Barley arabinoxylan arabinofuranohydrolases: purification, characterization and determination of primary structures from cDNA clones

2001 ◽  
Vol 356 (1) ◽  
pp. 181-189 ◽  
Author(s):  
Robert C. LEE ◽  
Rachel A. BURTON ◽  
Maria HRMOVA ◽  
Geoffrey B. FINCHER
Keyword(s):  
Catalytic Efficiency ◽  
Exchange Chromatography ◽  
Cdna Clones ◽  
Amino Acid Residues ◽  
Hordeum Vulgare L ◽  
Ph Optimum ◽  
Catalytic Rate Constant ◽  
Arabinoxylan Arabinofuranohydrolase ◽  
Mature Enzyme ◽  
Hydrolysis Of

A family 51 arabinoxylan arabinofuranohydrolase, designated AXAH-I, has been purified from extracts of 7-day-old barley (Hordeum vulgare L.) seedlings by fractional precipitation with (NH4)2SO4 and ion-exchange chromatography. The enzyme has an apparent molecular mass of 65kDa and releases l-arabinose from cereal cell wall arabinoxylans with a pH optimum of 4.3, a catalytic rate constant (kcat) of 6.9s−1 and a catalytic efficiency factor (kcat/Km) of 0.76 (ml·s−1·mg−1). Whereas the hydrolysis of α-l-arabinofuranosyl residues linked to C(O)3 of backbone (1 → 4)-β-xylosyl residues proceeds at the fastest rate, α-l-arabinofuranosyl residues on doubly substituted xylosyl residues are also hydrolysed, at lower rates. A near full-length cDNA encoding barley AXAH-I indicates that the mature enzyme consists of 626 amino acid residues and has a calculated pI of 4.8. A second cDNA, which is 81% identical with that encoding AXAH-I, encodes another barley AXAH, which has been designated AXAH-II. The barley AXAHs are likely to have key roles in wall metabolism in cereals and other members of the Poaceae. Thus the enzymes could participate in the modification of the fine structure of arabinoxylan during wall deposition, maturation or expansion, or in wall turnover and the hydrolysis of arabinoxylans in germinated grain.

scholarly journals Purification and Characterization of Phenylalanine Ammonia Lyase from Trichosporon cutaneum

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Andrea Goldson-Barnaby ◽  
Christine H. Scaman
Keyword(s):  
Phenylalanine Ammonia Lyase ◽  
Anion Exchange Chromatography ◽  
Exchange Chromatography ◽  
Hill Coefficient ◽  
Trichosporon Cutaneum ◽  
Amino Acid Residues ◽  
Ph Optimum ◽  
Ability To Act ◽  
Metal Cofactor ◽  
Intron Region

Trichosporon cutaneum phenylalanine ammonia lyase was selected as a model to investigate the dual substrate activity of this family of enzymes. Sequencing of the PAL gene identified an extensive intron region at the N-terminus. Five amino acid residues differing from a prior report were identified. Highest Phe : Tyr activities (1.6 ±0.3 : 0.4±0.1 μmol/h g wet weight) were induced by Tyr. The enzyme has a temperature optimum of 32°C and a pH optimum of 8–8.5 and shows no metal cofactor dependence. Michaelis-Menten kinetics (Phe, Km  5.0 ± 1.1 mM) and positive allostery (Tyr, K′  2.4 ± 0.6 mM, Hill coefficient 1.9±0.5) were observed. Anion exchange chromatography gave a purification fold of 50 with 20% yield. The His-Gln motif (substrate selectivity switch region) indicates the enzyme’s ability to act on both substrates.

scholarly journals Peptidase Activity of Amidinated Thrombin

1977 ◽  
Author(s):  
E.P. Kang
Keyword(s):  
Amino Acid ◽  
Catalytic Efficiency ◽  
Enzymic Activity ◽  
Peptidase Activity ◽  
Amino Acid Residues ◽  
Small Peptides ◽  
Human Thrombin ◽  
Small Change ◽  
Hydrolysis Of ◽  
Hydrolysis Activity

Human thrombin, free of plasminogen and plasmin, was treated with ethyl acetimidate hydrochloride in order to modify the lysyl residues of the protein. By monitoring the enzymic activity in the modification mixture, it was found that the reaction was completed in about one hour and the loss of activity of thrombin was proportional to the amount of modification. After the removal of the excess ethyl acetimidate, approximately 25% of the clotting activity and of the hydrolysis activity for small peptides remained. Amino acid analysis of this modified thrombin indicated about 80% of the lysyl residues had been modified with no apparent change of other amino acid residues. By studying the thrombolytic hydrolysis of Bz-phe-val-arg-pNA, the kcat of the amidinated thrombin was about 8% of the control while the KM Secreased to 0.056 μM from 0.098 μM. The modification of the lysyl residues of thrombin, therefore, has lowered the catalytic efficiency of the enzyme with a rather small change in binding affinity. This suggests that modification of lysyl residues in the neighborhood of the active site hinders the catalytic hydrolysis of the small peptides.

scholarly journals Characterization of β-galactosidase and α-galactosidase activities from the halophilic bacterium Gracilibacillus dipsosauri

2021 ◽  
Vol 71 (1) ◽  
Author(s):  
Charles E. Deutch ◽  
Amy M. Farden ◽  
Emily S. DiCesare
Keyword(s):  
Gel Filtration ◽  
Halophilic Bacterium ◽  
Peptide Sequencing ◽  
Exchange Chromatography ◽  
Galactosidase Activity ◽  
Ph Optimum ◽  
Whole Cells ◽  
Cell Extracts ◽  
Genes Encoding ◽  
Hydrolysis Of

Abstract Purpose Gracilibacillus dipsosauri strain DD1 is a salt-tolerant Gram-positive bacterium that can hydrolyze the synthetic substrates o-nitrophenyl-β-d-galactopyranoside (β-ONP-galactose) and p-nitrophenyl-α-d-galactopyranoside (α-PNP-galactose). The goals of this project were to characterize the enzymes responsible for these activities and to identify the genes encoding them. Methods G. dipsosauri strain DD1 was grown in tryptic soy broth containing various carbohydrates at 37 °C with aeration. Enzyme activities in cell extracts and whole cells were measured colorimetrically by hydrolysis of synthetic substrates containing nitrophenyl moieties. Two enzymes with β-galactosidase activity and one with α-galactosidase activity were partially purified by ammonium sulfate fractionation, ion-exchange chromatography, and gel-filtration chromatography from G. dipsosauri. Coomassie Blue-stained bands corresponding to each activity were excised from nondenaturing polyacrylamide gels and subjected to peptide sequencing after trypsin digestion and HPLC/MS analysis. Result Formation of β-galactosidase and α-galactosidase activities was repressed by d-glucose and not induced by lactose or d-melibiose. β-Galactosidase I had hydrolytic and transgalactosylation activity with lactose as the substrate but β-galactosidase II showed no activity towards lactose. The α-galactosidase had hydrolytic and transgalactosylation activity with d-melibiose but not with d-raffinose. β-Galactosidase I had a lower Km with β-ONP-galactose as the substrate (0.693 mmol l−1) than β-galactosidase II (1.662 mmol l−1), was active at more alkaline pH, and was inhibited by the product d-galactose. β-Galactosidase II was active at more acidic pH, was partially inhibited by ammonium salts, and showed higher activity with α-PNP-arabinose as a substrate. The α-galactosidase had a low Km with α-PNP-galactose as the substrate (0.338 mmol l−1), a pH optimum of about 7, and was inhibited by chloride-containing salts. β-Galactosidase I activity was found to be due to the protein A0A317L6F0 (encoded by gene DLJ74_04930), β-galactosidase II activity to the protein A0A317KZG3 (encoded by gene DLJ74_12640), and the α-galactosidase activity to the protein A0A317KU47 (encoded by gene DLJ74_17745). Conclusions G. dipsosauri forms three intracellular enzymes with different physiological properties which are responsible for the hydrolysis of β-ONP-galactose and α-PNP-galactose. BLAST analysis indicated that similar β-galactosidases may be formed by G. ureilyticus, G. orientalis, and G. kekensis and similar α-galactosidases by these bacteria and G. halophilus.

scholarly journals Lactose hydrolysis by free and fibre-entrapped β-galactosidase from Streptococcus thermophilus

1993 ◽  
Vol 2 (5) ◽  
pp. 395-401
Author(s):  
Zhennai Yang ◽  
Eero Pahkala ◽  
Tuomo Tupasela
Keyword(s):  
Skim Milk ◽  
Milk Proteins ◽  
Streptococcus Thermophilus ◽  
Exchange Chromatography ◽  
Concentration Addition ◽  
Lactose Hydrolysis ◽  
Ph Optimum ◽  
Glass Column ◽  
Ammonium Sulphate Fractionation ◽  
Hydrolysis Of

To study lactose hydrolysis by β-galactosidase, this enzyme was produced from Streptococcus thermophilus strain 11F and partially purified by acetone and ammonium sulphate fractionation, and ion exchange chromatography on a Q Sepharose FF column. Lactose hydrolysis by the enzyme was affected by lactose concentrations, sugars and milk proteins. The maximum extent of lactose hydrolysis in buffer was obtained with a 15% lactose concentration. Addition of 2% of lactose, glucose, galactose or sucrose in milk inhibited the enzymatic hydrolysis. The enzyme was activated by bovine serum albumin and a combination of αs-casein and β-casein. Of the casein fractions, the principal fraction, αs-casein, was less effective than β-casein and κ-casein. The fibre entrapped enzyme had a temperature optimum of 57°C, and a pH optimum from 7.5 to at least 9.0 with O-nitrophenyl-β-D-galactopyranoside as substrate. By recycling with whey and skim milk through a jacketed glass column (1.6 cm x 30 cm) loaded with fibre-entrapped enzyme at 55°C, a lactose hydrolysis of 49.5% and 47.9% was achieved in 11 h and 7 h respectively.

scholarly journals The Modified β-Ketoadipate Pathway in Rhodococcus rhodochrous N75: Enzymology of 3-Methylmuconolactone Metabolism

1998 ◽  
Vol 180 (24) ◽  
pp. 6668-6673 ◽  
Author(s):  
Chang-Jun Cha ◽  
Ronald B. Cain ◽  
Neil C. Bruce
Keyword(s):  
Ammonium Sulfate ◽  
Gel Filtration ◽  
Sole Source ◽  
Anion Exchange Chromatography ◽  
Exchange Chromatography ◽  
Rhodococcus Rhodochrous ◽  
Natural Substrate ◽  
Ph Optimum ◽  
A Subunit ◽  
Hydrolysis Of

ABSTRACT Rhodococcus rhodochrous N75 is able to metabolize 4-methylcatechol via a modified β-ketoadipate pathway. This organism has been shown to activate 3-methylmuconolactone by the addition of coenzyme A (CoA) prior to hydrolysis of the butenolide ring. A lactone-CoA synthetase is induced by growth of R. rhodochrous N75 on p-toluate as a sole source of carbon. The enzyme has been purified 221-fold by ammonium sulfate fractionation, hydrophobic chromatography, gel filtration, and anion-exchange chromatography. The enzyme, termed 3-methylmuconolactone-CoA synthetase, has a pH optimum of 8.0, a native M r of 128,000, and a subunitM r of 62,000, suggesting that the enzyme is homodimeric. The enzyme is very specific for its 3-methylmuconolactone substrate and displays little or no activity with other monoene and diene lactone analogues. Equimolar amounts of these lactone analogues brought about less than 30% (most brought about less than 15%) inhibition of the CoA synthetase reaction with its natural substrate.

scholarly journals Expression in Escherichia Coli, Purification, and Functional Reconstitution of Human Steroid 5α-Reductases

Endocrinology ◽  
2020 ◽  
Vol 161 (8) ◽  
Author(s):  
Hwei-Ming Peng ◽  
Juan Valentín-Goyco ◽  
Sang-Choul Im ◽  
Bing Han ◽  
Jiayan Liu ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Functional Characterization ◽  
Catalytic Efficiency ◽  
Biochemical Properties ◽  
Exchange Chromatography ◽  
Structural Basis ◽  
Cancer Drug ◽  
Ph Optimum ◽  
Hek 293 ◽  
Triton X

Abstract The potent androgen 5α-dihydrotestosterone irreversibly derives from testosterone via the activity of steroid 5α-reductases (5αRs). The major 5αR isoforms in most species, 5αR1 and 5αR2, have not been purified to homogeneity. We report here the heterologous expression of polyhistidine-tagged, codon-optimized human 5αR1 and 5αR2 cDNAs in Escherichia coli. A combination of the nonionic detergents Triton X-100 and Nonidet P-40 enabled solubilization of these extremely hydrophobic integral membrane proteins and facilitated purification with affinity and cation-exchange chromatography methods. For functional reconstitution, we incorporated the purified isoenzymes into Triton X-100-saturated dioleoylphosphatidylcholine liposomes and removed excess detergent with polystyrene beads. Kinetic studies indicated that the 2 isozymes differ in biochemical properties, with 5αR2 having a lower apparent Km for testosterone, androstenedione, progesterone, and 17-hydroxyprogesterone than 5αR1; however, 5αR1 had a greater capacity for steroid conversion, as reflected by a higher Vmax than 5αR2. Both enzymes preferred progesterone as substrate over other steroids, and the catalytic efficiency of purified reconstituted 5αR2 exhibited a sharp pH optimum at pH 5. Intriguingly, we found that the prostate-cancer drug-metabolite 3-keto-∆ 4-abiraterone is metabolized by 5αR1 but not 5αR2, which may serve as a structural basis for isoform selectivity and inhibitor design. The functional characterization results with the purified reconstituted isoenzymes paralleled trends obtained with HEK-293 cell lines stably expressing native 5αR1 and 5αR2. Access to purified human 5αR1 and 5αR2 will advance studies of these important enzymes and might help to clarify their contributions to steroid anabolism and catabolism.

scholarly journals A new chromophoric substrate for penicillopepsin and other fungal aspartic proteinases

1982 ◽  
Vol 203 (3) ◽  
pp. 603-610 ◽  
Author(s):  
Theo Hofmann ◽  
Robert S. Hodges
Keyword(s):  
Catalytic Efficiency ◽  
Aspartic Proteinase ◽  
Spectrophotometric Assay ◽  
Water Soluble ◽  
Burst Release ◽  
Penicillium Roqueforti ◽  
Aspartic Proteinases ◽  
Catalytic Rate Constant ◽  
Human Renin ◽  
Hydrolysis Of

The hexapeptide N-α-acetylalanylalanyl-lysyl-p- nitrophenylalanylalanylalanylamide has been synthesized and was found to be a good substrate for fungal aspartic proteinases that possess trypsinogen-activating activity, namely penicillopepsin, Rhizopus aspartic proteinase, Endothia aspartic proteinase and the aspartic proteinases from Aspergillus oryzae and Penicillium roqueforti. The peptide is rapidly cleaved between the lysine and p-nitrophenylalanine residues. Calf chymosin and human renin cleave the same bond, but only very slowly. The cleavage is accompanied by an absorbance decrease with a maximum at 296nm (Δε —1800m−1·cm−1). Pig pepsin and the aspartic proteinases from two Rhizomucor species cleave the peptide slowly on the carboxy side of p-nitrophenylalanine. For the five enzymes that hydrolysed the peptide rapidly, Km values range from 0.16 to 0.42mm and kcat. from 6 to 46.6s−1 at pH 4.5 and 25°C. A comparison of the kinetic parameters of the hexapeptide with those of the dipeptide N-α-acetyllysyl-p-nitrophenylalanylamide obtained with penicillopepsin shows that at pH 6.0 the catalytic rate constant kcat. is over 5000-fold greater for the hexapeptide, whereas the Km values are essentially the same, showing that the catalytic efficiency is strongly dependent on secondary binding. The new substrate with a p-nitrophenylalanine residue in the P′1 position has advantages over previously used substrates for aspartic proteinases in that it offers a more sensitive spectrophotometric assay that is independent of pH up to 5.5 and can readily be used up to pH 7.0. The presence of lysine makes it very water-soluble. Stopped-flow spectrophotometric experiments with penicillopepsin gave clear evidence that the hydrolysis of the substrate by penicillopepsin is not accompanied by a ‘burst’ release of p-nitrophenylalanylalanylalanylamide.

Formaldehyde as an Active Site Label of α-Chymotrypsin

1972 ◽  
Vol 50 (10) ◽  
pp. 1114-1121 ◽  
Author(s):  
Charles J. Martin ◽  
Narendra B. Oza ◽  
Mario A. Marini
Keyword(s):  
Active Site ◽  
Competitive Inhibition ◽  
Catalytic Efficiency ◽  
Formaldehyde Concentration ◽  
Binding Studies ◽  
Photometric Analysis ◽  
Limit Values ◽  
Catalytic Rate Constant ◽  
Catalytic Rate ◽  
Hydrolysis Of

The effect of formaldehyde concentration on the steady state parameters of the chymotrypsin-catalyzed hydrolysis of specific ester substrates has been investigated. At the limit values which are attained in about 3 M formaldehyde, the catalytic rate constant is decreased eightfold and [Formula: see text] increased ca. 2.5-foid. The reduction in activity does not conform to competitive, noncompetitive, uncompetitive, or partially competitive inhibition. The effect of increasing formaldehyde concentration is, however, in accord with an equimolar equilibrium reaction between chymotrypsin and formaldehyde with Kassoc of 5 M−1. Spectro-photometric analysis of the same reaction (J. Biol. Chem. 242, 5736 (1967)) and binding studies with 14C-elabeled formaldehyde (Biochim. Biophys. Acta, 242, 320 (1971)) have shown that both histidine residues react with formaldehyde.From a study of the imidazole group catalyzed hydrolysis of p-nitrophenyl acetate, the effect of formaldehyde on such processes is qualitatively similar to that observed for reactions catalyzed by chymotrypsin. The Kassoc values, however, are higher: 36 M−1 for imidazole and 25 M−1 for acetylhistidine.On the basis of these and other results, it is concluded that formaldehyde reacts with the active site of chymotrypsin to form a modified enzyme with decreased catalytic efficiency. The causative event is most probably due to the formation of an N-hydroxymethyl derivative of the His-57 residue.

scholarly journals Role of Asp104 in the SHV β-Lactamase

2006 ◽  
Vol 50 (12) ◽  
pp. 4124-4131 ◽  
Author(s):  
Christopher R. Bethel ◽  
Andrea M. Hujer ◽  
Kristine M. Hujer ◽  
Jodi M. Thomson ◽  
Mark W. Ruszczycky ◽  
...  
Keyword(s):  
Amino Acid ◽  
Catalytic Efficiency ◽  
Saturation Mutagenesis ◽  
Amino Acid Residues ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Threefold Increase ◽  
Rate Limiting ◽  
Hydrolysis Of

ABSTRACT Among the TEM-type extended-spectrum β-lactamases (ESBLs), an amino acid change at Ambler position 104 (Glu to Lys) results in increased resistance to ceftazidime and cefotaxime when found with other substitutions (e.g., Gly238Ser and Arg164Ser). To examine the role of Asp104 in SHV β-lactamases, site saturation mutagenesis was performed. Our goal was to investigate the properties of amino acid residues at this position that affect resistance to penicillins and oxyimino-cephalosporins. Unexpectedly, 58% of amino acid variants at position 104 in SHV expressed in Escherichia coli DH10B resulted in β-lactamases with lowered resistance to ampicillin. In contrast, increased resistance to cefotaxime was demonstrated only for the Asp104Arg and Asp104Lys β-lactamases. When all 19 substitutions were introduced into the SHV-2 (Gly238Ser) ESBL, the most significant increases in cefotaxime and ceftazidime resistance were noted for both the doubly substituted Asp104Lys Gly238Ser and the doubly substituted Asp104Arg Gly238Ser β-lactamases. Correspondingly, the overall catalytic efficiency (k cat/Km ) of hydrolysis for cefotaxime was increased from 0.60 ± 0.07 μM−1 s−1 (mean ± standard deviation) for Gly238Ser to 1.70 ± 0.01 μM−1 s−1 for the Asp104Lys and Gly238Ser β-lactamase (threefold increase). We also showed that (i) k 3 was the rate-limiting step for the hydrolysis of cefotaxime by Asp104Lys, (ii) the Km for cefotaxime of the doubly substituted Asp104Lys Gly238Ser variant approached that of the Gly238Ser β-lactamase as pH increased, and (iii) Lys at position 104 functions in an energetically additive manner with the Gly238Ser substitution to enhance catalysis of cephalothin. Based on this analysis, we propose that the amino acid at Ambler position 104 in SHV-1 β-lactamase plays a major role in substrate binding and recognition of oxyimino-cephalosporins and influences the interactions of Tyr105 with penicillins.

scholarly journals Acyl and amino intermediates in reactions catalysed by pig pepsin. Analysis of transpeptidation products

1976 ◽  
Vol 153 (3) ◽  
pp. 691-699 ◽  
Author(s):  
T T Wang ◽  
T Hofmann
Keyword(s):  
Reaction Rates ◽  
Major Product ◽  
Conclusive Evidence ◽  
Acyl Transfer ◽  
High Yield ◽  
Amino Acid Residues ◽  
Small Peptides ◽  
Ph Optimum ◽  
Covalent Intermediate ◽  
Hydrolysis Of

The action of pig pepsin on a variety of small peptides including Leu-Trp-Met-Arg, Leu-Trp-Met, Leu-Leu-NH2, benzyloxycarbonyl-Phe-Leu and Gly-Leu-Tyr was studied. Leu-Leu-Leu was found to be the major product from the substrates Leu-Trp-Met-Arg and Leu-Trp-Met, indicating that the predominant reaction at pH 3.4 was a transpeptidation of the acyl-transfer type. Leu-Leu-Leu was also formed in high yield by amino transfer from benzyloxycarbonyl-Phe-Leu. Like the amino-transfer reactions the acyl transfer proceeded via a covalent intermediate, since [14C]leucine was not incorporated into transpeptidation products and did not exchange with enzyme-bound leucine in the presence of acceptors. With Leu-Trp-Met both acyl and amino transpeptidation products, namely Leu-Leu, Leu-Leu-Leu, Met-Met and Met-Met-Met, were formed in addition to methionine and leucine. With Leu-Trp-Met-Arg (1 mM) the pH optimum for the rates of hydrolysis and acyl transfer is about pH 3.4. At this pH the rate of acyl transfer exceeds that of hydrolysis; at pH 2, however, hydrolysis was faster than transfer. A comparison of the effect of the length of substrates and products on the reaction rates allows the conclusion that the binding site can extend over eight to nine amino acid residues. Although the experiments provide no conclusive evidence for or against the involvement of amino and/or acyl intermediates in the hydrolysis of long peptides and proteins, the high yield of transpeptidation reactions of both types observed with some substrates suggests a major role for the intermediates in pepsin-catalysed reactions. The results also show that when pig pepsin is used for the digestion of proteins for sequence work, the likelihood of the formation of transpeptidation products is considerable. In this way peptides not present in the original sequence could easily form in a reasonably good yield.

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