Starch metabolism in Pseudomonas stutzeri. I. Studies on maltotetraose-forming amylase.

The extracellular maltotetraose-forming amylase of Pseudomonas stutzeri was purified to homogeneity by a combination of affinity and hydroxyapatite chromatography. Sodium dodecyl sulfate-gel electrophoresis indicated that the oligomeric enzyme contains two different subunits with molecular weights of 48 000 and 58 000. Cross-linking studies using dimethyl suberimidate have demonstrated that the native enzyme consists of dimers. Seven isozymes of the amylase have been identified after polyacrylamide gel electrophoresis and amylose-digestion zymograms. The amylase of Ps. stutzeri is known to produce maltotetraose from linear and branched alpha-glucans by an exomechanism. The relatively high conversion rate of starch (75% hydrolysis), and the hydrolysis of cross-linked blue starch by this amylase indicate that the enzyme can cleave its substrates also by an endomechanism. Further strong evidence for an endomechanism was obtained from the action of the amylase on maltotetraose units which are located within the pullulan molecule. Dextran, pullulan, and maltotetraose are compeititve inhibitors. EDTA caused reversible inactivation. Amylase activity could be restored by addition of Ca2+. Heavy metals are inhibitory.     

Enzymatic synthesis of p-nitrophenyl alpha-maltopentaoside in an aqueous-methanol solvent system by maltotetraose-forming amylase: a substrate for human amylase in serum

Transglycosylation from maltopentaose to the 4-position of p-nitrophenyl alpha-glucoside was efficiently induced through the use of maltotetraose-forming amylase from Pseudomonas stutzeri in an aqueous solution containing methanol at a high concentration. The enzyme specifically formed p-nitrophenyl alpha-maltopentaoside (12% of the enzyme-catalyzed net decrease of maltopentaose) from maltopentaose as a donor and p-nitrophenyl alpha-glucoside as an acceptor. The rate of the transglycosylation depended on the concentration of methanol solvent, the pH and the temperature. Use of the aqueous methanol system in this reaction not only ensured a sufficient solubility of p-nitrophenyl alpha-glucoside but also resulted in a remarkable increase in the formation of p-nitrophenyl alpha-maltopentaoside, which is a useful substrate for assay of human amylase in serum and urine.     

Roles of cysteinyl residues of phosphoribulokinase as examined by site-directed mutagenesis.

The Calvin Cycle enzyme phosphoribulokinase is activated in higher plants by the reversible reduction of a disulfide bond, which is located at the active site. To determine the possible contribution of the two regulatory residues (Cys16 and Cys55) to catalysis, site-directed mutagenesis has been used to replace each of them in the spinach enzyme with serine or alanine. The only other cysteinyl residues of the kinase, Cys244 and Cys250, were also replaced individually by serine or alanine. A comparison of specific activities of native and mutant enzymes reveals that substitutions at positions 244 or 250 are inconsequential. The position 16 mutants retain 45-90% of the wild-type activity and display normal Km values for both ATP and ribulose 5-phosphate. In contrast, substitution at position 55 results in 85-95% loss of wild-type activity, with less than a 2-fold increase in the Km for ATP and a 4-8-fold increase in the Km for ribulose 5-phosphate. These results are consistent with moderate facilitation of catalysis by Cys55 and demonstrate that the other three cysteinyl residues do not contribute significantly either to structure or catalysis. The enhanced stability, relative to wild-type enzyme, of the Ser16 mutant protein to a sulfhydryl reagent supports earlier suggestions that Cys16 is the initial target of the oxidative deactivation process.     

Continuous production of maltotetraose using a dual immobilized enzyme system of maltotetraose-forming amylase and pullulanase

In order to produce a product with a high content of maltotetraose, dual-enzyme systems composed of immobilized maltotetraose-forming amylase (G(4)-forming amylase) and pullulanase were studied. The thermostability of individually immobilized enzymes was examined in continuous operation; studies revealed that the enzyme immobilized on "Chitopearl" was much more stable than that immobilized on Diaion HP-50. The effects of operating conditions on the stability of G(4) forming amylase immobilized on "Chitopearl" were examined to confirm that the apparent half-life data could be arranged using the immobilized enzyme stability factor, f(s). As for the dual immobilized enzyme system, six methods of usage were considered, with five yielding a 7-10% (w/w) higher content of maltotetraose product than the single-enzyme system. The effects of operating conditions on the maltotetraose production reaction were examined to confirm that the maltotetraose content of the products could be analyzed using the specific space velocity,SSV. In dual immobilized enzyme systems, pullulanase immobilized on the same carrier as the G(4)-forming amylase was found to be more stable than pullulanase immobilized on separate carriers. The effectiveness of using immobilized pullulanase along with the G(4)-forming amylase was confirmed from constant-conversion operations in which the maltotetraose content in the product was kept at 50% (w/w) in laboratory-scale experimentation.     

Proteases involved in generation of beta- and alpha-amylases from a large amylase precursor in Bacillus polymyxa.

The genes for extracellular neutral protease (Npr) and intracellular serine protease (Isp) were cloned from Bacillus polymyxa in order to elucidate the process involved in the generation of multiple beta-amylases and an alpha-amylase from a large amylase precursor. The npr gene was composed of 1,770 bp and 570 amino acids, while the isp gene was composed of 978 bp and 326 amino acids. Both proteases produced by E. coli cleaved the amylase precursor to generate beta- and alpha-amylases. Furthermore, several other proteases produced the same products from the precursor. A 130-kDa amylase precursor has two large domain structures responsible for the generation of beta- and alpha-amylases. The junction region of approximately 200 amino acids may be exposed on the surface of the molecule and susceptible to proteolytic enzymes, which results in the formation of multiple amylases.     

The alpha-amylases as glycosylases, with wider catalytic capacities than envisioned or explained by their representation as hydrolases

In a study undertaken to illustrate the inadequacy of the familiar concept of carbohydrases as hydrolases, crystalline α-amylases from six different sources, as well as crude salivary amylase, were examined and found to catalyze the synthesis of maltose and maltosaccharides from α-d-glucopyranosyl fluoride, a stereoanalog of α-d-glucopyranose. These syntheses apparently involve initial formation of maltosyl fluoride and higher maltosaccharide 1-fluorides, traces of which were found in digests with certain α-amylases. That the reactions are due to the α-amylases themselves and not to some accompanying enzyme(s) appears certain from the purity and diversity of the preparations; their failure (with one exception) to attack α- or β-maltose; the correspondence of the synthesized products with the known specificity of α-amylases for α-1,4-d-glucosidic linkages (and capacity of different α-amylases to hydrolyze saccharides of different sizes). The “saccharifying” α-amylase of B. sublilis var amylosacchariticus was unique in producing maltosaccharides from both α- and β-maltose (i.e., by α-d-glucosyl transfer). However, the entire group of α-amylases had the capacity to promote α-d-glucosyl transfer from α-d-glucosyl fluoride to C₄-carbinol sites, demonstrating for the first time that the catalytic range of α-amylase extends beyond hydrolysis and its reversal. Indeed, all transferred the glucosyl group of α-d-glycosyl fluoride preferentially to C₄-carbinols rather than water—a finding neither anticipated nor explained by the representation of α-amylases as hydrolases.     

Identification of Asp174 and Asp175 as the key catalytic residues of human O-GlcNAcase by functional analysis of site-directed mutants

O-GlcNAcase is a family 84 beta-N-acetylglucosaminidase catalyzing the hydrolytic cleavage of beta-O-linked 2-acetamido-2-deoxy-d-glycopyranose (O-GlcNAc) from serine and threonine residues of posttranslationally modified proteins. O-GlcNAcases use a double-displacement mechanism involving formation and breakdown of a transient bicyclic oxazoline intermediate. The key catalytic residues of any family 84 enzyme facilitating this reaction, however, are unknown. Two mutants of human O-GlcNAcase, D174A and D175A, were generated since these residues are highly conserved among family 84 glycoside hydrolases. Structure-reactivity studies of the D174A mutant enzyme reveals severely impaired catalytic activity across a broad range of substrates alongside a pH-activity profile consistent with deletion of a key catalytic residue. The D175A mutant enzyme shows a significant decrease in catalytic efficiency with substrates bearing poor leaving groups (up to 3000-fold), while for substates bearing good leading groups the difference is much smaller (7-fold). This mutant enzyme also cleaves thioglycosides with essentially the same catalytic efficiency as the wild-type enzyme. As well, addition of azide as an exogenous nucleophile increases the activity of this enzyme toward a substrate bearing an excellent leaving group. Together, these results allow unambiguous assignment of Asp(174) as the residue that polarizes the 2-acetamido group for attack on the anomeric center and Asp(175) as the residue that functions as the general acid/base catalyst. Therefore, the family 84 glycoside hydrolases use a DD catalytic pair to effect catalysis.     

Cloning and nucleotide sequence of the gene (amyP) for maltotetraose-forming amylase from Pseudomonas stutzeri MO-19.

The gene (amyP) coding for maltotetraose-forming amylase (exo-maltotetraohydrolase) of Pseudomonas stutzeri MO-19 was cloned. Its nucleotide sequence contained an open reading frame coding for a precursor (547 amino acid residues) of secreted amylase. The precursor had a signal peptide of 21 amino acid residues at its amino terminus. An extract of Escherichia coli carrying the cloned amyP had amylolytic activity with the same mode of action as the extracellular exo-maltotetraohydrolase obtained from P. stutzeri MO-19. A region in the primary structure of this amylase showed homology with those of other amylases of both procaryotic and eucaryotic origins. The minimum 5' noncoding region necessary for the expression of amyP in E. coli was determined, and the sequence of this region was compared with those of Pseudomonas promoters.     

Co-oligopeptides of aromatic amino acids and glycine with a variable distance between the aromatic residues. V. pH-dependent conformational changes in peptides containing two adjacent tryptophyl residues as evidenced by circular dichroism studies.

The influence of pH upon CD spectra of H-Trp-Trp-OH, H-Trp-Trp-Gly-OH, and H-Gly-Trp-Trp-OH is investigated and data are compared with those obtained for peptides containing only one tryptophyl residue. A negative Cotton effect at around 225 nm, which in previous work has been related to an increase of the conformational rigidity in compounds having the sequence -CO-Trp-Trp, is also observed in the case of H-Trp-Trp-OH and H-Trp-Trp-Gly-OH upon deprotonation of the terminal α-amino group. These data, together with observations arising from solvent and temperature effects, give evidence that H-Trp-Trp-OH undergoes a conformational change upon going from acid to alkaline conditions, where the two aromatic side chains become conformationally more rigid relative to each other. This rigidity generates an exciton coupling between the B_b transitions of the two indoles. Hydrophobic forces, including stacking interactions, do not appear important in stabilizing this conformationally rigid structure. Rather, intramolecular electrostatic interactions (e.g., hydrogen bondings or polar interactions between the aromatic side chain and the peptide backbone) as well as interactions with the OH group(s) of the solvent, are suggested to be the salient forces. Possible structures which obey these requisites are discussed.     

Conserved residues of liquefying alpha-amylases are concentrated in the vicinity of active site

Three dimensional structure of three liquefying type Bacillus alpha-amylases were modeled based on sequence analyses and refined structure of Aspergillus oryzae enzyme. The models suggest that the overall folding motif of alpha-amylases is conserved. The active site, substrate binding and stabilizing calcium binding residues are conserved and concentrated in a cleft between two domains. They constitute the core of alpha-amylases to which other, less conserved regions are attached. The bacterial enzymes have a loop of about 45 residues near the active site and Ca2+ binding region. The loop may be important for the liquefying function of these enzymes.     

Roles of three well-conserved arginine residues in mediating the catalytic activity of tobacco acetohydroxy acid synthase

Acetohydroxy acid synthase (AHAS, EC 2.2.1.6; also known as acetolactate synthase, ALS) catalyzes the first common step in the biosynthesis of valine, leucine, and isoleucine in plants and microorganisms. AHAS is the target of several classes of herbicides. In the present study, the role of three well-conserved arginine residues (R141, R372, and R376) in tobacco AHAS was determined by site-directed mutagenesis. The mutated enzymes, referred to as R141A, R141F, and R376F, were inactive and unable to bind to the cofactor, FAD. The inactive mutants had the same secondary structure as that of the wild type. The mutants R141K, R372F, and R376K exhibited much lower specific activities than the wild type, and moderate resistance to herbicides such as Londax, Cadre, and/or TP. The mutation R141K showed a strong reduction in activation efficiency by ThDP, while the mutations R372K and R376K showed a strong reductions in activation efficiency by FAD in comparison to the wild type enzyme. Taking into account the data presented here and the homology model constructed previously [Le et al. (2004) Biochem. Biophys. Res. Commun. 317, 930-938], it is suggested that the three amino acid residues studied (R141, R372, and R376) are located essentially at the enzyme active site, and, furthermore, that residues R372 and R376 are possibly responsible for the binding of the enzyme to FAD.     

P-cats: prediction of catalytic residues in proteins from their tertiary structures

SUMMARY: P-cats is a web server that predicts the catalytic residues in proteins from the atomic coordinates. P-cats receives a coordinate file of the tertiary structure and sends out analytical results via e-mail. The reply contains a summary and two URLs to allow the user to examine the conserved residues: one for interactive images of the prediction results and the other for a graphical view of the multiple sequence alignment. AVAILABILITY: P-cats is freely available at http://p-cats.hgc.jp/p-cats CONTACT: kino@ims.u-tokyo.ac.jp     

Catalytic function of tyrosine residues in para-hydroxybenzoate hydroxylase as determined by the study of site-directed mutants

The role of protein residues in activating the substrate in the reaction catalyzed by the flavoprotein p-hydroxybenzoate hydroxylase was studied. X-ray crystallography (Schreuder, H. A., Prick, P.A.J., Wieringa, R.K., Vriend, G., Wilson, K.S., Hol, W.G. J., and Drenth, J. (1989) J. Mol. Biol. 208, 679-696) indicates that Tyr-201 and Tyr-385 form a hydrogen bond network with the 4-OH of p-hydroxybenzoate. Therefore, site directed mutants were constructed, converting each of these tyrosines into phenylalanines. Spectral (visible and fluorescence) properties, reduction potentials, and binding constants are very similar to those of wild type, indicating that there are no major structural changes in the mutants. In the absence of substrate, the mutants and wild type exhibit similar pH-dependent changes in the FAD spectrum. However, the enzyme-substrate complex of Tyr-201----Phe lacks an ionization observed in both wild type and Tyr-385----Phe, which preferentially bind the phenolate form of substrates. Tyr-201----Phe shows no preference, indicating that Tyr-201 is required to ionize the substrate. The mutants have less than 6% the activity of the wild type enzyme. The effects on catalysis were studied by stopped flow techniques. Reduction of FAD by NADPH is slower by 10-fold in Tyr-201----Phe and 100-fold in Tyr-385----Phe. When the reduced Tyr-201----Phe-p-hydroxybenzoate complex reacts with oxygen, a long-lived flavin-C(4a)-hydroperoxide is observed, which slowly eliminates H2O2 with very little hydroxylation. Thus, the role of Tyr-201 is to activate the substrate by stabilizing the phenolate. Tyr-385----Phe reacts with oxygen to form 25% oxidized enzyme, and 75% flavin hydroperoxide, which successfully hydroxylates the substrate. This mutant also hydroxylates the product (3, 4-dihydroxybenzoate) to form gallic acid.     

Instability of three-dimensional structures in ribosomal cores evidenced by microcalorimetric studies

In this paper we show a microcalorimetric investigation carried out on the so-called cores, i.e. ribosomes deprived of select proteins by LiCl treatment. Thermal degradation of native ribosomes gives rise to two thermal transitions occurring at different temperatures. In the cores the high temperature peak persists even after treatment at very high ion strength (2 M LiCl). This strongly suggests the existence of a very stable structure that was previously observed also in particles treated with agents that hydrolyze the RNA moiety. The low temperature peak gradually but dramatically decreases even though it never disappears completely. This indicates that the treatment to obtain ribosomal cores does not cause complete unfolding of the particle but only the destabilization of a structural three-dimensional domain present in native ribosomes. These data are discussed in the light of previous results obtained by dielectric spectroscopy and microcalorimetric studies on ribosomal particles.     

Crystal structures of the FXIa catalytic domain in complex with ecotin mutants reveal substrate-like interactions

Thrombosis can lead to life-threatening conditions such as acute myocardial infarction, pulmonary embolism, and stroke. Although commonly used anti-coagulant drugs, such as low molecular weight heparin and warfarin, are effective, they carry a significant risk of inducing severe bleeding complications, and there is a need for safer drugs. Activated Factor XI (FXIa) is a key enzyme in the amplification phase of the coagulation cascade. Anti-human FXI antibody significantly reduces thrombus growth in a baboon thrombosis model without bleeding problems (Gruber, A., and Hanson, S. R. (2003) Blood 102, 953-955). Therefore, FXIa is a potential target for anti-thrombosis therapy. To determine the structure of FXIa, we derived a recombinant catalytic domain of FXI, consisting of residues 370-607 (rhFXI370-607). Here we report the first crystal structure of rhFXI370-607 in complex with a substitution mutant of ecotin, a panserine protease protein inhibitor secreted by Escherichia coli, to 2.2 A resolution. The presence of ecotin not only assisted in the crystallization of the enzyme but also revealed unique structural features in the active site of FXIa. Subsequently, the sequence from P5 to P2' in ecotin was mutated to the FXIa substrate sequence, and the structures of the rhFXI370-607-ecotin mutant complexes were determined. These structures provide us with an understanding of substrate binding interactions of FXIa, the structural information essential for the structure-based design of FXIa-selective inhibitors.     

Dissecting structural and electrostatic interactions of charged groups in alpha-sarcin. An NMR study of some mutants involving the catalytic residues

The cytotoxic ribonuclease alpha-sarcin is the best characterized member of the ribotoxin family. Ribotoxins share a common structural core, catalytic residues, and active site topology with members of the broader family of nontoxic microbial extracellular RNases. They are, however, much more specific in their biological action. To shed light on the highly specific alpha-sarcin activity, we have evaluated the structural and electrostatic interactions of its charged groups, by combining the structural and pK(a) characterization by NMR of several variants with theoretical calculations based on the Tanford-Kirkwood and Poisson-Boltzmann models. The NMR data reveal that the global conformation of wild-type alpha-sarcin is preserved in the H50Q, E96Q, H137Q, and H50/137Q variants, and that His137 is involved in an H-bond that is crucial in maintaining the active site structure and in reinforcing the stability of the enzyme. The loss of this H-bond in the H137Q and H50/137Q variants modifies the local structure of the active site. The pK(a) values of active site groups H50, E96, and H137 in the four variants have been determined by two-dimensional NMR. The catalytic dyad of E96 and H137 is not sensitive to charge replacements, since their pK(a) values vary less than +/-0.3 pH unit with respect to those of the wild type. On the contrary, the pK(a) of His50 undergoes drastic changes when compared to its value in the intact protein. These amount to an increase of 0.5 pH unit or a decrease of 1.1 pH units depending on whether a positive or negative charge is substituted at the active site. The main determinants of the pK(a) values of most of the charged groups in alpha-sarcin have been established by considering the NMR results in conjunction with those derived from theoretical pK(a) calculations. With regard to the active site residues, the H50 pK(a) is chiefly influenced by electrostatic interactions with E96 and H137, whereas the effect of the low dielectric constant and the interaction with R121 appear to be the main determinants of the altered pK(a) value of E96 and H137. Charge-charge interactions and an increased level of burial perturb the pK(a) values of the active site residues of alpha-sarcin, which can account for its reduced ribonucleolytic activity and its high specificity.     

Differences in conformational stability between native and phosphorylated acetylcholinesterase as evidenced by a monoclonal antibody.

Monoclonal antibody 25B1 generated against diisopropyl phosphorofluoridate inhibited fetal bovine serum acetylcholinesterase has been extensively characterized with respect to its anticholinesterase properties. This antibody demonstrated considerably different properties from previously reported inhibitory antibodies raised against acetylcholinesterase in terms of the degree of inhibition (greater than 98%), the high degree of specificity, and the stability of the antigen-antibody complex. Monoclonal antibody 25B1 appears to be directed against a conformational epitope located in close proximity to the catalytic center of the enzyme and was found to be most suitable for studying the stabilization of the active site of acetylcholinesterase against denaturation by heat or guanidine following phosphorylation by organophosphorus anticholinesterase compounds. This approach allowed the determination of stability rank order of various phosphorylated acetylcholinesterases. Among all the organophosphates tested, the combination of a methyl group and a negatively charged oxygen attached to the P atom, CH3P(O)(O-)-AChE, conferred the greatest protection to the active site of aged or nonaged organophosphoryl conjugates of acetylcholinesterase.     

Functional site of human placental estradiol 17 beta-dehydrogenase involves tyrosine residues, as evidenced by reaction to p-nitrobenzenesulfonyl fluoride

Native estradiol 17 beta-dehydrogenase (EC 1.1.1.62) from human placenta was inactivated in time dependent manner by p-nitrobenzenesulfonyl fluoride (NBSF), which is a reagent for chemical modification of tyrosine. The sulfhydryl-blocked enzyme by 5,5'-dithio-bis(2-nitrobenzoic acid) (DTNB) was also reacted with NBSF more slowly in pseudo-first-order kinetics. After the sequential treatments with DTNB, NBSF and dithiothreitol (DTT), the enzyme in which tyrosine residues alone were modified was isolated, and its activity was decreased. These results suggest that tyrosyl residues of the estradiol 17 beta-dehydrogenase from human placenta are located at or near its catalytic site, and play a functional role in the enzyme reaction.