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PubMed2000

Do sequence repeats play an equivalent role in the choline-binding module of pneumococcal LytA amidase?

LytA amidase breaks down the N-acetylmuramoyl-l-alanine bonds in the peptidoglycan backbone of Streptococcus pneumoniae. Its polypeptide chain has two modules: the NH(2)-terminal module, responsible for the catalytic activity, and the COOH-terminal module, constructed by six tandem repeats of 20 or 21 amino acids (p1-p6) and a short COOH-terminal tail. The polypeptide chain must contain at least four repeats to efficiently anchor the autolysin to the choline residues of the cell wall. Nevertheless, the catalytic efficiency decreases by 90% upon deletion of the final tail. The structural implications of deleting step by step the two last (p5 and p6) repeats and the final COOH-tail and their effects on choline-amidase interactions have been examined by comparing four truncated mutants with LytA amidase by means of different techniques. Removal of this region has minor effects on secondary structure content but significantly affects the stability of native conformations. The last 11 amino acids and the p5 repeat stabilize the COOH-terminal module; each increases the module transition temperature by about 6 degrees C. Moreover, the p5 motif also seems to participate, in a choline-dependent way, in the stabilization of the NH(2)-terminal module. The effects of choline binding on the thermal stability profile of the mutant lacking the p5 repeat might reflect a cooperative pathway providing molecular communication between the choline-binding module and the NH(2)-terminal region. The three sequence motives favor the choline-amidase interaction, but the tail is an essential factor in the monomer <--> dimer self-association equilibrium of LytA and its regulation by choline. The final tail is required for preferential interaction of choline with LytA dimers and for the existence of different sets of choline-binding sites. The p6 repeat scarcely affects the amidase stability but could provide the proper three-dimensional orientation of the final tail.

Choline↗

PubMed1990

Characterization of the pneumococcal bacteriophage HB-3 amidase: cloning and expression in Escherichia coli.

HB-3, a temperate bacteriophage of Streptococcus pneumoniae, synthesizes its own murein hydrolase activity when multiplying on cultures of pneumococcus. The enzyme (HBL) was purified and biochemically characterized as an N-acetylmuramoyl-L-alanine amidase of 36,000 daltons, and a 2.1-kilobase DraI fragment containing the lysin gene (hbl) was cloned and expressed in Escherichia coli. Our results demonstrated that the primary product of the hbl gene is a form with low enzyme activity that can be converted to a more active form under conditions similar to those previously described for the major pneumococcal autolysin (E. García, J.L. García, C. Ronda, P. García, and R. López, Mol. Gen. Genet. 201:225-230, 1985). The phage-encoded amidase requires the presence of choline in the teichoic acids of the pneumococcal cell walls for in vivo and in vitro activity. Comparative biochemical and immunological tests of the phage-encoded and host amidases revealed a remarkable similarity between these enzymes, although analyses of their N-terminal amino acid sequences allowed us to conclude that the amidases are similar but not identical. This appears to be the first description of the cloning of a phage-encoded amidase in gram-positive bacteria.

Amidohydrolases↗

PubMed1984

Two immunologically different penicillin amidases synthetized by Escherichia coli PCM 271.

From Escherichia coli PCM 271 cells two penicillin amidases were separated by affinity chromatography on immunoadsorbent column. In cells grown in organic medium the activities of the amidase 1 and 2 were 30 and 70% respectively, whereas the activity of the amidase 1 in the cells grown in inorganic medium increased up to 98%. The amidase 1 migrated faster in polyacrylamide gel electrophoresis and was retained on DEAE-cellulose in 10 mM phosphate buffer, pH 8. No catalytic differences were demonstrated between the amidases.

Amidohydrolases↗

PubMed1998

Determination of anandamide amidase activity using ultraviolet-active amine derivatives and reverse-phase high-performance liquid chromatography.

Anandamide amidase catalyzes the hydrolysis of anandamide (AEA) to arachidonic acid (AA) and ethanolamine (EA). Recently, we published a method for determining anandamide amidase activity based on the measurement of arachidonic acid with direct UV detection at 204 nm. However, this method cannot be used to determine the hydrolysis of non-UV-active AEA analogs. It also cannot be used to study AEA amidase inhibitors that contain the arachidonic acid tail, and which are also enzyme substrates. Here we report a novel, more general method for measuring amidase activity by o-phthaldialdehyde (OPA) precolumn derivatization and reverse-phase high-performance liquid chromatography (HPLC). The hydrolysis product, ethanolamine, after separation from protein was derivatized with OPA to form a UV-active isoindole derivative which was then detected at 230 nm. The detection limit for derivatized ethanolamine was 1.0 pmol and retention times were typically less than 8 min. Our new method can detect non-UV-active analogs through derivatization of the amine product. It can thus be used after careful selection of the HPLC conditions in competition experiments between AEA and AEA analogs possessing different head groups. The most effective competitive inhibitor tested was (R)-N-(1-methyl-2-hydroxyethyl)arachidonylamide (AM356), which is resistant to enzymatic hydrolysis and yet inhibits AEA hydrolysis in a competition experiment by 43%. Moreover, this method offers several advantages over existing methodologies using radioisotopes or solvent extraction procedures. Our work to date has shown that small structural changes in the AEA molecule can result in significant variation in both affinity and turnover rate for each analog with respect to AEA amidase.

Amidohydrolases↗

PubMed1978

Relationship between mutant amidases of Pseudomonas aeruginosa and hydroxyurea as an inhibitor.

Hydroxyurea inhibited growth of Pseudomonas aeruginosa strain AI 3 on media containing either acetanilide (N-phenyl acetamide) or acetamide as sole carbon sources. Mutants resistant to hydroxyurea inhibition of growth on acetanilide (OUCH strains) and acetamide (AmOUCH strains) displayed altered growth properties on various amide media compared with the parent strain AI3. AI3 amidase, which catalyses the initial step in the metabolism of acetanilide and acetamide, was inhibited by hydroxyurea in a time-dependent reaction that was slowly reversible at pH 7.2. Compared with AI3 amidase, amidases from the OUCH mutants were much less sensitive to inhibition by hydroxyurea and showed altered substrate specificities and pH/activity profiles; amidases from the AmOUCH mutants were more sensitive to hydroxyurea inhibition but showed increased activity towards acetamide. Association of resistance to hydroxyurea inhibition with a mutation in the amidase structural gene of strain OUCH 4 was confirmed by transduction.

Amidohydrolases↗

PubMed1982

Regulation of amidase formation in mutants from Pseudomonas aeruginosa PAO lacking glutamine synthetase activity.

The formation of amidase was studied in mutants from Pseudomonas aeruginosa PAO lacking glutamine synthetase activity. It appeared that catabolite repression of amidase synthesis by succinate was partially relieved when cellular growth was limited by glutamine. Under these conditions, a correlation between amidase and urease formation was observed. The results suggest that amidase formation in strain PAO is subject to nitrogen control and that glutamine or some compound derived from it mediates the nitrogen repression of amidase.

Amidohydrolases↗

PubMed2004

Purification and properties of an enantioselective and thermoactive amidase from the thermophilic actinomycete Pseudonocardia thermophila.

A constitutively expressed thermoactive amidase from the thermophilic actinomycete Pseudonocardia thermophila was purified to homogeneity by applying hydrophobic interaction, anion exchange and gel filtration chromatography, giving a yield of 26% and a specific activity of 19.5 units mg(-1). The purified enzyme has an estimated molecular mass of 108 kDa and an isoelectric point of 4.2. The amidase is active at a broad pH range (pH 4-9) and temperature range (40-80 degrees C) and has a half-life of 1.2 h at 70 degrees C. Inhibition of enzyme activity was observed in the presence of metal ions, such as Co(2+), Hg(2+), Cu(2+), Ni(2+), and thiol reagents. The amidase has a broad substrate spectrum, including aliphatic, aromatic and amino acid amides. The presence of a double bond or a methyl group near the carboxamide group of aliphatic and amino acid amides enhances the enzymatic activity. Among aromatic amides with substitutions at the o-, m-, or p-position, the p-substituted amides are the preferred substrates. The highest acyl transferase activity was detected with hexanoamide, isobutyramide and propionamide. The K(m) values for propionamide, methacrylamide, benzamide and 2-phenylpropionamide are 7.4, 9.2, 4.9 and 0.9 mM, respectively. The amidase is highly S-stereoselective for 2-phenylpropionamide; and the racemic amide was converted to the corresponding S-acid with an enantiomeric excess of >95% at 50% conversion of the substrate. In contrast, the D,L-tryptophanamide and D,L-methioninamide were converted to the corresponding D,L-acids at the same rate. This thermostable enzyme represents the first reported amidase from a thermophilic actinomycete.

Actinobacteria↗

PubMed2006

Remaining acetamide in acetonitrile degradation using nitrile hydratase- and amidase-producing microorganisms.

The tandem conversion process involving nitrile hydratase- and amidase-producing microorganisms has potential for use in the treatment of acetonitrile-containing wastes. In that process, the acetamide hydrolysis step catalyzed by amidase is very slow compared with the acetonitrile hydration step catalyzed by nitrile hydratase, and a small amount of acetamide remains in the resulting solution. This study aimed to improve the efficiency of the acetamide hydrolysis step. An amidase-producing microorganism, Rhodococcus sp. S13-4, was newly obtained, whose use enabled rapid acetamide degradation. Though residual acetamide was still detected, it was successfully reduced by the addition of cation/anion mixed ion exchange resin or calcium hydroxide after the acetamide hydrolysis reaction using Rhodococcus sp. S13-4 cells. This result implies that acetamide hydrolysis and acetamide formation are in equilibrium. The incubation of Rhodococcus sp. S13-4 cells with high concentrations of ammonium acetate produced acetamide. The purified amidase from Rhodococcus sp. S13-4 revealed the acetamide formation activity (specific activity of 30.6 U/mg protein). This suggests that the amidase-catalyzed amide formation may cause the remaining of acetamide in the acetonitrile conversion process.

Acetamides↗

PubMed2005

Purification, characterization, gene cloning and nucleotide sequencing of D: -stereospecific amino acid amidase from soil bacterium: Delftia acidovorans.

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.

Amidohydrolases↗

PubMed1995

Pseudomonas aeruginosa aliphatic amidase is related to the nitrilase/cyanide hydratase enzyme family and Cys166 is predicted to be the active site nucleophile of the catalytic mechanism.

A database search indicated homology between some members of the nitrilase/cyanide hydratase family, Pseudomonas aeruginosa and Rhodococcus erythropolis amidases and several other proteins, some of unknown function. BLOCK and PROFILE searches confirmed these relationships and showed that four regions of the P. aeruginosa amidase had significant homology with corresponding regions of nitrilases. A phylogenetic tree placed the P. aeruginosa and R. erythropolis amidases in a group with nitrilases but separated other amidases into three groups. The active site cysteine in nitrilases is conserved in the P. aeruginosa amidase indicating that Cys166 is the active site nucleophile.

Amidohydrolases↗

PubMedDate not supplied

One-step affinity purification of amidase from mutant strains of Pseudomonas aeruginosa.

Amidases (acylamide amidohydrolase EC 3.5.1.4) from mutant strains (i.e., B6, AI3, AIU1N, OUCH 4 and L10) of Pseudomonas aeruginosa were purified in one-step by ligand affinity chromatography using Epoxy-activated Sepharose 4B-acetamide. The yields of the purified enzymes were about 90% for all mutant strains with purification factors of about 10 and were apparently homogeneous when analysed by SDS-PAGE and native PAGE. The protein bands on native PAGE coincided with the stained band of enzyme activity for all amidase preparations. Affinity columns had a maximum binding capacity of 0.5 mg amidase protein/ml of sedimented gel and could be regenerated and reused several times without any loss of binding capacity and resolution. Affinity gels containing either semicarbazide or urea were also found useful for the isolation of amidase. The differences in substrate specificity of these amidases reported previously were also observed in the elution behaviour of these enzymes from the affinity columns.

Acetamides↗

PubMed1977

Relationship between culture density and catabolite repression of an inducible aliphatic amidase in a thermophilic bacillus.

A direct correlation between the absorbance of a thermophilic bacillus and specific amidase activity was observed, which was found to depend on the cell density of the culture rather than on the time of contact of the culture with the inducer. Dilution of high density cultures caused the specific amidase activity to decrease. Environmental factors such as pH, concentration of inducer or degree of aeration, and level of NH+4 and glutamate had no effect on amidase synthesis. The decrease in amidase activity upon dilution could not be ascribed to destruction by oxygen or by inactivation or decay. Several lines of evidence suggest that catabolite repression is responsible for the phenomenon described. Succinate-grown cultures gave a stronger dilution effect thatn glutamate-grown cells. The mutant strain E-21, relatively resistant to catabolite repression, did not show the characteristic dilution effect nor the direct correlation between absorbance and specific amidase activity.

Acetamides↗

PubMed2005

Application of Fourier transform infrared spectroscopy for monitoring hydrolysis and synthesis reactions catalyzed by a recombinant amidase.

This study demonstrates the use of Fourier transform infrared (FTIR) spectroscopy for monitoring both synthesis and hydrolysis reactions catalyzed by a recombinant amidase (EC 3.5.1.4) from Pseudomonas aeruginosa. The kinetics of hydrolysis of acetamide, propionamide, butyramide, acrylamide, benzamide, phenylalaninamide, alaninamide, glycinamide, and leucinamide were determined. This revealed that very short-chain substrates displayed higher amidase activity than did branched side-chain or aromatic substrates. In addition, on reducing the polarity and increasing the substrates' bulkiness, a reduction of the amidase affinity for the substrates took place. Using FTIR spectroscopy it was possible to monitor and quantify the synthesis of several hydroxamic acid derivatives and ester hydrolysis products. These products may occur simultaneously in a reaction catalyzed by the amidase. The substrates used for the study of such reactions were ethyl acetate and glycine ethyl ester. Hydroxylamine was the nucleophile substrate used for the synthesis of acetohydroxamate compounds. Results presented in this article demonstrate the usefulness of FTIR spectroscopy as an important tool for understanding the enzyme structure-activity relationship because it provides a simple and rapid real-time assay for the detection and quantification of amidase hydrolysis and synthesis reactions in situ.

Amidohydrolases↗

PubMed2005

Expression and purification of a recombinant enantioselective amidase.

Microbacterium sp. AJ115 metabolises a wide range of nitriles using the two-step nitrile hydratase/amidase pathway. In this study, the amidase gene of Microbacterium sp. AJ115 has been inserted into the pCal-n-EK expression vector and expressed in Escherichia coli BL21(DE3)pLysS. The expressed protein is active in E. coli and expression of the amidase gene allows E. coli to grow on acetamide as sole carbon and/or nitrogen source. Expression of active amidase in E. coli was temperature dependent with high activity found when cultures were grown between 20 and 30 degrees C but no activity at 37 degrees C. On induction, the amidase represents 28% of the total soluble protein in E. coli. The expressed amidase has been purified in a single step from the crude lysate using the calmodulin-binding peptide (CBP) affinity tag. The V(max) and K(m) of the purified enzyme with acetamide (50 mM) were 4.4 micromol/min/mg protein and 4.5mM, respectively. The temperature optimum was found to be 50 degrees C. Purified enzyme demonstrated enantioselectivity with the ability to preferentially act on the S enantiomer of racemic (R,S)-2-phenylpropionamide. S-2-phenylpropionic acid is produced with an enantiomeric excess of >82% at 50% conversion of the parent amide.

Actinomycetales↗

PubMed2002

Support for a three-dimensional structure predicting a Cys-Glu-Lys catalytic triad for Pseudomonas aeruginosa amidase comes from site-directed mutagenesis and mutations altering substrate specificity.

The aliphatic amidase from Pseudomonas aeruginosa belongs to the nitrilase superfamily, and Cys(166) is the nucleophile of the catalytic mechanism. A model of amidase was built by comparative modelling using the crystal structure of the worm nitrilase-fragile histidine triad fusion protein (NitFhit; Protein Data Bank accession number 1EMS) as a template. The amidase model predicted a catalytic triad (Cys-Glu-Lys) situated at the bottom of a pocket and identical with the presumptive catalytic triad of NitFhit. Three-dimensional models for other amidases belonging to the nitrilase superfamily also predicted Cys-Glu-Lys catalytic triads. Support for the structure for the P. aeruginosa amidase came from site-direct mutagenesis and from the locations of amino acid residues that altered substrate specificity or binding when mutated.

Amidohydrolases↗

PubMed1999

Transcriptional analysis of the nitrile-degrading operon from Rhodococcus sp. ACV2 and high level production of recombinant amidase with an Escherichia coli-T7 expression system.

Northern blotting analysis with RNA probes derived from amidase and nitrile hydratase genes from Rhodococcus sp. ACV2 revealed that both genes are part of the same operon. RNase protection mapping and sequence analysis indicated that the operon is probably under the control of a sigma 70-like promoter located upstream from the amidase gene. Plasmids were constructed with the cloned genes under tac and lac promoter control. Expression of amdA was demonstrated in Escherichia coli. In another construction, the amdA gene was inserted under the control of the bacteriophage T7 promoter. Large amounts of recombinant amidase (at least 20% of total proteins) in a soluble and active form were obtained with the E. coli-T7 expression system by lowering the growth temperature to 29 degrees C, without IPTG induction. The ratio of amidase activity of strain ACV2 to E. coli was approximately 1:3. Purification of the recombinant amidase was carried out in one chromatographic step, giving an enzyme preparation that could be used directly in a biotechnological process.

Amidohydrolases↗

PubMedDate not supplied

Lipases specifically degrading lipopolysaccharide: fatty acyl amidases from Dictyostelium discoideum.

Two specific fatty acyl amidases that hydrolyze lipopolysaccharide have been isolated from the slime mold Dictyostelium discoideum. Esterases as well as phosphatases acting on lipid A derivatives were also observed. The first amidase (I) hydrolyzes the fatty amide adjacent to the C-1 phosphate on the disaccharide backbone of lipid A. Amidase II cleaves the distal amide, but only after deacylation of the first site. The range of specificity and the structural determinants important to specificity of the amidases were evaluated in studies of specifically modified derivatives of lipid A. In light of the effects of lipopolysaccharide on the biology of D. discoideum, a role for the amidases and other lipopolysaccharide-specific catabolic enzymes is discussed.

Amidohydrolases↗

PubMed1980

A nonpancreatic source of the proteolytic-enzyme amidase and bacteriology in experimental acute pancreatitis.

In previous studies of human and experimental acute pancreatitis, three main assumptions have been made. First, that the disease is due to activation of pancreatic proteolytic enzymes in the pancreas with resulting "autodigestion" of the gland. Second, that interstitial pancreatitis is a mild form of hemorrhagic pancreatitis into which it may progress, and third, that bacteria play little part, if any, in the initiation of the disease. These assumptions are now questioned. In the present study in dogs, levels of proteolytic enzymes in blood, thoracicduct lymph and peritoneal fluid were measured using benzoylarginine amide. Raised levels of amidase were found in hemorrhagic, but not with interstitial, pancreatitis, and biochemical examination of amidase suggested it was not a pancreatic protease, but with its broad specificity and stability derived from bacteria. Addition of antibiotic to the blind duodenal loop in hemorrhagic pancreatitis reduced the level of blood amidase, but Trasylol given intravenously did not, nor did it inhibit amidase in vitro. In all animals, histological examination was made of the pancreas at time of death. On bacteriology, it is concluded that experimental interstitial pancreatitis results from damage to the pancreatic duct system without infection, and haemorrhagic pancreatitis mainly from reflux of bacteria into the pancreatic ducts from the duodenum. Only bacteria such as Escherichia coli and Clostridium welchii that produce proteolytic enzymes and cytotoxins appear to be able to cause haemorrhagic pancreatitis, and these bacteria may explain the release of vasoactive polypeptides and the vascular effects. In hemorrhagic pancreatitis such bacteria were found in the pancreas, but none in interstitial pancreatitis. Evidence is given to suggest that pancreatic proteolytic enzymes are unlikely to cause the cell necrosis which is a pathological feature of hemorrhagic pancreatitis, and that "autodigestion" is likewise unlikely to be a cause of this condition. An extrapancreatic source of proteolytic enzymes from bacteria is now suggested in haemorrhagic pancreatitis, and more attention to bacteriology in human acute pancreatitis is urgently needed. Amidase levels were highest in peritoneal fluid, suggesting a rationale for peritoneal lavage in the treatment of acute pancreatitis, and it is unlikely that Trasylol can give any benefit. The assessment of treatment of acute pancreatitis will be unsatisfactory as long as the proportion of haemorrhagic to interstitial pancreatitis in any series is not known accurately.

Acute Disease↗