Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:3.5.1.4 (deaminase)
5,113 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

A comparative study of amino acid sequence and physicochemical properties indicates the affiliation of an amidase from Rhodococcus rhodochrous M8 (EC 3.5.1.4) to the nitrilase/cyanide hydratase family. Cluster analysis and multiple alignments show that Cys166 is an active site nucleophile. The enzyme has been shown to be a typical aliphatic amidase, being the most active toward short-chain linear amides. Small polar molecules such as hydroxylamine and O-methyl hydroxylamine can serve as effective external nucleophiles in acyl transfer reactions. The kinetics of the industrially important amidase-catalyzed acrylamide hydrolysis has been studied over a wide range of substrate concentrations; inhibition during enzymatic hydrolysis by the substrate and product (acrylic acid) has been observed; an adequate kinetic scheme has been evaluated and the corresponding kinetic parameters have been determined.
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PMID:Aliphatic amidase from Rhodococcus rhodochrous M8 is related to the nitrilase/cyanide hydratase family. 1633 90

This study aimed to construct an acetonitrile-containing waste treatment process by using nitrile-degrading microorganisms. To degrade high concentrations of acetonitrile, the microorganisms were newly acquired from soil and water samples. Although no nitrilase-producing microorganisms were found to be capable of degrading high concentrations of acetonitrile, the resting cells of Rhodococcus pyridinivorans S85-2 containing nitrile hydratase could degrade acetonitrile at concentrations as high as 6 M. In addition, an amidase-producing bacterium, Brevundimonas diminuta AM10-C-1, of which the resting cells degraded 6 M acetamide, was isolated. The combination of R. pyridinivorans S85-2 and B. diminuta AM10-C-1 was tested for the conversion of acetonitrile into acetic acid. The resting cells of B. diminuta AM10-C-1 were added after the first conversion involving R. pyridinivorans S85-2. Through this tandem process, 6 M acetonitrile was converted to acetic acid at a conversion rate of >90% in 10 h. This concise procedure will be suitable for practical use in the treatment of acetonitrile-containing wastes on-site.
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PMID:Convenient treatment of acetonitrile-containing wastes using the tandem combination of nitrile hydratase and amidase-producing microorganisms. 1640 66

In soil the herbicide 2,6-dichlorobenzonitrile (dichlobenil) is degraded to the persistent metabolite 2,6-dichlorobenzamide (BAM) which has been detected in 19% of samples taken from Danish groundwater. We tested if common soil bacteria harbouring nitrile-degrading enzymes, nitrile hydratases or nitrilases, were able to degrade dichlobenil in vitro. We showed that several strains degraded dichlobenil stoichiometrically to BAM in 1.5-6.0 days; formation of the amide intermediate thus showed nitrile hydratase rather than nitrilase activity, which would result in formation of 2,6-dichlorobenzoic acid. The non-halogenated analogue benzonitrile was also degraded, but here the benzamide intermediate accumulated only transiently showing nitrile hydratase followed by amidase activity. We conclude that a potential for dichlobenil degradation to BAM is found commonly in soil bacteria, whereas further degradation of the BAM intermediate could not be demonstrated.
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PMID:Transformation of the herbicide 2,6-dichlorobenzonitrile to the persistent metabolite 2,6-dichlorobenzamide (BAM) by soil bacteria known to harbour nitrile hydratase or nitrilase. 1649 93

It is shown that potentially persistent transformation products can be formed from the herbicides bromoxynil (3,5-dibromo-4-hydroxybenzonitrile) and ioxynil (3,5-diiodo-4-hydroxybenzonitrile), and possible leaching to groundwater is discussed. A similar process to the formation of BAM (2,6-dichlorobenzamide) from the herbicide dichlobenil (2,6-dichlorobenzonitrile) can be anticipated as bromoxynil and ioxynil are analogues of dichlobenil and they are degraded by the enzymes nitrilase, nitrile hydratase and amidase. A biodegradation study using cultured Variovorax sp. DSM 11402, a species commonly found in soil, demonstrated that ioxynil and bromoxynil were fully transformed into their corresponding amides in 2-5 days. These amides were not further degraded within 18 days, and formation of other degradation products was not observed. These results are in agreement with biodegradation experiments with dichlobenil. In soil, dichlobenil is transformed into its only observed degradation product BAM, which is persistent and mobile, and has been found in 19% of 5000 samples of Danish groundwater. Variovorax sp. is known to degrade the non-halogenated analogue benzamide, suggesting that degradation of the three amides may be hindered by the halogenated substituents (meta-Br; meta-I; ortho-Cl). This hypothesis is supported by QSAR modelling of fundamental properties. Using a new optimised liquid chromatography-tandem mass spectrometry (LC-MS/MS) method, the sorption and desorption properties of bromoxynil and ioxynil were characterised in sandy topsoil at four concentration levels. The estimated sorption coefficient K(d) was 1.4 L kg(-1) for bromoxynil and 5.4 L kg(-1) for ioxynil, indicating weak to moderate sorption to topsoil. Desorption of the herbicides showed that they were strongly and irreversible bound to the soil (K(des) > K(d)). The amount of herbicide desorbed depended on the initial concentration level. At low levels, K(des) values were higher, indicating stronger binding than at higher levels. The isocratic LC-MS/MS method developed for simultaneous detection of bromoxynil, ioxynil and their main degradation products is described. Using negative electrospray ionisation (ESI-), the detection limits were 0.4-1.0 microg L(-1), with relative standard deviations of 4-10% (n = 10) using direct injection without clean-up steps. The standard curves showed linearity in the range 5-100 microg L(-1) with r(2) > 0.992.
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PMID:Demonstrating formation of potentially persistent transformation products from the herbicides bromoxynil and ioxynil using liquid chromatography-tandem mass spectrometry (LC-MS/MS). 1712 53

The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase enzyme superfamily. It converts amides to the corresponding acids and ammonia and has application as an industrial catalyst. RAPc8 amidase has been cloned and functionally expressed in Escherichia coli and has been purified by heat treatment and a number of chromatographic steps. The enzyme was crystallized using the hanging-drop vapour-diffusion method. Crystals produced in the presence of 1.2 M sodium citrate, 400 mM NaCl, 100 mM sodium acetate pH 5.6 were selected for X-ray diffraction studies. A data set having acceptable statistics to 1.96 A resolution was collected under cryoconditions using an in-house X-ray source. The space group was determined to be primitive cubic P4(2)32, with unit-cell parameter a = 130.49 (+/-0.05) A. The structure was solved by molecular replacement using the backbone of the hypothetical protein PH0642 from Pyrococcus horikoshii (PDB code 1j31) with all non-identical side chains substituted with alanine as a probe. There is one subunit per asymmetric unit. The subunits are packed as trimers of dimers with D3 point-group symmetry around the threefold axis in such a way that the dimer interface seen in the homologues is preserved.
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PMID:The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packing. 1714 91

Helicobacter pylori AmiF formamidase that hydrolyzes formamide to produce formic acid and ammonia belongs to a member of the nitrilase superfamily. The crystal structure of AmiF was solved to 1.75A resolution using single-wavelength anomalous dispersion methods. The structure consists of a homohexamer related by 3-fold symmetry in which each subunit has an alpha-beta-beta-alpha four-layer architecture characteristic of the nitrilase superfamily. One exterior alpha layer faces the solvent, whereas the other one associates with that of the neighbor subunit, forming a tight alpha-beta-beta-alpha-alpha-beta-beta-alpha dimer. The apo and liganded crystal structures of an inactive mutant C166S were also determined to 2.50 and 2.30 A, respectively. These structures reveal a small formamide-binding pocket that includes Cys(166), Glu(60), and Lys(133) catalytic residues, in which Cys(166) acts as a nucleophile. Analysis of the liganded AmiF and N-carbamoyl d-amino acid amidohydrolase binding pockets reveals a common Cys-Glu-Lys triad, another conserved glutamate, and different subsets of ligand-binding residues. Molecular dynamic simulations show that the conserved triad has minimal fluctuations, catalyzing the hydrolysis of a specific nitrile or amide in the nitrilase superfamily efficiently.
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PMID:Crystal structure of Helicobacter pylori formamidase AmiF reveals a cysteine-glutamate-lysine catalytic triad. 1730 42

An amidase (EC 3.5.1.4) in branch 2 of the nitrilase superfamily, from the thermophilic strain Geobacillus pallidus RAPc8, was produced at high expression levels (20 U/mg) in small-scale fermentations of Escherichia coli. The enzyme was purified to 90% homogeneity with specific activity of 1,800 U/mg in just two steps, namely, heat-treatment and gel permeation chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and electron microscopic (EM) analysis of the homogenous enzyme showed the native enzyme to be a homohexamer of 38 kDa subunits. Analysis of the biochemical properties of the amidase showed that the optimal temperature and pH for activity were 50 and 7.0 degrees C, respectively. The amidase exhibited high thermal stability at 50 and 60 degrees C, with half-lives greater than 5 h at both temperatures. At 70 and 80 degrees C, the half-life values were 43 and 10 min, respectively. The amidase catalyzed the hydrolysis of low molecular weight aliphatic amides, with D: -selectivity towards lactamide. Inhibition studies showed activation/inhibition data consistent with the presence of a catalytically active thiol group. Acyl transfer reactions were demonstrated with acetamide, propionamide, isobutyramide, and acrylamide as substrates and hydroxylamine as the acyl acceptor; the highest reaction rate being with isobutyramide. Immobilization by entrapment in polyacrylamide gels, covalent binding on Eupergit C beads at 4 degrees C and on Amberlite-XAD57 resulted in low protein binding and low activity, but immobilization on Eupergit C beads at 25 degrees C with cross-linking resulted in high protein binding yield and high immobilized specific activity (80% of non-immobilized activity). Characterization of Eupergit C-immobilized preparations showed that the optimum reaction temperature was unchanged, the pH range was somewhat broadened, and stability was enhanced giving half-lives of 52 min at 70 degrees C and 30 min at 80 degrees C. The amidase has potential for application under high temperature conditions as a biocatalyst for D: -selective amide hydrolysis producing enantiomerically pure carboxylic acids and for production of novel amides by acyl transfer.
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PMID:A novel thermostable nitrilase superfamily amidase from Geobacillus pallidus showing acyl transfer activity. 1734 19

A microbial process for the degradation of three types of structurally distinct organonitriles (i.e., saturated and unsaturated aliphatic nitrile and aromatic nitrile) was studied. Microorganisms were enriched from the activated sludge of a pharmaceutical wastewater treatment plant and adapted through providing acetonitrile as the sole carbon and nitrogen source for their growth. The adapted mixed culture was then examined for their capability of degrading acetonitrile, acrylonitrile and benzonitrile under various operational conditions. The performance of biodegradation and the metabolic intermediate- and end-products in the process were monitored. The results show that an average removal rate of 0.083 g acetonitrile g(-1)-VSS h(-1), 0.0074 g acrylonitrile g(-1)-VSS h(-1) or 0.0029 g benzonitrile g(-1)-VSS h(-1) was achieved in the batch bioreactor under the common operational condition of 25 degrees C and pH 7. The biodegradation of acetonitrile and acrylonitrile showed a two-step pathway, with the generation of acetamide followed by acetic acid and ammonia for acetonitrile or acrylamide followed by acrylic acid and ammonia for acrylonitrile. However, the biodegradation of benzonitrile appeared to have only one step, with the direct production of benzoic acid and ammonia, but without benzamide being detected in the process. The results suggest that, depending on the substrates, the adapted mixed culture can develop very different degradation pathways, such as nitrile hydratase plus amidase for acetonitrile or acrylonitrile and nitrilase for benzonitrile. Therefore, the adapted mixed culture has a great potential and flexibility for actual applications in biodegradation of various organonitrile compounds.
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PMID:Biodegradation of organonitriles by adapted activated sludge consortium with acetonitrile-degrading microorganisms. 1754 72

The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase superfamily and catalyzes the conversion of amides to the corresponding carboxylic acids and ammonia. It shows both amide-hydrolysis and acyl-transfer activities and also exhibits stereoselectivity for some enantiomeric substrates, thus making it a potentially important industrial catalyst. The crystal structure of G. pallidus RAPc8 amidase at a resolution of 1.9 A was solved by molecular replacement from a crystal belonging to the primitive cubic space group P4(2)32. G. pallidus RAPc8 amidase is homohexameric in solution and its monomers have the typical nitrilase-superfamily alpha-beta-beta-alpha fold. Association in the hexamer preserves the eight-layered alpha-beta-beta-alpha:alpha-beta-beta-alpha structure across an interface which is conserved in the known members of the superfamily. The extended carboxy-terminal tail contributes to this conserved interface by interlocking the monomers. Analysis of the small active site of the G. pallidus RAPc8 amidase suggests that access of a water molecule to the catalytic triad (Cys, Glu, Lys) side chains would be impeded by the formation of the acyl intermediate. It is proposed that another active-site residue, Glu142, the position of which is conserved in the homologues, acts as a general base to catalyse the hydrolysis of this intermediate. The small size of the substrate-binding pocket also explains the specificity of this enzyme for short aliphatic amides and its asymmetry explains its enantioselectivity.
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PMID:Structure of an aliphatic amidase from Geobacillus pallidus RAPc8. 1788 22

Resting cells of Bacillus subtilis ZJB-063 were used for the direct transformation of MOPAN (p-methoxyphenylacetonitrile) to MOPAA (p-methoxyphenylacetic acid), which is an important pharmaceutical intermediate. The B. subtilis ZJB-063 culture conditions for the production of nitrilase and the reaction conditions for this nitrilase-mediated conversion were optimized. The maximum production of nitrilase was achieved when glucose and a combination of ammonium sulfate and yeast powder were added as carbon and nitrogen sources respectively. Previously reported inducers were found to be unnecessary for the production of nitrilase from B. subtilis ZJB-063, which indicated that this nitrilase appeared to be constitutive. However, when epsilon-caprolactam (6-hexanolactam) was added as the inducer, B. subtilis ZJB-063 exhibited nitrile hydratase and amidase activity. The maximum conversion of MOPAN into MOPAA (specific activity 17.03 units.g(-1)(DCW); DCW is dry cell weight) was observed in a solution containing 50 mM phosphate buffer (pH 7.0), 10 mM MOPAN, 2.7 mg DCW.ml(-1) wet resting cells and 5% (v/v) DMSO for 4 h at 32 degrees C. MOPAN (10 mM) was completely converted into MOPAA (9.65 mM) in 5 h in shake flasks without the formation of p-methoxyphenylacetamide. The small deviation of MOPAA (9.65 mM) from the theoretical amount (10 mM) may be due to partial consumption of the products by B. subtilis ZJB-063. Both MOPAN and MOPAA inhibited the hydrolysis at concentrations above 15 mM. Scale up of the reaction to 200 ml in a bubble bioreactor shortened the reaction time compared with the reactions performed in shake flasks.
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PMID:Biotransformation of p-methoxyphenylacetonitrile into p-methoxyphenylacetic acid by resting cells of Bacillus subtilis. 1791 May 34


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