Loop engineering of amadoriase II and mutational cooperativity

Amadori compounds and their cross-linked products have been implicated in diabetic complications and some age-related diseases. Fructosyl amine oxidases (FAOXs) are a family of enzymes that can cleave the amadori compounds. However, the natural enzymes are only active on small substrates (fructosyl amino acids or dipeptides), which limits the therapeutic and diagnostic applications of these enzymes. In this study, amadoriase II, a member of the FAOX family from Aspergillus fumigatus was engineered to broaden its substrate range using a modified combinatorial active site saturation testing approach. The two loops at the entrance of the substrate channel were targeted. Saturation mutagenesis was carried out to search for hot-spot sites, followed by pairwise mutagenesis and subsequent combination of active mutations. Five sites on the loops were found to be critical for accessibility for two model bulky substrates, fructosyl adamantanamine and fructosyl-polylysine (3–13 lysines). Two best mutants (with three and five mutations, respectively) were obtained, with a specific activity toward the model substrates 20.6-fold and 16.8-fold that of the wild-type, respectively. Deconvolution experiments revealed the cooperativity of the mutations.     

Occurrence, characteristics, and applications of fructosyl amine oxidases (amadoriases)

Amadori compounds, formed by the Maillard reaction between reducing sugars (e.g., glucose) and amines (e.g., lysine residues in proteins), are ubiquitous in nature and have been implicated in aging and several chronic diseases. Fructosyl amine oxidases (FAOXs) are a relatively new class of enzymes that cleave amadori compounds and have been found in fungi, yeast, and bacteria. This mini-review summarizes over a dozen of FAOXs with different substrate specificities have been isolated, characterized, and engineered to date. All known FAOX sequences except one have the consensus motif for the ADP-binding βαβ-fold common to all FAD and NAD enzymes, and a recently solved crystal structure provides important clues for this class of enzymes. FAOXs have been explored for applications in diabetes diagnosis, detergents, and food processing. Given that naturally occurring FAOXs can only react directly with small glycated amino acids or short peptides, it is of great interest to engineer and expand the accessibility of the substrate binding sites of these enzymes.     

Cyanide as a copper-directed inhibitor of amine oxidases: implications for the mechanism of amine oxidation

 The interactions of five copper-containing amine oxidases with substrates and substrate analogues in the presence of the copper ligands cyanide, azide, chloride, and 1,10-phenanthroline have been investigated. While cyanide inhibits, to varying degrees, the reaction of phenylhydrazine with porcine kidney amine oxidase (PKAO), porcine plasma amine oxidase (PPAO), bovine plasma amine oxidase (BPAO), and pea seedling amine oxidase (PSAO), it enhances the reaction of Arthrobacter P1 amine oxidase (APAO) with this substrate analogue. This indicates that cyanide exerts an indirect effect on topa quinone (TPQ) reactivity via coordination to Cu(II) rather than through cyanohydrin formation at the TPQ organic cofactor. Moreover, cyanide binding to the mechanistically relevant TPQ^• semiquinone form of substrate-reduced APAO and PSAO was not observable by EPR or resonance Raman spectroscopy. Hence, cyanide most likely inhibits enzyme reoxidation by binding to Cu(I) and trapping the Cu(I)-TPQ^• form of amine oxidases, and thus preventing the reaction of O₂ with Cu(I). In contrast, ligands such as azide, chloride, and 1,10-phenanthroline, which preferentially bind to Cu(II), inhibit by stabilizing the aminoquinol Cu(II)-TPQ_red redox state, which is in equilibrium with Cu(I)-TPQ^•. Received: 12 December 1996 / Accepted: 20 March 1997     

Donor substrate recognition in the raffinose-bound E342A mutant of fructosyltransferase <Emphasis Type="Italic">Bacillus subtilis</Emphasis> levansucrase

Background  

Fructans – β-D-fructofuranosyl polymers with a sucrose starter unit – constitute a carbohydrate reservoir synthesised by a considerable number of bacteria and plant species. Biosynthesis of levan (αGlc(1–2)βFru [(2–6)βFru]_n), an abundant form of bacterial fructan, is catalysed by levansucrase (sucrose:2,6-β-D-fructan-6-β-D-fructosyl transferase), utilizing sucrose as the sole substrate. Previously, we described the tertiary structure of Bacillus subtilis levansucrase in the ligand-free and sucrose-bound forms, establishing the mechanistic roles of three invariant carboxylate side chains, Asp86, Asp247 and Glu342, which are central to the double displacement reaction mechanism of fructosyl transfer. Still, the structural determinants of the fructosyl transfer reaction thus far have been only partially defined.     

Construction of engineered fructosyl peptidyl oxidase for enzyme sensor applications under normal atmospheric conditions

Current enzymatic methods for the analysis of glycated proteins use flavoenzymes that catalyze the oxidative deglycation of fructosyl peptides, designated as fructosyl peptidyl oxidases (FPOXs). However, as FPOXs are oxidases, the signals derived from electron mediator-type electrochemical monitoring based on them are affected by dissolved O₂. Improvement of dye-mediated dehydrogenase activity of FPOXs and its application to enzyme electrode construction were therefore undertaken. Saturation mutagenesis study on Asn56 of FPOX from Phaeosphaeria nodorum, produced mutants with marked decreases in the catalytic ability to employ O₂ as the electron acceptor, while showing higher dye-mediated dehydrogenase activity employing artificial electron acceptors than the parental enzyme. Thus constructed virtually fructosyl peptide dehydrogenase, Asn56Ala, was then applied to produce an enzyme electrode for the measurement of fructosyl-^α N-valyl-histidine (f-^αVal-His), the protease-digested product of HbA1c. The enzyme electrode could measure f-^αVal-His in the physiological target range in air.     

Comparison of Kinetic Properties Between Plant and Fungal Amine Oxidases

Abstract

Kinetic properties of novel amine oxidases isolated from a mold Aspergillus niger AKU 3302 were compared to those of typical plant amine oxidase from pea seedling (EC 1.4.3.6). Pea amine oxidase showed highest affinity with diamines, such as putrescine and cadaverine, while fungal enzymes oxidized preferably n-hexylamine and tyramine. All enzymes were inhibited by carbonyl reagents, copper chelating agents, some substrate analogs and alkaloids, but there were quite significant differences in the sensitivity and inhibition modes. Aminoguanidine, which strongly inhibited pea amine oxidases showed only little effect on fungal enzymes. Substrate analogs such as 1,5-diamino-3-pentanone and l-amino-3-phenyl-3-propanone, which were potent competitive inhibitors of pea amine oxidases, inhibited fungal enzymes much more weakly and non competitively. Also various alkaloids behaving as competitive inhibitors of pea amine oxidases inhibited the fungal enzymes non competitively. Very surprising was the potent inhibition of fungal enzymes by artificial substrates of pea amine oxidases, E- and Z-1,4-diamino-2-butene. The relationships between the different inhibition modes and possible binding at the active site are discussed.     

The cation-π interaction between Lys53 and the flavin of fructosamine oxidase (FAOX-II) is critical for activity

Fructosamine oxidases (FAOXs) are flavin-containing enzymes that catalyze the oxidative deglycation of low molecular weight fructosamines or Amadori products. The fructosamine substrate is oxidized by the flavin in the reductive half-reaction, and the reduced flavin is then oxidized by molecular oxygen in the oxidative half-reaction. The crystal structure of FAOX-II from Aspergillus fumigatus reveals a unique interaction between Lys53 and the isoalloxazine. The ammonium nitrogen of the lysine is in contact with and nearly centered over the aromatic ring of the flavin on the si-face. Here, we investigate the importance of this unique interaction on the reactions catalyzed by FAOX by studying both half-reactions of the wild-type and Lys53 mutant enzymes. The positive charge of Lys53 is critical for flavin reduction but plays very little role in the reaction with molecular oxygen. The conservative mutation of Lys53 to arginine had minor effects on catalysis. However, removing the charge by replacing Lys53 with methionine caused more than a million-fold decrease in flavin reduction, while only slowing the oxygen reaction by ～30-fold.     

Active site analysis of fructosyl amine oxidase using homology modeling and site-directed mutagenesis

A three-dimensional structural model of fructosyl amine oxidase from the marine yeast Pichia N1-1 was generated using the crystal structure of monomeric sarcosine oxidase from Bacillus sp. B-0618 as template. The putative active site region was investigated by site-directed mutagenesis, identifying several amino acid residues likely playing important roles in the enzyme reaction. Asn354 was identified as a residue that plays an important role in substrate recognition and that can be substituted in order to change substrate specificity while maintaining high catalytic activity. While the Asn354Ala substitution had no effect on the V _max K _m⁻¹ value for fructosyl valine, the V _max K _m⁻¹ value for fructosyl-^ε N-lysine was decreased 3-fold, thus resulting in a 3-fold improvement in specificity for fructosyl valine over fructosyl-^ε N-lysine.     

Preliminary kinetic characterization of a copper amine oxidase from rat liver mitochondria matrix

Kinetic measurements of a novel copper-dependent amine oxidase, purified from rat liver mitochondria matrix, were carried out using various substrates in a large pH (5.6–10.2) and ionic strength range (5–200 mM), in order to study the docking of substrates to the enzyme and, as a consequence, to verify the physicochemical characteristics of the active site. Relatively small changes of V _max values (approx. 2.5-folds) over the substrates tested, suggest that the rate determining step of the catalysis is only slightly affected by amine chemical structure. In contrast, the strong change of K _M and k _c/K _M values (approx. two orders of magnitude) indicates electrostatic control of the docking process, since the changes of K _M and k _c/K _M values appear due to the presence of positively charged groups in the substrate molecules. These results suggest the presence in the enzyme active site of two negatively charged amino acid residues which seem to interact with positively charged groups of the substrate molecules. Analogies and differences with bovine serum amine oxidase are also described.     

Analysis of Substrate Specificity and Endopeptidyl Activities of the Cathepsin B-like Proteinase from <Emphasis Type="Italic">Helicoverpa armigera</Emphasis>

The cathepsin B-like proteinase from Helicoverpa armigera (HCB) is involved in the degradation of yolk proteins during embryonic development. In order to gain insight into the substrate specificity of this proteinase, various proteins from animals and plants were tested as substrates. The specific cleavage sites of this enzyme on endopeptide bonds were assayed using bovine serum albumin (BSA) as a substrate. Results showed that BSA was degraded into several fragments, which suggests that HCB cleaves BSA at specific endopeptidyl sites. The amino acid sequences of the BSA derived peptides were determined, revealing cleavage of the bonds between residues Arg⁸¹–Glu⁸², Val⁴²³–Glu⁴²⁴ and Gly⁴³⁰–Lys⁴³¹. This suggests that the minimum requirement for a scissile bond to be recognized by HCB is the presence of an ionic amino acid at the P₁^′ position and the P₁ position can vary. These observations suggest that HCB cleaves bonds at the N-terminal side of ionic amino acid residues giving HCB a wide range of substrates, though other factors dictating the substrate specificity of this enzyme remains to be clarified. Our results provide new evidence that HCB functions as an endopeptidase on some proteins.     

Fungal delignification of lignocellulosic biomass improves the saccharification of cellulosics

The biological delignification of lignocellulosic feedstocks, Prosopis juliflora and Lantana camara was carried out with Pycnoporus cinnabarinus, a white rot fungus, at different scales under solid-state fermentation (SSF) and the fungal treated substrates were evaluated for their acid and enzymatic saccharification. The fungal fermentation at 10.0 g substrate level optimally delignified the P. juliflora by 11.89% and L. camara by 8.36%, and enriched their holocellulose content by 3.32 and 4.87%, respectively, after 15 days. The fungal delignification when scaled up from 10.0 g to 75.0, 200.0 and 500.0 g substrate level, the fungus degraded about 7.69–10.08% lignin in P. juliflora and 6.89–7.31% in L. camara, and eventually enhanced the holocellulose content by 2.90–3.97 and 4.25–4.61%, respectively. Furthermore, when the fungal fermented L. camara and P. juliflora was hydrolysed with dilute sulphuric acid, the sugar release was increased by 21.4-42.4% and the phenolics content in hydrolysate was decreased by 18.46 and 19.88%, as compared to the unfermented substrate acid hydrolysis, respectively. The reduction of phenolics in acid hydrolysates of fungal treated substrates decreased the amount of detoxifying material (activated charcoal) by 25.0–33.0% as compared to the amount required to reduce almost the same level of phenolics from unfermented substrate hydrolysates. Moreover, an increment of 21.1–25.1% sugar release was obtained when fungal treated substrates were enzymatically hydrolysed as compared to the hydrolysis of unfermented substrates. This study clearly shows that fungal delignification holds potential in utilizing plant residues for the production of sugars and biofuels.     

Enzymatic deglycation of Amadori products in bacteria: mechanisms,occurrence and physiological functions

Amadori products (fructosamines)—ubiquitously occurring in nature—are precursors of the toxic and cell damaging ‘advanced glycation endproducts’; thus, it is not surprising that numerous organisms have developed systems to degrade such compounds. The deglycating enzymes differ with respect to their mechanisms as well as to their substrate specificities. Furthermore, different physiological functions are proposed for the different enzymes. The fructosamine 3-kinases of mammals and homologous proteins (fructosamine 3-kinase related proteins), which are common to all taxa, are thought to focus on intracellular repair functions. In contrast, in Bacillus subtilis and Escherichia coli, the cooperative action of a kinase and a deglycase facilitates Amadori degradation. As genes encoding these enzymes are co-transcribed with ABC transporter genes, it is thought that these genes facilitate the utilisation of extracellular Amadori products. Indeed, it has been shown that fructosamines can serve as the sole carbon and nitrogen sources. Here, we provide an overview of known deglycating systems with the emphasis on Amadori product degradation in bacteria.     

Molecular cloning and expression of novel fructosyl peptide oxidases and their application for the measurement of glycated protein

Fructosyl peptide oxidases, enzymes that are active against a model compound of glycated hemoglobin, N(alpha)-fructosyl valyl-histidine, were characterized. To identify the primary structure of fructosyl peptide oxidases, we have prepared cDNA libraries from Eupenicillium terrenum ATCC18547 and Coniochaeta sp. NISL9330. The coding regions, both fungal fructosyl peptide oxidases consisting of 1314-bp, were obtained with degenerated primers based on the amino acid sequences and specific primers by 3(') and 5(') RACE (rapid amplification of cDNA ends). By their sequence similarities and substrate specificities, fructosyl peptide oxidases and their homologs could be categorized into two groups: (A) enzymes that preferably oxidize alpha-glycated molecules and (B) enzymes that preferably oxidize epsilon-glycated molecules. We showed that recombinant fructosyl peptide oxidases could be used to detect protease-treated fructosyl-hexapeptide, a glycated peptide that is released from HbA(1C) by endoproteinase Glu-C, suggesting these enzymes could be useful for the enzymatic measurement of HbA(1C).     

Kinetic characterization of enhanced lipase activity on oil bodies

Enzyme access, kinetic behavior, and protein–protein interactions are critical for explaining reaction of the metabolites contained within the myriad compartments of biological systems. To explore these relationships, the reaction kinetics of oil bodies versus oil emulsions as substrates for lipolytic reactions were measured. The initial rate of hydrolysis for the oil body system was comparatively very low due to a brief latency period. However, the complete activation of the lipase at the interface resulted in an enzyme–membrane complex that was catalytically enhanced 3–15-fold over the emulsion system for substrate concentrations in the measured range of approximately 1–5.5 mM. This disparity is explained by the availability of substrate to the enzyme active site (defined as the availability parameter “A”) which varies between the two substrates by 40-fold. A simple hyperbolic kinetic mechanism is proposed with K _m replaced by the parameter, A, to account for this phenomenon, leading to a maximum rate of approximately 1450 IU/mg protein. The interaction is verified through separation of the enzyme–membrane complex which shows nearly double the activity towards an emulsified soybean oil substrate (activity ratio of 5:3) when compared to the native enzyme.     

Enhancement of thermostability of fungal deglycating enzymes by directed evolution

Fructosyl peptide oxidases are valuable for the determination of glycoproteins such as hemoglobin A1c. For practical use in clinical diagnosis, we applied directed evolution to improve the thermostability of these enzymes. After two rounds of random mutagenesis and high-throughput screening, six thermostabilizing amino acid substitutions were identified. Therefore, site-directed and cassette mutageneses were applied to combine these six stabilizing mutations. The simultaneous mutants showed that the stabilizing effect of the amino acid replacement was cumulative. The sextuple mutant enzyme, R94K/G184D/F265L/N272D/H302R/H388Y, had a half-life of thermal inactivation at 50°C that was 79.8-fold longer than that of the parental fructosyl peptide oxidase. The thermostable variants also showed increased tolerance to digestion by a protease. The sextuple mutant enzyme did not lose its activity on incubation with neutral protease, while the wild-type enzyme almost completely lost its activity. Furthermore, three amino acid substitutions were introduced into another fructosyl peptide oxidase with a different substrate specificity. The half-life of inactivation at 50°C was 3.61-fold longer than that of the parent enzyme. These engineered fructosyl peptide oxidases will be useful for industrial application to clinical diagnosis.     

Efficient synthesis of optically pure alcohols by asymmetric hydrogen-transfer biocatalysis: application of engineered enzymes in a 2-propanol–water medium

We describe an efficient method for producing both enantiomers of chiral alcohols by asymmetric hydrogen-transfer bioreduction of ketones in a 2-propanol (IPA)–water medium with E. coli biocatalysts expressing phenylacetaldehyde reductase (PAR: wild-type and mutant enzymes) from Rhodococcus sp. ST-10 and alcohol dehydrogenase from Leifsonia sp. S749 (LSADH). We also describe the detailed properties of mutant PARs, Sar268, and HAR1, which were engineered to have high activity and productivity in media composed of polar organic solvent and water, and the construction of three-dimensional structure of PAR by homology modeling. The K _m and V _max values for some substrates and the substrate specificity of mutant PARs were quite different from those of wild-type PAR. The results well explained the increased productivity of engineered PARs in IPA–water medium.     

Structure and biogenesis of topaquinone and related cofactors

 The structure of a new biological redox cofactor – topaquinone (TPQ), the quinone of 2,4,5-trihydroxyphenylalanine – was elucidated in 1990. TPQ is the cofactor in most copper-containing amine oxidases. It is produced by post-translational modification of a strictly conserved active-site tyrosine residue. Recent work has established that TPQ biogenesis proceeds via a novel self-processing pathway requiring only the protein, copper, and molecular oxygen. The oxidation of tyrosine to TPQ by dioxygen is a six-electron process, which has intriguing mechanistic implications because copper is a one-electron redox agent, and dioxygen can function as either a two-electron or four-electron oxidant. This review adopts an historical perspective in discussing the structure and reactivity of TPQ in amine oxidases, and then assesses what is currently understood about the mechanism of the oxidation of tyrosine to produce TPQ. Aspects of the structures and chemistry of related cofactors, such as the Tyr-Cys radical in galactose oxidase and the lysine tyrosylquinone of lysyl oxidase, are also discussed. Received: 23 May 1998 / Accepted: 19 October 1998     

Occurrence of Fructosyl-Amino Acid Oxidase-Reactive Compounds in Fungal Cells

Fructosyl-amino acid oxidase (FAOD)-reactive fraction (FRY) was found in commercial yeast extract. FRY showed very hydrophilic property and was adsorbed to phenylboronate silica gel, indicating that it contained the Amadori compound. TLC and amino acid analyses revealed that glucosone, lysine, and arginine were produced from FRY after incubation with FAOD. TOF-MS analysis confirmed that FRY is a mixture of fructosyl lysine and fructosyl arginine. These compounds were also detected in mycelial extract of an FAOD-producer, Aspergillus terreus GP1, grown on the minimum medium, suggesting that a glycation reaction occurs in fungal cells and that FAOD acts toward the resultant Amadori compounds.     

Genetic and functional characterization of <Emphasis Type="Italic">Lactobacillus panis</Emphasis> levansucrase

Exopolysaccharides (EPS) can affect the rheological properties of foods, act as stabilizers or stimulate preferential growth of bifidobacteria in the gut and therefore function as prebiotics. The latter is referred to fructans, which are synthesized from sucrose by fructosyl transferases (FTFs). In this work, the FTF enzyme of Lactobacillus panis TMW1.648 isolated from sourdough was characterized. The coding gene was identified, sequenced and expressed heterologously in E. coli. Enzyme activity was maximal at pH 4.0–4.6, 45°C and a substrate concentration of 300 mmol l⁻¹. It produced free fructose, a high molecular fructan and the oligosaccharide kestose from sucrose. Calcium ions proved to be essential for the enzymatic activity. In comparison to published data of other FTF enzymes of lactobacilli the described enzyme showed significant differences.     

Kinetic studies, mechanism, and substrate specificity of amadoriase I from Aspergillus sp.

Amadoriase is a flavoenzyme that catalyzes the oxidative deglycation of Amadori products (fructosyl amino acids or aliphatic amines) to yield free amine, glucosone, and hydrogen peroxide. The mechanism of action of amadoriase I from Aspergillus sp. has been investigated by stopped-flow kinetic studies using fructosyl propylamine and O(2) as substrates in 10 mM Tris HCl, pH 7.9, 4 degrees C. Using both substrate analogues and fast kinetic techniques, the active configuration of the substrate was found to be the beta-pyranose form. Stopped-flow studies showed that the reductive half-reaction is triphasic and generates intermediates that absorb at long wavelengths and is consistent either with (i) the reaction of the substrate with the flavin followed by iminium deprotonation or hydrolysis and then product release or with (ii) the formation of flavin reduction intermediates (carbanion equivalents or adducts), followed by product release. The rate of product release after flavin reduction is lower than the aerobic turnover rate, 14.4 s(-1), suggesting that it is not involved in the catalytic cycle and that reoxidation of the reduced enzyme occurs in the E(red)-product complex. In the oxidative half-reaction, the reduced flavin is oxidized by O(2) in a single phase. The observed rate constant has a linear dependence on oxygen concentration, giving a bimolecular rate constant of 4.9 x 10(4) M(-1) s(-1) in the absence of product, and 3.6 x 10(4) M(-1) s(-1) when the product is bound. The redox potentials of amadoriase have been measured at pH 7.0, 25 degrees, giving values of +48 and -52 mV for the oxidized enzyme/anionic semiquinone and anionic semiquinone/reduced enzyme couples, respectively.