scholarly journals Enhancing the Promiscuous Phosphotriesterase Activity of a Thermostable Lactonase (GkaP) for the Efficient Degradation of Organophosphate Pesticides

2012 ◽  
Vol 78 (18) ◽  
pp. 6647-6655 ◽  
Author(s):  
Yu Zhang ◽  
Jiao An ◽  
Wei Ye ◽  
Guangyu Yang ◽  
Zhi-Gang Qian ◽  
...  
Keyword(s):  
Catalytic Efficiency ◽  
Dynamics Simulation ◽  
Saturation Mutagenesis ◽  
Divergent Evolution ◽  
Laboratory Evolution ◽  
Content Type ◽  
Hydrolytic Activities ◽  
Geobacillus Kaustophilus ◽  
Amidohydrolase Superfamily

ABSTRACTThe phosphotriesterase-like lactonase (PLL) enzymes in the amidohydrolase superfamily hydrolyze various lactones and exhibit latent phosphotriesterase activities. These enzymes serve as attractive templates forin vitroevolution of neurotoxic organophosphates (OPs) with hydrolytic capabilities that can be used as bioremediation tools. Here, a thermostable PLL fromGeobacillus kaustophilusHTA426 (GkaP) was targeted for joint laboratory evolution with the aim of enhancing its catalytic efficiency against OP pesticides. By a combination of site saturation mutagenesis and whole-gene error-prone PCR approaches, several improved variants were isolated. The most active variant, 26A8C, accumulated eight amino acid substitutions and demonstrated a 232-fold improvement over the wild-type enzyme in reactivity (kcat/Km) for the OP pesticideethyl-paraoxon. Concomitantly, this variant showed a 767-fold decrease in lactonase activity with δ-decanolactone, imparting a specificity switch of 1.8 × 105-fold. 26A8C also exhibited high hydrolytic activities (19- to 497-fold) for several OP pesticides, including parathion, diazinon, and chlorpyrifos. Analysis of the mutagenesis sites on the GkaP structure revealed that most mutations are located in loop 8, which determines substrate specificity in the amidohydrolase superfamily. Molecular dynamics simulation shed light on why 26A8C lost its native lactonase activity and improved the promiscuous phosphotriesterase activity. These results permit us to obtain further insights into the divergent evolution of promiscuous enzymes and suggest that laboratory evolution of GkaP may lead to potential biological solutions for the efficient decontamination of neurotoxic OP compounds.

scholarly journals Characterization of the Inhibitor-Resistant SHV β-Lactamase SHV-107 in a Clinical Klebsiella pneumoniae Strain Coproducing GES-7 Enzyme

2011 ◽  
Vol 56 (2) ◽  
pp. 1042-1046 ◽  
Author(s):  
Vera Manageiro ◽  
Eugénia Ferreira ◽  
Antony Cougnoux ◽  
Luís Albuquerque ◽  
Manuela Caniça ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Inhibitory Concentration ◽  
Catalytic Efficiency ◽  
Dynamics Simulation ◽  
Inhibitory Effects ◽  
Content Type ◽  
High Affinity ◽  
Amoxicillin Clavulanate ◽  
Lactamase Gene

ABSTRACTThe clinicalKlebsiella pneumoniaeINSRA6884 strain exhibited nonsusceptibility to all penicillins tested (MICs of 64 to >2,048 μg/ml). The MICs of penicillins were weakly reduced by clavulanate (from 2,048 to 512 μg/ml), and tazobactam restored piperacillin susceptibility. Molecular characterization identified the genesblaGES-7and a new β-lactamase gene,blaSHV-107, which encoded an enzyme that differed from SHV-1 by the amino acid substitutions Leu35Gln and Thr235Ala. The SHV-107-producingEscherichia colistrain exhibited only a β-lactam resistance phenotype with respect to amoxicillin, ticarcillin, and amoxicillin-clavulanate combination. The kinetic parameters of the purified SHV-107 enzyme revealed a high affinity for penicillins. However, catalytic efficiency for these antibiotics was lower for SHV-107 than for SHV-1. No hydrolysis was detected against oxyimino-β-lactams. The 50% inhibitory concentration (IC50) for clavulanic acid was 9-fold higher for SHV-107 than for SHV-1, but the inhibitory effects of tazobactam were unchanged. Molecular dynamics simulation suggested that the Thr235Ala substitution affects the accommodation of clavulanate in the binding site and therefore its inhibitory activity.

scholarly journals Exploring the Enantioselective Mechanism of Halohydrin Dehalogenase from Agrobacterium radiobacter AD1 by Iterative Saturation Mutagenesis

2015 ◽  
Vol 81 (8) ◽  
pp. 2919-2926 ◽  
Author(s):  
Chao Guo ◽  
Yanpu Chen ◽  
Yu Zheng ◽  
Wei Zhang ◽  
Yunwen Tao ◽  
...  
Keyword(s):  
Catalytic Efficiency ◽  
Significant Loss ◽  
Saturation Mutagenesis ◽  
Active Site Residues ◽  
Agrobacterium Radiobacter ◽  
Content Type ◽  
Halohydrin Dehalogenase ◽  
Aromatic Substrates ◽  
Chiral Epoxides ◽  
Iterative Saturation Mutagenesis

ABSTRACTHalohydrin dehalogenase fromAgrobacterium radiobacterAD1 (HheC) shows great potential in producing valuable chiral epoxides and β-substituted alcohols. The wild-type (WT) enzyme displays a highR-enantiopreference toward most aromatic substrates, whereas noS-selective HheC has been reported to date. To obtain more enantioselective enzymes, seven noncatalytic active-site residues were subjected to iterative saturation mutagenesis (ISM). After two rounds of screening aspects of both activity and enantioselectivity (E), three outstanding mutants (Thr134Val/Leu142Met, Leu142Phe/Asn176His, and Pro84Val/Phe86Pro/Thr134Ala/Asn176Ala mutants) with divergent enantioselectivity were obtained. The two double mutants displayed approximately 2-fold improvement inR-enantioselectivity toward 2-chloro-1-phenylethanol (2-CPE) without a significant loss of enzyme activity compared with the WT enzyme. Strikingly, the Pro84Val/Phe86Pro/Thr134Ala/Asn176Ala mutant showed an inverted enantioselectivity (from anERof 65 [WT] to anESof 101) and approximately 100-fold-enhanced catalytic efficiency toward (S)-2-CPE. Molecular dynamic simulation and docking analysis revealed that the phenyl side chain of (S)-2-CPE bound at a different location than that of itsR-counterpart; those mutations generated extra connections for the binding of the favored enantiomer, while the eliminated connections reduced binding of the nonfavored enantiomer, all of which could contribute to the observed inverted enantiopreference.

scholarly journals Development of a Single-Gene, Signature-Tag-Based Approach in Combination with Alanine Mutagenesis To Identify Listeriolysin O Residues Critical for theIn VivoSurvival of Listeria monocytogenes

2012 ◽  
Vol 80 (6) ◽  
pp. 2221-2230 ◽  
Author(s):  
Jody A. Melton-Witt ◽  
Susannah L. McKay ◽  
Daniel A. Portnoy
Keyword(s):  
Listeria Monocytogenes ◽  
Single Gene ◽  
Saturation Mutagenesis ◽  
Single Amino Acid ◽  
Screening Methods ◽  
Listeriolysin O ◽  
Phenotypic Analysis ◽  
Content Type

ABSTRACTListeriolysin O (LLO) is a pore-forming toxin of the cholesterol-dependent cytolysin (CDC) family and a primary virulence factor of the intracellular pathogenListeria monocytogenes. LLO mediates rupture of phagosomal membranes, thereby releasing bacteria into the growth-permissive host cell cytosol. Several unique features of LLO allow its activity to be precisely regulated in order to facilitate phagosomal escape, intracellular growth, and cell-to-cell spread. To improve our understanding of the multifaceted contribution of LLO to the pathogenesis ofL. monocytogenes, we developed a screen that combined saturation mutagenesis and signature tags, termedinvivoanalysis bysaturation mutagenesis andsignature tags (IVASS). We generated a library of LLO mutant strains, each harboring a single amino acid substitution and a signature tag, by using the previously described pPL2 integration vector. The signature tags acted as molecular barcodes, enabling high-throughput, parallel analysis of 40 mutants in a single animal and identification of attenuated mutants by negative selection. Using the IVASS technique we were able to screen over 90% of the 505 amino acids present in LLO and identified 60 attenuated mutants. Of these, 39 LLO residues were previously uncharacterized and potentially revealed novel functions of the toxin during infection. The mutants that were subsequently analyzedin vivoeach conferred a 2- to 4-orders of magnitude loss in virulence compared to wild type, thereby validating the screening methods. Phenotypic analysis of the LLO mutant library using commonin vitrotechniques suggested that the functional contributions of some residues could only have been revealed throughin vivoanalysis.

scholarly journals Substrate Specificity of the Bacillus licheniformis Lyxose Isomerase YdaE and Its Application inIn VitroCatalysis for Bioproduction of Lyxose and Glucose by Two-Step Isomerization

2011 ◽  
Vol 77 (10) ◽  
pp. 3343-3350 ◽  
Author(s):  
Darshan H. Patel ◽  
Seung Gon Wi ◽  
Seong-Gene Lee ◽  
Dae-Seok Lee ◽  
Youn-ho Song ◽  
...  
Keyword(s):  
Bacillus Licheniformis ◽  
Thermus Thermophilus ◽  
Xylose Isomerase ◽  
Catalytic Efficiency ◽  
Sugar Production ◽  
Uncharacterized Protein ◽  
Easy Method ◽  
Content Type ◽  
Substrate Specificities

ABSTRACTEnzymatic processes are useful for industrially important sugar production, andin vitrotwo-step isomerization has proven to be an efficient process in utilizing readily available sugar sources. A hypothetical uncharacterized protein encoded byydaEofBacillus licheniformiswas found to have broad substrate specificities and has shown high catalytic efficiency ond-lyxose, suggesting that the enzyme isd-lyxose isomerase.Escherichia coliBL21 expressing the recombinant protein, of 19.5 kDa, showed higher activity at 40 to 45°C and pH 7.5 to 8.0 in the presence of 1.0 mM Mn2+. The apparentKmvalues ford-lyxose andd-mannose were 30.4 ± 0.7 mM and 26 ± 0.8 mM, respectively. The catalytic efficiency (kcat/Km) for lyxose (3.2 ± 0.1 mM−1s−1) was higher than that ford-mannose (1.6 mM−1s−1). The purified protein was applied to the bioproduction ofd-lyxose andd-glucose fromd-xylose andd-mannose, respectively, along with the thermostable xylose isomerase ofThermus thermophilusHB08. From an initial concentration of 10 mMd-lyxose andd-mannose, 3.7 mM and 3.8 mMd-lyxose andd-glucose, respectively, were produced by two-step isomerization. This two-step isomerization is an easy method forin vitrocatalysis and can be applied to industrial production.

scholarly journals Improving the Stability and Activity of Arginine Decarboxylase at Alkaline pH for the Production of Agmatine

2021 ◽  
Vol 1 ◽  
Author(s):  
Eun Young Hong ◽  
Sun-Gu Lee ◽  
Hyungdon Yun ◽  
Byung-Gee Kim
Keyword(s):  
Disulfide Bond ◽  
Specific Activity ◽  
Catalytic Efficiency ◽  
Arginine Decarboxylase ◽  
Saturation Mutagenesis ◽  
Alkaline Ph ◽  
Wild Type ◽  
Active Site Residues ◽  
Cellular Mechanisms

Agmatine, involved in various modulatory actions in cellular mechanisms, is produced from arginine (Arg) by decarboxylation reaction using arginine decarboxylase (ADC, EC 4.1.1.19). The major obstacle of using wild-type Escherichia coli ADC (ADCes) in agmatine production is its sharp activity loss and instability at alkaline pH. Here, to overcome this problem, a new disulfide bond was rationally introduced in the decameric interface region of the enzyme. Among the mutants generated, W16C/D43C increased both thermostability and activity. The half-life (T1/2) of W16C/D43C at pH 8.0 and 60°C was 560 min, which was 280-fold longer than that of the wild-type, and the specific activity at pH 8.0 also increased 2.1-fold. Site-saturation mutagenesis was subsequently performed at the active site residues of ADCes using the disulfide-bond mutant (W16C/D43C) as a template. The best variant W16C/D43C/I258A displayed a 4.4-fold increase in the catalytic efficiency when compared with the wild-type. The final mutant (W16C/D43C/I258A) was successfully applied to in vitro synthesis of agmatine with an improved yield and productivity (>89.0% yield based on 100 mM of Arg within 5  h).

scholarly journals Engineering Pseudochelin Production inMyxococcus xanthus

2018 ◽  
Vol 84 (22) ◽  
Author(s):  
Juliane Korp ◽  
Lea Winand ◽  
Angela Sester ◽  
Markus Nett
Keyword(s):  
Iron Homeostasis ◽  
Condensation Reaction ◽  
Myxococcus Xanthus ◽  
Inducible Promoter ◽  
Content Type ◽  
Intramolecular Condensation ◽  
Amidohydrolase Superfamily ◽  
Interesting Alternative

ABSTRACTMyxobacteria utilize the catechol natural products myxochelin A and B in order to maintain their iron homeostasis. Recently, the production of these siderophores, along with a new myxochelin derivative named pseudochelin A, was reported for the marine bacteriumPseudoalteromonas piscicidaS2040. The latter derivative features a characteristic imidazoline moiety, which was proposed to originate from an intramolecular condensation reaction of the β-aminoethyl amide group in myxochelin B. To identify the enzyme catalyzing this conversion, we compared the myxochelin regulons of two myxobacterial strains that produce solely myxochelin A and B with those ofP. piscicidaS2040. This approach revealed a gene exclusive to the myxochelin regulon inP. piscicidaS2040, coding for an enzyme of the amidohydrolase superfamily. To prove that this enzyme is indeed responsible for the postulated conversion, the reaction was reconstitutedin vitrousing a hexahistidine-tagged recombinant protein made inEscherichia coli, with myxochelin B as the substrate. To test the production of pseudochelin A underin vivoconditions, the amidohydrolase gene was cloned into the myxobacterial plasmid pZJY156 and placed under the control of a copper-inducible promoter. The resulting vector was introduced into the myxobacteriumMyxococcus xanthusDSM 16526, a native producer of myxochelin A and B. Following induction with copper, the myxobacterial expression strain was found to synthesize small quantities of pseudochelin A. Replacement of the copper-inducible promoter with the constitutivepilApromoter led to increased production levels inM. xanthus, which facilitated the isolation and subsequent structural verification of the heterologously produced compound.IMPORTANCEIn this study, an enzyme for imidazoline formation in pseudochelin biosynthesis was identified. Evidence for the involvement of this enzyme in the postulated reaction was obtained afterin vitroreconstitution. Furthermore, the function of this enzyme was demonstratedin vivoby transferring the corresponding gene into the bacteriumMyxococcus xanthus, which thereby became a producer of pseudochelin A. In addition to clarifying the molecular basis of imidazoline formation in siderophore biosynthesis, we describe the heterologous expression of a gene in a myxobacterium without chromosomal integration. Due to its metabolic proficiency,M. xanthusrepresents an interesting alternative to established host systems for the reconstitution and manipulation of biosynthetic pathways. Since the plasmid used in this study is easily adaptable for the expression of other enzymes as well, we expand the conventional expression strategy for myxobacteria, which is based on the integration of biosynthetic genes into the host genome.

scholarly journals The Tape Measure Protein of the Staphylococcus aureus Bacteriophage vB_SauS-phiIPLA35 Has an Active Muramidase Domain

2012 ◽  
Vol 78 (17) ◽  
pp. 6369-6371 ◽  
Author(s):  
Lorena Rodríguez-Rubio ◽  
Dolores Gutiérrez ◽  
Beatriz Martínez ◽  
Ana Rodríguez ◽  
Friedrich Götz ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Lytic Activity ◽  
Structural Proteins ◽  
Tape Measure Protein ◽  
Content Type ◽  
Double Stranded Dna ◽  
Tape Measure ◽  
Hydrolytic Activities ◽  
Muramidase Activity

ABSTRACTTailed double-stranded DNA (dsDNA) bacteriophages frequently harbor structural proteins displaying peptidoglycan hydrolytic activities. The tape measure protein fromStaphylococcus aureusbacteriophage vB_SauS-phiIPLA35 has a lysozyme-like and a peptidase_M23 domain. This report shows that the lysozyme-like domain (TG1) has muramidase activity and exhibitsin vitrolytic activity against liveS. aureuscells, an activity that could eventually find use in the treatment of infections.

scholarly journals N152G, -S, and -T Substitutions in CMY-2 β-Lactamase Increase Catalytic Efficiency for Cefoxitin and Inactivation Rates for Tazobactam

2013 ◽  
Vol 57 (4) ◽  
pp. 1596-1602 ◽  
Author(s):  
Marion J. Skalweit ◽  
Mei Li ◽  
Benjamin C. Conklin ◽  
Magdalena A. Taracila ◽  
Rebecca A. Hutton
Keyword(s):  
Catalytic Efficiency ◽  
Enzyme Inactivation ◽  
Inactivation Kinetics ◽  
Content Type ◽  
New Class ◽  
Fold Reduction ◽  
Class C ◽  
Functional Mutants

ABSTRACTClass C cephalosporinases are a growing threat, and clinical inhibitors of these enzymes are currently unavailable. Previous studies have explored the role of Asn152 in theEscherichia coliAmpC and P99 enzymes and have suggested that interactions between C-6′ or C-7′ substituents on penicillins or cephalosporins and Asn152 are important in determining substrate specificity and enzymatic stability. We sought to characterize the role of Asn152 in the clinically important CMY-2 cephalosporinase with substrates and inhibitors. Mutagenesis of CMY-2 at position 152 yields functional mutants (N152G, -S, and -T) that exhibit improved penicillinase activity and retain cephamycinase activity. We also tested whether the position 152 substitutions would affect the inactivation kinetics of tazobactam, a class A β-lactamase inhibitor within vitroactivity against CMY-2. Using standard assays, we showed that the N152G, -S, and -T variants possessed increased catalytic activity against cefoxitin compared to the wild type. The 50% inhibitory concentration (IC50) for tazobactam improved dramatically, with an 18-fold reduction for the N152S mutant due to higher rates of enzyme inactivation. Modeling studies have shown active-site expansion due to interactions between Y150 and S152 in the apoenzyme and the Michaelis-Menten complex with tazobactam. Substitutions at N152 might become clinically important as new class C β-lactamase inhibitors are developed.

scholarly journals Roles of Two Glutathione-Dependent 3,6-Dichlorogentisate Dehalogenases inRhizorhabdus dicambivoransNdbn-20 in the Catabolism of the Herbicide Dicamba

2018 ◽  
Vol 84 (17) ◽  
Author(s):  
Na Li ◽  
Ren-Lei Tong ◽  
Li Yao ◽  
Qing Chen ◽  
Xin Yan ◽  
...  
Keyword(s):  
Large Scale ◽  
Catalytic Efficiency ◽  
Catabolic Pathway ◽  
High Identity ◽  
Content Type ◽  
Phylogenetic Status ◽  
Sphingobium Chlorophenolicum ◽  
Sequence Identities

ABSTRACTThe herbicide dicamba is initially demethylated to 3,6-dichlorosalicylate (3,6-DCSA) inRhizorhabdus dicambivoransNdbn-20 and is subsequently 5-hydroxylated to 3,6-dichlorogentisate (3,6-DCGA). In the present study, two glutathione-dependent 3,6-DCGA dehalogenases, DsmH1 and DsmH2, were identified in strain Ndbn-20. DsmH2 shared a low identity (only 31%) with the tetrachlorohydroquinone (TCHQ) dehalogenase PcpC fromSphingobium chlorophenolicumATCC 39723, while DsmH1 shared a high identity (79%) with PcpC. In the phylogenetic tree of related glutathioneS-transferases (GSTs), DsmH1 and DsmH2, together with PcpC and the 2,5-dichlorohydroquinone dehalogenase LinD, formed a separate clade. DsmH1 and DsmH2 were synthesized inEscherichia coliBL21 and purified as His-tagged enzymes. Both enzymes required glutathione (GSH) as a cofactor and could 6-dechlorinate 3,6-DCGA to 3-chlorogentisatein vitro. DsmH2 had a significantly higher catalytic efficiency toward 3,6-DCGA than DsmH1. Transcription and disruption analysis revealed that DsmH2 but not DsmH1 was responsible for the 6-dechlorination of 3,6-DCGA in strain Ndbn-20in vivo. Furthermore, we propose a novel eta class of GSTs to accommodate the four bacterial dehalogenases PcpC, LinD, DsmH1, and DsmH2.IMPORTANCEDicamba is an important herbicide, and its use and leakage into the environment have dramatically increased since the large-scale planting of genetically modified (GM) dicamba-resistant crops in 2015. However, the complete catabolic pathway of dicamba has remained unknown, which limits ecotoxicological studies of this herbicide. Our previous study revealed that 3,6-DCGA was an intermediate of dicamba degradation in strain Ndbn-20. In this study, we identified two glutathione-dependent 3,6-DCGA dehalogenases, DsmH1 and DsmH2, and demonstrated that DsmH2 is physiologically responsible for the 6-dechlorination of 3,6-DCGA in strain Ndbn-20. GSTs play an important role in the detoxification and degradation of a variety of endogenous and exogenous toxic compounds. On the basis of their sequence identities, phylogenetic status, and functions, the four bacterial GSH-dependent dehalogenases (PcpC, LinD, DsmH1, and DsmH2) were reclassified as a new eta class of GSTs. This study helps us to elucidate the microbial catabolism of dicamba and enhances our understanding of the diversity and functions of GSTs.

scholarly journals Targeting the Homoserine Dehydrogenase of Paracoccidioides Species for Treatment of Systemic Fungal Infections

2017 ◽  
Vol 61 (9) ◽  
Author(s):  
Mariane C. Bagatin ◽  
Arethusa L. Pimentel ◽  
Débora C. Biavatti ◽  
Ernani A. Basso ◽  
Erika S. Kioshima ◽  
...  
Keyword(s):  
Tertiary Structure ◽  
Fungal Infections ◽  
Paracoccidioides Brasiliensis ◽  
Pathogenic Fungi ◽  
Dynamics Simulation ◽  
Homoserine Dehydrogenase ◽  
Content Type ◽  
Zinc Database ◽  
Etiological Agents

ABSTRACT This work evaluated new potential inhibitors of the enzyme homoserine dehydrogenase (HSD) of Paracoccidioides brasiliensis, one of the etiological agents of paracoccidioidomycosis. The tertiary structure of the protein bonded to the analogue NAD, and l-homoserine was modeled by homology. The model with the best output was subjected to gradient minimization, redocking, and molecular dynamics simulation. Virtual screening simulations with 187,841 molecules purchasable from the Zinc database were performed. After the screenings, 14 molecules were selected and analyzed by the use of absorption, distribution, metabolism, excretion, and toxicity criteria, resulting in four compounds for in vitro assays. The molecules HS1 and HS2 were promising, exhibiting MICs of 64 and 32 μg · ml−1, respectively, for the Pb18 isolate of P. brasilensis, 64 μg · ml−1 for two isolates of P. lutzii, and also synergy with itraconazole. The application of these molecules to human-pathogenic fungi confirmed that the HSD enzyme may be used as a target for the development of drugs with specific action against paracoccidioidomycosis; moreover, these compounds may serve as leads in the design of new antifungals.

Sign in / Sign up

Export Citation Format

Share Document