Dimeric Enzyme Molecule Research Articles

Molecular Dynamics Study of Escherichia coli Thymidine Phosphorylase in a Complex with 3'-Azidothymidine Inhibitor and Phosphate

—Using a molecular dynamics method, the state of the dimeric thymidine phosphorylase molecule from Escherichia coli in a complex with noncompetitive enzyme inhibitor 3'-azidothymidine and phosphate ion was studied on a trajectory of 50 ns. Previously obtained atomic coordinates of a complex of thymidine phosphorylase with azidothymidine and sulfate at a resolution of 1.52 Å were used as a starting model. It was demonstrated that both subunits of a dimeric enzyme molecule function asynchronously in a given time interval; moreover, each subunit maintains an open conformation. It was found that the nature of ligand at the nucleoside center affects the binding strength of phosphate in the phosphate center. In a complex with an inhibitor, both ligands over the entire time interval remain bound to the enzyme, while the release of phosphate from the active center is observed when simulating the behavior of thymidine phosphorylase in the presence of phosphate and thymidine substrate. The stabilizing effect of azidothymidine on phosphate binding is consistent with the behavior of azidothymidine as a noncompetitive inhibitor of thymidine phosphorylase.

Trypanosoma cruzi as a model system to study the expression of exogenous genes coding for polyamine biosynthetic enzymes. Induction of DFMO resistance in transgenic parasites

Trypanosoma cruzi, the etiologic agent of Chagas' disease, is a polyamine auxotroph organism because its genome contains neither ornithine decarboxylase (ODC) nor arginine decarboxylase (ADC) genes, presumably lost during evolution. After transformation with a recombinant plasmid bearing the complete coding region of Crithidia fasciculata ODC gene, the transgenic parasites were able to synthesize putrescine and simultaneously became susceptible to α-difluoromethylornithine (DFMO), an irreversible inhibitor of ODC. We have studied the emergence of DFMO-resistant T. cruzi after one-step selection of ODC-transformed parasites cultivated in the presence of high levels of the drug (5 mM). Our results have indicated a duplication of the ODC gene copy number in the drug-resistant cell line. The ODC transcripts and the corresponding translation products showed very significant increases (about 7- and 25-fold, respectively) in DFMO-resistant parasites, while the ODC enzymatic activity was 5 times higher than in drug-sensitive T. cruzi. The unequal increases of ODC protein and enzymatic activity in DFMO-resistant protozoa strongly suggest that in addition to gene amplification and enhanced transcription and translation, the assembly of ODC polypeptide chains into dimeric active enzyme molecules might also contribute to regulate the development of DFMO resistance.

Direct monitoring of EcoRII restriction enzyme reactions on a 27MHz quartz-crystal microbalance

EcoRII is a type IIe restriction endonuclease characterized by a highly cooperative reaction mechanism that depends on simultaneous binding of the dimeric enzyme molecule to two copies of its recognition site. Gaining insights about reaction property of EcoRII binding to its recognition site and effect of divalent metal ion on DNA cleavage process, a DNA-immobilized quartz crystal microbalance (QCM), which enables real-time monitoring both the binding of enzyme and the cleavage reaction on DNA strands as mass changes, was utilized.

Divalent cation induced changes in structural properties of the dimeric enzyme glucose oxidase: dual effect of dimer stabilization and dissociation with loss of cooperative interactions in enzyme monomer.

Glucose oxidase (GOD) from Aspergillus niger is a dimeric enzyme having high localization of negative charges on the enzyme surface and at the dimer interface. The monovalent cations induce compaction of the native conformation of GOD and enhance stability against thermal and urea denaturation [Ahmad et al. (2001) Biochemistry 40, 1947-1955]. In this paper we report the effect of the divalent cations Ca2+ and Mg2+ on the structural and stability properties of GOD. A divalent cation concentration dependent change in native conformation and subunit assembly of GOD was observed. Low concentration (up to 1 M) of CaCl2 or MgCl2 induced compaction of the native conformation of GOD, and the enzyme showed higher stability as compared to the native enzyme against urea denaturation. However, higher concentration (> or =2.0 M) of CaCl2 or MgCl2 induced dissociation of the native dimeric enzyme, resulting in stabilization of the enzyme monomer. An interesting observation was that the 3 M CaCl2-stabilized monomer of GOD retained about 70% secondary structure present in the native GOD dimer; however, there was a complete loss of cooperative interactions between these secondary structural elements present in the enzyme. Regarding the mechanism of divalent cation induced structural changes in GOD, the studies suggest that organization of water molecules by divalent cation results in stabilization of enzyme at low divalent cation concentration, whereas direct binding of these cations to the enzyme, at higher divalent cation concentration, results in dissociation and partial unfolding of the dimeric enzyme molecule.

Combined kinetic mechanism describing activation and inhibition of muscle glycogen phosphorylase b by adenosine 5′-monophosphate

The kinetic analysis of the glycogen chain growth reaction catalyzed by glycogen phosphorylase b from rabbit skeletal muscle has been carried out over a wide range of concentrations of AMP under the saturation of the enzyme by glycogen. The applicability of 23 different variants of the kinetic model involving the interaction of AMP and glucose 1-phosphate binding sites in the dimeric enzyme molecule is considered. A kinetic model has been proposed which assumes: (i) the independent binding of one molecule of glucose 1-phosphate in the catalytic site on the one hand, and AMP in both allosteric effector sites and both nucleoside inhibitor sites of the dimeric enzyme molecule bound by glycogen on the other hand; (ii) the binding of AMP in one of the allosteric effector sites results in an increase in the affinity of other allosteric effector site to AMP; (iii) the independent binding of AMP to the nucleoside inhibitor sites of the dimeric enzyme molecule; (iv) the exclusive binding of the second molecule of glucose 1-phosphate in the catalytic site of glycogen phosphorylase b containing two molecules of AMP occupying both allosteric effector sites; and (v) the catalytic act occurs exclusively in the complex of the enzyme with glycogen, two molecules of AMP occupying both allosteric effector sites, and two molecules of glucose 1-phosphate occupying both catalytic sites.

Kinetic mechanism of allosteric regulation of muscle glycogen phosphorylase B by adenosine 5'-monophosphate.

Kinetic analysis of the glycogen chain growth reaction catalyzed by glycogen phosphorylase b from rabbit skeletal muscle has been carried out over a wide range of AMP concentration under the saturation of the enzyme by glycogen. Applicability of some variants of the kinetic model involving the interaction of AMP- and glucose 1-phosphate-binding sites in the dimeric enzyme molecule is considered. A kinetic model of the enzymatic reaction describing adequately the activation of the enzyme by AMP and inhibition at sufficiently high concentrations of AMP is proposed.

Imaging DNA Loops Induced by Restriction Endonuclease EcoRII: A SINGLE AMINO ACID SUBSTITUTION UNCOUPLES TARGET RECOGNITION FROM COOPERATIVE DNA INTERACTION AND CLEAVAGE

EcoRII is a type IIE restriction endonuclease characterized by a highly cooperative reaction mechanism that depends on simultaneous binding of the dimeric enzyme molecule to two copies of its DNA recognition site. Transmission electron microscopy provided direct evidence that EcoRII mediates loop formation of linear DNA containing two EcoRII recognition sites. Specific DNA binding of EcoRII revealed a symmetrical DNase I footprint occupying 16-18 bases. Single amino acid replacement of Val(258) by Asn yielded a mutant enzyme that was unaffected in substrate affinity and DNase I footprinting properties, but exhibited a profound decrease in cooperative DNA binding and cleavage activity. Because the electrophoretic mobility of the mutant enzyme-DNA complexes was significantly higher than that of the wild-type, we investigated if mutant V258N binds as a monomer to the substrate DNA. Analysis of the molecular mass of mutant V258N showed a high percentage of protein monomers in solution. The dissociation constant of mutant V258N confirmed a 350-fold decrease of the enzyme dimerization capability. We conclude that Val(258) is located in a region of EcoRII involved in homodimerization. This is the first report of a specific amino acid replacement in a restriction endonuclease leading to the loss of dimerization and DNA cleavage while retaining specific DNA binding.

On the mechanism and specificity of soluble, quinoprotein glucose dehydrogenase in the oxidation of aldose sugars.

Kinetic and optical studies were performed on the reductive half-reaction of soluble, quinoprotein glucose dehydrogenase (sGDH), i.e., on the conversion of sGDHox plus aldose sugar into sGDHred plus corresponding aldonolactone. It appears that the nature and stereochemical configuration of the substituents at certain positions in the aldose molecule determine the substrate specificity pattern: absolute specificity exists with respect to the C1-position (only sugars being oxidized which have the same configuration of the H/OH substituents at this site as the beta-anomer of glucose, not those with the opposite one) and with respect to the overall conformation of the sugar molecule (sugars with a 4C1 chair conformation are substrates, those with a 1C4 one are not); the nature and configuration of the substituents at the 3-position are hardly relevant for activity, and an equatorial pyranose group at the 4-position exhibits only aspecific hindering of the binding of the aldose moiety of a disaccharide. The pH optimum determined for glucose oxidation appeared to be 7.0, implying that reoxidation of sGDHred is rate-limiting with those electron acceptors displaying a different value under steady-state conditions. The kinetic mechanism of sGDH consists of (a) step(s) in which a fluorescing intermediate is formed, and a subsequent, irreversible step, determining the overall rate of the reductive half-reaction. The consequences of this for the likeliness of chemical mechanisms where glucose is oxidized by covalent catalysis in which a C5-adduct of glucose and PQQ are involved, or by hydride transfer from glucose to PQQ, followed by tautomerization of C5-reduced PQQ to PQQH2, are discussed. The negative cooperative behavior of sGDH seems to be due to substrate-occupation-dependent subunit interaction in the dimeric enzyme molecule, leading to a large increase of the turnover rate under saturating conditions.

The significance of distance and orientation of restriction endonuclease recognition sites in viral DNA genomes

Studies on phage T3 and T7 have shown that these viruses avoid restriction not only by the phage-coded Ocr (and S-adenosylmethionine hydrolase) protein functions or by the complete loss of specific recognition sites for certain restriction endonucleases from their genomes, but also that there are two additional modes: resistance towards EcoP15 (which recognizes a non-symmetrical sequence) is achieved by an identical orientation of all the recognition sites in the virus genome (strand bias) and in the case of EcoRII by the extreme reduction in number and thereby greater distance between recognition sites in the genome. These observations led to the discovery that certain restriction endonucleases require the simultaneous cooperation with two DNA sites for their function, as well as to the ongoing elucidation of the molecular modes of action of these enzymes. Type II and type III enzymes display fundamentally different mechanisms of protein-DNA interaction. For EcoRII we favor a model of simultaneous binding of two DNA sites to a dimeric enzyme molecule (neighbouring sites of the same, looping, DNA molecule or sites located on different DNA molecules), while the action of EcoP15 seems to conform with a tracking-collision model of two enzyme molecules bound to inversely oriented recognition sites. In addition to podoviruses T3 and T7, strand bias of recognition sequences for different type III DNA modification-restriction enzymes is also observed in the inoviruses M13, IKE and PF3.

The significance of distance and orientation of restriction endonuclease recognition sites in viral DNA genomes

Studies on phage T3 and T7 have shown that these viruses avoid restriction not only by the phage-coded Ocr (and S-adenosylmethionine hydrolase) protein functions or by the complete loss of specific recognition sites for certain restriction endonucleases from their genomes, but also that there are two additional modes: resistance towards EcoP15 (which recognizes a non-symmetrical sequence) is achieved by an identical orientation of all the recognition sites in the virus genome (strand bias) and in the case of EcoRII by the extreme reduction in number and thereby greater distance between recognition sites in the genome. These observations led to the discovery that certain restriction endonucleases require the simultaneous cooperation with two DNA sites for their function, as well as to the ongoing elucidation of the molecular modes of action of these enzymes. Type II and type III enzymes display fundamentally different mechanisms of protein—DNA interaction. For EcoRII we favor a model of simultaneous binding of two DNA sites to a dimeric enzyme molecule (neighbouring sites of the same, looping, DNA molecule or sites located on different DNA molecules), while the action of EcoP15 seems to conform with a tracking-collision model of two enzyme molecules bound to inversely oriented recognition sites. In addition to podoviruses T3 and T7, strand bias of recognition sequences for different type III DNA modification—restriction enzymes is also observed in the inoviruses M13, IKE, and PF3.

Overproduction of His-tagged EcoRII restriction endonuclease and terminally deleted mutant proteins

EcoRII was the first restriction endonuclease (ENase) reported requiring the cooperative interaction with at least two DNA sites for activity. Using two different expression systems the enzyme could be purified and its special substrate requirements were further analyzed. At the present state of knowledge we suggest a model of simultaneous binding of two DNA sites to one dimeric enzyme molecule (see Krüger et al., FEMS Microbiol. Rev. (1995) in press).

Immediate Interaction between the Nascent Subunits and Two Conserved Amino Acids Trp34 and Thr206 Are Needed for the Catalytic Activity of Aspartylglucosaminidase

Aspartylglucosaminidase (AGA, EC 3.5.1.26) is a dimeric lysosomal hydrolase involved in the degradation of glycoproteins. The synthesized precursor polypeptide of AGA is rapidly activated in the endoplasmic reticulum by proteolysis into two subunits. Expression of the alpha- and beta-subunits of AGA in separate cDNA constructs showed that independently folded subunits totally lack enzyme activity, and even when co-expressed in vitro they fail to produce an active heterodimer of the enzyme. Both of the subunits are required for the enzyme activity, and the immediate interaction of the subunits in the endoplasmic reticulum is necessary for the correct folding of the dimeric enzyme molecule. The specific amino acid residues essential for the active site of the AGA enzyme were further analyzed by site-directed mutagenesis and in vitro expression of mutagenized constructs. Replacement of Thr206, the most amino-terminal residue of the beta-subunit, with Ser resulted in a complete loss of enzyme activity without influencing intracellular processing or transport of the mutant polypeptide to the lysosomes. Analogously, replacement of the most amino-terminal tryptophan, Trp34 with Phe or Ser in the alpha-subunit, resulted in a totally inactive enzyme without influencing the intracellular processing or stability of the polypeptide. These results suggest that the catalytic center of this amidase is formed by the interaction of the amino-terminal parts of two subunits and requires both Trp34 in the alpha-subunit and Thr206 in the beta-subunit.

Kinetic Mechanism of Activation of Muscle Glycogen Phosphorylase b by Adenosine 5′-Monophosphate

The kinetic analysis of the enzymatic reaction catalyzed by glycogen phosphorylase b from the rabbit skeletal muscle has been carried out in the direction of glycogen synthesis under the conditions of the saturation of the enzyme by glycogen. The applicability of 12 different variants of the Monod-Wyman-Changeux model and 6 kinetic schemes involving the interaction of AMP- and glucose-1-phosphate-binding sites in the dimeric enzyme molecule is considered. The kinetic model has been proposed, which assumes (i) the independent binding of AMP and one molecule of glucose 1-phosphate with the enzyme saturated by glycogen, (ii) the exclusive binding of the second molecule of glucose 1-phosphate by the enzyme containing two molecules of AMP and one molecule of glucose 1-phosphate, and (iii) the exclusive ability of the complex of the enzyme with glycogen, two molecules of AMP, and two molecules of glucose 1-phosphate to undergo the catalytic transformation. The parameters of the equation of the initial steady-state rate of the enzymatic reaction are calculated by the nonlinear regression method. The proposed kinetic scheme is shown to satisfy to the following criteria: (i) the convergence under the regressional analysis, (ii) the reliability of the values of the parameters of the model, (iii) the minimality of the sum of the weighted squares of the differences between the experimental and calculated values of the reaction rate.

Crystal structure of yeast Cu,Zn superoxide dismutase: Crystallographic refinement at 2.5 Å resolution

The structure of Cu,Zn yeast superoxide dismutase has been determined to 2.5 Å resolution. The enzyme crystallizes in the P2 12 12 space group with two dimeric enzyme molecules per asymmetric unit. The structure has been solved by molecular replacement techniques using the dimer of the bovine enzyme as the search model, and refined by molecular dynamics with crystallographic pseudo-energy terms, followed by conventional crystallographic restrained refinement. The R-factor for 32,088 unique reflections in the 10.0 to 2.5 Å resolution range (98.2% of all possible reflections) is 0.158 for a model comprising two protein dimers and 516 bound solvent molecules, with a root-mean-square deviation of 0.016 Å from the ideal bond lengths, and an average B-factor value of 29.9 Å 2. A dimeric molecule of the enzyme is composed of two identical subunits related by a noncrystallographic 2-fold axis. Each subunit (153 amino acid residues) has as its structural scaffolding a flattened antiparallel eight-stranded β-barrel, plus three external loops. The overall three-dimensional structure is quite similar to the phylogenetically distant bovine superoxide dismutase (55% amino acid homology), the largest deviations can be observed in the regions of amino acid insertions. The major insertion site hosting residues Ser25A and Gly25B, occurs in the 2,3 β-turn between strands 2b and 3c, resulting in the structural perturbations of the two neighbouring strands. The second insertion site, at the end of the 3c β-strand in the wide Greek-key loop, hosts the Asn35A residue, having an evident effect on the structure of the loop and possibly on the neighbouring 5,4 β-turn. The salt bridge Arg77-Asp99 and the disulphide bridge Cys55-Cys144 stabilize the loop regions containing the metal ligands. The stereochemistry of the two metal centres is conserved, with respect to the bovine enzyme. The Cu 2+ ligands show an uneven distortion from a square plane, while Zn 2+ co-ordination geometry is distorted tetrahedral. The imidazole ring of the His61 residue forms a bridge between Cu and Zn ions. A solvent peak compatible with a fifth ligand is observed 2.0 Å away from the copper in the active site channel, which is filled by ordered water molecules that possibly contribute to the stability and function of the enzyme. The charged residues responsible for the electrostatic guidance of the substrate to the active site (Glu130, Glu131, Lys134 and Arg141) are fairly conserved in their positions, some of them showing different interactions in the four chains due to the intermolecular contacts between the dimers. The β-barrel of the bovine enzyme is closed at opposite ends by apolar interactions involving Leu104 and Leu36; the latter is substituted by Ser36 in the yeast enzyme. Three concerted substitutions Ala87 → Thr, His41 → Arg and Glu119 → Ala allow for the formation of a “plug” for the β-barrel by means of a hydrogen bonding scheme.

Crystallization and preliminary X-ray diffraction studies of the human erythrocyte bisphosphoglycerate mutase

Bisphosphoglycerate mutase (EC 2.7.5.4) catalyzes the synthesis and breakdown of 2,3-diphosphoglycerate in red cells. The human enzyme, cloned and expressed in Escherichia coli has been crystallized in the rhombohedral space group R32 with a = b = c = 100·4 A ̊ and α = β = γ = 81·2 ° . The asymmetric unit contains either a dimeric enzyme molecule or a monomer.

Preliminary crystallographic data for NAD(P)H quinone reductase isolated from the Walker 256 rat carcinoma cell line

An NAD(P)H quinone reductase isolated from Walker rat 256 carcinoma cells has been crystallized in a form suitable for high-resolution structural analysis. The crystals belong to orthorhombic space group P2 12 12 1 with cell parameters a = 168.15 A ̊ , b = 105.09 A ̊ and c = 67.38 A ̊ and contain four monomeric or two dimeric enzyme molecules per asymmetric unit. Diffraction extends beyond 2.3 Å resolution.

Characterization of a functional recombinant rat liver aldehyde dehydrogenase: Expression as a non-fusion protein in E. Coli

A cDNA encoding a rat liver inducible aldehyde dehydrogenase carried in a pUC8 plasmid is expressed in E. coli as a dimeric enzyme molecule functionally and physically identical to the authentic rat enzyme. The cDNA appears to be transcribed using the lac promoter, but is translated from an initiator codon 174 base pairs from the 5' end of the cDNA. The aldehyde dehydrogenase polypeptide is not produced as a fusion protein. This is the first example of the production by E. coli of a catalytically active, multimeric eukaryotic protein which is not a fusion protein.

Crystallization and a preliminary X-ray diffraction study of isozyme 3-3 of glutathione S-transferase from rat liver

Crystals of the homodimeric isozyme 3-3 of glutathione S-transferase from rat liver have been obtained with the hanging drop method of vapor diffusion from ammonium sulfate solutions. The successful crystallization of the enzyme required the presence of both the enzyme inhibitor (9R,10R)-9,10-dihydro-9-( S-glutathionyl)-10-hydroxyphenanthrene and the detergent β-octylglucopyranoside. The crystals belong to the monoclinic space group C2, with cell dimensions of a = 88.24(8) A ̊ , b = 69.44(4) A ̊ , c = 81.28(5) A ̊ , β = 106.01(6)∘ , and contain four dimeric enzyme molecules per unit cell. The crystals diffract to at least 2.2 Å and are suitable for X-ray crystallographic structure determination at high resolution.

Suppression of high-affinity ligand binding to the major glutathione S-transferase from Galleria mellonella by physiological concentrations of glutathione

The major glutathione S-transferase from larvae of Galleria mellonella binds a number of synthetic triphenylmethane dyes with dissociation constants of the order of 10(-6) M or less. The organ distribution of the enzyme activity does not parallel the uptake of such dyes by the insect's organs in vivo. The affinity of the protein for such dyes is decreased by about an order of magnitude by the presence of glutathione in normal physiological concentration. This appears to be the cause of this protein's lack of efficacy as a 'ligandin' in vivo. The dyes appear to be acting as ineffective substrate analogues, binding at the catalytic site and impeding, in a reciprocal fashion, the binding of glutathione. Fluorescence-quenching titration and kinetic experiments together indicate the existence of a single ligand-binding and catalytic site per dimeric enzyme molecule.

Nucleoside Phosphotransferase front Malt Sprouts. III. Studies on Metal Ion Requirement, Solvent Effects, Kinetics and Reaction Mechanism

The nucleoside phosphotransferase from malt sprouts contains one Mg2 per dimeric enzyme molecule. This cation can be removed by EDTA, while other chelating agents are less efficient. The metal-free apoenzyme is inactive. Activity can be restored to its initial value by Mg2 or Co2 and to a minor extent by Mn2, Zn2, Cu2, Ni2 and Fe2. Thermal stability is reduced when the metal is removed but can be restored by addition of Mg2. Adenosine 3',5'-phosphate (cAMP) and arsenate, strong competitive inhibitors, reduce the rate of inactivation by EDTA considerably but do not reduce the rate for the reconstitution with Mg2. We therefore conclude that the phosphate group interacts electrostatically with Mg2 and that the inhibitor is not bound to the apoenzyme. The Sp-isomer of adenosine 3',5'-thionophosphate is a hundred times stronger inhibitor than the Rp-isomer and ten times stronger than cAMP; this allowed us to determine the relative position of the Mg2 in the active site. The imidazolium cation, previously detected as an essential part of the active site, obviously forms a salt bridge to the carboxylate group which attacks the phosphorus opposite to the leaving alcohol group. This conclusion is derived from the fact that organic solvents increase the rate of formation of the phospho-intermediate considerably, while higher concentrations of salt decrease it strongly. In addition, the imidazolium cation seems to polarize the P = O bond and to stabilize the negative charge at the phosphoryl oxygen in the pentacoordinate transition state; this is followed from the pH-dependence of the hydrolysis reaction. The kinetic results reveal that Km does not represent a binding equilibrium, but is the ratio of the rates for decay and formation of the covalent intermediate, while kcat/Km is an indicator for the formation step of the acyl phosphate. On the basis of all these informations it should be allowed to formulate a reaction mechanism, in which all steps of the transferase reaction have to be microscopically reversible.