Enzymic memory studies with nucleoside-5'-diphosphate kinase

The ROK kinase N-acetylglucosamine kinase uses a sequential random enzyme mechanism with successive conformational changes upon each substrate binding

N-acetyl-d-glucosamine (GlcNAc) is a major component of bacterial cell walls. Many organisms recycle GlcNAc from the cell wall or metabolize environmental GlcNAc. The first step in GlcNAc metabolism is phosphorylation to GlcNAc-6-phosphate. In bacteria, the ROK family kinase N-acetylglucosamine kinase (NagK) performs this activity. Although ROK kinases have been studied extensively, no ternary complex showing the two substrates has yet been observed. Here, we solved the structure of NagK from the human pathogen Plesiomonas shigelloides in complex with GlcNAc and the ATP analog AMP-PNP. Surprisingly, PsNagK showed distinct conformational changes associated with the binding of each substrate. Consistent with this, the enzyme showed a sequential random enzyme mechanism. This indicates that the enzyme acts as a coordinated unit responding to each interaction. Our molecular dynamics modeling of catalytic ion binding confirmed the location of the essential catalytic metal. Additionally, site-directed mutagenesis confirmed the catalytic base and that the metal-coordinating residue is essential. Together, this study provides the most comprehensive insight into the activity of a ROK kinase.

Kinetics of membrane-bound nitrate reductase A from Escherichia coli with analogues of physiological electron donors--different reaction sites for menadiol and duroquinol

We have compared the steady-state kinetics of wild-type nitrate reductase A and two mutant forms with altered beta subunits. To mimic conditions in vivo as closely as possible, we used analogues of the physiological quinols as electron donors and membranes with overexpressed nitrate reductase A in preference to a purified alpha beta gamma complex. With the wild-type enzyme both menadiol and duroquinol supply their electrons for the reduction of nitrate at rates that depend on the square of the quinol concentration, menadiol having the higher catalytic constant. The results as a whole are consistent with a substituted-enzyme mechanism for the reduction of nitrate by the quinols. Kinetic experiments suggest that duroquinol and menadiol deliver their electrons at different sites on nitrate reductase, with cross-inhibition. Menadiol inhibits the duroquinol reaction strongly, suggesting that menaquinol may be the preferred substrate in vivo. To examine whether electron transfer from menadiol and duroquinol for nitrate reduction requires the presence of all of the Fe-S centres, we have studied the steady-state kinetics of mutants with beta subunits that lack an Fe-S centre. The loss of the highest-potential Fe-S centre results in an enzyme without menadiol activity, but retaining duroquinol activity; the kinetic parameters are within a factor of two of those of the wild-type enzyme, indicating that this centre is not required for the duroquinol activity. The loss of a low-potential Fe-S centre affects the activity with both quinols: the enzyme is still active but the catalytic constants for both quinols are decreased by about 75%, indicating that this centre is important but not essential for the activity. The existence of a specific site of reaction on nitrate reductase for each quinol, together with the differences in the effects on the two quinols produced by the loss of the Fe-S centre of +80 mV, suggests that the pathways for transfer of electrons from duroquinol and menadiol are not identical.

Kinetic studies of a soluble alpha beta complex of nitrate reductase A from Escherichia coli. Use of various alpha beta mutants with altered beta subunits

A soluble alpha beta complex of nitrate reductase can be obtained from a strain of Escherichia coli that lacks the narI gene and expresses only the alpha and beta subunits. The beta subunit contains four Fe-S centres and the alpha subunit contains the molybdenum cofactor, which is the site at which nitrate is reduced. Despite the lack of the gamma subunit of the complete enzyme, this complex can still catalyse the reduction of nitrate with artificial electron donors such as benzyl viologen, so that it is suitable for studying the transfer of electrons between these two types of redox centre. To examine whether the electrons from reduced benzyl viologen are initially delivered to the Fe-S centres, or directly to the molybdenum cofactor, or both, we have studied the steady-state kinetics and the binding of benzyl viologen to the alpha beta complex and mutants alpha beta* with altered beta subunits. Reduction of the enzyme by reduced benzyl viologen in the absence of nitrate showed that all four Fe-S centres and the molybdenum cofactor could be reduced. Two classes of site with different equilibrium constants could be distinguished. The kinetic results suggest that benzyl viologen supplies its electrons directly to the molybdenum cofactor, at a rate showing a hyperbolic dependence on the square of the concentration of the electron donor. A reaction mechanism is proposed for the reduction of nitrate catalysed by the alpha beta complex of nitrate reductase with artificial electron donors.

Potential memory and hysteretic effects in transcription

Kinetic results of RNA-chain elongation catalysed by wheat-germ RNA polymerase II are analysed according to the concept that DNA-dependent conformational transitions of the transcription complex intervene during transcription. A model is presented, involving participation of several forms of the transcription complex with different catalytic properties, generated by the sequence and/or conformation of the DNA template and/or the experimental conditions. The available experimental data suggest that these forms are interconvertible. Examples in which hysteretic transitions might occur are outlined, such as termination of transcription and transition from abortive to productive elongation in the first steps of RNA synthesis. The slow catalytic adaptation of the transcription complex to the template sequence might be a more general phenomenon for enzyme systems acting on polynucleotide templates, in view of the recent proposal that enzyme memory effects may also have some importance in DNA replication and messenger RNA (mRNA) translation.

Co-operativity in monomeric enzymes

It has been known for at least 20 years that monomeric enzymes can in principle show kinetic behaviour similar in appearance to the binding of ligands to oligomeric proteins in which there are co-operative interactions between multiple binding sites. However, the initial lack of experimental examples of kinetic co-operativity suggested that in nature co-operativity always arose from interactions between binding sites. Now, however, several examples are known, most of which cannot be explained in terms of multiple binding sites on one polypeptide chain. All current theoretical models for monomeric co-operativity postulate that it arises from the presence in the mechanism of parallel pathways for substrate binding that are slow compared with the possible rate of the catalytic reaction. Rapid removal of the intermediates produced in the slow steps prevents them from approaching equilibrium and allows the appearance of kinetic properties that would not be possible in systems at equilibrium.

Kinetic implications of the occurrence of several relaxations in the conformational transition of mnemonical enzymes

If the conformational transition involved in enzyme memory occurs in several elementary steps, the time constant of the overall 'slow' relaxation is mostly determined by the individual values of the rate constants pertaining to the overall transconformation. The extent of kinetic co-operativity of the enzyme reaction, however, is mostly controlled by the degree of reversibility of the elementary steps of the conformational transition. There is then no simple relation between the time scale of the 'slow' transition and the extent of kinetic co-operativity of the enzyme reaction. A slow transition of about 10(-3) s-1 is therefore perfectly compatible with a strong positive or negative co-operativity and in particular with the negative co-operativity observed with wheat germ hexokinase LI. The relationship that has been established recently [Pettersson, G. (1986) Eur. J. Biochem. 154, 167-170] between the 'slow' enzyme relaxation and the extent of kinetic co-operativity holds only in the specific case where the transconformation occurs in one step. Owing to the possible occurrence of a multistep conformation change, the lack of this relationship means nothing as to the validity, or the invalidity, of the concept of mnemonical transition. More informative than the time scale of the 'slow' transition is its dependence with respect to glucose and glucose 6-phosphate, which both react with the enzyme. The effect of reaction products on the modulation of kinetic co-operativity is also of cardinal importance in the diagnosis of enzyme memory. Since an alternative model has been recently proposed by Pettersson (cited above) to explain the mechanistic origin of kinetic co-operativity of monomeric enzymes, the effect of products on the kinetic co-operativity predicted by this alternative model has been studied theoretically, in order to determine whether it is consistent with the experimental results obtained with wheat germ hexokinase LI. This analysis shows that the predictions of this model are in total disagreement with both the predictions of the mnemonical model and the experimental results obtained with wheat germ hexokinase LI, as well as with other enzymes. This alternative model cannot therefore be considered as a sensible explanation of the mechanistic origin of co-operativity of monomeric enzymes. It is therefore concluded that the mnemonical model which rests on numerous experimental results, obtained by different research groups, on different enzymes is the simplest and most likely explanation of the kinetic subtleties displayed by some monomeric enzymes, and in particular wheat germ hexokinase LI.

Binding of nucleotides to nucleoside diphosphate kinase monitored by rose Bengal

The binding of nucleotides to nucleoside-diphosphate kinase from pig heart was studied using the dye rose Bengal as an optical probe. By difference absorption spectroscopy and by equilibrium dialysis it was shown that one dye molecule strongly bound per enzyme subunit. By competition with nucleotides it was shown that two nucleotide-binding sites exist on each subunit of either unphosphorylated or phosphorylated enzyme: one of them binds ATP or ADP tightly, the other one binds rose Bengal tightly and ADP loosely. As detected by different affinities for rose Bengal the enzyme exists in two conformations: a 'relaxed' conformation induced by the binding of ADP, and a 'tense' conformation induced by the binding of ATP or by phosphorylation.

Kinetic co-operativity of monomeric mnemonical enzymes. The significance of the kinetic Hill coefficient

The expression of the kinetic Hill coefficient for a two-substrate, two-product mnemonical enzyme has been derived. Its relation with the gamma coefficient, that is the slope of the reciprocal plots for 1/[A]----O, has been established. The variation of this Hill coefficient, as a function of the second substrate and product concentrations, has been studied theoretically. Whereas the gamma coefficient does not vary as a function of the substrate and first product concentrations, the kinetic Hill coefficient does. If the enzyme is positively co-operative, the Hill coefficient increases upon increasing the second substrate concentration and decreases if the first product concentration is increased. The converse is expected to occur if the enzyme displays a negative co-operativity. The last product may either reverse a positive co-operativity into a negative one or, alternatively, strengthen an already negative co-operativity. The co-operativity generated by the mnemonical model has been compared to the kinetic behaviour of a random model. These two models have been shown to be discriminated on the basis of the departure they show with respect to the Michaelis-Menten behaviour. These theoretical considerations have been applied to previously published data, obtained with wheat germ hexokinase LI. This monomeric enzyme has a negative co-operativity with respect to the preferred substrate, glucose. The Hill coefficient decreases with MgATP concentration, increases with MgADP concentration and decreases with glucose-6-phosphate concentration. This is exactly what is to be expected on the basis of the above theory of kinetic co-operativity.