Kinetic and magnetic resonance studies of the role of metal ions in the mechanism of Escherichia coli GDP-mannose mannosyl hydrolase, an unusual nudix enzyme

Escherichia coli GDP-mannose mannosyl hydrolase (GDPMH), a homodimer, catalyzes the hydrolysis of GDP-alpha-D-sugars to yield the beta-D-sugar and GDP by nucleophilic substitution with inversion at the C1' carbon of the sugar [Legler, P. M., Massiah, M. A., Bessman, M. J., and Mildvan, A. S. (2000) Biochemistry 39, 8603-8608]. GDPMH requires a divalent cation for activity such as Mn2+ or Mg2+, which yield similar kcat values of 0.15 and 0.13 s(-1), respectively, at 22 degrees C and pH 7.5. Kinetic analysis of the Mn2+-activated enzyme yielded a K(m) of free Mn2+ of 3.9 +/- 1.3 mM when extrapolated to zero substrate concentration (K(a)Mn2+), which tightened to 0.32 +/- 0.18 mM when extrapolated to infinite substrate concentration (K(m)Mn2+). Similarly, the K(m) of the substrate extrapolated to zero Mn2+ concentration (K(S)(GDPmann) = 1.9 +/- 0.5 mM) and to infinite Mn2+ concentration (K(m)(GDPmann) = 0.16 +/- 0.09 mM) showed an order of magnitude decrease at saturating Mn2+. Such mutual tightening of metal and substrate binding suggests the formation of an enzyme-metal-substrate bridge complex. Direct Mn2+ binding studies, monitoring the concentration of free Mn2+ by EPR and of bound Mn2+ by its enhanced paramagnetic effect on the longitudinal relaxation rate of water protons (PRR), detected three Mn2+ binding sites per enzyme monomer with an average dissociation constant (K(D)) of 3.2 +/- 1.0 mM, in agreement with the kinetically determined K(a)Mn2+. The enhancement factor (epsilon(b)) of 11.5 +/- 1.2 indicates solvent access to the enzyme-bound Mn2+ ions. No cross relaxation was detected among the three bound Mn2+ ions, suggesting them to be separated by at least 10 A. Such studies also yielded a weak dissociation constant for the binary Mn2+-GDP-mannose complex (K1 = 6.5 +/- 1.0 mM) which significantly exceeded the kinetically determined K(m) values of Mn2+, indicating the true substrate to be GDP-mannose rather than its Mn2+ complex. Substrate binding monitored by changes in 1H-15N HSQC spectra yielded a dissociation constant for the binary E-GDP-mannose complex (K(S)(GDPmann)) of 4.0 +/- 0.5 mM, comparable to the kinetically determined K(S) value (1.9 +/- 0.5 mM). To clarify the metal stoichiometry at the active site, product inhibition by GDP, a potent competitive inhibitor (K(I) = 46 +/- 27 microM), was studied. Binding studies revealed a weak, binary E-GDP complex (K(D)(GDP) = 9.4 +/- 3.2 mM) which tightened approximately 500-fold in the presence of Mn2+ to yield a ternary E-Mn2+-GDP complex with a dissociation constant, K3(GDP) = 18 +/- 9 microM, which overlaps with the K(I)(GDP). The tight binding of Mn2+ to 0.7 +/- 0.2 site per enzyme subunit in the ternary E-Mn2+-GDP complex (K(A)' = 15 microM) and the tight binding of GDP to 0.8 +/- 0.1 site per enzyme subunit in the ternary E-Mg2+-GDP complex (K3 < 0.5 mM) indicate a stoichiometry close to 1:1:1 at the active site. The decrease in the enhancement factor of the ternary E-Mn2+-GDP complex (epsilon(T) = 4.9 +/- 0.4) indicates decreased solvent access to the active site Mn2+, consistent with an E-Mn2+-GDP bridge complex. Fermi contact splitting (4.3 +/- 0.2 MHz) of the phosphorus signal in the ESEEM spectrum established the formation of an inner sphere E-Mn2+-GDP complex. The number of water molecules coordinated to Mn2+ in this ternary complex was determined by ESEEM studies in D2O to be two fewer than on the average Mn2+ in the binary E-Mn2+ complexes, consistent with bidentate coordination of enzyme-bound Mn2+ by GDP. Kinetic, metal binding, and GDP binding studies with Mg2+ yielded dissociation constants similar to those found with Mn2+. Hence, GDPMH requires one divalent cation per active site to promote catalysis by facilitating the departure of the GDP leaving group, unlike its homologues the MutT pyrophosphohydrolase, which requires two, or Ap4A pyrophosphatase, which requires three.     

Stereospecific ring opening of conduritol-B-epoxide by an active site asparatate residue of sucrase-isomaltase

Conduritol-B-epoxide inactivates sucrase-isomaltase (sucrose alpha-glucohydrolase, EC 3.2.1.48-dextrin 6-alpha-glucohydrolase, EC 3.2.1.10) irreversibly with incorporation of 1 mol inhibitor/mol subunit, the affinity label being bound in both subunits to a beta-carboxyl group of an aspartic acid (Quaroni, A. and Semnza; G. (1976) J. Biol. Chem. 251, 3250-3253). Conduritol-B-epoxide is a racemic mixture of 1-L-1,2-anhydro-myo-inositol and 1-D-1,2-anhydro-myo-inositol, but only the latter one is the reactive component, since 1-L-1,2-anhydro-myo-inositol alone did not inactivate the enzyme. After inactivation by 1-D-1,2-anhydro-myo-inositol the label was released by hydroxylamine and identified as scyllo-inositol. One can decide now which C atom of the epoxide ring has been attacked by the enzyme's aspartate residue. This explains why only the D-enantiomer is the reactive species and provides further information about the role of the carboxylate residue during enzymic hydrolysis.     

Perchlorate and nitrate remediation efficiency and microbial diversity in a containerized wetland bioreactor

We have developed a method to remove perchlorate (14-27 microg/L) and nitrate (48 mg/L) from contaminated groundwater using a wetland bioreactor. The bioreactor has operated continuously in a remote field location for more than 2 yr with a stable ecosystem of indigenous organisms. This study assesses the bioreactorfor long-term perchlorate and nitrate remediation by evaluating influent and effluent groundwater for oxidation-reduction conditions and nitrate and perchlorate concentrations. Total community DNA was extracted and purified from 10-g sediment samples retrieved from vertical coring of the bioreactor during winter. Analysis by denaturing gradient gel electrophoresis of short, 16S rDNA, polymerase-chainreaction products was used to identify dominant microorganisms. Bacteria genera identified were closely affiliated with bacteria widely distributed in soils, mud layers, and fresh water. Of the 17 dominant bands sequenced, most were gram negative and capable of aerobic or anaerobic respiration with nitrate as the terminal electron acceptor (Pseudomonas, Acinetobacter, Halomonas, and Nitrospira). Several identified genera (Rhizobium, Acinetobactor, and Xanthomonas) are capable of fixing atmospheric nitrogen into a combined form (ammonia) usable by host plants. Isolates were identified from the Proteobacteria class, known for the ability to reduce perchlorate. Initial bacterial assessments of sediments confirm the prevalence of facultative anaerobic bacteria capable of reducing perchlorate and nitrate in situ.     

Biochemical and genetic evidence of benzylsuccinate synthase in toluene-degrading,ferric iron-reducing Geobacter metallireducens

In vitro assays demonstrated that toluene-grown cells of Geobacter metallireducens catalyzed the addition of toluene to fumarate to form benzylsuccinate under anaerobic conditions. The specific in vitro rate of benzylsuccinate formationwas ca. 45% of the specific in vivo rate of toluene consumption. In addition, bssA and bssB, which code for the and subunits of benzylsuccinate synthase (BSS), respectively, were found to have sequences in G. etallireducens similar to the only sequences heretofore available (for three denitrifying strains). This is the first report of the presence of BSS in a ferriciron-reducing bacterium; BSS activity has previously been reported in denitrifying, sulfate-reducing, and anoxygenic phototrophic toluene degraders, as well as in a highly enriched methanogenic, toluene-degrading culture.     

GDP-mannose mannosyl hydrolase catalyzes nucleophilic substitution at carbon, unlike all other Nudix hydrolases

GDP-mannose mannosyl hydrolase (GDPMH) from Escherichia coli is a 36. 8 kDa homodimer which, in the presence of Mg(2+), catalyzes the hydrolysis of GDP-alpha-D-mannose or GDP-alpha-D-glucose to yield sugar and GDP. On the basis of its amino acid sequence, GDPMH is a member of the Nudix family of enzymes which catalyze the hydrolysis of nucleoside diphosphate derivatives by nucleophilic substitution at phosphorus. However, GDPMH has a sequence rearrangement (RE to ER) in the conserved Nudix motif and is missing a Glu residue characteristic of the Nudix signature sequence. By (1)H NMR, the initial hydrolysis product of GDP-alpha-D-glucose is beta-D-glucose, indicating nucleophilic substitution with inversion at C1' of glucose. Substitution at carbon was confirmed by two-dimensional (1)H-(13)C HSQC spectra of the products of hydrolysis in 48.4% (18)O-labeled water which showed an additional C1' resonance of beta-D-glucose with a typical upfield (18)O isotope shift of 18 ppb and an intensity of 47.6% of the total signal. No (18)O isotope-shifted resonances (<4%) were found in the (31)P NMR spectrum of the GDP product. Thus, unlike all other Nudix enzymes studied so far, GDPMH catalyzes nucleophilic substitution at carbon rather than at phosphorus. A small solvent kinetic deuterium isotope effect on k(cat) of 1.76 +/- 0.25, independent of pH over the range of 6.0-9.3, suggests that the deprotonation of water may be part of the rate-limiting step.     

Active site directed inhibition of a cytosolic beta-glucosidase from calf liver by bromoconduritol B epoxide and bromoconduritol F

Hydrolysis of p-nitrophenyl-beta-D-glucoside by cytosolic beta-glucosidase proceeds with retention of the anomeric configuration. Whereas inactivation of the enzyme by the glucosidase inhibitor conduritol B epoxide (CBE) was extremely slow (ki(max)/Ki 0.57 M-1 min-1) it reacted 130 times more rapidly with 6-bromo-6-deoxy-CBE (Br-CBE). The beta-glucosidase could be labeled with [3H]Br-CBE; incorporation of 1 mol inhibitor/mol enzyme resulted in complete loss of activity. Most of the bound inhibitor was released after denaturation and treatment with ammonia as (1,3,4/2,5,6)-6-bromocyclohexanepentol, thus demonstrating the formation of an ester bond with an active site carboxylate by trans-diaxial opening of the epoxide ring. It was concluded from the Ki values for the epoxide inhibitors and for coduritol B with the cytosolic enzyme and corresponding data for the lysosomal beta-glucosidase that the unusually low reactivity with CBE and Br-CBE is probably due to the inability of the cytosolic enzyme to effectively donate a proton to the epoxide oxygen. An extremely rapid inactivation of the cytosolic beta-glucosidase was caused by bromoconduritol F ((1,2,4/3)-1-bromo-2,3,4-trihydroxycyclohex-5-ene) with ki(max)/Ki 10(5) M-1 min-1. In contrast with the Br-CBE-inhibited enzyme the beta-glucosidase inhibited by bromoconduritol F was subject to spontaneous reactivation with t1/2 approximately 20 min.     

Multimode sensors as new tools for molecular recognition of testosterone,dihydrotestosterone and estradiol in children's saliva

Increased levels of testosterone (T₂), dihydrotestosterone (DHT) and estradiol (E₂) in children may be responsible for their early/delayed puberty and obesity conditions. Therefore, multimode sensors based on carbon matrices, such as graphite, graphene, fullerene C₆₀ and multiwall carbon nanotubes modified with maltodextrin, were designed to assess reliably T₂, DHT and E₂ in children saliva. The modes used for the assay of hormones were stochastic mode (for qualitative and quantitative determination of hormones) and differential pulse voltammetry mode (for quantitative determination of hormones). The advantage of this type of sensors, for hormone analysis, is their possibility to reach low concentration levels— are placed for children saliva under the detection limit of standard methods (e.g. ELISA used for the determination of these hormones in saliva). This made the multimode sensors an excellent tool for clinical analysis and especially for determination of substances of clinical importance in saliva samples. The proposed method is fast and simple, and no sampling of saliva is required. Copyright © 2014 John Wiley & Sons, Ltd.     

Standardizing the analysis of conditioned fear in rodents: a multidimensional software approach

Data comparability between different laboratories strongly depends on the individually applied analysis method. This factor is often a critical source of variation in rodent phenotyping and has never been systematically investigated in Pavlovian fear conditioning paradigms. In rodents, fear is typically quantified in terms of freezing duration via manual observation or automated systems. While manual analysis includes biases such as tiredness or inter‐personal scoring variability, computer‐assisted systems are unable to distinguish between freezing and immobility. Consequently, the novel software called MOVE follows a semi‐automatized approach that prefilters video sequences of interest for the final human judgment. Furthermore, MOVE allows integrating additional data sources (e.g. force‐sensitive platform, EEG) to reach the most accurate and precise results. MOVE directly supports multi‐angle video recordings with webcams or standard laboratory equipment. The integrated manual key logger and internal video player complement this all‐in‐one software solution. Calculating the interlaboratory variability of manual freezing evaluation revealed significantly different freezing scores in two out of six laboratories. This difference was minimized when all experiments were analyzed with MOVE. Applied to a genetically modified mouse model, MOVE revealed higher fear responses of CB1 deficient mice compared to their wild‐type littermates after foreground context fear conditioning. Multi‐angle video analysis compared to the single‐camera approach reached up to 15% higher accuracy and two fold higher precision. Multidimensional analysis provided by integration of additional data sources further improved the overall result. We conclude that the widespread usage of MOVE could substantially improve the comparability of results from different laboratories.     

Introduction of a disulfide bond leads to stabilization and crystallization of a ricin immunogen

RTA1-33/44-198 is a catalytically inactive, single-domain derivative of the ricin toxin A-chain (RTA) engineered to serve as a stable protein scaffold for presentation of native immunogenic epitopes (Olson et al., Protein Eng Des Sel 2004;17:391-397). To improve the stability and solubility of RTA1-33/44-198 further, we have undertaken the design challenge of introducing a disulfide (SS) bond. Nine pairs of residues were selected for placement of the SS-bond based on molecular dynamics simulation studies of the modeled single-domain chain. Disulfide formation at either of two positions (R48C/T77C or V49C/E99C) involving a specific surface loop (44-55) increased the protein melting temperature by ~5°C compared with RTA1-33/44-198 and by ~13°C compared with RTA. Prolonged stability studies of the R48C/T77C variant (> 60 days at 37°C, pH 7.4) confirmed a > 40% reduction in self-aggregation compared with RTA1-33/44-198 lacking the SS-bond. The R48C/T77C variant retained affinity for anti-RTA antibodies capable of neutralizing ricin toxin, including a monoclonal that recognizes a human B-cell epitope. Introduction of either R48C/T77C or V49C/E99C promoted crystallization of RTA1-33/44-198, and the X-ray structures of the variants were solved to 2.3 A or 2.1 A resolution, respectively. The structures confirm formation of an intramolecular SS-bond, and reveal a single-domain fold that is significantly reduced in volume compared with RTA. Loop 44 to 55 is partly disordered as predicted by simulations, and is positioned to form self-self interactions between symmetry-related molecules. We discuss the importance of RTA loop 34 to 55 as a nucleus for unfolding and aggregation, and draw conclusions for ongoing structure-based minimalist design of RTA-based immunogens.