Search

Abstract The term vitamin B6 is a designation for the vitamers pyridoxal, pyridoxamine, pyridoxine and the respective phosphate esters pyridoxal-5′-phosphate (PLP), pyridoxamine-5′-phosphate and pyridoxine-5′-phosphate. Animals and humans are unable to synthesise vitamin B6. These organisms have to take up vitamin B6 with their diet. Therefore, vitamin B6 is of commercial interest as a food additive and for applications in the pharmaceutical industry. As yet, two naturally occurring routes for de novo synthesis of PLP are known. Both routes have been genetically engineered to obtain bacteria overproducing vitamin B6. Still, major genetic engineering efforts using the existing pathways are required for developing fermentation processes that could outcompete the chemical synthesis of vitamin B6. Recent suppressor screens using mutants of the Gram-negative and Gram-positive model bacteria Escherichia coli and Bacillus subtilis, respectively, carrying mutations in the native pathways or heterologous genes uncovered novel routes for PLP biosynthesis. These pathways consist of promiscuous enzymes and enzymes that are already involved in vitamin B6 biosynthesis. Thus, E. coli and B. subtilis contain multiple promiscuous enzymes causing a so-called underground metabolism allowing the bacteria to bypass disrupted vitamin B6 biosynthetic pathways. The suppressor screens also show the genomic plasticity of the bacteria to suppress a genetic lesion. We discuss the potential of the serendipitous pathways to serve as a starting point for the development of bacteria overproducing vitamin B6. Key points • Known vitamin B6 routes have been genetically engineered. • Underground metabolism facilitates the emergence of novel vitamin B6 biosynthetic pathways. • These pathways may be suitable to engineer bacteria overproducing vitamin B6.

The polypeptide N-acetylgalactosaminyl transferase (GalNAc-T) enzyme family initiates O-linked mucin-type glycosylation. The family constitutes 20 isozymes in humans—an unusually large number—unique to O-glycosylation. GalNAc-Ts exhibit both redundancy and finely tuned specificity for a wide range of peptide substrates. In this work, we deciphered the sequence and structural motifs that determine the peptide substrate preferences for the GalNAc-T2 isoform. Our approach involved sampling and characterization of peptide–enzyme conformations obtained from Rosetta Monte Carlo-minimization–based flexible docking. We computationally scanned 19 amino acid residues at positions −1 and +1 of an eight-residue peptide substrate, which comprised a dataset of 361 (19×19) peptides with previously characterized experimental GalNAc-T2 glycosylation efficiencies. The calculations recapitulated experimental specificity data, successfully discriminating between glycosylatable and non-glycosylatable peptides with a probability of 96.5% (ROC-AUC score), a balanced accuracy of 85.5% and a false positive rate of 7.3%. The glycosylatable peptide substrates viz. peptides with proline, serine, threonine, and alanine at the −1 position of the peptide preferentially exhibited cognate sequon-like conformations. The preference for specific residues at the −1 position of the peptide was regulated by enzyme residues R362, K363, Q364, H365 and W331, which modulate the pocket size and specific enzyme-peptide interactions. For the +1 position of the peptide, enzyme residues K281 and K363 formed gating interactions with aromatics and glutamines at the +1 position of the peptide, leading to modes of peptide-binding sub-optimal for catalysis. Overall, our work revealed enzyme features that lead to the finely tuned specificity observed for a broad range of peptide substrates for the GalNAc-T2 enzyme. We anticipate that the key sequence and structural motifs can be extended to analyze specificities of other isoforms of the GalNAc-T family and can be used to guide design of variants with tailored specificity.

Graphical abstract, Pharmaceutical heparin’s activity arises from a key high affinity and high selectivity antithrombin binding motif, which forms the basis for its use as an anticoagulant. The current problems with the supply of pig heparin raises the emphasis of understanding heparin biosynthesis so as to control and advance recombinantly expressed agent that could bypass the need for animals. Unfortunately, much remains to be understood about the generation of the antithrombin-binding motif by the key enzyme involved in its biosynthesis, 3-O-sulfotransferase–1 (3OST-1). In this work, we present a novel computational approach to understand recognition of oligosaccharide sequences by 3OST-1. Application of combinatorial virtual library screening (CVLS) algorithm on hundreds of tetrasaccharide and hexasaccharide sequences shows that 3OST-1 belongs to the growing number of proteins that recognize glycosaminoglycans with very high selectivity. It prefers very well defined pentasaccharide sequences carrying distinct groups in each of the five residues to generate the antithrombin binding motif. CVLS also identifies key residues including His271, Arg72, Arg197 and Lys173, which interact with 6-sulfate, 5-COO¯, 2-/6-sulfates and 2-sulfate at the −2, −1, +2, and +1 positions of the precursor pentasaccharide, respectively. Additionally, uncharged residues, especially Gln163 and Asn167, were also identified as playing important roles in recognition. Overall, the success of CVLS in predicting 3OST-1 recognition characteristics that help engineer selectivity lead to the expectation that recombinant enzymes could be designed to help resolve the current problems in the supply of anticoagulant heparin.

N-glycosylation is one of the most abundant posttranslational modifications of proteins, essential for many physiological processes, including protein folding, protein stability, oligomerization and aggregation, and molecular recognition events. Defects in the N-glycosylation pathway cause diseases that are classified as congenital disorders of glycosylation. The ability to manipulate protein N-glycosylation is critical not only to our fundamental understanding of biology but also for the development of new drugs for a wide range of human diseases. Chemoenzymatic synthesis using engineered endo-β-N-acetylglucosaminidases (ENGases) has been used extensively to modulate the chemistry of N-glycosylated proteins. However, defining the molecular mechanisms by which ENGases specifically recognize and process N-glycans remains a major challenge. Here we present the X-ray crystal structure of the ENGase EndoBT-3987 from Bacteroides thetaiotaomicron in complex with a hybrid-type glycan product. In combination with alanine scanning mutagenesis, molecular docking calculations and enzymatic activity measurements conducted on a chemically engineered monoclonal antibody substrate unveil two mechanisms for hybrid-type recognition and processing by paradigmatic ENGases. Altogether, the experimental data provide pivotal insight into the molecular mechanism of substrate recognition and specificity for GH18 ENGases and further advance our understanding of chemoenzymatic synthesis and remodeling of homogeneous N-glycan glycoproteins.

The substrate specificity of enzymes is bound to be imperfect, because of unavoidable physicochemical limits. In extant metabolic enzymes, furthermore, such limits are seldom approached, suggesting that the degree of specificity of these enzymes, on average, is much lower than could be attained. During biological evolution, the activity of a single enzyme with available alternative substrates may be preserved to a significant or even substantial level for different reasons - for example when the alternative reaction contributes to fitness, or when its undesirable products are nevertheless dispatched by metabolite repair enzymes. In turn, the widespread occurrence of promiscuous reactions is a consistent source of metabolic 'messiness', from which both liabilities and opportunities ensue in the evolution of metabolic systems.

Agmatine is the product of the decarboxylation of L-arginine by the enzyme arginine decarboxylase. This amine has been attributed to neurotransmitter functions, anticonvulsant, anti-neurotoxic, and antidepressant in mammals and is a potential therapeutic agent for diseases such as Alzheimer’s, Parkinson’s, and cancer. Agmatinase enzyme hydrolyze agmatine into urea and putrescine, which belong to one of the pathways producing polyamines, essential for cell proliferation. Agmatinase from Escherichia coli (EcAGM) has been widely studied and kinetically characterized, described as highly specific for agmatine. In this study, we analyze the amino acids involved in the high specificity of EcAGM, performing a series of mutations in two loops critical to the active-site entrance. Two structures in different space groups were solved by X-ray crystallography, one at low resolution (3.2 Å), including a guanidine group, and other at high resolution (1.8 Å) which presents urea and agmatine in the active site. These structures made it possible to understand the interface interactions between subunits that allow the hexameric state and postulate a catalytic mechanism according to the Mn2+ and urea/guanidine binding site. Molecular dynamics simulations evaluated the conformational dynamics of EcAGM and residues participating in non-binding interactions. Simulations showed the high dynamics of loops of the active site entrance and evidenced the relevance of Trp68, located in the adjacent subunit, to stabilize the amino group of agmatine by cation-pi interaction. These results allow to have a structural view of the best-kinetic characterized agmatinase in literature up to now.

We examined the roles of Mg2+ ions in DNA polymerization by kinetic analysis of single nucleotide incorporation catalyzed by HIV reverse transcriptase and by molecular dynamics simulation of Mg2+ binding. Binding of the Mg-nucleotide complex induces a conformational change of the enzyme from open to closed states in a process that is independent of free Mg2+ concentration. Subsequently, the second Mg2+ binds weakly to the closed state of the enzyme-DNA-Mg.dNTP complex with an apparent Kd = 3.7 mM and facilitates the catalytic reaction. This weak binding of the catalytic Mg2+ is important to maintain fidelity in that the Mg2+ samples the correctly aligned substrate without perturbing the equilibrium at physiological Mg2+ concentrations. The binding of the catalytic Mg2+ increases nucleotide specificity (kcat/Km) by increasing the rate of the chemistry and decreasing the rate of enzyme opening allowing nucleotide release. Changing the free Mg2+ concentration from 0.25 to 10 mM increased nucleotide specificity (kcat/Km) by 12-fold. Mg2+ binds very weakly to the open state of the enzyme in the absence of nucleotide (Kd ≈ 34 mM) and competes with Mg.dNTP. Analysis based on publish crystal structures showed that HIV RT binds only two metal ions during incorporation of a correct base-pair. MD simulations support the kinetic studies suggesting weak binding of the catalytic Mg2+ in open and closed states. They also support the two-metal ion mechanism, although the polymerase may bind a third metal ion in the presence of a mismatched nucleotide.

Background Fungal beta-glucosidases (BGs) from glucoside hydrolase family 3 (GH3) are industrially important enzymes, which convert cellooligosaccharides into glucose; the end product of the cellulolytic process. They are highly active against the β-1,4 glycosidic bond in soluble substrates but typically reported to be inactive against insoluble cellulose. Results We studied the activity of four fungal GH3 BGs on cellulose and found significant activity. At low temperatures (10 ℃), we derived the approximate kinetic parameters kcat = 0.3 ± 0.1 s−1 and KM = 80 ± 30 g/l for a BG from Aspergillus fumigatus (AfBG) acting on Avicel. Interestingly, this maximal turnover is higher than reported values for typical cellobiohydrolases (CBH) at this temperature and comparable to those of endoglucanases (EG). The specificity constant of AfGB on Avicel was only moderately lowered compared to values for EGs and CBHs. Conclusions Overall these observations suggest a significant promiscuous side activity of the investigated GH3 BGs on insoluble cellulose. This challenges the traditional definition of a BG and supports suggestions that functional classes of cellulolytic enzymes may represent a continuum of overlapping modes of action.

There are more than one million described insect species. This species richness is reflected in the diversity of insect metabolic processes. In particular, biosynthesis of secondary metabolites, such as defensive compounds and chemical signals, encompasses an extraordinarily wide range of chemicals that are generally unparalleled among natural products from other organisms. Insect genomes, transcriptomes and proteomes thus offer a valuable resource for discovery of novel enzymes with potential for biotechnological applications. Here, we focus on fatty acid (FA) metabolism-related enzymes, notably the fatty acyl desaturases and fatty acyl reductases involved in the biosynthesis of FA-derived pheromones. Research on insect pheromone-biosynthetic enzymes, which exhibit diverse enzymatic properties, has the potential to broaden the understanding of enzyme specificity determinants and contribute to engineering of enzymes with desired properties for biotechnological production of FA derivatives. Additionally, the application of such pheromone-biosynthetic enzymes represents an environmentally friendly and economic alternative to the chemical synthesis of pheromones that are used in insect pest management strategies.

Kinetic characteristics of specific recognition of damaged base by the DNA glycosylase MutY in model DNA substrates, containing oxoG/A-, G/A-, oxoG/C- and F/G pairs in the central position, were investigated. Conformational changes of the MutY enzyme during the recognition of the damaged base in DNA have been recorded by the change in the fluorescence intensity of tryptophan residues using the stopped-flow technique in real time. DNA duplexes containing a fluorescein residue were used for the registration of DNA conformational changes. Analysis of the kinetic curves allowed us to determine the values of rate constants for the kinetic stages of the interaction. It was shown that nonspecific contacts between the DNA-binding site of the enzyme and the DNA duplex are formed at the first stage of the interaction. It was found that the discrimination of Gua and oxoGua bases occurs at the second stage of the MutY interaction with the DNA duplex. The data obtained for the oxoG/C-substrate showed that the recognition of the base located opposite oxoGua also occurs at this stage.

Beta-lactam antibiotics comprise one of the earliest known classes of antibiotic therapies. These molsecules covalently inhibit enzymes from the family of penicillin-binding proteins, which are essential to the construction of the bacterial cell wall. As a result, beta-lactams have long been known to cause striking changes to cellular morphology. The exact nature of the changes tend to vary by the precise PBPs engaged in the cell since beta-lactams exhibit a range of PBP enzyme specificity. The traditional method for exploring beta-lactam polyspecificity is a gel-based binding assay which is low-throughput and typically runex situin cell extracts. Here, we describe a medium-throughput, image-based assay combined with machine learning methods to automatically profile the activity of beta-lactams inE. colicells. By testing for morphological change across a panel of strains with perturbations to individual PBP enzymes, our approach automatically and quantifiably relates different beta-lactam antibiotics according to their preferences for individual PBPs in cells. We show the potential of our approach for guiding the design of novel inhibitors towards different PBP-binding profiles by recapitulating the activity of two recently-reported PBP inhibitors.

MtsZ is a molybdenum-containing methionine sulfoxide reductase that supports virulence in the human respiratory pathogen Haemophilus influenzae (Hi). HiMtsZ belongs to a group of structurally and spectroscopically uncharacterized S-/N-oxide reductases, all of which are found in bacterial pathogens. Here, we have solved the crystal structure of HiMtsZ, which reveals that the HiMtsZ substrate-binding site encompasses a previously unrecognized part that accommodates the methionine sulfoxide side chain via interaction with His182 and Arg166. Charge and amino acid composition of this side chain-binding region vary and, as indicated by electrochemical, kinetic, and docking studies, could explain the diverse substrate specificity seen in closely related enzymes of this type. The HiMtsZ Mo active site has an underlying structural flexibility, where dissociation of the central Ser187 ligand affected catalysis at low pH. Unexpectedly, the two main HiMtsZ electron paramagnetic resonance (EPR) species resembled not only a related dimethyl sulfoxide reductase but also a structurally unrelated nitrate reductase that possesses an Asp-Mo ligand. This suggests that contrary to current views, the geometry of the Mo center and its primary ligands, rather than the specific amino acid environment, is the main determinant of the EPR properties of mononuclear Mo enzymes. The flexibility in the electronic structure of the Mo centers is also apparent in two of three HiMtsZ EPR-active Mo(V) species being catalytically incompetent off-pathway forms that could not be fully oxidized.

Eversa&reg, Transform (ET), and the lipase from Thermomyces lanuginosus (TLL), liquid commercial lipases formulations, have been immobilized on octyl agarose beads and their stabilities were compared. Immobilized and free ET forms were more thermostable than TLL formulations at pH 5.0, 7.0, and 9.0, and the ET immobilized form was more stable in the presence of 90% methanol or dioxane at 25 &deg, C and pH 7. Specific activity versus p-nitrophenyl butyrate was higher for ET than for TLL. However, after immobilization the differences almost disappeared because TLL was very hyperactivated (2.5-fold) and ET increased the activity only by 1.6 times. The enzymes were also immobilized in octadecyl methacrylate beads. In both cases, the loading was around 20 mg/g. In this instance, activity was similar for immobilized TLL and ET using triacetin, while the activity of immobilized ET was lower using (S)-methyl mandelate. When the immobilized enzymes were used to produce biodiesel from sunflower oil and methanol in tert-butanol medium, their performance was fairly similar.

C. neoformans Dnmt5 is an unusually specific maintenance-type CpG methyltransferase (DNMT) that mediates long-term epigenome evolution. It harbors a DNMT domain and SNF2 ATPase domain. We find that the SNF2 domain couples substrate specificity to an ATPase step essential for DNA methylation. Coupling occurs independent of nucleosomes. Hemimethylated DNA preferentially stimulates ATPase activity, and mutating Dnmt5’s ATP-binding pocket disproportionately reduces ATPase stimulation by hemimethylated versus unmethylated substrates. Engineered DNA substrates that stabilize a reaction intermediate by mimicking a ‘flipped-out’ conformation of the target cytosine bypass the SNF2 domain’s requirement for hemimethylation. This result implies that ATP hydrolysis by the SNF2 domain is coupled to the DNMT domain conformational changes induced by preferred substrates. These findings establish a new role for a SNF2 ATPase: controlling an adjoined enzymatic domain’s substrate recognition and catalysis. We speculate that this coupling contributes to the exquisite specificity of Dnmt5 via mechanisms related to kinetic proofreading.

A bifunctional alginate lyase (ALFA3) and mannuronate-specific alginate lyase (ALFA4) genes were found in the genome of polysaccharide-degrading marine bacterium Formosa algae KMM 3553T. They were classified to PL7 and PL6 polysaccharide lyases families and expressed in E. coli. The recombinant ALFA3 appeared to be active both on mannuronate- and guluronate-enriched alginates, as well as pure sodium mannuronate. For all substrates, optimum conditions were pH 6.0 and 35 &deg, C, Km was 0.12 &plusmn, 0.01 mg/ml, and half-inactivation time was 30 min at 42 &deg, C. Recombinant ALFA4 was active predominately on pure sodium mannuronate, with optimum pH 8.0 and temperature 30 &deg, C, Km was 3.01 &plusmn, 0.05 mg/ml. It was stable up to 30 &deg, half-inactivation time was 1h 40 min at 37 &deg, C. 1H NMR analysis showed that ALFA3 degraded mannuronate and mannuronate-guluronate blocks, while ALFA4 degraded only mannuronate blocks, producing mainly disaccharides. Products of digestion of pure sodium mannuronate by ALFA3 at 200 &micro, g/ml inhibited anchorage-independent colony formation of human melanoma cells SK-MEL-5, SK-MEL-28, and RPMI-7951 up to 17% stronger compared to native polymannuronate. This fact supports previous data and suggests that mannuronate oligosaccharides may be useful for synergic tumor therapy.

A wide number of Lactic Acid Bacteria (LAB) species produce ?-glucans with their ability to synthesize glucansucrases (GS) which use sucrose as substrate for the glucan production. Recently another group of enzymes in LAB gained special interest for their ability to produce ?-glucans targeting the substrates containing ?1-4-linkages and synthesizing new (?1-6) or (?1-3)–linkages as ??glucanotransferases. In this study, a putative 4,6???glucanotransferase (GTFB) from sourdough isolate Lactobacillus reuteri E81 was identified and expressed in Escherichia coli. The biochemical characterization of the GTFB-E81 confirmed its function as it cleaved the ?1-4-linkages in different substrates and produced new gluco-oligomers/polymers containing ?1-6 linkages together with the ?1-4-linkages detected by NMR analysis. GTFB-E81 produced malto-oligosaccharides targeting maltose and maltoheptaose as substrates with up to DP 8 detected by TLC and ESI-MS/MS analysis. The functional roles of these malto-oligosaccharides were determined by testing their immune-modulatory functions in HT29 cells and they triggered the production of anti-inflammatory 1L-4 and pro-inflammatory IL-12 cytokines. © 2018 Elsevier B.V.

Benzimidazole carboxyphosphonates and bisphosphonates have been prepared and evaluated for their activity as inhibitors of protein prenylation or isoprenoid biosynthesis. The nature of the phosphonate head group was found to dictate enzyme specificity. The lead carboxyphosphonate inhibits geranylgeranyl transferase II while its corresponding bisphosphonate analogue potently inhibits farnesyl diphosphate synthase. The most active inhibitors effectively disrupted protein prenylation in human multiple myeloma cells.

Many nanomaterials have been reported to have enzyme-like activities and are considered as nanozymes. As a multifunctional nanozyme, nanoceria has received much attention due to the dual oxidation states of Ce3+/Ce4+ which facilitate redox reactions at the particle surface. Despite the advantages of nanozymes, their limited activity and lack of enzyme specificity are still problems to be resolved. DNA is used to modulate the oxidase activity of nanoceria because it has recently become an important molecule in bionanotechnology. However, the current research on the effect of DNA on the oxidase mimetic activity of nanoceria is contradictory. It has been discovered that nanoceria used in recent works are different, including in particle size, doping and concentration, and these differences may affect the interaction between DNA and nanoceria, and then affect the oxidase mimetic activity of nanoceria. Hence, it is important to clarify the factors that affect the interaction between DNA with nanoceria. In this work, the interactions between DNA and nanoceria with three different morphologies (nanoparticles, nanocubes, and nanorods) have been investigated. Experimental results show that DNA has different influences on the oxidase mimetic activity of nanoceria with different morphologies. The oxidase mimetic activity of CeO2 nanoparticles and nanocubes increased, but that of CeO2 nanorods decreased, after DNA modification. The mechanism of these experimental results has been explored, and it has been found that it is the interaction between cerium and the phosphate backbone of DNA that changes with the different morphologies, resulting in the varying effect of DNA on the oxidase mimetic activity of nanoceria. These results may provide a better understanding of the effect of DNA on the oxidase mimetic activity of nanoceria and promote the applications of nanoceria.

International audience; Poly(ADP-ribose) polymerases (PARPs) act as DNA break sensors and catalyze the synthesis of polymers of ADP-ribose (PAR) covalently attached to acceptor proteins at DNA damage sites. It has been demonstrated that both mammalian PARP1 and PARP2 PARylate double-strand break termini in DNA oligonucleotide duplexes in vitro. Here, we show that mammalian PARP2 and PARP3 can PARylate and mono(ADP-ribosyl)ate (MARylate), respectively, 5-and 3-terminal phosphate residues at double-and single-strand break termini of a DNA molecule containing multiple strand breaks. PARP3catalyzed DNA MARylation can be considered a new type of reversible post-replicative DNA modification. According to DNA substrate specificity of PARP3 and PARP2, we propose a putative mechanistic model of PARP-catalyzed strand break-oriented ADP-ribosylation of DNA termini. Notably, PARPmediated DNA ADP-ribosylation can be more effective than PARPs' auto-ADP-ribosylation depending on the DNA substrates and reaction conditions used. Finally, we show an effective PARP3-or PARP2catalyzed ADP-ribosylation of high-molecular-weight (∼3-kb) DNA molecules, PARP-mediated DNA PARylation in cell-free extracts and a persisting signal of anti-PAR antibodies in a serially purified genomic DNA from bleomycin-treated poly(ADP-ribose) glycohydrolase-depleted HeLa cells. These results suggest that certain types of complex DNA breaks can be effectively ADP-ribosylated by PARPs in cellular response to DNA damage.

The patchoulol synthase (PTS) is a multi-product sesquiterpene synthases which is the central enzyme for biosynthesis of patchouli essential oil in the patchouli plant. Sesquiterpene synthases catalyse the formation of various complex carbon backbones difficult to approach by organic synthesis. Here, we report the characterisation of a recombinant patchoulol synthase complementary DNA (cDNA) variant (PTS var. 1), exhibiting significant amino acid exchanges compared to the native PTS. The product spectrum using the natural substrate E,E-farnesyl diphosphate (FDP) as well as terpenoid products resulting from conversions employing alternative substrates was analysed by GC-MS. In respect to a potential use as a biocatalyst, important enzymatic parameters such as the optimal reaction conditions, kinetic behaviour and the product selectivity were studied as well. Adjusting the reaction conditions, an increased patchoulol ratio in the recombinant essential oil was achieved. Nevertheless, the ratio remained lower than in plant-derived patchouli oil. As alternative substrates, several prenyl diposphates were accepted and converted in numerous compounds by the PTS var. 1, revealing its great biocatalytic potential. The final publication is available at Springer via http://dx.doi.org/10.1007/s12010-015-1707-y EFRE/ZW-8-80130940

To screen soil metagenomic libraries for novel enzymes with enhanced activities. To screen soil metagenomic libraries for novel enzymes with enhanced activities. A novel l-asparaginase was identified from forest soil metagenome and its characteristics were studied. The purified protein had a specific activity of 696 IU mg−1 and optimum activity at pH 7 and 35 °C. Enhanced enzyme activities were observed in the presence of Mg2+, Ca2+ and K+. The Km value, 2 mM, and enzyme specificity constant 7.7 mM−1s−1 indicated that the recombinant enzyme has good substrate affinity to l-asparagine compared with commercially-available Escherichia coli asparaginase. The IC50 value of 0.78 µg ml−1 (0.47 IU ml−1) was observed with HL60 cell line and 0.39 µg ml−1(0.23 IU ml−1) with MOLT-3 and MOLT-4 cell lines, which is better than that of commercially-available drugs. The soil metagenome derived l-asparaginase with enhanced activities could be a potential candidate to develop as a drug in Acute Lymphoblastic Leukemia (ALL) therapy.

At present, few organisms are known to and capable of naturally producing laccases and white rot fungi are one such group. In the present study, three fungal species, namely,Ganoderma lucidum-CDBT1, Ganoderma japonicum,andLentinula edodes, isolated from their native habitat in Nepal were screened for laccase production, andG. lucidum-CDBT1 was found to express highest levels of enzyme (day 10 culture media showed 0.92 IU/mg total protein or 92 IU/mL laccase activity with ABTS as substrate). Lignin extracted from rice straw was used in Olga medium for laccase production and isolation fromG. lucidum-CDBT1. Presence of lignin (5 g/L) and copper sulfate (30 μM) in the media increased the extracellular laccase content by 111% and 114%, respectively. The laccase enzyme produced byG. lucidum-CDBT1 was fractionated by ammonium sulfate and purified by DEAE Sepharose anion exchange chromatography. The purified enzyme was found to have a molecular mass of 43 kDa and exhibits optimal activity at pH 5.0 and 30°C. The isolated laccase was thermally stable for up to 70°C for 1 h and exhibited broad pH stability. The kinetic constants,Km,Vmax, andKcat, determined using 2,2′-azinobis-(-3-ethylbenzothiazoline-6-sulfonic acid) as substrate were found to be 110 μM, 36 μmol/min/mg, and 246 min−1, respectively. The isolated thermostable laccase will be used in future experiments for delignification process.

International audience; Poly(ADP-ribose) polymerases (PARPs/ARTDs) use nicotinamide adenine dinucleotide (NAD +) to catalyse the synthesis of a long branched poly(ADPribose) polymer (PAR) attached to the acceptor amino acid residues of nuclear proteins. PARPs act on single-and double-stranded DNA breaks by recruiting DNA repair factors. Here, in in vitro biochemical experiments, we found that the mammalian PARP1 and PARP2 proteins can directly ADP-ribosylate the termini of DNA oligonucleotides. PARP1 preferentially catalysed covalent attachment of ADP-ribose units to the ends of recessed DNA duplexes containing 3-cordycepin, 5-and 3phosphate and also to 5-phosphate of a singlestranded oligonucleotide. PARP2 preferentially ADPribosylated the nicked/gapped DNA duplexes containing 5-phosphate at the double-stranded termini. PAR glycohydrolase (PARG) restored native DNA structure by hydrolysing PAR-DNA adducts generated by PARP1 and PARP2. Biochemical and mass spectrometry analyses of the adducts suggested that PARPs utilise DNA termini as an alternative to 2-hydroxyl of ADP-ribose and protein acceptor residues to catalyse PAR chain initiation either via the 2 ,1-O-glycosidic ribose-ribose bond or via phosphodiester bond formation between C1 of ADPribose and the phosphate of a terminal deoxyribonucleotide. This new type of post-replicative modification of DNA provides novel insights into the molecular mechanisms underlying biological phenomena of ADP-ribosylation mediated by PARPs.

Oxidative enzymatic reactions using horseradish peroxidase (HRP) were carried out in water-in-oil (w/o) microemulsions composed of olive oil/lecithin/1-propanol/water, a model biomimetic system. The substrates used (gallic acid, octyl gallate and 2,2′-azino-bis[3-ethylbenzo-thiazoline-6- sulfonic acid] (ABTS)) have different hydrophobicities and possible locations in the microemulsion system. HRP reactivity with reference to substrate hydrophobicity and structural characteristics of the microemulsions is discussed. The nature of the enzyme microenvironments was examined using dynamic light scattering (DLS), differential scanning calorimetry (DSC) and diffusion NMR (DOSY) methodologies while the location of various enzymatic substrates in the microemulsion phase was assessed by solubility measurements and by taking pressure-area isotherms of mixed monolayers of the substrates with dipalmitoyl-phosphatidylcholine (DPPC), which is a major constituent of lecithin. In contrast to the bulk aqueous phase, in the severely restricted environment of the polar domains of the microemulsion HRP reacted faster with octyl gallate, a substrate that is solubilized at the lipid interfaces. HRP was deactivated in the olive oil microemulsions within a few hours, a phenomenon that has also been observed in other microemulsion systems. © 2011 American Chemical Society. 27 6 2692 2700 Cited By :9

Tyrosinase (Ty) is a copper-containing enzyme ubiquitously distributed in nature. In recent years, Ty has attracted interest as a potential detoxifying agent for xenobiotic compounds with phenolic structure. Among these, chlorophenols are particularly relevant pollutants, commonly found in waste waters. The activity of Streptomyces antibioticus tyrosinase toward isomeric monochlorophenols was studied. Tyrosinase oxidizes both 3- and 4-chlorophenol to the same product, 4-chloro-1,2-ortho-quinone, which subsequently undergoes a nucleophilic substitution reaction at the chlorine atom by excess phenol to give the corresponding phenol-quinone adduct. By contrast, 2-chlorophenol is not reactive and acts as a competitive inhibitor. Docking calculations suggest that the substrates point to one of the copper atoms of the dinuclear center (copper B) and appear to interact preferentially with one of the two coordinated oxygen atoms. The approach of the substrate toward the active site is favored by a π-stacking interaction with one of the copper-coordinated histidines (His194) and by a hydrogen bonding interaction with the O1 oxygen. With this study, we provide the first characterization of the early intermediates in the biotechnologically relevant reaction of Ty with chlorophenols. Additionally, combining experimental evidences with molecular modeling simulations, we propose a detailed reaction scheme for Ty-mediated oxidation of monochlorophenols. © 2010 Elsevier Inc. All rights reserved.

In this issue of Structure, Hoyland and colleagues describe the structure of a peptidoglycan L,D-carboxypeptidase in both substrate-bound and apoenzyme forms. These studies reveal the basis for enzyme specificity and assist greatly in a field where form and function overlap.

The enzyme specificity in the biosynthesis of prostaglandins has been investigated by incubation of a particulate fraction of sheep vesicular glands with substituted cis-8,cis-11,cis-14-eicosatrienoic acids. Conversions were always lower than with the unsubstituted acid (20:3). In the 2-substituted series, a conversion of up to 50% was found for 2-methoxycarbonyl- ; 2-methyl- ; 2-hydroxymethyl- ; 2-butyl- ; 2-methoxy- ; 2-methoxymethylene- ; 2-fluoro- ; 2-bromo- ; 2-cyano- ; and 2-phenyl-20:3. No conversion was found for 2-hydroxycarbonyl- ; 2-heptoxycarbonyl- ; 2-amino- ; and 2-acetamido-20:3. In some cases, a slight preference of the enzymes for the R configuration (2-phenyl- ; 2-methyl-20:3) was noted. For di-substituted acids, yields of up to 70% were found for 2-cyano-2-butyl- ; 2,3-cis- and 2,3-trans-methylene- ; 3,3-dimethyl-20:3, but 4,4-dimethyl-20:3 was not converted. However, 5-yne-20:3 was again a substrate (25% conversion). Substitution at the methyl end of the precursor acid resulted in 34% conversion with 19-methyl-20:3, but 18-methyl-20:3 was not converted. Biological activities of substituted prostaglandins were, in general, much less than those of PGE1, but for 19-methyl-PGE1, smooth muscle-stimulating activity was 1.6 times that of PGE1. For some substituted prostaglandins (2-fluoro- ; 2-cyano-PGE1), an appreciable activity in one biological test system was found but very little in others.

Microbial lipase from Thermomyces lanuginosus (formerly Humicola lanuginosa ) was immobilized by covalent binding on a novel microporous styrene–divinylbenzene polyglutaraldehyde copolymer (STY–DVB–PGA). The response surface methodology (RSM) was used to optimize the conditions for the maximum activity and to understand the significance and interaction of the factors affecting the specific activity of immobilized lipase. The central composite design was employed to evaluate the effects of enzyme concentration (4–16%, v/v), pH (6.0–8.0), buffer concentration (20–100 mM) and immobilization time (8–40 h) on the specific activity. The results indicated that enzyme concentration, pH and buffer concentration were the significant factors on the specific activity of immobilized lipase and quadratic polynomial equation was obtained for specific activity. The predicted specific activity was 8.78 μmol p -NP/mg enzyme min under the optimal conditions and the subsequent verification experiment with the specific activity of 8.41 μmol p -NP/mg enzyme min confirmed the validity of the predicted model. The lipase loading capacity was obtained as 5.71 mg/g support at the optimum conditions. Operational stability was determined with immobilized lipase and it indicated that a small enzyme deactivation (12%) occurred after being used repeatedly for 10 consecutive batches with each of 24 h. The effect of methanol and tert -butanol on the specific activity of immobilized lipase was investigated. The immobilized lipase was almost stable in tert -butanol (92%) whereas it lost most of its activity in methanol (80%) after 15 min incubation.

Serum sphingomyelin (SM) has predictive value in the development of atherosclerosis. Furthermore, SM plays important roles in cell membrane structure, signal transduction pathways, and lipid raft formation. A convenient enzymatic method for SM is available for routine laboratory practice, but the enzyme specificity is not sufficient because of nonspecific reactions with lysophosphatidylcholine (LPC). Based on the differential specificity of selected enzymes toward choline-containing phospholipids, a two-step assay for measuring SM was constructed and its performance was evaluated using sera from healthy individuals on a Hitachi 7170 autoanalyzer. Results from this assay were highly correlated with theoretical serum SM concentrations estimated by subtracting phosphatidylcholine (PC) and LPC concentrations from that of total phospholipids determined using previously established methods. There was a good correlation between the results of SM assayed by the proposed method and the existing enzymatic method in sera from healthy individuals. Moreover, the proposed method was superior to the existing method in preventing nonspecific reactions with LPC present in sera. The proposed method does not require any pretreatment, uses 2.5 μl of serum samples, and requires only 10 min on an autoanalyzer. This high-throughput method can measure serum SM with sufficient specificity for clinical purposes and is applicable in routine laboratory practice.

How different helicase families with a conserved catalytic ‘helicase core’ evolved to function on varied RNA and DNA substrates by diverse mechanisms remains unclear. In this study, we used Mss116, a yeast DEAD-box protein that utilizes ATP to locally unwind dsRNA, to investigate helicase specificity and mechanism. Our results define the molecular basis for the substrate specificity of a DEAD-box protein. Additionally, they show that Mss116 has ambiguous substrate-binding properties and interacts with all four NTPs and both RNA and DNA. The efficiency of unwinding correlates with the stability of the ‘closed-state’ helicase core, a complex with nucleotide and nucleic acid that forms as duplexes are unwound. Crystal structures reveal that core stability is modulated by family-specific interactions that favor certain substrates. This suggests how present-day helicases diversified from an ancestral core with broad specificity by retaining core closure as a common catalytic mechanism while optimizing substrate-binding interactions for different cellular functions. DOI: http://dx.doi.org/10.7554/eLife.04630.001, eLife digest Living cells store their genetic material as DNA, which can be copied to make another molecule called RNA. DNA consists of two strands that are wound around each other in a double helix. RNA is made in a similar way to DNA, but it is usually present as a single strand that folds into a three-dimensional structure that is held in shape by regions of the molecule interacting with each other. Before DNA and RNA can perform their essential tasks in cells, enzymes called helicases must separate the interacting strands. A large group of helicases, known as superfamily 1 and 2, are involved in virtually all aspects of the control of RNA and DNA structure. All of these helicases contain a region called the ‘helicase core’, but they work in different ways. For example, some move along the DNA or RNA strand whilst they unwind it, while others can unwind RNA without moving. It remains unclear how these helicases have evolved different ways to unwind DNA and RNA structures using the same helicase core. Mallam et al. have now analyzed a helicase from yeast called Mss116, which belongs to superfamily 2. It is known from previous work that Mss116 binds to many different RNA molecules and—unlike most other helicases—it does not require any extra proteins to help. This makes it an ideal model to study the properties of a helicase core on its own. Helicases use the energy released from breaking down molecules called nucleotides to pull apart the bonds that hold DNA and RNA strands together. The experiments found that for Mss116, a nucleotide called ATP is the best for providing the energy needed to unwind RNA but other nucleotides can work less efficiently. The experiments also show that in addition to RNA, Ms116 is able to unwind double-stranded DNA molecules that have a certain shape. Using a technique called X-ray crystallography, Mallam et al. observed the structure of the Mss116 core when it is bound to RNA and DNA. While there are some shared points of contact between the helicase and the DNA or RNA, there are more points of contact between Mss116 and RNA than between Mss116 and DNA. Mallam et al. propose that present-day helicases have diversified from enzymes that had broad specificity for RNA and DNA, by optimizing interactions that favor the binding of particular nucleotides and nucleic acids. These changes enabled the helicases to become a versatile set of tools that control the structure of RNA or DNA in different ways. DOI: http://dx.doi.org/10.7554/eLife.04630.002

SummaryWe created a metagenome expression library from the brine:seawater interface of the Urania hypersaline basin, screened it for esterases, and characterized five of these. Two had no significant sequence homology to known esterases, hydrolyzed both carboxylesters and thioesters, and exhibited unusual, habitat-specific characteristics (preference for high hydrostatic pressure and salinity). One has an unusual structural signature incorporating three catalytic active centers mediating distinct hydrolytic activities and an adaptive tertiary-quaternary structure that alters between three molecular states, according to the prevailing physicochemical conditions. Some of the esterases have high activities, specificities, enantioselectivities, and exceptional stability in polar solvents, and they are therefore potentially useful for industrial biotransformations. One possesses the highest enantioselectivity toward an ester of the important chiral synthon solketal (E: 126[S]; 98%ee).

We present a rapid screening method for monitoring enzyme specificity using both combinatorial chemistry and mass spectrometry where, as an example, the substrate specificity of peptidylglycine alpha-amidating enzyme was determined and compared against a conventional quantitative technique. Whereas alternative methods for library screening are generally limited to certain enzymes and can present difficulties in the synthesis or derivatization of potential substrates, the approach we call chirality-based isotope labeling for a library of substrates (CHILLS) does not fall short to such limitations, since we exploit the inherent stereospecificity of enzymes to determine preferred substrates. Additionally, the CHILLS method generates accurate results, as compared to typical screening procedures that require tedious method development, because the synthesized library contains a structurally similar internal standard for each individual library component in order to quantitate the progress of enzymatic reactions.

Chagas' disease, caused by Trypanosoma cruzi, affects about 18 million people in Latin America, and no effective treatment is available to date. To acquire sialic acid from the host glycoconjugates, T. cruzi expresses an unusual surface sialidase with trans-sialidase activity (TcTS) that transfers the sugar to parasite mucins. Surface sialic acid was shown to have relevant functions in protection of the parasite against the lysis by complement and in mammalian host cell invasion. The recently determined 3D structure of TcTS allowed a detailed analysis of its catalytic site and showed the presence of a lactose-binding site where the β-linked galactose accepting the sialic acid is placed. In this article, the acceptor substrate specificity of lactose derivatives was studied by high pH anion-exchange chromatography with pulse amperometric detection. The lactose open chain derivatives lactitol and lactobionic acid, as well as other derivatives, were found to be good acceptors of sialic acid. Lactitol, which was the best of the ones tested, effectively inhibited the transfer of sialic acid to N-acetyllactosamine. Furthermore, lactitol inhibited parasite mucins re-sialylation when incubated with live trypanosomes and TcTS. Lactitol also diminished the T. cruzi infection in cultured Vero cells by 20-27%. These results indicate that compounds directed to the lactose binding site might be good inhibitors of TcTS. © Oxford University Press 2004; all rights reserved. Fil:Agustí, R. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Ratier, L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:de Lederkremer, R.M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.

The stability of almond ?-glucosidase in five different organic media was evaluated. After 1 hour of incubation at 30�C, the enzyme retained 95, 91, 81, 74 and 56% relative activity in aqueous solutions [30% (v/v)] of dioxane, DMSO, DMF, acetone and acetonitrile, respectively. Transglucosylation involving p-nitrophenyl ?-D-glucopyranoside as donor and ?-1-N-acetamido-D-glucopyranose, which is a glycosylasparagine mimic, as acceptor was explored under different reaction conditions using almond ?-glucosidase and cloned Pichia etchellsii ?-glucosidase II. The yield of disaccharides obtained in both reactions turned out to be 3%. Both enzymes catalyzed the formation of (1 ? 3)- as well as (1 ? 6)-regioisomeric disaccharides, the former being the major product in cloned ?-glucosidase II reaction while the latter predominated in the almond enzyme catalyzed reaction. Use of ?-1-N-acetamido-D-mannopyranose and ?-1-N-acetamido-2-acetamido-2-deoxy-D-glucopyranose as acceptors in almond ?-glucosidase catalyzed reactions, however, did not afford any disaccharide products revealing the high acceptor specificity of this enzyme. ? 2004 Taylor & Francis Ltd.

The biosynthesis of monolignols is one of the most studied pathways of plant natural product biosynthesis. However, the pathway has recently undergone considerable revision, and it would appear that our understanding of the exact routes for synthesis of the building blocks of lignin and lignans is still not fully understood. Early studies of in vitro enzyme specificity failed to appreciate the catalytic promiscuity of some of the enzymes of the monolignol pathway, and the evolving model of a metabolic grid for monolignol biosynthesis may fail to appreciate the possible extent of metabolic channeling within the pathway. New approaches to the study of monolignol biosynthesis include genomics, advanced cellular imaging techniques, and transgenic manipulation. This article summarizes the use of these approaches to gain a better understanding of the operation of a complex metabolic pathway.

Azo dyes, which re characterized by azo bonds, are a predominant class of colorants used in tattooing, cosmetics, foods, textile and consumer products. Laccases (EC 1.10.3.2), lignin peroxidases (EC 1.11.1.14) , Azo reductases (EC 1.7.1.6) of different micro organisms are mainly useful for the development of biodegradation systems as they catalyse reductive cleavage of azo groups (­N=N­) . Laccases have very broad substrate specificity with respect to the electron donor and is capable of oxidizing phenols and aromatic amines. Azoreductase belongs to the family of oxidoreductases, acting on other nitrogenous compounds as donors with NAD+ or NADP+ as acceptor. Lignin peroxidase enzymes are highly non-specific and are well reported to decolourize various dyes We have developed BiodEnz database by collecting information like strains that produce particular enzymes, azo dyes that are degraded , substrate specificity, molecular weight, the optimum temperature and pH, sequence data of the above enzymes ,as the most effective inoculants used for bioremediation are able to degrade dyes over a broad concentration range, tolerate a range of environmental conditions of temperature, pH, and activity of the enzymes. The database can be searched by using a user friendly web interface. Availability The database is available for free at http://www.biodenzdatabase.in

An aerobic xylanolytic moderately halophilic and alkali-tolerant bacterium, Gracilibacillus sp. TSCPVG, produces multiple xylanases of unusual halo-acid-alkali-thermo-stable nature. The purification of a major xylanase from TSCPVG culture supernatant was achieved by hydrophobic and gel permeation chromatographic methods followed by electroelution from preparatory PAGE. The molecular mass of the purified xylanase was 42 kDa, as analyzed by SDS-PAGE, with a pI value of 6.1. It exhibited maximal activity in 3.5 % NaCl and retained over 75 % of its activity across the broad salinity range of 0-30 % NaCl, indicating a high halo-tolerance. It showed maximal activity at pH 7.5 and had retained 63 % of its activity at pH 5.0 and 73 % at pH 10.5, signifying the tolerance to broad acid to alkaline conditions. With birchwood xylan as a substrate, K m and specific activity values were 21 mg/ml and 1,667 U/mg, respectively. It is an endoxylanase that degrades xylan to xylose and xylobiose and had no activity on p-nitrophenyl-?-d-xylopyranoside, p-nitrophenyl-?-d-glucopyranoside, p-nitrophenyl acetate, carboxymethylcellulose, and filter paper. Since it showed remarkable stability over different salinities, broad pH, and temperature ranges, it is promising for application in many industries. � 2014 Springer Science+Business Media.

SMO (spermine oxidase) and APAO (acetylpolyamine oxidase) are flavoenzymes that play a critical role in the catabolism of polyamines. Polyamines are basic regulators of cell growth and proliferation and their homoeostasis is crucial for cell life since dysregulation of polyamine metabolism has been linked with cancer. In vertebrates SMO specifically catalyses the oxidation of spermine, whereas APAO displays a wider specificity, being able to oxidize both N1 -acetylspermine and N1 -acetylspermidine, but not spermine. The molecular bases of the different substrate specificity of these two enzymes have remained so far elusive. However, previous molecular modelling, site-directed mutagenesis and biochemical characterization studies of the SMO enzyme–substrate complex have identified Glu216–Ser218 as a putative active site hot spot responsible for SMO substrate specificity. On the basis of these analyses, the SMO double mutants E216L/S218A and E216T/S218A have been produced and characterized by CD spectroscopy and steady-state and rapid kinetics experiments. The results obtained demonstrate that mutation E216L/S218A endows SMO with N1 -acetylspermine oxidase activity, uncovering one of the structural determinants that confer the exquisite and exclusive substrate specificity of SMO for spermine. These results provide the theoretical bases for the design of specific inhibitors either for SMO or APAO. Abbreviations: APAO, acetylpolyamine oxidase; FMS1, fenpropimorph-resistance multicopy suppressor 1; MmSMO, Mus musculus SMO; N1-AcSpd, N1-acetylSpd; N1-AcSpm, N1-acetylSpm; PA, polyamine; PAO, PA oxidase; Spd, spermidine; Spm, spermine; SMO, Spm oxidase

In the past decade, mass spectrometry (MS), coupled with electrospray ionization (ESI) has been extensively applied to the study of intact proteins and their complexes, often without the requirement of labels. Solvent conditions (for example, pH, ionic strength, and concentration) affect the observed desolvated species; the ease of altering such extrinsic factors renders ESI-MS an appropriate method by which to consider the range of conformational states that proteins may occupy, including natively folded, disordered and arnyloid. Rotationally averaged collision cross sections of the ionized forms of proteins, provided by the combination of mass spectrometry and ion mobility (IM-MS), are also instructive in exploring conformational landscapes in the absence of solvent Here, we ask the following question: "If the only technique you had was ESI-IM-MS, what information would it provide on the structural preferences of an unknown protein?" We have selected 20 different proteins, both monomeric and multimeric, ranging in mass from 2846 Da (melittin) to 150 kDa (Immunoglobulin G), and we consider how they are presented to a mass spectrometer under different solvent conditions Mass spectrometery allows us to distinguish which of these proteins are structured (melittin, human beta defensin 1, truncated human lymphotactin, Cytochrome C, holo hemoglobin a, ovalbumin, human transthyretin, avidin, bovine serum albumin, concanavalin, human serum amyloid protein, and Immunoglobulin G) from those that contain at least some regions of disorder (human lynaphotactin, N-terminal p53, alpha-Synuclein, N-terminal MDM2, and p53 DNA binding domain) or denatured due to solvent conditions (ubiquitin, apo hemoglobin-alpha, apo hemoglobin-beta) by considering two experimental parameters: the range of charge states occupied by the protein (Delta z) and the range of collision cross sections in which the protein is observed (Delta CCS). We also provide a simple model to predict the difference between the collision cross sections of the most compact and the most extended form of a given protein, based on the volume of the amino acids it contains. We compare these calculated parameters with experimental values. In addition, we consider the occupancy of conformations based on the intensities of ions in the mass spectra. This allows us to qualitatively predict the potential energy landscape of each protein. Our empirical approach to assess order or disorder is shown to be more accurate than the use of charge hydropathy plots, which are frequently used to predict disorder, and could provide an initial route to characterization. Finally, we present an ESI-IM-MS methodology to determine if a given protein is structured or disordered.

Benzyl alcohol dehydrogenase fromAcinetobacter calcoaceticus(AC-BADH) and TOL plasmid-encoded benzyl alcohol dehydrogenase fromPseudomonas putida(TOL-BADH) have previously been shown to oxidize a variety of aromatic alcohols but not aliphatic substrates. Here, we have expressed the genes for AC-BADH and TOL-BADH inEscherichia coli,purified the resulting over-expressed enzymes, and shown that each is an effective catalyst of both benzylic and allylic alcohol oxidation, but not of oxidation of nonallylic analogs. Enzyme specificity (kcat/Km) for both enzymes was higher with an aliphatic, allylic alcohol (3-methyl-2-buten-1-ol) than with benzyl alcohol. These results suggest that bacterial benzyl alcohol dehydrogenases use the resonance stabilization provided by allylic and benzylic alcohols to promote catalysis.

3,4-Dihydroxyphenylalanine (Dopa) decarboxylase is a stereospecific pyridoxal 5′-phosphate (PLP)-dependent α-decarboxylase that converts l-aromatic amino acids into their corresponding amines. We now report that reaction of the enzyme with d-5-hydroxytryptophan or d-Dopa results in a time-dependent inactivation and conversion of the PLP coenzyme to pyridoxamine 5′-phosphate and PLP-d-amino acid Pictet-Spengler adducts, which have been identified by high performance liquid chromatography. We also show that the reaction specificity of Dopa decarboxylase toward aromatic amines depends on the experimental conditions. Whereas oxidative deamination occurs under aerobic conditions (Bertoldi, M., Moore, P. S., Maras, B., Dominici, P., and Borri Voltattorni, C. (1996) J. Biol. Chem. 271, 23954–23959; Bertoldi, M., Dominici, P., Moore, P. S., Maras, B., and Borri Voltattorni, C. (1998)Biochemistry 37, 6552–6561), half-transamination and Pictet-Spengler reactions take place under anaerobic conditions. Moreover, we examined the reaction specificity of nicked Dopa decarboxylase, obtained by selective tryptic cleavage of the native enzyme between Lys334 and His335. Although this enzymatic species does not exhibit either decarboxylase or oxidative deamination activities, it retains a large percentage of the native transaminase activity toward d-aromatic amino acids and displays a slow transaminase activity toward aromatic amines. These transamination reactions occur concomitantly with the formation of cyclic coenzyme-substrate adducts. Together with additional data, we thus suggest that native Dopa decarboxylase can exist as an equilibrium among “open,” “half-open,” and “closed” forms.

The in vitro use of enzymes for polymer synthesis is considered as a means of attempting to emulate and extend the range of polymers found in nature which are readily biodegradable and have superb control over structure and properties. The issues raised in the use of non-conventional reaction environments are discussed. These include (i) the environmental compatibility of the synthesised polymer, the (often modified) enzyme, and the other components of the system such as organic solvents and additives, (ii) the factors which need to be considered in order to control the enzyme specificity and stability, and (iii) tests and their validity for assessing the biodegradability of all of the materials in the system. Examples of a wide range of synthesised polymers are provided. These include those from smaller units composed of various saccharides, lignins and proteins and related compounds. In addition, examples of enzymic modification of the architecture of existing polymers composed of these substances are given. Finally, cases are described where saccharides, lignins and protein-based substances are incorporated into other polymeric materials, either as grafts or by inclusion in the main chain, using either enzymic or chemicoenzymic procedures. © 1998 Society of Chemical Industry

A time-resolved kinetic study in acetonitrile and a theoretical investigation of hydrogen abstraction reactions from N,N-dimethylformamide (DMF) and N,N-dimethylacetamide (DMA) by the cumyloxyl (CumO•) and benzyloxyl (BnO•) radicals was carried out. CumO • reacts with both substrates by direct hydrogen abstraction. With DMF, abstraction occurs from the formyl and N-methyl C-H bonds, with the formyl being the preferred abstraction site, as indicated by the measured k H/kD ratios and by theory. With DMA, abstraction preferentially occurs from the N-methyl groups, whereas abstraction from the acetyl group represents a minor pathway, in line with the computed C-H BDEs and the kH/kD ratios. The reactions of BnO• with both substrates were best described by the rate-limiting formation of hydrogen-bonded prereaction complexes between the BnO• α-C-H and the amide oxygen, followed by intramolecular hydrogen abstraction. This mechanism is consistent with the very large increases in reactivity measured on going from CumO• to BnO• and with the observation of kH/kD ratios close to unity in the reactions of BnO•. Our modeling supports the different mechanisms proposed for the reactions of CumO• and BnO • and the importance of specific substrate/radical hydrogen bond interactions, moreover providing information on the hydrogen abstraction selectivity. © 2013 American Chemical Society.

Co-metabolism is a term used for biochemically undefined observations in catabolic enzyme substrate specificity, the interplay between enzyme specificity and metabolic regulation, the metabolic interdependence of microorganisms, and co-substrate requirements in the catabolism of xenobiotic compounds. Recent findings in these four areas of microbial biochemistry necessitate a re-evaluation of the widespread use of the term.

1. Four different rat glutathione S-transferase (GST) isoenzymes, belonging to three different classes, were examined for their GSH conjugating capacity towards 11 2-substituted 1-chloro-4-nitrobenzene derivatives. Significant differences were found in their enzyme kinetic parameters K(m), k(cat) and k(cat)/K(m). 2. Substrates with bulky substituents on the ortho-position appeared to have high affinities (low K(m)'s) for the active site of the GST-isoenzymes, suggesting that there is sufficient space in this area of the active site. A remarkably high K(m) (low affinity) was found for 2-chloro-5-nitropyridine towards all GST-isoenzymes examined. 3. GST 3-3 catalysed the reaction between GSH and the substrates most efficiently (high k(cat)) compared with the other GST-isoenzymes. Moreover, GST 3-3 showed clear substrate selectivities towards the substrates with a trifluoromethyl-, chlorine- and bromine-substituent. 1-Chloro-2,4-dinitrobenzene and 2-chloro-5-nitrobenzonitrile were most efficiently conjugated by all four GST-isoenzymes examined. 4. When the rate of the conjugation reactions was followed, a linear increase of formation of GS-conjugate could be seen for 2-chloro-5-nitrobenzonitrile during a much longer period of time than for 1-chloro-2,4-dinitrobenzene with all GST-isoenzymes examined. Therefore, it is suggested that 2-chloro-5-nitrobenzonitrile might be recommended as an alternative model substrate in GST-research. Chemicals/CAS: Dinitrochlorobenzene, 97-00-7; Glutathione Transferase, EC 2.5.1.18; Isoenzymes

Cyclohexylamine oxidase (CHAO) is a flavoprotein first described in Brevibacterium oxydans strain IH-35A that carries out the initial step of the degradation of the industrial chemical cyclohexylamine to cyclohexanone. We have cloned and expressed in Escherichia coli the CHAO-encoding gene (chaA) from B. oxydans, purified CHAO and determined the structures of both the holoenzyme form of the enzyme and a product complex with cyclohexanone. CHAO is a 50 kDa monomer with a PHBH fold topology. It belongs to the flavin monooxygenase family of enzymes and exhibits high substrate specificity for alicyclic amines and sec-alkylamines. The overall structure is similar to that of other members of the flavin monooxygenase family, but lacks either of the C- or N-terminal extensions observed in these enzymes. Active site features of the flavin monooxygenase family are conserved in CHAO, including the characteristic aromatic cage. Differences in the orientations of residues of the CHAO aromatic cage result in a substrate-binding site that is more open than those of its structural relatives. Since CHAO has a buried hydrophobic active site with no obvious route for substrates and products, a random acceleration molecular dynamics simulation has been used to identify a potential egress route. The path identified includes an intermediate cavity and requires transient conformation changes in a shielding loop and a residue at the border of the substrate-binding cavity. These results provide a foundation for further studies with CHAO aimed at identifying features determining substrate specificity and for developing the biocatalytic potential of this enzyme. © 2013 Mirza et al.

A recently solved Dnmt1-DNA crystal structure revealed several enzyme–DNA contacts and large structural rearrangements of the DNA at the target site, including the flipping of the non-target strand base of the base pair flanking the CpG site and formation of a non-canonical base pair between the non-target strand Gua and the flanking base pair. Here, we show that the contacts of the enzyme to the target base and the Gua:5mC base pair that are observed in the structure are very important for catalytic activity. The contacts to the non-target strand Gua are not important since its exchange by Ade stimulated activity. Except target base flipping, we could not find evidence that the DNA rearrangements have a functional role.

Submitted by Vitor Silverio Rodrigues (vitorsrodrigues@reitoria.unesp.br) on 2014-05-27T11:26:27Z No. of bitstreams: 0Bitstream added on 2014-05-27T14:42:13Z : No. of bitstreams: 1 2-s2.0-84860325647.pdf: 962503 bytes, checksum: 3c968603a10dad95fcadd1d5620a13a7 (MD5) Made available in DSpace on 2014-05-27T11:26:27Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-04-27 l-Amino acid oxidases (LAAOs) are flavoenzymes that catalytically deaminate l-amino acids to corresponding α-keto acids with the concomitant production of ammonia (NH 3) and hydrogen peroxide (H 2O 2). Particularly, snake venom LAAOs have been attracted much attention due to their diverse clinical and biological effects, interfering on human coagulation factors and being cytotoxic against some pathogenic bacteria and Leishmania ssp. In this work, a new LAAO from Bothrops jararacussu venom (BjsuLAAO) was purified, functionally characterized and its structure determined by X-ray crystallography at 3.1å resolution. BjsuLAAO showed high catalytic specificity for aromatic and aliphatic large side-chain amino acids. Comparative structural analysis with prokaryotic LAAOs, which exhibit low specificity, indicates the importance of the active-site volume in modulating enzyme selectivity. Surprisingly, the flavin adenine dinucleotide (FAD) cofactor was found in a different orientation canonically described for both prokaryotic and eukaryotic LAAOs. In this new conformational state, the adenosyl group is flipped towards the 62-71 loop, being stabilized by several hydrogen-bond interactions, which is equally stable to the classical binding mode. © 2012 Elsevier Inc. Centro Multiusuário de Inovação Biomolecular Departamento de Física Universidade Estadual Paulista (UNESP), 15054-000 São José do Rio Preto, SP Laboratório Nacional de Biociências Centro Nacional de Pesquisa em Energia e Materiais, Campinas, 13083-970 SP Institute of Biochemistry and Molecular Biology University of Hamburg Laboratory of Structural Biology of Infection and Inflammation, C/o DESY, Notkestrasse 85, Build. 22a, D-22603 Hamburg Centro Multiusuário de Inovação Biomolecular Departamento de Física Universidade Estadual Paulista (UNESP), 15054-000 São José do Rio Preto, SP

Crown ethers first came to prominence in the late 1960s through the pioneering work of Charles Pedersen. The discovery that they bind cations based on complementarity between the crown ether cavity and the size of the cation has been a driving force in macrocyclic and supramolecular chemistry ever since. Many derivatives have been synthesized, including those with side arms known collectively as lariat ethers, and their cation selectivity used in molecular sensors. The history of crown and lariat ethers is discussed together with their syntheses, structural and binding evidence for size selectivity, and their industrial and clinical applications. Crown and lariat ethers have found use as phase-transfer catalysts, modifiers for chromatographic media, sensors for numerous chemical species, critical analyte detectors, and can even enhance insecticide activity. They have been used to probe important biological phenomena, including enzyme specificity, the nature of in vivo cation-π interactions in proteins and transmembrane ion transport, through the synthesis of model compounds. Keywords: crown ether; lariat ether; macrocycle; template synthesis; azacrown; thiacrown, anticrown

The effective flux between phospholipids and neutral lipids is critical for a high level of biosynthesis and accumulation of very-long-chain polyunsaturated fatty acids (VLCPUFAs), such as arachidonic acid (ARA; 20:4n-6), eicosapentaenoic acid (EPA; 20:5n-3), and docosahexaenoic acid (DHA; 22:6n-3). Here we describe a cDNA ( PiCPT1 ) from Phytophthora infestans , a VLCPUFA-producing oomycete, that may have a role in acyl trafficking between diacylglycerol (DAG) and phosphatidylcholine (PC) during the biosynthesis of VLCPUFAs. The cDNA encodes a polypeptide of 393 amino acids with a conserved CDP-alcohol phosphotransferase motif and approximately 27% amino acid identity to the Saccharomyces cerevisiae cholinephosphotransferase (ScCPT1). In vitro assays indicate that PiCPT1 has high cholinephosphotransferase (CPT) activity but no ethanolaminephosphotransferase (EPT) activity. Substrate specificity assays show that it prefers VLCPUFA-containing DAGs, such as ARA DAG and DHA DAG, as substrates. Real-time PCR analysis reveals that expression of PiCPT1 was upregulated in P. infestans organisms fed with exogenous VLCPUFAs. These results lead us to conclude that PiCPT1 is a VLCPUFA-specific CPT which may play an important role in shuffling VLCPUFAs from DAG to PC in the biosynthesis of VLCPUFAs in P. infestans .