The crystal structure of Pyrococcus furiosus UMP kinase provides insight into catalysis and regulation in microbial pyrimidine nucleotide biosynthesis

UMP kinase (UMPK), the enzyme responsible for microbial UMP phosphorylation, plays a key role in pyrimidine nucleotide biosynthesis, regulating this process via feed-back control and via gene repression of carbamoyl phosphate synthetase (the first enzyme of the pyrimidine biosynthesis pathway). We present crystal structures of Pyrococcus furiosus UMPK, free or complexed with AMPPNP or AMPPNP and UMP, at 2.4 A, 3 A and 2.55 A resolution, respectively, providing a true snapshot of the catalytically competent bisubstrate complex. The structure proves that UMPK does not resemble other nucleoside monophosphate kinases, including the UMP/CMP kinase found in animals, and thus UMPK may be a potential antimicrobial target. This enzyme has a homohexameric architecture centred around a hollow nucleus, and is organized as a trimer of dimers. The UMPK polypeptide exhibits the amino acid kinase family (AAKF) fold that has been reported in carbamate kinase and acetylglutamate kinase. Comparison with acetylglutamate kinase reveals that the substrates bind within each subunit at equivalent, adequately adapted sites. The UMPK structure contains two bound Mg ions, of which one helps stabilize the transition state, thus having the same catalytic role as one lysine residue found in acetylglutamate kinase, which is missing from P.furiosus UMPK. Relative to carbamate kinase and acetylglutamate kinase, UMPK presents a radically different dimer architecture, lacking the characteristic 16-stranded beta-sheet backbone that was considered a signature of AAKF enzymes. Its hexameric architecture, also a novel trait, results from equatorial contacts between the A and B subunits of adjacent dimers combined with polar contacts between A or B subunits, and may be required for the UMPK regulatory functions, such as gene regulation, proposed here to be mediated by hexamer-hexamer interactions with the DNA-binding protein PepA.     

A comparative study of the age-related patterns of decay of some nucleoside monophosphate kinases in human red cells

The nucleoside monophosphate kinases, adenylate kinase (AK), guanylate kinase (GUK), and uridine monophosphate kinase (UMPK), were studied electrophoretically and quantitatively in density gradient fractions of human red cells from normal adults which contain red cells of differing mean age. The enzymes were found to differ both in their rates and patterns of decay and in secondary isozyme formation during the life of the red cell in the circulation. AK showed no appreciable enzyme decay and slight genetation of secondary isozymes; UMPK showed a rapid monophasic decline and no secondary isozyme formation; GUK showed intermediate overall loss of activity with a biphasic pattern of decay and marked secondary isozyme formation. A comparative study of the two common phenotypes of UMPK (UMPK 1 and UMPK 2-1) and of AK (AK 1 and AK 2-1) was made. The UMPK 2 isozyme showed a more rapid decay than the UMPK 1 isozyme, whereas no difference was observed between the AK 1 and AK 2 isozymes.     

First-time crystallization and preliminary X-ray crystallographic analysis of a bacterial-archaeal type UMP kinase, a key enzyme in microbial pyrimidine biosynthesis

UMP phosphorylation, a key step for pyrimidine nucleotide biosynthesis, is catalyzed in bacteria by UMP kinase (UMPK), an enzyme specific for UMP that is dissimilar to the eukaryotic UMP/CMP kinase or to other nucleoside monophosphate kinases. UMPK is allosterically regulated and participates in pyrimidine-triggered gene repression. As first step towards determining UMPK structure, the putative UMPK-encoding gene of the hyperthermophilic archaeon Pyrococcus furiosus was cloned and overexpressed in Escherichia coli. The protein product was purified and confirmed to be a genuine UMPK. It was crystallized at 294 K in hanging drops by the vapor diffusion technique using 3.5-4 M Na formate. Cubic 0.2-mm crystals diffracted synchrotron X-rays to 2.4-angstroms resolution. Space group was I23 (a=b=c=144.95 angstroms), and the asymmetric unit contained two monomers, with 52% solvent content. The self-rotation function suggests that the enzyme is hexameric, which agrees with biochemical studies on bacterial UMPKs.     

Pyrimidine nucleoside monophosphate kinase from rat bone marrow cells: purification to high specific activity by a two-step affinity chromatography procedure

This report describes a two-column scheme for purifying a pyrimidine nucleoside monophosphate kinase from rat bone marrow cells. Purification was achieved by affinity chromatography on Blue Sepharose and cellulose phosphate, with selective elution of the enzyme by substrates (UMP, ATP). The enzyme preparation appeared to be about 90% pure upon polyacrylamide gel electrophoresis, exhibited an exceptionally high specific activity (greater than 600 mumol/min/mg protein), and was obtained with 30-36% recovery of enzyme activity. It was concluded that UMP, dUMP, and CMP serve as phosphate acceptors for the enzyme, based on the parallel behavior displayed by enzyme activity with these substrates both during the purification process and during other procedures. The purified enzyme preparation did not display dTMP kinase activity. This report also describes a simplified radiotracer assay for pyrimidine nucleoside monophosphate kinases. Thin-layer chromatography on polyethyleneimine-cellulose is used to resolve residual substrates and products. Because both nucleoside di- and triphosphates remain at the origin, the assay is insensitive to the action of nucleoside diphosphate kinases and does not require the use of marker compounds. A variety of radiolabeled substrates can be used with this assay, including UMP, dUMP, CMP, and dTMP.     

Biochemical characterization of a red cell UMP kinase variant found in the Warao Indians of Venezuela

UMPK 3 is a rare variant of the polymorphic enzyme of human red cells, uridine monophosphate kinase. This homozygote phenotype was detected among the Warao Indians of Venezuela. The UMPK 1 and UMPK 3 enzymes were partially purified following the method described by Tend et al. (1976). The biochemical and kinetic parameters of both variants were studied in crude hemolysates and in partially purified enzymes. A comparison was made with the results previously reported by Teng for UMPK 1 and UMPK 2, and it was concluded that UMPK 3 seems to resemble the other two allelic gene products in Km values for UMP, CMP, and ATP but differs from them in electrophoretic mobility, pH optimum, and thermal stability.     

Red cell uridine monophosphate kinase: effects of red cell aging on the activity of two UMPK gene products.

We have previously reported that uridine monophosphate kinase (UMPK) is genetically polymorphic in man, and that the UMPK2 gene product has less activity than that of UMPK1 when measured in normal red cells. In this paper we present evidence that the activity of UMPK, like that of many other enzymes, declines during red cell aging, and that the lower activity of UMPK 2, as compared with UMPK 1, is best explained by its more rapid catabolism.     

Uridine monophosphate kinase polymorphism in two Venezuelan populations.

A study of the uridine monophosphate kinase (UMPK) electrophoretic patterns in Venezuelan individuals from the mestizo population of Caracas and from the Warao Indians of the Nabasanuka village in the Delta of the Orinoco River are reported. Among the mestizo population, the frequency of the UMPK1, UMPK2, and UMPK3 alleles was .979, .020, and .001, respectively. A higher frequency of the UMPK3 gene was seen in the highly inbred Warao Indians than any other population studied to date.     

Human nucleoside diphosphate kinase B (Nm23-H2) from melanoma cells shows altered phosphoryl transfer activity due to the S122P mutation.

The Ser122 --> Pro mutation in human nucleoside diphosphate kinase (NDK)-B/Nm23-H2 was recently found in melanoma cells. In comparison to the wild-type enzyme, steady state activity of NDKS122P with ATP and TDP as substrates was slowed down 5-fold. We have utilized transient kinetic techniques to analyze phosphoryl transfer between the mutant enzyme and various pairs of nucleoside triphosphates and nucleoside diphosphates. The two half-reactions of phosphorylation and dephosphorylation of the active site histidine residue (His118) were studied separately by making use of the intrinsic fluorescence changes which occur during these reactions. All apparent second order rate constants are drastically reduced, falling 5-fold for phosphorylation and 40-200-fold for dephosphorylation. Also, the reactivity of the mutant with pyrimidine nucleotides and deoxy nucleotides is more than 100-fold reduced compared with the wild-type. Thus, the rate-limiting step of the NDK-BS122P-catalyzed reaction is phosphoryl transfer from the phospho-enzyme intermediate to the nucleoside diphosphate and not phosphoryl transfer from the nucleoside triphosphate to the enzyme as was found for the wild-type protein. This results in a pronounced shift of the equilibrium between unphosphorylated and phosphorylated enzyme. Moreover, like the Killer-of-prune mutation in Drosophila NDK and the neuroblastoma Ser120 --> Gly mutation in human NDK-A/Nm23-H1, the Ser122 --> Pro substitution in NDK-B affects the stability of the protein toward heat and urea. These significantly altered properties may be relevant to the role of the mutant enzyme in various intracellular processes.     

Potential application of thymidylate kinase in nucleoside analogue activation in Plasmodium falciparum

Plasmodium falciparum thymidylate kinase (PfTMPK) shows a broad range of substrate tolerance when compared to the corresponding human enzyme. Besides 2′-deoxythymidine monophosphate (dTMP), PfTMPK can phosphorylate 3′-azido-2′,3′-dideoxythymidine monophosphate (AZTMP) very efficiently. In contrast, human thymidylate kinase (hTMPK) is 200 times less active towards AZTMP. We were interested to see if we could use PfTMPK to activate 3′-azido-2′,3′-deoxythymidine (AZT) derivatives as a strategy to treat malaria. P. falciparum lacks a pyrimidine nucleoside kinase which usually activates nucleoside and nucleoside analogues to the corresponding monophosphates. Therefore, several prodrug analogues of AZT and related nucleoside monophosphates were prepared and analysed for antiparasitic activity. The prodrugs showed an increase in activity over the parent nucleoside analogues, which showed no inhibition of parasite growth at the concentration tested. The evidence here reported provides a strategy that could be exploited for further anti-malarial design.     

Activation of rat liver pyrimidine nucleoside monophosphate kinase.

The activity of the pyrimidine nucleoside monophosphate kinase (ATP:dCMP phosphotransferase, EC 2.7.4.14) from rat liver is dependent upon the presence of sulfhydryl-reducing agents. Addition to the inactive enzyme of 2-mercaptoethanol (5 mM), a reagent specific for cleavage of disulfide bonds, effects a reduction in molecular weight from approx. 53 000 to 17 000, measured by molecular sieve chromatography. This low molecular weight form is partially active in the presence of 2-mercaptoethanol (f mM). In absence of 2-mercaptoethanol, the low molecular weight form is inactive. Higher concentrations of 2-mercaptoethanol (50 mM) fully reactivate the CMP(ATP) kinase activity followed by dCMP(ATP) and CMP(dCTP) kinase activities in a sequential manner, without further change in moelcular weight. Alkylation by iodoacetamide of the enzyme at different stages of reactivation in dithiothreitol suggests an ordered appearance of the various enzyme activities. Furthermore, iodoacetamide inactivates the fully active enzyme. Thioredoxin was found to activate the enzyme in a manner similar to 2-mercaptoethanol and dithiothreitol. These results are consistent with the interpretation that the mechanism of activation of the enzyme involves cleavage of inter- and intramolecular disulfide bonds.     

Synthesis of sugar-modified nucleoside 5'-triphosphates with partially purified nucleotide kinases from calf thymus.

The partial purification of some nucleoside monophosphate kinases (ATP:nucleosidemonophosphate phosphotransferases, EC 2.7.4.4) from calf thymus by chromatography on Blue Sepharose to remove interfering phosphatase activity is described. Their specificities towards nucleoside monophosphates modified in the sugar are investigated. Pyrimidine nucleoside monophosphate kinase is not very much affected by such modifications, whereas GMP kinase does not tolerate such alteration. The effect on AMP kinase is intermediate.     

Substrate specificity of vaccinia virus thymidylate kinase

Anti-poxvirus therapies are currently limited to cidofovir [(S)-1-(3-hydroxy-2-phosphonylmethoxypropyl)cytosine], but drug-resistant strains have already been characterized. In the aim of finding a new target, the thymidylate (TMP) kinase from vaccinia virus, the prototype of Orthopoxvirus, has been overexpressed in Escherichia coli after cloning the gene (A48R). Specific inhibitors and alternative substrates of pox TMP kinase should contribute to virus replication inhibition. Biochemical characterization of the enzyme revealed distinct catalytic features when compared to its human counterpart. Sharing 42% identity with human TMP kinase, the vaccinia virus enzyme was assumed to adopt the common fold of nucleoside monophosphate kinases. The enzyme was purified to homogeneity and behaves as a homodimer, like all known TMP kinases. Initial velocity studies showed that the Km for ATP-Mg2+ and dTMP were 0.15 mm and 20 microM, respectively. Vaccinia virus TMP kinase was found to phosphorylate dTMP, dUMP and also dGMP from any purine and pyrimidine nucleoside triphosphate. 5-Halogenated dUMP such as 5-iodo-2'-deoxyuridine 5'-monophosphate (5I-dUMP) and 5-bromo-2'-deoxyuridine 5'-monophosphate (5Br-dUMP) were also efficient alternative substrates. Using thymidine-5'-(4-N'-methylanthraniloyl-aminobutyl)phosphoramidate as a fluorescent probe of the dTMP binding site, we detected an ADP-induced conformational change enhancing the binding affinity of dTMP and analogues. Several thymidine and dTMP derivatives were found to bind the enzyme with micromolar affinities. The present study provides the basis for the design of specific inhibitors or substrates for poxvirus TMP kinase.     

Deoxyguanosine kinase. Distinct molecular forms in mitochondria and cytosol.

Two distinct deoxyguanosine kinase activities have been identified in calf thymus tissue. They can be differentiated by subcellular location, electrophoretic mobility, chromatographic behavior, nucleoside specificity, apparent Km values, and end product inhibition. After a 130-fold purification from mitochondrial extract, the newly discovered kinase was specific primarily for deoxyguanosine and deoxyinosine. Unlike the cytosol enzyme, which proved to be the broadly specific deoxycytidine kinase studied previously, the mitochondrial enzyme does not phosphorylate deoxycytidine. Its apparent Km for deoxyguanosine, 6 micromolar, is 2 orders of magnitude lower than that of the cytosol enzyme. The mitochondrial enzyme is strongly inhibited by dGTP and dITP and activated up to 6-fold by dTDP and UDP, whereas neither dCTP nor dATP had much effect.     

Human erythrocyte pyrimidine 5'-nucleotidase, PN-I.

Erythrocyte maturation is accompanied by RNA degradation and release of mononucleotides. Pyrimidine 5'-nucleotidase, PN-I, has been purified and characterized. The molecular and enzymatic properties determined for the enzyme shows a 36-kDa and 5.1 pI monomeric protein with no disulfide bridges and no phosphate content. The activity is dependent on Mg(2+), while it is inactivated by heavy metals and by thiol-reactive reagents. PN-I is specific for pyrimidine nucleoside monophosphates, including the antineoplastic agents 5'-AZTMP and 5'-Ara-CMP. PN-I possess phosphotransferase activity able to exchange phosphate between pyrimidine nucleoside monophosphates and pyrimidine nucleosides, including AZT and Ara-Cyd. Amino acid sequence has been obtained from tryptic and CNBr peptides. PN-I cDNA sequence, coding for a 286-residue protein, has been retrieved from tag database, amplified by PCR, and expressed in Escherichia coli. The recombinant protein was fully active and showed identical properties with respect to PN-I. Substantial identity has been revealed with the partial sequences reported for p36, an alpha-interferon-induced protein. The significance of this identity is discussed.     

Ribonuclease of cultured mammalian cells

KB cell ribonuclease has been purified 260-fold and the fundamental properties have been studied. Though the enzyme is concentrated in the lysosomal fraction, appreciable quantities are present in the cell sap and nuclear fractions. Comparison of the optimal temperature and pH for activity, and the heat stability of enzyme from these three fractions suggests that only one species of this enzyme exists in these cells. The enzyme behaves as an endonuclease, cleaving synthetic pyrimidine polynucleotides to smaller oligonucleotides with cyclic 2′:3′ end-groups. The final product is pyrimidine nucleoside 3′ monophosphate. Polyadenylic acid is not hydrolyzed. Of the properties examined in this study only two differences were noted between KB cell and pancreatic ribonuclease. KB cell enzyme acts optimally at pH 6 as opposed to an optimum at pH 7 to 8 for pancreatic enzyme. In addition ribonuclease from KB cells is definitely less stable to heating at 100°C than is the enzyme isolated from pancreas.     

Active site mutants of Drosophila melanogaster multisubstrate deoxyribonucleoside kinase.

The multisubstrate deoxyribonucleoside kinase of Drosophila melanogaster (Dm-dNK) is sequence-related to three human deoxyribonucleoside kinases and to herpes simplex virus type-1 thymidine kinase. Dm-dNK phosphorylates both purine and pyrimidine deoxyribonucleosides and nucleoside analogues although it has a preference for pyrimidine nucleosides. We performed site-directed mutagenesis on residues that, based on structural data, are involved in substrate recognition. The aim was to increase the phosphorylation efficiency of purine nucleoside substrates to create an improved enzyme to be used in suicide gene therapy. A Q81N mutation showed a relative increase in deoxyguanosine phosphorylation compared with the wild-type enzyme although the efficiency of deoxythymidine phosphorylation was 10-fold lower for the mutant. In addition to residue Q81 the function of amino acids N28, I29 and F114 was investigated by different substitutions. All of the mutated enzymes showed decreased efficiency of thymidine phosphorylation in comparison with the wild-type enzyme supporting their importance for substrate binding and/or catalysis as proposed by the recently solved structure of Dm-dNK.     

Linkage group VI of fish of the genus Xiphophorus (Poeciliidae): Assignment of genes coding for glutamine synthetase,uridine monophosphate kinase,and transferrin

Electrophoretic variation ascribable to three protein-coding loci, coding for glutamine synthetase (GS), uridine monophosphate kinase (UMPK), and transferrin (Tf), was observed in three species of fish of the genus Xiphophorus. Electrophoretic patterns in interspecific F1 hybrid heterozygotes suggested monomeric subunit structures of UMPK and Tf and a multimeric structure of undetermined subunit number of GS. Linkage analyses in backcross hybrids indicated a recombination map of GS-0%-Tf-10.8%-UMPK. This group (designated Xiphophorus linkage group VI) was shown to assort independently from the 14 enzyme loci assigned to linkage groups I-V and from 19 other informative markers within the limits of the data.     

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 the reaction mechanism is sequential and nonequilibrium in nature. Substrates bind to the enzyme in a random order. Substrate binding is cooperative. That is, the binding of the first substrate facilitates the binding of the second substrate. UMP can bind to the purine site on the enzyme, resulting in substrate inhibition. 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.     

Kinetics and equilibria of pyrimidine nucleoside monophosphate kinase from human erythrocytes.

The common type of pyrimidine nucleoside monophosphate kinase (ATP:CMP phosphotransferase, EC 2.7.4.14), purified 50 000-fold from human erythrotes, reacted with a wide variety of nucleotides, but only ATP, dATP, UMP and CMP were good substrates. The optimum Mg2+ concentration, 2-3 mM, was generally independent of substrate concentration, of the nature of the substrate, and of the direction of the reaction. Kinetic studies indicated that a ternary complex was formed, that the substrates were bound at two unlike sites, and that the order of addition of substrates was random. Equilibrium constants were ATP + UMP 0.98, ATP + CMP 1.59, dATP + UMP 1.13, and ATP + AMP 1.20.     

Characterization of undecaprenol kinase from Lactobacillus plantarum.

A membrane-bound undecaprenol kinase from Lactobacillus has been identified by observing the ATP-dependent phosphorylation of [14C]undercaprenol. The product of this reaction was shown to be [14C]undecaprenyl monophosphate by comparison of its chromatographic mobilities with authentic undecaprenyl monophosphate. It was shown that 32P from [gamma-32P]ATP was incorporated into undecaprenyl monophosphate. The kinase was partially solubilized by a variety of methods utilizing Triton X-100. Both the membrane-associated and solubilized enzymes required Mg2+, Triton X-100 and dimethylsulfoxide for activity. The enzyme preferentially phosphorylated the C34, C50 AND C 55 polyprenols. Geranylgeraniol (C20) and dolichol (C100), however, were utilized only 6% and 13% as well as undecaprenol, respectively. Despite the 8-fold difference in apparent V values, the apparent Km values for dolichol and undecaprenol were both 14 microM. The apparent Km for the nucleotide cosubstrate, ATP, was 2 mM. No other nucleoside triphosphate could substitute for ATP.