The mechanism of ATP inhibition of wild type and mutant phosphofructo-1-kinase from Escherichia coli

Divalent cations in human liver pyruvate kinase exemplify the combined effects of complex-equilibrium and allosteric regulation

There is growing recognition that the functional outcome of binding of an allosteric regulator to a protein/enzyme is influenced by the presence of other ligands. Here, this complexity is exemplified in the allosteric regulation of human liver pyruvate kinase (hLPYK) that is influenced by the presence of a range of divalent cation types and concentrations. For this system, fructose-1,6-bisphosphate (activator) and alanine (inhibitor) both influence the protein's affinity for the substrate, phosphoenolpyruvate (PEP). Mg2+, Mn2+, Ni2+, and Co2+ were the primary divalent cations evaluated, although Zn2+, Cd2+, V2+, Pb2+, Fe2+, and Cu2+also supported activity. Allosteric coupling between Fru-1,6-BP and PEP and between Ala and PEP varied depending on divalent cation type and concentration. Due to complicating interactions among small molecules, we did not attempt the fitting of response trends and instead we discuss a range of potential mechanisms that may explain those observed trends. Specifically, observed "substrate inhibition" may result from substrate A in one active site acting as an allosteric regulator for the affinity for substrate B in a second active site of a multimer. We also discuss apparent changes in allosteric coupling that can result from a sub-saturating concentration of a third allosteric ligand.

Sulfoglycolysis: catabolic pathways for metabolism of sulfoquinovose

Sulfoquinovose (SQ), a derivative of glucose with a C6-sulfonate, is produced by photosynthetic organisms and is the headgroup of the sulfolipid sulfoquinovosyl diacylglycerol. The degradation of SQ allows recycling of its elemental constituents and is important in the global sulfur and carbon biogeochemical cycles. Degradation of SQ by bacteria is achieved through a range of pathways that fall into two main groups. One group involves scission of the 6-carbon skeleton of SQ into two fragments with metabolic utilization of carbons 1-3 and excretion of carbons 4-6 as dihydroxypropanesulfonate or sulfolactate that is biomineralized to sulfite/sulfate by other members of the microbial community. The other involves the complete metabolism of SQ by desulfonylation involving cleavage of the C-S bond to release sulfite and glucose, the latter of which can enter glycolysis. The discovery of sulfoglycolytic pathways has revealed a wide range of novel enzymes and SQ binding proteins. Biochemical and structural characterization of the proteins and enzymes in these pathways have illuminated how the sulfonate group is recognized by Nature's catalysts, supporting bioinformatic annotation of sulfoglycolytic enzymes, and has identified functional and structural relationships with the pathways of glycolysis.

Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis

The sulfosugar sulfoquinovose (SQ) is produced by essentially all photosynthetic organisms on Earth and is metabolized by bacteria through the process of sulfoglycolysis. The sulfoglycolytic Embden-Meyerhof-Parnas pathway metabolizes SQ to produce dihydroxyacetone phosphate and sulfolactaldehyde and is analogous to the classical Embden-Meyerhof-Parnas glycolysis pathway for the metabolism of glucose-6-phosphate, though the former only provides one C3 fragment to central metabolism, with excretion of the other C3 fragment as dihydroxypropanesulfonate. Here, we report a comprehensive structural and biochemical analysis of the three core steps of sulfoglycolysis catalyzed by SQ isomerase, sulfofructose (SF) kinase, and sulfofructose-1-phosphate (SFP) aldolase. Our data show that despite the superficial similarity of this pathway to glycolysis, the sulfoglycolytic enzymes are specific for SQ metabolites and are not catalytically active on related metabolites from glycolytic pathways. This observation is rationalized by three-dimensional structures of each enzyme, which reveal the presence of conserved sulfonate binding pockets. We show that SQ isomerase acts preferentially on the β-anomer of SQ and reversibly produces both SF and sulforhamnose (SR), a previously unknown sugar that acts as a derepressor for the transcriptional repressor CsqR that regulates SQ-utilization. We also demonstrate that SF kinase is a key regulatory enzyme for the pathway that experiences complex modulation by the metabolites SQ, SLA, AMP, ADP, ATP, F6P, FBP, PEP, DHAP, and citrate, and we show that SFP aldolase reversibly synthesizes SFP. This body of work provides fresh insights into the mechanism, specificity, and regulation of sulfoglycolysis and has important implications for understanding how this biochemistry interfaces with central metabolism in prokaryotes to process this major repository of biogeochemical sulfur.

ROS and pentose phosphate pathway: mathematical modelling of the metabolic regulation in response to xenobiotic-induced oxidative stress and the proposed Impact of the gluconate shunt

Elevated intracellular levels of reactive oxygen species (ROS), e.g. resulting from exposure to xenobiotics, can cause severe damages. Antioxidant defence mechanisms, which involve regulation of enzyme activities, protect cells to a certain extent. Nevertheless, continuous or increased exposure can overwhelm this system resulting in an adverse cellular state. To simulate exposure scenarios and to investigate the transition to an adverse cellular state, a mathematical model for the dynamics of ROS in response to xenobiotic-induced oxidative stress has been developed. It is based on exposure experiments of human urothelial cells (RT4) to the nitrated polycyclic aromatic hydrocarbon 3-nitrobenzanthrone (3-NBA), a component of diesel engine exhaust, and takes into account the following metabolic pathways of the antioxidant defence system: glutathione redox cycle scavenging directly ROS, the pentose phosphate pathway and the gluconate shunt as NADPH supplier and the beginning of glycolysis. In addition, ROS generation due to the bioactivation of 3-NBA has been implemented. The regulation of enzyme activities plays an important role in the presented mathematical model. The in silico model consists of ordinary differential equations on the basis of enzyme kinetics and mass action for the metabolism of 3-NBA. Parameters are either estimated from performed in vitro experiments via least-squares fitting or obtained from the literature. The results underline the importance of the pentose phosphate pathway to cope with oxidative stress and suggest an important role of the gluconate shunt during low-dose exposure.

The Interplay between Feedback and Buffering in Cellular Homeostasis

Buffering, the use of reservoirs of molecules to maintain concentrations of key molecular species, and negative feedback are the primary known mechanisms for robust homeostatic regulation. To our knowledge, however, the fundamental principles behind their combined effect have not been elucidated. Here, we study the interplay between buffering and negative feedback in the context of cellular homeostasis. We show that negative feedback counteracts slow-changing disturbances, whereas buffering counteracts fast-changing disturbances. Furthermore, feedback and buffering have limitations that create trade-offs for regulation: instability in the case of feedback and molecular noise in the case of buffering. However, because buffering stabilizes feedback and feedback attenuates noise from slower-acting buffering, their combined effect on homeostasis can be synergistic. These effects can be explained within a traditional control theory framework and are consistent with experimental observations of both ATP homeostasis and pH regulation in vivo. These principles are critical for studying robustness and homeostasis in biology and biotechnology.

Development of a novel catalytic amyloid displaying a metal-dependent ATPase-like activity

Amyloids are protein aggregates of highly regular structure that are involved in diverse pathologies such as Alzheimer's and Parkinson's disease. Recent evidence has shown that under certain conditions, small peptides can self-assemble into amyloids that exhibit catalytic reactivity towards certain compounds. Here we report a novel peptide with a sequence derived from the active site of RNA polymerase that displays hydrolytic activity towards ATP. The catalytic reaction proceeds in the presence of the divalent metal manganese and the products are ADP and AMP. The kinetic data shows a substrate-dependent saturation of the activity with a maximum rate achieved at around 1 mM ATP. At higher ATP concentrations, we also observed substrate inhibition of the activity. The self-assembly of the peptide into amyloids is strictly metal-dependent and required for the catalysis. Our results show that aspartate-containing amyloids can also be catalysts under conditions that include interactions with metals. Moreover, we show for the first time an amyloid that exerts reactivity towards a biologically essential molecule.

Ligand chirality effects on the dynamics of human 3-phosphoglycerate kinase: comparison between D- and L-nucleotides

l-nucleoside analogues are now largely used as antiviral drugs for the treatment of viral infections like HBV, HCV and HIV. However, in order to be fully active, they need to be phosphorylated by cellular or viral kinases. Human 3-phosphogycerate kinase (hPGK) was shown to catalyze the last step of activation of l-enantiomers and thus constitutes an attractive target for theoretical predictions of its phosphorylation efficiency. Molecular dynamics simulations were carried out with four different nucleotides (d-/l-ADP and d-/l-CDP) in complex with hPGK and 1,3-bisphospho-d-glycerate (bPG). The binding affinities of CDPs (both enantiomers) for hPGK were found very weak while d- and l-ADP were better substrates. Interestingly, the binding affinity of the bPG substrate was found to be lower in presence of d-ADP than l-ADP which indicates a potential antagonistic effect on one substrate to the other. A detailed analysis of the simulations unravels important dynamic conditions for efficient phosphorylation. Indeed, as previously described for the natural substrate, the hinge bending motion of the domains upon substrates binding should be more correlated and directional. Interestingly, the unforeseen finding was the larger dynamics freedoms observed for the substrates that was favored by the protein atoms flexibility around the nucleobase binding site.

Interaction of human 3-phosphoglycerate kinase with its two substrates: is substrate antagonism a kinetic advantage?

Substrate antagonism has been described for a variety of enzymes with more than one substrate and is characterized by a lowering of the affinity of one substrate in the presence of the other(s). 3-Phosphoglycerate kinase (PGK) catalyzes phosphotransfer from 1,3-bisphosphoglycerate (bPG) to ADP to give 3-phosphoglycerate (PG) and ATP, and is subject to substrate antagonism. Because of the instability of bPG, antagonism has only been described between PG and ATP or ADP. Here, we show that antagonism also occurs between bPG and ADP. Using the stopped-flow method, we show that the dissociation constant for one substrate increases in the presence of the other, and that this decrease in affinity is mainly due to an increase in the dissociation rate constant. As a consequence, there is an increase in the overall interaction kinetics. Interestingly, in the presence of the mirror image of natural d-ADP, l-ADP (a good substrate for PGK), antagonism is absent. Using rapid-quench-flow, we studied the kinetics of ATP formation. The time courses present the following: (1) a lag with l-ADP, but not with d-ADP, the kinetics of which were similar to the interaction kinetics measured by stopped-flow; (2) a burst that is directed by the phosphotransfer; and (3) a steady-state that is rate limited by the release of product kinetics. Structural explanations for these results are proposed by analyzing the crystallographic structure of the fully closed conformation of PGK in complex with l-ADP, PG, and the transition-state analogue AlF(4)(-) compared to previously determined structures.

Influence of culture conditions and medium composition on the production of cellulose by shiga toxin-producing Escherichia coli cells

Culture conditions favoring cellulose production by Shiga toxin-producing Escherichia coli included a 28 degrees C incubation temperature, an aerobic atmosphere, and the presence of 2% ethanol in Luria-Bertani no-salt agar with pH 6.0 and a water activity of 0.99. These findings will assist in formulating microbiological media useful for cellulose and biofilm research.

ADP-dependent 6-phosphofructokinase from Pyrococcus horikoshii OT3: structure determination and biochemical characterization of PH1645

Some hyperthermophilic archaea use a modified glycolytic pathway that employs an ADP-dependent glucokinase (ADP-GK) and an ADP-dependent phosphofructokinase (ADP-PFK) or, in the case of Methanococcus jannaschii, a bifunctional ADP-dependent glucophosphofructokinase (ADP-GK/PFK). The crystal structures of three ADP-GKs have been determined. However, there is no structural information available for ADP-PFKs or the ADP-GK/PFK. Here, we present the first crystal structure of an ADP-PFK from Pyrococcus horikoshii OT3 (PhPFK) in both apo- and AMP-bound forms determined to 2.0-A and 1.9-A resolution, respectively, along with biochemical characterization of the enzyme. The overall structure of PhPFK maintains a similar large and small alpha/beta domain structure seen in the ADP-GK structures. A large conformational change accompanies binding of phosphoryl donor, acceptor, or both, in all members of the ribokinase superfamily characterized thus far, which is believed to be critical to enzyme function. Surprisingly, no such conformational change was observed in the AMP-bound PhPFK structure compared with the apo structure. Through comprehensive site-directed mutagenesis of the substrate binding pocket we identified residues that were critical for both substrate recognition and the phosphotransfer reaction. The catalytic residues and many of the substrate binding residues are conserved between PhPFK and ADP-GKs; however, four key residues differ in the sugar-binding pocket, which we have shown determine the sugar-binding specificity. Using these results we were able to engineer a mutant PhPFK that mimics the ADP-GK/PFK and is able to phosphorylate both fructose 6-phosphate and glucose.

Crystallographic structure of phosphofructokinase-2 from Escherichia coli in complex with two ATP molecules. Implications for substrate inhibition

Phosphofructokinase-1 and -2 (Pfk-1 and Pfk-2, respectively) from Escherichia coli belong to different homologous superfamilies. However, in spite of the lack of a common ancestor, they share the ability to catalyze the same reaction and are inhibited by the substrate MgATP. Pfk-2, an ATP-dependent 6-phosphofructokinase member of the ribokinase-like superfamily, is a homodimer of 66 kDa subunits whose oligomerization state is necessary for catalysis and stability. The presence of MgATP favors the tetrameric form of the enzyme. In this work, we describe the structure of Pfk-2 in its inhibited tetrameric form, with each subunit bound to two ATP molecules and two Mg ions. The present structure indicates that substrate inhibition occurs due to the sequential binding of two MgATP molecules per subunit, the first at the usual site occupied by the nucleotide in homologous enzymes and the second at the allosteric site, making a number of direct and Mg-mediated interactions with the first. Two configurations are observed for the second MgATP, one of which involves interactions with Tyr23 from the adjacent subunit in the dimer and the other making an unusual non-Watson-Crick base pairing with the adenine in the substrate ATP. The oligomeric state observed in the crystal is tetrameric, and some of the structural elements involved in the binding of the substrate and allosteric ATPs are also participating in the dimer-dimer interface. This structure also provides the grounds to compare analogous features of the nonhomologous phosphofructokinases from E. coli.

Uncoupling the MgATP-induced inhibition and aggregation of Escherichia coli phosphofructokinase-2 by C-terminal mutations

Binding of MgATP to an allosteric site of Escherichia coli phosphofructokinase-2 (Pfk-2) provoked inhibition and a dimer-tetramer (D-T) conversion of the enzyme. Successive deletions of up to 10 residues and point mutations at the C-terminal end led to mutants with elevated K(Mapp) values for MgATP which failed to show the D-T conversion, but were still inhibited by the nucleotide. Y306 was required for the quaternary packing involved in the D-T conversion and the next residue, L307, was crucial for the ternary packing necessary for the catalytic MgATP-binding site. These results show that the D-T conversion could be uncoupled from the conformational changes that lead to the MgATP-induced allosteric inhibition.

Extraction of elementary rate constants from global network analysis of E. coli central metabolism

Background

As computational performance steadily increases, so does interest in extending one-particle-per-molecule models to larger physiological problems. Such models however require elementary rate constants to calculate time-dependent rate coefficients under physiological conditions. Unfortunately, even when in vivo kinetic data is available, it is often in the form of aggregated rate laws (ARL) that do not specify the required elementary rate constants corresponding to mass-action rate laws (MRL). There is therefore a need to develop a method which is capable of automatically transforming ARL kinetic information into more detailed MRL rate constants.

Results

By incorporating proteomic data related to enzyme abundance into an MRL modelling framework, here we present an efficient method operating at a global network level for extracting elementary rate constants from experiment-based aggregated rate law (ARL) models. The method combines two techniques that can be used to overcome the difficult properties in parameterization. The first, a hybrid MRL/ARL modelling technique, is used to divide the parameter estimation problem into sub-problems, so that the parameters of the mass action rate laws for each enzyme are estimated in separate steps. This reduces the number of parameters that have to be optimized simultaneously. The second, a hybrid algebraic-numerical simulation and optimization approach, is used to render some rate constants identifiable, as well as to greatly narrow the bounds of the other rate constants that remain unidentifiable. This is done by incorporating equality constraints derived from the King-Altman and Cleland method into the simulated annealing algorithm. We apply these two techniques to estimate the rate constants of a model of E. coli glycolytic pathways. The simulation and statistical results show that our innovative method performs well in dealing with the issues of high computation cost, stiffness, local minima and uncertainty inherent with large-scale non-convex nonlinear MRL models.

Conclusion

In short, this new hybrid method can ensure the proper solution of a challenging parameter estimation problem of nonlinear dynamic MRL systems, while keeping the computational effort reasonable. Moreover, the work provides us with some optimism that physiological models at the particle scale can be rooted on a firm foundation of parameters generated in the macroscopic regime on an experimental basis. Thus, the proposed method should have applications to multi-scale modelling of the real biological systems allowing for enzyme intermediates, stochastic and spatial effects inside a cell.

Differences in the transient kinetics of the binding of D-ADP and its mirror image L-ADP to human 3-phosphoglycerate kinase revealed by the presence of 3-phosphoglycerate

L-Nucleosides comprise a new class of antiviral and anticancer agents that are converted in vivo by a cascade of kinases to pharmacologically active nucleoside triphosphates. The last step of the cascade may be catalyzed by 3-phosphoglycerate kinase (PGK), an enzyme that has low specificity for nucleoside diphosphate (NDP): NDP + 1,3-bisphosphoglycerate <--> NTP + 3-phosphoglycerate. Here we compared the kinetics of the formation of the complexes of human PGK with d- and its mirror image l-ADP and the effect of 3-phosphoglycerate (PG) on these by exploiting the fluorescence signal of PGK that occurs upon its interaction with nucleotide substrate. Two types of experiment were carried out: equilibrium (estimation of dissociation constants) and stopped-flow (transient kinetics of the interactions). We show that under our experimental conditions (buffer containing 30% methanol, 4 degrees C) PGK binds d- and l-ADP with similar kinetics. However, whereas PG increased the dissociation rate constant for d-ADP by a factor of 8-which is a kinetic explanation for "substrate antagonism"-PG had little effect on this constant for l-ADP. We explain this difference by a molecular modeling study that showed that the beta-phosphates of d- and l-ADP have different orientations when bound to the active site of human PGK. The difference is unexpected because l-ADP is almost as catalytically competent as d-ADP [ Varga, A. et al. (2008) Biochem. Biophys. Res. Commun. 366, 994-1000].

Constitutive activation and transgenic evaluation of the function of an arabidopsis PKS protein kinase

A novel family of SOS2 (salt overly sensitive 2)-like protein kinase genes (designated PKSes) have been recently identified in Arabidopsis. The biochemical characteristics as well as in vivo roles of most of the PKSes are unclear at present. In this work, we isolated and characterized one of the PKSes, PKS18. PKS18 was expressed in leaves of mature Arabidopsis plants. The glutathione S-transferase (GST)-PKS18 fusion protein was inactive by itself in substrate phosphorylation. An activation loop Thr(169) to Asp mutation, however, highly activated this kinase in vitro (designated PKS18T/D). Kinase activity of the PKS18T/D preferred Mn(2+) to Mg(2+). The activated kinase showed a substrate specificity, and high catalytic efficiency for a peptide substrate p3 and for ATP. Interestingly, PKS18T/D transgenic plants were hypersensitive to the phytohormone abscisic acid (ABA) in seed germination and seedling growth, whereas silencing the kinase gene by RNA interference (RNAi) conferred ABA-insensitivity, indicating the involvement of PKS18 in plant ABA signaling.

Influence of a sulfhydryl cross-link across the allosteric-site interface of E. coli phosphofructokinase

To assess the role of quaternary stability on the properties of Escherichia coli phosphofructokinase (PFK), a disulfide bond has been introduced across the subunit interface containing the allosteric binding sites in E. coli phosphofructokinase by changing N288 to cysteine. N288 is located in close proximity to the equivalent residue on an adjacent subunit. Although SDS-PAGE of oxidized N288C indicates monomeric protein, blocking the six native cysteine residues with N-ethyl maleimide (NEM) reveals dimers of N288C on non-native gels. Subsequent addition of dithiothreitol (DTT) to NEM-labeled N288C regenerates the monomer on SDS-PAGE, reflecting the reversibility of intersubunit disulfide bond formation. KSCN-induced hybrid formation between N288C and the charged-tagged mutant E195,199K exhibits full monomer-monomer exchange only upon DTT addition, providing a novel assessment of disulfide bond formation without NEM treatment. N288C also exhibits a diminished tendency toward nonspecific aggregation under denaturing conditions, a phenomenon associated with monomer formation in PFK. Pressure-induced dissociation and urea denaturation studies further indicate that oxidized N288C exhibits increased quaternary stability along both interfaces of the tetramer, suggesting a synergistic relationship between active site and allosteric site formation. Although the apparent binding affinities of substrates and effectors change somewhat upon disulfide formation in N288C, little difference is evident between the maximally inhibited and activated forms of the enzyme in oxidizing versus reducing conditions. Allosteric influence, therefore, is not correlated to subunit-subunit affinity, and does not involve substantial interfacial rearrangement.

The two phosphofructokinase gene products of Entamoeba histolytica

Two phosphofructokinase genes have been described previously in Entamoeba histolytica. The product of the larger of the two genes codes for a 60-kDa protein that has been described previously as a pyrophosphate (PP(i))-dependent enzyme, and the product of the second, coding for a 48-kDa protein, has been previously reported to be a PP(i)-dependent enzyme with extremely low specific activity. Here it is found that the 48-kDa protein is not a PP(i)-dependent enzyme but a highly active ATP-requiring enzyme (k(cat) = 250 s(-)1) that binds the cosubstrate fructose 6-phosphate (Fru-6-P) with relatively low affinity. This enzyme exists in concentration- and ATP-dependent tetrameric active and dimeric inactive states. Activation is achieved in the presence of nucleoside triphosphates, ADP, and PP(i), but not by AMP, P(i), or the second substrate Fru-6-P. Activation by ATP is facilitated by conditions of molecular crowding. Divalent cations are not required, and no phosphoryl transfer occurs during activation. Kinetics of the activated enzyme show cooperativity with Fru-6-P (Fru-6-P(0.5) = 3.8 mm) and inhibition by high ATP and phosphoenolpyruvate. The enzyme is active without prior activation in extracts of E. histolytica. The level of mRNA, the amount of enzyme protein, and the enzyme activity of the 48-kDa enzyme are about one-tenth that of the 60-kDa enzyme in extracts of E. histolytica trophozoites.

An essential methionine residue involved in substrate binding by phosphofructokinases

An alignment of all PPi-dependent phosphofructokinases and all allosteric ATP-dependent PFKs shows relatively few residues that are fully conserved. One residue that is conserved is a methionine residue that appears from the crystal structure of Escherichia coli PFK to be interacting with fructose 6-P. Very conservative substitutions for this methionine with leucine or isoleucine by site-directed mutagenesis of E. coli ATP-PFK and Entamoeba histolytica PPi-PFK produced profound decreases either in the apparent affinity for fructose 6-P or in maximal velocity, or both. Methionine provides a highly specific interaction with fructose 6-P for binding and for transition state stabilization.

A chimeric bacterial phosphofructokinase exhibits cooperativity in the absence of heterotropic regulation

The phosphofructokinases (PFKs) from the bacteria Escherichia coli and Bacillus stearothermophilus differ markedly in their regulation by ATP. Whereas E. coli PFK (EcPFK) is profoundly inhibited by ATP, B. stearothermophilus PFK (BsPFK) is only slightly inhibited. The structural basis for this difference could be closure of the active site via a conformational transition that occurs in the ATP-binding domain of EcPFK, but is absent in BsPFK. To investigate the role of this transition in ATP inhibition of EcPFK, we have constructed a chimeric enzyme that contains the "rigid" ATP-binding domain of BsPFK grafted onto the remainder of the EcPFK subunit. The chimeric PFK has the following characteristics: (i) tetrameric structure and kinetic parameters similar to those of the native enzymes, (ii) insensitivity to regulation by the effector phosphoenolpyruvate despite its ability to bind to the enzyme, and (iii) a sigmoidal (nH around 2) fructose 6-phosphate saturation curve. From the results, it is concluded that the active site regions of the two native enzymes are remarkably similar, but their effector sites and their mechanisms of heterotropic regulation are different. The chimeric subunit is locked in a structure resembling that of activated E. coli PFK, yet the enzyme can exist in two different conformational states. Mechanisms for its sigmoidal kinetics are discussed.

Pyrophosphate-dependent phosphofructo-1-kinase complements fructose 1,6-bisphosphatase but not phosphofructokinase deficiency in Escherichia coli

The gene from Propionibacterium freudenreichii for PPi-dependent phosphofructo-1-kinase, an enzyme that is found in some bacteria, in a number of anaerobic protists, and in plants, complements the absence of fructose 1,6-bisphosphatase in Escherichia coli but does not complement the deficiency of the ATP-dependent phosphofructokinase.