RESUMO
Hydroxynitrile lyase (HNL) from the cyanogenic millipede Oxidus gracillis (OgraHNL) is a crucial enzyme in the cyanogenesis pathway. Here, the crystal structures of OgraHNL complexed with sulfate, benzaldehyde (BA), (R)-mandelonitrile ((R)-Man), (R)-2-chloromandelonitrile ((R)-2-Cl-Man), and acetone cyanohydrin (ACN) were solved at 1.6, 1.7, 2.3, 2.1, and 2.0â Å resolutions, respectively. The structure of OgraHNL revealed that it belonged to the lipocalin superfamily. Based on this structure, positive variants were designed to further improve the catalytic activity and enantioselectivity of the enzyme for asymmetric hydrocyanation and Henry reactions.
Assuntos
Aldeído Liases , Mutagênese Sítio-Dirigida , Aldeído Liases/metabolismo , Aldeído Liases/química , Aldeído Liases/genética , Animais , Benzaldeídos/metabolismo , Benzaldeídos/química , Acetonitrilas/química , Acetonitrilas/metabolismo , Modelos Moleculares , Cristalografia por Raios X , Nitrilas/metabolismo , Nitrilas/química , EstereoisomerismoRESUMO
Nitriles (R-CN) comprise a broad group of chemicals industrially produced and used in fine chemicals, pharmaceuticals, and bulk applications, polymer chemistry, solvents, etc. Nitriles are important starting materials for producing carboxylic acids, amides, amines, and several other compounds. In addition, some volatile nitriles have been evaluated for their potential as ingredients in fragrance and flavor formulations. However, many nitrile synthesis methods have drawbacks, such as drastic reaction conditions, limited substrate scope, lack of readily available reagents, poor yields, and long reaction times. In contrast to chemical synthesis, biocatalytic approaches using enzymes can produce nitriles without harsh conditions, such as high temperatures and pressures, or toxic compounds. In this review, we summarize the nitrile-synthesizing enzymes from microorganisms, plants, and animals. Furthermore, we introduce several examples of biocatalytic synthesis of volatile nitrile compounds, particularly those using aldoxime dehydratase.
Assuntos
Hidroliases , Nitrilas , Nitrilas/química , Hidroliases/metabolismo , Biocatálise , AmidasRESUMO
MAIN CONCLUSION: Cytochrome P450 CYP77A59 is responsible for the biosynthesis of phenylacetonitrile in loquat flowers. Flowers of some plants emit volatile nitrile compounds, but the biosynthesis of these compounds is unclear. Loquat (Rhaphiolepis bibas) flowers emit characteristic N-containing volatiles, such as phenylacetonitrile (PAN), (E/Z)-phenylacetaldoxime (PAOx), and (2-nitroethyl)benzene (NEB). These volatiles likely play a defense role against pathogens and insects. PAN and NEB are commonly biosynthesized from L-phenylalanine via (E/Z)-PAOx. Two cytochrome P450s-CYP79D80 and "promiscuous fatty acid ω-hydroxylase" CYP94A90, which catalyze the formation of (E/Z)-PAOx from L-phenylalanine and NEB from (E/Z)-PAOx, respectively-are involved in NEB biosynthesis. However, the enzymes catalyzing the formation of PAN from (E/Z)-PAOx in loquat have not been identified. In this study, we aimed to identify candidate cytochrome P450s catalyzing PAN formation in loquat flowers. Yeast whole-cell biocatalyst assays showed that among nine candidate cytochrome P450s, CYP77A58 and CYP77A59 produced PAN from (E/Z)-PAOx. CYP77As catalyzed the dehydration of aldoximes, which is atypical of cytochrome P450; the reaction was NADPH-dependent, with an optimum temperature and pH of 40 °C and 8.0, respectively. CYP77As acted on (E/Z)-PAOx, (E/Z)-4-hydroxyphenylacetaldoxime, and (E/Z)-indole-3-acetaldoxime. Previously characterized CYP77As are known to hydroxylate fatty acids; loquat CYP77As did not act on tested fatty acids. We observed higher expression of CYP77A59 in flowers than in buds; expression of CYP77A58 was remarkably reduced in the flowers. Because the flowers, but not buds, emit PAN, CYP77A59 is likely responsible for the biosynthesis of PAN in loquat flowers. This study will help us understand the biosynthesis of floral nitrile compounds.
Assuntos
Eriobotrya , Nitrilas , Nitrilas/análise , Nitrilas/metabolismo , Sistema Enzimático do Citocromo P-450/genética , Flores/metabolismo , Fenilalanina , Ácidos Graxos/análiseRESUMO
The production of recombinant proteins in Escherichia coli is an important application of biotechnology. 2-Oxoglutarate-dependent l-pipecolic acid hydroxylase derived from Xenorhabdus doucetiae (XdPH) is an excellent biocatalyst that catalyzes the hydroxylation of l-pipecolic acid to produce cis-5-hydroxy-l-pipecolic acid. However, the enzyme tends to form aggregates in the E. coli expression system. Our group established two rules, namely, the "α-helix rule" and the "hydropathy contradiction rule," to select residues to be altered for improving the heterologous recombinant production of proteins, by analyzing their primary structure. We rationally designed XdPH variants that are expressed in highly soluble and active forms in the E. coli expression system using these hotspot prediction methods, and the L142R variant showed a remarkably high soluble expression level compared to the wild-type XdPH. Further mutations were introduced into the L142R gene by site-directed mutagenesis. Moreover, the I28P/L142R and C76Y/L142R double variants displayed improved soluble expression levels compared to the single variants. These variants were also more thermostable than the wild-type XdPH. To analyze the effect of the alteration on one of the hotspots, L142 was replaced with various hydrophilic and positively charged residues. The remarkable increase in soluble protein expression caused by the alterations suggests that the decrease in the hydrophobicity of the protein surface and the enhancement of the interaction between nearby residues are important factors determining the solubility of the protein. Overall, this study demonstrated the effectiveness of our protocol in identifying aggregation hotspots for recombinant protein production and in basic biochemical research.
RESUMO
Microbial production of bioactive glucosides using uridine diphosphate glucosyltransferase (UGT) is an efficient glucoside production method. Here, we describe a detailed method for the construction of a UDP-glucose biosynthetic enzyme gene coexpression plasmid, that is, pCDF-PGP and the microbial production of prunasin from racemic mandelonitrile using Escherichia coli possessing UGT85A47 obtained from Japanese apricot. Furthermore, this constructed vector can find application in the production of various other glucosides that utilize other UGTs and aglycons.
Assuntos
Escherichia coli , Uridina Difosfato Glucose , Escherichia coli/genética , Glucose , Glucosídeos , Nitrilas , Plasmídeos/genética , Difosfato de UridinaRESUMO
Aldoxime dehydratase (Oxd) is a heme enzyme that catalyzes aldoxime dehydration to the corresponding nitriles. Unlike many other heme enzymes, Oxd has a unique feature that the substrate binds directly to the heme. Therefore, it is thought that structural differences around the bound heme directly relate to differences in substrate selection. However sufficient structural information to discuss the substrate specificity has not been obtained. Oxd from Bacillus sp. OxB-1 (OxdB) shows unique substrate specificity and enantioselectivity compared to the Oxds whose crystal structures have already been reported. Here, we report the crystal structure of OxdB, which has not been reported previously. Although the crystallization of OxdB has been difficult, by adding a site-specific mutation to Glu85 located on the surface of the protein, we succeeded in crystallizing OxdB without reducing the enzyme activity. The catalytic triad essential for Oxd activity were structurally conserved in OxdB. In addition, the crystal structure of the Michaelis complex of OxdB and the diastereomerically pure substrate Z-2-(3-bromophenyl)-propanal oxime implied the importance of several hydrophobic residues for substrate specificity. Mutational analysis implicated Ala12 and Ala14 in the E/Z selectivity of bulky compounds. The N-terminal region of OxdB was shown to be shorter than those of Oxds from Pseudomonas chlororaphis and Rhodococcus sp. N-771, and have high flexibility. These structural differences possibly result in distinct preferences for aldoxime substrates based on factors such as substrate size.
Assuntos
Bacillus , Cristalização , Heme/química , Hidroliases , Oximas/química , Especificidade por SubstratoRESUMO
Hydroxynitrile lyase from Linum usitatissimum (LuHNL) is an enzyme involved in the catabolism of cyanogenic glycosides to release hydrogen cyanide upon tissue damage. This enzyme strictly conserves the substrate- and NAD(H)-binding domains of Zn2+-containing alcohol dehydrogenase (ADH); however, there is no evidence suggesting that LuHNL possesses ADH activity. Herein, we determined the ligand-free 3D structure of LuHNL and its complex with acetone cyanohydrin and (R)-2-butanone cyanohydrin using X-ray crystallography. These structures reveal that an A-form NAD+ is tightly but not covalently bound to each subunit of LuHNL. The restricted movement of the NAD+ molecule is due to the "sandwich structure" on the adenine moiety of NAD+. Moreover, the structures and mutagenesis analysis reveal a novel reaction mechanism for cyanohydrin decomposition involving the cyano-zinc complex and hydrogen-bonded interaction of the hydroxyl group of cyanohydrin with Glu323/Thr65 and H2O/Lys162 of LuHNL. The deprotonated Lys162 and protonated Glu323 residues are presumably stabilized by a partially desolvated microenvironment. In summary, the substrate binding geometry of LuHNL provides insights into the differences in activities of LuHNL and ADH, and identifying this novel reaction mechanism is an important contribution to the study of hydroxynitrile lyases.
Assuntos
Aldeído Liases , Linho , Proteínas de Plantas , Aldeído Liases/química , Aldeído Liases/metabolismo , Sítios de Ligação , Cristalografia por Raios X , Linho/enzimologia , Modelos Moleculares , NAD/metabolismo , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Zinco/química , Zinco/metabolismoRESUMO
Thermostable l-glutamate oxidases (LGOXs) are desirable for use in l-glutamate (L-Glu) assay kits, enzymatic synthesis of α-ketoglutarate and for biosensor development. However, protein engineering efforts to improve thermostability often lead to a decrease in enzymatic activity. In this report, we aimed to enhance the thermostability (melting temperature, Tm) of a mesophilic LGOX from Streptomyces sp. NT1 (LGOXNT1) without a reduction in activity by a sequence-based protein design approach, termed full consensus (Fc) protein design. Among the 690 amino acids of LGOXNT1, 104 amino acids were substituted by the Fc protein design. The mutant gene was artificially synthesized and expressed in Escherichia coli BL21(DE3) cells. The Tm of the purified, recombinant LGOX mutant (FcLGOX) was determined to be â¼72 °C, which is an increase on the Tm of 65 °C for LGOXNT1 and the highest among known LGOXs. Importantly, purified FcLGOX showed no loss of specific activity or substrate specificity after a 30-min incubation at 70 °C. Our findings provide a new approach to improve the thermostability of enzymes.
Assuntos
Streptomyces , Aminoácido Oxirredutases/química , Aminoácido Oxirredutases/genética , Aminoácido Oxirredutases/metabolismo , Proteínas de Bactérias/metabolismo , Consenso , Estabilidade Enzimática/genética , Streptomyces/metabolismo , TemperaturaRESUMO
Recently, the program INTMSAlign_HiSol for identifying aggregation hotspots in proteins only requiring secondary structure data was introduced. We explored the utility of this program further and applied it for engineering of the aldoxime dehydratase from Bacillus sp. OxB-1. Towards this end, the effect of inverting the hydropathy at selected positions of the amino acid sequence on the enzymatic activity was studied leading to 60% of our constructed variants, which showed improved activity. In part, this activity increase can be rationalised by an improved heme incorporation of the variants. For example, a single mutation gave a 1.8 fold increased enzymatic activity and 30% improved absolute heme incorporation.
Assuntos
Hidroliases/metabolismo , Engenharia de Proteínas/métodos , Bacillus/enzimologia , Bacillus/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Biocatálise , Hidroliases/química , Alinhamento de Sequência , Especificidade por SubstratoRESUMO
Consensus design (CD) is a representative sequence-based protein design method that enables the design of highly functional proteins by analyzing vast amounts of protein sequence data. This study proposes a partial consensus design (PCD) of a protein as a derivative approach of CD. The method replaces the target protein sequence with a consensus sequence in a secondary-structure-dependent manner (i.e., regionally dependent and divided into α-helix, ß-sheet, and loop regions). In this study, we generated several artificial partial consensus l-threonine 3-dehydrogenases (PcTDHs) by PCD using the TDH from Cupriavidus necator (CnTDH) as a target protein. Structural and functional analysis of PcTDHs suggested that thermostability would be independently improved when consensus mutations are introduced into the loop region of TDHs. On the other hand, enzyme kinetic parameters (kcat/Km) and average productivity would be synergistically enhanced by changing the combination of the mutations-replacement of one region of CnTDH with a consensus sequence provided only negative effects, but the negative effects were nullified when the two regions were replaced simultaneously. Taken together, we propose the hypothesis that there are protein regions that encode individual protein properties, such as thermostability and activity, and that the introduction of consensus mutations into these regions could additively or synergistically modify their functions.
Assuntos
Oxirredutases do Álcool/química , Proteínas de Bactérias/química , Cupriavidus necator/química , Oxirredutases do Álcool/genética , Proteínas de Bactérias/genética , Sequência Consenso , Cristalografia por Raios X , Cupriavidus necator/genética , Modelos Moleculares , Mutagênese , Mutação , Engenharia de Proteínas , Estabilidade Proteica , Estrutura Secundária de Proteína , TemperaturaRESUMO
Nitro groups are often associated with synthetically manufactured compounds such as medicines and explosives, and rarely with natural products. Loquat emits a nitro compound, (2-nitroethyl)benzene, as a flower scent. The nitro compound exhibits fungistatic activity and is biosynthesised from l-phenylalanine via (E/Z)-phenylacetaldoxime. Although aldoxime-producing CYP79s have been intensively studied, it is unclear what enzymes form nitro groups from aldoximes either in plants or in other organisms. Here, we report the identification of two cytochrome P450s that are likely to be involved in (2-nitroethyl)benzene biosynthesis in loquat through differential gene expression analysis using RNA-seq and functional identification using yeast and tobacco. CYP79D80 and CYP94A90 catalysed the formation of (E/Z)-phenylacetaldoxime from l-phenylalanine and (2-nitroethyl)benzene from the aldoxime, respectively. Expression profiles of CYP79D80 and CYP94A90 were correlated with the emission of (2-nitroethyl)benzene from loquat flowers. CYP94A90 also functioned as a fatty acid ω-hydroxylase as do other CYP94A fatty acid ω-hydroxylases. The CYP94As tested from other plants were all found to catalyse the formation of (2-nitroethyl)benzene from (E/Z)-phenylacetaldoxime. CYP79D80 and CYP94A90 are likely to operate in concert to biosynthesise (2-nitroethyl)benzene in loquat. CYP94A90 and other CYP94As are 'promiscuous fatty acid ω-hydroxylases', catalysing the formation of nitro groups from aldoximes, and are widely distributed in dicot plants.
Assuntos
Eriobotrya , Citocromo P-450 CYP4A , Flores , Nitrocompostos , OdorantesRESUMO
In this contribution, the unique and unprecedented stereochemical phenomenon of an aldoxime dehydratase-catalyzed enantioselective dehydration of racemic E- and Z-aldoximes with selective formation of both enantiomeric forms of a chiral nitrile is rationalized by means of molecular modelling, comprising in silico mutations and docking studies. This theoretical investigation gave detailed insight into why with the same enzyme the use of racemic E- and Z-aldoximes leads to opposite forms of the chiral nitrile. The calculated mutants with a larger or smaller cavity in the active site were then prepared and used in biotransformations, showing the theoretically predicted decrease and increase of the enantioselectivities in these nitrile syntheses. This validated model also enabled the rational design of mutants with a smaller cavity, which gave superior enantioselectivities compared to the known wild-type enzyme, with excellent E-values of up to E>200 when the mutant OxdRE-Leu145Phe was utilized.
Assuntos
Hidroliases/metabolismo , Simulação de Acoplamento Molecular , Nitrilas/metabolismo , Hidroliases/química , Estrutura Molecular , Nitrilas/química , EstereoisomerismoRESUMO
An enzyme showing l-histidine oxidase (HisO) activity by the formation of hydrogen peroxide was newly purified from Achromobacter sp. TPU 5009. This enzyme was found to be a heterodimer of two proteins (molecular mass, 53.8 and 58.3 kDa), the partial determination of which indicated they are homologs of l-histidine ammonia-lyase (AchHAL) and urocanate hydratase (AchURO). The enzyme was stable in a pH range of 5.0-11.0, with >90% of the original activity maintained below 60°C at pH 7.0. To characterize AchHAL and AchURO, each of their genes was cloned and expressed in a heterologous expression system. Heterologous AchHAL catalyzed the elimination of the α-amino group of l-histidine to urocanate and ammonia, while heterologous AchURO catalyzed the hydration of urocanate to imidazolone propionate. Since imidazolone propionate is highly unstable in the presence of oxygen at neutral pH, it was immediately decomposed and hydrogen peroxide was non-enzymatically produced. Our results indicate that this natural enzyme showing apparent HisO activity is composed of AchHAL and AchURO, which formed hydrogen peroxide after the spontaneous decomposition of imidazolone propionate.
Assuntos
Achromobacter/enzimologia , Histidina Amônia-Liase/metabolismo , Histidina/metabolismo , Biocatálise , Histidina/análise , Concentração de Íons de Hidrogênio , Imidazóis/química , Imidazóis/metabolismo , Peso MolecularRESUMO
Hydroxynitrile lyases (HNLs) catalyze the cleavage of cyanohydrin into cyanide and the corresponding aldehyde or ketone. Moreover, they catalyze the synthesis of cyanohydrin in the reverse reaction, utilized in industry for preparation of enantiomeric pure pharmaceutical ingredients and fine chemicals. We discovered a new HNL from the cyanogenic millipede, Chamberlinius hualienensis. The enzyme displays several features including a new primary structure, high stability, and the highest specific activity in (R)-mandelonitrile ((R)-MAN) synthesis (7420 U·mg-1 ) among the reported HNLs. In this study, we elucidated the crystal structure and reaction mechanism of natural ChuaHNL in ligand-free form and its complexes with acetate, cyanide ion, and inhibitors (thiocyanate or iodoacetate) at 1.6, 1.5, 2.1, 1.55, and 1.55 Å resolutions, respectively. The structure of ChuaHNL revealed that it belongs to the lipocalin superfamily, despite low amino acid sequence identity. The docking model of (R)-MAN with ChuaHNL suggested that the hydroxyl group forms hydrogen bonds with R38 and K117, and the nitrile group forms hydrogen bonds with R38 and Y103. The mutational analysis showed the importance of these residues in the enzymatic reaction. From these results, we propose that K117 acts as a base to abstract a proton from the hydroxyl group of cyanohydrins and R38 acts as an acid to donate a proton to the cyanide ion during the cleavage reaction of cyanohydrins. The reverse mechanism would occur during the cyanohydrin synthesis. (Photo: Dr. Yuko Ishida) DATABASES: Structural data are available in PDB database under the accession numbers 6JHC, 6KFA, 6KFB, 6KFC, and 6KFD.
Assuntos
Acetonitrilas/química , Aldeído Liases/química , Proteínas de Artrópodes/química , Artrópodes/química , Lipocalinas/química , Acetonitrilas/metabolismo , Aldeído Liases/genética , Aldeído Liases/metabolismo , Sequência de Aminoácidos , Animais , Proteínas de Artrópodes/genética , Proteínas de Artrópodes/metabolismo , Artrópodes/enzimologia , Sítios de Ligação , Biocatálise , Clonagem Molecular , Cristalografia por Raios X , Inibidores Enzimáticos/química , Inibidores Enzimáticos/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Expressão Gênica , Vetores Genéticos/química , Vetores Genéticos/metabolismo , Ácido Iodoacético/química , Ácido Iodoacético/metabolismo , Cinética , Lipocalinas/genética , Lipocalinas/metabolismo , Simulação de Acoplamento Molecular , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Especificidade por Substrato , Tiocianatos/química , Tiocianatos/metabolismoRESUMO
While belonging to the most fundamental functional groups, nitriles represent a class of compound that still raises challenges in terms of an efficient, cost-effective, general and, at the same time, sustainable way for their synthesis. Complementing existing chemical routes, recently a cyanide-free enzymatic process technology based on the use of an aldoxime dehydratase (Oxd) as a biocatalyst component has been developed and successfully applied for the synthesis of a range of nitrile products. In these biotransformations, the Oxd enzymes catalyze the dehydration of aldoximes as readily available substrates to the nitrile products. Herein, these developments with such enzymes are summarized, with a strong focus on synthetic applications. It is demonstrated that this biocatalytic technology has the potential to "cross the bridge" between the production of fine chemicals and pharmaceuticals, on one hand, and bulk and commodity chemicals, on the other.
Assuntos
Cianetos , Nitrilas , Desidratação , Humanos , Oximas , ÁguaRESUMO
Hydroxynitrile lyase (HNL) catalyzes the reversible synthesis and degradation of cyanohydrins, which are important synthetic intermediates for fine chemical and pharmaceutical industries. Here, we report the discovery of HNL from Parafontaria laminata (PlamHNL) millipedes, purification of the HNL to homogeneity, expression of the gene for the enzyme in heterologous expression hosts, and increase in the reaction rate and enantioselectivity in the synthesis of 2-chloromandelonitrile by protein engineering. The recombinant PlamHNL expressed in Pichia pastoris is glycosylated and has a higher thermostability and pH stability than the nonglycosylated HNL expressed in Escherichia coli. PlamHNL showed a unique wide substrate specificity among other millipede HNLs acting on various cyanohydrins, including 2-chloromandelonitrile, a key intermediate for the antithrombotic agent clopidogrel. We solved the X-ray crystal structure of the PlamHNL and found that the catalytic residues were almost identical to those of HNL from Chamberlinius hualienensis, although the forming binding cavity was different. In order to improve the catalytic activity and stereoselectivity, a computational structure-guided directed evolution approach was performed by an enzyme-substrate docking simulation at all of the residues that were exposed on the surface of the active site. The PlamHNL-N85Y mutant showed higher conversion (91% conversion with 98.2% ee of the product) than the wild type (76% conversion with 90% ee of the product) at pH 3.5 and 25 °C for 30 min of incubation. This study shows the diversity of millipede HNLs and reveals the molecular basis for improvement of the activity and stereoselectivity of the wild-type HNL to increase the reaction rate and enantioselectivity in the synthesis of 2-chloromandelonitrile.
RESUMO
An R-stereoselective amine oxidase and variants with markedly altered substrate specificity toward (R)-amines were generated from porcine d-amino acid oxidase (pkDAO), based on the X-ray crystallographic analysis of the wild-type enzyme. The new R-amine oxidase, a pkDAO variant (Y228L/R283G), acted on α-MBA and its derivatives, α-ethylbenzylamine, alkylamine, and cyclic secondary amines, totally losing the activities toward the original substrates, d-amino acids. The variant is enantiocomplementary to the flavin-type S-stereoselective amine oxidase variant from Aspergillus niger. Moreover, we solved the structure of pkDAO variants and successfully applied the obtained information to generate more variants through rational protein engineering, and used them in the synthesis of pharmaceutically attractive chiral compounds. The pkDAO variant Y228L/R283G and a variant I230A/R283G were used to synthesize (S)-amine and (R)-4-CBHA through deracemization, from racemic α-methylbenzylamine and benzhydrylamine, respectively, by selective oxidation of one of the enantiomers in the presence of a chemical reductant such as NaBH4. From a mechanistic point of view, we speculated that the imine intermediate, synthesized by oxidases or dehydrogenases, could be converted into primary α-aminonitrile by nucleophilic addition of cyanide in aqueous solutions. Nitriles and some unnatural amino acids were synthesized through a cascade reaction by oxidative cyanation reaction with the variant and a wide substrate specificity nitrilase.
Assuntos
D-Aminoácido Oxidase/química , Rim/enzimologia , Engenharia de Proteínas , Aminoácidos , Animais , Especificidade por Substrato , SuínosRESUMO
Exponentially increasing protein sequence data enables artificial enzyme design using sequence-based protein design methods, including full-consensus protein design (FCD). The success of artificial enzyme design is strongly dependent on the nature of the sequences used. Hence, sequences must be selected from databases and curated libraries prepared to enable a successful design by FCD. In this study, we proposed a selection approach regarding several key residues as sequence motifs. We used l-threonine 3-dehydrogenase (TDH) as a model to test the validity of this approach. In the classification, four residues (143, 174, 188, and 214) were used as key residues. We classified thousands of TDH homologous sequences into five groups containing hundreds of sequences. Utilizing sequences in the libraries, we designed five artificial TDHs by FCD. Among the five, we successfully expressed four in soluble form. Biochemical analysis of artificial TDHs indicated that their enzymatic properties vary; half of the maximum measured enzyme activity (t1/2) and activation energies were distributed from 53 to 65 °C and from 38 to 125 kJ/mol, respectively. The artificial TDHs had unique kinetic parameters, distinct from one another. Structural analysis indicates that consensus mutations are mainly introduced in the secondary or outer shell. The functional diversity of the artificial TDHs is due to the accumulation of mutations that affect their physicochemical properties. Taken together, our findings indicate that our proposed approach can help generate artificial enzymes with unique enzymatic properties.
Assuntos
Oxirredutases do Álcool/metabolismo , Bactérias/enzimologia , Proteínas de Bactérias/metabolismo , Engenharia de Proteínas , Oxirredutases do Álcool/química , Oxirredutases do Álcool/genética , Sequência de Aminoácidos , Bactérias/química , Bactérias/genética , Bactérias/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Estabilidade Enzimática , Cinética , Modelos Moleculares , Especificidade por Substrato , TermodinâmicaRESUMO
l-Lysine oxidase/monooxygenase (l-LOX/MOG) from Pseudomonas sp. AIU 813 catalyzes the mixed bioconversion of l-amino acids, particularly l-lysine, yielding an amide and carbon dioxide by an oxidative decarboxylation (i.e. apparent monooxygenation), as well as oxidative deamination (hydrolysis of oxidized product), resulting in α-keto acid, hydrogen peroxide (H2O2), and ammonia. Here, using high-resolution MS and monitoring transient reaction kinetics with stopped-flow spectrophotometry, we identified the products from the reactions of l-lysine and l-ornithine, indicating that besides decarboxylating imino acids (i.e. 5-aminopentanamide from l-lysine), l-LOX/MOG also decarboxylates keto acids (5-aminopentanoic acid from l-lysine and 4-aminobutanoic acid from l-ornithine). The reaction of reduced enzyme and oxygen generated an imino acid and H2O2, with no detectable C4a-hydroperoxyflavin. Single-turnover reactions in which l-LOX/MOG was first reduced by l-lysine to form imino acid before mixing with various compounds revealed that under anaerobic conditions, only hydrolysis products are present. Similar results were obtained upon H2O2 addition after enzyme denaturation. H2O2 addition to active l-LOX/MOG resulted in formation of more 5-aminopentanoic acid, but not 5-aminopentamide, suggesting that H2O2 generated from l-LOX/MOG in situ can result in decarboxylation of the imino acid, yielding an amide product, and extra H2O2 resulted in decarboxylation only of keto acids. Molecular dynamics simulations and detection of charge transfer species suggested that interactions between the substrate and its binding site on l-LOX/MOG are important for imino acid decarboxylation. Structural analysis indicated that the flavoenzyme oxidases catalyzing decarboxylation of an imino acid all share a common plug loop configuration that may facilitate this decarboxylation.
Assuntos
Aminoácido Oxirredutases/metabolismo , Oxigenases de Função Mista/metabolismo , Pseudomonas/enzimologia , Catálise , Peróxido de Hidrogênio/metabolismo , Hidrólise , Especificidade por SubstratoRESUMO
The development of enantioselective syntheses of nitriles gained increasing interest due to, e.g., an increasing demand for chiral nitriles for drug synthesis. Complementing existing routes, recently catalytic processes enabling an enantioselective formation of the chiral nitrile moiety without the need to utilize cyanide were accomplished. It is noteworthy that these processes are complementary to each other as they are based on different types of substrates, catalytic methods (utilizing chemo- and biocatalysts), and stereochemical reaction concepts (asymmetric synthesis versus resolution).