Quaternary structure of pigeon liver malic enzyme

Pigeon liver malic enzyme (EC 1.1.1.40) has a double dimer quaternary structure. The NADP+ analogs, aminopyridine adenine dinucleotide phosphate and nicotinamide-1,N6-ethenoadenosine dinucleotide phosphate, bind to the enzyme anti-cooperatively. In the presence of non-cooperative competing ligand NADP+, the binding parameter Hill coefficients of these analogues changed very little. Binding of L-malate with enzyme-AADP+ complex first enhanced then reduced the nucleotide fluorescence. Two L-malate binding sites, with Kd values of 23-30 and 270-400 microM, respectively. for the tight and weak binding sites were postulated. A hybrid model between the sequential and pre-existing asymmetrical models was proposed for the pigeon liver malic enzyme.     

Characterization of the tetramer-dimer-monomer equilibrium of the enzymatically active subunits of pigeon liver malic enzyme.

The tetrameric malic enzyme from pigeon liver was reversibly dissociated in the sequence of tetramer-dimer-monomer in an acidic environment (pH 4.5) or when the ionic strength or temperature of the solution was perturbed (0.2 M ammonium sulfate or < 10 degrees C). The dissociated monomer was enzymatically active according to the following criteria: (a) separation and direct activity staining of the monomer in the native gradient polyacrylamide gel, (b) activity staining of the monomer at its pI region in the isoelectric focusing gel, and (c) the enzyme showing lower but definite enzyme activity under conditions where only monomer existed in the solution. The catalytic constant (kcat) and specificity constant (kcat/KmMal) for the monomer were found to be 19 +/- 6 s-1 and 58 x 10(3) s-1.M-1, respectively, only one-seventh and one-seventeenth of those for the tetramer. Different types of interactions are involved in the monomer-monomer and dimer-dimer associations: (a) Two dissociation processes showed different pH dependences. The monomer-monomer interactions involve an amino acid with a side chain pKa value around 5.7, and an amino acid with a side chain pKa value of 7.2 is involved in the dimer-dimer association. (b) Ammonium sulfate up to 0.2 M only affects the monomer-monomer but not the dimer-dimer interactions. The Gibb's free energy, enthalpy, and entropy all have negative values for the above subunits' dissociations. The overall dissociation is an enthalpy-driven process. Association of the subunits to form dimers and tetramers involves salt-bridge, van der Waals, and hydrogen-bonding interactions.(ABSTRACT TRUNCATED AT 250 WORDS)     

Purification of pigeon liver malic enzyme by affinity chromatography

A simple and rapid method for the purification of malic enzyme (EC 1.1.1.40) from pigeon liver is described. Malic enzyme in the crude tissue extract was partially purified by heat treatment, ammonium sulfate fractionation, and DEAE-cellulose chromatography. Final purification was achieved by affinity chromatography on immobilized N⁶-(6-aminohexyl)-adenosine 2′,5′-bisphosphate. Apparently homogeneous enzyme was obtained in 2 days with 54% yield.     

Fluorescence studies on the dissociation and denaturation of pigeon liver malic enzyme

Exposure of pigeon liver malic enzyme [S)-malate:NADP+ oxidoreductase (oxaloacetate-decarboxylating), EC 1.1.1.40) in medium concentrations of guanidine-HCl at 25 degrees C and pH 7.45 caused biphasic conformational changes of the enzyme molecule. Molecular weight determination confirmed that the enzyme tetramers were dissociated to monomers in phase I transition. Enzymatic activity was completely lost in this phase. Recovery of the enzyme activity was only possible in the early stages of the phase I transition. Phase II was due to enzyme unfolding, as judged by circular dichroism and the fluorescence parameters of the enzyme. The steps of the transformation of native malic enzyme into a completely denatured state were in the following sequence: tetramer----monomer----random coil. Extensive denaturation of the enzyme molecule resulted in irreversible aggregation. Dissociation and denaturation were accompanied by a red-shift of the fluorescence spectrum (328----368 nm). Fluorescence quenching studies indicated that tryptophan residues of the enzyme molecule were buried deeply in the interior of the molecule. The tryptophan residues were only partially accessible by acrylamide and almost inaccessible by KI. Dissociation and denaturation were accompanied by exposure of the tryptophan residues, as manifested by the accessibility of the enzyme molecule toward KI or acrylamide.     

Mechanism of pigeon liver malic enzyme: modification of essential carboxyl groups

The maximum velocity of the reaction catalyzed by the pigeon liver malic enzyme depends on the ionization of a functional group of pKa 6.7. This pKa value is independent of temperature within the range 30 degrees-49 degrees C, suggesting the ionization of a carboxyl group. The enzyme activity is inactivated by N-ethyl-5-phenylisoxazolium-3'-sulfonate (Woodward reagent K) at pH 6.0 and 25 degrees C. N-Methylhydroxamine regenerates the enzymatic activity whereas glycine ethyl ester does not. The addition of Mn2+, NADP+, and L-malate to the incubation mixture decreases the inactivation rate, suggesting that the reaction takes place in the active center. The binding capacities of the modified enzyme with NADP+, L-malate, pyruvate, and Mn2+ are not impaired. The kinetic and chemical evidence indicates that the inactivation is due to the modification of a carboxyl group which may be from glutamyl or aspartyl residues of the enzyme. This carboxyl group might function as a general acid-base catalyst. A detailed mechanism in terms of the exact amino acid residues involved is proposed.     

Effect of metal binding on the structural stability of pigeon liver malic enzyme.

The cytosolic malic enzyme from the pigeon liver is sensitive to chemical denaturant urea. When monitored by protein intrinsic fluorescence or circular dichroism spectral changes, an unfolding of the enzyme in urea at 25 degrees C and pH 7.4 revealed a biphasic phenomenon with an intermediate state detected at 4-5 m urea. The enzyme activity was activated by urea up to 1 m but was completely lost before the intermediate state was detected. This suggests that the active site region of the enzyme was more sensitive to chemical denaturant than other structural scaffolds. In the presence of 4 mm Mn(2+), the urea denaturation pattern of malic enzyme changed to monophasic. Mn(2+) helped the enzyme to resist phase I urea denaturation. The [urea](0.5) for the enzyme inactivation shifted from 2.2 to 3.8 m. Molecular weight determined by the analytical ultracentrifuge indicated that the tetrameric enzyme was dissociated to dimers in the early stage of phase I denaturation. In the intermediate state at 4-5 m urea, the enzyme showed polymerization. However, the polymer forms were dissociated to unfolded monomers at a urea concentration greater than 6 m. Mn(2+) retarded the polymerization of the malic enzyme. Three mutants of the enzyme with a defective metal ligand (E234Q, D235N, E234Q/D235N) were cloned and purified to homogeneity. These mutant malic enzymes showed a biphasic urea denaturation pattern in the absence or presence of Mn(2+). These results indicate that the Mn(2+) has dual roles in the malic enzyme. The metal ion not only plays a catalytic role in stabilization of the reaction intermediate, enol-pyruvate, but also stabilizes the overall tetrameric protein architecture.     

Oxidized NADP as a potential active-site-directed reagent of pigeon liver malic enzyme.

Pigeon liver malic enzyme (malate dehydrogenase (decarboxylating), EC 1.1.1.40) was reversibly inactivated by periodate-oxidized NADP in a biphasic manner. The reversibility could be made irreversible by treating the modified enzyme with sodium borohydride. The inactivation showed saturation kinetics and could be prevented by nucleotide (NADP or NADPH). Fully protection was afforded by the combination of NADP, Mn²⁺ and L-malate. Oxidized NADP was also found to be a coenzyme and noncompetitive inhibitor of L-malate in the oxidative decarboxylase reaction catalyzed by malic enzyme.     

Mechanism of pigeon liver malic enzyme modification of histidyl residues by ethoxyformic anhydride.

Incubation of malic enzyme (L-malate:NADP+ oxidoreductase (oxaloacetate-decarboxylating), EC 1.1.1.40) with ethoxyformic anhydride caused the time-dependent loss of its ability to catalyze reactions requiring the nucleotide cofactor NADP+ or NADPH, such as the oxidative decarboxylase, the NADP+ - stimualted oxalacetate decarboxylase, the pyruvate reductase, and the pyruvate-medium proton exchange activities. Similar loss of oxidative decarboxylase and pyruvate reductase activities was affected by photo-oxidation in the presence of rose bengal. The inactivation of oxidative decarboxylase activity by ethoxyformic anhydride was accompanied by the reaction of greater than or equal to 2.3 histidyl residues per enzyme site and was strongly inhibited by NADP+. Ethoxyformylation also impaired the ability of malic enzyme to bind NADP+ or NADPH. These results support the involvement of histidyl residue(s) at the nucleotide binding site of malic enzyme.     

Slow binding of metal ions to pigeon liver malic enzyme: a general case

Pigeon liver malic enzyme was inhibited by lutetium ion through a slow-binding process, which resulted in a concave down tracing of the enzyme activity assay. The fast initial rates were independent of lutetium ion concentration, while the slow steady-state rates decreased with increasing Lu(3+) concentration. The observed rate constant for the transition from initial rate to steady-state rate, k(obs), exhibited saturation kinetics as a function of Lu(3+) concentration, suggesting the involvement of an isomerization process between two enzyme forms (R-form and T-form). The binding affinity of Lu(3+) to the R-form is weaker (K(d,Lu) = 14 microM) than that of Mn(2+) (K(m,Mn) = 1.89 microM); however, Lu(3+) has much tighter binding affinity with the T-form ( = 0.83 microM). Lu(3+) was shown to be a competitive inhibitor with respect to Mn(2+), which suggests that Lu(3+) and Mn(2+) are competing for the same metal binding site of the enzyme. These observations are in accordance with the available crystal structure information, which shows a distorted active site region of the Lu(3+)-containing enzyme. Other divalent cations, i.e., Fe(2+), Cu(2+), or Zn(2+), also act as time-dependent slow inhibitors for malic enzyme. The dynamic quenching constants of the intrinsic fluorescence for the metal-free and Lu(3+)-containing enzymes are quite different, indicating the conformational differences between the two enzyme forms. The secondary structure of these two enzyme forms, on the other hand, was not changed. The above results indicated that replacement of the catalytically essential Mn(2+) by other metal ions leads to a slow conformational change of the enzyme and consequently alters the geometry of the active site. The transformed enzyme conformation, however, is unfavorable for catalysis. Both the chemical nature of the metal ion and its correct coordination in the active site are essential for catalysis.     

Structural characteristics of the nonallosteric human cytosolic malic enzyme

Human cytosolic NADP⁺-dependent malic enzyme (c-NADP-ME) is neither a cooperative nor an allosteric enzyme, whereas mitochondrial NAD(P)⁺-dependent malic enzyme (m-NAD(P)-ME) is allosterically activated by fumarate. This study examines the molecular basis for the different allosteric properties and quaternary structural stability of m-NAD(P)-ME and c-NADP-ME. Multiple residues corresponding to the fumarate-binding site were mutated in human c-NADP-ME to correspond to those found in human m-NAD(P)-ME. Additionally, the crystal structure of the apo (ligand-free) human c-NADP-ME conformation was determined. Kinetic studies indicated no significant difference between the wild-type and mutant enzymes in K_m,NADP, K_m,malate, and k_cat. A chimeric enzyme, [51-105]_c-NADP-ME, was designed to include the putative fumarate-binding site of m-NAD(P)-ME at the dimer interface of c-NADP-ME; however, this chimera remained nonallosteric. In addition to fumarate activation, the quaternary structural stability of c-NADP-ME and m-NAD(P)-ME is quite different; c-NADP-ME is a stable tetramer, whereas m-NAD(P)-ME exists in equilibrium between a dimer and a tetramer. The quaternary structures for the S57K/N59E/E73K/S102D and S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G mutants of c-NADP-ME are tetrameric, whereas the K57S/E59N/K73E/D102S m-NAD(P)-ME quadruple mutant is primarily monomeric with some dimer formation. These results strongly suggest that the structural features near the fumarate-binding site and the dimer interface are highly related to the quaternary structural stability of c-NADP-ME and m-NAD(P)-ME. In this study, we attempt to delineate the structural features governing the fumarate-induced allosteric activation of malic enzyme.     

Possible alternative functions of rat liver malic enzyme

The induction of rat liver malic enzyme by restriction of protein intake has been studied in conjunction with the biosynthesis of fatty acids, fatty acid synthetase, glutathione reductase, and other “lipogenic” enzymes in the various experimental animals. No correlation has been detected between malic enzyme activity and lipogenesis under these conditions. Conversely, a positive correlation between malic enzyme and glutathione reductase has been noted. Possible functions of malic enzyme which appear consistent with these observations are postulated.     

High malic enzyme activity in tumor cells and its cross-reaction with antipigeon liver malic enzyme serum

Summary Rabbit antibodies against pigeon liver malic enzyme (EC 1.1.1.40) were prepared. The antiserum gave single precipitation line with crude pigeon liver extract. Cross reaction was observed with partially purified malic enzyme or crude extract from chicken liver. Positive cross reaction was also observed with the concentrated cytosolic fraction of two human carcinoma cell lines which were demonstrated to contain high malic enzyme activity. All other proteins examined did not react with the antibodies. When purified pigeon liver malic enzyme was mixed with the antiserumin vitro, a time-dependent inactivation of the enzyme activity was observed. Protection of the enzyme activity against antiserum inactivation was afforded by NADP⁺ orL-malate. Metal Mn²⁺ gave little protection.     

Coding nucleotide sequence of rat liver malic enzyme mRNA

The nucleotide sequence of the mRNA for malic enzyme ((S)-malate NADP+ oxidoreductase (oxaloacetate-decarboxylating, EC 1.1.1.40) from rat liver was determined from three overlapping cDNA clones. Together, these clones contain 2078 nucleotides complementary to rat liver malic enzyme mRNA. The single open reading frame of 1761 nucleotides codes for a 585-amino acid polypeptide with a calculated molecular mass of about 65,460 daltons. The cloned cDNAs contain the complete 3'-noncoding region of 301 nucleotides for the major mRNA species of rat liver and 16 nucleotides of the 5'-noncoding region. Amino acid sequences of seven tryptic peptides (67 amino acids) from the purified protein are distributed through the single open reading frame and show excellent correspondence with the translated nucleotide sequence. The putative NADP-binding site for malic enzyme was identified by amino acid sequence homology with the NADP-binding site of the enoyl reductase domain of fatty acid synthetase.     

Involvement of single residue tryptophan 548 in the quaternary structural stability of pigeon cytosolic malic enzyme

Pigeon cytosolic malic enzyme has a double dimer quaternary structure with three tryptophanyl residues in each monomer distributed in different structural domains. The enzyme showed a three-state unfolding phenomenon upon increasing the urea concentration (Chang, H. C., Chou, W. Y., and Chang, G. G. (2002) J. Biol. Chem. 277, 4663-4671). At urea concentration of 4-4.5 m, where the intermediate form was detected, the enzyme existed as partially unfolded dimers, which were easily polymerized. Mn2+ provided full protection against the polymerization. To further characterize this phenomenon, three mutants of the enzyme (W129, W321, and W548), each with only one tryptophanyl residue left, were constructed. All these mutants were successfully overexpressed in Escherichia coli cells and purified to homogeneity. Changes in the circular dichroism spectra of all mutants revealed a three-state urea-unfolding process in the absence of Mn2+. In the presence of 4 mm Mn2+, W548 and wild type (WT) enzymes shifted to monophasic, while W129 and W321 were still biphasic. Similar results were obtained from the fluorescence spectral changes, except for W321, which showed monophasic denaturation curve with or without Mn2+. Analytical ultracentrifugation analysis indicated that the mutant enzymes were polymerized at 4.5 m urea, and Mn2+ provided protective effect on W548 and WT enzymes only. Other mutants with mutated Trp-548 polymerized at 4.5 m urea in the absence or presence of 4 mm Mn2+. The above results indicate that a single residue, Trp-548, in the subunit interface region, is responsible for the integrity of the quaternary structure of the pigeon cytosolic malic enzyme.     

Structural and functional analysis of the rat malic enzyme gene promoter.

We have characterized sequences of genomic DNA 5' to the coding region of the rat malic enzyme gene. This sequence possesses neither TATA nor CCAAT sequences in their usual positions but is rich in GC residues. Sequences similar to those found in the regulatory regions of other genes are discussed. Deletion analyses have revealed that sequences +1 to -41 are sufficient to initiate expression, although inclusion of information up to -177 is necessary for maximal promoter activity.