Substrate deactivation of phenylalanine-sensitive 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase by erythrose 4-phosphate.

3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS, EC 4.1.2.15) catalyzes the condensation of phosphoenolpyruvate (PEP) with erythrose 4-phosphate (E4P) to give DAH7P via an ordered sequential mechanism. In the absence of PEP (the first substrate to bind), E4P binds covalently to the phenylalanine-sensitive DAH7PS of Escherichia coli, DAH7PS(Phe), deactivating the enzyme. Activity is restored on addition of excess PEP but not if deactivation was carried out in the presence of sodium cyanoborohydride. Electrospray mass spectrometry indicates that a single E4P is bound to the protein. These data are consistent with a slow, reversible Schiff base reaction of the aldehydic functionality of E4P with a buried lysine. Molecular modeling indicates that Lys186, a residue at the base of the substrate-binding cavity involved in hydrogen bonding with PEP, is well placed to react with E4P forming an imine linkage that is substantially protected from solvent water.     

A new erythrose 4-phosphate dehydrogenase coupled assay for transketolase

The standard assay for transketolase (E.C 2.2.1.1) has depended upon the use of d-xylulose 5-phosphate as the ketose donor substrate since the production of d-glyceraldehyde 3-phosphate can be readily coupled to a reaction that consumes NADH allowing the reaction to be followed spectrophotometrically. Unfortunately, commercial supplies of d-xylulose 5-phosphate recently became unavailable. In this article we describe the coupling of a transketolase reaction (using Leishmania mexicana transketolase) that converts d-fructose 6-phosphate to d-erythrose 4-phosphate. d-Erythrose 4-phosphate can then be converted to 4-phosphate d-erythronate using erythrose-4-phosphate dehydrogenase (E.C 1.2.1.72), a reaction that reduces NAD⁺ to NADH and can be easily followed spectrophotometrically. d-Ribose 5-phosphate and d-glyceraldehyde 3-phosphate can both be used as ketol acceptor substrates in the reaction although d-ribose 5-phosphate is also a substrate for the coupling enzyme.     

Characterization of Aspergillus niger phosphoglucose isomerase. Use for quantitative determination of erythrose 4-phosphate.

Phosphoglucose isomerase (PGI) was purified from Aspergillus niger and the in vitro kinetic properties of the enzyme were related to its functioning in vivo. A new assay method was developed to study the forward reaction making use of mannitol 1-P dehydrogenase as the coupling enzyme. In this simple assay system mannitol 1-P dehydrogenase converts fructose 6-P and NADH to mannitol 1-P and NAD+, respectively. At pH 7.5 the Km for glucose 6-P was 0.48 mM, whereas the Km for fructose 6-P was 0.32 mM. The pentose phosphate pathway intermediates 6-phosphogluconate and erythrose 4-P (E4P) were competitive inhibitors of PGI with Ki values of approximately 0.2 mM and 1 microM respectively. In citric acid producing A. niger mycelium inhibition by 6-phosphogluconate is of minor physiological significance (10% inhibition). Since E4P could not be detected by an existing procedure, a novel assay was developed based on the strong inhibition of PGI by E4P. Although the new assay is very sensitive (detection limit 25 pmol), E4P could still not be detected in metabolite extracts indicating that a very low level of E4P is present in the cells. Using in vitro kinetics and concentrations of intracellular metabolites the in vivo activity of PGI was calculated and closely matched the steady state glycolytic flux observed during citric acid production.     

Competitive inhibition of spinach leaf phosphoglucose isomerase isoenzymes by erythrose 4-phosphate

In plant cells, the reversible isomerization between fructose 6-phosphate (Fru6P) and glucose 6-phosphate (Glc6P) is catalyzed by a cytosolic and a chloroplastic isoenzyme of phosphoglucose isomerase (PGI, EC 5.3.1.9). The extractable activities of both PGI isoenzymes are in large excess compared with the flux required for product synthesis, but the measured Glu6P/Fru6P ratio in illuminated chloroplasts and in whole leaves is always displaced from equilibrium. Cytosolic (PGI 2) and stromal (PGI 1) isoenzymes were purified from spinach leaves and used to investigate the possibility of metabolic regulation at this step. Several metabolites were found to inhibit PGI, but within the physiological concentration range, only erythrose 4-phosphate (Ery4P) inhibited significantly. The inhibition was competitive, with K_i values below 10 μM for PGI 2 and 1. The physiological significance of the inhibition of PGI by Ery4P was assessed in isolated intact spinach chloroplasts. We conclude that, in vivo, this inhibition is probably responsible for the observed displacement from equilibrium in the chloroplasts, but limits the carbon flow towards starch synthesis only when Fru6P is low. In contrast, the inhibition by Ery4P is unlikely to play any role in the cytosolic carbon metabolism because both Fru6P concentration and PGI activity, are much higher than in the chloroplast stroma.     

Biochemical characterization of gapB-encoded erythrose 4-phosphate dehydrogenase of Escherichia coli K-12 and its possible role in pyridoxal 5'-phosphate biosynthesis.

One step in de novo pyridoxine (vitamin B6) and pyridoxal 5'-phosphate biosynthesis was predicted to be an oxidation catalyzed by an unidentified D-erythrose-4-phosphate dehydrogenase (E4PDH). To help identify this E4PDH, we purified the Escherichia coli K-12 gapA- and gapB-encoded dehydrogenases to homogeneity and tested whether either uses D-erythrose-4-phosphate (E4P) as a substrate. gapA (gap1) encodes the major D-glyceraldehyde-3-phosphate dehydrogenase (GA3PDH). The function of gapB (gap2) is unknown, although it was suggested that gapB encodes a second form of GA3PDH or is a cryptic gene. We found that the gapB-encoded enzyme is indeed an E4PDH and not a second GA3PDH, whereas gapA-encoded GA3PDH used E4P poorly, if at all, as a substrate under the in vitro reaction conditions used in this study. The amino terminus of purified E4PDH matched the sequence predicted from the gapB DNA sequence. Purified E4PDH was a heat-stable tetramer with a native molecular mass of 132 kDa. E4PDH had an apparent Km value for E4P [Kmapp(E4P)] of 0.96 mM, an apparent kcat catalytic constant for E4P [kcatapp(E4P)] of 200 s-1, Kmapp(NAD+) of 0.074 mM, and kcatapp(NAD+) of 169 s-1 in steady-state reactions in which NADH formation was determined. From specific activities in crude extracts, we estimated that there are at least 940 E4PDH tetramer molecules per bacterium growing in minimal salts medium plus glucose at 37 degrees C. Thin-layer chromatography confirmed that the product of the E4PDH reaction was likely the aldonic acid 4-phosphoerythronate. To establish a possible role of E4PDH in pyridoxal 5'-phosphate biosynthesis, we showed that 4-phosphoerythronate is a likely substrate for the 2-hydroxy-acid dehydrogenase encoded by the pdxB gene. Implications of these findings in the evolution of GA3PDHs are also discussed. On the basis of these results, we propose renaming gapB as epd (for D-erythrose-4-phosphate dehydrogenase).     

Investigating the role of the hydroxyl groups of substrate erythrose 4-phosphate in the reaction catalysed by the first enzyme of the shikimate pathway

3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAH7P) synthase catalyses the first step of the shikimate pathway, which is responsible for the biosynthesis of aromatic amino acids in microorganisms and plants. This enzyme catalyses an aldol reaction between phosphoenolpyruvate and D-erythrose 4-phosphate to generate DAH7P. Both 2-deoxyerythrose 4-phosphate and 3-deoxyerythrose 4-phosphate were synthesised and tested as alternative substrates for the enzyme. Both compounds were found to be substrates for the DAH7P synthases from Escherichia coli, Pyrococcus furiosus and Mycobacterium tuberculosis, consistent with an acyclic mechanism for the enzyme for which neither C2 nor C3 hydroxyl groups are required for catalysis. The enzymes all showed greater tolerance for the loss of the C2 hydroxyl group than the C3 hydroxyl group.     

Dimerization of the insulin-like growth factor II/mannose 6-phosphate receptor

The insulin-like growth factor II/mannose 6-phosphate receptor (IGF2R) interacts with lysosomal enzymes through two binding domains in its extracytoplasmic domain. We report in the accompanying article (Byrd, J. C., and MacDonald, R. G. (2000) J. Biol. Chem. 275, 18638-18646) that only one of the two extracytoplasmic mannose 6-phosphate (Man-6-P) binding domains is necessary for high affinity Man-6-P ligand binding, suggesting that, like the cation-dependent Man-6-P receptor, oligomerization of the IGF2R contributes to high affinity interaction with lysosomal enzymes. In the present study, we have directly characterized both naturally occurring and engineered forms of the IGF2R for their ability to form oligomeric structures. Whereas gel filtration chromatography suggested that purified bovine IGF2R species exist in a monomeric form, native gel electrophoresis allowed for the separation of dimeric and monomeric forms of the receptors with distinct phosphomannosyl ligand binding characteristics. The ability of the IGF2R to form oligomeric complexes was confirmed and localized to the extracytoplasmic domain through the use of epitope-tagged soluble IGF2R constructs bearing deletions of the transmembrane and cytoplasmic domains. Finally, chimeric receptors were engineered containing the extracytoplasmic and transmembrane domains of the IGF2R fused to the cytoplasmic domain of the epidermal growth factor receptor with which dimerization of the chimeras could be monitored by measuring autophosphorylation. Collectively, these results show that the IGF2R is capable of forming oligomeric complexes, most likely dimers, in the absence of Man-6-P ligands.     

SUMO Chain-Induced Dimerization Activates RNF4

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Computational study of mutarotation in erythrose and threose

For the first time the mutarotation mechanism of furanose rings has been investigated, with and without solvent. The transformations from open-chain furanose to d-erythrose and d-threose have been studied at B3LYP/6-311++G(d,p) and G3MP2B3 levels, in vacuum and in solution through continuum solvation models. We studied the catalytic influence of one, two or three water molecules, as well as simplified models of carbohydrates, that is, methanol and 1,2-ethanediol. Water molecules significantly reduce the energy barrier of the hemiacetal formation occurring between the open-chain and furanose configurations. The energy barrier is optimally reduced by two water molecules. Methanol yields a smaller transition state barrier than the one obtained with a single water molecule. In contrast, 1,2-ethanediol does not provide a lower transition state compared to the barrier in the presence of two water molecules.     

Inhibition of ribose-5-phosphate isomerase by 4-phosphoerythronate.

Hoping to exploit the special affinity of enzymes for unstable intermediates in substrate transformation, we have determined the effectiveness of possible analogs of ene-diolate intermediates as inhibitors of spinach ribose-5-phosphate isomerase. 4-Phosphoerythronic acid was found to be a very strong competitive inhibitor, with a Ki value almost 3 orders of magnitude lower than the Km value of ribose 5-phosphate, and very much lower than the Ki value of any other inhibitor that was examined.     

Dimerization of mammalian adenylate cyclases.

Mammalian adenylate cyclases are predicted to possess complex topologies, comprising two cassettes of six transmembrane-spanning motifs followed by a cytosolic, catalytic ATP-binding domain. Recent studies have begun to provide insights on the tertiary assembly of these proteins; crystallographic analysis has revealed that the two cytosolic domains dimerize to form a catalytic core, while more recent biochemical and cell biological analysis shows that the two transmembrane cassettes also associate to facilitate the functional assembly and trafficking of the enzyme. The older literature had suggested that adenylate cyclases might form higher order aggregates, although the methods used did not necessarily provide convincing evidence of biologically relevant events. In the present study, we have pursued this question by a variety of approaches, including rescue or suppression of function by variously modified molecules, coimmunoprecipitation and fluorescence resonance energy transfer (FRET) analysis between molecules in living cells. The results strongly suggest that adenylate cyclases dimerize (or oligomerize) via their hydrophobic domains. It is speculated that this divalent property may allow adenylate cyclases to participate in multimeric signaling assemblies.     

Dimerization of phospholipase d isozymes.

Two mammalian phospholipase D (PLD) isozymes (PLD1 and PLD2) have been reported. In this study, we differentially tagged these isozymes with enhanced green fluorescent protein (EGFP-rPLD1 and EGFP-rPLD2) or Xpress peptide epitope (Xpress-rPLD1 and Xpress-rPLD2) to examine the association between these isozymes. Overexpressed EGFP-rPLD1 coimmunoprecipitated with Xpress-rPLD1 using anti-Xpress antibody. However, the coimmunoprecipitation was independent of the activity of rPLD1. Xpress-rPLD2 also bound to EGFP-rPLD1 although the binding was less efficient than observed with Xpress-rPLD1. The association between rPLD2 and rPLD1 was confirmed by coimmunoprecipitation of EGFP-rPLD2 with Xpress-rPLD1. EGFP-rPLD2 also bound to Xpress-rPLD2 as shown by coimmunoprecipitation. Immunofluorescence staining of COS-7 cells coexpressing EGFP-rPLDs and Xpress-rPLDs showed that the PLD isozymes colocalized in the perinuclear and plasma membrane regions, suggesting that they could associate in a cellular setting. These results suggest that rPLD1 and rPLD2 can exist as homodimers and can form heterodimers.     

Mechanism of enzymic isomerization and epimerization of D-erythrose 4-phosphate.

The mechanism of the enzymic isomerization and epimerization of D-erythrose 4-phosphate (Ery4P) by an enzyme preparation from bovine liver was investigated with the use of 2H2O. The incorporation of 2H was quantitatively determined by a procedure using gas chromatography-mass spectrometry. About one atom of 2H was incorporated per molecule of the enzymic epimerization reaction product of Ery4P (D-threose 4-phosphate) or that of D-ribulose 5-phosphate. Computer simulation of the Ery4P isomerization reaction indicated that the 2H of 2H2O was not directly incorporated into the enzymic reaction product (D-erythrulose 4-phosphate). Instead, intramolecular transfer of hydrogen atoms had occurred.     

Dimerization of SLX4 contributes to functioning of the SLX4-nuclease complex

The Fanconi anemia protein SLX4 assembles a genome and telomere maintenance toolkit, consisting of the nucleases SLX1, MUS81 and XPF. Although it is known that SLX4 acts as a scaffold for building this complex, the molecular basis underlying this function of SLX4 remains unclear. Here, we report that functioning of SLX4 is dependent on its dimerization via an oligomerization motif called the BTB domain. We solved the crystal structure of the SLX4_BTB dimer, identifying key contacts (F681 and F708) that mediate dimerization. Disruption of BTB dimerization abrogates nuclear foci formation and telomeric localization of not only SLX4 but also of its associated nucleases. Furthermore, dimerization-deficient SLX4 mutants cause defective cellular response to DNA interstrand crosslinking agent and telomere maintenance, underscoring the contribution of BTB domain-mediated dimerization of SLX4 in genome and telomere maintenance.     

An enyzmic method for the analysis of D-erythrose 4-phosphate.

Two modifications of an enzymic method for the measurement of erythrose 4-phosphate, based on reactions catalyzed by transketolase, are described. Unlike the method generally employed, the new procedure is sensitive and highly specific and applicable to the assay of erythrose 4-phosphate in tissue extracts.     

Immunochemical characterization of phosphatidylinositol 4-phosphate kinase from rat brain.

Affinity-purified antibodies were used to identify a protein of molecular mass 45 kDa (45 kDa protein) in rat brain cytosol as phosphatidylinositol 4-phosphate (PtdIns4P) kinase. Antibodies were raised in rabbits by immunization with the purified 45 kDa protein. Anti-(45 kDa protein) immunoglobulins were isolated by affinity chromatography of the antiserum on a solid immunosorbent, which was prepared by coupling a soluble rat brain fraction, the DEAE-cellulose pool containing 10-15% 45 kDa protein, to CNBr-activated Sepharose 4B. The purified IgGs were specific for the 45 kDa protein as judged by immunoblot and by immunoprecipitation. The purified anti-(45 kDa protein) IgGs inhibited the enzyme activity of partially purified PtdIns4P kinase, whereas preimmune IgGs were ineffective. Immunoprecipitation of the 45 kDa protein from the partially purified enzyme preparation with the purified IgGs resulted in a concomitant decrease in the amount of 45 kDa protein and in PtdIns4P kinase activity. The amount of 45 kDa protein remaining in the supernatant and the activity of PtdIns4P kinase correlated with a coefficient of r = 0.87. The evidence presented lends further support for the notion that the catalytic activity of PtdIns4P kinase in rat brain cytosol resides in a 45 kDa protein.