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PubMed2001

NaCl-activated nucleoside diphosphate kinase from extremely halophilic archaeon, Halobacterium salinarum, maintains native conformation without salt.

Enzymes from extremely halophilic archaea are readily denatured in the absence of a high salt concentration. However, we have observed here that a nucleoside diphosphate kinase prepared from Halobacterium salinarum was active and stable in the absence of salt, though it has the amino acid composition characteristic of halophilic enzymes. Recombinant nucleoside diphosphate kinase expressed in Escherichia coli requires salt for activation in vitro, but once it acquires the proper folding, it no longer requires the presence of salts for its activity and stability.

Amino Acid Sequence↗
PubMed1997

Intrinsic nucleoside diphosphate kinase-like activity as a novel function of 14-3-3 proteins.

14-3-3 proteins play a role in many cellular functions as molecular chaperone and adapter proteins: they bind to and modulate several proteins involved in cell proliferation and differentiation, and also function ATP-dependently in targeting of precursors to mitochondria. We show here that 14-3-3 purified from a human lymphoblastoma and also its recombinant tau isoform exhibited intrinsic nucleoside diphosphate (NDP) kinase-like activity. 14-3-3 proteins preferentially catalyzed the transfer of the gamma-phosphate group from ATP, dATP or dGTP to all nucleoside diphosphates and this transfer involved acid-labile phosphoenzyme intermediates. They also simultaneously catalyzed the reverse reaction of ATP hydrolysis. These properties of 14-3-3 are similar to those of NDP kinase, but not to those of adenylate kinase.

14-3-3 Proteins↗
PubMed2000

Nucleoside diphosphate kinase of Trypanosoma brucei.

Nucleoside diphosphate kinase (NDPK) is a highly conserved, multifunctional enzyme. Its originally described function is the phosphorylation of nucleoside diphosphates to the corresponding triphosphates, using ATP as the phosphate donor and a high-energy phosphorylated histidine residue as the reaction intermediate. More recently, a host of additional functions of NDPK have been discovered. Some of these correlate with the capacity of NDPK to transphosphorylate other proteins, in a manner reminiscent of bacterial two-component systems. Other functions may be mediated by direct DNA-binding of NDPK. This study describes the identification of NDPK from the parasitic protozoon Trypanosoma brucei. The genome of this major disease agent contains a single gene for NDPK. The predicted amino acid sequence of the trypanosomal enzyme is highly conserved with respect to all other species. The protein is constitutively expressed and is present in procyclic and in bloodstream forms. Immunofluorescence and immuno-electron microscopy demonstrate that trypanosomal NDPK (TbNDPK) is predominantly localized in the cell nucleus. Histidine phosphorylation of TbNDPK is essentially resistant to the experimental compound LY266500, a potent inhibitor of histidine phosphorylation of trypanosomal succinyl coenzyme A synthase.

Amino Acid Sequence↗
PubMed2002

Rapid photolytic release of cytidine 5'-diphosphate from a coumarin derivative: a new tool for the investigation of ribonucleotide reductases.

In order to study the long-range radical transfer in the Escherichia coli ribonucleotide reductase (RNR), caged cytidine 5'-diphosphate (CDP) 1 was synthesized, which contains the photolabile (7-diethylaminocoumarin-4-yl)methyl moiety. The caged CDP 1 triggers the release of CDP when irradiated at wavelengths between 365 and 436 nm. The rate constant of the formation of alcohol 2 and cytidine 5'-diphosphate 3 is 2x10(8) s(-1) and the quantum efficiency for the disappearance of caged CDP 1 is 2.9%.

Coumarins↗
PubMed2000

Oxidative modification of nucleoside diphosphate kinase and its identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

Nucleoside diphosphate kinase (NDPK, Nm23) has been implicated as a multifunctional protein. However, the regulatory mechanism of NDPK is poorly understood. We have examined the modification of NDPK in oxidative stresses. We found that oxidative stresses including diamide and H(2)O(2) treatment cause disulfide cross-linking of NDPK inside cells. This cross-linking was reversible in response to mild oxidative stress, and irreversible to strong stress. This suggests that disulfide cross-linked NDPK may be a possible mechanism in the modification of cellular regulation. To confirm this idea, oxidative modification of NDPK has been performed in vitro using purified human NDPK H(2)O(2) inactivated the nucleoside diphosphate (NDP) kinase activity of NDPK by producing intermolecular disulfide bonds. Disulfide cross-linking of NDPK also dissociated the native hexameric structure into a dimeric form. The oxidation sites were identified by the analysis of tryptic peptides of oxidized NDPK, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Intermolecular cross-linking between Cys109-Cys109, which is highly possible based on the X-ray crystal structure of NDPK-A, and oxidations of four methionine residues were identified in H(2)O(2)-treated NDPK. This cross-linkng was confirmed using mutant C109A (NDPK-A(C109A)) which had similar enzymatic activity as a wild NDPK-A. Mutant NDPK-A(C109A) was not cross-linked and was not easily denatured by the oxidant. Therefore, enzymatic activity and the quaternary structure of NDPK appear to be regulated by cross-linking with oxidant. These findings suggest one of the regulatory mechanisms of NDPK in various cellular processes.

Amino Acid Sequence↗
PubMed2000

Stathmin slows down guanosine diphosphate dissociation from tubulin in a phosphorylation-controlled fashion.

Stathmin is an important protein that interacts with tubulin and regulates microtubule dynamics in a phosphorylation-controlled fashion. Here we show that the dissociation of guanosine 5'-diphosphate (GDP) from beta-tubulin is slowed 20-fold in the (tubulin)(2)-stathmin ternary complex (T(2)S). The kinetics of GDP or guanosine 5'-triphosphate (GTP) dissociation from tubulin have been monitored by the change in tryptophan fluorescence of tubulin upon exchanging 2-amino-6-mercapto-9-beta-ribofuranosylpurine 5'-diphosphate (S6-GDP) for tubulin-bound guanine nucleotide. At molar ratios of stathmin to tubulin lower than 0.5, biphasic kinetics were observed, indicating that the dynamics of the complex is extremely slow, consistent with its high stability. The method was used to characterize the effects of phosphorylation of stathmin on its interaction with tubulin. The serine-to-glutamate substitution of all four phosphorylatable serines of stathmin (4E-stathmin) weakens the stability of the T(2)S complex by about 2 orders of magnitude. The phosphorylation of serines 16 and 63 in stathmin has a more severe effect and weakens the stability of T(2)S 10(4)-fold. The rate of GDP dissociation is lowered only 7-fold and 4-fold in the complexes of tubulin with 4E-stathmin and diphosphostathmin, respectively. Sedimentation velocity studies support the conclusions of nucleotide exchange data and show that the T(2)S complexes formed between tubulin and 4E-stathmin or diphosphostathmin are less compact than the highly stable T(2)S complex. The correlation between the effect of phosphorylation of stathmin on the stability of T(2)S complex measured in vitro and on the function of stathmin in vivo is discussed.

Animals↗
PubMed1983

Resonance energy transfer between the adenosine 5'-diphosphate site of glutamate dehydrogenase and a guanosine 5'-triphosphate site containing a tyrosine labeled with 5'-[p-(fluorosulfonyl)benzoyl]-1,N6-ethenoadenosine.

The fluorescent nucleotide analogue 5'-[p-(fluorosulfonyl)benzoyl]-1,N6-ethenoadenosine (5'-FSB epsilon A) reacts irreversibly with bovine liver glutamate dehydrogenase and modifies one of the natural inhibitory guanosine 5'-triphosphate (GTP) sites [Jacobson, M.A., & Colman, R.F. (1982) Biochemistry 21, 2177-2186]. Enzyme with 1.28 mol of 5'-(p-sulfonylbenzoyl)-1,N6-ethenoadenosine/mol of subunit incorporated and exhibiting maximum change in sensitivity to GTP inhibition is now shown by amino acid analysis to contain 0.95 mol of O-[(4-carboxyphenyl)sulfonyl]tyrosine (CBS-Tyr) and 0.33 mol of N epsilon-[(4-carboxyphenyl)sulfonyl]-lysine (CBS-Lys), quantitatively accounting for the total incorporation prior to acid hydrolysis. As a function of time of incubation with 5'-FSB epsilon A, the amount of CBS-Tyr formed was directly proportional to the change in GTP inhibition. In contrast, an initial formation of CBS-Lys was observed, followed by relatively little additional CBS-Lys although the percent change in GTP inhibition continued to increase. It was concluded that the tyrosine is an essential residue in the GTP binding site of glutamate dehydrogenase, while the lysine modified is not involved in the inhibitory action of GTP. The nucleotide analogue 2'(3')-O-(2,4,6-trinitrophenyl)adenosine 5'-diphosphate (TNP-ADP) was evaluated for its ability to occupy the adenosine 5'-diphosphate (ADP) activator site and to function as an energy acceptor conjointly with 5'-SB epsilon A covalently bound at the GTP site as the energy donor. TNP-ADP activates native enzyme 2-fold and competes kinetically with ADP. As determined by fluorometric titration, the maximum number of TNP-ADP binding sites on native enzyme was 0.5 mol/mol of subunit in the absence and 1 mol/mol of subunit in the presence of reduced coenzyme. The 5'-SB epsilon A-modified enzyme also binds TNP-ADP: 0.5 mol/mol of subunit in the absence or presence of reduced coenzyme. TNP-ADP competes for binding with ADP to native and 5'-SB epsilon A-modified enzyme, indicating that this nucleotide analogue is a satisfactory fluorescent probe of the ADP site of glutamate dehydrogenase. An energy-transfer efficiency of 0.77 was determined from the decrease in donor fluorescence upon addition of TNP-ADP in the absence of reduced coenzyme to modified enzyme containing 1.23 mol of 5'-SB epsilon A/mol of subunit. A value of 18 A was calculated as the average distance between the GTP and ADP regulatory sites. This result indicates that the inhibitory GTP and the activatory ADP sites are close but not identical.

Adenosine↗
PubMed1984

6-[(4-bromo-2,3-dioxobutyl)thio]-6-deaminoadenosine 5'-monophosphate and 5'-diphosphate: new affinity labels for purine nucleotide sites in proteins.

Two new adenine nucleotide analogues have been synthesized and characterized: 6-[(4-bromo-2,3-dioxobutyl)thio]-6-deaminoadenosine 5'-monophosphate and 5'-diphosphate. The bromoketo and dioxobutyl moieties have the ability to react with the nucleophilic side chains of several amino acids, as well as with arginine. 6-[(4-Bromo-2,3-dioxobutyl)thio]-6-deaminoadenosine 5'-monophosphate reacts irreversibly with rabbit muscle pyruvate kinase, causing inactivation. Addition of ADP to the reaction mixture (in the presence of Mg2+) markedly decreases the rate of inactivation. Pig heart NAD-dependent isocitrate dehydrogenase is allosterically activated by ADP, which reduces the Km for isocitrate. 6-[(4-Bromo-2,3-dioxobutyl)thio]-6-deaminoadenosine 5'-diphosphate reacts irreversibly with isocitrate dehydrogenase, causing, rapidly, a loss of the ability of ADP to increase the initial velocity of assays conducted at low isocitrate concentrations and, more slowly, inactivation. Addition of ADP to the reaction mixture (in the presence of Mn2+) protects this enzyme against the loss of allosteric activation. It is proposed that the 6-[(4-bromo-2,3-dioxobutyl)thio]-6-deaminoadenine nucleotides react at the active site of pyruvate kinase and at the ADP activating site of isocitrate dehydrogenase and that these compounds may have general applicability as affinity labels of catalytic and regulatory adenine nucleotide sites in proteins.

Adenosine Diphosphate↗
PubMed1985

Mechanism of inhibition of protein glycosylation by the antiviral sugar analogue 2-deoxy-2-fluoro-D-mannose: inhibition of synthesis of man(GlcNAc)2-PP-Dol by the guanosine diphosphate ester.

2-Deoxy-2-fluoro-D-mannose (2FMan), an antiviral mannose analogue, inhibited the dolichol cycle of protein glycosylation. To specifically inhibit oligosaccharide-lipid synthesis, and not (viral) protein synthesis in influenza virus infected cells, the addition of guanosine to the 2FMan-treated cells was required. Under these conditions an early step in the assembly of the oligosaccharide-lipid was inhibited, and as a consequence, the glycosylation of proteins was strongly inhibited. Low-molecular-weight, lipid-linked oligosaccharides accumulated in cells treated with 2FMan plus guanosine, although dolichol phosphate (Dol-P) and GDP-Man were still present in the treated cells, and membranes from these cells were not defective in assembly of lipid-linked oligosaccharides. Thus, the presence of a soluble inhibitor of oligosaccharide-lipid assembly in these cells was postulated, and GDP-2FMan and UDP-2FMan, two metabolites found in 2FMan-treated cells, were synthesized and used to study in cell-free systems the inhibition of oligosaccharide-lipid assembly. GDP-2FMan inhibited the synthesis of Man(GlcNAc)2-PP-Dol from (GlcNAc)2-PP-Dol and GDP-Man, and in addition, it caused a trapping of Dol-P as 2FMan-P-Dol, whereas UDP-2FMan only inhibited Glc-P-Dol synthesis. However, it is probable that neither trapping of Dol-P nor inhibition of Glc-P-Dol synthesis by UDP-2FMan contributed to inhibition of protein glycosylation in cells treated with 2FMan. Incorporation of 2FMan from GDP-2FMan or UDP-2FMan into dolichol diphosphate linked oligosaccharides and interference of GDP-2FMan with the latter steps of assembly of the dolichol diphosphate linked oligosaccharide could not be shown.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1980

Interactions of tris buffer with nucleotides: the crystal structure of tris(hydroxymethyl)methylammonium adenosine 5'-diphosphate dihydrate.

The crystal and molecular structures of the Tris salt of adenosine 5'-diphosphate were determined from X-ray diffraction data. The crystals are monoclinic, space P21, and Z = 2 with a=9.198 (2) A, b=6.894 (1) A, c=18.440 (4) A, and beta = 92.55 (2) degrees. Intensity data were collected on an automated diffractometer. The structure was solved by the heavy-atom technique and refined by least squares to R = 0.047. The ADP molecule adopts a folded conformation. The conformation about the glycosidic bond is anti. The conformation of the ribose ring is close to a perfect C(2')-endo-C-(3')-exo puckering. The conformation about C(4')-C(5') is gauche-gauche, similar to other nucleotide structures. The pyrophosphate chain displays a nearly eclipsed geometry when viewed down the P-P vector, unlike the staggered conformation observed in crystal structures of other pyrophosphates. The less favorable eclipsed conformation probably results from the observed association of Tris molecules with the polar diphosphate chain through electrostatic interactions and hydrogen bonds. Such interactions may play an important role in Tris-buffered aqueous solutions of nucleotides and metal ions.

Adenosine Diphosphate↗
PubMed1976

Binding of adenosine 5'-diphosphate to creatine kinase. An investigation using intermolecular nuclear Overhauser effect measurements.

Measurements of the nuclear Overhauser effect (NOE), which is a nuclear magnetic resonance (NMR) double resonance technique, for the H-2 proton on ADP have been used to identify the amino acid residue binding ADP at the active site of creatine kinase. Application of a strong radio-frequency field H2 at a frequency of 0.9 ppm or 1.7 ppm downfield from the proton resonance of 2,2-dimethyl-2-silapentane-5-sulfonate results in a negative NOE for the H2-2 proton resonance of ADP in its complex with creatine kinase. The magnitude of the NOE for the ADPH-2 proton depends on the ratio of ADP to creatine kinase binding site concentration; the dependence indicates that there is rapid exchange between free and bound ADP. Comparable values of the NOE for the H-2 proton of adenosine 5'-mono-, 5'-di-, and 5'-triphosphate and inosine 5'-diphosphate in binary complexes with creatine kinase show that the binding site for these nucleotides is the same. The large negative NOE for the H-2 proton of ADP is maintained for the various binary, ternary, quaternary, and pentenary complexes of creatine kinase with ADP formed by addition of the activator Mg(II), the other substrate creatine, and the planar anion nitrate which is an inhibitor. These results indicate that the conformational changes known to occur upon addition of the other ligands do not involve the entire active site. In particular, the environment around the nucleotide is unperturbed. Inactivation of creatine kinase by reaction with iodoacetamide causes considerable conformational changes. However, as indicated by the large negative NOE for the H-2 proton of ADP in a binary complex with the inactivated enzyme, the environment around the base is altered minimally. Experiments were performed to identify the proton groups on the enzyme, resonating at 0.9 and 1.7 ppm, which interact with the ADPH-2 proton. An NOE was not observed when the aromatic protons of the enzyme were irradiated with the strong radiofrequency field H2 implying that aromatic protons are not near the H-2 proton of ADP in the enzyme complex. The H-2 proton of 1-N6-ethenoadenosine 5'-diphosphate, an analogue of ADP with the 1-nitrogen and 6-nitrogen blocked from potentially hydrogen bonding, still exhibits a large NOE in the nucleotide-enzyme complex. The indication is that the protons promoting the H-2 proton NOE are not on an amino acid residue which binds ADP by hydrogen binding. Creatine kinase was inactivated by reacting the single essential arginyl residue per subunit with diacetyl. No NOE for the H-2 proton of ADP in the presence of the inactivated enzyme was observed. Observation of the H-2 proton resonance of the inhibitor adenosine in the presence of the enzyme revealed no NOE in contrast to the observations with the adenine nucleotides.

Adenosine Diphosphate↗
PubMed2001

Kinetics in the pre-steady state of the formation of cystines in ribonucleoside diphosphate reductase: evidence for an asymmetric complex.

Two folded polypeptides, designated R1 and R2, respectively, combine in an as yet undefined stoichiometry to form ribonucleoside diphosphate reductase (ribonucleotide reductase) from Escherichia coli. Two pairs of cysteines in each R1 protomer have been implicated in the enzymatic mechanism. One pair, cysteines 225 and 462, is located in the active site of the enzyme and forms a cystine concomitant with the reduction of the ribonucleotide. The other pair, cysteines 754 and 759, is located near the carboxy terminus and is thought to reduce the cystine in the active site by disulfide interchange; either thioredoxin or glutaredoxin is then thought to reduce the cystine that results. Rapid quenching and site-directed immunochemistry have been used to follow the formation of the cystine in the active site and the peripheral cystine simultaneously during the pre-steady state. Prereduced R1 dimer of ribonucleoside diphosphate reductase, in the presence of ATP and CDP, was mixed with R2 dimer in an apparatus for quench flow. The reaction was quenched with a solution of acetic acid and N-ethylmaleimide, the protein was then precipitated with trichloroacetic acid, and the precipitate was separated into two portions. The percent of the cystine in the active site in one of the portions was determined as described previously [Erickson, H. K. (2000) Biochemistry 39, 9241-9250]. A similar method was employed to determine the percent of the peripheral cystine in the other portion of the precipitate. It was found that while the formation of both of these cystines was initiated by the addition of R2 dimer, presumably as products of the reduction of CDP, the peripheral cystine appeared to form more rapidly and in a higher yield than the cystine in the active site. These results demonstrate that the formation of the cystine between cysteines 754 and 759 of ribonucleotide reductase from E. coli is kinetically competent. A mechanism consistent with the prior formation of the cystine between cysteine 225 and cystene 462 as well as the kinetics for the formation of each cystine with time is presented. Because twice as much of the peripheral cystine than cystine in the active site had formed during the pre-steady state, it follows that the enzymatically competent complex between R1 dimers and R2 dimers cannot be symmetric.

Binding Sites↗
PubMed1996

Inactivation of Escherichia coli ribonucleotide reductase by 2'-deoxy-2'-mercaptouridine 5'-diphosphate. Electron paramagnetic resonance evidence for a transient protein perthiyl radical.

Ribonucleotide reductase catalyzes a key step in DNA biosynthesis and repair, supplying the cell with the four common deoxyribonucleotides. It is thus the target of antiproliferative agents. The enzyme consists of two subunits named protein R1 and protein R2. R1 provides the sites for the nucleotide substrates and redox-active cysteines required for catalysis. R2 harbors a tyrosyl radical essential for activity. We show here that 2'-deoxy-2'-mercaptouridine 5'-diphosphate, a substrate analog, is a very efficient inactivator of ribonucleotide reductase (Ki = 35 microM, Kinact = 0.18 s-1). Inactivation is due to specific scavenging of the protein R2 tyrosyl radical. This unique feature sets this compound apart from other mechanism-based inhibitors such as 2'-azido-or 2'-chloro-2'-deoxyribonucleotide which induce partial or total protein R1 inactivation. During reaction, a transient organic radical was detected by EPR spectroscopy. Its g anisotropy (gz = 2.0620, gy = 2.0265, and gx = 2.0019) and its hyperfine structure are consistent with a perthiyl RSS. radical. The loss of the hyperfine structure by deuterium labeling of the beta protons of R1 cysteines unambiguously shows that the perthiyl radical is located on protein R1. We thus conclude that inactivation of ribonucleotide reductase by 2'-deoxy-2'-mercaptouridine 5'-diphosphate is due to an irreversible transfer of the radical located on protein R2 to a cysteine residue of protein R1.

Electron Spin Resonance Spectroscopy↗
PubMed1996

Phosphorylation of nucleoside diphosphate kinase at the active site studied by steady-state and time-resolved fluorescence.

Nucleoside diphosphate (NDP) kinase is the enzyme responsible in the cell for the phosphorylation of nucleoside or deoxynucleoside diphosphates into the corresponding triphosphates at the expense of ATP. Transfer of the gamma-phosphate is very fast (turnover number above 1000 s-1) and involves the phosphorylation of a histidine residue at the active site of the enzyme. We have used intrinsic protein fluorescence of the single tryptophan of Dictyostelium discoideum NDP kinase as a sensitive probe for monitoring the interaction of the enzyme with its substrates. We demonstrate that the 20% quenching of steady-state fluorescence observed upon addition of ATP is due to formation of the phosphorylated intermediate. Time-resolved fluorescence indicates that the Trp-137 side chain is rigidly bound to the protein core with a unique lifetime of 4.5 ns for the free enzyme at 20 degrees C and that it remains tightly immobilized during the time course of the reaction. Phosphorylation of this catalytic residue (His-122) in the presence of ATP induces a similar decrease in mean lifetime, due to the splitting of the signal and the appearance of a shorter decay. This splitting is discussed in terms of a slow conformational equilibrium. We demonstrate that, in the wild-type enzyme, the conserved His-55 quenches the fluorescence of Trp-137 as the H55A mutant protein fluorescence displays an increase in quantum yield. Even though H55A mutant enzyme is active, the absence of the imidazole ring prevents the detection of the phosphorylated state of His-122 by Trp-137. We conclude that His-55 serves as a relay between His-122 and Trp-137.

Animals↗
PubMed1997

Evaluation of the kinetic mechanism of Escherichia coli uridine diphosphate-N-acetylmuramate:L-alanine ligase.

Initial velocity methods were used to probe the kinetic mechanism of Escherichia coli uridine diphosphate-N-acetylmuramate:L-alanine ligase (UNAM:L-Ala ligase). When the activity (in the forward direction) versus substrate concentration data were plotted in double-reciprocal form, all line patterns were intersecting. The best fit of these data was to the equation for an ordered mechanism with the following parameters: k(cat), 1000 +/- 100 min(-1); Kma, 210 +/- 40 microM; Kmb, 84 +/- 20 microM; Kmc, 70 +/- 15 microM; Kia, 180 +/- 50 microM; Kib, 68 +/- 24 microM. Initial velocity line patterns were also determined when the concentration of one substrate was varied at different fixed concentrations of a second substrate while the third substrate was held at a concentration more than 100 times its Km value. Reciprocal plots of data collected with either ATP or L-alanine present at more than 100 times their Km values resulted in intersecting line patterns. Data collected with UNAM present at 100 times its Km value gave a set of parallel lines. These data are consistent with UNAM binding as the second substrate in an ordered mechanism. ADP, uridine diphosphate-N-acetylmuramoyl-L-alanine (UNAMA), and phosphate were tested as product inhibitors versus substrates. None of the products were competitive inhibitors versus L-alanine or UNAM, while the only observed competitive inhibition was ADP versus ATP. These results are consistent with an ordered kinetic mechanism wherein ATP binds first, UNAM binds second, and ADP is the last product released. Rapid quench experiments were performed in the presence of all three substrates or in the presence of ATP and UNAM. The production of acid-labile phosphate as a function of time is characterized by a burst phase followed by a slower linear phase with the rate close to k(cat) in the presence of all three substrates. Only a burst phase was observed for the time course of the reaction in the presence of ATP and UNAM. In both cases, the burst rate was identical. These observations are consistent with L-alanine being the third substrate to bind in a sequential mechanism involving a putative acyl-phosphate intermediate.

Adenosine Triphosphate↗
PubMed1999

Catalytic mechanism of nucleoside diphosphate kinase investigated using nucleotide analogues, viscosity effects, and X-ray crystallography.

Nucleoside diphosphate (NDP) kinases display low specificity with respect to the base moiety of the nucleotides and to the 2'-position of the ribose, but the 3'-hydroxyl is found to be important for catalysis. We report in this paper the enzymatic analysis of a series of derivatives of thymidine diphosphate (TDP) where the 3'-OH group was removed or replaced by fluorine, azido, and amino groups. With Dictyostelium NDP kinase, kcat decreases 15-200-fold from 1100 s-1 with TDP, and (kcat/Km)NDP decreases from 12 x 10(6) to 10(3) to 5 x 10(4) M-1 s-1, depending on the substrate. The poorest substrates are 3'-deoxyTDP and 3'-azido-3'-deoxyTDP, while the best modified substrates are 2',3'-dehydro-3'-deoxyTDP and 3'-fluoro-3'-deoxyTDP. In a similar way, 3'-fluoro-2',3'-dideoxyUDP was found to be a better substrate than 2',3'-dideoxyUDP, but a much poorer substrate than 2'-deoxyUDP. (kcat/Km)NDP is sensitive to the viscosity of the solution with TDP as the substrate but not with the modified substrates. To understand the poor catalytic efficiency of the modified nucleotides at a structural level, we determined the crystal structure of Dictyostelium NDP kinase complexed to 3'-fluoro-2',3'-dideoxyUDP at 2.7 A resolution. Significant differences are noted as compared to the TDP complex. Substrate-assisted catalysis by the 3'-OH, which is effective in the NDP kinase reaction, cannot occur with the modified substrate. With TDP, the beta-phosphate, which is the leaving group when a gamma-phosphate is transferred to His122, hydrogen bonds to the 3'-hydroxyl group of the sugar; with 3'-fluoro-2',3'-dideoxyUDP, the beta-phosphate hydrogen bonds to Asn119 and moves away from the attacking Ndelta of the catalytic His122. Since all anti-AIDS nucleoside drugs are modified at the 3'-position, these results are relevant to the role of NDP kinase in their cellular metabolism.

Animals↗
PubMed2002

Recombinant squalene synthase. A mechanism for the rearrangement of presqualene diphosphate to squalene.

Squalene synthase (SQase) catalyzes the condensation of two molecules of farnesyl diphosphate (FPP) to form presqualene diphosphate (PSPP) and the subsequent rearrangement and NADPH-dependent reduction of PSPP to squalene (SQ). These reactions are the first committed steps in cholesterol biosynthesis. When recombinant SQase was incubated with FPP in the presence of dihydroNADPH (NADPH3, an unreactive analogue lacking the 5,6-double bond in the nicotinamide ring), three products were formed: dehydrosqualene (DSQ), a C30 analogue of phytoene; 10(S)-hydroxysqualene (HSQ), a hydroxy analogue of squalene; and rillingol (ROH), a cyclopropylcarbinyl alcohol formed by addition of water to the tertiary cyclopropylcarbinyl cation previously proposed as an intermediate in the rearrangement of PSPP to SQ (Poulter, C. D. Acc. Chem. Res. 1990, 23, 70-77). The structure and absolute stereochemistry of the tertiary cyclopropylcarbinyl alcohol were established by synthesis using two independent routes. Isolation of ROH from the enzyme-catalyzed reaction provides strong evidence for a cyclopropylcarbinyl-cyclopropylcarbinyl rearrangement in the biosynthesis of squalene. By comparing the SQase-catalyzed solvolysis of PSPP in the absence of NADPH3 to the reaction in the presence of NADPH3, it is apparent that the binding of the cofactor analogue substantially enhances the ability of SQase to control the regio- and stereochemistry of the rearrangements of PSPP.

Amino Acid Sequence↗
PubMed1985

Inhibitors of blood platelet aggregation. Effects of some 1,2-benzisothiazol-3-ones on platelet responsiveness to adenosine diphosphate and collagen.

A series of substituted 1,2-benzisothiazol-3-ones was synthesized, and the compounds were tested for ability to inhibit platelet aggregation induced by adenosine diphosphate and collagen in rats and guinea pigs ex vivo. Alkyl substituents at the 2-position bearing a basic group were necessary for ex vivo activity. Several of the compounds were potent inhibitors of adenosine diphosphate induced first-phase aggregation, but adverse toxicological findings terminated their further development. Preliminary studies suggested that inhibition of aggregation was not attributable to inhibition of prostanoid synthesis or to raised levels of cyclic 3',5'-adenosine monophosphate.

Adenosine Diphosphate↗