ArnT proteins that catalyse the glycosylation of lipopolysaccharide share common features with bacterial N-oligosaccharyltransferases

ArnT is a glycosyltransferase that catalyses the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) to the lipid A moiety of the lipopolysaccharide. This is a critical modification enabling bacteria to resist killing by antimicrobial peptides. ArnT is an integral inner membrane protein consisting of 13 predicted transmembrane helices and a large periplasmic C-terminal domain. We report here the identification of a functional motif with a canonical consensus sequence DEXRYAX(5)MX(3)GXWX(9)YFEKPX(4)W spanning the first periplasmic loop, which is highly conserved in all ArnT proteins examined. Site-directed mutagenesis demonstrated the contribution of this motif in ArnT function, suggesting that these proteins have a common mechanism. We also demonstrate that the Burkholderia cenocepacia and Salmonella enterica serovar Typhimurium ArnT C-terminal domain is required for polymyxin B resistance in vivo. Deletion of the C-terminal domain in B. cenocepacia ArnT resulted in a protein with significantly reduced in vitro binding to a lipid A fluorescent substrate and unable to catalyse lipid A modification with L-Ara4N. An in silico predicted structural model of ArnT strongly resembled the tertiary structure of Campylobacter lari PglB, a bacterial oligosaccharyltransferase involved in protein N-glycosylation. Therefore, distantly related oligosaccharyltransferases from ArnT and PglB families operating on lipid and polypeptide substrates, respectively, share unexpected structural similarity that could not be predicted from direct amino acid sequence comparisons. We propose that lipid A and protein glycosylation enzymes share a conserved catalytic mechanism despite their evolutionary divergence.

2,4-dinitrophenol as an activating reagent in a facile preparation of cyclic phosphate trimesters

Abstract 2,4-Dinitrophenol was employed with benzyloxy-bis-(diisopropylamino)phosphine to synthesise the cyclic phosphate derivatives of a series of alkane diols (HO–(CH2)n–OH, n=2–6) in good isolated yields. Tetrazole and DNP were compared by 31P NMR spectroscopy for their ability to catalyse the cyclisation at the P(III) stage. Investigation of the phosphate triester stability under various oxidation and chromatographic conditions resulted in the optimisation of the isolation procedures of the chemically unstable cyclic compounds. Conditions for debenzylation were developed to yield the corresponding cyclic phosphodiesters quantitatively. The methodology was further applied to the preparation and isolation of the cyclic phosphate derivative of a carbohydrate.

Element partitioning and potential mobility within surface dusts on buildings in a polluted urban environment, Budapest.

A voluminous literature exists on the analysis of water-soluble ions extracted from gypsum crusts and patinas formed on building surfaces. However, less data is available on the intermediate dust layer and the important role its complex matrix and constituents play in crust/patina formation. To address this issue, surface dust samples were collected from two buildings in the city of Budapest. Substrate properties, different pollution levels and environmental variations were considered by collecting samples from a city centre granite building exposed to intense traffic conditions and from an oolitic limestone church situated in a pedestrian area outside and high above the main pollution zone. Selective extraction examines both water-soluble ions (Ca2+, Mg2+, Na+, K+, Cl-, NO3- SO42-) and selected elements (Fe, Mn, Zn, Cu, Cr, Pb, Ni) from the water-soluble, exchangeable/carbonate, amorphous Mn, amorphous Fe/Mn, crystalline Fe/Mn, organic and residual phases, their mobility and potential to catalyse heterogeneous surface reactions. Salt weathering processes are highlighted by high concentrations of water-soluble Ca2+, Na+, Cl- and SO42-- at both sites. Manganese, Zn and Cu and to a lesser extent Pb and Ni, are very mobile in the city centre dust, where 30%, 54%, 38%, 11% and 11% of their totals are bound by the water-soluble phase, respectively. Church dust shows a sharp contrast for Mn, Zn, Cu and Pb with only 3%, 1%, 12% and 3% of their totals being bound by the water-soluble phase respectively. This may be due to (a) different environmental conditions at the church e.g. lower humidity (b) continuous replenishment of salts under intensive city centre traffic conditions (c) enrichment in oxidisable organic carbon by a factor of 4.5 and a tenfold increase in acidity in the city centre dust.

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.

Aromatic dioxygenases: Molecular biocatalysis and applications

Aromatic dioxygenases have been found to catalyse single and tandem oxidation reactions of conjugated polyenes. Rational selection and design of dioxygenases, allied to substrate shape, size and substitution pattern, has been used to control regiochemistry and stereochemistry during the oxygenation process. The resulting enantiopure bioproducts have been increasingly utilised as precursors for new and alternative routes in chiral synthesis.

Efficient heterogeneous asymmetric catalysis of the Mukaiyama aldol reaction by silica- and ionic liquid-supported Lewis acid copper(II) complexes of bis(oxazolines)

Lewis acid complexes based on copper(II) and an imidazolium-tagged bis(oxazoline) have been used to catalyse the asymmetric Mukaiyama aldol reaction between methyl pyruvate and 1-methoxy-1-tri-methylsilyloxypropene under homogeneous and heterogeneous conditions. Although the ees obtained in ionic liquid were similar to those found in dichloromethane, there was a significant rate enhancement in the ionic liquid with reactions typically reaching completion within 2 min compared with only 55% conversion after 60 min in dichloromethane. However, this rate enhancement was offset by lower chemoselectivity in ionic liquids due to the formation of 3-hydroxy-1,3-diphenylbutan-1-one as a by-product. Supporting the catalyst on silica or an imidazolium-modified silica using the ionic liquid or in an ionic liquid-diethyl ether system completely suppressed the formation of this by-product without reducing the enantioselectivity. Although the heterogeneous systems were characterised by a drop in catalytic activity the system could be recycled up to five times without any loss in conversion or ee.

Supported and liquid phase task specific ionic liquids for base catalysed Knoevenagel reactions

A series of Hunig's base tethered ammonium ionic liquids have been used to catalyse the Knoevenagel condensation of aldehydes/ketones with malononitrile and ethyl cyanoacetate. The reactions were performed under homogeneous and under biphasic, liquid-liquid and liquid-silica supported ionic liquid, conditions with the biphasic systems employing cyclohexene as the second phase. By increasing the distance between the ammonium head group and Hunig's base the activity of the catalyst was found to increase. Higher activity, in general, was found under homogeneous reaction conditions; however, the recyclability of the catalyst was improved by supporting the BIL under biphasic conditions. (c) 2007 Elsevier B.V. All rights reserved.

Polymer-supported phosphoramidites: highly efficient and recyclable catalysts for asymmetric hydrogenation of dimethylitaconate and dehydroamino acids and esters

Several novel phosphoramidites have been prepared by reaction of the primary amines para-vinylaniline, ortho-anisidine, 2-methoxyphenyl(4-vinylbenzyl)amine, 8-aminoquinoline and 3-vinyl-8-aminoquinoline with (S)-1,1'-bi-2-naphthylchlorophosphite, in the presence of base. Rhodium(l) complexes of these phosphoramidites catalyse the asymmetric hydrogenation of dimethylitaconate and dehydroamino acids and esters giving ee values up to 95%. Soluble non-cross linked polymers of the para-vinylaniline and 3-vinyl-8-aminoquinoline-based phosphoramidites have been prepared by free radical co-polymerisation with styrene in the presence of AIBN as initiator. The corresponding [Rh(COD)](+) complexes serve as recyclable catalysts for the asymmetric hydrogenation dimethylitaconate and dehydroamino acids and esters to give ee values up to 80%. (C) 2003 Elsevier Science Ltd. All rights reserved.

Stereochemical and mechanistic aspects of dioxygenase-catalysed benzylic hydroxylation of indene and chromane substrates

Toluene dioxygenase (TDO)-catalysed benzylic hydroxylation of indene substrates (8, 16 and 17), using whole cell cultures of Pseudomonas putida UV4, was found to yield inden-1-ol (14 and 22) and indan-1-one bioproducts (15 and 23). The formation of these bioproducts is consistent with the involvement of carbon-centred radical intermediates. TDO-catalysed oxidation of indenes 8 and 16 also gave cis-diols 13 and 18 respectively. TDO and naphthalene dioxygenase (NDO), used as both whole-cell preparations and as purified enzymes, were found to catalyse the benzylic hydroxylation of chromane 30, deuteriated (+/-)-chromane 30(D) and enantiomers (4S)-30(D) and (4R)-30(D) to yield (4R)- and (4S)-chroman-4-ols 31/31(D) respectively. The mechanism of benzylic hydroxylation of chromane 30/30(D) involves the stereoselective abstraction of a pro-R (with TDO) or a pro-S (with NDO) hydrogen atom at C-4 and a marked preference for retention of configuration.

Increased Promiscuity of Human Galactokinase Following Alteration of a Single Amino Acid Residue Distant from the Active Site

Galactokinase catalyses the site-and stereospecific phosphorylation of galactose at the expense of ATP. The specificity of bacterial galactokinase enzymes can be broadened by alteration of a tyrosine residue to a histidine. The effects of altering the equivalent residue in human galactokinase (Tyr379) were investigated by testing all 19 possible variants. All of these alterations, except Y379P, resulted in soluble protein on expression in Escherichia coli and all the soluble variants could catalyse the phosphorylation of galactose, except Y379A and Y379E. The variants Y379C, Y379K, Y379R, Y379S and Y379W were all able to catalyse the phosphorylation of a variety of monosaccharides, including ones that are not acted on by the wild-type enzyme. Novel substrates for these variant galactokinases included D-mannose and D-fructose. The latter monosaccharide is presumed to react in the pyranose configuration. Molecular modelling suggested that the alterations do not cause changes to the overall structure of the enzyme. However, alteration of Tyr379 increases the flexibility of the peptide backbone in regions surrounding the active site. Therefore, it is proposed that alteration of Tyr379 affects the substrate specificity by the propagation of changes in flexibility to the active site, permitting a broader range of compounds to be accommodated.

Structural mimics for the active site of [NiFe] hydrogenase

Hydrogenases are enzymes that catalyse the reversible two-electron oxidation of H-2. The [NiFe] hydrogenases have been characterised spectroscopically and by single crystal X-ray diffraction, and show an active site incorporating a heterobinuclear [NiFe] centre bridged by two cysteine S-donors. Low molecular weight synthetic complex models, which structurally mimic the dithiolate-bridged [NiFe] centre, serve as important probes of structure and chemistry at the active site and are the subject of this review. (C) 2001 Elsevier Science B.V. All rights reserved.

N-acetylgalactosamine kinase: a naturally promiscuous small molecule kinase

N-acetylgalactosamine kinase is a member of the GHMP family of small molecule kinases which catalyses the ATP-dependent phosphorylation of N-acetylgalactosamine. It is highly similar in structure and sequence to galactokinase. Alteration of galactokinase at a key tyrosine residue (Tyr-379 in the human enzyme) has been shown to dramatically enhance the substrate range of this enzyme. Here, we investigated the substrate specificity of the wild type N-acetylgalactosamine kinase and demonstrated that it can also catalyse the phosphorylation of N-acetylglucosamine and N-acetylmannosamine. In human N-acetylgalactosamine kinase, the equivalent residue to Tyr-379 in galactokinase is Phe-444. Alteration of this residue did not result in dramatic changes to the specificity of the enzyme. The more relaxed substrate specificity of N-acetylgalactosamine kinase, compared to galactokinase, can be explained by the greater flexibility of a glycine rich loop in the active site of the enzyme. These results suggest that N-acetylgalactosamine kinase is a potential biocatalyst for the phosphorylation of N-acetyl sugars. However, it is unlikely that it will be possible to further broaden the substrate range by alteration of Phe-444.

Catalysing open innovation through publicly funded R&D: A Comparison of University and Company-based research centres

Public funding of university and company-based R&D centres of excellence is widespread both in core and more peripheral regions. What is less well-known is whether these R&D centres can catalyse multi-directional, multi-actor and iterative innovation. Based on data from a real-time monitoring study, this article explores the development of 18 R&D centres’ external connections. University-based R&D centres establish more new connections than company-based centres and are more likely to be interacting with small or micro-firms. However, there is a general bias towards links with larger firms; micro, small and medium-sized enterprises also are less likely to be involved in collaborative R&D with research centres than other types of relationships. The results suggest the potential for R&D centres to act as a catalyst for open innovation but emphasise the need to ensure that the focus of the R&D being conducted is relevant to the needs of smaller firms.

An Escherichia coli undecaprenyl-pyrophosphate phosphatase implicated in undecaprenyl phosphate recycling

Undecaprenyl phosphate (Und-P) is a universal lipid carrier of glycan biosynthetic intermediates for carbohydrate polymers that are exported to the bacterial cell envelope. Und-P arises from the dephosphorylation of undecaprenyl pyrophosphate (Und-PP) molecules produced by de novo synthesis and also from the recycling of released Und-PP after the transfer of the glycan component to other acceptor molecules. The latter reactions take place at the periplasmic side of the plasma membrane, while cytoplasmic enzymes catalyse the de novo synthesis. Four Und-PP pyrophosphatases were recently identified in Escherichia coli. One of these, UppP (formerly BacA), accounts for 75 % of the total cellular Und-PP pyrophosphatase activity and has been suggested to participate in the Und-P de novo synthesis pathway. Unlike UppP, the other three pyrophosphatases (YbjG, YeiU and PgpB) have a typical acid phosphatase motif also found in eukaryotic dolichyl-pyrophosphate-recycling pyrophosphatases. This study shows that double and triple deletion mutants in the genes uppP and ybjG, and uppP, ybjG and yeiU, respectively, are supersensitive to the Und-P de novo biosynthesis inhibitor fosmidomycin. In contrast, single or combined deletions including pgpB have no effect on fosmidomycin supersensitivity. Experimental evidence is also presented that the acid phosphatase motifs of YbjG and YeiU face the periplasmic space. Furthermore, the quadruple deletion mutant DeltauppP-DeltaybjG-DeltayeiU-DeltawaaL has a growth defect and abnormal cell morphology, suggesting that accumulation of unprocessed Und-PP-linked O antigen polysaccharides is toxic for these cells. Together, the results support the notion that YbjG, and to a lesser extent YeiU, exert their enzymic activity on the periplasmic side of the plasma membrane and are implicated in the recycling of periplasmic Und-PP molecules.

The GalF protein of Escherichia coli is not a UDP-glucose pyrophosphorylase but interacts with the GalU protein possibly to regulate cellular levels of UDP-glucose

We report the functional characterization of the galF gene of strain VW187 (Escherichia coli O7:K1), which encodes a polypeptide displaying structural features common to bacterial UDP-glucose pyrophosphorylases, including the E. coli GalU protein. These enzymes catalyse a reversible reaction converting UTP and glucose-1-phosphate into UDP-glucose and PPi. We show that, although the GalF protein is expressed in vivo, GalF-expressing plasmids cannot complement the phenotype of a galU mutant and extracts from this mutant which only produces GalF are enzymatically inactive. In contrast, the presence of GalU and GalF proteins in the same cell-free extract caused a significant reduction in the rate of pyrophosphorolysis (conversion of UDP-glucose into glucose-1-phosphate) but no significant effect on the kinetics of synthesis of UDP-glucose. The presence of GalF also increased the thermal stability of the enzyme in vitro. The effect of GalF in the biochemical properties of the UDP-glucose pyrophosphorylase required the co-synthesis of GalF and GalU, suggesting that they could interact as components of the oligomeric enzyme. The physical interaction of GalU and GalF was demonstrated in vivo by the co-expression of both proteins as fusion products using a yeast two-hybrid system. Furthermore, using a pair of galF-/galU+ and galF/galU+ isogenic strains, we demonstrated that the presence of GalF is associated with an increased concentration of intracellular UDP-glucose as well as with an enhancement of the thermal stability of the UDP-glucose pyrophosphorylase in vivo. We propose that GalF is a non-catalytic subunit of the UDP-glucose pyrophosphorylase modulating the enzyme activity to increase the formation of UDP-glucose, and this function is important for bacterial adaptation to conditions of stress.