Molecular enzymology of lipoxygenases

Lipoxygenases (LOXs) are lipid peroxidizing enzymes, implicated in the pathogenesis of inflammatory and hyperproliferative diseases, which represent potential targets for pharmacological intervention. Although soybean LOX1 was discovered more than 60 years ago, the structural biology of these enzymes was not studied until the mid 1990s. In 1993 the first crystal structure for a plant LOX was solved and following this protein biochemistry and molecular enzymology became major fields in LOX research. This review focuses on recent developments in molecular enzymology of LOXs and summarizes our current understanding of the structural basis of LOX catalysis. Various hypotheses explaining the reaction specificity of different isoforms are critically reviewed and their pros and cons briefly discussed. Moreover, we summarize the current knowledge of LOX evolution by profiling the existence of LOX-related genomic sequences in the three kingdoms of life. Such sequences are found in eukaryotes and bacteria but not in archaea. Although the biological role of LOXs in lower organisms is far from clear, sequence data suggests that this enzyme family might have evolved shortly after the appearance of atmospheric oxygen on earth.     

Structure of human carnitine acetyltransferase. Molecular basis for fatty acyl transfer

Carnitine acyltransferases are a family of ubiquitous enzymes that play a pivotal role in cellular energy metabolism. We report here the x-ray structure of human carnitine acetyltransferase to a 1.6-A resolution. This structure reveals a monomeric protein of two equally sized alpha/beta domains. Each domain is shown to have a partially similar fold to other known but oligomeric enzymes that are also involved in group-transfer reactions. The unique monomeric arrangement of the two domains constitutes a central narrow active site tunnel, indicating a likely universal feature for all members of the carnitine acyltransferase family. Superimposition of the substrate complex of a related protein, dihydrolipoyl trans-acetylase, reveals that both substrates localize to the active site tunnel of human carnitine acetyltransferase, suggesting the location of the ligand binding sites for carnitine and coenzyme A. Most significantly, this structure provides critical insights into the molecular basis for fatty acyl chain transfer and a possible common mechanism among a wide range of acyltransferases utilizing a catalytic dyad.     

Cardiac carnitine deficiency and altered carnitine transport in cardiomyopathic hamsters

The Bio 14.6 hamster has a well-documented cardiomyopathy which leads to congestive heart failure. Previous work demonstrated that hearts from these hamsters have depressed fatty acid oxidation and depressed carnitine concentrations compared to those of normal hamsters. Analyses of tissue carnitine concentrations from 40 to 464 days of age demonstrate that the cardiomyopathic hamsters have a cardiac carnitine deficiency throughout life. Therefore, the carnitine deficiency is not a secondary effect of an advanced stage of the cardiomyopathy. Both the observation that other tissues of the cardiomyopathic hamster have normal or markedly elevated carnitine concentrations and the observation that oral carnitine treatment could not increase the cardiac carnitine concentrations to those of normal hamsters are consistent with the hypothesis that the cardiac carnitine deficiency is the result of a defective cardiac transport mechanism. Cardiac carnitine-binding protein (which may function in the cardiac carnitine transport mechanism) prepared from hearts of cardiomyopathic hamsters had a lower maximal carnitine binding and an increased dissociation constant for carnitine compared to the cardiac carnitine-binding protein prepared from normal hamsters. Thus, several types of data indicate that the cardiomyopathic hamster has an altered cardiac carnitine transport mechanism.     

Abnormal sodium stimulation of carnitine transport in primary carnitine deficiency

Primary carnitine deficiency is an autosomal recessive disorder of fatty acid oxidation characterized by hypoketotic hypoglycemia and skeletal and cardiac myopathy. It is caused by mutations in the sodium-dependent carnitine cotransporter OCTN2. The majority of natural mutations identified in this and other Na(+)/solute symporters introduce premature termination codons or impair insertion of the mutant transporter on the plasma membrane. Here we report that a missense mutation (E452K) identified in one patient with primary carnitine deficiency did not affect membrane targeting, as assessed with confocal microscopy of transporters tagged with the green fluorescent protein, but reduced carnitine transport by impairing sodium stimulation of carnitine transport. The natural mutation increased the concentration of sodium required to half-maximally stimulate carnitine transport (K(Na)) from the physiological value of 11.6 to 187 mm. Substitution of Glu(452) with glutamine (E452Q), aspartate (E452D), or alanine (E452A) caused intermediate increases in the K(Na). Carnitine transport decreased exponentially with increased K(Na). The E452K mutation is the first natural mutation in a mammalian cotransporter affecting sodium-coupled solute transfer and identifies a novel domain of the OCTN2 cotransporter involved in transmembrane sodium/solute transfer.     

The enzymology of the bacterial phosphoenolpyruvate-dependent sugar transport systems

Summary The phosphoenolpyruvate-dependent sugar transport system (PTS) is present in a large variety of bacteria. It catalyzes transport and phosphorylation of hexoses and hexitols at the expense of phosphoenolpyruvate. Only three of four enzymes are required for this entire sequence. Each component has been isolated and purified to the homogeneity from one bacterial species or another allowing recent investigations intomechanistic aspects of energy coupling, energy conservation, transport and regulation using well-characterized enzymes. In each case the phosphorylation of the enzyme is a key element in that enzymes function.The initial step in the energy conversion process is the E_I catalyzed conversion of phosphoenolpyruvate to pyruvate and P-HPr. E_II is a metal requiring hydrophobic enzyme which is active only as a dimer. Kinetic and gel filtration data confirm that it forms functional ternary complexes with HPr or P-Hpr and phosphoenolpyruvate or pyruvate which influence both the degree of dimerization and the specific activity of the dimer. The dimer appears to carry only one phosphoryl group suggesting that negative cooperativity or a flip-flop mechanism may be involved in the sequence of phosphoryl group transfer.Many of the PTS phosphoenzyme intermediates carry the phosphoryl group as a phospho-histidine. A general mechanism for the transfer of the phosphoryl group to and from the active site histidine residue in each protein has been established with high resolution ¹H NMR data. At physiological pH the active site histidine is deprotonated, whereas the phosphohistidine is protonated. Consequently the histidine, as a strong nucleophile, can abstract the phosphoryl group from the donor while protonation destabilizes the phosphohistidine facilitating passage of the phosphoryl group to the following enzyme intermediate. The change in protonation state accompanies a phosphorylation induced conformational change in the carrier.The ability of the PTS to regulate the activity of other permeases and catabolic enzymes has been attributed to E_III ^Glc. Data obtained with mutants suggest that changes in the phosphorylation state alter the regulatory properties of the enzyme. The nonphosphorylated species blocks various permeases and suppresses adenylate cyclase activity thereby inhibiting the synthesis of catabolic enzyme systems. The phosphorylated species stimulates adenylate cyclase and permits the uptake of inducers leading to the initiation of catabolic enzyme synthesis. Experiments with the isolated E_III ^Glc confirm that a phosphoenzyme intermediate exists.Transport and phosphorylation of the sugar are catalyzed by a membrane-bound E_II via a phosphoenzyme intermediate which can be reached from P-HPr, P-E_III or sugar-P. The phosphorylation state controls the affinity of the enzyme for its substrates. E_II is high affinity for P-HPr or P-E_III and low affinity for sugar. P-E_II is high affinity for sugar and low affinity for P-HPr or P-E_III. The affinity of the enzyme for sugar substrates is controlled by the oxidation state of a dithiol. The reduced, dithiol form is high affinity for sugar substrates. The oxidized, disulfide form, is low affinity. Phosphorylation of the enzyme chould shift the affinity for substrates by altering the oxidation state of the enzyme.     

Molecular enzymology of phage T4 Dam DNA-methyltransferase

The review reflects results of studies on the molecular mechanism of phage T4 Dam DNA-methyltransferase action. The enzyme (T4Dam) catalyzes methyl group transfer from S-adenosyl-l-methionine (AdoMet) to N6-adenine position in the palindromic recognition sequence GATC (EC 2.1.1.72). The enzyme subunit structure, substrate-binding and kinetic parameters for a wide range of native and modified oligonucleotide duplexes, as well as steady-state reaction kinetic scheme, included T4Dam isomerization to catalytically active form, are considered. The found mechanisms of DNA induced T4Dam dimerization, target base flipping, enzyme reorientation in an asymmetrically modified recognition sequence, effector action of reaction substrates and processive methylation of DNA substrates, containing more than one specific site, are discussed. The results obtained with T4Dam may be useful for understanding mechanisms of action of other homologous enzymes, most of all for specimens of numerous family of Dam DNA-methyltransferases.     

Carnitine transport and tissue carnitine accretion in rats

In rats, circulating carnitine levels were highly correlated with skeletal muscle and heart carnitine concentrations over the range of 26-69 microM serum carnitine, but not at higher extracellular carnitine concentrations (70-188 microM). By contrast, circulating carnitine levels over the entire range studied (26-188 microM) correlated with liver and kidney carnitine concentrations. For each tissue the range of extracellular carnitine concentrations which correlated with the tissue carnitine concentration corresponded with the linear or nearly linear portion of the Michaelis-Menten curve for transport of carnitine in vitro.     

Properties of carnitine transport in rat kidney cortex slices

The properties of carnitine transport were studied in rat kidney cortex slices. Tissue: medium concentration gradients of 7.9 for L-[methyl-¹⁴C]carnitine were attained after 60-min incubation at 37°C in 40 μM substrate. L- and D-carnitine uptake showed saturability. The concentration curves appeared to consist of (1) a high-affinity component, and (2) a lower affinity site. When corrected for the latter components, the estimated K_m for L-carnitine was 90 μM and $\text{V = 22}\text{nmol/min}$ per ml intracellular fluid; for D-carnitine, $\text{K}{}_{\mathrm{<mtext>m</mtext>}}\text{= 166}\text{μM}$ and $\text{V = 15}\text{nmol/min}$ per ml intracellular fluid. The system was stereospecific for L-carnitine. The uptake of L-carnitine was inhibited by (1) D-carnitine, γ-butyrobetaine, and (2) acetyl-L-carnitine. γ-Butyrobetaine and acetyl-L-carnitine were competitive inhibitors of L-carnitine uptake. Carnitine transport was not significantly reduced by choline, betaine, lysine or γ-aminobutyric acid. Carnitine uptake was inhibited by 2,4-dinitrophenol, carbonyl cyanide $\text{m-}\text{chlorophenylhydrazone}$, N₂ atmosphere, KCN, $\text{N-}\text{ethylmaleimide}$, low temperature (4°C) and ouabain. Complete replacement of Na⁺ in the medium by Li⁺ reduced L- and D-carnitine uptake by 75 and 60%, respectively. Complete replacement of K⁺ or Ca²⁺ in the medium also significantly reduces carnitine uptake. Two roles for the carnitine transport system in kidney are proposed: (1) a renal tubule reabsorption system for the steady-state maintenance of plasma carnitine; and (2) maintenance of normal carnitine levels in kidney cells, which is required for fatty acid oxidation.     

Characterization of the unidirectional transport of carnitine catalyzed by the reconstituted carnitine carrier from rat liver mitochondria

The carnitine carrier from rat liver mitochondria was purified by chromatography on hydroxyapatite and celite and reconstituted in egg yolk phospholipid vesicles by adsorbing the detergent on polystyrene beads. In the reconstituted system, in addition to the carnitine/carnitine exchange, the purified protein catalyzed a uni-directional transport (uniport) of carnitine measured as uptake into unloaded proteoliposomes as well as efflux from prelabelled proteoliposomes. In both cases the reaction followed a first-order kinetics with a rate constant of 0.023-0.026 min-1. Besides carnitine, also acylcarnitines were transported in the uniport mode. N-Ethylmaleimide inhibited the uni-directional transport of carnitine completely. The uniport of carnitine is not influenced by the delta pH and the electric gradient across the membrane. The activation energy for uniport was 115 kJ/mol and the half-saturation constant on the external side of the proteoliposomes was 0.53 mM. The maximal rate of the uniport at 25 degrees C was 0.2 mumol/min per mg protein, i.e. about 10 times lower than that of the reconstituted carnitine transport in exchange mode.     

Molecular enzymology of 5-aminolevulinate synthase, the gatekeeper of heme biosynthesis

Chlorophyll(Chl)-c pigments in algae, diatoms and some prokaryotes are characterized by the fully conjugated porphyrin π-system as well as the acrylate residue at the 17-position. The precise structural characterization of Chl-c(3) from the haptophyte Emiliania huxleyi was performed. The conformations of the π-conjugated peripheral substituents, the 3-/8-vinyl, 7-methoxycarbonyl and 17-acrylate moieties were evaluated, in a solution, using nuclear Overhauser enhancement correlations and molecular modeling calculations. The rotation of the 17-acrylate residue was considerably restricted, whereas the other three substituents readily rotated at ambient temperature. Moreover, the stereochemistry at the 132-position was determined by combination of chiral high-performance liquid chromatography (HPLC) with circular dichroism (CD) spectroscopy. Compared with the CD spectra of the structurally related, synthetic (132R)- and (132S)-protochlorophyllide(PChlide)-a, naturally occurring Chl-c? had exclusively the (132R)-configuration. To elucidate this natural selection of a single enantiomer, we analyzed the three major Chl-c pigments (Chl-c?, c? and c?) in four phylogenetically distinct classes of Chl-c containing algae, i.e., heterokontophyta, dinophyta, cryptophyta and haptophyta using chiral HPLC. All the photosynthetic organisms contained only the (132R)-enantiomerically pure Chls-c, and lacked the corresponding enantiomeric (132S)-forms. Additionally, Chl-c? was found in all the organisms as the common Chl-c. These results throw a light on the biosynthesis as well as photosynthetic function of Chl-c pigments: Chl-c? is derived from 8-vinyl-PChlide-a by dehydrogenation of the 17-propionate to acrylate residues as generally proposed, and the (132R)-enantiomers of Chls-c function as photosynthetically active, light-harvesting pigments together with the principal Chl-a and carotenoids.     

Tyrosine residues affecting sodium stimulation of carnitine transport in the OCTN2 carnitine/organic cation transporter

Primary carnitine deficiency is a disorder of fatty acid oxidation caused by mutations in the Na+-dependent carnitine/organic cation transporter OCTN2. Studies with tyrosyl group-modifying reagents support the involvement of tyrosine residues in Na+ binding by sodium-coupled transporters. Here we report two new patients with carnitine deficiency caused by mutations affecting tyrosyl residues (Y447C and Y449D) close to a residue (Glu-452) previously shown to affect sodium stimulation of carnitine transport. Kinetic analysis indicated that the Y449D substitution, when expressed in Chinese hamster ovary cells, increased the concentration of sodium required to half-maximally stimulate carnitine transport from 14.8 +/- 1.8 to 34.9 +/- 5.8 mM (p<0.05), whereas Y447C completely abolished carnitine transport. Substitution of these tyrosine residues with phenylalanine restored normal carnitine transport in Y449F but resulted in markedly impaired carnitine transport by Y447F. This was associated with an increase in the concentration of sodium required to half-maximally stimulate carnitine transport to 57.8 +/- 7.4 mM (p<0.01 versus normal OCTN2). The Y447F and Y449D mutant transporters retained their ability to transport the organic cation tetraethylammonium indicating that their effect on carnitine transport was specific and likely associated with the impaired sodium stimulation of carnitine transport. By contrast, the Y447C natural mutation abolished the transport of organic cations in addition to carnitine. Confocal microscopy of OCTN2 transporters tagged with green fluorescent protein indicated that the Y447C mutant transporters failed to reach the plasma membrane, whereas Y447F, Y449D, and Y449F had normal membrane localization. These natural mutations identify tyrosine residues possibly involved in coupling the sodium electrochemical gradient to transmembrane solute transfer in the sodium-dependent co-transporter OCTN2.     

Molecular basis for sterol transport by StART‐like lipid transfer domains

Lipid transport proteins at membrane contact sites, where two organelles are closely apposed, play key roles in trafficking lipids between cellular compartments while distinct membrane compositions for each organelle are maintained. Understanding the mechanisms underlying non‐vesicular lipid trafficking requires characterization of the lipid transporters residing at contact sites. Here, we show that the mammalian proteins in the lipid transfer proteins anchored at a membrane contact site (LAM) family, called GRAMD1a‐c, transfer sterols with similar efficiency as the yeast orthologues, which have known roles in sterol transport. Moreover, we have determined the structure of a lipid transfer domain of the yeast LAM protein Ysp2p, both in its apo‐bound and sterol‐bound forms, at 2.0 Å resolution. It folds into a truncated version of the steroidogenic acute regulatory protein‐related lipid transfer (StART) domain, resembling a lidded cup in overall shape. Ergosterol binds within the cup, with its 3‐hydroxy group interacting with protein indirectly via a water network at the cup bottom. This ligand binding mode likely is conserved for the other LAM proteins and for StART domains transferring sterols.     

Interaction of mildronate with the mitochondrial carnitine/acylcarnitine transport protein

The interaction of mildronate [3-(2,2,2-trimethylhydrazine) propionate] with the purified mitochondrial carnitine/acylcarnitine transporter reconstituted in liposomes has been studied. Mildronate, externally added to the proteoliposomes, strongly inhibited the carnitine/carnitine antiport catalyzed by the reconstituted transporter with an IC(50) of 560 muM. A kinetic analysis revealed that the inhibition is completely competitive, that is, mildronate interacts with the substrate-binding site. The half-saturation constant of the transporter for external mildronate (K(i)) is 530 muM. Carnitine/mildronate antiport has been measured as [(3)H]carnitine uptake into proteoliposomes containing internal mildronate or as [(3)H]carnitine efflux from proteoliposomes in the presence of external mildronate, indicating that mildronate is transported by the carnitine/acylcarnitine transporter and that the inhibition observed was due to the transport of mildronate in the place of carnitine. The intraliposomal half-saturation constant for mildronate transport (K(m)) has been determined. Its value, 18 mM, is much higher than the external half-saturation constant (K(i)) in agreement with the asymmetric properties of the transporter. In vivo, the antiport reaction between cytosolic (administered) mildronate and matrix carnitine may cause intramitochondrial carnitine depletion. This effect, together with the inhibition of the physiological transport, will lead to impairment of fatty acid utilization.     

Conformations of carnitine and acetylcarnitine and the relationship to mitochondrial transport of fatty acids

The conformations of carnitine and acetylcarnitine by EHT and CNDO/2 molecular orbital calculations show that carnitine has two low energy conformers. One of these is an extended conformer corresponding to a charge separated species, while the other is a folded conformer having a charged onium head and carboxylate anion in close proximity forming an internal ionic bond. These results suggest that the folded conformation is responsible for the active transport of acetyl- and acyl-carnitine by enzymes which transfer acyl groups into the mitochondria for subsequent fatty acid oxidation.     

Biosynthesis of carnitine octanoyltransferase and carnitine palmitoyltransferase

Male Wistar rats were fed a diet with or without di(2-ethylhexyl)phthalate (DEHP) for 2 weeks. Carnitine octanoyltransferase (COT) in the liver was increased 23.5-fold in rats given DEHP. It was found by in vivo experiments using L-[4,5-3H]leucine and the immunoprecipitation technique that the rate of synthesis of COT was 14.1-fold higher and that of its degradation was 1.5-fold lower in the DEHP group. COT was translated much more effectively in free polysomes than in membrane-bound polysomes. The molecular size of the in vitro product was the same as that of the mature enzyme. The translation activity of mRNA coding for COT measured with total hepatic RNA was 16.6-fold higher in the DEHP group. Carnitine palmitoyltransferase (CPT) was increased 5.9-fold after administration of DEHP. The rate of synthesis of CPT measured in the in vivo experiment was 5.0-fold higher in the DEHP group. The rate of its degradation was the same in the two groups. CPT was also translated much more effectively in free polysomes. The size of the preenzyme was larger than that of the subunit of the mature enzyme by about 2,400 daltons. In contrast to COT, the increase in the translation activity of mRNA for CPT by administration of DEHP was markedly higher than the increase in the rate of its synthesis measured in the in vivo experiment.