Nucleoside Monophosphate Kinase Research Articles

A Continuous Spectrophotometric Assay for Glycosyltransferases

This paper describes a continuous spectrophotometric assay for glycosyltransferases. In this assay, a nucleotide diphosphate is coupled to NADH oxidation via pyruvate kinase and lactate dehydrogenase. The nucleotide diphosphate is produced either directly during the glycosyltransferase mediated reaction, or indirectly by the production of a nucleotide monophosphate during the glycosyltransferase mediated reaction, and subsequent conversion of the nucleotide monophosphate to nucleotide diphosphate using nucleoside monophosphate kinase. Using this assay, kinetic parameters for fucosyl-, sialyl-, and N-acetylglucosaminyltransferases were determined. The assay not only allows continual monitoring of the enzymatic reaction, but is rapid and allows the processing of 96 samples at once since it is performed in 96-well microtiter plates. In addition, the procedure provides a means of monitoring the activity of these enzymes using sugar-nucleotide donor analogs, where radiochemical procedures cannot be used.

Improved Spectrophotometric Assay of Nucleoside Monophosphate Kinase Activity Using the Pyruvate Kinase/Lactate Dehydrogenase Coupling System

Improved Spectrophotometric Assay of Nucleoside Monophosphate Kinase Activity Using the Pyruvate Kinase/Lactate Dehydrogenase Coupling System

The Structure of Uridylate Kinase with Its Substrates, Showing the Transition State Geometry

Uridylate kinase from Saccharomyces cerevisiae is a member of the nucleoside mono-phosphate (NMP) kinase family and catalyzes the reaction ATP+NMP ⇌ ADP+NDP with moderate specificity for UMP. The recombinant enzyme crystallized together with two substrate molecules. The structures was solved, by multiple isomorphous replacement and solvent flattening, at 3·0 Å and then refined at 2·13 Å resolution. The present R-factor is 19%. Superposition onto the structure of a substrate-free adenylate kinase revealed the motions induced by substrate binding. A further superposition onto an adenylate kinase with bound P 1,P 5-bis(5′-adenosyl)pentaphosphate (Ap 5A), a two-substrate-mimicking inhibitor, failed to explain the UMP preference of the uridylate kinase, but superimposed the nucleosides and in particular the non-transferred phosphates at the ATP- and NMP-site rather well. The coincidence of the phosphates indicate strongly that these groups assume their final positions during catalysis. This locates the transition state, which can be modeled with reasonable geometry in agreement with an in-line associative S N2 mechanism.

Multicopy suppressors, mssA and mssB, of an smbA mutation of Escherichia coli.

We have isolated and characterized two multicopy suppressors, mssA and mssB, which suppress the cold-sensitive growth phenotype of the smbA2 mutant of Escherichia coli. The mssA gene is located immediately upstream of the rpsA gene (20.5 min). MssA protein was found to be related to nucleoside monophosphate kinases. The mssB gene was found to be identical to the deaD gene (69 min), which encodes a putative RNA helicase. The SmbA protein belongs to the aspartokinase family and probably represents a new, fourth aspartokinase species in E. coli. Expression of the smbA gene is essential for cell growth. The smbA2 mutant shows a pleiotropic phenotype characterized by cold-sensitive growth, hypersensitivity to the detergent sodium dodecyl sulfate, and formation of a translucent segment at midcell or at a pole of the cell when grown at 22 degrees C. In addition, some cellular proteins were either increased or decreased in amount in the smbA2 mutant. SmbA may be a regulatory factor in the expression of a battery of genes. MssA and MssB might also relate to the expression of some of these genes. Multiple copies mssA and mssB suppressed the various phenotypic features of the smbA2 mutant to various extents, suppressing the cold-sensitive growth completely.

Molecular analysis of the essential gene for adenylate kinase from the fission yeast Schizosaccharomyces pombe

The enzyme-catalyzed transfer of the terminal phosphoryl group from ATP to an acceptor molecule is an important reaction in a wide variety of biological processes. I demonstrate here the essential function of an ATP:AMP phosphotransferase (adenylate kinase) in the fission yeast Schizosaccharomyces pombe. A cDNA clone encoding immunoreactive adenylate kinase from S. pombe was isolated from a lambda gt11 expression library by cross-reaction with antibodies raised against the recently characterized ADK1 enzyme from the budding yeast Saccharomyces cerevisiae. Subsequent cloning and nucleotide sequence analysis of the S. pombe adenylate kinase gene, adk1, revealed a coding region of 660 nucleotides. The alignment of the two amino acid sequences from S. cerevisiae and S. pombe shows 67% identity. By gene disruption and tetrad analysis it is demonstrated that adk1 is absolutely essential for cell viability. This is in contrast to the ADK1 gene of S. cerevisiae, the deletion of which was shown to lead to a slower cell growth rate rather than to a lethal phenotype. Expression of adk1 in the S. cerevisiae ADK1 deletion strain restored normal cell growth, demonstrating that ADK1 and adk1 are functionally interchangeable. However, despite lack of absolute substrate specificity of adenylate kinases, adk1 could not complement the loss of function of the guanylate kinase encoding gene in a S. cerevisiae null mutant strain, thus highlighting the functional uniqueness of each nucleoside monophosphate kinase. Using suitable expression vectors, large amounts of active adk1 enzyme were produced in either yeast species and in E. coli. The purified enzyme exhibits a high preference for adenine nucleotides, with ATP being a 10 times more efficient phosphoryl donor than GTP.

Nucleoside monophosphate kinase may be the key enzyme preventing salvage of DNA 5-methylcytosine

Nucleoside monophosphate kinase (EC 2.7.4.4) catalyzes the phosphorylation of various nucleoside monophosphates to their corresponding diphosphates. We investigated whether 5-methyl-2′-deoxycytidine 5′-monophosphate (5MedCMP) could serve as a substrate for the enzyme isolated from bovine liver. Although the substrate activity of UMP, CMP and dCMP was readily demonstrable, no activity was recorded with 5MedCMP as the candidate substrate. Moreover, 5MedCMP did not affect the active site of the enzyme, since no inhibition in the phosphorylation of UMP was recorded in the presence of 5MedCMP. This metabolic step appears to be the key phase where the incorporation of exogenous 5-methylcytosine (5MeCyt) into DNA is prevented. Hence, very little or no salvage of DNA 5MeCyt can be expected.

The adenylate kinase family in yeast: identification of URA6 as a multicopy suppressor of deficiency in major AMP kinase

The gene URA6 encoding uridylate kinase (UK) from Saccharomyces cerevisiae was isolated as a multicopy suppressor of the respiratory-deficient phenotype of an S. cerevisiae mutant defective in the gene AKY2 encoding AMP kinase (AK). The URA6 gene also restored temperature resistance to two different temperature-sensitive mutations in the gene encoding Escherichia coli AK. By contrast, the gene encoding UK of Dictyostelium discoideum on a multicopy yeast shuttle plasmid, expressed under control of the constitutive yeast AKY2 promoter, failed to complement the deficiency in yeast, although such transformants expressed high UK activity. We show that yeast UK exerts significant AK activity which is responsible for the complementation and is absent in the analogous enzyme from D. discoideum. Since UK also significantly phosphorylates CMP (but not GMP), it must be considered an unspecific short-form nucleoside monophosphate kinase. Wild-type mitochondria lack UK activity, but import AKY2. Since multicopy transformation with URA6 heals the Pet − phenotype of AKY2 disruption mutants, the presence of AKY2 in the mitochondrial intermembrane space is not required to maintain respiratory competence. However, furnishing UK with the bipartite intermembrane space-targeting presequence of cytochrome c 1 improves the growth rates of AKY2 mutants with nonfermentable substrates, suggesting that AK activity in mitochondria is helpful, though not essential for oxidative growth.

Decreased Pyrimidine Nucleoside Monophosphate Kinase Activity in Sickle Erythrocytes

We have previously shown that physiologic concentrations of hemin cause marked inhibition of several red blood cell (RBC) enzymes. Because endogenous heme content is elevated in sickle RBCs, we have examined the activity of hemin-sensitive enzymes in these RBCs. One of the hemin-sensitive enzymes, pyrimidine nucleoside monophosphate kinase (PNMK), was shown to have decreased activity in sickle RBCs relative to RBCs of equivalent cell age. The other hemin-sensitive enzymes, including adenylate kinase (AK), pyrimidine 5'-nucleotidase (P5N), 6-phosphogluconate dehydrogenase (6PGD), and aldolase, had activities that were appropriate for cell age. We have also examined the affinity of the hemin-sensitive enzymes to hemin. Using two different methods, PNMK was shown to have the highest binding affinity to hemin. The exquisite sensitivity of PNMK to inhibition by hemin, coupled with the enzyme's high affinity to hemin, may account for the decrease in PNMK activity and the lack of significant decrease in the other hemin-sensitive enzymes in sickle RBCs. These results suggest that the increased endogenous heme content in sickle RBCs may be responsible for the decrease in PNMK activity. Whether the increased endogenous heme content of sickle RBCs can cause hemolysis indirectly by inhibiting RBC enzymes remains to be determined.

Decreased pyrimidine nucleoside monophosphate kinase activity in sickle erythrocytes

We have previously shown that physiologic concentrations of hemin cause marked inhibition of several red blood cell (RBC) enzymes. Because endogenous heme content is elevated in sickle RBCs, we have examined the activity of hemin-sensitive enzymes in these RBCs. One of the hemin- sensitive enzymes, pyrimidine nucleoside monophosphate kinase (PNMK), was shown to have decreased activity in sickle RBCs relative to RBCs of equivalent cell age. The other hemin-sensitive enzymes, including adenylate kinase (AK), pyrimidine 5′-nucleotidase (P5N), 6- phosphogluconate dehydrogenase (6PGD), and aldolase, had activities that were appropriate for cell age. We have also examined the affinity of the hemin-sensitive enzymes to hemin. Using two different methods, PNMK was shown to have the highest binding affinity to hemin. The exquisite sensitivity of PNMK to inhibition by hemin, coupled with the enzyme's high affinity to hemin, may account for the decrease in PNMK activity and the lack of significant decrease in the other hemin- sensitive enzymes in sickle RBCs. These results suggest that the increased endogenous heme content in sickle RBCs may be responsible for the decrease in PNMK activity. Whether the increased endogenous heme content of sickle RBCs can cause hemolysis indirectly by inhibiting RBC enzymes remains to be determined.

A new member of the adenylate kinase family in yeast: PAK3 is highly homologous to mammalian AK3 and is targeted to mitochondria.

Making use of the polymerase chain reaction primed by oligonucleotides corresponding to regions conserved between members of the nucleoside monophosphate kinase family, we have isolated the yeast gene PAK3. Pak3p belongs to the subgroup of long-form adenylate kinase isozymes (deduced molecular mass 25.3 kDa) and exhibits highest sequence similarity to bovine AK3 rather than to the yeast isozyme, Aky2p. The gene is shown to be non-essential because haploid disruption mutants are viable, both in the presence and absence of a functional AKY2 allele. It maps on chromosome V upstream of RAD3. Its expression level is low when cells are grown on glucose or other fermentable carbon sources and about threefold higher on glycerol, but can be significantly induced by ethanol. A PAK3/mouse dihydrofolate reductase fusion construct expressed in yeast is targeted to mitochondria. Transformation with PAK3 on a multicopy plasmid complements neither adenylate kinase deficiency in an aky2-disrupted yeast strain nor in Escherichia coli cells conditionally defective in adenylate kinase.

Metabolism of 1-(S)-(3-Hydroxy-2-phosphonomethoxypropyl)cytosine (HPMPC) in Human Embryonic Lung Cells

The acyclic nucleotide analogue HPMPC is in human embryonic lung cells, cultured in vitro, transformed to its mono- and diphosphates (HPMPCp and HPMPCpp) and HPMPCp-choline; the synthesis of HPMPCp is catalysed by pyrimidine nucleoside monophosphate kinase (EC 2.7.4.14); HPMPCp-choline (analogue of CDP-choline) is formed from HPMPCpp and choline phosphate in the presence of CTP:phosphorylcholine cytidylyltransferase (EC 2.7.7.15). These metabolites persist for a long time in the cellular pool even after HPMPC has been removed from the medium; on the other hand, they efflux to the medium. Neither HPMPC, nor any of its metabolites interfere with intracellular CDP-choline level.

Structural and functional consequences of amino acid substitutions in the second conserved loop of Escherichia coli adenylate kinase.

All known nucleoside monophosphate kinases contain an invariant sequence Asp-Gly-Phe(Tyr)-Pro-Arg. In order to understand better the structural and functional role of individual amino acid residues belonging to the above sequence, three mutants of Escherichia coli adenylate kinase (D84H, G85V, and F86L) were produced by site-directed mutagenesis. Circular dichroism spectra revealed that the secondary structure dichroism spectra revealed that the secondary structure of all three mutant proteins is very similar to that of the wild-type enzyme. However, each of the substitutions resulted in a decreased thermodynamic stability of the protein, as indicated by differential scanning calorimetry measurements and equilibrium unfolding experiments in guanidine HCl. The destabilizing effect was most pronounced for the G85V mutant, in which case the denaturation temperature was decreased by as much as 11 degrees C. The catalytic activity of the three mutants represented less than 1% of that of the wild-type enzyme. Furthermore, for the D84H-modified form of adenylate kinase, the impaired binding of nucleotide substrates was accompanied by a markedly decreased affinity for magnesium ion. These observations support the notion that Asp84 is directly involved in binding of nucleotide substrates and that this binding is mediated by interaction of the aspartic acid residue with divalent cation. The two remaining residues probed in this study, Gly85 and Phe86, belong to a beta-turn which appears to play a major role in stabilizing the three-dimensional structure of adenylate kinase.

Enzymatic synthesis of cytidine 5′-diphosphate using pyrimidine nucleoside monophosphate kinase

Nucleoside monophosphate kinase (NMPK, EC 2.7.4.4, from bovine liver or yeast) has been used to prepare cytidine 5′-diphosphate (CDP). The enzyme catalyses the reversible ( K eq ≅ 1) reaction of a pyrimidine nucleoside 5′-monophosphate and ATP to produce a nucleoside 5′-diphosphate and ADP. Equilibrium mixtures of CMP, CDP, ADP, and ATP were obtained from the reaction of CMP, ATP, and magnesium chloride with NMPK. The soluble enzyme could be recovered and reused but an enzyme activity half-life of only ca. 2 days was observed. Stabilization of enzyme activity by immobilization via covalent bonding to a carrier surface, and by gel entrapment, was examined. Immobilization yields were optimized by varying protein loading, pH, temperature, ionic strength, type of buffer, and concentration of enzyme substrates. The highest yields of immobilized NMPK activity were obtained by gel entrapment in a poly(acrylamide-co- N-acryloxysuccinimide) gel crosslinked with triethylenetetramine (PAN-500); NMPK immobilized using this method exhibited increased stability of enzyme activity compared to the unimmobilized enzyme.

Ketone body and phosphoenolpyruvate formation by isolated hepatic mitochondria from Squalus acanthias (spiny dogfish)

AbstractIn elasmobranchs, triglycerides are stored in the liver, which appears to be the primary site for lipolysis and oxidation of fatty acids, a major product being ketone bodies. The objective of this study was to obtain comparative information about properties of ketone body and phosphoenolpyruvate formation by liver of Squalus acanthias (spiny dogfish, a representative elasmobranch) by using an isolated hepatic mitochondrial system we have previously described for studying respiration and glutamine‐dependent citrulline synthesis. Acetate and palmitoyl‐CoA are stoichiometrically converted to ketone bodies at a rapid rate. The capability of mitochondria to convert short‐chain fatty acids to ketone bodies indicates that the previously reported inability of dogfish mitochondria to utilize short‐chain fatty acids to support respiration is not due to absence of nucleoside monophosphate kinase activity. At least two acyl‐CoA synthetase activities are present in mitochondrial extracts, one specific for acetate and another with specificity for longer‐chain fatty acids. Utilization of palmitoyl‐CoA is carnitine‐dependent and is inhibited by low concentrations of malonyl‐CoA. Pyruvate and alanine are also rapidly metabolized to ketone bodies. Phosphoenolpyruvate is formed at a significant rate from a number of substrates, including in particular aspartate and malate in the presence of α‐ketoglutarate. The osmolytes urea and trimethylamine oxide activate and inhibit, respectively, phosphoenolpyruvate formation; in contrast, these osmolytes inhibit and activate, respectively, ketone body and citrulline formation by isolated mitochondria. The results are consistent with the reported unique functions of dogfish liver in lipid metabolism and indicate that the basic enzymatic processes at the level of mitochondria appear to be analogous to those present in mammalian species.

The use of immobilised glycosyltransferases in the synthesis of sialyloligosaccharides

The CMP-sialic acids, cytidine 5′-(5-acetamido-3,5-dideoxy-β- d- glycero- d- galacto-2-nonulopyranosylonic acid monophosphate) ( 1) and cytidine 5′-(5-acetamido-9- O-acetyl-3,5-dideoxy-β- d- glycero- d- galacto-2-nonulopyranosylonic acid monophosphate ( 2) were prepared from CMP, phosphoenolpyruvate, N-acetylneuraminic acid or its 9-acetate, and a catalytic amount of ATP in the presence of immobilised pyruvate kinase, nucleoside monophosphate kinase, inorganic pyrophosphatase, and CMP-sialic acid synthetase. CMP-NeuAc ( 1) was used as a donor of N-acetylneuraminic acid in the reaction catalysed by immobilised porcine liver β- d-Gal p-(1→4)-α- d-Glc pNAc-(2→6)-sialytransferase. α- d-Neu p5Ac-(2→6)-β- d-Gal p-(1→4)-β- d-Glc pNAc-(1→2)-α- d-Man-OMe ( 5) was obtained on a 0.1-mmol scale by enzymic sialylation of β- d-Gal p-(1→4)-β- d-Glc pNAc-(1→2)-α- d-Man-OME 4), prepared by enzymic galactosylation of β- d-Glc pNAc-(1→2)-α- d-Man-OMe ( 3). Likewise, using 2, α- d-Neu p-5,9Ac 2-(2→6)-β- d-Gal p- (1→4)- d-Glc pNAc ( 7) was obtained from N-acetyl-lactosamine ( 6).

Preparation of a mixture of nucleoside triphosphates suitable for use in synthesis of nucleotide phosphate sugars from ribonucleic acid using nuclease P1, a mixture of nucleoside monophosphokinases and acetate kinase

This paper (1) describes the enzymatic synthesis of a mixture of adenosine, guanosine, cytidine, and uridine triphosphates (ATP, GTP, CTP, and UTP) from ribonucleic acid (RNA). RNA was hydrolyzed by nuclease P1 to a mixture of 5'-nucleoside monophosphates. This mixture was converted to the nucleoside triphosphates using a mixture of nucleoside monophosphate kinases and acetate kinase, with acetyl phosphate as the ultimate phosphoryl donor. The nucleoside monophosphokinases were extracted from brewer's yeast in a four-step procedure. The specific activity of the yeast enzyme preparation after gel permeation chromatography was sufficiently high that the yeast kinases could be immobilized in volumes that were practical for laboratory scale syntheses. Conversions from NMP to NTP in a mixture containing 0.34 mol of total nucleoside phosphates were: ATP, 90%; GTP, 90%; CTP, 60%; and UTP, 40%.

Nucleotide interconversions in microtubule protein preparations, a significant complication for accurate measurement of GTP hydrolysis in the presence of adenosine 5'-(beta, gamma-imidotriphosphate).

Pursuing the observation of Carlier and Pantaloni [Carlier, M.-F., & Pantaloni, D. (1982) Biochemistry 21, 1215-1224] that adenosine 5'-(beta, gamma-imidotriphosphate) (pNHppA) strongly inhibited tubulin-independent phosphatases in microtubule protein preparations, we observed with a number of commercial preparations of pNHppA that a major proportion of the terminal phosphate of [gamma-32P]GTP added to microtubule protein preparations was rapidly converted into ATP. Initially postulating degradation of pNHppA to AMP followed by stepwise conversion of AMP to ATP, we isolated two nucleoside monophosphate kinase activities from microtubule protein capable of generating ATP from AMP + GTP. The amounts of these enzymes in microtubule protein preparations, however, are probably too low to account for rapid ATP formation. Instead, ATP formation most likely is caused by nucleoside diphosphate kinase acting on ADP contaminating commercial pNHppA preparations. Such ADP contamination was demonstrated by high-performance liquid chromatography, with the amount of ATP formed with different pNHppA preparations proportional to the amount of ADP contamination. Repurification of commercial pNHppA until it was free of contaminating ADP also resulted in the elimination of ATP formation. The repurified pNHppA potently inhibited GTP hydrolysis in microtubule protein preparations. In addition, especially when supplemented with equimolar Mg2+, the repurified pNHppA strongly inhibited GTP hydrolysis and microtubule assembly in reaction mixtures containing purified tubulin and heat-treated microtubule-associated proteins (which contain negligible amounts of tubulin-independent phosphatase activity). We conclude that studies of microtubule-dependent GTP hydrolysis which make use of pNHppA must be interpreted with extreme caution.

Pyrimidine nucleoside monophosphate kinase hyperactivity in hereditary erythrocyte pyrimidine 5'-nucleotidase deficiency.

The pyrimidine nucleoside triphosphates (CTP, UTP) increase in the pyrimidine 5'-nucleotidase (P5N) deficient red blood cell (RBC) to a greater degree than do the pyrimidine nucleoside monophosphates (CMP, UMP). Pyrimidine nucleoside monophosphate (PNMP) kinase phosphorylates CMP and UMP to their respective phosphodiesters. We tested the hypothesis that increased PNMP kinase activity contributes to the disproportionate increase in CTP and UTP in the P5N deficient RBC. CMP and UMP kinase activities were increased in high reticulocyte (4.4 +/- 2.1 and 8.5 +/- 3.3 mumol/ml RBC per minute) compared to normal RBC (2.8 +/- 1.0 and 6.0 +/- 2.5 mumol/ml RBC per minute). P5N deficient RBC (n = 2) had significantly increased CMP and UMP kinase activities (14.0 and 26.5 mumol/ml RBC per minute). UMP and CDP-ethanolamine were able to increase the activity of CMP kinase in crude haemolysate and the activity of partially purified enzyme. Since the Km for CMP of CMP kinase was 33 mumol/l in P5N deficient RBC and since the CMP concentration is 25-90 mumol/l in the P5N deficient RBC, the enzyme should be nearly saturated with CMP in the P5N deficient RBC. Thus, PNMP kinase hyperactivity appears to contribute to the disproportionate increase in CTP and UTP in the P5N deficient RBC.

Pyrimidine nucleoside monophosphate kinase from rat bone marrow cells: A kinetic analysis of the reaction mechanism

A kinetic analysis of the reaction mechanism of pyrimidine nucleoside monophosphate kinase was carried out with a highly purified enzyme preparation from rat bone marrow cells. The results of initial rate and product inhibition studies provided insight into the mode of action of the enzyme. The data support the views that (i) the reaction mechanism is sequential and nonequilibrium in nature, (ii) Substrates bind to the enzyme in a random order, (iii) Substrate binding is cooperative. That is, the binding of the first substrate facilitates the binding of the second substrate, (iv) UMP can bind to the purine site on the enzyme, resulting in substrate inhibition, (v) Product inhibition can result from the binding of UDP to either the pyrimidine or purine site, or from the binding of ADP to the purine site.

Analysis of the energy metabolism after incubation of Saccharomyces cerevisiae with sulfite or nitrite.

After addition of 5 mM sulfite or nitrite to glucose-metabolizing cells of Saccharomyces cerevisiae a rapid decrease of the ATP content and an inversely proportional increase in the level of inorganic phosphate was observed. The concentration of ADP shows only small and transient changes. Cells of the yeast mutant pet 936, lacking mitochondrial F1 ATPase, after addition of 5 mM sulfite or nitrite exhibit changes in ATP, ADP and inorganic phosphate very similar to those observed in wild type cells. They key enzyme of glucose degradation, glyceraldehyde-3-phosphate dehydrogenase was previously shown to be the most sulfite- or nitrite-sensitive enzyme of the glycolytic pathway. This enzyme shows the same sensitivity to sulfite or nitrite in cells of the mutant pet 936 as in wild type cells. It is concluded that the effects of sulfite or nitrite on ATP, ADP and inorganic phosphate are the result of inhibition of glyceraldehyde-3-phosphate dehydrogenase and not of inhibition of phosphorylation processes in the mitochondria. Levels of GTP, UTP and CTP show parallel changes to ATP. This is explained by the presence of very active nucleoside monophosphate kinases which cause a rapid exchange between the nucleoside phosphates. The effects of the sudden inhibition of glucose degradation by sulfite or nitrite on levels of ATP, ADP and inorganic phosphate are discussed in terms of the theory of Lynen (1942) on compensating phosphorylation and dephosphorylation in steady state glucose metabolizing yeast.