Polarographic studies on the peroxidase activity of liganded deuterohemin]

The peroxidase activity of deuterohemin and deuterohemin complexes relative to the substrates pyrogallol and ascorbic acid was studied using d.c. polarography in aqueous solution. Imidazole and pyridine served as complex ligands. In the absence of the ligands, a continual rise in the substrate conversion rate with increasing H2O2 initial concentration is observed. Imidazole or pyridine were found to considerably increase the peroxidase activity of deuterohemin at low H2O2 concentrations. At high H2O2 concentrations, the dependence of the reaction rate on H2O2 concentration shows a bend, the reaction rate being in each case higher than that of free hemin under the same conditions. The reason of this fact is discussed to be a retarded formation of activated H2O2 hemin-ligand complexes at high H2O2 concentrations.     

Detailed reaction mechanism of macrophomate synthase. Extraordinary enzyme catalyzing five-step transformation from 2-pyrones to benzoates

Macrophomate synthase from the fungus Macrophoma commelinae IFO 9570 is a Mg(II)-dependent dimeric enzyme that catalyzes an extraordinary, complex five-step chemical transformation from 2-pyrone and oxalacetate to benzoate involving decarboxylation, C-C bond formation, and dehydration. The catalytic mechanism of the whole pathway was investigated in three separate chemical steps. In the first decarboxylation step, the enzyme loses oxalacetate decarboxylation activity upon incubation with EDTA. Activity is fully restored by addition of Mg(II) and is not restored with other divalent metal cations. The dissociation constant of 0.93 x 10(-)(7) for Mg(II) and atomic absorption analysis established a 1:1 stoichiometric complex. Inhibition of pyruvate formation with 2-pyrone revealed that the actual product in the first step is a pyruvate enolate, which undergoes C-C bond formation in the presence of 2-pyrone. Incubation of substrate analogs provided aberrant adducts that were produced via C-C bond formation and rearrangement. This strongly indicates that the second step is two C-C bond formations, affording a bicyclic intermediate. Based on the stereospecificity, involvement of a Diels-Alder reaction at the second step is proposed. Incubation of the stereospecifically deuterium-labeled malate with 2-pyrones in the presence of malate dehydrogenase provided information for the stereochemical course of the reaction catalyzed by macrophomate synthase, indicating that the first decarboxylation provides pyruvate (Z)-[3-(2)H]enolate and that dehydration at the final step occurs with anti-elimination accompanied by concomitant decarboxylation. Examination of kinetic parameters in the individual steps suggests that the third step is the rate-determining step of the overall transformation.     

Mechanism of the severe inhibition of tetrachlorohydroquinone dehalogenase by its aromatic substrates

Tetrachlorohydroquinone (TCHQ) dehalogenase catalyzes the conversion of TCHQ to 2,6-dichlorohydroquinone during degradation of pentachlorophenol by Sphingobium chlorophenolicum. TCHQ dehalogenase is a member of the glutathione S-transferase superfamily. Members of this superfamily typically catalyze nucleophilic attack of glutathione upon an electrophilic substrate to form a glutathione conjugate and contain a single glutathione binding site in each monomer of the typically dimeric enzyme. TCHQ dehalogenase, in contrast to most members of the superfamily, is a monomer and uses 2 equiv of glutathione to catalyze a more complex reaction. The first glutathione is involved in formation of a glutathione conjugate, while the second is involved in the final step of the reaction, a thiol-disulfide exchange reaction that regenerates the free enzyme and forms GSSG. TCHQ dehalogenase is severely inhibited by its aromatic substrates, TCHQ and trichlorohydroquinone (TriCHQ). TriCHQ acts as a noncompetitive inhibitor of the thiol-disulfide exchange reaction required to regenerate the free form of the enzyme. In addition, dissociation of the GSSG product is inhibited by TriCHQ. The thiol-disulfide exchange reaction is the rate-limiting step in the reductive dehalogenation reaction under physiological conditions.     

Kinetic mechanism for formation of the active,dimeric UvrD helicase-DNA complex

Escherichia coli UvrD protein is a 3' to 5' SF1 helicase required for DNA repair as well as DNA replication of certain plasmids. We have shown previously that UvrD can self-associate to form dimers and tetramers in the absence of DNA, but that a UvrD dimer is required to form an active helicase-DNA complex in vitro. Here we have used pre-steady state, chemical quenched flow methods to examine the kinetic mechanism for formation of the active, dimeric helicase-DNA complex. Experiments were designed to examine the steps leading to formation of the active complex, separate from the subsequent DNA unwinding steps. The results show that the active dimeric complex can form via two pathways. The first, faster path involves direct binding to the DNA substrate of a pre-assembled UvrD dimer (dimer path), whereas the second, slower path proceeds via sequential binding to the DNA substrate of two UvrD monomers (monomer path), which then assemble on the DNA to form the dimeric helicase. The rate-limiting step within the monomer pathway involves dimer assembly on the DNA. These results show that UvrD dimers that pre-assemble in the absence of DNA are intermediates along the pathway to formation of the functional dimeric UvrD helicase.     

A base triple in the Tetrahymena group I core affects the reaction equilibrium via a threshold effect

Previous work on group I introns has suggested that a central base triple might be more important for the first rather than the second step of self-splicing, leading to a model in which the base triple undergoes a conformational change during self-splicing. Here, we use the well-characterized L-21 ScaI ribozyme derived from the Tetrahymena group I intron to probe the effects of base-triple disruption on individual reaction steps. Consistent with previous results, reaction of a ternary complex mimicking the first chemical step in self-splicing is slowed by mutations in this base triple, whereas reaction of a ternary complex mimicking the second step of self-splicing is not. Paradoxically, mechanistic dissection of the base-triple disruption mutants indicates that active site binding is weakened uniformly for the 5'-splice site and the 5'-exon analog, mimics for the species bound in the first and second step of self-splicing. Nevertheless, the 5'-exon analog remains bound at the active site, whereas the 5'-splice site analog does not. This differential effect arises despite the uniform destabilization, because the wild-type ribozyme binds the 5'-exon analog more strongly in the active site than in the 5'-splice site analog. Thus, binding into the active site constitutes an additional barrier to reaction of the 5'-splice site analog, but not the 5'-exon analog, resulting in a reduced reaction rate constant for the first step analog, but not the second step analog. This threshold model explains the self-splicing observations without the need to invoke a conformational change involving the base triple, and underscores the importance of quantitative dissection for the interpretation of effects from mutations.     

Activation process of pepsinogen.

The activation process of pepsinogen was analyzed by a combination of computer simulation and experiment. In order to investigate in detail the behavior of the basic schemes proposed in the previous study, further computer simulations were conducted. Some experiments were performed based on the information obtained. The changes in the UV difference spectrum in the early stage was measured by the stopped-flow technique and the conversion of pepsinogen to pepsin [EC 3.4.23.1] was followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Furthermore, on the basis of the experimental results, the most reasonable scheme was selected and modified. As a result, a scheme for the activation process of pepsinogen was obtained (Scheme 8). On the basis of the above analyses, it was assumed that the first step and the third step are pH-dependent based on the change in the UV spectrum, that the second step is a nonlinear reaction containing a looped reaction with a dimeric intermediate (in this step, peptide fragments are released and pepsinogen is converted to a pepsin-like molecule), and that the third step is an equilibrium reaction involving proton binding.     

Reversible and irreversible hemichrome generation by the oxygenation of nitrosylmyoglobin

The repeated oxygenation/reduction/nitrosylation of nitrosylmyoglobin produces low-spin ferric heme hemichromes which have been characterized by electron spin resonance spectroscopy. The predominant myoglobin hemichrome is a chemically reversible dihistidyl complex identified by the g values 1.53, 2.21, and 2.97. Also present is a low-spin ferric hydroxide derivative which is represented by the g values 1.83, 2.18, and 2.59. The formation of these species goes undetected by UV-vis spectroscopy, but the oxygenation of myoglobin to metmyoglobin is correlated with complete conversion of nitric oxide to nitrate which is released following a clear induction period. These results are interpreted in terms of the intermediates generated during the MbNO oxygenation reaction.     

The physical chemistry of Hemes II. Electron paramagnetic resonance study of the interaction of some iron(III)-porphyrins with fluoride ion in dimethylformamide

The interaction of F⁻ with high and low spin ferric deuteroporphyrin IX dimethyl ester and a low spin model compound, bis(histidine methyl ester) deuterohemin IX has been studied in dimethylformamide solution by low-temperature EPR. The reaction of F⁻ with these complexes leads to high spin compounds. The structure of the EPR line at g = 2 is due to superhyperfine interactions with axial fluoride ligands. It allows their identification as mono- or difluoride complexes. Their optical absorption spectra are reported. In the particular cases of bis(imidazole) deuterohemin IX dimethyl ester and of the model compound, the variations of the EPR spectra as functions of concentration of ionic ligand are reported. Three new low spin complexes are thus obtained. They are characterized by a specific interaction of F⁻ with the NH group of the imidazole ring. This is proved following a second independent study in which we report the changes in g tensor principal values of low spin ferric porphyrins with the basicity (pK_a) of various nitrogenous bases.     

Reconstitution of native Escherichia coli pyruvate oxidase from apoenzyme monomers and FAD

Pyruvate oxidase, a tetrameric enzyme consisting of 4 identical subunits, dissociates into apoenzyme monomers and free FAD when treated with acid ammonium sulfate in the presence of high concentrations of potassium bromide. Reconstitution of the native enzymatically active protein can be accomplished by incubating equimolar concentrations of apomonomers and FAD at pH 6.5. The kinetics of the reconstitution reaction have been measured by 1) enzyme activity assays, 2) spectrophotometric assays to measure FAD binding, and 3) high performance liquid chromatography analysis measuring the distribution of monomeric, dimeric, and tetrameric species during reconstitution. The kinetic analysis indicates that the second order reaction of apomonomers with FAD to form an initial monomer-FAD complex is fast. The rate-limiting step for enzymatic reactivation appears to be the folding of the polypeptide chain in the monomer-FAD complex to reconstitute the three-dimensional FAD binding site prior to subunit reassociation. The subsequent formation of native tetramers appears to proceed via an essentially irreversible dimer assembly pathway.     

Reactions between half- and full-FLP recombination target sites. A model system for analyzing early steps in FLP protein-mediated site-specific recombination.

The FLP recombination target (FRT) can be cut in half so that only one FLP protein binding site is present (a "half site"). FLP protein binds the half sites and joins them into dimeric, asymmetric head-to-head complexes held together chiefly by strong noncovalent interactions. These complexes react with full (normal) FRT sites to generate a variety of products. Analysis of these DNA species reveals that the reaction follows a well-defined reaction pathway that generally parallels the normal reaction pathway. The system is useful in analyzing early steps in recombination, since the identity of the products in a given recombination event unambiguously pinpoints the order in which the cleavage and strand exchange reactions occur. Two conclusions are derived from the present study: (i) Formation of the dimeric head-to-head complex of half sites is a prerequisite to further steps in recombination. (ii) The identity of the base pairs at positions 6 and -6 within the FRT site has a subtle effect in directing the first strand exchange event in the reaction to predominantly one of two possible cleavage sites. In addition, results are presented that suggest that a DNA-DNA pairing intermediate involving only two base pairs of the core sequence is formed prior to the first cleavage and strand exchange. DNA-DNA interactions may therefore not be limited to the isomerization step that follows the first strand exchange.     

Quantitative structure-activity relationships for the pre-steady-state inhibition of cholesterol esterase by 4-nitrophenyl-N-substituted carbamates

4-Nitrophenyl-N-substituted carbamates (1-6) are the pseudo-substrate inhibitors of porcine pancreatic cholesterol esterase. Thus, the first step of the inhibition (Ki step) is the formation of the enzyme inhibitor tetrahedral adduct and the second step of the inhibition (kc) is the formation of the carbamyl enzyme. The formation of the enzyme inhibitor tetrahedral adduct is further divided into two steps, the formation of the enzyme-inhibitor complex with the dissociation constant, KS, at the first step and the formation of the enzyme-inhibitor tetrahedral adduct from the complex at the second step. The two-step mechanism for the formation of the enzyme-inhibitor tetrahedral adduct is confirmed by the pre-steady-state kinetics. The results of quantitative structure-activity relationships for the pre-steady-state inhibitions of cholesterol esterase by carbamates 1-6 indicate that values of -logKs and logk2/k-2 are correlated with the Taft substituent constant, sigma*, and the rho* values from these correlations are -0.33 and 0.1, respectively. The negative rho* value for the -logKS-sigma*-correlation indicates that the first step of the two-step formation of the enzyme-inhibitor tetrahedral adduct (KS step) is the formation of the positive enzyme inhibitor complex. The positive rho* value for the logk2/k-2 -sigma*-correlation indicates that the enzyme inhibitor tetrahedral adduct is more negative than the enzyme inhibitor complex. Finally, the two-step mechanism for the formation of the enzyme inhibitor tetrahedral adduct is proposed according to these results. Thus, the partially positive charge is developed at nitrogen of carbamates 1-6 in the enzyme-inhibitor complex probably due to the hydrogen bonding between the lone pair of nitrogen of carbamates 1-6 and the amide hydrogen of the oxyanion hole of the enzyme. The second step of the two-step formation of the enzyme-inhibitor tetrahedral adduct is the nucleophilic attack of the serine of the enzyme to the carbonyl group of carbamates 1-6 in the enzyme-inhibitor complex and develops the negative-charged oxygen in the adduct.     

Effect of Asp-235-->Asn substitution on the absorption spectrum and hydrogen peroxide reactivity of cytochrome c peroxidase.

The spectroscopic properties of a mutant cytochrome c peroxidase, in which Asp-235 has been replaced by an asparagine residue, were examined in both nitrate and phosphate buffers between pH 4 and 10.5. The spin state of the enzyme is pH dependent, and four distinct spectroscopic species are observed in each buffer system: a predominantly high-spin Fe(III) species at pH 4, two distinct low-spin forms between pH 5 and 9, and the denatured enzyme above pH 9.3. The spectrum of the mutant enzyme at pH 4 is dependent upon specific ion effects. Increasing the pH above 5 converts the mutant enzyme to a predominantly low-spin hydroxy complex. Subsequent conversion to a second low-spin form is essentially complete at pH 7.5. The second low-spin form has the distal histidine, His-52, coordinated to the heme iron. To evaluate the effect of the changes in coordination state upon the reactivity of the enzyme, the reaction between hydrogen peroxide and the mutant enzyme was also examined as a function of pH. The reaction of CcP(MI,D235N) with peroxide is biphasic. At pH 6, the rapid phase of the reaction can be attributed to the bimolecular reaction between hydrogen peroxide and the hydroxy-ligated form of the mutant enzyme. Despite the hexacoordination of the heme iron in this form, the bimolecular rate constant is approximately 22% that of pentacoordinate wild-type yeast cytochrome c peroxidase. The bimolecular reaction of the mutant enzyme with peroxide exhibits the same pH dependence in nitrate-containing buffers that has been described for the wild-type enzyme, indicating a loss of reactivity with the protonation of a group with an apparent pKa of 5.4. This observation eliminates Asp-235 as the source for this heme-linked ionization and strengthens the hypothesis that the pKa of 5.4 is associated with His-52. The slower phase of the reaction between peroxide and the mutant enzyme saturates at high peroxide concentration and is attributed to conversion of unreactive to reactive forms of the enzyme. The fraction of enzyme which reacts via the slow phase is dependent upon both pH and specific ion effects.     

Time-resolved dissociation of the light-harvesting 1 complex of Rhodospirillum rubrum,studied by infrared laser temperature jump

For the first time, data are presented on the time-resolved disassembly reaction of a highly organized membrane protein complex in vitro. The photosynthetic core light-harvesting complex of the bacterial strain Rhodospirillum rubrum G9 consists of 12-16 dimeric subunits that in vivo are associated with the photosynthetic reaction center in a ringlike manner. Isolated in a detergent solution, its appearance either as a ringlike complex (called B873 and absorbing at 873 nm), subunit dimer (called B820 and absorbing at 820 nm), or monomeric form (called B777 and absorbing at 777 nm) is strongly temperature-dependent. In thermodynamic equilibria between B820 and B873, intermediate-sized complexes have also been observed that have absorption maxima around 850 nm. It is unknown whether these structures appear as intermediates in the kinetic B820-B873 (dis)assembly reaction. In this paper disassembly of the light-harvesting complex into its dimeric subunits was followed spectroscopically on a time scale up to 200 ms, upon applying an infrared laser-induced temperature jump. The full dissociation process appears to take place on a time scale of tens to hundreds of milliseconds, the rates becoming faster at higher starting temperatures. Applying the same technique, the dissociation reaction of dimeric subunits into monomers also could be established. This dissociation process occurred on a much faster time scale and took place within the 500 micros response time of our detection system.     

Hydrolysis of aryl beta-D-glucopyranosides and beta-D-xylopyranosides by an induced beta-D-glucosidase from Stachybotrys atra.

The induced beta-D-glucosidase from Stachybotrys atra hydrolyzes aryl beta-D-glucopyranosides and aryl beta-D-xylopyranosides by the same basic two-step mechanism. In the first step the aglycon group is split of with simultaneous formation of an enzyme-glycosyl complex. In the second step this intermediate complex reacts with water yeilding beta-D-glucose or beta-D-xylose. For beta-D-xyloside hydrolysis each of the two steps is partially rate-controlling, whereas for beta-D-glucoside hydrolysis the second step is rate-limiting. The enzyme is inhibited by high concentrations of substrate and the exact rate-concentration equation is a second-order equation. 1-Thio-beta-D-glycopyranosides with an aromatic aglycon inhibit the reaction in both a competitive and non-competitive way. A tentative mechanism is proposed to explain all types of inhibition. In this mechanism substrates and inhibitors with an aromatic aglycon group bind through hydrophobic forces to the 'aglycon subsite' of the intermediate enzyme-glycosyl complex. Binding of the second substrate molecule or of the inhibitor to this complex does not prevent the reaction of the glycosyl moiety with water, it only decreases the rate of the second step.     

Troubleshooting in gene splicing by overlap extension

A step-wise method for cloning intron-containing genes from genomic DNA is described. The two exons of the human proinsulin gene were separately amplified in two steps using, in the first step, completely homologous primers. This reduces unwanted interactions between mismatched primers and a complex DNA template such as genomic DNA. The fragments were amplified in a second step polymerase chain reaction (PCR) using mismatched primers that incorporated additional bases complementary to the other exon, and these products were spliced together in a third step PCR.     

Theoretical calculations on hydrogenase kinetics: explanation of the lag phase and the enzyme concentration dependence of the activity of hydrogenase uptake

Two models of the hydrogenase reaction cycle were investigated by means of theoretical calculations and model simulations. The first model is the widely accepted triangular hydrogenase reaction cycle with minor modifications; the second is a modified triangular model, where we have introduced an autocatalytic step into the reaction cycle. Both models include a one-step activation reaction. The theoretical calculations and model simulations corroborate the assumed autocatalytic reaction step concluded from the experimental characteristics of the hydrogenase reaction.     

Monolayers of long chain lecithins at the air/water interface and their hydrolysis by phospholipase A2

The behavior of phosphatidylcholine monolayers at the air/water interface was studied by measuring their surface isotherm, surface potential, surface viscosity, and rate of hydrolysis by the dimeric phospholipase A2 from the venom of Crotalus atrox. The monolayers showed typical liquid-expanded behavior. In this phase, the surface potential was linearly dependent on surface concentration and extrapolated at zero concentration to a value characteristic of a liquid hydrocarbon/water interface. The rate of the reaction was measured by monitoring changes in area at constant surface pressure for 1,2-dioctanoyl- and 1,2-didecanoyl-3-sn-phosphatidylcholines, and by monitoring changes in surface potential for 1,2-dimyristoyl-, 1,2-dipalmitoyl-, 1-palmitoyl-2-oleoyl-, and 1-oleoyl-2-palmitoyl-sn-glycero-3-phosphocholines. The enzymatic hydrolysis is first order with respect to the enzyme-calcium complex which forms with a Kd = 1.5 mM. A mechanism is proposed to account for the dependency of the reaction rates on the surface concentration of the substrate. We postulate that the rate-limiting step is the decomposition of a quaternary complex formed from two phospholipid molecules, one calcium ion and one dimeric enzyme. The rate is independent of the surface pressure per se; addition of inert lipids to a monolayer at constant area, and hence constant surface concentration of the substrate, increases the surface pressure without changing the surface density of the substrate yielding maximal enzymatic rate. The enzyme is specific for loosely packed substrate molecules in the liquid-expanded state: transition into the liquid-condensed state or compression of the liquid-expanded layer beyond 80 A2/phospholipid strongly inhibits the enzymatic reaction. Our results show that surface recognition is a direct consequence of a bifunctional active site since it is only at a phospholipid surface that the distance between two substrate molecules is optimal for forming a catalytically competent enzyme-Ca2+-(substrate)2 complex.     

19F NMR study of protein-induced rhombic perturbations on the electronic structure of the active site of myoglobin

 A novel C ₂-symmetric ring-fluorinated hemin, 13,17-bis(2-carboxyethyl)-2,8,12,18-tetramethyl-3,7-difluoroporphyrinatoiron(III), has been synthesized and was incorporated into sperm whale apomyoglobin to investigate protein-induced rhombic perturbations on the electronic structure of the active site of myoglobin (Mb) using ¹⁹F NMR spectroscopy. NMR signals for ¹⁹F atoms introduced as substituents on the present heme in ferrous low-spin and high-spin and ferric low-spin complexes have been observed and their shifts sharply reflect not only the electronic nature of the heme iron, but also in-plane asymmetry of the heme electronic structure. The two-fold symmetric electronic structure of the ring-fluorinated hemin is clearly manifested in the ¹⁹F and ¹H NMR spectra of its dicyano complex. The chemical equivalence of the two fluorine atoms of the heme is removed in the active site of myoglobin and the splitting of the two ¹⁹F NMR signals provides a quantitative probe for characterizing the rhombic perturbation of the heme electronic structure induced by the heme-protein interaction. The in-plane asymmetry of heme electronic structures in carbonmonoxy and deoxy Mbs have been analyzed for the first time on the basis of the shift difference between the two ¹⁹F NMR signals of the heme and is interpreted in terms of iron-ligand binding and/or the orbital ground state of the heme. A potential utility of ¹⁹F NMR, combined with the use of a symmetric fluorinated hemin, in characterizing the heme electronic structure of myoglobin in a variety of iron oxidation, spin, and ligation states, is presented. Received: 23 December 1999 / Accepted: 3 April 2000     

Rational design of a lipase to accommodate catalysis of Baeyer–Villiger oxidation with hydrogen peroxide

The mechanism and potential energy surface for the Baeyer-Villiger oxidation of acetone with hydrogen peroxide catalyzed by a Ser105-Ala mutant of Candida antarctica Lipase B has been determined using ab initio and density functional theories. Initial substrate binding has been studied using an automated docking procedure and molecular dynamics simulations. Substrates were found to bind to the active site of the mutant. The activation energy for the first step of the reaction, the nucleophilic attack of hydrogen peroxide on the carbonyl carbon of hydrogen peroxide, was calculated to be 4.4 kcal x mol(-1) at the B3LYP/6-31+G* level. The second step, involving the migration of the alkyl group, was found to be the rate-determining step with a computed activation energy of 19.9 kcal x mol(-1) relative the reactant complex. Both steps were found to be lowered considerably in the reaction catalyzed by the mutated lipase, compared to the uncatalyzed reaction. The first step was lowered by 36.0 kcal x mol(-1) and the second step by 19.5 kcal x mol(-1). The second step of the reaction, the rearrangement step, has a high barrier of 27.7 kcal x mol(-1) relative to the Criegee intermediate. This could lead to an accumulation of the intermediate. It is not clear whether this result is an artifact of the computational procedure, or an indication that further mutations of the active site are required. Figure Second TS (18TS) in the Baeyer-Villiger oxidation in a mutant of CALB. Distances in A     

Single turnover kinetics of phage T4 DNA-(N6-adenine)methyltransferase

Interaction of T4 DNA-(N6-adenine)-methyltransferase [EC 2.1.1] was studied with a variety of synthetic oligonucleotide substrates containing the native recognition site GATC or its modified variants. The data obtained in the decisecond and second intervals of the reaction course allowed for the first time the substrate methylation rates to be compared with the parameters of the steady-state reaction. It was established that the substrate reaction proceeds in two stages. Because it is shown that in steady-state conditions T4 MTase forms a dimeric structure, the following sequence of events is assumed. Upon collision of a T4 MTase monomer with an oligonucleotide duplex, an asymmetrical complex forms in which the enzyme randomly oriented relative to one of the strands of the specific recognition site catalyzes a fast transfer of the methyl group from S-adenosylmethionine to the adenosine residue (k1 = 0.21 s-1). Simultaneously, a second T4 MTase subunit is added to the complex, providing for the continuation of the reaction. In the course of a second stage, which is by an order of magnitude slower (k2 = 0.023 s-1 for duplex with the native site), the dimeric T4 MTase switches over to the second strand and the methylation of the second residue, target. The rate of the methyl group transfer from donor, S-adenosylmethionine, to DNA is much higher than the overall rate of the T4 MTase-catalyzed steady-state reaction, although this difference is considerably less than that shown for EcoRI Mtase. Substitutions of bases and deletions in the recognition site affect the substrate parameters in different fashions. When the GAT sequence is disrupted, the proportion of the initial productive enzyme-substrate complexes is usually sharply reduced. The flipping of the adenosine residue, a target for the modification in the recognition site, revealed by fluorescence titration, upon interaction with the enzyme supports the existing notions about the involvement of such a DNA deformation in reactions catalyzed by various DNA-MTases.