Structure of the adenylation domain of an NAD+-dependent DNA ligase

Background: DNA ligases catalyse phosphodiester bond formation between adjacent bases in nicked DNA, thereby sealing the nick. A key step in the catalytic mechanism is the formation of an adenylated DNA intermediate. The adenyl group is derived from either ATP (in eucaryotes and archaea) or NAD+4 (in bacteria). This difference in cofactor specificity suggests that DNA ligase may be a useful antibiotic target.

Results: The crystal structure of the adenylation domain of the NAD+-dependent DNA ligase from Bacillus stearothermophilus has been determined at 2.8 Å resolution. Despite a complete lack of detectable sequence similarity, the fold of the central core of this domain shares homology with the equivalent region of ATP-dependent DNA ligases, providing strong evidence for the location of the NAD+-binding site.

Conclusions: Comparison of the structure of the NAD+4-dependent DNA ligase with that of ATP-dependent ligases and mRNA-capping enzymes demonstrates the manifold utilisation of a conserved nucleotidyltransferase domain within this family of enzymes. Whilst this conserved core domain retains a common mode of nucleotide binding and activation, it is the additional domains at the N terminus and/or the C terminus that provide the alternative specificities and functionalities in the different members of this enzyme superfamily.

Divergence of chemical function in the alkaline phosphatase superfamily: Structure and mechanism of the P-C bond cleaving enzyme phosphonoacetate hydrolase

Phosphonates constitute a class of natural products that mimic the properties of the more common organophosphate ester metabolite yet are not readily degraded owing to the direct linkage of the phosphorus atom to the carbon atom. Phosphonate hydrolases have evolved to allow bacteria to utilize environmental phosphonates as a source of carbon and phosphorus. The work reported in this paper examines one such enzyme, phosphonoacetate hydrolase. By using a bioinformatic approach, we circumscribed the biological range of phosphonoacetate hydrolase to a select group of bacterial species from different classes of Proteobacteria. In addition, using gene context, we identified a novel 2-aminoethylphosphonate degradation pathway in which phosphonoacetate hydrolase is a participant. The X-ray structure of phosphonoformate-bound phosphonoacetate hydrolase was determined to reveal that this enzyme is most closely related to nucleotide pyrophosphatase/diesterase, a promiscuous two-zinc ion metalloenzyme of the alkaline phosphatase enzyme superfamily. The X-ray structure and metal ion specificity tests showed that phosphonoacetate hydrolase is also a two-zinc ion metalloenzyme. By using site-directed mutagenesis and P-32-labeling strategies, the catalytic nucleophile was shown to be Thr64. A structure-guided, site-directed mutation-based inquiry of the catalytic contributions of active site residues identified Lys126 and Lys128 as the most likely candidates for stabilization of the aci-carboxylate dianion leaving group. A catalytic mechanism is proposed which combines Lys12/Lys128 leaving group stabilization with zinc ion activation of the Thr64 nucleophile and the substrate phosphoryl group.

The role of the active site residues in human galactokinase: implications for the mechanisms of GHMP kinases.

Galactokinase catalyses the phosphorylation of galactose at the expense of ATP. Like other members of the GHMP family of kinases it is postulated to function through an active site base mechanism in which Asp-186 abstracts a proton from galactose. This asparate residue was altered to alanine and to asparagine by site-directed mutagenesis of the corresponding gene. This resulted in variant enzyme with no detectable galactokinase activity. Alteration of Arg-37, which lies adjacent to Asp-186 and is postulated to assist the catalytic base, to lysine resulted in an active enzyme. However, alteration of this residue to glutamate abolished activity. All the variant enzymes, except the arginine to lysine substitution, were structurally unstable (as judged by native gel electrophoresis in the presence of urea) compared to the wild type. This suggests that the lack of activity results from this structural instability, in addition to any direct effects on the catalytic mechanism. Computational estimations of the pK(a) values of the arginine and aspartate residues, suggest that Arg-37 remains protonated throughout the catalytic cycle whereas Asp-186 has an abnormally high pK(a) value (7.18). Quantum mechanics/molecular mechanics (QM/MM) calculations suggest that Asp-186 moves closer to the galactose molecule during catalysis. The experimental and theoretical studies presented here argue for a mechanism in which the C-1-OH bond in the sugar is weakened by the presence of Asp-186 thus facilitating nucleophilic attack by the oxygen atom on the gamma-phosphorus of ATP.

Evidence To Challenge the Universality of the Horiuti-Polanyi Mechanism for Hydrogenation in Heterogeneous Catalysis:Origin and Trend of the Preference of a Non-Horiuti-Polanyi Mechanism

The Horiuti-Polanyi mechanism has been considered to be universal for explaining the mechanisms of hydrogenation reactions in heterogeneous catalysis for several decades. In this work, we examine this mechanism for the hydrogenation of acrolein, the simplest alpha,beta-unsaturated aldehyde, in gold-based systems as well as some other metals using extensive first-principles calculations. It is found that a non-Horiuti-Polanyi mechanism is favored in some cases. Furthermore, the physical origin and trend of this mechanism are revealed and discussed regarding the geometrical and electronic effects, which will have a significant influence on current understandings on heterogeneous catalytic hydrogenation reactions and the future catalyst design for these reactions.

Facet-Dependent Catalytic Activity of Platinum Nanocrystals for Triiodide Reduction in Dye-Sensitized Solar Cells

Platinum (Pt) nanocrystals have demonstrated to be an effective catalyst in many heterogeneous catalytic processes. However, pioneer facets with highest activity have been reported differently for various reaction systems. Although Pt has been the most important counter electrode material for dye-sensitized solar cells (DSCs), suitable atomic arrangement on the exposed crystal facet of Pt for triiodide reduction is still inexplicable. Using density functional theory, we have investigated the catalytic reaction processes of triiodide reduction over {100}, {111} and {411} facets, indicating that the activity follows the order of Pt(111) > Pt(411) > Pt(100). Further, Pt nanocrystals mainly bounded by {100}, {111} and {411} facets were synthesized and used as counter electrode materials for DSCs. The highest photovoltaic conversion efficiency of Pt(111) in DSCs confirms the predictions of the theoretical study. These findings have deepened the understanding of the mechanism of triiodide reduction at Pt surfaces and further screened the best facet for DSCs successfully.

Understanding catalytic reactions over zeolites: A density functional theory study of selective catalytic reduction of NOX by NH3 over Cu-SAPO-34

Metal exchanged CHA-type (SAPO-34 and SSZ-13) zeolites are promising catalysts for selective catalytic reduction (SCR) of NOx by NH3. However, the understanding of the process at the molecular level is still limited, which hinders the identification of its mechanism and the design of more efficient zeolite catalysts. In this work, modelling the reaction over Cu-SAPO-34, a periodic density functional theory (DFT) study of NH3-SCR was performed using hybrid functional with the consideration of van der Waals (vdW) interactions. A mechanism with a low N–N coupling barrier is proposed to account for the activation of NO. The redox cycle of Cu2+ and Cu+, which is crucial for the SCR process, is identified with detailed analyses. Besides, the decomposition of NH2NO is shown to readily occur on the Brønsted acid site by a hydrogen push-pull mechanism, confirming the collective efforts of Brønsted acid and Lewis acid (Cu2+) sites. The special electronic and structural properties of Cu-SAPO-34 are demonstrated to play an essential role the reaction, which may have a general implication on the understanding of zeolite catalysis.

Catalytic Water Formation on Platinum: A First-Principles Study

The study of catalytic behavior begins with one seemingly simple process, namely the hydrogenation of O to H2O on platinum. Despite the apparent simplicity its mechanism has been much debated. We have used density functional theory with,gradient corrections to examine microscopic reaction pathways for several elementary steps implicated in this fundamental catalytic process. We find that H2O formation from chemisorbed O and H atoms is a highly activated process. The largest barrier along this route, with a value of similar to1 eV, is the addition of the first H to O to produce OH. Once formed, however, OH groups are easily hydrogenated to H2O with a barrier of similar to0.2 eV. Disproportionation reactions with 1:1 and 2:1 stoichiometries of H2O and O have been examined as alternative routes for OH formation. Both stoichiometries of reaction produce OH groups with barriers that are much lower than that associated with the O + H reaction. H2O, therefore, acts as an autocatalyst in the overall H O formation process. Disproportionation with a 2:1 stoichiometry is thermodynamically and kinetically favored over disproportionation with a l:I stoichiometry. This highlights an additional (promotional) role of the second H2O molecule in this process. In support of our previous suggestion that the key intermediate in the low-temperature H2O formation reaction is a mixed OH and H2O overlayer we find that then is a very large barrier for the dissociation of the second H2O molecule in the 2:1 disproportionation process. We suggest that the proposed intermediate is then hydrogenated to H2O through a very facile proton transfer mechanism.

State defining experiment in chemical kinetics. Primary characterization of catalyst activity in a TAP experiment

This paper presents a new strategy, “state-by-state transient screening”, for kinetic characterization of states of a multicomponent catalyst as applied to TAP pulse-response experiments. The key idea is to perform an insignificant chemical perturbation of the catalytic system so that the known essential characteristics of the catalyst (e.g. oxidation degree) do not change during the experiment. Two types of catalytic substances can be distinguished: catalyst state substances, which determine the catalyst state, and catalyst dynamic substances, which are created by the perturbation. The general methodological and theoretical framework for multi-pulse TAP experiments is developed, and the general model for a one-pulse TAP experiment is solved. The primary kinetic characteristics, basic kinetic coefficients, are extracted from diffusion–reaction data and calculated as functions of experimentally measured exit-flow moments without assumptions regarding the detailed kinetic mechanism. The new strategy presented in this paper provides essential information, which can be a basis for developing a detailed reaction mechanism. The theoretical results are illustrated using furan oxidation over a VPO catalyst.

Structure and kinetics of phosphonopyruvate hydrolase from Variovorax sp. Pal2: New insight into the divergence of catalysis within the PEP mutase/isocitrate lyase superfamily .

Phosphonopyruvate (P-pyr) hydrolase (PPH), a member of the phosphoenolpyruvate (PEP) mutase/isocitrate lyase (PEPM/ICL) superfamily, hydrolyzes P-pyr and shares the highest sequence identity and functional similarity with PEPM. Recombinant PPH from Variovorax sp. Pal2 was expressed in Escherichia coli and purified to homogeneity. Analytical gel filtration indicated that the protein exists in solution predominantly as a tetramer. The PPH pH rate profile indicates maximal activity over a broad pH range.The steady-state kinetic constants determined for a rapid equilibrium ordered kinetic mechanism with Mg+2 binding first (Kd =140 ± 40 M), are kcat = 105 ± 2 s-1 and P-pyr Km = 5 ± 1 M. PEP (slow substrate kcat = 2 × 10-4 s-1), oxalate, and sulfopyruvate are competitive inhibitors with Ki values of 2.0 ± 0.1 mM, 17 ± 1 M, and 210 ± 10 M, respectively. Three PPH crystal structures have been determined, that of a ligand-free enzyme, the enzyme bound to Mg2+ and oxalate (inhibitor), and the enzyme bound to Mg2+ and P-pyr (substrate). The complex with the inhibitor was obtained by cocrystallization, whereas that with the substrate was obtained by briefly soaking crystals of the ligand-free enzyme with P-pyr prior to flash cooling. The PPH structure resembles that of the other members of the PEPM/ICL superfamily and is most similar to the functionally related enzyme, PEPM. Each monomer of the dimer of dimers exhibits an (/)8 barrel fold with the eighth helix swapped between two molecules of the dimer. Both P-pyr and oxalate are anchored to the active site by Mg2+. The loop capping the active site is disordered in all three structures, in contrast to PEPM, where the equivalent loop adopts an open or disordered conformation in the unbound state but sequesters the inhibitor from solvent in the bound state. Crystal packing may have favored the open conformation of PPH even when the enzyme was cocrystallized with the oxalate inhibitor. Structure alignment of PPH with other superfamily members revealed two pairs of invariant or conservatively replaced residues that anchor the flexible gating loop. The proposed PPH catalytic mechanism is analogous to that of PEPM but includes activation of a water nucleophile with the loop Thr118 residue.

Differential effects of an anti-oxidant intervention on cardiomyocyte expression of adrenomedullin and intermedin and their receptor components in chronic nitric oxide deficiency

Background: Chronic inhibition of nitric oxide (NO) synthesis is associated with hypertension, myocardial oxidative stress and hypertrophic remodeling. Up-regulation of the cardiomyocyte adrenomedullin (AM) / intermedin (IMD) receptor signaling cascade is also apparent in NO-deficient cardiomyocytes: augmented expression of AM and receptor activity modifying proteins RAMP2 and RAMP3 is prevented by blood pressure normalization while that of RAMP1 and intermedin (IMD) is not, indicating that the latter is regulated by a pressure-independent mechanism. Aims: to verify the ability of an anti-oxidant intervention to normalize cardiomyocyte oxidant status and to investigate the influence of such an intervention on expression of AM, IMD and their receptor components in NO-deficient cardiomyocytes. Methods: NO synthesis inhibitor, NG-nitro-L-arginine methyl ester (L-NAME, 35mg/kg/day) was given to rats for 8 weeks, with/without con-current administration of antioxidants (Vitamin C (25mg/kg/day) and Tempol (25mg/kg/day)). Results: In left ventricular cardiomyocytes isolated from L-NAME treated rats, increased oxidative stress was indicated by augmented (3.6 fold) membrane protein oxidation, enhanced expression of catalytic and regulatory subunits of pro-oxidant NADPH oxidases (NOX1, NOX2) and compensatory increases in expression of anti-oxidant glutathione peroxidase and Cu/Zn superoxide dismutases (SOD1, SOD3). Vitamin C plus Tempol did not reduce systolic blood pressure but normalized augmented plasma levels of IMD, but not of AM, and in cardiomyocytes: (i) abolished increased membrane protein oxidation; (ii) normalized augmented expression of prepro-IMD and RAMP1, but not prepro-AM, RAMP2 and RAMP3; (iii) attenuated (by 42%) increased width and normalized expression of hypertrophic markers, skeletal-�-actin and prepro-endothelin-1 similarly to blood pressure normalization but in contrast to blood pressure normalization did not attenuate augmented brain natriuretic peptide (BNP) expression. Conclusion: normalization specifically of augmented IMD/RAMP1 expression in NO-deficient cardiomyocytes by antioxidant intervention in the absence of blood pressure reduction indicates that these genes are likely to be induced directly by myocardial oxidative stress. Although oxidative stress contributed to cardiomyocyte hypertrophy, induction of IMD and RAMP1 is unlikely to be secondary to cardiomyocyte hypertrophy.

A review of the selective reduction of NOx, with hydrocarbons under lean-burn conditions with non-zeolitic oxide and platinum group metal catalysts

Research on the selective reduction of NOx with hydrocarbons under lean-burn conditions using non-zeolitic oxides and platinum group metal (PGM) catalysts has been critically reviewed. Alumina and silver-promoted alumina catalysts have been described in detail with particular emphasis on an analysis of the various reaction mechanisms that have been put forward in the literature. The influence of the nature of the reducing agent, and the preparation and structure of the catalysts have also been discussed and rationalised for several other oxide systems. It is concluded for non-zeolitic oxides that species that are strongly adsorbed on the surface, such as nitrates/nitrites and acetates, could be key intermediates in the formation of various reduced and oxidised species of nitrogen, the further reaction of which leads eventually to the formation of molecular nitrogen. For the platinum group metal catalysts, the different mechanisms that have been proposed in the literature have been critically assessed. It is concluded that although there is indirect, mainly spectroscopic, evidence for various reaction intermediates on the catalyst surface, it is difficult to confirm that any of these are involved in a critical mechanistic step because of a lack of a direct quantitative correlation between infrared and kinetic measurements. A simple mechanism which involves the dissociation of NO on a reduced metal surface to give N(ads) and O(ads), with subsequent desorption of N-2 and N2O and removal of O(ads) by the reductant can explain many of the results with the platinum group metal catalysts, although an additional contribution from organo-nitro-type species may contribute to the overall NOx reduction activity with these catalysts.

Friedel-Crafts Benzoylation of Anisole in Ionic Liquids: Catalysis, Separation, and Recycle Studies

The comparison of three ionic liquid-mediated catalytic processes for the benzoylation of anisole with benzoic anhydride is presented. A detailed understanding of the mechanism by which the zeolite and metal triflate reactions in bis{trifluoromethanesulfonyl}imide-based ionic liquids has been reported previously, and these routes are considered together with an indium chloride-based ionic liquid system. Solvent extraction and vacuum/steam distillation have been assessed as possible workup procedures, and an overall preliminary economic evaluation of each overall process is reported. Although the predominant activity is associated with the in situ formation of a homogeneous acid catalyst, the low cost and facile separation of the zeolite-catalysed process leads to this route being the most economically viable overall option. The results of a continuous flow miniplant based on the zeolite catalyst are also presented and compared with the reaction using a small plug How reactor.

Persistent measles virus infection of mouse neural cells lacking known human entry receptors

Aims: Infection of the mouse central nervous system with wild type (WT) and vaccine strains of measles virus (MV) results in lack of clinical signs and limited antigen detection. It is considered that cell entry receptors for these viruses are not present on murine neural cells and infection is restricted at cell entry.

Methods: To examine this hypothesis, virus antigen and caspase 3 expression (for apoptosis) was compared in primary mixed, neural cell cultures infected in vitro or prepared from mice infected intracerebrally with WT, vaccine or rodent neuroadapted viruses. Viral RNA levels were examined in mouse brain by nested and real-time reverse transcriptase polymerase chain reaction.

Results: WT and vaccine strains were demonstrated for the first time to infect murine oligodendrocytes in addition to neurones despite a lack of the known MV cell receptors. Unexpectedly, the percentage of cells positive for viral antigen was higher for WT MV than neuroadapted virus in both in vitro and ex vivo cultures. In the latter the percentage of positive cells increased with time after mouse infection. Viral RNA (total and mRNA) was detected in brain for up to 20 days, while cultures were negative for caspase 3 in WT and vaccine virus infections.

Conclusions: WT and vaccine MV strains can use an endogenous cell entry receptor(s) or alternative virus uptake mechanism in murine neural cells. However, viral replication occurs at a low level and is associated with limited apoptosis. WT MV mouse infection may provide a model for the initial stages of persistent MV human central nervous system infections.

Identification of the mitochondrial ND3 subunit as a structural component involved in the active/deactive enzyme transition of respiratory complex I

Mitochondrial complex I (NADH: ubiquinone oxidoreductase) undergoes reversible deactivation upon incubation at 30-37 degrees C. The active/deactive transition could play an important role in the regulation of complex I activity. It has been suggested recently that complex I may become modified by S-nitrosation under pathological conditions during hypoxia or when the nitric oxide: oxygen ratio increases. Apparently, a specific cysteine becomes accessible to chemical modification only in the deactive form of the enzyme. By selective fluorescence labeling and proteomic analysis, we have identified this residue as cysteine-39 of the mitochondrially encoded ND3 subunit of bovine heart mitochondria. Cysteine-39 is located in a loop connecting the first and second transmembrane helix of this highly hydrophobic subunit. We propose that this loop connects the ND3 subunit of the membrane arm with the PSST subunit of the peripheral arm of complex I, placing it in a region that is known to be critical for the catalytic mechanism of complex I. In fact, mutations in three positions of the loop were previously reported to cause Leigh syndrome with and without dystonia or progressive mitochondrial disease.

Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus.

Bursaphelenchus xylophilus is the nematode responsible for a devastating epidemic of pine wilt disease in Asia and Europe, and represents a recent, independent origin of plant parasitism in nematodes, ecologically and taxonomically distinct from other nematodes for which genomic data is available. As well as being an important pathogen, the B. xylophilus genome thus provides a unique opportunity to study the evolution and mechanism of plant parasitism. Here, we present a high-quality draft genome sequence from an inbred line of B. xylophilus, and use this to investigate the biological basis of its complex ecology which combines fungal feeding, plant parasitic and insect-associated stages. We focus particularly on putative parasitism genes as well as those linked to other key biological processes and demonstrate that B. xylophilus is well endowed with RNA interference effectors, peptidergic neurotransmitters (including the first description of ins genes in a parasite) stress response and developmental genes and has a contracted set of chemosensory receptors. B. xylophilus has the largest number of digestive proteases known for any nematode and displays expanded families of lysosome pathway genes, ABC transporters and cytochrome P450 pathway genes. This expansion in digestive and detoxification proteins may reflect the unusual diversity in foods it exploits and environments it encounters during its life cycle. In addition, B. xylophilus possesses a unique complement of plant cell wall modifying proteins acquired by horizontal gene transfer, underscoring the impact of this process on the evolution of plant parasitism by nematodes. Together with the lack of proteins homologous to effectors from other plant parasitic nematodes, this confirms the distinctive molecular basis of plant parasitism in the Bursaphelenchus lineage. The genome sequence of B. xylophilus adds to the diversity of genomic data for nematodes, and will be an important resource in understanding the biology of this unusual parasite.