Dichotomic phylogenetic tree of the pyruvate kinase family: K+ -dependent and -independent enzymes

K+ dependence was assumed to be a feature of all pyruvate kinases until it was discovered that some enzymes express K+ -independent activity. Almost all the K+ -independent pyruvate kinases have Lys at position 117, instead of the Glu present in the K+ -dependent muscle enzyme. Mutagenesis studies show that the internal positive charge substitutes for the K+ requirement (Laughlin, L. T. & Reed, G. H. (1997) Arch. Biochem. Biophys. 348, 262-267). In this work a phylogenetic analysis of pyruvate kinase was performed to ascertain the abundance of K+ -independent activities and to explore whether the K+ activating effect is related to the evolutionary history of the enzyme. Of the 230 studied sequences, 46% have Lys at position 117, and the rest have Glu. Pyruvate kinases with Lys117 and Glu117 are separated in two clusters. All of the enzymes of the Glu117 cluster that have been characterized are K+ -dependent, whereas those of the Lys117 cluster are K+ -independent. Thus, there is a strict correlation between the dichotomy of the tree and the dependence of activity on K+. 77% of the pyruvate kinases that possess Lys117 have Lys113/Gln114; they also have Ile, Val, or Leu at position 120. These residues are replaced by Glu117 and Thr113/Lys114/Thr120 in 80% of K+ -dependent pyruvate kinases. Structural analysis indicates that these residues are in a hinge region involved in the acquisition of the catalytic conformation of the enzyme. The route of conversion from K+ -independent to K+ -dependent pyruvate kinases is described. A plausible explanation of how enzymes developed K+ dependence is put forth.     

K+-independent active transport of Na+ by the (Na+ and K+)-stimulated adenosine triphosphatase

The (Na+ and K+)-stimulated adenosine triphosphatase (Na+,K+)-ATPase) from canine kidney reconstituted into phospholipid vesicles showed an ATP-dependent, ouabain-inhibited uptake of 22Na+ in the absence of added K+. This transport occurred against a Na+ concentration gradient, was not affected by increasing the K+ concentration to 10 microM (four times the endogenous level), and could not be explained in terms of Na+in in equilibrium Na+out exchange. K+-independent transport occurred with a stoichiometry of 0.5 mol of Na+ per mol of ATP hydrolyzed as compared with 2.9 mol of Na+ per mol of ATP for K+-dependent transport.     

Selectivity of pyruvate kinase for Na+ and K+ in water/dimethylsulfoxide mixtures.

In aqueous media, muscle pyruvate kinase is highly selective for K+ over Na+. We now studied the selectivity of pyruvate kinase in water/dimethylsulfoxide mixtures by measuring the activation and inhibition constants of K+ and Na+, i.e. their binding to the monovalent and divalent cation binding sites of pyruvate kinase, respectively [Melchoir J.B. (1965) Biochemistry 4, 1518-1525]. In 40% dimethylsulfoxide the K0.5 app for K+ and Na+ were 190 and 64-fold lower than in water. Ki app for K+ and Na+ decreased 116 and 135-fold between 20 and 40% dimethylsulfoxide. The ratios of Ki app/K0.5 app for K+ and Na+ were 34-3.5 and 3.3-0.2, respectively. Therefore, dimethylsulfoxide favored the partition of K+ and Na+ into the monovalent and divalent cation binding sites of the enzyme. The kinetics of the enzyme at subsaturating concentrations of activators show that K+ and Mg2+ exhibit high selectivity for their respective cation binding sites, whereas when Na+ substitutes K+, Na+ and Mg2+ bind with high affinity to their incorrect sites. This is evident by the ratio of the affinities of Mg2+ and K+ for the monovalent cation binding site, which is close to 200. For Na+ and Mg2+ this ratio is approximately 20. Therefore, the data suggest that K+ induces conformational changes that prevent the binding of Mg2+ to the monovalent cation binding site. Circular dichroism spectra of the enzyme and the magnitude of the transfer and apparent binding energies of K+ and Na+ indicate that structural arrangements of the enzyme induced by dimethylsulfoxide determine the affinities of pyruvate kinase for K+ and Na+.     

The regulatory properties of yeast pyruvate kinase. Effects of NH4+ and K+ concentrations.

The kinetics of pyruvate kinase from Saccharomyces cerevisiae were studied at 25 degrees C and pH 6.2 as a function of the concentrations of ADP, phosphoenolpyruvate, Mg2+ and either NH4+ or K+. The data were analysed by the exponential model for four substrates, obtained by extension of the model described by Ainsworth, Kinderlerer & Gregory [(1983) Biochem. J. 209, 401-411]. On that basis, it was concluded that NH4+ binding is almost non-interactive but leads to the appearance of positive interaction in the velocity response to increase in its concentration because of positive interactions with phosphoenolpyruvate and Mg2+. The data obtained with K+ lead to the same conclusions and differ only in suggesting that NH4+ is bound more strongly to the enzyme than is K+. Both data sets are used as the basis for a discussion of the substrate interactions of pyruvate kinase and it appears therefrom that the heterotropic interactions accord with what is known of the events that take place at the active site during catalysis. The paper also reports a determination of the dissociation constants for the NH4+ complexes with ADP and phosphoenolpyruvate and an examination of the simultaneous activation of pyruvate kinase by K+ and NH4+ ions.     

Alteration in liver pyruvate kinase protein and catalytic activity upon starvation and refeeding

Liver pyruvate kinase (L-type isozyme) was purified from the livers of rats fed a high carbohydrate, low protein diet for 4 days. The protein was homogeneous as judged by polyacrylamide-gel electrophoresis with and without added sodium dodecyl sulfate and as judged by high speed sedimentation and low speed equilibrium centrifugation. The specific activity of the purified protein was 190–220 international units (IU)/mg. A precipitating antiserum directed specifically against liver pyruvate kinase was obtained from rabbits and was used to determine the amount of liver pyruvate kinase protein present in the 80,000g supernatant fraction of rat liver homogenates in response to the dietary status of the animal. Rats maintained on a high carbohydrate, low protein diet for 4 days prior to sacrifice have at least 20 mg of precipitable liver pyruvate kinase protein per liver. Starvation of the animal results in a marked reduction in liver pyruvate kinase so that by 3 days of starvation less than 7 mg of liver pyruvate kinase protein per liver remains. Refeeding the animal a high carbohydrate, low protein diet results in a return of the liver pyruvate kinase protein to the prestarvation level of 20 mg per liver. The liver pyruvate kinase activity per liver varies in the same direction as does the liver pyruvate kinase protein but does not parallel the change in protein. Animals fed a high carbohydrate, low protein diet for 4 days have 60–70 IU/mg of liver pyruvate kinase protein whereas animals starved for periods exceeding 30 h have greater than 100 IU/mg of liver pyruvate kinase protein. Refeeding starved animals with a high carbohydrate, low protein diet initially causes a large increase in activity per milligram of liver pyruvate kinase protein followed by a return of this value to the prestarvation level. The observed rise in the ratio of activity per milligram of liver pyruvate kinase protein during starvation suggests a modification in the enzyme protein resulting either in an increase in the specific activity of the enzyme or in a decrease in the affinity of the enzyme for the antibody.     

K(+)-independent gastric H(+),K(+)-atpase activity. Dissociation of K(+)-independent dephosphorylation and preference for the E1 conformation by combined mutagenesis of transmembrane glutamate residues

Several mutations of residues Glu(795) and Glu(820) present in M5 and M6 of the catalytic subunit of gastric H(+),K(+)-ATPase have resulted in a K(+)-independent, SCH 28080-sensitive ATPase activity, caused by a high spontaneous dephosphorylation rate. The mutants with this property also have a preference for the E(1) conformation. This paper investigates the question of whether these two phenomena are coupled. This possibility was studied by combining mutations in residue Glu(343), present in M4, with those in residues 795 and 820. When in combined mutants Glu and/or Gln residues were present at positions 343, 795, and 820, the residue at position 820 dominated the behavior: a Glu giving K(+)-activated ATPase activity and an E(2) preference and a Gln giving K(+)-independent ATPase activity and an E(1) preference. With an Asp at position 343, the enzyme could be phosphorylated, but the dephosphorylation was blocked, independent of the presence of either a Glu or a Gln at positions 795 and 820. However, in these mutants, the direction of the E(2) <--> E(1) equilibrium was still dominated by the 820 residue: a Glu giving E(2) and a Gln giving E(1). This indicates that the preference for the E(1) conformation of the E820Q mutation is independent of an active dephosphorylation process.     

Src homology domains of v-Src stabilize an active conformation of the tyrosine kinase catalytic domain

To examine the interactions between Src homology,domains and the tyrosine kinase catalytic domain of v-Src, various combinations of domains have been expressed in bacteria as fusion proteins. Constructs containing the isolated catalytic domain, SH2 + catalytic domain, and SH3 + SH2 + catalytic domains were active in autophosphorylation assays. For the catalytic domain of v-Src, but not for v-Abl, addition of exogenous Src SH3-SH2 domains stimulated the autophosphorylation activity. In contrast to results for autophosphorylation, constructs containing Src homology domains were more active towards a synthetic peptide substrate than the isolated catalytic domain. The ability of the SH2 and SH3 domains of v-Src to stabilize an active enzyme conformation was also confirmed by refolding after denaturation in guanidinium hydrochloride. Collectively the data suggest that, in addition to their roles in intermolecular protein-protein interactions, the Src homology regions of v-Src exert a positive influence on tyrosine kinase function, potentially by maintaining an active conformation of the catalytic domain.     

Analysis of the catalytic mechanism of pyruvate dehydrogenase kinase

It has been proposed that "Glu238" within the N-box of pyruvate dehydrogenase kinase (PDK) is a base catalyst. The pH dependence of k(cat) of Arabidopsis thaliana PDK indicates that ionizable groups with pK values of 6.2 and 8.4 are necessary for catalysis, and the temperature dependence of these values suggests that the acidic pK is due to a carboxyl- or imidazole-group. The E238 and K241 mutants had elevated K(m,ATP) values. The acidic pK value of the E238A mutant was shifted to 5.5. The H233A, L234H, and L234A mutants had the same pK values as wild-type AtPDK, contrary to the previous proposal of a "Glu-polarizing" His. Instead, we suggest that the conserved Glu, Lys, and Asn residues of the N-box contribute to coordinating Mg2+ in a position critical for formation of the PDK-MgATP-substrate ternary complex.     

Adipose-tissue pyruvate kinase. Properties and interconversion of two active forms

1. Extraction of rat epididymal adipose tissue with buffer containing EDTA yields a pyruvate kinase, provisionally called PyK-A, the properties of which resemble in several respects those of the allosteric pyruvate kinase of liver. These properties include co-operative interactions with phosphoenolpyruvate, Mg(2+), K(+), NH(4) (+) and ATP, and sensitivity to activation by fructose 1,6-diphosphate. 2. Extraction in the absence of EDTA yields predominantly a form, PyK-B, that shows both normal Michaelis-Menten kinetics with phosphoenolpyruvate, Mg(2+) and ATP, and co-operative interactions with K(+) and NH(4) (+); this form is insensitive towards fructose 1,6-diphosphate. 3. Both forms yield simple kinetics with ADP, though K(m) values differ in the two systems. In all cases where co-operativity has been demonstrated, Hill-plot n values are between 1.4 and 2.0. 4. The conversion of PyK-A into PyK-B is mediated specifically by fructose 1,6-diphosphate; the reverse reaction is occasioned by EDTA, ATP or citrate. It is thought that a bivalent cation may be involved in this interconversion. 5. Attempts at partial purification have revealed that the enzyme resembles the pyruvate kinase of skeletal muscle, rather than that of liver, in its solubility in ammonium sulphate and elution from DEAE-cellulose. 6. The relevance of these properties in the regulation of pyruvate kinase activity in vivo in adipose tissue is discussed.     

Affinity purification and catalytic properties of a soluble, Ca2+-independent, diacylglycerol kinase

We used a new procedure that involved selective enzyme binding to lipid vesicles to partially purify a soluble diacylglycerol kinase, then studied the relation between enzyme-vesicle binding and activity in vesicle-based assays. The vesicle-binding procedure required about 2 h, increased the enzyme's specific activity 50-fold with a 50% yield of activity, and combined well with additional purification steps. Studies of the activity of the partially purified diacylglycerol kinase toward vesicle-associated diacylglycerols revealed linear reaction kinetics that reflected enzyme binding to the vesicles; factors known to influence enzyme binding to the vesicles affected enzyme activity only indirectly, not by influencing the diacylglycerol kinase reaction itself. On the other hand, special incubation experiments that caused both substrate depletion in vesicles and enzyme stalling provided evidence that the diacylglycerol kinase could desorb from these vesicles, adsorb to freshly added, substrate-containing vesicles, and resume catalysis of phosphorylation reactions. The molecular basis for this enzyme-vesicle "hopping" behavior remains to be clarified. But enzyme-catalyzed conversion of diacylglycerol to phosphatidic acid may not have been a contributing factor because separate, enzyme-vesicle binding experiments showed that the enzyme had only a marginally higher affinity for diacylglycerol-containing vesicles than it did for vesicles that contained comparable amounts of phosphatidic acid. The combined results of our experiments suggest that the linear rates of diacylglycerol phosphorylation observed in standard assays with diacylglycerol-containing vesicles may have been combined functions of both the rate of enzyme hopping among vesicles and the rate of diacylglycerol phosphorylation by enzyme that was bound transiently on substrate-containing vesicles.     

Inhibitory effect of Li+ on cell growth and pyruvate kinase activity of Escherichia coli.

Li+ inhibited growth of Escherichia coli when glucose, galactose, fructose, or glycerol was added as the sole source of carbon. Growth inhibition was not observed when lactate or a mixture of amino acids was used as the carbon source. A mutant possessing elevated activity of Li+ extrusion was not inhibited by Li+. These results suggested that intracellular Li+ inhibited the glycolytic pathway, most likely triose metabolism, without affecting gluconeogenesis. We also found that pyruvate kinase I was inhibited by Li+.     

On the temperature- and salt-dependent conformation change in human erythrocyte pyruvate kinase

The influence of temperature, K+, Mg2+ and fructose 1,6-bisphosphate on human red cell pyruvate kinase was investigated. Kinetic measurements between 4 degrees C and 43 degrees C revealed a remarkable influence of the temperature on the allosteric behaviour of the enzyme. Below a transition region between 15 degrees C and 20 degrees C (as obtained from an Arrhenius plot) the enzyme shows non-cooperative behaviour, as can be deduced from Michaelis-Menten, Hill and Scatchard plots. At temperatures above 20 degrees C cooperativity increases with rising temperature. This effect becomes even more pronounced at higher temperatures upon addition of increasing amounts of K+ and Mg2+ accompanied by a slight decrease of the reaction velocity. Fructose 1,6-bisphosphate, however, abolishes cooperativity at every temperature and salt concentration measured. Difficulties which arise in evaluating the correct values of V, Km and the Hill coefficient nH with cooperative systems are met by using a computer program of Wieker, Johannes and Hess, especially designed for the determination of kinetic parameters obtained from sigmoidal steady-state kinetics.     

Phosphoenolpyruvate hydrolase activity of rabbit muscle pyruvate kinase.

Rabbit muscle pyruvate kinase catalyzes the hydrolysis of P-enolpyruvate at the same active site which catalyzes the physiologically important kinase reaction. The hydrolase activity is lower than the kinase activity by a factor of at least 10(3). There are specific monovalent cation and divalent cation requirements. No other cofactors are required. The relative activation of the pyruvate kinase for the hydrolase reaction is: Ni(II) greater than Co(II) greater than Mg(II) greater than Mn(II). This parallels the rates of nonenzymatic hydrolysis of P-enolpyruvate (Benkovic, S.J., and Schray, K.J. (1968) Biochemistry 7, 4097-4102). The pH rate profiles of the hydrolase and kinase reactions activated by Ni(II) and Co(II) are similar, suggesting common features in their mechanisms. In contrast to the kinase reaction, the reaction velocity of the hydrolase increases at high Co(II) concentrations indicating a second mode for hydrolysis.     

The active conformation of the PAK1 kinase domain

The p21-activated kinases (PAKs) participate in cytoskeletal control networks, downstream of Rho-family GTPases. A structure of PAK1 in an autoregulated, "off" state showed that a regulatory region, N-terminal to the kinase domain, forces the latter into an inactive conformation, prevents phosphorylation of Thr423 in the activation loop, and promotes dimerization. We have now determined structures at 1.8 A resolution for the free PAK1 kinase domain, with a mutation in the active site that blocks enzymatic activity, and for the same domain with a "phosphomimetic" mutation in the activation loop. The two very similar structures show that even in the absence of a phosphorylated Thr423, the kinase has an essentially active conformation. When Cdc42 binds the regulatory region and dissociates the dimer, PAK1 will be in an "intermediate-active" state, with a capacity to phosphorylate itself or other substrates even prior to modification of its activation loop.     

Energy-dependent changes in conformation and catalytic activity of the chloroplast ATP synthase.

Energy-dependent activation of the chloroplast ATP synthase (CF0CF1) has been elucidated by investigating the conformational changes, the ADP effect, and the catalytic cooperativity of ATP hydrolysis. Conformational change was observed by measuring the reactivity of Lys-109 of the epsilon subunit of chloroplast coupling factor 1 with pyridoxal 5'-phosphate. In the postillumination dark, the Lys-109 reactivity decreased biphasically with half-times of less than 1 and 17 s. NH4Cl accelerated the slow phase decrease. Addition of ADP (0.2 microM) in the postillumination dark inactivated CF0CF1 (0.05 microM) with a half-time of 12 s. At high concentration of CF0CF1 (1.2 microM), inactivation occurred without exogenously added ADP with a half-time of 12 s. Accompanying the inactivation, the positive catalytic cooperativity of ATP hydrolysis decreased. Addition of 10 mM NH4Cl before ADP (0.2 microM) decelerated the ADP-induced inactivation to a half-time of 64 s. Throughout this inactivation, the positive catalytic cooperativity was maintained at a high level. These results suggest three distinct conformations of CF0CF1, EH, EM, and EL, and their ADP binding forms EM-ADP and EL-ADP. EH, EM, and EL have a low affinity for ADP, a high affinity for ADP, and low accessibility to ADP, respectively. EM and EL exhibit highly cooperative ATP hydrolysis. ATP hydrolysis catalyzed by EM-ADP exhibits no cooperativity. EL-ADP is inactive.     

Monitoring active site alterations upon mutation of yeast pyruvate kinase using 205Tl+ NMR

The interaction of the monovalent cation with wild type (WT) yeast pyruvate kinase (YPK) and with the T298S, T298C, and T298A mutants was investigated by 205Tl+ NMR to monitor possible structural alterations at the active site by Thr-298 mutation. TlNO3 activates WT YPK with a kcat value similar to that obtained with KCl and an apparent Ka of 0.96 +/- 0.07 mm in the presence of Mn2+ and fructose 1,6-bisphosphate. With the three mutants, Tl+ is a better activator than is K+ based on kcat values. Tl+ activation and inhibition of YPK is affected by mutation of the active site Thr-298. The effect of Mn2+ on the 1/T value of 205Tl+1 in the presence of the WT and mutant YPK complexes was determined at 173 MHz (300 MHz, 1H) and 346 MHz (600 MHz, 1H). For each complex studied, 1/pT2p > 1/pT1p and 1/pT1p is frequency-dependent suggesting fast exchange conditions. The values of 1/pT1p differ for each mutant. A correlation time of 0.65 +/- 0.35 ns was estimated for the Mn2+-205Tl+ interaction. The Tl+-Mn2+ distances at the active site of YPK were calculated from the paramagnetic contribution of Mn2+ to 1/T1M of YPK-bound 205Tl+. The calculated Tl+-Mn2+ distance for the Thr-298 mutants is decreased by about 1 A from 6.0 +/- 0.2 A observed with WT. The results suggest conformational alterations at the active site of YPK where phosphoryl transfer occurs upon mutation of Thr-298. These conformational changes may, in part, explain the alteration in kcat and kcat/Km,PEP observed with the Thr-298 mutants.