Preliminary crystallographic study of aspartate: 2-oxoglutarate aminotransferase from pig heart

Pyridoxal 5'-phosphate dependent reactions: Analyzing the mechanism of aspartate aminotransferase

Enzyme catalysis is the primary activity in energy and information metabolism and enzyme cofactors are key to the catalytic ability of most enzymes. Pyridoxal 5'-phosphate (PLP) cofactor, derived from Vitamin B6, is widely distributed in nature and has significant latitude in catalytic diversity. X-ray crystallography has revealed the structures of diverse PLP dependent enzymes from multiple families. But these structures are incomplete, lacking the positions of protons essential for understanding enzymatic mechanisms. Here, we review the diversity of PLP and discuss the use of neutron crystallography and joint X-ray/neutron refinement of Fold Type I aspartate aminotransferase to visualize the positions of protons in both the internal and external aldimine forms. Strategies used to prepare extremely large crystals required for neutron diffraction and the approach to data refinement including the PLP cofactor are discussed. The observed positions of protons, including one located in a previously unknown low-barrier hydrogen bond, have been used to create more accurate models for computational analysis. The results revealed a new mechanism for the transaminase reaction where hyperconjugation is key to reducing the energy barrier which finally provides a clear explanation of the Dunathan alignment.

Noncoded amino acid replacement probes of the aspartate aminotransferase mechanism

The primary role of Tyr225 in the aspartate aminotransferase mechanism is to provide a hydrogen bond to stabilize the 3'O- functionality of bound pyridoxal phosphate. The strength of this hydrogen bond is perturbed by replacement of Tyr225 with 3-fluoro-L-tyrosine (FlTyr) by in vitro transcription/translation. This mutant enzyme exhibits kcat/values that are near to those of wild type enzyme; however, the kcat/vs pH profile is much sharper with similar pKas of approximately 7.5 for both the ascending and descending limbs. The pKas are assigned to the endocyclic proton of the internal aldimine and to the bridging hydrogen bond, respectively. The pKas in the kcat vs pH profile of 7.2 and 8.7 are assigned to the epsilon-NH3+ of lysine 258 and to the endocyclic protons of the ketimine complex, respectively. Arginine 292 forms a salt bridge with the beta-COOH of the substrate, aspartate. An improvement on the earlier attempt to invert the substrate charge specificity via R292D mutation-induced arginine transaminase activity [Cronin, C. N., & Kirsch, J. F. (1988) Biochemistry 27, 4572-4579] is described. Here Arg292 is replaced with homoglutamate (R292hoGlu). This construct exhibits 6.8 x 10(4)-fold greater activity for the cationic substrate D,L-[Calpha-3H]-alpha-amino-beta-guanidinopropionic acid (D,L-[Calpha-3H]AGPA) than does wild type enzyme. The gain in selectivity for this substrate is at least 4500-fold greater than that achieved in the 1988 experiment, i.e., [(kcat/KM)R292hoGlu/(kcat/KM)WT (D,L-[Calpha-3H]AGPA)] >/= 4500 x [(kcat/KM)R292D/(kcat/KM)WT (L-arginine)]. The value of (kcat/KM)R292D is 0.43 M-1 s-1 with L-Arg while (kcat/KM)R292hoGlu is 29 M-1 s-1 with D,L-[Calpha-3H]AGPA (it is assumed that the D-enantiomer is unreactive). The latter value is the lower limit because of the uncertain value of 3H kinetic isotope effect.

High-resolution electron microscopic studies on the quaternary structure of ornithine aminotransferase from pig kidney

The ornithine aminotransferase (OAT) from pig kidney has been studied on the basis of high-resolution electron microscopy and the morphological appearance of the apoenzyme and holoenzyme have been examined. The quaternary structure of the OAT molecules in the presence of 5 mM pyridoxal 5'-phosphate could be established. The enzyme molecule appears to be built up of two morphological units, called M1. The native holoenzyme, termed morphological unit M2, measures 10.9 nm in length and 5.8 nm in width and its molecular mass is approximately 168 kDa, based on electron microscopical calculations. Since the enzyme is composed of only one type of 45-kDa subunit, the holoenzyme is a homotetramer. Each M1 is composed of two subunits and, as seen in top-view projection, has an oval to triangular shape. Upon tilting to 40 degrees the triangular shape changes into three distinct centers of mass. This morphological differentiation reflects the inner organization of M1, i.e. the shape of the individual subunit deviates from strictly globular proteins. This observation is compatible with the notion that the 45-kDa subunit consists of one large and one small domain. By tilting to 40 degrees, both large domains in M1 represent two of the three centers of mass, while the third center of mass is attributed to the superposition of both small domains. Thus, the four domains of both subunits in M1, in accordance with the triangular top-view projection, are quasi-tetrahedrally arranged. Since the change in shape of M1 upon tilting is only obvious in one of the two halves of the native OAT, it suggests that both morphological units of M2 are oriented asymmetrically relative to one another.

A comparison of pyridoxal 5'-phosphate dependent decarboxylase and transaminase enzymes at a molecular level

Pyridoxal 5'-phosphate is a coenzyme for a number of enzymes which catalyse reactions at C alpha of amino acid substrates including transaminases, decarboxylases and serine hydroxymethyltransferase. Using the X-ray coordinates for a transaminase, aspartate aminotransferase, and the results of stereochemical and mechanistic studies for decarboxylases and serine hydroxymethyltransferase, an active-site structure for the decarboxylase group is constructed. The structure of the active-site is further refined through active-site pyridoxyllysine peptide sequence comparison and a 3-D catalytic mechanism for the L-alpha-amino acid decarboxylases is proposed. The chemistry of serine hydroxymethyltransferase is re-examined in the light of the proposed decarboxylase mechanism.

Trigonal crystals of porcine mitochondrial aspartate aminotransferase

Crystals suitable for X-ray analysis of porcine mitochondrial aspartate aminotransferase in the closed conformation were obtained after the apoenzyme was reconstituted with N-5'-phosphopyridoxyl-L-aspartate, an inhibitor in which the cofactor is covalently bound to the substrate. This results in a crystal form that has not been encountered previously in studies of aspartate aminotransferases. The crystals belong to the trigonal space group P3121 (or the enantiomeric P3221) with unit cell dimensions alpha = b = 202.0 A, c = 58.0 A, alpha = beta = 90 degrees, gamma = 120 degrees and contain one dimer in the asymmetric unit.

The unfolding and refolding of cytoplasmic aspartate aminotransferase from pig heart

The unfolding of cytoplasmic aspartate aminotransferase from pig heart in solutions of guanidinium chloride (GdnHCl) was studied. Data from protein fluorescence, c.d. and thiol-group reactivity indicated that the enzyme was unfolded in 6 M-GdnHCl. Spectroscopic studies showed that this unfolding was accompanied by dissociation of the pyridoxal 5'-phosphate cofactor. On dilution of the GdnHCl, re-activation of the enzyme occurred in reasonable yield, provided that dithiothreitol and pyridoxal 5'-phosphate were present. The regain of activity obeyed second-order kinetics. In the absence of added dithiothreitol and pyridoxal 5'-phosphate, substantial formation of high-Mr aggregates occurred.

An appreciation of Professor Alexander E. Braunstein. The discovery and scope of enzymatic transamination

Nonenzymatic transamination was discovered in the early 1930s. In the mid-1930s Braunstein and associates discovered the process of enzymatic transamination and established the biological significance of this reaction. Over the next 50 years, Braunstein and coworkers continued to contribute many new ideas and make important discoveries in the field of aminotransferases and other pyridoxal 5'-phosphate enzymes. This review outlines (1) the events leading to the discovery of enzymatic transamination, (2) how the discovery was made, (3) the findings that led to the recognition by the mid-1950s of the very wide scope and biological importance of aminotransferase reactions, and (4) the elucidation of the primary amino acid sequence and three-dimensional structure of aspartate aminotransferases.

Specific labeling of cytosolic and mitochondrial aspartate aminotransferases

The apoisozymes of cytosolic and mitochondrial aspartate aminotransferase are both irreversibly inhibited by alpha-N-fluorodinitrophenyl-beta-N-phosphopyridoxyldiaminopropi onate, an affinity-labeling reagent analog of the coenzyme. Analysis of the modified peptides shows that the active-site Lys-258, which in the holoenzyme binds the coenzyme pyridoxal 5'-phosphate, is labeled in both isozymes. Comparison with the results obtained using the parent compound 4'-N-fluorodinitrophenylpyridoxamine 5'-phosphate, which labels only the cytosolic enzyme, provides information about differences in active-site reactivity and geometry. Labeling external to the active site occurs in both isozymes. In the cytosolic enzyme the very reactive Cys-45 is modified, in the mitochondrial enzyme the surface residue Lys-342 reveals a peculiar reactivity.

Interaction of a coenzyme analog with aspartate aminotransferase isoenzymes in the crystal

The interaction between the coenzyme derivative 4'-N-(2,4-dinitro-5-fluorophenyl)-pyridoxamine 5'-phosphate with cytoplasmic and mitochondrial apo-aspartate aminotransferase in the crystalline state was investigated to establish whether the structural differences, known to exist between the active sites of the two isoenzymes in solution, are maintained in the crystal although they are not apparent from the available crystallographic data. In the crystal, as in solution, both apo-isoenzymes reversibly bind the coenzyme derivative and catalyze a slow cleavage reaction, by which pyridoxal 5'-phosphate is produced and bound to the active-site lysine. In the case of the cytoplasmic isoenzyme, however, in the crystal as in solution, the initial complex can follow an alternative reaction path that leads to the formation of a covalent bond between the active-site lysine and the C-5 of the 2,4-dinitrophenyl moiety of the reagent. Therefore, crystal-packing forces neither abolish the active site properties that are needed to cleave the specifically bound reagent and are common to the two isoenzymes nor mask the subtle differences that allow for the selective irreversible labeling of the cytoplasmic isoenzyme.

Primary structure of aspartate aminotransferase from horse heart and comparison with that of other homotopic and heterotopic isoenzymes

Sulphydryl groups of mitochondrial aspartate aminotransferase from horse heart were titrated with 5,5'-dithiobis (2-nitrobenzoic acid). From analysis of peptic peptides, 378 amino acid residues (94.3% of the total) in the protein were identified. The results of amino acid sequence analysis are compared with those of cytosolic and mitochondrial aspartate aminotransferases from other sources.

Circular-dichroism study of the interaction of aspartate-aminotransferase isoenzymes with a coenzyme analog

The interaction between a coenzyme derivative, 4'-N-(2,4-dinitro-5-fluorophenyl)-pyridoxamine 5'-phosphate, and the apoenzyme of cytoplasmic and mitochondrial aspartate aminotransferase, was studied by circular dichroism. The specific complexes initially formed were characterized by their circular dichroic spectra. The spectra indicate that the complex is very probably the same for the two isoenzymes. In contrast the spectra recorded during further reaction, in agreement with previous results, monitor different reaction paths and characterize the irreversible labeling at the active site of the cytoplasmic enzyme and regeneration of pyridoxal 5'-phosphate in the mitochondrial enzyme. By following circular dichroic changes in the mitochondrial enzyme, initial kinetic characterization of the cleavage of 4'-N-(2,4-dinitro-5-fluorophenyl)-pyridoxamine 5'-phosphate to form pyridoxal 5'-phosphate at the active site, is provided.

Reactivity of sulphydryl groups of cytosolic and mitochondrial bovine aspartate aminotransferases

Reactivity of sulphydryl groups of cytosolic and mitochondrial aspartate aminotransferases from ox heart has been studied. A total of 5 and 7 cysteine residues per monomer are present in cAATo and mAATo, respectively. In native conditions only a single sulphydryl group can be titrated by Nbs2 while the catalytic activity remains unchanged, however in the mitochondrial isozyme the reactivity depends on the functional state of the enzyme. Reactivity toward NEM reveals the existence of a syncatalytic sulphydryl group in the cytosolic isozyme. Titration of cAATo with pMB at pH 8 and pH 5 confirms the existence of two exposed sulphydryl groups with a different reactivity. The results compared with those reported on the corresponding isozymes from pig and chicken heart show that syncatalytic sulphydryl groups are of general occurrence in these enzymes.

Three-dimensional structure of a pyridoxal-phosphate-dependent enzyme, mitochondrial aspartate aminotransferase

X-ray diffraction studies to 2.8-A resolution have yielded the three-dimensional structure of mitochondrial aspartate aminotransferase (L-aspartate:2-oxoglutarate aminotransferase, EC 2.6.1.1), an isologous alpha 2 dimer (Mr = 2 x 45,000). The subunits are rich in secondary structure and contain two domains, one of which anchors the coenzyme, pyridoxal 5'-phosphate. Each active site lies between the subunits and is composed of residues from both of them.

Electron density map of chicken heart cytosol aspartate transaminase at 3.5 A resolution

Aspartate transaminase (EC 2.6.1.1., Asp-transaminase) has been studied extensively, and much is now known about its physico-chemical, catalytic and other properties. X-ray studies that can provide a structural foundation for the events that occur during the transamination reaction are under way on three species of Asp-transaminase: the cytosolic enzyme from pig and chicken hearts, and the mitochondrial chicken heart enzyme. We describe here the interpretation of an electron density map of Asp-transaminase from chicken heart cytosol at 3.5 A.

Catalytic activity of aspartate aminotransferase in the crystal. Equilibrium and kinetic analysis

Natural substrates and analogs rapidly diffuse through crystals of pig heart mitochondrial aspartate aminotransferase and react at the active sites causing spectral changes that can be measured by single-crystal microspectrophotometry. Dissociation constants for natural substrates and rate constants of transamination for slowly reacting substrates have been determined. A comparison between the data obtained in the crystal and in solution shows that the crystalline enzyme is catalytically competent and that events occurring in the crystal essentially parallel those occurring in solution, even though minor differences have been detected.

Fluorescence of aromatic amino acids in a pyridoxal phosphate enzyme: aspartate aminotransferase

At pH 8.3, the fluorescence spectrum of apoaspartate aminotransferase is characteristic of buried tryptophans (maximum at 330 nm and width at half-height equal to 51 nm). Its quantum yield is 1.69 times larger than for tryptophan in H2O and the mean decay time is 2.5 ns for the fluorescence emitted at wavelengths higher than 335 nm. Polarization of excitation spectrum (minimum at 305 nm for an emission at 360 nm), suggests an inter-tryptophan energy transfer. Accessibility to a quencher of fluorescence indicates that 34% of the fluorescence can be extinguished by iodide with a quenching constant of 4 M-1; as shown by solvent perturbation spectroscopy, this partial accessibility is related to two tryptophan residues accessible to solvent. At pH 5, the relative quantum yield is slightly lower than at pH 8.3 (1.65). Binding of the pyridoxal-P coenzyme diminishes the fluorescence quantum yield relative to tryptophan to 0.51 at pH 8.3 and 0.595 at pH 5; the decrease is smaller in the presence of pyridoxamine-P. Since the fluorescence of the coenzyme is very weak it is difficult to observe its emission sensitized by tryptophan, nevertheless, since the quenching is larger for pyridoxal-P that absorbs at 360 nm than for reduced pyridoxal-P that absorbs at 330 nm, it is deduced that the energy is transferred preferentially from exposed tryptophans. It is proposed that conformational changes in the vicinity of buried tryptophans are responsible for the remaining quenching. This hypothesis of conformational changes induced by the binding of the coenzyme is in agreement with the observed fluorescence emission of tyrosine. In the apoenzyme the tyrosine quantum yield is zero and the energy is entirely transferred to tryptophan. In the holoenzyme the quantum yield is low and the efficiency of transfer to tryptophan is 0.13 in pyridoxal-P form and 0.7 in pyridoxamine-P form. According to the Förster theory of long-range energy transfer, a change of transfer efficiency can be attributed to a modification either of the mutual orientation of tyrosine and tryptophan residues or of the distance between these residues: both interpretations correspond to a conformational change.

Active-site labeling of aspartate aminotransferases by the beta,gamma-unsaturated amino acid vinylglycine

The pyridoxal form of both cytosolic and mitochondrial aspartate aminotransferase is irreversibly inactivated consequent to its interaction with the beta,gamma-unsaturated substrate analogue vinylglycine. Per catalytic cycle, 90% of the enzyme molecules are inactivated while 10% escape inactivation by transamination to the pyridoxamine form. In the presence of vinylglycine plus 2-oxoglutarate, inactivation is complete because of retransamination of the pyridoxamine form to the susceptible pyridoxal form. Peptide analyses after inactivation with [1-14C]vinylglycine showed that vinylglycine alkylates the active-site lysine residue 258 which forms the internal aldimine with the coenzyme pyridoxal 5'-phosphate. The coenzyme itself is left intact; resolution of the inactivated enzyme by base or trichloroacetic acid yields pyridoxal-5'-P. The absorption spectrum of the inactivated enzyme (lambdamax 335 nm) suggests that the cofactor is bound as a substituted aldimine. The proposed pathway of alkylation of Lys-258 involves abstraction of the alpha proton from vinylglycine, isomerization to the alpha,beta-unsaturated enamine, and subsequent nucleophilic attack of the epsilon-amino group of the lysyl residue at the beta carbon of the inhibitor. The determination of the amino acid sequence around the coenzyme-binding lysyl residue in the mitochondrial isoenzyme from chicken gave Ala-(epsilon-Pxy)Lys-Asn-Met-(Gly,Leu,Tyr) which is identical with the other mitochondrial transaminases examined so far.