity after complete dephosphorylation of the enzyme, and via the rapid reversible shift of the inactive to the active form, resulting from the ratio between the two enzyme forms. The latter mechanism for the modulation of cholesterol synthesis cannot be tested in cell cultures because full activation of the enzyme occurs during hepatocyte plating.     

Differential regulation of the active and inactive forms of Saccharomyces cerevisiae acid phosphatase

Summary Acid phosphatase in S. cerevisiae exists as an enzymatically active, cell wall associated form and as an enzymatically inactive, probably membrane-bound form (Schweingruber and Schweingruber, in press). Orthophosphate dependent and independent regulation determines the level of acid phosphatase activity. To deduce the regulation mechanisms we purified and quantified active and inactive acid phosphatase from cells grown under different physiological conditions and displaying variable levels of enzyme activity. Orthophosphate dependent regulation does not include significant changes in the amount of total (active and inactive) acid phosphatase protein synthesized. Under the experimental conditions chosen increased activity is achieved by preferential synthesis of the active form and by increasing the specific activity of the active enzyme. Orthophosphate independent regulation seems to occur by similar mechanisms.     

Purification and properties of glycogen phosphorylase isolated from bovine skeletal muscles

Glycogen phosphorylase isolated from bovine skeletal muscles was found to be homogeneous during polyacrylamide gel electrophoresis. The enzyme phosphorylation by phosphorylase kinase is accompanied by the incorporation of one mole of labeled phosphate per protein dimer; therefore the enzyme is represented by a partly phosphorylated form. The presence of a phosphate group prevents the removal of the protein-bound pyridoxal phosphate. The partly phosphorylated bovine phosphorylase possesses a low affinity for AMP and is inactive in the presence of IMP. Bovine phosphorylase a obtained from the partly phosphorylated enzyme has a molecular mass corresponding to a dimer. Both forms of bovine phosphorylase exhibit high cooperativity towards the substrate. The mechanism of phosphorylase a activation by AMP and IMP is identical: the nucleotides increase the enzyme affinity for the substrate as well as the maximal rate of the enzymatic reaction. Study of the enzyme inhibition by caffeine revealed the cooperativity of caffeine-binding centers. The equilibrium between the active and inactive enzyme conformations in the presence of caffeine is markedly shifted towards the inactive (T) form of glycogen phosphorylase.     

Activation of the coenzyme at the early step of the catalytic cycle of tryptophanase

Tryptophanase is catalytically more competent in alkaline pH even though the coenzyme exists as an inactive aldamine structure in this pH region. The binding of a substrate analog, 3-indolepropionate to the enzyme shifts the equilibrium from the substituted aldamine to the ketoenamine form in the entire pH region studied. The resultant ketoenamine form is favorable for transaldimination with the substrate amino group, a prerequisite for subsequent catalysis. This implies that the binding of tryptophan in alkaline pH, where the enzyme shows maximum activity, converts the inactive aldamine form of the coenzyme to the active ketoenamine form, which is favorable for undergoing the next step of the catalytic process.     

Long‐range molecular dynamics show that inactive forms of Protein Kinase A are more dynamic than active forms

Many protein kinases are characterized by at least two structural forms corresponding to the highest level of activity (active) and low or no activity, (inactive). Further, protein dynamics is an important consideration in understanding the molecular and mechanistic basis of enzyme function. In this work, we use protein kinase A (PKA) as the model system and perform microsecond range molecular dynamics (MD) simulations on six variants which differ from one another in terms of active and inactive form, with or without bound ligands, C‐terminal tail and phosphorylation at the activation loop. We find that the root mean square fluctuations in the MD simulations are generally higher for the inactive forms than the active forms. This difference is statistically significant. The higher dynamics of inactive states has significant contributions from ATP binding loop, catalytic loop, and αG helix. Simulations with and without C‐terminal tail show this differential dynamics as well, with lower dynamics both in the active and inactive forms if C‐terminal tail is present. Similarly, the dynamics associated with the inactive form is higher irrespective of the phosphorylation status of Thr 197. A relatively stable stature of active kinases may be better suited for binding of substrates and detachment of the product. Also, phosphoryl group transfer from ATP to the phosphosite on the substrate requires precise transient coordination of chemical entities from three different molecules, which may be facilitated by the higher stability of the active state.     

Effect of phospholipids on the thermal stability of microsomal UDP-glucuronosyltransferase

The GT2P isoform of microsomal UDP-glucuronosyltransferase from pig liver is a lipid-dependent enzyme. The data in the present work indicate that, in addition to regulation of activity, the thermal stability of the enzyme also is modulated by the acyl chain composition of phosphatidylcholines (PC) used to reconstitute the activity of pure enzyme. There was a reversible, temperature-dependent change in the state of the pure enzyme to an inactive form with onset at T greater than 38 degrees C, depending on the environment of the enzyme. The midpoint for the transition shifted from 39.8 degrees C for enzyme in a bilayer of distearoylphosphatidylcholine (DSPC) to 47.5 degrees C for enzyme in a bilayer of 1-stearoyl-2-oleoylphosphatidylcholine (SOPC). For all lipids, the transition from a catalytically active to an inactive form of the enzyme was associated with large compensating changes in H and S. Lipid-induced stabilization of the active form of UDP-glucuronosyltransferase at T greater than 37 degrees C was associated with decreases in delta H and delta S, but the decreases in delta S were larger, indicating that lipid-induced stabilization of the active form of the enzyme was entropic. The transition between the active and inactive forms of the enzyme was too rapid in either direction to measure in a standard spectrophotometer. In addition to reversible inactivation of the enzyme, there was a slower irreversible, temperature-dependent inactivation. The rate of this process depended on the acyl chains of the phosphocholines interacting with the enzyme. However, there was no obvious correlation between the structures of lipids that stabilized the different inactivation reactions.     

Comparative kinetic studies on the two interconvertible forms of Streptococcus faecalis inorganic pyrophosphatase.

In this work the two interconvertible forms of inorganic pyrophosphatase (EC 3.6.1.1) of Streptococcus faecalis were shown to differ in kinetics. The highly active form of the enzyme was more sensitive to the changes in the Mg2+ concentration, and thus also more sensitive to the inhibition caused by ATP, which competes with PPi for the chelation of Mg2+ ions. We have previously described a kinetic model for the less-active form of S. faecalis inorganic pyrophosphatase [Lahti & Jokinen (1985) Biochemistry 24, 3526-3530]. The kinetic model of the highly active enzyme form is proposed to be a modification of the model of the less-active form in which enzyme activation by free Mg2+ is necessary for the reaction to occur. In this model the enzyme exists in two states, referred to as R- and T-states. In the absence of ligands the enzyme is in the T-state. R-state, i.e. the catalytically active state, exists only in the presence of free Mg2+. Mg1PPi2- is the primary substrate, and free pyrophosphate is a weak inhibitor that cannot serve as a substrate for the highly active form of S. faecalis inorganic pyrophosphatase. This model closely resembles that previously presented for yeast inorganic pyrophosphatase.     

Generation mechanism and purification of an inactive form convertible in vivo to the active form of quinoprotein alcohol dehydrogenase in Gluconobacter suboxydans.

Alcohol dehydrogenase (ADH) of acetic acid bacteria is a membrane-bound quinohemoprotein-cytochrome c complex involved in vinegar production. In Gluconobacter suboxydans grown under acidic growth conditions, it was found that ADH content in the membranes was largely increased but the activity was not much changed, suggesting that such a condition produces an inactive form of ADH (inactive ADH). A similar phenomenon could be also observed in Acetobacter aceti, another genus of acetic acid bacteria. Furthermore, aeration conditions were also shown to affect ADH production; the ADH level was increased and was present as an active form under low-aeration conditions, while the ADH level was decreased and was present mainly as an inactive form under high-aeration conditions. Inactive ADH was solubilized from the membranes of G. suboxydans grown in acidic and high-aeration conditions and was purified separately from the normal, active form of ADH (active ADH). In spite of having 10 times less enzyme activity than active ADH, inactive ADH could not be distinguished from active ADH with respect to their subunit compositions, molecular sizes, and prosthetic groups. Inactive ADH, however, had a relatively loose conformation with a partially oxidized state, while active ADH had a tight conformation with a completely reduced state, suggesting that inactive ADH may lack a right subunit's interaction and that one of the heme c components may be inactivated. Reactivation from such an inactive ADH occurred either by shifting of the pH of the culture medium up during the cultivation or by incubation of the resting cells at the neutral pH region in the presence of an energy source such as D-sorbitol. Such an activation of ADH was repressed by the addition of a proton uncoupler and could not occur in the spheroplasts. Thus, the results suggest that inactive ADH could be generated abundantly under acidic growth conditions and converted to the active form at a neutral culture pH. The data also suggest that some periplasmic component may be involved in the conversion of inactive ADH into the active form by consuming some forms of energy.     

Factors affecting the oligomeric structure of yeast external invertase

It has been assumed that yeast external invertase is a dimer, with each subunit composed of a 60-kDa polypeptide chain. We now present evidence that at its optimal pH of 5.0, the predominant form of external invertase is an octamer with an average size of 8 X 10(5) Da. During ultracentrifugation the octamer dissociated to lower molecular weight forms, including a hexamer, tetramer, and dimer. All forms of the enzyme were shown to possess identical specific activities and to contain a similar carbohydrate to protein ratio. Although the monomer subunits (1 X 10(5) Da) were heterogenous in carbohydrate content, each subunit possessed nine oligosaccharide chains. When stained for protein and enzyme activity following sodium dodecyl sulfate-polyacrylamide gel electrophoresis, only the oligomeric form of the enzyme appeared to be active. Thus, on partially inactivating invertase with 4 M guanidine hydrochloride both octamer and monomer were evident on the gels but only the former was active. Similarly, incubating at pH 2.5 in the presence of sodium dodecyl sulfate yielded only inactive monomer. The monomer, unlike the active oligomeric aggregate, was unable to hydrolyze sucrose after sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Consistent with the in vitro studies, freshly prepared yeast lysate was shown to contain the octameric species of external invertase as the major active form of this enzyme. From these studies and others which employed deglycosylated invertase, it is concluded that the carbohydrate component of external invertase contributes not only to stabilizing enzyme activity, but also to maintaining its oligomeric structure.     

Conversion of Tyrosine Hydroxylase to Stable and Inactive Form by the End Products

We have reported previously that tyrosine hydroxylase in the crude extract from rat striatum exists in the inactive form showing almost no activity at the physiological pH and that the inactive form is produced by the action of the end products of the enzyme, such as dopamine. The incubation of the enzyme with the end products resulted in not only the inactivation but also a remarkable stabilization of the enzyme. Catechols possessing amino groups but no negatively charged groups on the side chains (catecholamine-type catechols) were effective at a concentration as low as 10(-7) M in both the inactivation and stabilization of the enzyme. In contrast, catechols not possessing positively or negatively charged side chains (3,4-dihydroxyphenylethyleneglycol-type catechols) were ineffective at a concentration of 10(-7) M but effective at a concentration of 10(-6) M for both the inactivation and stabilization. Catechols possessing negatively charged groups (3,4-dihydroxyphenylacetic acid-type catechols) were ineffective even at a concentration of 10(-6) M. Thus, the end products of tyrosine hydroxylase appear to serve to keep the enzyme inactive and stable. The reaction mechanism of the conversion of the enzyme from the active/labile form to the inactive/stable form by dopamine was also investigated.     

A model for the regulation of the activity of L-asparaginase/ kinase enzyme of Tetrahymena pyriformis

L-Asparaginase of Tetrahymena pyriformis is a lipoprotein with relative M(r) approximately 200 kDa and one subunit size of 39 kDa. This enzyme also exhibits protein kinase activity and it is autophosphorylated in tyrosine residues. Phosphorylation-dephosphorylation of L-asparaginase resulted in complete loss or activation by more than 10-fold of its catalytic activity. Both native and dephosphorylated forms of L-asparaginase are inactivated by phospholipase C and this inactivation can be reversed by the addition of lipids. Based on these results a working hypothesis is suggested that L-asparaginase of T. pyriformis exists in four interconvertible forms: Form A, phosphorylated complexed with lipids, form HA, dephosphorylated (highly active), form I, free of lipids, (inactive) and form B, free of lipids and phosphate.     

Secretion of both partially unfolded and folded apoproteins of dimethyl sulfoxide reductase by spheroplasts from a molybdenum cofactor-deficient mutant of Rhodobacter sphaeroides f. sp. denitrificans.

Spheroplasts prepared from a molybdenum cofactor-deficient mutant of Rhodobacter sphaeroides f. sp. denitrificans secreted dimethyl sulfoxide (DMSO) reductase which had no molybdenum cofactor and therefore no activity, whereas those from wild-type cells secreted the active reductase. The inactive DMSO reductase proteins were separated by nondenaturing electrophoresis into two forms: form I, with the same mobility as the native enzyme, and form II, with slower mobility. Both forms had the same mobility on denaturing gel. Form I and active DMSO reductase had the same profile on gel filtration chromatography. Form II was eluted a little faster than the native enzyme, suggesting that DMSO reductase form II was not an aggregated form but a compactly folded form very similar to the native enzyme. Form II was digested by trypsin and denatured with urea, whereas form I was unaffected, like native DMSO reductase. These results suggested that form II was a partially unfolded but compactly folded apoprotein of DMSO reductase.     

Coordination and geometry of the nickel atom in active methyl-coenzyme M reductase from Methanothermobacter marburgensis as detected by X-ray absorption spectroscopy

Methyl-coenzyme M reductase (MCR) catalyzes the reduction of methyl-coenzyme M (CH(3)-S-CoM) to methane. The enzyme contains as a prosthetic group the nickel porphinoid F(430) which in the active enzyme is in the EPR-detectable Ni(I) oxidation state. Crystal structures of several inactive Ni(II) forms of the enzyme but not of the active Ni(I) form have been reported. To obtain structural information on the active enzyme-substrate complex we have now acquired X-ray absorption spectra of active MCR in the presence of either CH(3)-S-CoM or the substrate analog coenzyme M (HS-CoM). For both MCR complexes the results are indicative of the presence of a five-coordinate Ni(I), the five ligands assigned as four nitrogen ligands from F(430) and one oxygen ligand. Analysis of the spectra did not require the presence of a sulfur ligand indicating that CH(3)-S-CoM and HS-CoM were not coordinated via their sulfur atom to nickel in detectable amounts. As a control, X-ray absorption spectra were evaluated of three enzymatically inactive MCR forms, MCR-silent, MCR-ox1-silent and MCR-ox1, in which the nickel is known to be six-coordinate. Comparison of the edge position of the X-ray absorption spectra revealed that the Ni(I) in the active enzyme is more reduced than the Ni in the two EPR-silent Ni(II) states. Surprisingly, the edge position of the EPR-active MCR-ox1 state was found to be the same as that of the two silent states indicating similar electron density on the nickel.