Pentitol phosphate dehydrogenases: Discovery, characterization and use in D-arabitol and xylitol production by metabolically engineered Bacillus subtilis

The ultimate goal of this study has been to construct metabolically engineered microbial strains capable of fermenting glucose into pentitols D-arabitol and, especially, xylitol. The path that was chosen to achieve this goal required discovery, isolation and sequencing of at least two pentitol phosphate dehydrogenases of different specificity, followed by cloning and expression of their genes and characterization of recombinant arabitol and xylitol phosphate dehydrogenases. An enzyme of a previously unknown specificity, D-arabitol phosphate dehydrogenase (APDH), was discovered in Enterococcus avium. The enzyme was purified to homogenity from E. avium strain ATCC 33665. SDS/PAGE revealed that the enzyme has a molecular mass of 41 ± 2 kDa, whereas a molecular mass of 160 ± 5 kDa was observed under non-denaturing conditions implying that the APDH may exist as a tetramer with identical subunits. Purified APDH was found to have narrow substrate specificity, converting only D-arabitol 1-phosphate and D-arabitol 5-phosphate into D-xylulose 5-phosphate and D-ribulose 5-phosphate, respectively, in the oxidative reaction. Both NAD+ and NADP+ were accepted as co-factors. Based on the partial protein sequences, the gene encoding APDH was cloned. Homology comparisons place APDH within the medium chain dehydrogenase family. Unlike most members of this family, APDH requires Mn2+ but no Zn2+ for enzymatic activity. The DNA sequence surrounding the gene suggests that it belongs to an operon that also contains several components of phosphotransferase system (PTS). The apparent role of the enzyme is to participate in arabitol catabolism via the arabitol phosphate route similar to the ribitol and xylitol catabolic routes described previously. Xylitol phosphate dehydrogenase (XPDH) was isolated from Lactobacillus rhamnosus strain ATCC 15820. The enzyme was partially sequenced. Amino acid sequences were used to isolate the gene encoding the enzyme. The homology comparisons of the deduced amino acid sequence of L. rhamnosus XPDH revealed several similar enzymes in genomes of various species of Gram-positive bacteria. Two enzymes of Clostridium difficile and an enzyme of Bacillus halodurans were cloned and their substrate specificities together with the substrate specificity of L. rhamnosus XPDH were compared. It was found that one of the XPDH enzymes of C. difficile and the XPDH of L. rhamnosus had the highest selectivity towards D-xylulose 5-phosphate. A known transketolase-deficient and D-ribose-producing mutant of Bacillus subtilis (ATCC 31094) was further modified by disrupting its rpi (D-ribose phosphate isomerase) gene to create D-ribulose- and D-xylulose-producing strain. Expression of APDH of E. avium and XPDH of L. rhamnosus and C. difficile in D-ribulose- and D-xylulose-producing strain of B. subtilis resulted in strains capable of converting D-glucose into D-arabitol and xylitol, respectively. The D-arabitol yield on D-glucose was 38 % (w/w). Xylitol production was accompanied by co-production of ribitol limiting xylitol yield to 23 %.

Magnetic behaviour in metal-organic frameworks-Some recent examples

The article describes the synthesis, structure and magnetic investigations of a series of metal-organic framework compounds formed with Mn+2 and Ni+2 ions. The structures, determined using the single crystal X-ray diffraction, indicated that the structures possess two- and three-dimensional structures with magnetically active dimers, tetramers, chains, two-dimensional layers connected by polycarboxylic acids. These compounds provide good examples for the investigations of magnetic behaviour. Magnetic studies have been carried out using SQUID magnetometer in the range of 2-300 K and the behaviour indicates a predominant anti-ferromagnetic interactions, which appears to differ based on the M-O-C-O-M and/or the M-O-M (M = metal ions) linkages. Thus, compounds with carboxylate (Mn-O-C-O-Mn) connected ones, [C3N2H [Mn(H2O)''C6H3(COO)(3)''], I, [''Mn(H2O (3)''aEuroeC(12)H(8)O(COO)(2)'']center dot H2O, II, [''Mn(H2O)''aEuroeC(12)H(8)O(COO)(2)''], III, show simple anti-ferromagnetic behaviour. The compounds with Mn-O/OH-Mn connected dimer and tetramer units in [NaMn''C6H3(COO)(3)''], IV, [Mn-2(A mu(3)-OH) (H2O)(2)''C6H3(COO)(3)'']center dot 2H(2)O, V, show canted-antiferromagnetic and anti-ferromagnetic behaviour, respectively. The presence of infinite one-dimensional -Ni-OH-Ni- chains in the compound, [Ni-2(H2O)(A mu(3)-OH)(2)(C8H5NO4], VI, gives rise to ferromagnet-like behaviour at low temperatures. The compounds, [Mn-3''C6H3(COO)(3)''(2)], VII and [''Mn(OH)''(2)''C12H8O(COO)(2)''], VIII, have two-dimensional infinite -Mn-O/OH-Mn- layers with triangular magnetic lattices, which resemble the Kagome and brucite-like layer. The magnetic studies indicated canted-antiferromagnetic behaviour in both the cases. Variable temperature EPR and theoretical magnetic modelling studies have been carried out on selected compounds to probe the nature of the magnetic species and their interactions with them.

Insight into the early stages of thermal unfolding of peanut agglutinin by molecular dynamics simulations

Peanut agglutinin is a homotetrameric nonglycosylated protein. The protein has a unique open quaternary structure. Molecular dynamics simulations have been employed follow the atomistic details of its unfolding at different temperatures. The early events of the deoligomerization of the protein have been elucidated in the present study. Simulation trajectories of the monomer as well as those of the tetramer have been compared and the tetramer is found to be substantially more stable than its monomeric counterpart. The tetramer shows retention of most of its.. secondary structure but considerable loss of the tertiary structure at high temperature. e generation of a This observation impies the molten globule-like intermediate in the later stages of deoligomerization. The quaternary structure of the protein has weakened to a large extent, but none of the subunits are separated. In addition, the importance of the metal-binding to the stability of the protein structure has also been investigated. Binding of the metal ions not only enhances the local stability of the metal-ion binding loop, but also imparts a global stability to the overall structure. The dynamics of different interfaces vary significantly as probed through interface clusters. The differences are substantially enhanced at higher temperatures. The dynamics and the stability of the interfaces have been captured mainly by cluster analysis, which has provided detailed information on the thermal deoligomerization of the protein.

Thermodynamic analysis of three state denaturation of Peanut Agglutinin

Peanut Agglutinin (PNA) is a homotetrameric protein with a very unusual open quaternary structure. During denaturation, it first dissociates into a molten globule like state, which subsequently undergoes complete denaturation. Urea denaturation of PNA at neutral pH has been studied by intrinsic fluorescence spectroscopy and has been fitted to a three state model, A(4) double left right arrow 4I double left right arrow 4U, to get all the relevant thermodynamic parameters. Urea denaturation leads to continuous red shift of wavelength maxima. The molten globule like state is formed in a short range of urea concentration. Refolding of the denatured PNA has been attempted by intrinsic fluorescence study. Refolding by instantaneous dilution shows the occurrence of the formation of an intermediate at a relatively rapid rate, within few seconds. The transition from PNA tetramer to molten globule like state is found to have a Delta G value of similar to 33 kcal/mole while it is similar to 8 kcal/mole for the transition from molten globule like state to a completely denatured state. This in turn indicates that the tetramerization in PNA contributes significantly to the stability of the oligomer.

Thermodynamics of monosaccharide binding to concanavalin A, pea (Pisum sativum) lectin, and lentil (Lens culinaris) lectin

Titration calorimetry measurements of the binding of methyl alpha-D-mannopyranoside (Me alpha Man), D-mannopyranoside (Man), methyl alpha-D-glucopyranoside (Me alpha Glu), and D-glucopyranoside (Glu) to concanavalin A (Con A), pea lectin, and lentil lectin were performed at 281 and 292 K in 0.01 M dimethylglutaric acid-NaOH buffer (pH 6.9) containing 0.15 M NaCl and Mn+2 and Ca+2 ions. The site binding enthalpies, delta H, are the same at both temperatures and range from -28.4 +/- 0.9 (Me alpha Man) to -16.6 +/- 0.5 kJ mol-1 (Glu) for Con A, from -26.2 +/- 1.1 (Me alpha Man) to -12.8 +/- 0.4 kJ mol-1 (Me alpha Glu) for pea lectin, and from -16.6 +/- 0.7 (Me alpha Man) to -8.0 +/- 0.2 kJ mol-1 (Me alpha Glu) for lentil lectin. The site binding constants range from 17 +/- 1 x 10(3) M-1 (Me alpha Man to Con A at 281.2 K) to 230 +/- 20 M-1 (Glu to lentil lectin at 292.6 K) and exhibit high specificity for Con A where they are in the Me alpha Man:Man:Me alpha Glu:Glu ratio of 21:4:5:1, while the corresponding ratio is 5:2:1.5:1 for pea lectin and 4:2:2:1 for lentil lectin. The higher specificity for Con A indicates more interactions between the amino acid residues at the binding site and the carbohydrate ligand than for the pea and lentil lectin-carbohydrate complexes. The carbohydrate-lectin binding results exhibit enthalpy-entropy compensation in that delta Hb (kJ mol-1) = -1.67 +/- 0.06 x 10(4) + (1.30 +/- 0.12)T(K) delta Sb (J mol-1K-1). Differential scanning calorimetry measurements on the thermal denaturation of the lectins and their carbohydrate complexes show that the Con A tetramer dissociates into monomers, while the pea and lentil lectin dimers dissociate into two submonomer fragments. At the denaturation temperature, one carbohydrate binds to each monomer of Con A and the pea and lentil lectins. Complexation with the carbohydrate increases the denaturation temperature of the lectin and the magnitude of the increases yield binding constants in agreement with the determinations from titration calorimetry.

Crystallization and preliminary X-ray crystallographic analysis of a galactose-specific lectin from Dolichos lablab

The galactose-specific lectin from the seeds of Dolichos lablab has been crystallized using the hanging-drop vapour-diffusion technique. The crystals belong to space group P1, with unit-cell parameters a = 73.99, b = 84.13, c = 93.15 angstrom, alpha = 89.92, beta = 76.01, gamma = 76.99 degrees. X-ray diffraction data to a resolution of 3.0 angstrom have been collected under cryoconditions ( 100 K) using a MAR imaging-plate detector system mounted on a rotating-anode X-ray generator. Molecular-replacement calculations carried out using the available structures of legume lectins as search models revealed that the galactose-specific lectin from D. lablab forms a tetramer similar to soybean agglutinin; two such tetramers are present in the asymmetric unit.

X-ray and molecular-dynamics studies on Mycobacterium leprae single-stranded DNA-binding protein and comparison with other eubacterial SSB structures

The crystal structures of two forms of Mycobacterium leprae single-stranded DNA-binding protein (SSB) have been determined at 2.05 and 2.8 A resolution. Comparison of these structures with the structures of other eubacterial SSBs indicates considerable variation in their quaternary association, although the DNA-binding domains in all of them exhibit the same OB-fold. This variation has no linear correlation with sequence variation, but could be related to variation in protein stability. Molecular-dynamics simulations have been carried out on tetrameric molecules derived from the two forms and the prototype Escherichia coli SSB and the individual subunits of both proteins. Together, the X-ray studies and molecular-dynamics simulations yield information on the relatively rigid and flexible regions of the molecule and on the effect of oligomerization on flexibility. The simulations provide insight into the changes in subunit structure on oligomerization. They also provide insight into the stability and time evolution of the hydrogen bonds/water bridges that connect the two pairs of monomers in the tetramer.

Studies on nucleotidases in plants: Fluorescence and kinetic properties of nucleotide pyrophosphatase from mung bean (Phaseolus aureus) seedlings

Nucleotide pyrophosphatase of mung bean seedlings has earlier been isolated in our laboratory in a dimeric form (Mr 65,000) and has been shown to be converted to a tetramer by AMP and to a monomer by p-hydroxymercuribenzoate. All the molecular forms were enzymatically active with different kinetic properties. By a modified procedure using blue-Sepharose affinity chromatography, we have now obtained a dimeric form of the enzyme which is desensitized to AMP interaction. The molecular weight of the desensitized form of the enzyme was found to be the same as that of the native dimeric enzyme. However, the desensitized enzyme functioned with a linear time course, contrary to the biphasic time course exhibited by the native enzyme. In addition, it was not converted to a tetramer on the addition of AMP, had only one binding site for adenine nucleotides, and p-hydroxy-mercuribenzoate had no effect on the time course of the reaction or on the molecular weight of the enzyme. The temperature optimum of the desensitized enzyme was found to be 67 °C in contrast to the optimum of 49 °C for the native dimer. Fifty percent of the tryptophan residues of the desensitized enzyme were not accessible for quenching by iodide. Fluorescence studies gave Kd values of 0.34, 2.2, and 0.8 mImage for AMP, ADP, and ATP, which were close to the Ki values of 0.12, 2.2, and 0.9 mImage , respectively, for these nucleotides. The binding and inhibition studies with AMP and its analogs showed that the 6-amino group and the 5′-phosphate group were essential for the inhibition of the enzyme activity.

Purification and characterization of an extracellular β-glucosidase from the thermophilic fungus Sporotrichum thermophile and its influence on cellulase activity

Multiple forms of beta-glucosidase (EC 3.2.1.21) of Sporotrichum thermophile were produced when the fungus was grown in a cellulose medium. One beta-glucosidase was purified 16-fold from 6-d-old culture filtrates by ion-exchange and gel-filtration chromatography. The purified enzyme was free of cellulase activity. It hydrolysed aryl beta-D-glucosides and beta-D-linked diglucosides. It was optimally active at pH 5.4, at 65-degrees-C. The apparent K(m) values for p-nitrophenyl beta-D-glucoside (PNPG) and cellobiose were 0.29 and 0.83 mm, respectively. Glucose, fucose, nojirimycin and gluconolactone inhibited beta-glucosidase competitively. At high (> 1 mm) substrate concentration, beta-glucosidase catalysed a parallel transglycosylation reaction. The transglycosylation product formed from cellobiose appeared to be a beta-linked tetramer of glucose. Admixtures of beta-glucosidase and cellulase components showed that the concept of cellobiose inhibition of cellulases was not valid for all components of the cellulase system of S. thermophile. Beta-Glucosidase supplementation also stimulated cellulose hydrolysis by cellulases when there was no accumulation of cellobiose in reaction mixture.

Variations in the copper(I)-copper(I) distances in multinuclear clusters with identical coordination geometries. Short metal-metal contacts induced by oligomerization

Factors contributing to the variations in the Cu(I)-Cu(I) distances in two clusters with identical ligand and coordination geometries have been analyzed. While the hexamer, 4, exhibits metal-metal distances in the range 2.81-3.25 Angstrom, shorter contacts are found in the corresponding tetramer, 3 (2.60-2.77 Angstrom). EHT calculations reveal relatively little attractive interactions in the corresponding Cu-4(4+) and Cu-6(6+) cores. Introduction of the ligands lowers the reduced overlap populations between the metals further. MNDO calculations with model electrophiles have been carried out to determine the bite angle requirements of the ligands. These are satisfactorily met in the structures of both 3 and 4. The key geometric feature distinguishing 3 and 4 is the Cu-S-Cu angle involving the bridging S- unit. In 4, the corresponding angles are about 90 degrees, while the values in 3 are smaller (70-73 degrees). Wider angles are computed to be energetically favored and are characterized by an open three-center bond and a long Cu-Cu distance. The bridging angles are suggested to be primarily constrained by the mode of oligomerization. Implications of these results for the stability and reactivity of these clusters and for short metal-metal distances in d(10) systems in general are discussed.

Lanthanide Sulfate Frameworks: Synthesis, Structure, and Optical Properties

Layered lanthanide sulfate compounds with three different structures have been prepared and characterized. The compounds C10H10N2] La(SO4)(2)]center dot 2H(2)O (I), C10H10N2] La(SO4)(2)(H2O)(2)](2) (Ha), C10H10N2]Pr(SO4)(2)(H2O)(2)](2) (IIb), C10H10N2]Nd-2(SO4)(4)(H2O)(2)](2) (IIIa), C10H10N2]Sm-2(SO4)(4)(H2O)(2)](2) (IIIb), and C10H10N2]Eu-2(SO4)(4)(H2O)(2)] 2 (IIIC) have anionic lanthanide sulfate layers separated by protonated bipyridine molecules. The layers are formed by the connectivity between the lanthanide polyhedra and sulfate tetrahedra. The formation of a two-dimensional La-O-La layer (la), Pr-O-Pr chains (IIb), and a tetramer cluster (IIIa) is noteworthy. The compounds exhibit honeycomb (I), square (IIa, IIb), and honeycomb (IIIa-IIIc) net arrangements, when the connectivity between the lanthanide ions is considered. Optical studies indicate the observation of characteristic metal-centered emission at room temperature. The Nd compound (IIIa) exhibits a two-photon upconversion behavior.

The role of lysine-256 in the structure and function of sheep liver recombinant serine hydroxymethyltransferase

The active site lysine residue, K256, involved in Schiffs base linkage with pyridoxal-5'-phosphate (PEP) in sheep liver recombinant serine hydroxymethyltransferase (rSHMT) was changed to glutamine or arginine by site-directed mutagenesis. The purified K256Q and K256R SHMTs had less than 0.1% of catalytic activity with serine and H(4)folate as substrates compared to rSHMT. The mutant enzymes also failed to exhibit the characteristic visible absorbance spectrum (lambda(max) 425 nm) and did not produce the quinonoid intermediate (lambda(max) 495 nm) upon the addition of glycine and H(4)folate. The mutant enzymes were unable to catalyze aldol cleavage of beta-phenylserine and transamination of D-alanine. These results suggested that the mutation of the lysine had resulted in the inability of the enzyme to bind to the cofactor. Therefore, the K256Q SHMT was isolated as a dimer and the K256R SHMT as a mixture of dimers and tetramers which were converted to dimers slowly. On the other hand, rSHMT was stable as a tetramer for several months, further confirming the role of PLP in maintenance of oligomeric structure. The mutant enzymes also failed to exhibit the increased thermal stability upon the addition of serine, normally observed with rSHMT. The enhanced thermal stability has been attributed to a change in conformation of the enzyme from open to closed form leading to reaction specificity. The mutant enzymes were unable to undergo this conformational change probably because of the absence of bound cofactor.

Probing the limits of steric constraints in the oligomerization of copper(I) complexes: structures of two sterically congested oligomers

Oligomeric copper(I) clusters are formed by the insertion reaction of copper(I) aryloxides into heterocumulenes. The effect of varying the steric demands of the heterocumulene and the aryloxy group on the nuclearity of the oligomers formed has been probed. Reactions with copper(I)2-methoxyphenoxide and copper(I)2-methylphenoxide with PhNCS result in the formation of hexameric complexes hexakis[N-phenylimino(aryloxy)methanethiolato copper(I)] 3 and 4 respectively. Single crystal X-ray data confirmed the structure of 3. Similar insertion reactions of CS2 with the copper(I) aryloxides formed by 2,6-di-tert-butyl-4-methylphenol and 2,6-dimethylphenol result in oligomeric copper(I) complexes 7 and 8 having the (aryloxy)thioxanthate ligand. Complex 7 was confirmed to be a tetramer from single crystal X-ray crystallography. Reactions carried out with 2-mercaptopyrimidine, which has ligating properties similar to N-alkylimino(aryloxy)methanethiolate, result in the formation of an insoluble polymeric complex 11. The fluorescence spectra of oligomeric complexes are helpful in determining their nuclearity. Ir has been shown that a decrease in the steric requirements of either the heterocumulene or aryloxy parts of the ligand can compensate for steric constraints acid facilitate oligomerization. (C) 1999 Elsevier Science Ltd. All rights reserved.

Supramolecular hydrogen-bonded structures in organic amine squarates

Structures of monohydrogen squarates of methylamine, ethylenediamine, 1,3-diaminopropane, 1,4-diaminobutane, 1,5-diaminopentane, N,N'-diemethylpiperazine and N,N,N,N-tetramethylguanidine have been studied in detail. The supramolecular hydrogen-bonded molecular networks are formed by the monoanion of squaric acid by itself or in association with the parent acid. Three types of hydrogen-bonded motifs are observed in these compounds, namely a liner chain, a cyclic dimer and a cyclic tetramer. These hydrogen-bonded motifs formed by the squaric acid species interact with the amine through N-H...O hydrogen-bonding and give rise to predominantly layered structures, while some of them also exhibit three-dimensional structures. Two of the monohydrogen squarate structures also exhibit pi-pi interactions between two squarate rings. The various hydrogen-bonding parameters in the amine squarates are discussed at length. (C) 2002 Elsevier Science B.V. All rights reserved.

Conformational changes of the chaperone SecB upon binding to a model substrate - bovine pancreatic trypsin inhibitor (BPTI)

SecB is a homotetrameric cytosolic chaperone that forms part of the protein translocation machinery in E. coli. Due to SecB, nascent polypeptides are maintained in an unfolded translocation-competent state devoid of tertiary structure and thus are guided to the translocon. In vitro SecB rapidly binds to a variety of ligands in a non-native state. We have previously investigated the bound state conformation of the model substrate bovine pancreatic trypsin inhibitor (BPTI) as well as the conformation of SecB itself by using proximity relationships based on site-directed spin labeling and pyrene fluorescence methods. It was shown that SecB undergoes a conformational change during the process of substrate binding. Here, we generated SecB mutants containing but a single cysteine per subunit or an exposed highly reactive new cysteine after removal of the nearby intrinsic cysteines. Quantitative spin labeling was achieved with the methanethiosulfonate spin label (MTS) at positions C97 or E90C, respectively. Highfield (W-band) electron paramagnetic resonance (EPR) measurements revealed that with BPTI present the spin labels are exposed to a more polar/hydrophilic environment. Nanoscale distance measurements with double electron-electron resonance (DEER) were in excellent agreement with distances obtained by molecular modeling. Binding of BPTI also led to a slight change in distances between labels at C97 but not at E90C. While the shorter distance in the tetramer increased, the larger diagonal distance decreased. These findings can be explained by a widening of the tetrameric structure upon substrate binding much like the opening of two pairs of scissors.