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PubMed1995

Structural determinants of allosteric regulation in alternatively spliced AMPA receptors.

The flip and flop splice variants of AMPA receptors show strikingly different sensitivity to allosteric regulation by cyclothiazide; heteromers assembled from GluR-A and GluR-B also exhibit splice variant-dependent differences in efficacy for activation by glutamate and kainate. The sensitivity for attenuation of desensitization by cyclothiazide for homomeric GluR-A was solely dependent upon exchange of Ser-750 (flip) and Asn-750 (flop), and was unaffected by mutagenesis of other divergent residues. In contrast, substantial alteration of the relative efficacy of glutamate versus kainate required mutation of multiple residues in the flip/flop region. Modulation by cyclothiazide was abolished by mutation of Ser-750 to Gin, the residue found at the homologous site in kainate-preferring subunits, whereas introduction of Ser at this site in GluR6 imparted sensitivity to cyclothiazide.

Allosteric Regulation↗
PubMed2003

Comprehensive model for allosteric regulation of mammalian ribonucleotide reductase: refinements and consequences.

Reduction of NDPs by murine ribonucleotide reductase (mRR) requires catalytic (mR1) and free radical-containing (mR2) subunits and is regulated by nucleoside triphosphate allosteric effectors. Here we present the results of several studies that refine the recently presented comprehensive model for the allosteric control of mRR enzymatic activity [Kashlan, O. B., et al. (2002) Biochemistry 41, 462-474], in which nucleotide binding to the specificity site (s-site) drives formation of an active R1(2)R2(2) dimer, ATP or dATP binding to the adenine site (a-site) drives formation of a tetramer, mR1(4a), which isomerizes to an inactive form, mR1(4b), and ATP binding to the hexamerization site (h-site) drives formation of an active R1(6)R2(6) hexamer. Analysis of the a-site D57N variant of mR1, which differs from wild-type mR1 (wt-mR1) in that its RR activity is activated by both ATP and dATP, demonstrates that dATP activation of the D57N variant RR arises from a blockage in the formation of mR1(4b) from mR1(4a), and provides strong evidence that mR1(4a) forms active complexes with mR2(2). We further demonstrate that (a) differences in the effects of ATP versus dATP binding to the a-site of wt-mR1 provide specific mechanisms by which the dATP/ATP ratio in mammalian cells could modulate in vivo RR enzymatic activity, (b) the comprehensive model is valid over a range of Mg(2+) concentrations that include in vivo concentrations, and (c) equilibrium constants derived for the comprehensive model can be used to simulate the distribution of R1 among dimer, tetramer, and hexamer forms in vivo. Such simulations indicate that mR1(6) predominates over mR1(2) in the cytoplasm of normal mammalian cells, where the great majority of RR activity is located, but that mR1(2) may be important for nuclear RR activity and for RR activity in cells in which the level of ATP is depleted.

Adenosine Triphosphate↗
PubMed2005

Allosteric regulation and communication between subunits in uracil phosphoribosyltransferase from Sulfolobus solfataricus.

Uracil phosphoribosyltransferase (UPRTase) catalyzes the conversion of 5-phosphate-alpha-1-diphosphate (PRPP) and uracil to uridine 5'-monophosphate (UMP) and diphosphate. The UPRTase from Sulfolobus solfataricus has a unique regulation by nucleoside triphosphates compared to UPRTases from other organisms. To understand the allosteric regulation, crystal structures were determined for S. solfataricus UPRTase in complex with UMP and with UMP and the allosteric inhibitor CTP. Also, a structure with UMP bound in half of the active sites was determined. All three complexes form tetramers but reveal differences in the subunits and their relative arrangement. In the UPRTase-UMP complex, the peptide bond between a conserved arginine residue (Arg80) and the preceding residue (Leu79) adopts a cis conformation in half of the subunits and a trans conformation in the other half and the tetramer comprises two cis-trans dimers. In contrast, four identical subunits compose the UPRTase-UMP-CTP tetramer. CTP binding affects the conformation of Arg80, and the Arg80 conformation in the UPRTase-UMP-CTP complex leaves no room for binding of the substrate PRPP. The different conformations of Arg80 coupled to rearrangements in the quaternary structure imply that this residue plays a major role in regulation of the enzyme and in communication between subunits. The ribose ring of UMP adopts alternative conformations in the cis and trans subunits of the UPRTase-UMP tetramer with associated differences in the interactions of the catalytically important Asp209. The active-site differences have been related to proposed kinetic models and provide an explanation for the regulatory significance of the C-terminal Gly216.

Allosteric Regulation↗
PubMed1990

Phosphofructokinase from Plasmodium berghei: a kinetic model of allosteric regulation.

As in mammalian cells, phosphofructokinase (PFK) is of major regulatory importance in the glucose metabolism of Plasmodium berghei. The malarial enzyme shows allosteric properties similar to PFK from various sources; it is activated by fructose-6-phosphate and inhibited by ATP, but differs with respect to allosteric regulation. Enzyme activity is only marginally increased by AMP, a potent activator of many phosphofructokinases. Phosphoenolpyruvate, which is reported to inhibit PFK activity, efficiency activates the malarial enzyme. No activation by ADP was observed. Instead, ADP inhibits the enzyme non-allosterically and competitively to the substrate MgATP. Phosphate stimulates the catalytic activity of malarial PFK independently of the activation by F6P and PEP.

Adenosine Diphosphate↗
PubMed2000

Phosphorylation of recombinant human ATP:citrate lyase by cAMP-dependent protein kinase abolishes homotropic allosteric regulation of the enzyme by citrate and increases the enzyme activity. Allosteric activation of ATP:citrate lyase by phosphorylated sugars.

Recombinantly expressed human ATP:citrate lyase was purified from E. coli, and its kinetic behavior was characterized before and after phosphorylation. Cyclic AMP-dependent protein kinase catalyzed the incorporation of only 1 mol of phosphate per mole of enzyme homotetramer, and glycogen synthase kinase-3 incorporated an additional 2 mol of phosphate into the phosphorylated protein. Isoelectric focusing revealed that all of the phosphates were incorporated into only one of the four enzyme subunits. Phosphorylation resulted in a 6-fold increase in V(max) and the conversion of citrate dependence from sigmoidal, displaying negative cooperativity, to hyperbolic. The phosphorylated recombinant enzyme is more similar to the enzyme isolated from mammalian tissues than unphosphorylated enzyme with respect to the K(m) for citrate, CoA, and ATP, and the specific activity. Fructose 6-phosphate was found to be a potent activator (60-fold) of the unphosphorylated recombinant enzyme, with half-maximal activation at 0.16 mM, which results in a decrease in the apparent K(m) for citrate and ATP, as well as an increase in the V(max) of the reaction. Thus, human ATP:citrate lyase activity is regulated in vitro allosterically by phosphorylated sugars as well as covalently by phosphorylation.

ATP Citrate (pro-S)-Lyase↗
PubMed1990

Calcium flux mediated by purified inositol 1,4,5-trisphosphate receptor in reconstituted lipid vesicles is allosterically regulated by adenine nucleotides.

When incorporated into lipid vesicles, the purified inositol 1,4,5-trisphosphate (IP3) receptor protein mediates 45Ca2+ flux. We observe a potent, selective allosteric regulation by ATP of IP3 actions on Ca2+ flux. The action of ATP is selective for adenine nucleotides with ADP and AMP less potent and GTP inactive. At 1-10 microM, ATP increases maximal IP3-induced flux by 50% with no change in IP3 potency. The enhancing effect of ATP diminishes between 0.1 and 1 mM. Concentration-response curves are steep for both the increasing and the decreasing effects of ATP on IP3 actions, suggesting a physiological regulatory role of ATP in IP3-induced Ca2+ release. Diminishing local ATP concentrations coincident with filling of Ca2+ stores by the Ca2(+)-ATPase may enhance IP3 release of Ca2+, an effect that would decline as ATP returns to physiological levels. ATP regulation of Ca2+ release may also play a role in oscillations of intracellular Ca2+ concentration.

Adenine Nucleotides↗
PubMed1998

Allosteric regulation of pyruvate kinase M2 isozyme involves a cysteine residue in the intersubunit contact.

Pyruvate kinase M2 isozyme mutants with amino acid substitutions in the subunit interface were prepared and characterized. The substitutions were made in the allosteric M2 isozyme by the corresponding residues of the nonallosteric M1 isozyme to identify the residue involved in the allosteric effects. The replacement of Cys-423 by Leu led to substantial loss of both homotropic and heterotropic allosteric effects while the substitutions at Phe-389, Arg-398, Ala-401, Pro-402, Thr-408, and Ile-427 did not. The altered kinetic properties of the Cys-423-substituted mutant resulted from the shift of the allosteric transition toward the active R-state since the mutant exhibits the allosteric properties in the presence of an allosteric inhibitor, L-phenylalanine. The inverse correlation between the hydrophobicity of residue 423 and the extent of stabilization of the R-state was found by analysis of mutants with un-ionizable amino acids at position 423. Furthermore, the modification of Cys-423 with methyl methanethiosulfonate led to a shift of the allosteric transition toward the R-state, probably the result of increased hydrophobicity of the residue. These results suggest that Cys-423 is involved in the allosteric regulation of the enzyme through hydrophobic interactions.

Allosteric Regulation↗
PubMed1998

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.

Adenosine Triphosphate↗
PubMed1996

Allosteric regulation of the thermostability and DNA binding activity of human p53 by specific interacting proteins. CRC Cell Transformation Group.

Conformational stability is a prerequisite for the physiological activity of the tumor suppressor protein p53. p53 protein can be allosterically activated for DNA binding by phosphorylation or through noncovalent interaction with proteins such as DnaK, the Escherichia coli homologue of the heat shock protein Hsp70. We present in vitro evidence for a rapid temperature-dependent change in the conformation and tetrameric nature of wild-type p53 upon incubation at 37 degrees C, which correlates with a permanent loss in DNA binding activity. We show that p53 is allosterically regulated for stabilization of the wild-type conformation and DNA binding activity at 37 degrees C by binding of two classes of ligands to regulatory sites on the N and C terminus of the molecule through which an intrinsic instability of p53 is neutralized. Deletion of the domain conferring instability at the C terminus is sufficient to confer enhanced stability to the total protein. DnaK binding to the C terminus can profoundly protect p53 at 37 degrees C from a temperature-dependent loss of the DNA binding activity but does not renature or activate denatured p53. In contrast, another activator of the DNA binding activity of latent p53, the monoclonal antibody PAb421, which also interacts with the C terminus of the protein, is not able to protect p53 from thermal denaturation. Two monoclonal antibodies to the N terminus of p53, PAb1801 and DO-1, do not activate the latent DNA binding function of p53 but can protect the p53 wild-type conformation at 37 degrees C. Thus, activation of the DNA binding function of p53 is not synonymous with protection from thermal denaturation, and therefore, both of these pathways may be used in cells to control the physiological activity of p53. The protection of p53 conformation from heat denaturation by interacting proteins suggests a novel mechanism by which p53 function could be regulated in vivo.

Allosteric Regulation↗
PubMed1996

The mechanism of velocity modulated allosteric regulation in D-3-phosphoglycerate dehydrogenase. Cross-linking adjacent regulatory domains with engineered disulfides mimics effector binding.

D-3-Phosphoglycerate dehydrogenase (PGDH) (EC 1.1.1.95) from Escherichia coli is an allosterically regulated enzyme of the Vmax type. It is a tetramer of identical subunits and each subunit is made up of three identifiable domains, the cofactor binding domain, the substrate binding domain, and the regulatory domain. Each subunit contacts two other subunits through adjacent cofactor binding domains and through adjacent regulatory domains. L-Serine, the physiological effector, inhibits catalytic activity by apparently tethering regulatory domains from adjacent subunits together through the formation of hydrogen bonds to each subunit. This investigation demonstrates that cross-linking adjacent regulatory domains with engineered disulfides produces catalytic inhibition in the absence of inhibitor in a manner similar to that produced by the inhibitor. The inhibition due to cross-linking can be completely reversed in a concentration dependent manner by dithiothreitol. The active mutant enzyme, containing the engineered cysteines in the reduced state, retains its ability to be inhibited by L-serine, although at a 100-fold higher concentration. Hill plots of the serine inhibition of mutant and native enzyme indicate that the number of interacting sites remains at 2 in the mutant enzyme. The reversible inhibition of enzyme activity that results from tethering adjacent regulatory domains with engineered disulfides suggests that these domains move in some manner relative to one another during the active to inhibited state transition. These observations support the model which predicts that catalytic activity is regulated by the movement of rigid domains about flexible hinges and that effector binding prevents this by locking the regulatory domains in a state that produces an open active site cleft.

Allosteric Regulation↗
PubMed1978

Enhanced allosteric regulation of threonine deaminase and acetohydroxy acid synthase from Escherichia coli in a permeabilized-cell assay system.

A permeabilized-cell technique for rapid assay of enzyme activity has revealed enhanced allosteric regulation of both threonine deaminase (L-threonine hydrolyase (deaminating), EC 4.2.1.16) and acethohydroxy acid synthease (acetolactate pyruvate-lyase (carboxylating), EC 4.1.3.18) in Escherichia col K-12. In the permeabilized cell assay threonine deaminase exhibited a higher Hill coefficient for inhibition by L-isoleucine, and acetohydroxy acid synthase exhibited a hypersensensitivity to allosteric inhibition by L-valine when compared to studies on crude extracts. We propose that these effects reflect the in situ microenvironments of both enzymes. Preliminary evidence further indicates that acetohydroxy acid synthase may loosely associate with the cell membrane.

Acetolactate Synthase↗
PubMed1995

Allosteric regulation of the ATP sulfurylase associated GTPase.

ATP sulfurylase catalyzes and chemically links the hydrolysis of GTP and the synthesis of activated sulfate (APS). Like many GTPases, its GTPase activity is allosterically regulated, in this case, by APS-forming reactants and their analogues. Using these activators, we have been able to mimic many of the complexes that form in the native reaction, including an E.AMP intermediate. The effects of each of these complexes on GTP hydrolysis are determined. The results of pre-steady-state and isotope trapping studies demonstrate that the binding of activator and substrate to the enzyme are near equilibrium and that the rate-determining step appears to be scission of the beta, gamma-bond of GTP. These properties of the system allow the energetic consequences of activator binding on the ground- and transition-state complexes to be evaluated. Activation occurs predominantly by transition-state stabilization, resulting in kcat increases. The values for kcat span a 180-fold range and vary with each activator. Km, or ground-state, effects are relatively small, approximately 3-fold, and are uniform throughout the activator series. These studies provide an in-depth view of the energetic interactions between the two active sites at each step of the APS-forming reaction.

Acid Anhydride Hydrolases↗
PubMed1987

Enzymic arrangement and allosteric regulation of the aromatic amino acid pathway in Neisseria gonorrhoeae.

The pathway construction and allosteric regulation of phenylalanine and tyrosine biosynthesis was examined in Neisseria gonorrhoeae. A single 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase enzyme sensitive to feedback inhibition by L-phenylalanine was found. Chorismate mutase and prephenate dehydratase appear to co-exist as catalytic components of a bifunctional enzyme, known to be present in related genera. The latter enzyme activities were both feedback inhibited by L-phenylalanine. Prephenate dehydratase was strongly activated by L-tyrosine. NAD+-linked prephenate dehydrogenase and arogenate dehydrogenase activities coeluted following ion-exchange chromatography, suggesting their identity as catalytic properties of a single broad-specificity cyclohexadienyl dehydrogenase. Each dehydrogenase activity was inhibited by 4-hydroxyphenylpyruvate, but not by L-tyrosine. Two aromatic aminotransferases were resolved, one preferring the L-phenylalanine:2-ketoglutarate substrate combination and the other preferring the L-tyrosine: 2-ketoglutarate substrate combination. Each aminotransferase was also able to transaminate prephenate. The overall picture of regulation is one in which L-tyrosine modulates L-phenylalanine synthesis via activation of prephenate dehydratase. L-Phenylalanine in turn regulates early-pathway flow through inhibition of DAHP synthase. The recent phylogenetic positioning of N. gonorrhoeae makes it a key reference organism for emerging interpretations about aromatic-pathway evolution.

3-Deoxy-7-Phosphoheptulonate Synthase↗
PubMed2006

Ionic contacts at DnaK substrate binding domain involved in the allosteric regulation of lid dynamics.

To gain further insight into the interactions involved in the allosteric transition of DnaK we have characterized wild-type (wt) protein and three mutants in which ionic interactions at the interface between the two subdomains of the substrate binding domain, and within the lid subdomain have been disrupted. Our data show that ionic contacts, most likely forming an electrically charged network, between the N-terminal region of helix B and an inner loop of the beta-sandwich are involved in maintaining the position of the lid relative to the beta-subdomain in the ADP state but not in the ATP state of the protein. Disruption of the ionic interactions between the C-terminal region of helix B and the outer loops of the beta-sandwich, known as the latch, does not have the same conformational consequences but results equally in an inactive protein. This indicates that a variety of mechanisms can inactivate this complex allosteric machine. Our results identify the ionic contacts at the subdomain and interdomain interfaces that are part of the hinge region involved in the ATP-induced allosteric displacement of the lid away from the peptide binding site. These interactions also stabilize peptide-Hsp70 complexes at physiological (37 degrees C) and stress (42 degrees C) temperatures, a requirement for productive substrate (re)folding.

Adenosine Diphosphate↗
PubMed1996

The mechanism of velocity modulated allosteric regulation in D-3-phosphoglycerate dehydrogenase. Site-directed mutagenesis of effector binding site residues.

D-3-Phosphoglycerate dehydrogenase (EC 1.1.1.95) from Escherichia coli catalyzes the first committed step in serine biosynthesis and is allosterically regulated by L-serine, the end product of the pathway. Each subunit of the homotetramer is made up of three distinct domains with one of the intersubunit contacts being between adjacent regulatory domains. Each regulatory domain interface contains two symmetrical serine binding sites such that serine forms hydrogen bonds to both domains across the interface. Previous work (Al-Rabiee, R., Lee, E. J., and Grant, G. A. (1996) J. Biol. Chem. 271, 13013-13017) demonstrated that when adjacent regulatory domains are covalently linked to one another by engineered disulfide bonds, the enzyme was inactivated. Breaking the disulfide bonds by reduction restored enzymatic activity. This study demonstrates that the complementary situation is also true. Site-directed mutagenesis of three residues at the effector binding site, His344, Asn346, and Asn364', render the enzyme increasingly less susceptible to inhibition by the effector. When mutations result in a situation where it is no longer possible to establish a stable hydrogen bonding network across the regulatory domain interface, the inhibitory capacity of the effector is lost. Furthermore, mutations that produce as much as 5 orders of magnitude decrease in the ability of L-serine to inhibit the enzyme have no appreciable effect on the Km or kcat of the enzyme. These observations support the model that predicts that catalytic activity in D-3-phosphoglycerate dehydrogenase is regulated by the movement of adjacent regulatory domains about a flexible hinge and that effector binding tethers the regulatory domains together producing a state that results in a stable, open active site cleft that is no longer able to promote catalysis.

Allosteric Regulation↗
PubMed2000

Allosteric regulation of the light-harvesting system of photosystem II.

Non-photochemical quenching of chlorophyll fluorescence (NPQ) is symptomatic of the regulation of energy dissipation by the light-harvesting antenna of photosystem II (PS II). The kinetics of NPQ in both leaves and isolated chloroplasts are determined by the transthylakoid delta pH and the de-epoxidation state of the xanthophyll cycle. In order to understand the mechanism and regulation of NPQ we have adopted the approaches commonly used in the study of enzyme-catalysed reactions. Steady-state measurements suggest allosteric regulation of NPQ, involving control by the xanthophyll cycle carotenoids of a protonation-dependent conformational change that transforms the PS II antenna from an unquenched to a quenched state. The features of this model were confirmed using isolated light-harvesting proteins. Analysis of the rate of induction of quenching both in vitro and in vivo indicated a bimolecular second-order reaction; it is suggested that quenching arises from the reaction between two fluorescent domains, possibly within a single protein subunit. A universal model for this transition is presented based on simple thermodynamic principles governing reaction kinetics.

Allosteric Regulation↗
PubMed1978

Allosteric regulation of calf thymus ribonucleotide reductase.

Ribonucleotide reductase was purified 3400-fold from calf thymus. The enzyme preparation was essentially free of kinases and phosphatases and therefore allowed a conclusive study of the allosteric regulation of a eukaryotic ribonucleotide reductase to be made for the first time. Comparable maximal activities were obtained for the reduction of all four ribonucleotide substrates in the presence of their optimal stimulatory effectors. These and other results strongly argue for the existence of only one ribonucleotide reductase in mammalian cells. No reduction was observed in the absence of effector. The reduction of CDP and UDP both required ATP, with no stimulatory effect of any other nucleoside triphosphate. The only activator of GDP reduction was dTTP and the only activator of ADP reduction was dGTP. Reduction of the purine ribonucleotides was further stimulated by ATP but only in combination with dTTP or dGTP. The reduction of all four ribonucleotides was strongly inhibited by dATP, the inhibition being partly released by ATP. The data can be integrated into a scheme which links ribonucleotide reduction to DNA synthesis.

Allosteric Regulation↗
PubMed2000

Role of residue Phe225 in the cofactor-mediated, allosteric regulation of the serine protease coagulation factor VIIa.

Functional regulation by cofactors is fundamentally important for the highly ordered, consecutive activation of the coagulation cascade. The initiating protease of the coagulation system, factor VIIa (VIIa), retains zymogen-like features after proteolytic cleavage of the activating Arg(15)-Ile(16) peptide bond and requires the binding of the cofactor tissue factor (TF) to stabilize the protease domain in an active enzyme conformation. Structural comparison of TF-bound and free VIIa failed to provide a conclusive mechanism for this catalytic activation. This study provides novel insight into the cofactor-dependent regulation of VIIa by demonstrating that the side chain of Phe(225), an aromatic residue that is common to allosterically regulated serine proteases, is necessary for optimal TF-mediated activation of VIIa's catalytic function. However, mutation of Phe(225) did not abolish the cofactor-induced stabilization of the Ile(16)-Asp(194) salt bridge, previously considered the primary switch mechanism for activating VIIa. Moreover, mutation of other residue side chains in the VIIa protease domain resulted in a reduced level of or no stabilization of the amino-terminal insertion site upon TF binding, with little or no effect on the TF-mediated enhancement of catalysis. This study thus establishes a crucial role for the aromatic Phe(225) residue position in the allosteric network that transmits the activating switch from the cofactor interface to the catalytic cleft, providing insight into the highly specific conformational linkages that regulate serine protease function.

Allosteric Regulation↗