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)

Ammonia production is of great importance for the gastric pathogen Helicobacter pylori as a nitrogen source, as a compound protecting against gastric acidity, and as a cytotoxic molecule. In addition to urease, H. pylori possesses two aliphatic amidases responsible for ammonia production: AmiE, a classical amidase, and AmiF, a new type of formamidase. Both enzymes are part of a regulatory network consisting of nitrogen metabolism enzymes, including urease and arginase. We examined the role of the H. pylori amidases in vivo by testing the gastric colonization of mice with H. pylori SS1 strains carrying mutations in amiE and/or amiF and in coinfection experiments with wild-type and double mutant strains. A new cassette conferring resistance to gentamicin was used in addition to the kanamycin cassette to construct the double mutation in strain SS1. Our data indicate that the amidases are not essential for colonization of mice. The search for amiE and amiF genes in 53 H. pylori strains from different geographic origins indicated the presence of both genes in all these genomes. We tested for the presence of the amiE and amiF genes and for amidase and formamidase activities in eleven Helicobacter species. Among the gastric species, H. acinonychis possessed both amiE and amiF, H. felis carried only amiF, and H. mustelae was devoid of amidases. H. muridarum, which can colonize both mouse intestine and stomach, was the only enterohepatic species to contain amiE. Phylogenetic trees based upon the sequences of H. pylori amiE and amiF genes and their respective homologs from other organisms as well as the amidase gene distribution among Helicobacter species are strongly suggestive of amidase acquisition by horizontal gene transfer. Since amidases are found only in Helicobacter species able to colonize the stomach, their acquisition might be related to selective pressure in this particular gastric environment.
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PMID:Presence of active aliphatic amidases in Helicobacter species able to colonize the stomach. 1450 Apr 81

The endometrium stroma cells and properties of such key enzymes as acetylcholinesterase, Mg2+, Ca(2+)-ATPase, AMP-deaminase have been investigated in them. The activity of acetylcholinesterase in suspension of cells compounds is 9.8 +/- 0.2 mumol of tiocholinbromide/mg protein/hour and is reduced under influence of exogenous ATP, NO2-, H2O2 and Triton X-100. Common Mg2+, Ca(2+)-ATPase activity of compounds of 36 +/- 2 mumol Pi/mg protein/hour, is depressed by sodium azide and thapsigargine, that specifies presence of an investigated enzyme in mitochondria and endoplasmic reticulum of investigated cells. In a suspension of stroma cells with addition of 0.2% of Triton X-100 for augmentation of permeability of cellular membranes and 1.5 M KCl for a dissociation of complexes AMP-deaminase with proteins and membranes, the deamination exogenous AMP up to IMP and NH3, is registered generated in the given response. The supposition about NH3 role as the paracrine regulator in the system endometrium-myometrium of the uterus is expressed.
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PMID:[Enzymes and processes of activation of the endometrium stromal cells]. 1514 16

This paper describes the enzymatic synthesis of the C-terminal fragment H-Gly-Trp-Met-Asp-Phe-NH2 of cholecystokinin. Immobilized enzymes were used for the formation of all peptide bonds except thermolysin. Beginning the synthesis with phenylacetyl (PhAc) glycine carboxamidomethyl ester (OCam) and H-Trp-OMe by using immobilized papain as biocatalyst in buffered ethyl acetate, the dipeptide methyl ester was then coupled directly with Met-OEt.HCl by alpha-chymotrypsin/Celite 545 in a solvent free system. For the 3+2 coupling PhAc-Gly-Trp-Met-OEt had to be converted into its OCam ester. The other fragment H-Asp(OMe)-Phe-NH2 resulted from the coupling of Cbo-Asp(OMe)-OH with H-Phe-NH2.HCl and thermolysin as catalyst, followed by catalytic hydrogenation. Finally PhAc-Gly-Trp-Met-Asp-Phe-NH2 was obtained in a smooth reaction from PhAc-Gly-Trp-Met-OCam and H-Asp(OMe)-Phe-NH2 with alpha-chymotrypsin/Celite 545 in acetonitrile, followed by basic hydrolysis of the beta-methyl ester. The PhAc-group is removed with penicillin G amidase and CCK-5 is obtained in an overall isolated yield of 19.6%.
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PMID:Total enzymatic synthesis of cholecystokinin CCK-5. 1530 78

Peptide amidase (Pam), a hydrolytic enzyme that belongs to the amidase signature (AS) family, selectively catalyzes the hydrolysis of the C-terminal amide bond (CO-NH(2)) of peptides. The recent availability of the X-ray structures of Pam, fatty acid amide hydrolase, and malonamidase E2 has led to the proposal of a novel Ser-Ser-Lys catalytic triad mechanism for the amide hydrolysis by the AS enzymes. The molecular dynamics (MD) simulations using the CHARMM force field were performed to explore the catalytic mechanism of Pam. The 1.8 A X-ray crystal structure of Pam in complex with the amide analogue of chymostatin was chosen for the initial coordinates for the MD simulations. The five systems that were investigated are as follows: (i) enzyme.substrate with Lys123-NH(2), (ii) enzyme.substrate with Lys123-NH(3)(+), (iii) enzyme.substrate with Lys123-NH(3)(+) and Ser226-O(-), (iv) enzyme.transition state, and (v) enzyme.tetrahedral intermediate. Our data support the presence of the hydrogen bonding network among the catalytic triad residues, Ser226, Ser202, and Lys123, where Ser226 acts as the nucleophile and Ser202 bridges Ser226 and Lys123. The MD simulation supports the catalytic role of the crystallographic waters, Wat1 and Wat2. In all the systems that have been studied, the backbone amide nitrogens of Asp224 and Thr223 create an oxyanion hole by hydrogen bonding to the terminal amide oxygen of the substrate, and stabilize the oxyanion tetrahedral intermediate. The results from both our computational investigation and previously published experimental pH profile support two mechanisms. In a mechanism that is relevant at lower pH, the Lys123-NH(3)(+)-Ser202 dyad provides structural support to the catalytic residue Ser226, which in turn carries out a nucleophilic attack at the substrate amide carbonyl in concert with Wat1-mediated deprotonation and stabilization of the tetrahedral transition state by the oxyanion hole. In the mechanism operating at higher pH, the Lys123-NH(2)-Ser202 catalytic dyad acts as a general base to assist addition of Ser226 to the substrate amide carbonyl. The results from the MD simulation of the tetrahedral intermediate state show that both Ser202 and Lys123 are possible candidates for protonation of the leaving group, NH(2), to form the acyl-enzyme intermediate.
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PMID:Probing the Ser-Ser-Lys catalytic triad mechanism of peptide amidase: computational studies of the ground state, transition state, and intermediate. 1559 22

Two open reading frames (nhpS and acsA) were identified immediately downstream of the previously described Pseudomonas chlororaphis B23 nitrile hydratase (NHase) gene cluster (encoding aldoxime dehydratase, amidase, the two NHase subunits, and an uncharacterized protein). The amino acid sequence deduced from acsA shows similarity to that of acyl-CoA synthetase (AcsA). The acsA gene product expressed in Escherichia coli showed acyl-CoA synthetase activity toward butyric acid and CoA as substrates, with butyryl-CoA being synthesized. From the E. coli transformant, AcsA was purified to homogeneity and characterized. The quality of the recombinant protein was verified by the NH2-terminal amino acid sequence and the results of matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The apparent Km values for butyric acid, CoA, and ATP were 0.32 +/- 0.04, 0.37 +/- 0.02, and 0.22 +/- 0.02 mm, respectively. AcsA was shown to be a short-chain acyl-CoA synthetase, according to the catalytic efficiencies (kcat/Km) for various acids. The substrate specificity of AcsA was similar to those of aldoxime dehydratase, NHase, and amidase, the genes of which coexist in the same orientation in the gene cluster. P. chlororaphis B23 grew when cultured in a medium containing butyraldoxime as the sole carbon and nitrogen source. The activities of aldoxime dehydratase, NHase, and amidase were detected together with that of acyl-CoA synthetase under the culture conditions used. Moreover, on culture in a medium containing butyric acid as the sole carbon source, acyl-CoA synthetase activity was also detected. Together with the adjacent locations of the aldoxime dehydratase, NHase, amidase, and acyl-CoA synthetase genes, these findings suggest that the four enzymes are sequentially correlated with one another in vivo to utilize butyraldoxime as a carbon and nitrogen source. This is the first report of an overall "nitrile pathway" (aldoxime-->nitrile-->amide-->acid-->acyl-CoA) comprising these enzymes.
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PMID:Nitrile pathway involving acyl-CoA synthetase: overall metabolic gene organization and purification and characterization of the enzyme. 1563 96

An opportunity of formation of ammonia (NH3) in utera endometrium and its influence on exchange of Ca2+ and H+ in plasmalemma of myometrium was investigated. Dissociation of endometrium stroma cells and myocytes suspension was carried from utera of pigs and rats in accordance with the traditional techniques. In suspension of stroma cells a rather high AMP-deaminase activity (53 +/- 2 mmol IMP/hour on 1 mg of protein) was determined. It was demonstrated that ammonia release in extracellular space (measured by the changes of colouring of trinitrobenzolsulfonate acid) was significantly amplified by 1 mM acetylcholine and decreased by 0,1 mM fluoride ions, nonspecific AMP-deaminase inhibitor. It enables to assume a role of AMP-deaminase in formation of NH3 by endometrium stroma cells and its release into extracellular space during acetylcholine stimulation. The addition of ammonia (4 mM) to suspension of myocytes is accompanied by significant increase in pH (measured by the change in BCECF fluorescence) in extracellular and intracellular space, and the last parameter is inhibited by the blockers of passive H+ transport across the membrane: 0,1 mM 4-aminopyridine and tetraethylammonium. It is possible that addition of ammonia-containing solution results in increase in proton gradient on myocyte membrane and in amplification of H+ efflux. The opportunity of stimulation ofacetylcholine-activated passive Ca2+ transport in myocytes by 4 mM NH4+ that was suppressed by 1 mM cadmium and 1 nM nifedipine was also shown using fluorescent probe FURA-2AM. The increase in Ca2+ concentration in cytoplasm in the given conditions is intensively oppressed by protonophore (0.04% 2,4-dinitrophenol) and is effectively amplified by Na+/H+-exchange inhibitor 0,1 mM amyloride. It is possible to assume an amplification of lygand-activated passive Ca2+ transport caused by dispersion of transmembrane proton gradient which exists on plasmalemma and can be increased by ammonia formation in endometrium. The role of diffused from endometrium NH3 in regulation of utera functional activity requires further investigation, however already at this stage it is possible to assume, that NH3 molecules (or ion NH4+) can carry out a role of paracrine regulator in the system endometrium-myometrium.
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PMID:[Possible role of ammonium as a paracrine regulator in the uterine tissue]. 1573 59

The D-amino acid amidase-producing bacterium was isolated from soil samples using an enrichment culture technique in medium broth containing D-phenylalanine amide as a sole source of nitrogen. The strain exhibiting the strongest activity was identified as Delftia acidovorans strain 16. This strain produced intracellular D-amino acid amidase constitutively. The enzyme was purified about 380-fold to homogeneity and its molecular mass was estimated to be about 50 kDa, on sodium dodecyl sulfate polyacrylamide gel electrophoresis. The enzyme was active preferentially toward D-amino acid amides rather than their L-counterparts. It exhibited strong amino acid amidase activity toward aromatic amino acid amides including D-phenylalanine amide, D-tryptophan amide and D-tyrosine amide, yet it was not specifically active toward low-molecular-weight D-amino acid amides such as D-alanine amide, L-alanine amide and L-serine amide. Moreover, it was not specifically active toward oligopeptides. The enzyme showed maximum activity at 40 degrees C and pH 8.5 and appeared to be very stable, with 92.5% remaining activity after the reaction was performed at 45 degrees C for 30 min. However, it was mostly inactivated in the presence of phenylmethanesulfonyl fluoride or Cd2+, Ag+, Zn2+, Hg2+ and As3+ . The NH2 terminal and internal amino acid sequences of the enzyme were determined; and the gene was cloned and sequenced. The enzyme gene damA encodes a 466-amino-acid protein (molecular mass 49,860.46 Da); and the deduced amino acid sequence exhibits homology to the D-amino acid amidase from Variovorax paradoxus (67.9% identity), the amidotransferase A subunit from Burkholderia fungorum (50% identity) and other enantioselective amidases.
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PMID:Purification, characterization, gene cloning and nucleotide sequencing of D: -stereospecific amino acid amidase from soil bacterium: Delftia acidovorans. 1595 27

Acquisition of nutrients by plants is primarily dependent on root growth and bioavailability of nutrients in the rooting medium. Most of the beneficial bacteria enhance root growth, but their effectiveness could be influenced by the nutrient status around the roots. In this study, two 1-aminocyclopropane-1-carboxylate (ACC)-deaminase containing plant-growth-promoting rhizobacteria (PGPR), Pseudomonas fluorescens and P. fluorescens biotype F were tested for their effect on growth, yield, and nutrient use efficiency of wheat under simultaneously varying levels of all the three major nutrients N, P, and K (at 0%, 25%, 50%, 75%, and 100% of recommended doses). Results of pot and field trials revealed that the efficacy of these strains for improving growth and yield of wheat reduced with the increasing rates of NPK added to the soil. In most of the cases, significant negative linear correlations were recorded between percentage increases in growth and yield parameters of wheat caused by inoculation and increasing levels of applied NPK fertilizers. It is highly likely that under low fertilizer application, the ACC-deaminase activity of PGPR might have caused reduction in the synthesis of stress (nutrient)-induced inhibitory levels of ethylene in the roots through ACC hydrolysis into NH(3) and alpha-ketobutyrate. The results of this study imply that these Pseudomonads could be employed in combination with appropriate doses of fertilizers for better plant growth and savings of fertilizers.
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PMID:Fertilizer-dependent efficiency of Pseudomonads for improving growth, yield, and nutrient use efficiency of wheat (Triticum aestivum L.). 1834 Apr 43

The search for diverse plant growth-promoting (PGP) diazotrophic bacteria is gaining momentum as efforts are made to exploit them as biofertilizers for various economically important crops. In the present study, 17 diazotrophic strains belonging to eight different genera isolated from rice paddy fields were screened for multiple PGP traits and evaluated for their inoculation effects on canola and rice plants. All of the strains tested positive for 1- aminocyclopropane-1-carboxylate (ACC) deaminase activity and production of indole 3-acetic acid (IAA) and ammonia (NH3). Additionally, four of the strains were able to solubilize phosphorus (P), five tested positive for zinc (Zn) solubilization and sulfur (S) oxidation, and eight strains produced siderophores. Based on the presence of multiple PGP traits, 10 strains were selected for inoculation studies. Treatment with Herbaspirillum sp. RFNB26 resulted in maximum root length (54.3%), seedling vigor, and dry biomass in canola, whereas Paenibacillus sp. RFNB4 exhibited the lowest activity under gnotobiotic conditions. However, under pot culture conditions, Paenibacillus sp. RFNB4 significantly increased plant height and dry biomass production by 42.3% and 29.5%, respectively. Canola plants and rhizosphere soils inoculated with Bacillus sp. RFNB6 exhibited significantly higher nitrogenase activity. In greenhouse experiments, Serratia sp. RFNB18 increased rice plant height by 35.1%, Xanthomonas sp. RFNB24 enhanced biomass production by 84.6%, and rice rhizosphere soils inoculated with Herbaspirillum sp. RFNB26 exhibited the highest nitrogenase activity. Our findings indicate that most of the selected strains possess multiple PGP properties that significantly improve the growth parameters of the two plants when tested under controlled conditions.
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PMID:Characterization of plant growth-promoting traits of free-living diazotrophic bacteria and their inoculation effects on growth and nitrogen uptake of crop plants. 1988 83

The extensive and enduring challenges in soil microbiology depend on the development of efficient methods to be acquainted with the types of microbes present in soil, and to determine the functional performance of the overall microbial groups in situ. This study aims to investigate the combined uses of species richness and diversity as well as to estimate the combinatorial effect of species richness and diversity in order to understand their role and distribution in their habitat. To achieve this objective a study was designed targeting the rhizosphere of Jatropha curcas L. which were planted in various soil conditions on five distinctive sites of Gujarat state (India). These sites were constantly monitored and studied for the species richness and evenness ("heterogeneity"). The isolates were checked for their PGPR potentials like Phosphate solubilisation, Siderophore production, Indole acetic acid production, ACC deaminase production, HCN production, EPS production and Ammonia production. The results obtained were used to calculate richness, evenness and diversity indices. Results reveal the total heterogeneity in the site of fertile Jatropha rhizosphere (GS4) as well as sodic soil site (GS5) than other three sites. Absence of equitability under the selected and defined condition was also observed in GS4 and GS5 sites. The combinatorial estimates provide the information on their distribution and roles in the habitat. In particular, such an empirical relationship from a single rhizosphere of a distinctive species Jatropha is useful to test diversity predictions in natural sites, and further it can be applied to either by performing trials over larger spatial and temporal scales or by conducting correlational studies of biodiversity gradients.
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PMID:Combinatorial assessment on dominance and informative diversity of PGPR from rhizosphere of Jatropha curcas L. 2014 56


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