Formyl phloroglucinol meroterpenoids from the leaves of Eucalyptus globulus subsp. maidenii and their ATP-citrate lyase inhibitory activities

Three new formyl phloroglucinol meroterpenoids, eumaidials A-C (1-3), were isolated from the leaves of Eucalyptus globulus subsp. maidenii, along with ten known analogues (4-13). Their chemical structures were determined by various spectral data and electronic circular dichroism calculations. Eumaidial A (1) is the first β-caryophyllene-based formyl phloroglucinol meroterpenoids from the genus Eucalyptus. Compounds 1-4 and 10 exhibited ATP-citrate lyase inhibitory activities, and compounds 2 and 3 suppressed the hepatocyte lipogenesis.

The structure of succinyl-CoA synthetase bound to the succinyl-phosphate intermediate clarifies the catalytic mechanism of ATP-citrate lyase

Succinyl-CoA synthetase (SCS) catalyzes a three-step reaction in the citric acid cycle with succinyl-phosphate proposed as a catalytic intermediate. However, there are no structural data to show the binding of succinyl-phosphate to SCS. Recently, the catalytic mechanism underlying acetyl-CoA production by ATP-citrate lyase (ACLY) has been debated. The enzyme belongs to the family of acyl-CoA synthetases (nucleoside diphosphate-forming) for which SCS is the prototype. It was postulated that the amino-terminal portion catalyzes the full reaction and the carboxy-terminal portion plays only an allosteric role. This interpretation was based on the partial loss of the catalytic activity of ACLY when Glu599 was mutated to Gln or Ala, and on the interpretation that the phospho-citryl-CoA intermediate was trapped in the 2.85 Å resolution structure from cryogenic electron microscopy (cryo-EM). To better resolve the structure of the intermediate bound to the E599Q mutant, the equivalent mutation, E105αQ, was made in human GTP-specific SCS. The structure of the E105αQ mutant shows succinyl-phosphate bound to the enzyme at 1.58 Å resolution when the mutant, after phosphorylation in solution by Mg2+-ATP, was crystallized in the presence of magnesium ions, succinate and desulfo-CoA. The E105αQ mutant is still active but has a specific activity that is 120-fold less than that of the wild-type enzyme, with apparent Michaelis constants for succinate and CoA that are 50-fold and 11-fold higher, respectively. Based on this high-resolution structure, the cryo-EM maps of the E599Q ACLY complex reported previously should have revealed the binding of citryl-phosphate and CoA and not phospho-citryl-CoA.

ATP-citrate lyase B (ACLB) negatively affects cell death and resistance to Verticillium wilt

BACKGROUND

ATP-citrate lyase (ACL) plays a pivotal role in histone acetylation and aerobic glycolysis. In plant, ACL is a heteromeric enzyme composed of ACLA (45 kD) and ACLB (65 kD). So far, the function of ACL genes in cotton still remains unknown.

RESULTS

Here, we identified three ACLA homologous sequences and two ACLB homologous in each genome/sub-genome of cotton species. Silencing ACLB in cotton led to cell death at newly-grown leaves and stem apexes. Simultaneously, in ACLB-silenced plants, transcription factors related to senescence including SGR, WRKY23 and Osl57 were observed to be activated. Further investigation showed that excessive H₂O₂ was accumulated, salicylic acid-dependent defense response and pathogenesis-related gene expressions were evidently enhanced in ACLB-silenced plants, implying that knockdown of ACLB genes leads to hypersensitive response-like cell death in cotton seedlings. However, as noted, serious cell death happened in newly-grown leaves and stem apexes in ACLB-silenced plants, which led to the failure of subsequent fungal pathogenicity assays. To confirm the role of ACLB gene in regulating plant immune response, the dicotyledonous model plant Arabidopsis was selected for functional verification of ACLB gene. Our results indicate the resistance to Verticillium dahliae infection in the Arabidopsis mutant aclb-2 were enhanced without causing strong cell death. Ectopic expression of GausACLB-2 in Arabidopsis weakened its resistance to V. dahliae either in Col-0 or in aclb-2 background, in which the expression level of ACLB is negatively correlated with the resistance to V. dahliae.

CONCLUSIONS

These results indicate that ACLB has a new function in negatively affecting the induction of plant defense response and cell death in cotton, which provides theoretical guidance for developing cotton varieties with resistance against Verticillium wilt.

Ketogenic HMG-CoA lyase and its product β-hydroxybutyrate promote pancreatic cancer progression

Pancreatic ductal adenocarcinoma (PDA) tumor cells are deprived of oxygen and nutrients and therefore must adapt their metabolism to ensure proliferation. In some physiological states, cells rely on ketone bodies to satisfy their metabolic needs, especially during nutrient stress. Here, we show that PDA cells can activate ketone body metabolism and that β-hydroxybutyrate (βOHB) is an alternative cell-intrinsic or systemic fuel that can promote PDA growth and progression. PDA cells activate enzymes required for ketogenesis, utilizing various nutrients as carbon sources for ketone body formation. By assessing metabolic gene expression from spontaneously arising PDA tumors in mice, we find HMG-CoA lyase (HMGCL), involved in ketogenesis, to be among the most deregulated metabolic enzymes in PDA compared to normal pancreas. In vitro depletion of HMGCL impedes migration, tumor cell invasiveness, and anchorage-independent tumor sphere compaction. Moreover, disrupting HMGCL drastically decreases PDA tumor growth in vivo, while βOHB stimulates metastatic dissemination to the liver. These findings suggest that βOHB increases PDA aggressiveness and identify HMGCL and ketogenesis as metabolic targets for limiting PDA progression.

Stressed-Out T Cells Fragment the Mind

The immune system is increasingly recognized to play an integral role in regulating stress responses. In a recent article in Cell, Fan et al. demonstrate a novel mechanism through which stress drives mitochondrial fragmentation-induced xanthine accumulation in mouse CD4⁺ T cells, subsequently acting on oligodendrocytes to induce anxiety-like behaviors.

Quantitative analysis of sugar constituents of glycoproteins by capillary electrophoresis

A method for quantitative analysis of monosaccharides including N-acetylneuraminic acid derived from sialic acid-containing oligosaccharides and glycoproteins is presented. The analysis is based on the combination of chemical and enzymatic methods coupled with capillary electrophoretic (CE) separation and laser-induced fluorescence (LIF) detection. The present method utilizes a simplified acid hydrolysis procedure consisting of mild hydrolysis (0.1 M TFA) to release sialic acid and strong acid hydrolysis (2.0 N TFA) to produce amino and neutral sugars. Amino sugars released from strong acid hydrolysis of oligosaccharides and glycoproteins were reacetylated and derivatized with 8-aminopyrene-1,3,6-trisulfonate (APTS) along with neutral sugars in the presence of sodium cyanoborohydride to yield quantitatively the highly stable fluorescent APTS adducts. N-acetylneuraminic acid (Neu5Ac), a major component of most mammalian glycoproteins, was converted in a fast specific reaction by the action of neuraminic acid aldolase (N-acylneuraminate pyruvate-lyase EC 4.1.3.3) to N-acetylmannosamine (ManNAc) and pyruvate. ManNAc was then derivatized with APTS in the same manner as the other monosaccharides. This method was demonstrated for the quantitation of pure Neu5Ac and the species derived from mild acid hydrolysis of 6'-sialyl-N-acetyllactosamine and bovine fetuin glycan. Quantitative recovery of the N-acetylmannosamine was obtained from a known amount of Neu5Ac in a mixture of seven other monosaccharides or from the sialylated oligosaccharides occurring in glycoproteins. The sequence of procedures consists of acid hydrolysis, enzymatic conversion and APTS derivatization which produced quantitative recovery of APTS-monosaccharide adducts. The detection limits for sugars derivatized with APTS and detected by CE-LIF are 100 pmol for Neu5Ac and 50 pmol for the other sugars.

Role of citritase in acetoin formation by Streptococcus diacetilactis and Leuconostoc citrovorum

Harvey, R. J. (University of California, Davis) and E. B. Collins. Role of citritase in acetoin formation by Streptococcus diacetilactis and Leuconostoc citrovorum. J. Bacteriol. 82:954-959. 1961.-Cell-free extracts of Streptococcus diacetilactis and Leuconostoc citrovorum converted citrate to acetate, oxalacetate, pyruvate, carbon dioxide, and acetoin. The products, stoichiometry, and cofactor requirements of the citrate-splitting reaction were identical to those reported for citritase. Coenzyme A was not required; the reaction was stimulated by magnesium or manganous ions, and inhibited by calcium ions. In S. diacetilactis the enzyme is constitutive; it has been found inducible in all other organisms that have been studied. Ten strains of S. diacetilactis, three strains of Leuconostoc, and one strain of S. liquefaciens contained the enzyme; 21 strains of S. cremoris and 3 strains of S. lactis did not. Cell-free extracts of S. diacetilactis and L. citrovorum converted pyruvate to acetoin and carbon dioxide in the presence of manganous ions and thiamine pyrophosphate.

THE EQUILIBRIUM OF THE REACTION CATALYSED BY CITRATE OXALOACETATE-LYASE

1. A method of preparation and purification of citrate oxaloacetate-lyase (EC 4.1.3.6) from Aerobacter aerogenes is described. 2. The equilibrium of this reaction has been determined at pH 8.4 and 25 degrees . It has been shown that K, i.e. [citrate(3-)]/[oxaloacetate(keto) (2-)][acetate (-)], is 3.08+/-0.72, but that K(app.), i.e. [total citrate]/[total oxaloacetate][total acetate], is markedly affected by the initial concentrations of the reactants and magnesium. 3. The free-energy change during the cleavage of citrate has been calculated and compared with data from other sources. 4. The free energy of hydrolysis of acetyl-CoA has been evaluated from the present data. 5. A detailed knowledge of the interactions of the reactants with metal ions has been shown to be important in the calculation of the equilibrium constant and related thermodynamic functions.

Citrate lyase from Klebsiella pneumoniae. The complete primary structure of the acyl lyase subunit

The primary structure of the beta-subunit (acyl lyase subunit) of citrate lyase from Klebsiella pneumoniae (ATCC 13,882) was determined with protein chemical methods. The polypeptide chain consists of 289 amino acid residues and has a molecular mass of 31,352 Da. The two half-cystine residues of the subunit are present as cysteines and not involved in disulfide bridges. The sequence shows no homology to known sequences of proteins or nucleic acids and reads (sequence; see text)

Proposed mechanism for the condensation reaction of citrate synthase: 1.9-A structure of the ternary complex with oxaloacetate and carboxymethyl coenzyme A

The crystal structure of the ternary complex citrate synthase-oxaloacetate-carboxymethyl coenzyme A has been solved to a resolution of 1.9 A and refined to a conventional crystallographic R factor of 0.185. The structure resembles a proposed transition state of the condensation reaction and suggests that the condensation reaction proceeds through a neutral enol rather than an enolate intermediate. A mechanism for the condensation reaction is proposed which involves the participation of three key catalytic groups (Asp 375, His 274, and His 320) in two distinct steps. The proposed mechanism invokes concerted general acid-base catalysis twice to explain both the energetics of the reaction and the experimentally observed inversion of stereochemistry at the attacking carbon atom.

The unfolding and attempted refolding of citrate synthase from pig heart

The unfolding of the dimeric enzyme citrate synthase from pig heart in solutions of guanidinium chloride (GdnHCl) was studied. Data from fluorescence, circular dichroism (CD) and thiol group reactivity studies indicated that the enzyme was almost completely unfolded at GdnHCl concentrations greater than or equal to 4 M. On dilution of GdnHCl, essentially no reactivation of the enzyme occurred. The implications of this finding for the process of folding and assembly in vivo of this and other mitochondrial enzymes are discussed. Exposure of the enzyme to high pH (9-10) led to only a small loss of secondary structure and partial reactivation could be observed on readjustment of the pH to 8.0.

High sequence conservation between isocitrate lyase from Escherichia coli and Ricinus communis

The deduced amino acid sequences of isocitrate lyase (EC 4.1.3.1) from Escherichia coli and Ricinus communis (castor bean) were compared and regions of high homology between the two enzymes were identified. The castor-bean enzyme had a 14 amino acid amino-terminal, and a 25 amino acid carboxy-terminal extension and a 102 amino acid central insertion compared to the E. coli enzyme. Enzymatic data were used to attempt to identify specific amino acids in the active site. Comparisons with putative peroxisomal/gloxysomal targeting sequences were made and a region including part of the central insertion of the castor bean enzyme was tentatively identified.

Coenzyme A dithioesters: synthesis, characterization and reaction with citrate synthase and acetyl-CoA:choline O-acetyltransferase

Acyl dithioesters of CoA have been synthesized by transesterification. The alpha-hydrogens have a spectrally determined pKa of 12.5 +/- 0.14. The hydroxide catalyzed enolization rate is estimated to be 600 M-1.s-1. The absorbance of the dithioester, lambda max = 306 nm, can be used to monitor both the condensation and transesterification reactions that use CoA-Ac as a substrate. For citrate synthase at pH 7.4 Vmax = (4.0 +/- 0.4).10(-4) s-1 and Km = 53 +/- 7.5 microM, which are 2.10(-6) and 3.3-times the Vmax and Km values observed for CoAS-Ac, while for Ac-CoA: choline O-acetyltransferase (EC 2.3.1.6) at pH 7.0 Vmax = (1.1 +/- 0.2).10(-2) mumol.s-1.(mg protein)-1 and Km = 83 +/- 33 microM, which are 0.077 and 10-times the values observed with CoAS-Ac, respectively. The CoA dithioesters are stable at low pH, but hydrolyze with a second-order rate constant of 8.2.10(-2) M-1.s-1 at pH 11.4. The spectral properties of these dithioesters should allow these analogs to be used as probes of the structure of enzyme bound intermediates.

Determination of urinary citrate by ion chromatography

Ion chromatography was used to determine urinary citrate concentration. The technique is simple, requiring a 100-fold dilution of urine and 35 minutes at most for each analysis. The technique does, however, have the disadvantage that it requires a rather expensive automated system. The minimum detectable limit for citrate was 0.5 microgram/ml. in a standard solution, and the regression line for the standard curve from 0.5 to 50 micrograms/ml. citrate had a significant correlation coefficient (lnY = 1.048 X lnX-2.755, r = 0.997). The intra-run coefficient of variation was 0.9 per cent. The overall intra-run and inter-run coefficients of variation, including the sampling and dilution of urine, were 4.8 and 8.3 per cent respectively. There is a possibility that another ion is close enough to the citrate peak to interfere; however, this problem can be solved by the treatment of the sample with citrate lyase. When the present method was compared with the conventional enzyme method, a significant correlation between the results was obtained in both human and rat urine. The 24-hour urinary citrate excretion in eight normal human males was 73.8 to 378.4 mg./day (mean, 174.7 mg./day), while that in male Wistar-strain rats (approximately 150 gm.) was 1.5 to 18.6 mg./day (mean, 9.5 mg./day), as measured in more than 50 consecutive rat urine samples.

Metabolic labeling of sialic acids in tissue culture cell lines: methods to identify substituted and modified radioactive neuraminic acids

The parent sialic acid N-acetylneuraminic acid can be modified or substituted in various ways, giving rise to a family of more than 25 compounds. The definitive identification of these compounds has previously required isolation of nanomole amounts for mass spectrometry or NMR. We have explored the possibility of using the known metabolic precursors of the sialic acids, particularly N-acetyl-[6-3H]mannosamine, to label and identify various forms of sialic acids in tissue culture cells. Firstly, we defined several variables that affect the labeling of sialic acids with N-acetyl-[6-3H]mannosamine. Secondly, we have devised a simple screening method to identify cell lines that synthesize substituted or modified sialic acids. We next demonstrate that it is possible to definitively identify the natures of the various labeled sialic acids without the use of mass spectrometry, even though they are present only in tracer amounts. The methods used include paper chromatography, analytical de-O-acetylation, periodate release of the 9-3H as [3H]formaldehyde (which is subsequently converted to a specific 3H-labeled chromophore), acylneuraminate pyruvate lyase treatment with identification of [3H]acylmannosamines, gas-liquid chromatography with radioactive detection, and two new high-pressure liquid chromatography methods utilizing the amine-adsorption:ion suppression and ion-pair principles. The use of an internal N-acetyl-[4-14C]neuraminic acid standard in each of these methods assures precision and accuracy. The combined use of these methods now allows the identification of radioactive tracer amounts of the various types of sialic acids in well-defined populations of tissue culture cells; it may also allow the identification of hitherto unknown forms of sialic acids.

Enzymatic-ultraviolet determination of L-citric acid in wine: collaborative study

A collaborative study was carried out on an enzymatic method for the determination of L-citric acid in wine, using the enzymes citrate lyase, malate dehydrogenase, and lactate dehydrogenase and the coenzyme nicotinamide-adenine dinucleotide phosphate. The study was performed by 18 laboratories using 4 blind duplicates of commercial wine. The method is simple and shows good precision. Coefficients of variation (CV) for reproducibility ranged from 1.8 to 3.4%; CVs for repeatability ranged from 0.76 to 2.62%. Analysts are cautioned to check the linear absorbance response of their spectrophotometers when performing this assay and also to take care in pipetting the relatively small volumes used in this procedure. The method has been adopted official first action.

Evidence from 13C NMR for polarization of the carbonyl of oxaloacetate in the active site of citrate synthase

The carbon-13 NMR spectrum of oxaloacetate bound in the active site of citrate synthase has been obtained at 90.56 MHz. In the binary complex with enzyme, the positions of the resonances of oxaloacetate are shifted relative to those of the free ligand as follows: C-1 (carboxylate), -2.5 ppm; C-2 (carbonyl), +4.3 ppm; C-3 (methylene), -0.6 ppm; C-4 (carboxylate), +1.3 ppm. The change observed in the carbonyl chemical shift is successively increased in ternary complexes with the product [coenzyme A (CoA)], a substrate analogue (S-acetonyl-CoA), and an acetyl-CoA enolate analogue (carboxymethyl-CoA), reaching a value of +6.8 ppm from the free carbonyl resonance. Binary complexes are in intermediate to fast exchange on the NMR time scale with free oxaloacetate; ternary complexes are in slow exchange. Line widths of the methylene resonance in the ternary complexes suggest complete immobilization of oxaloacetate in the active site. Analysis of line widths in the binary complex suggests the existence of a dynamic equilibrium between two or more forms of bound oxaloacetate, primarily involving C-4. The changes in chemical shifts of the carbonyl carbon indicate strong polarization of the carbonyl bond or protonation of the carbonyl oxygen. Some of this carbonyl polarization occurs even in the binary complex. Development of positive charge on the carbonyl carbon enhances reactivity toward condensation with the carbanion/enolate of acetyl-CoA in the mechanism which has been postulated for this enzyme. The very large change in the chemical shift of the reacting carbonyl in the presence of an analogue of the enolate of acetyl-CoA supports this interpretation.

An enzymatic method for the determination of enantiomeric composition and absolute configuration of deuterated or tritiated succinic acid

The distribution of hydrogen isotope between pro-R and pro-S positions of succinic acid has been determined by comparison of its isotopic content before and after incubation with isocitrate lyase. This enzyme, in the presence of glyoxylate, exchanges exclusively the pro-S protons of succinate with water (M. Sprecher, R. Berger, and D. B. Sprinson (1964) J. Biol. Chem. 239, 4268-4271). With [1-14C,2(R,S)-3H]succinate as substrate, the exchange was easily followed by the decrease of 3H/14C ratio (dried aliquots), which accounted for the high isotopic effect of this reaction. The final ratio was within +/- 5% of the theoretical one. The evolution of the exchange of deuterated succinate added with [1-14C,2(R,S)-3H]succinate acid was again followed by 3H/14C ratio. The deuterium content of [2,3-2H2]succinic acid, [2-2H2]succinic acid (derived from L-[4-2H2]glutamic acid by oxidation) and of the corresponding succinates isolated after incubation with isocitrate lyase was determined by gas chromatography-mass spectroscopy of their dimethylester under NH4+ chemical ionization. This method provides the basis for a quantitative measurement of the distribution of hydrogen isotopes in unsymmetrically 2-labeled succinate or 4-labeled glutamate.

A kit for citrate in foodstuffs adapted for assay of serum and urine

A kit method for rapid analysis of citrate in foodstuffs, based on use of citrate lyase (EC 4.1.3.6), has been adapted and evaluated for use with clinical samples. Membrane filters removed serum proteins, which interfere with the analysis, and reagent and sample volumes were decreased from those in the manufacturer's protocol, thereby decreasing the cost of the assay. Using gravimetrically prepared citrate standards, we determined that assay results varied linearly with concentration up to sixfold the upper reference limit for serum citrate. Intra- and interassay variation were within acceptable limits (CVs less than 3% and less than 8.5%, respectively). Kit reagents were stable for four weeks at -20 degrees C. Assay results were unaffected by hemolysis or other biochemical interferences. The method evidently provides a rapid, convenient microassay for citrate in clinical samples.

Amino acid sequence of Escherichia coli citrate synthase

Detailed evidence for the amino acid sequence of allosteric citrate synthase from Escherichia coli is presented. The evidence confirms all but 11 of the residues inferred from the sequence of the gene as reported previously [Ner, S. S., Bhayana, V., Bell, A. W., Giles, I. G., Duckworth, H. W., & Bloxham, D. P. (1983) Biochemistry 22, 5243]; no information has been obtained about 10 of these (residues 101-108 and 217-218), and we find aspartic acid rather than asparagine at position 10. Substantial regions of sequence homology are noted between the E. coli enzyme and citrate synthase from pig heart, especially near residues thought to be involved in the active site. Deletions or insertions must be assumed in a number of places in order to maximize homology. Either of two lysines, at positions 355 and 356, could be formally homologous to the trimethyllysine of pig heart enzyme, but neither of these is methylated. It appears that E. coli and pig heart citrate synthases are formed of basically similar subunits but that considerable differences exist, which must explain why the E. coli enzyme is hexameric and allosterically inhibited by NADH, while the pig heart enzyme is dimeric and insensitive to that nucleotide.

Mechanisms of domain closure in proteins

Certain enzymes respond to the binding of substrates and coenzymes by the closure of an active site that lies in a cleft between two domains. We have examined the mechanism of the domain closure in citrate synthase, for which atomic co-ordinates are available for "open" and "closed" forms. We show that the mechanism of domain closure involves small shifts and rotations of packed helices within the two domains and at their interface. Large motions of distant segments of the structure are the cumulative effect of the small relative shifts in intervening pairs of packed segments. These shifts are accommodated not by changes in packing but rather by small conformational changes in side-chains. We call this the helix interface shear mechanism of domain closure. The relative movements of packed helices follow the principles suggested by our recent study of insulin. This mechanism of domain closure is quite different from the hinge mechanisms that allow the rigid body movements of domains in immunoglobulins. The large interface between the domains of citrate synthase precludes a simple hinge mechanism for its conformational change. The helix interface shear mechanism of conformational change occurs in other enzymes that contain extensive domain-domain interfaces.

Crystal structure analysis and molecular model of a complex of citrate synthase with oxaloacetate and S-acetonyl-coenzyme A

The crystal structure of the complex of pig heart citrate synthase and oxaloacetate in the presence of the potent inhibitor S-acetonyl coenzyme A has been determined at a nominal resolution of 2.9 A by Patterson search techniques and refined by restrained crystallographic refinement. The complex crystallizes in the presence of polyvinylpyrrolidone in space group P4(3)2(1)2 with a = 101.5 A and c = 224.6 A, with one dimeric molecule of molecular weight 100,000 in the asymmetric unit. The crystallographic R factor is 0.194 for the 14,332 unique reflections between 6.0 and 2.9 A resolution. The structures of two forms of citrate synthase in the presence and absence of product molecules have been determined recently and shown to differ in the relative arrangement of the large and small domains ("closed" and "open" forms). The third crystal form described here is also closed, but there is substantial rearrangement within the small domain relative to either of the other crystal forms. We conclude that this is a third structural state of the enzyme, and catalytic activity of the enzyme depends on structural changes during the course of the reaction affecting domain conformation also. The three structures are compared, and it is shown that the large domain is considerably more rigid than the small domain. The conformation of the small domain adapts to the ligand. The inhibitor, and the "coenzyme-A-binding segment" of the enzyme are disordered. No electron density is observed for the inhibitor, and only weak density for the coenzyme-A-binding segment. Electron density for oxaloacetate is well defined. It binds in a very similar manner to citrate.

A simple automated method for determination of citric acid levels in semen

An automated enzymatic method for determination of seminal citric acid by using an Abbott ABA-100 bichromic analyzer is presented. The technique recommended in this communication is a rapid and simple micromethod which does not require semen deproteinization and which has been optimized to provide satisfactory precision and accuracy.

Crystallographic studies of Escherichia coli citrate synthase

The citrate synthase from Escherichia coli B has been crystallized in a cubic space group with a unit cell spacing of 220 A. X-ray diffraction, electron microscopy, symmetry considerations, and low resolution projection Patterson syntheses are consistent with a model proposed in which 24 tetrameric molecules of Mr = 188,000 +/- 12,000 occupy the unit cell. The space group is apparently P23, although at low resolution the observed systematic absences in reflections are consistent with the space group P43n, a space group not allowed for asymmetric molecules. Estimates of VM suggest that in the true space group, P23, two tetrameric molecules occupy the asymmetric unit.

Complete amino acid sequence of porcine heart citrate synthase

The detailed proof of the 437-residue amino acid sequence (Mr 48,969) of porcine heart citrate synthase (EC 4.13.7) is described. The S-carboxymethylated protein has been cleaved at methionine (cyanogen bromide) and arginine (trypsin digest of citraconylated enzyme) residues to yield 14 and 17 major peptides, respectively. Peptides were initially fractionated by gel filtration, and those useful for sequence analysis were purified by high-performance liquid chromatography. Sequence analyses were performed on these primary peptides and on subpeptides generated by cleavage with the bromine adduct of 2-[(2-nitrophenyl)sulfenyl]-3-methylindole, Staphylococcus aureus V8 protease, trypsin, chymotrypsin, or acid. The overall sequence was confirmed by analyzing products of cleavage by hydroxylamine, acid, and subtilisin. A novel feature of the sequence is the identification of trimethyllysine at residue 368.

Enzymic determination of citrate in serum and urine, with use of the Worthington "ultrafree" device

We describe an enzymic method for conveniently measuring citrate in serum or urine. Interfering enzyme proteins are removed by a disposable ultrafilter ("Ultrafree"; Worthington Diagnostics), obviating the need for hazardous protein precipitants. A 50 mmol/L Tris buffer adequately controls pH, no lactate dehydrogenase is necessary in the reagents, and the reaction of citrate catalyzed by citrate lyase (EC 4.1.3.6) is complete in 2-3 min. Within-run and day-to-day coefficients of variation were 7.5% and 5.4%, respectively. Serum citrate concentrations for 20 apparently healthy persons ranged from 0.08 to 0.17 mmol/L (mean 0.12, SD 0.03). Urinary citrate excretion by six normal volunteers ranged from 2.2 to 4.4 mmol/24 h. We observed no detectable changes in citrate in whole blood stored at room temperature for 90 min or longer. Overall, the method is faster and less hazardous than other methods for citrate that require protein precipitation.

Primary structure of porcine heart citrate synthase

The sequence of 437 amino acid residues of porcine heart citrate synthase [citrate oxaloacetate-lyase (pro-3S-CH2COO leads to acetyl-CoA), EC 4. 1. 3. 7] has been determined by the alignment of fragments generated by cleavage with cyanogen bromide and with trypsin. Isolation of the peptides was facilitated by recent developments in the high-performance liquid chromatography of peptide mixtures. The alignment of these peptides was consistent with that previously deduced from fragments derived by restricted cleavage of citrate synthase by limited proteolysis and cleavage of aspartyl-prolyl bonds and asparaginyl-glycyl bonds. The enzyme contains a modified amino acid, trimethyllysine, at residue 368, showing that the enzyme is subjected to post-translational modification.

Thiamine deficiency and glyoxylic acid

The effect of thiamine deficiency on glyoxylic acid metabolism in mice and rats was investigated to determine whether the vitamin deficiency results in gross effects on glyoxylate levels via an alteration in the activity of alpha-ketoglutarate:glyoxylate carboligase. Thiamine-deprived or pyrithiamine-treated mice did not show a decreased oxidation of [1-14C]glyoxylate to respiratory CO2; there was some decrease in the conversion of [2-14C]glyoxylate into CO2 by pyrithiamine-treated mice, but not by thiamine-deprived animals. Dietary thiamine deprivation caused a decrease in carboligase levels in liver but no effect on levels in three brain regions. Pyrithiamine treatment had no significant effect on liver carboligase activities, but did decrease the levels in cerebrum, cerebellum and brainstem. Thiamine-deprived and pyrithiamine-treated mice showed decreased urinary glycolic acid excretion Glyoxylic acid excretion by thiamine-deprived rats was monitored in order to re-examine a previous report by another laboratory that glyoxyluria occurs under these conditions. Trace amounts of glyoxylate could be detected in the urine of rats fed thiamine-deficient diet for 3-5 weeks, but urinary glyoxylate was not detectable at later stages of thiamine deprivation. These results do not support a significant role for alpha-ketoglutarate:carboligase activity in the primary etiology of thiamine deficiency syndromes.

Enzymatic assay of serum sialic acid

Serum sialic acid has been assayed enzymatically. The reaction includes neuraminidase hydrolysis of glycoprotein, cleavage of sialic acid to pyruvate by N-acetyl neuraminic acid (NANA)-aldolase, oxidation of pyruvate by pyruvate oxidase which produces hydrogen peroxide, and colorimetry of hydrogen peroxide using the peroxidase-p-chlorophenol-4-amino-antipyrine method. This method showed good correlation between a chemical method (r = 0.984), good recovery (98.8%) and good reproducibility (within-run-precision: 1.0% C.V.; day-to-day precision: 1.9% C.V). Intrinsic serum pyruvate produces an equimolar positive effect. The normal value range is 1.94 +/- 0.29 mmol/l (mean +/- S.D.,n = 24).

Interaction of a paramagnetic analogue of oxaloacetate with citrate synthase

Electron paramagnetic resonance studies have indicated that nitrosodisulfonate binds to pig heart citrate synthase. Titration of the enzyme with nitrosodisulfonate revealed several binding sites for the probe per subunit with one site (KD approximately 0.1 mM) having a greater affinity than the others. The substrate, oxaloacetate, competed very effectively for one of the nitrosodisulfonate binding sites (KD less than 10(-2) mM) at the same time eliminating the weaker probe binding sites. Citrate and (R)- and (S)-malates also displaced the probe. Failure to resolve low- and high-field shoulder in the high gain--high modulation electron paramagnetic resonance spectra of the enzyme--nitrosodisulfonate system indicated that the bound probe was "weakly immobilized". However, the electron paramagnetic resonance spectrum of the bound probe changed to one typical of a "strongly immobilized" nitroxide upon the addition of a saturating concentration of the substrate acetyl coenzyme A (acetyl-CoA) to the enzyme--nitrosodisulfonate system, indicating the formation of a ternary acetyl-CoA-enzyme-probe complex. Titration of the acetyl-CoA saturated enzyme with the probe indicated one binding site per subunit (KD = 0.37 mM). Thus, nitrosodisulfonate may be considered as a paramagnetic analogue of oxaloacetate in its interaction with citrate synthase. These results are compared with our previous studies with this enzyme, employing a spin-labeled acyl coenzyme A (acyl-CoA) derivative [Weidman, S. W., Drysdale, G. R., & Mildvan, A. S. (1973) Biochemistry 12, 1874--1883].

Crystal structure analysis of the tetragonal crystal form are preliminary molecular model of pig-heart citrate synthase

The crystal structure of pig heart citrate synthase was analyzed at 0.35-nm resolution. Chain tracing was possible and an initial molecular model constructed. The dimensions of the dimer molecule (located on a crystallographic diad) are 7.5 x 6.0 x 9.0 nm. The chain folding is characterized by the predominance of helices and the absence of sheet structure. The electron density accounts for 355 residues per monomer, so that about 80 residues must be disordered in the crystal. The disordered segment in probably N-terminal. The ordered part consists of two closely associated domains, a large domain with 300 residues and a C-terminal domain of 55 residues consisting of 3(anti)parallel helices. The large domain is built from 12 helical segments, some of which are buried in the interior of the molecule. Inhibitor binding studies with citrate and CoA revealed citrate binding sites but showed no electron density for CoA. It is suggested that CoA binds to the disordered, flexible N-terminal domain. Experiments of limited proteolysis with trypsin showed that under conditions a segment of Mr 9000 is cleaved off selectively. The remaining 35 000-Mr part is dimeric.

Structural basis of the thermostability of monomeric malate synthase from a thermophilic Bacillus

Malate synthases from a thermophilic Bacillus and Escherichia coli have been isolated in a high state of purity. Molecular weights of these two proteins determined in the native state and after denaturation in sodium dodecyl sulfate-mercaptoethanol show that the enzymes are monomeric. This conclusion is supported, for the thermophile enzyme, by the result of an electrophoretic analysis of that protein after treatment with dimethylsuberimidate and denaturation. The thermophilic Bacillus malate synthase is considerably more thermostable than its mesophilic counterparts from E. coli, Bacillus licheniformis, and Pseudomonas indigofera. It is, however, markedly labilized by an increase in the ionic strength of the medium brought about by the addition of 0.2 M potassium chloride or in pH above 9. Increased ionic strength has little effect on the thermostability of the mesophilic bacterial malate synthases. These observations provide strong support for the idea that monomeric proteins in thermophiles owe their unusual heat stability to the presence of salt bridges in their tertiary structure.

Small-angle x-ray scattering on malate synthase from baker's yeast. Considerations on the effects of bound ligands

Binding of the substrates to the anisometric enzyme causes slight changes of some molecular parameters (Zipper and Durchschlag, Eur. J. Biochem., 1978). Estimations based on several plausible assumptions allow a separation of the experimentally observed effects into effects caused by the substrates or by the enzyme in the enzyme-substrate complexes or by binding of buffer molecules. The results show that the observed changes of molecular parameters are primarily due to structural changes in the enzyme molecule. From the changes in the radius of gyration upon substrate binding, the binding sites of the substrates may be localized to be at a radial distance of 5.3 nm from the centre of the enzyme particle. Binding of one or both of the substrates induces different structural changes of the enzyme particle. On formation of the [enzyme·acetyl-CoA], [enzyme·glyoxylate], or [enzyme·pyruvate] complexes, an increase of the short axis by 4.5 + 1% occurs, while the formation of the [enzyme·acetyl-CoA·pyruvate] complex does not change this axis significantly. A t the same time, binding of the substrates leads to a decrease of the long axes of the enzyme particle by 2.0 ± 0.2%, independent on the kind of the complex formed. These changes of the axes correspond to an increase of the axial ratio by 6.7 ± 1% on formation of the [enzyme·acetyl-CoA], [enzyme·glyoxylate], or [enzyme-pyruvate] complexes and by 2.7.% on formation of the [enzyme-acetyl·CoA·pyruvate] complex, i. e. in all cases to a decrease of anisometry of the enzyme particle.

Purification and properties of citrate lyase ligase from Streptococcus diacetilactis

Citrate lyase ligase (acetate: SH--[acyl-carrier protein] enzyme ligase (AMP) from Streptococcus diacetilactis was purified 920-fold with a yield of 6.3%. The molecular weight of the enzyme was estimated to be 41000; the ligase consisted of one polypeptide chain. The acetylation of 1 mol of deacetyl-citrate lyase to enzymatically active citrate lyase required 6 mol ATP. The formation of AMP and pyrophosphate in the acetylation reaction was demonstrated. Citrate lyase ligase was specific for the lyase from S. diacetilacitis and did not acetylate lyases from Rhodopseudomonas gelatinosa and Enterobacter aerogenes. The substract acetate and ATP could be replaced by propionate and dATP, repectively. The reaction rates for ATP, acetate and deacetyl-citrate lyase followed Michaelis-Menten kinetics (Km values: 26 micron for ATP, 25 mM for acetate and 38 nM for deacetyl-citrate lyase).

Sulfhydryl groups in relation to the structure and catalytic activity of 2-oxo-4-hydroxyglutarate aldolase from bovine liver

Bovine liver 2-oxo-4-hydroxyglutarate aldolase (suggested name: 2-oxo-4-hydroxyglutarate glyoxylate-lyase catalyzing the reaction: 2-oxo-4-hydroxyglutarate in equilibrium pyruvate + glyoxylate) contains eight to ten sulfhydryl groups as determined by titration of the enzyme with either 5,5'-dithiobis(2-nitrobenzoic acid) (Nbs2) or p-mercuribenzoate in the presence of 1% sodium dodecyl sulfate. In the absence of a denaturant, all of the cysteinyl residues react with p-mercuribenzoate whereas only four are accessible to titration with Nbs2. No differences in -SH group reactivity can be detected during titration of the aldolase with p-mercuribenzoate. In contrast, two classes of sulfhydryls can be differentiated in the disulfide exchange reaction with Nbs2 in the absence of a denaturant; one -SH group (Class I) reacts rapidly whereas three additional thiols (Class II) titrate at approx. 0.1 the rate of the Class I-SH residue. Both pyruvate and glyoxylate protect one of the three -SH residues in Class II from reaction with Nbs2. Either substrate also prevents titration of one to two thiol groups by p-mercuribenzoate and decreases the rate of reaction of aldolase -SH groups with Nbs2 in 8 M urea. These ligand-induced changes in -SH reactivity provide a sensitive indication that the enzyme exists in an altered conformational state in the presence of either of its cosubstrates. Titration of the enzyme with either Nbs2 or p-mercuribenzoate results in a progressive loss of aldolase activity which is not proportional to the number of -SH groups modified. The enzyme retains 50% of the activity of the native enzyme when Class I and Class II thiols (i.e. four -SH groups total) are modified with Nbs2; 15% residual activity is still observed following titration of all of the cysteinyl residues with p-mercuribenzoate. Pyruvate and glyoxylate provide partial protection against inactivation. It is concluded that inactivation of 2-oxo-4-hydroxyglutarate aldolase by Nbs2 or p-mercuribenzoate is a consequence of alterations in protein structure which accompany modification of -SH groups. The data argue against the direct participation of an active-site thiol group in the catalytic mechanism of 2-oxo-4-hydroxyglutarate aldolase, be that aldol cleavage and condensation or beta-decarboxylation.

A method for enzymatic determination of citrate in serum and urine

A method for determination of citrate in serum and urine using citrate lyase is described. The influence of pH, zinc, magnesium, and calcium ions on the reaction velocity is studied. Citrate lyase activity is found rather insensitive to variations in pH round the pH-optimum at 8.2. Zinc ions activate the reactions. The optimal concentration of zinc ions in the reaction mixture is found to depend on the calcium concentration of samples. Perchloric acid is used for precipitation of proteins. The perchloric ion inhibits the reaction, and a procedure for removing perchlorate is given. Sensitivity of analysis is 0.005 mmo1/1 for serum and urine samples, respectively. No contamination of citrate lyase is found, and therefore addition of lactate dehydrogenase is considered unneccessary.

Inactivation of bovine liver 2-keto-4-hydroxyglutarate aldolase by cyanide in the presence of aldehydes

Kinetic data show that the irreversible inactivation of liver 2-keto-4-hydroxyglutarate aldolase observed when the enzyme is incubated with an aldehydic substrate (or substrate analogue) in the presence of cyanide is a biphasic process and can, under certain conditions, involve a direct interaction between the enzyme and cyanide. The kinetic data are consistent with a scheme consisting of three competing reactions: (1) irreversible addition of cyanide to the enzyme-substrate Schiff base intermediate, (2) reversible cyanohydrin formation between cyanide and the aldehydic substrate (or substrate analogue), and (3) an interaction of cyanide with the enzyme which is not substrate dependent. Approximately 0.4 mol of cyanide is associated with 1 mol (120 000 g) of enzyme when 2-keto-4-hydroxyglutarate aldolase is incubated with [14-C]-cyanide followed by exhaustive dialysis; an ionic attachment possibly at a carboxylate binding site, is suggested. Whereas native enzyme, not treated with cyanide, has ten Nbs2-titratable sulfhydryl groups, approximately one less such group reacts with Nbs2 when the aldolase is incubated with cyanide (in the absence of aldehydic substrate). It is suggested that the binding of cyanide results in a conformational change of the enzyme; conformational changes in the presence of cyanide are confirmed by circular dichroism spectra.