Active Site Of Aspartate Aminotransferase Research Articles

A QM/MM simulation study of transamination reaction at the active site of aspartate aminotransferase: Free energy landscape and proton transfer pathways

Transaminase is a key enzyme for amino acid metabolism, which reversibly catalyzes the transamination reaction with the help of PLP (pyridoxal 5' -phosphate) as its cofactor. Here we have investigated the mechanism and free energy landscape of the transamination reaction involving the aspartate transaminase (AspTase) enzyme and aspartate-PLP (Asp-PLP) complex using QM/MM simulation and metadynamics methods. The reaction is found to follow a stepwise mechanism where the active site residue Lys258 acts as a base to shuttle a proton from α-carbon (CA) to imine carbon (C4A) of the PLP-Asp Schiff base. In the first step, the Lys258 abstracts the CA proton of the substrate leading to the formation of a carbanionic intermediate which is followed by the reprotonation of the Asp-PLP Schiff base at C4A atom by Lys258. It is found that the free energy barrier for the proton abstraction by Lys258 and that for the reprotonation are 17.85 and 3.57 kcal/mol, respectively. The carbanionic intermediate is 7.14 kcal/mol higher in energy than the reactant. Hence, the first step acts as the rate limiting step. The present calculations also show that the Lys258 residue undergoes a conformational change after the first step of transamination reaction and becomes proximal to C4A atom of the Asp-PLP Schiff base to favor the second step. The active site residues Tyr70* and Gly38 anchor the Lys258 in proper position and orientation during the first step of the reaction and stabilize the positive charge over Lys258 generated at the intermediate step.

Transimination Reaction at the Active Site of Aspartate Aminotransferase: A Proton Hopping Mechanism through Pyridoxal 5′-Phosphate

The transimination reaction involves conversion of an internal aldimine involving pyridoxal 5′-phosphate (PLP) and an enzyme to an external aldimine involving PLP and a substrate amino acid and it ...

A hybrid QM/MM simulation study of intramolecular proton transfer in the pyridoxal 5'-phosphate in the active site of transaminase: influence of active site interaction on proton transfer.

Pyridoxal 5'-phosphate (PLP) Schiff base, a versatile cofactor, exhibits a tautomeric equilibrium that involves an intramolecular proton transfer between the N-protonated zwitterionic ketoenamine tautomer and the O-protonated covalent enolimine tautomer. It has been postulated that for the catalytic activity, the PLP has to be in the zwitterionic ketoenamine tautomeric form. However, the exact position of the tautomeric equilibrium of Schiff base in the active site of PLP-dependent enzyme is not known yet. In the present work, we investigated the tautomeric equilibrium for the external aldimine state of PLP aspartate (PLP-Asp) Schiff base in the active site of aspartate aminotransferase (AspAT) using combined quantum mechanical and molecular mechanical simulations. The main focus of the present study is to analyze the factors that control the tautomeric equilibrium in the active sites of various PLP-dependent enzymes. The results show that the ketoenamine tautomer is more preferred than the enolimine tautomer both in the gas and aqueous phases as well as in the active site of AspAT. Current simulations show that the active site of AspAT is more suitable for the ketoenamine tautomer compared to the enolimine tautomer. Interestingly, the Tyr225 acts as a proton donor to the phenolic oxygen in the ketoenamine tautomer, while in the covalent enolimine tautomer, it acts as a proton acceptor to the phenolic oxygen. Finally, the metadynamics study confirms this result. The calculated free energy barrier is about 7.5 kcal/mol. A comparative analysis of the microenvironment created by the active site residues of three different PLP-dependent enzymes (aspartate aminotransferase, Dopa decarboxylase, and Ala-racemase) has been carried out to understand the controlling factor(s) of the tautomeric equilibrium. The analysis shows that the intermolecular hydrogen bonding between active site residues and the phenolic oxygen of PLP shifts the tautomeric equilibrium toward the N-protonated ketoenamine tautomeric form.

Substitution of apolar residues in the active site of aspartate aminotransferase by histidine. Effects on reaction and substrate specificity.

In an attempt to change the reaction and substrate specificity of aspartate aminotransferase, several apolar active-site residues were substituted in turn with a histidine residue. Aspartate aminotransferase W140H (of Escherichia coli) racemizes alanine seven times faster (Kcat' = 2.2 x 10(-4) s-1) than the wild-type enzyme, while the aminotransferase activity toward L-alanine was sixfold decreased. X-ray crystallographic analysis showed that the structural changes brought about by the mutation are limited to the immediate environment of H140. In contrast to the tryptophan side chain in the wild-type structure, the imidazole ring of H140 does not form a stacking interaction with the coenzyme pyridine ring. The angle between the two ring planes is about 50 degrees. Pyridoxamine 5'-phosphate dissociates 50 times more rapidly from the W140H mutant than from the wild-type enzyme. A model of the structure of the quinonoid enzyme substrate intermediate indicates that H140 might assist in the reprotonation of C alpha of the amino acid substrate from the re side of the deprotonated coenzyme-substrate adduct in competition with si-side reprotonation by K258. In aspartate aminotransferase I17H (of chicken mitochondria), the substituted residue also lies on the re side of the coenzyme. This mutant enzyme slowly decarboxylates L-aspartate to L-alanine (Kcat' = 8 x 10(-5) s-1). No beta-decarboxylase activity is detectable in the wild-type enzyme. In aspartate aminotransferase V37H (of chicken mitochondria), the mutated residue lies besides the coenzyme in the plane of the pyridine ring; no change in reaction specificity was observed. All three mutations, i.e. W140-->H, I17-->H and V37--H, decreased the aminotransferase activity toward aromatic amino acids by 10-100-fold, while decreasing the activity toward dicarboxylic substrates only moderately to 20%, 20% and 60% of the activity of the wild-type enzymes, respectively. In all three mutant enzymes, the decrease in aspartate aminotransferase activity at pH values lower than 6.5 was more pronounced than in the wild-type enzyme, apparently due to the protonation of the newly introduced histidine residues. The study shows that substitutions of single active-site residues may result in altered reaction and substrate specificities of pyridoxal-5'-phosphate-dependent enzymes.

The tyrosine-225 to phenylalanine mutation of Escherichia coli aspartate aminotransferase results in an alkaline transition in the spectrophotometric and kinetic pKa values and reduced values of both kcat and Km

Tyrosine-225 is hydrogen-bonded to the 3'-hydroxyl group of pyridoxal 5'-phosphate in the active site of aspartate aminotransferase. Replacement of this residue with phenylalanine (Y225F) results in a shift in the acidic limb of the pKa of the kcat/KAsp vs pH profile from 7.1 (wild-type) to 8.4 (mutant). The change in the kinetic pKa is mirrored by a similar shift in the spectrophotometrically determined pKa of the protonated internal aldimine. Thus, a major role of tyrosine-225 is to provide a hydrogen bond that stabilizes the reactive unprotonated form of the internal aldimine in the neutral pH range. The Km value for L-aspartate and the dissociation constant for alpha-methyl-DL-aspartate are respectively 20- and 37-fold lower in the mutant than in the wild-type enzyme, while the dissociation constant for maleate is much less perturbed. These results are interpreted in terms of competition between the Tyr225 hydroxyl group and the substrate or quasi-substrate amino group for the coenzyme. The value of kcat in Y225F is 450-fold less than the corresponding rate constant in wild type. The increased affinity of the mutant enzyme for substrates, combined with the lack of discrimination against deuterium in the C alpha position of L-aspartate in Y225F-catalyzed transamination [Kirsch, J. F., Toney, M. D., & Goldberg, J. M. (1990) in Protein and Pharmaceutical Engineering (Craik, C. S., Fletterick, R., Matthews, C. R., & Wells, J., Eds.) pp 105-118, Wiley-Liss, New York], suggests that the rate-determining step in the mutant is hydrolysis of the ketimine intermediate rather than C alpha-H abstraction which is partially rate-determining in wild type.

Site‐Specific Mutagenesis in the Active Site of Aspartate Aminotransferase

Site‐Specific Mutagenesis in the Active Site of Aspartate Aminotransferase

Modeling Inhibitors in the Active Site of Aspartate Aminotransferasea

Modeling Inhibitors in the Active Site of Aspartate Aminotransferase^a

Sequential protection–modification method for selective sulfhydryl group derivatization in proteins having more than one cysteine

The method of Smith and Hartman [J. Biol. Chem., 263, 4921-4925 (1988)] for introducing the non-natural lysine analog, S-(2-aminoethyl)cysteine, into specific sites in proteins by alkylation of a genetically introduced cysteine with 2-bromoethylamine has been generalized to be applicable to proteins containing one or more endogenous cysteines. The target cysteine residue introduced at the active site of aspartate aminotransferase is protected by bound cofactor. The enzyme is partially unfolded in low concentrations of urea, and the non-active site cysteine residues derivatized by a reversible thiol protecting reagent. The active site cysteine is then exposed and alkylated in 6 M urea. Enzyme activity is regenerated by removal of the thiol protecting groups and refolding of the protein.

Reactions of 3'-O-methylpyridoxal 5'-phosphate in aspartate aminotransferase.

The reaction of 3'-O-methylpyridoxal 5'-phosphate bound into the active site of aspartate aminotransferase with the substrate L-aspartate has been investigated. This methylated coenzyme is a very poor catalyst but it does function slowly to produce normal products of a transamination half-reaction. At pH 8.5 and above the characteristic absorption band of a quinonoid intermediate appears rapidly and becomes very intense when the aspartate concentration is raised to 2 M. At pH 6 the quinonoid band is not seen, but the conversion of the methylated coenzyme into 3'-O-methylpyridoxamine 5'-phosphate is about 7 times faster than at high pH with the pH dependence being determined by an apparent pKa of 8.1 at 30 degrees C. We suggest that the active site containing the methylated coenzyme carries a net charge 1 unit more positive than that of native enzyme. This causes a loss of some other proton from the active site and could leave the catalytic lysine-258 deprotonated in the quinonoid species. This may explain its inability to react rapidly. We have measured the spectral band shapes of the quinonoid species studied here and have compared it with that seen with native enzyme. Because of the close similarity we conclude that during normal transamination the proton bound to the imine nitrogen probably shifts onto the phenolic oxygen prior to or synchronously with the formation of the observed quinonoid species.

Stereospecific labilization of the C-4' pro-S hydrogen of pyridoxamine 5'-phosphate in aspartate aminotransferase. Activators and inhibitors.

Measurement of the stereospecific release of the pro-S proton from C-4' of enzyme-bound pyridoxamine 5'-phosphate provides an experimental means to probe parts of the active site of aspartate aminotransferase independently of substrate turnover (Tobler, H. P., Christen, P., and Gehring, H. (1986) J. Biol. Chem. 261, 7105-7108). The release of pro-S 3H from enzyme-bound [3H]pyridoxamine 5'-phosphate is 30,000 times faster than from free coenzyme. Enzyme-bound [3H]pyridoxine 5'-phosphate is not detritiated suggesting an essential role of the 4'-amino group. Formation of the unproductive complex of the [3H]pyridoxamine 5'-phosphate-enzyme with aspartate or glutamate results in a 400-fold acceleration of 3H release. In contrast, addition of borohydride or cyanoborohydride immediately stops 3H release. Experiments with a fluorescent reporter group and with differential chemical modifications indicate that the activating effect of aspartate on the release of 3H is accompanied by a shift of the so-called open/closed conformational equilibrium of the enzyme (Kirsch, J.F., Eichele, G., Ford, G. C., Vincent, M.G., Jansonius, J.N., Gehring, H., and Christen, P. (1984) J. Mol. Biol. 174, 497-525) toward the closed conformation; the inhibiting effect of borohydride and cyanoborohydride appears to be accompanied by a shift toward the open conformation. Apparently, at least part of the catalytic apparatus of aspartate aminotransferase becomes fully operative only in the closed conformation of the enzyme.

Phosphonate analogues of pyridoxal phosphate with shortened side chains.

A phosphonate analogue of pyridoxal 5'-phosphate containing a 5'-phosphonomethyl group and its monoethyl and diethyl esters have been prepared. Except for the diethyl ester, the compounds appear to bind into the active site of aspartate aminotransferase. However, they lack detectable catalytic activity with this enzyme and with glutamate decarboxylase of Escherichia coli. The phosphonomethyl analogue bound to aspartate aminotransferase does react slowly with substrates, as determined by spectrophotometric observations; the monomethyl ester reacts about 20 times less rapidly. Because of the stability of the phosphonate linkage, these compounds may be useful as modifying reagents for various proteins.

Pyrrolopyridine derivatives from pyridoxal 5'-sulfate.

A fluorescent derivative of lysine-258 isolated from the active site of aspartate aminotransferase modified by treatment of the apoenzyme with pyridoxal 5'-sulfate has been characterized as a substituted 2H-pyrrolo[3,4-c]pyridine. Similar pyrrolopyridines are produced in up to 20% yield by reaction of pyridoxal sulfate with simple alkylamines or with amino acids including lysine. The latter forms two products, one of which is identical with that isolated from the enzyme. The pyrrolopyridine derived from ethylamine has been characterized by proton and 13C NMR, ultraviolet-visible, and mass spectroscopy and by its chemical reactions.

Stereospecificity of sodium borohydride reduction of Schiff bases at the active site of aspartate aminotransferase.

Sodium boro[3H]hydride treatment of holoaspartate aminotransferase results in the reduction of the Schiff's base formed between pyridoxal phosphate and Lys 258. Treatment of the reduced enzyme with papain followed by acid hydrolysis liberates epsilon-N-[3H]pyridoxyl lysine which is degraded to [3H]pyridoxamine diHCl and stereochemically analyzed with apoaspartate aminotransferase. Sodium boro[3H]hydride treatment of active site carbamylated aspartate aminotransferase reconstituted with pyridoxyl phosphate and sodium aspartate results in the trapping of an enzyme x substrate complex through the reduction of the Schiff's base formed between pyridoxal phosphate and aspartate. Active site bound N-[3H]pyridoxyl aspartate is liberated by treatment with papain and degraded to [3H]pyridoxamine diHCl for stereochemical analysis. Borohydride reduction of the holoenzyme occurs from the re face of the pyridoxal phosphate Lys 258 Schiff's base. Similarly, reduction of active site carbamylated enzyme x substrate complex occurs from the re face of the pyridoxal phosphate-aspartate Schiff's base. These results indicate that when active site carbamylated enzyme binds substrate to pyridoxal phosphate it does so stereospecifically and without changing the face of the Schiff base that is available for reduction as compared to native enzyme.

On the conformation of pyridoxal phosphate imine in solution and in aspartate-aminotransferase active site.

The work comprises: Determination by nuclear magnetic resonance method of the conformation of the imino group of pyridoxal‐P oxime in solution. It has been found to be nearly coplanar with the aromatic ring. Theoretical calculation by the method of atom‐atom potentials of the permitted conformations of pyridoxal‐P imine and its analogs: 6‐methylpyridoxal‐P and 5′‐methylpyridoxal‐P. There have been found seven favourable conformations for pyridoxal‐P imine, some of which were prohibited in the analogs mentioned. Experimental estimation of the conformation of pyridoxal‐P imine in the active site of aspartate aminotransferase with the use of the above sterically hindered analogs and 5′‐deoxy‐5′‐carboxy‐methylenepyridoxal analog. In result, the number of the possible conformations for pyridoxal‐P imine in the active site has been reduced to a pair of symmetrical conformations.

Formate-induced Labeling of the Active Site of Aspartate Aminotransferase by β-Chloro-l-alanine

Abstract The pyridoxal form of both the supernatant and mitochondrial isoenzymes of aspartate aminotransferase (EC 2.6.1.1) catalyzes α, β elimination of pyruvate from β-chloro-l-alanine with concomitant inactivation. Rates of these reactions were greatly accelerated by formate ion. Acetate and propionate were much less effective and essentially ineffective with the mitochondrial isoenzyme. With both isoenzymes, dependency of rates of α, β elimination as well as inactivation on formate concentration showed sigmoidal curves; the rate enhancement was especially marked at formate concentrations from 1 to 3 m. Michaelis constants for β-chloro-l-alanine were identical in both the α β elimination reaction and the inactivation. These results suggest that both reactions occur via a common intermediate. The presence of formate did not affect the Michaelis constants for β-chloro-l-alanine. Formate increased only the maximal velocities of these reactions. The pH optimum for the inactivation of both isoenzymes was approximately pH 7.5 whereas the rate of the α, β elimination reaction was maximal at pH 7 and remained constant above this pH. Formate induced a considerable change in the absorption and circular dichroism spectra of the pyridoxal form of both isoenzymes in visible regions. Upon reacting with β-chloro-l-alanine in the presence of 3 m formate, the absorption band at 345 nm, which is attributed to the bound pyridoxal phosphate, shifted to 337 nm, which was accompanied by a marked decrease in ellipticity. Prolonged incubation of the inactivated enzymes resulted in the formation of a new spectral species absorbing at 455 nm. Removal of formate produced a drastic change in the spectrum, giving rise to three absorption bands at 333, 375, and 420 nm. Addition of formate to this solution reversed these spectral changes to give a single 455-nm band again. All these observations are consistent with the proposal that formate binds to a discrete subsite within the active site which normally binds the distal carboxyl group of a natural dicarboxylic substrate. Inactivation of both isoenzymes with β-chloro-l-[U-14C]-alanine and reduction with KBH4 resulted in a stoichiometric incorporation of the three-carbon moiety derived from chloroalanine as well as the pyridoxyl moiety into the enzyme protein via stable covalent linkages.

Selective modification of tyrosine and cysteine residues in aspartate aminotransferase from pig heart cytosol

In the region of the active site of aspartate amino-transferase two amino acid residues — one Tyr and one Cys — are accessible to selective modification by appropriate reagents. Modification of each of the two residues singly results in certain changes of the enzyme's physico-chemical properties, but does not abolish its ability to catalyse the transamination reaction. Complete inactivation, associated with irreversible amination of the protein-bound pyridoxal-P to pyridoxamine-P, is observed only on modification of both residues.

The presence of a histidine residue near the active site of aspartate aminotransferase

The presence of a histidine residue near the active site of aspartate aminotransferase