Effects of assembly and mutations outside the active site on the functional pH dependence of Escherichia coli aspartate transcarbamylase

Solvent perturbation of the allosteric regulation of aspartate transcarbamylase

Escherichia coli aspartate transcarbamylase (ATCase) catalyzes the first committed step in pyrimidine biosynthesis, the condensation of aspartate and carbamyl phosphate. ATCase is positively allosterically regulated by ATP and negatively regulated by CTP. We have used mild solvent perturbation to gain global molecular information about the mechanism of heterotropic allostery. The [NaCl], temperature, and osmotic pressure dependence of the enzymatic activity of ATCase has been examined in the presence and absence of allosteric effectors. The results indicate that: 1) Regulation of aspartate binding by CTP appears to involve a unique set of electrostatic interactions not involved in enzyme function in the presence of ATP or in the absence of effectors. 2) Aspartate binding is enthalpically driven in the presence and absence of allosteric effectors. 3) The apparent enthalpy and entropy of aspartate binding (delta H, delta S), and activation energy of catalysis (Ea) are substantially altered in the presence of CTP but not ATP. 4) The change in hydration of ATCase upon substrate binding is the same in the presence and absence of allosteric effectors. 5) The linkage between heterotropic and homotropic allostery is different for ATP and CTP.

Functionally linked hydration changes in Escherichia coli aspartate transcarbamylase and its catalytic subunit

Aspartate transcarbamylase (ATCase) is a highly regulated, dodecameric enzyme that catalyzes the first committed step in pyrimidine biosynthesis. Upon ligation, ATCase undergoes a conformational transition from a low-activity T-state to a high-activity R-state. This transition involves major changes in the molecular architecture, including structural rearrangements of several intersubunit interfaces and a 12 A expansion of the molecule along its 3-fold axis. Solute-induced osmotic stress experiments report that approximately 208 solvent waters are taken up by ATCase as it binds substrate. Solvent-accessible surface area calculations conducted on the T and R conformers of ATCase agree very well with this result, predicting that approximately 189 waters are taken up during this conformational change. Both osmotic stress measurements and surface area calculations on the catalytic trimer of ATCase predict water release upon ligation of the trimer. Specific aspects of the application of osmotic stress to ATCase are also discussed, including solute size effects, and an assessment of potential alternative explanations for these results.

'Late onset' ornithine transcarbamylase deficiency: function of three purified recombinant mutant enzymes

Although many mutations in the ornithine transcarbamylase gene have been correlated with 'late onset' of hyperammonemia in patients, the effects of these mutations on enzyme function are largely unknown. Three recurrent mutations (R40H, R277W and R277Q) found in patients with 'late onset' disease were incorporated into 'mature' human ornithine transcarbamylase cDNA and overexpressed in Escherichia coli. The three recombinant mutant enzymes were purified to homogeneity on an affinity column and their biochemical characteristics were compared to the wild type enzyme. The R277W and R277Q mutants display markedly reduced affinity for L-ornithine, loss of substrate inhibition, alkaline shift of pH optimum, and reduced thermal stability compared to the wild type enzyme. These differences, particularly the reduced affinity for L-ornithine, are sufficient to account for their biochemical effects. In contrast, the 'mature' R40H mutant was biochemically indistinguishable from the wild type enzyme in vitro.

A continuous spectrophotometric assay for aspartate transcarbamylase and ATPases

A new continuous coupled uv-spectrophotometric assay is described for two phosphate-releasing enzymes, aspartate transcarbamylase and ATPase of herpes simplex virus (HSV). Phosphate release is coupled to the phosphorolysis of the nucleoside analog 7-methylinosine (m7Ino) catalyzed by purine nucleoside phosphorylase. When this reaction is monitored at 291 nm, the coupled assay can readily detect 10 nmol Pi released/min. Our method offers advantages over a recently reported continuous assay devised for measuring aspartate transcarbamylase activity using the nucleoside analog methylthioguanosine (MESG) as the linking substrate. In contrast to MESG, m7Ino is easily and inexpensively synthesized and is also commercially available. The spectrophotometric signal at 291 nm, produced by the difference in the extinction coefficients between nucleoside substrate and the base product, is significant over a much wider pH range than the signal difference between MESG and its phosphorolysis product at 360 nm. Saturation curves for aspartate and carbamyl phosphate and pH rate profiles have been reproduced using the purine nucleoside phosphorylase/m7Ino coupled assay. Initial velocity patterns constructed over micromolar to millimolar concentrations of aspartate and carbamyl phosphate yielded four kinetic parameters simultaneously. To further illustrate the application of this coupled assay, kinetic parameters were determined for the DNA-dependent ATPase reaction of HSV helicase-primase.

Expression, purification and kinetic characterization of wild-type human ornithine transcarbamylase and a recurrent mutant that produces 'late onset' hyperammonaemia

Ornithine Transcarbamylase Deficiency, an X-linked disorder, is the most common cause of inherited urea cycle disorders. Approx. 90 mutations that produce reduced levels of ornithine transcarbamylase (OTCase) activity have been identified in patients [Tuchman (1993) Hum. Mutat. 2, 174-178; Tuchman and Plante (1995) Hum. Mutat. 5, 293-295]. A model of the three-dimensional structure of OTCase, developed on the basis of its homology to the catalytic subunit of Escherichia coli aspartate transcarbamylase (ATCase) [Tuchman, Morizono, Reish, Yuan and Allewell (1995) J. Med. Genet. 32, 680-688], and in good agreement with the crystal structure of Pseudomonas aeruginosa OTCase [Villeret, Tricot, Stalon and Dideberg (1995) Proc. Natl. Acad. Sci. U.S.A. 92, 10762-10766], indicates that many mutations that produce severe clinical symptoms are at the active site or buried in the interior of the protein. However, one of the few recurrent mutations, R277W, an alteration that produces a milder phenotype of ornithine transcarbamylase deficiency, is located in the model in a loop remote from the active site that is analogous to a similar loop (the 240's loop, a flexible loop of the catalytic chain of Escherichia coli aspartate transcarbamylase, comprised of residues 230-250) of ATCase. Human wild-type OTCase and the R277W mutant have been cloned and overexpressed in E. coli and a rapid and efficient purification method utilizing the bisubstrate analogue, Ndelta-(phosphonacetyl)-L-ornithine, has been developed and used to purify both proteins. Gel chromatography indicates both are trimeric. The pH dependence of the kinetic parameters of the wild-type enzyme is similar to that of E. coli OTCase [Kuo, Herzberg and Lipscomb (1985) Biochemistry 24, 4754-4761], suggesting that its catalytic mechanism is similar, although its maximal activity is approx. 10-fold less. Compared with the wild-type, the R277W mutant has nearly 70-fold lower affinity for L-ornithine, shows no substrate inhibition, and its thermal stability is reduced by 5 degrees C. Its reduced affinity for L-ornithine, which in turn results in lower activity at physiological concentrations of ornithine, as well as its reduced stability, may contribute to the clinical effects that it produces.

Is substrate inhibition a consequence of allostery in aspartate transcarbamylase?

Aspartate transcarbamylase (ATCase) is a highly regulated, multisubunit enzyme that catalyzes the first regulated step in pyrimidine biosynthesis. Although ATCase exhibits strong substrate inhibition (the reduction of enzyme activity at high substrate concentrations), the mechanism of substrate inhibition has not been investigated. At the molecular level, substrate inhibition may result either from local events at the active site or from global or specific long-range allosteric effects. We have compared the results of fitting kinetic data to several models: (a) a semi-empirical steady-state kinetic model that includes cooperative substrate binding (described by a Hill coefficient) and partial uncompetitive substrate inhibition, (b) a nested allosteric model developed to analyze substrate inhibition of the ATPase activity of GroEL, an enzyme with a quaternary structure analogous to ATCase (O. Yifrach and A. Horovitz, Biochemistry, 34 (1995) 5303), and (c) purely concerted models, including a model originally proposed by Monod et al. (J. Monod, J. Wyman and J.P. Changeux, J. Mol. Biol., 12 (1965) 88). Model (a) is the first kinetic equation for ATCase that both fits the data and returns physically realistic values for all parameters, but it is a modified Hill equation and thus returns little or no molecular mechanistic information. The nested allosteric model (b), which assumes concerted cooperativity within each catalytic trimer of ATCase and sequential cooperativity between trimers, is unlikely to be the correct model for ATCase, since isolated catalytic trimers, which cannot exhibit the sequential cooperativity of the model, still exhibit substrate inhibition. Analysis of concerted models (c) shows that a two-state model is inadequate to account for substrate inhibition in ATCase. Further, although unique fits to a three-state model cannot be obtained, because the parameters are highly correlated, several sets of parameter values fit the data well and are in accord with other experimental results. These results indicate that substrate inhibition in ATCase may be the consequence of allostery, and that further experimental investigation is warranted.

Identification and analysis of long-range electrostatic effects in proteins by computer modeling:aspartate transcarbamylase

While ion pairs are readily identified in crystal structures, longer range electrostatic interactions cannot be identified from the three-dimensional structure alone. These interactions are likely to be important in large, multisubunit proteins that are regulated by allosteric interactions. In this paper, we show that these interactions are readily detected by electrostatic modeling, using, as an example, unliganded Escherichia coli aspartate transcarbamylase, a widely studied allosteric enzyme with 12 subunits and a molecular weight of 310 kD. The Born, dipolar, and site-site interaction terms of the free energy of protonation of the 810 titratable sites in the holoenzyme were calculated using the multigrid solution of the nonlinear Poisson-Boltzmann equation. Calculated titration curves are in good agreement with experimental titration curves, and the structural asymmetry observed in the crystal structure is readily apparent in the calculated free energies and pK1/2 values. Most of the residues with pK1/2 values that differ substantially from those of model compounds are buried in the low dielectric medium of the protein, particularly at the intersubunit interfaces. The dependence of the site-site interaction free energies on distance is complex, with a steep dependence at distances less than 5 A and a more shallow dependence at longer distances. Interactions over distances of 6 to 15 A require a bridging residue and are often not apparent in the structure. The network of interactions between ionizable groups extends across and between subunits and provides a potential mechanism for transmitting long-range structural effects and allosteric signals.