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In this study, biochar derived from Jackfruit peel (JA) via the pyrolysis at 500 °C for 2 h was used as an adsorbent to remove Methylene Blue (MB) from aqueous solution. Effects of pH, contact time, and initial MB concentration were investigated. Isotherm models, such as Langmuir, Freundlich, Sips, and Dubinin-Radushkevich, were applied to estimate the adsorption in nature. The results indicated that the Sips and Freundlich models gave the best fit with experimental datas. The maximum adsorption capacity of MB calculated from Langmuir was 39.87 mg/g at 306K, pH = 11, and time = 60 min. The E value evaluated from Dubinin-Radushkevich smaller than 8 kJ/mol indicated that the MB adsorption of JA followed a physical process.

Xylan and pectin are major structural components of plant cell walls. There are two independent catabolic pathways for xylan and pectin. UxaE bridges these two pathways by reversibly epimerizing D-fructuronate and D-tagaturonate. The crystal structure of UxaE from Cohnella laeviribosi (ClUxaE) shows a core scaffold of TIM-barrel with a position-changing divalent metal cofactor. ClUxaE has the flexible metal-coordination loop to allow the metal shift and the extra domains to bind a phosphate ion in the active site, which are important for catalysis and substrate specificity. Elucidation of the structure and mechanism of ClUxaE will assist in understanding the catalytic mechanism of UxaE family members, which are useful for processing both xylan and pectin-derived carbohydrates for practical and industrial purposes, including the transformation of agricultural wastes into numerous valuable products.

To remove Ni(II) ions from an aqueous solution, researchers used red mud modified by chitosan (RM/CS) material as a new adsorbent. According to the findings, the surface area of red mud is nearly doubled after being treated with chitosan, from 68.6 m2/g to 105.7 m2/g. The effects of pH solution, contact time, and material dosage on the Ni(II) uptake were examined. In comparison with the pseudo-first-order and pseudo-second-order models, the intra-diffusion model was the most suitable kinetic model for the Ni(II) removal. Besides, the three-parameter Sips model was used to predict the Ni(II) adsorption of RM/CS from aqueous solution. Furthermore, the Langmuir maximum Ni(II) uptake capacity of this material was 31.66 mg/g at 323K, which was higher than red mud and several other natural materials. Notably, thermodynamic investigations demonstrated that Ni(II) adsorption on RM/CS is both exothermic and physic.

Red mud modified by chitosan (RM/CS) was utilized as an adsorbent to effectively remove Pb(II) from aqueous solution. The surface area of RM/CS was found to significantly increase by more than 50% compared to that of original red mud. Different factors that affected the Pb(II) removal on this material, such as initial Pb(II) concentration, pH, and contact time, were investigated. The pseudo-first-order, pseudo-second-order, and intra-diffusion models were used to fit the experimental data to investigate the Pb(II)'s removal kinetics. The Pb(II) removal followed the intra-diffusion model. Additionally, the non-zero C value obtained from this model indicates that the removal was controlled by many different mechanisms. We also found that the interaction of Pb(II) and carbonate group on the material's surface played a primary role once the adsorption equilibrium was reached. Finally, the maximum adsorptive capacity was found to be about 209 mg/g. This obtained value is higher than those obtained for some other materials. Therefore, the present RM/CS should be a potential material for removing Pb(II) from aqueous solution.

Manganese dioxide, in particular α-MnO2, is one of the advanced inorganic nanomaterials having wide applications in many areas. Hence, understanding the crystallization pathways, morphologies, and formation mechanism of defects in its structure is of particular importance, not only for fundamental science but also for practical applications. Herein, different physically and chemically based methods, such as Neutron Diffraction (ND), XRD, SEM, TPR- H2, TGA-DSC, FT-IR, Positron Annihilation Lifetime (PAL), Doppler Broadening (DB) of positron annihilation radiation, and Electron-Momentum Distribution (EMD) measurements combined with theoretical calculations, were utilized to systematically investigate the composition, structure, and morphology of α-MnO2 nanomaterial under different annealed temperatures. The investigated material was synthesized at room temperature using a facile chemical method with potassium permanganate (KMnO4) and ethanol (C2H5OH), prior to being treated by temperatures of 100 oC – 800 oC. Results demonstrated, for the first time, that the α-MnO2 nucleation can be formed even at room temperature and gradually developed to α-MnO2 nanorods at 600 oC. This novel finding, which cannot be explored by conventional XRD, was confirmed by ND analysis. In addition, PAL analysis combined with theoretical ab initio calculations indicated the existence of H+ ions in the tunnel [1x1] of α-MnO2. At the same time, DB and EMD measurements explored the presence of Mn and O vacancies in α-MnO2 crystals at low temperatures. Finally, the present study reported a remarkable finding that organic molecules may act as reactants as well as templates, which are entirely decomposed and disappeared at highly annealed temperatures.

In this report, the adsorption of Cr(VI) onto MnO

Human cytochrome P450 2B6 is an important hepatic enzyme for the metabolism of xenobiotics and clinical drugs. Recently, more attention has been paid to P450 2B6 because of the increasing number of drugs it metabolizes. It has been known to interact with terpenes, the major constituents of the essential oils used for various medicinal purposes. In this study, the effect of monoterpenes on P450 2B6 catalytic activity was investigated. Recombinant P450 2B6 was expressed in Escherichia coli and purified using Ni-affinity chromatography. The purified P450 2B6 enzyme displayed bupropion hydroxylation activity in gas-mass spectrometry (GC-MS) analysis with a kcat of 0.5 min−1 and a Km of 47 μM. Many terpenes displayed the type I binding spectra to purified P450 2B6 enzyme and α-terpinyl acetate showed strong binding affinity with a Kd value of 5.4 μM. In GC-MS analysis, P450 2B6 converted α-terpinyl acetate to a putative oxidative product. The bupropion hydroxylation activity of P450 2B6 was inhibited by α-terpinyl acetate and its IC50 value was 10.4 μM α-Terpinyl acetate was determined to be a competitive inhibitor of P450 2B6 with a Ki value of 7.6 μM. The molecular docking model of the binding site of the P450 2B6 complex with α-terpinyl acetate was constructed. It showed the tight binding of α-terpinyl acetate in the active site of P450 2B6, which suggests that it could be a competitive substrate for P450 2B6.

Aldehyde dehydrogenases (ALDHs) are NAD(P) + -dependent oxidoreductases that catalyze the oxidation of a variety of aldehydes to their acid forms. In this study, we determined the crystal structures of ALDH from Bacillus cereus ( Bc ALDH), alone, and in complex with NAD + and NADP + . This enzyme can oxidize all- trans -retinal to all- trans -retinoic acid using either NAD + or NADP + with equal efficiency, and atypically, as a minor activity, can reduce all- trans -retinal to all- trans -retinol using NADPH. Bc ALDH accommodated the additional 2′-phosphate of NADP + by expanding the cofactor-binding pocket and upshifting the AMP moiety in NADP + . The nicotinamide moiety in NAD + and NADP + had direct interactions with the conserved catalytic residues (Cys300 and Glu266) and caused concerted conformational changes. We superimposed the structure of retinoic acid bound to human ALDH1A3 onto the Bc ALDH structure and speculated a model of the substrate all- trans -retinal bound to Bc ALDH. We also proposed a plausible mechanism for the minor reducing activity of Bc ALDH. These Bc ALDH structures will be useful in understanding cofactor specificity and the catalytic mechanism of an atypical bacterial Bc ALDH and should help the development of a new biocatalyst to produce retinoic acid and related high-end products.

In this report, the adsorption of Zn(II) ion on g- and a-MnO2 nanostructures was compared. The results showed that the maximum adsorption was obtained at pH = 4.0 for both materials and after 60 minutes for g-MnO2 and 80 minutes for a-MnO2. Adsorption isotherm models demonstrated that the Langmuir was the best model to describe the adsorption of Zinc(II) on g- and a-MnO2 because of the highest correlation coefficient (R2), the smallest root mean square error (RMSE), and the nonlinear chi-squared test (c2) values. The maximum adsorption capacity of g-MnO2 calculated from Langmuir model was 55.23 mg/g, which was roughly double a-MnO2. The lower 1/n value from Freundlich model for a-MnO2 revealed that it was not as favourable as g-MnO2. The heat of the adsorption as well as the mean free energy estimated from Temkin and Dubinin - Radushkevich models to be less than 8 kJ/mol indicated that the adsorption on both materials followed a physical process. Kinetic studies showed that pseudo-second-order model was accurate to describe both materials in three stages.

Fructose 1,6-bisphosphate aldolase (FBA) is important for both glycolysis and gluconeogenesis in life. Class II (zinc dependent) FBA is an attractive target for the development of antibiotics against protozoa, bacteria, and fungi, and is also widely used to produce various high-value stereoisomers in the chemical and pharmaceutical industry. In this study, the crystal structures of class II Escherichia coli FBA (EcFBA) were determined from four different crystals, with resolutions between 1.8 A and 2.0 A. Native EcFBA structures showed two separate sites of Zn1 (interior position) and Zn2 (active site surface position) for Zn2＋ ion. Citrate and TRIS bound EcFBA structures showed Zn2＋ position exclusively at Zn2. Crystallographic snapshots of EcFBA structures with and without ligand binding proposed the rationale of metal shift at the active site, which might be a hidden mechanism to keep the trace metal cofactor Zn2＋ within EcFBA without losing it. [BMB Reports 2016; 49(12): 681-686].

In this report, the adsorption of Cr(VI) onto MnO2/CS nanocomposite material from aqueous solution is investigated. All the factors, which affect the adsorption, such as pH, adsorption time, Cr(VI) initial concentration and adsorbent dosage, are also examined. The results obtained show that the Cr(VI) uptake is strongly affected by pH and ion strength. Analysis within the nonlinear isotherm models indicates that the Sips isotherm combining with the Langmuir and Freundlich models offer the best fit to the experimental data due to the obtained highest R2 and smallest RMSE and χ2 values. The calculated Langmuir monolayer adsorption capacity is 61.56 mg g−1 at pH of 2.0 and adsorption time of 120 min. Moreover, the mechanism studies by combining theoretical models with analytical spectroscopies reveal that the electrostatic attraction plays the important role to the uptake of Cr(VI) onto MnO2/CS nanocomposite. Therefore, the present nanocomposite material can be applied to remove total Cr from wastewater produced by the galvanized manufacturing factory with a relatively high efficiency.

Thermococcus onnurineus NA1 is an anaerobic archaeon usually found in a deep-sea hydrothermal vent area, which can use elemental sulfur (S0) as a terminal electron acceptor for energy. Sulfur, essential to many biomolecules such as sulfur-containing amino acids and cofactors including iron-sulfur cluster, is usually mobilized from cysteine by the pyridoxal 5′-phosphate- (PLP-) dependent enzyme of cysteine desulfurase (CDS). We determined the crystal structures of CDS from Thermococcus onnurineus NA1 (ToCDS), which include native internal aldimine (NAT), gem-diamine (GD) with alanine, internal aldimine structure with existing alanine (IAA), and internal aldimine with persulfide-bound Cys356 (PSF) structures. The catalytic intermediate structures showed the dihedral angle rotation of Schiff-base linkage relative to the PLP pyridine ring. The ToCDS structures were compared with bacterial CDS structures, which will help us to understand the role and catalytic mechanism of ToCDS in the archaeon Thermococcus onnurineus NA1.

β-1,3-1,4-Glucanase (BGlc8H) from Paenibacillus sp. X4 was mutated by error-prone PCR or truncated using termination primers to improve its enzyme properties. The crystal structure of BGlc8H was determined at a resolution of 1.8 A to study the possible roles of mutated residues and truncated regions of the enzyme. In mutation experiments, three clones of EP 2-6, 2-10, and 5-28 were finally selected that exhibited higher specific activities than the wild type when measured using their crude extracts. Enzyme variants of BG2-6, BG2-10, and BG5-28 were mutated at two, two, and six amino acid residues, respectively. These enzymes were purified homogeneously by Hi-Trap Q and CHT-II chromatography. Specific activity of BG5-28 was 2.11-fold higher than that of wild-type BGwt, whereas those of BG2-6 and BG2-10 were 0.93- and 1.19-fold that of the wild type, respectively. The optimum pH values and temperatures of the variants were nearly the same as those of BGwt (pH 5.0 and 40 °C, respectively). However, the half-life of the enzyme activity and catalytic efficiency (k cat/K m) of BG5-28 were 1.92- and 2.12-fold greater than those of BGwt at 40 °C, respectively. The catalytic efficiency of BG5-28 increased to 3.09-fold that of BGwt at 60 °C. These increases in the thermostability and catalytic efficiency of BG5-28 might be useful for the hydrolysis of β-glucans to produce fermentable sugars. Of the six mutated residues of BG5-28, five residues were present in mature BGlc8H protein, and two of them were located in the core scaffold of BGlc8H and the remaining three residues were in the substrate-binding pocket forming loop regions. In truncation experiments, three forms of C-terminal truncated BGlc8H were made, which comprised 360, 286, and 215 amino acid residues instead of the 409 residues of the wild type. No enzyme activity was observed for these truncated enzymes, suggesting the complete scaffold of the α6/α6-double-barrel structure is essential for enzyme activity.

Thermococcus onnurineus NA1 is an anaerobic archaeon usually found in a deep-sea hydrothermal vent area, which can use elemental sulfur (S0) as a terminal electron acceptor for energy. Sulfur, essential to many biomolecules such as sulfur-containing amino acids and cofactors including iron-sulfur cluster, is usually mobilized from cysteine by the pyridoxal 5′-phosphate- (PLP-) dependent enzyme of cysteine desulfurase (CDS). We determined the crystal structures of CDS from Thermococcus onnurineus NA1 (ToCDS), which include native internal aldimine (NAT), gem-diamine (GD) with alanine, internal aldimine structure with existing alanine (IAA), and internal aldimine with persulfide-bound Cys356 (PSF) structures. The catalytic intermediate structures showed the dihedral angle rotation of Schiff-base linkage relative to the PLP pyridine ring. The ToCDS structures were compared with bacterial CDS structures, which will help us to understand the role and catalytic mechanism of ToCDS in the archaeon Thermococcus onnurineus NA1.

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight on rice; this species is one of the most destructive pathogenic bacteria in rice cultivation worldwide. Peptide deformylase (PDF) catalyzes the removal of the N-formyl group from the N-terminus of newly synthesized polypeptides in bacterial cells and is an important target to develop antibacterial agents. We determined crystal structures of Xoo PDF (XoPDF) at up to 1.9 A resolution, which include apo, two substrate-bound (methionine-alanine or methionine-alanine-serine), an inhibitor-bound (actinonin), and six fragment chemical-bound structures. Six fragment chemical compounds were bound in the substrate-binding pocket. The fragment chemical-bound structures were compared to the natural PDF inhibitor actinonin-bound structure. The fragment chemical molecules will be useful to design an inhibitor specific to XoPDF and a potential pesticide against Xoo.

Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of bacterial blight of rice, one of the most devastating rice diseases. We analysed the time-resolved transcriptional expression of aminoacyl-tRNA synthetase (aaRS) genes in Xoo cells treated with rice-leaf extract. Most aaRS genes showed decreased expression in the initial 30 min and recovered or increased expression in the later 30 min. The protein-synthetic machinery of bacterial cells is an important target for developing antibiotic agents; aaRSs play an essential role in peptide synthesis by attaching amino acids onto the corresponding tRNA. In bacteria, glutaminyl-tRNA (Gln-tRNAGln) is synthesised in two steps by glutamyl-tRNA synthetase (GluRS) and tRNA-dependent aminotransferase, the indirect biosynthetic mechanism of which is not present in eukaryotes. We determined the crystal structure of GluRS from Xoo (XoGluRS) at resolution of 3.0 Å, this being the first GluRS structure from a plant pathogen such as Xoo. The XoGluRS structure consists of five domains, which are conserved in other bacterial GluRS structures. In the bacterial GluRS structures, the Rossmann-fold catalytic domain and the stem-contact domain are most conserved in both sequence and structure. The anticodon-binding domain 1 is less conserved in sequence but overall structure is conserved. The connective-polypeptide domain and the anticodon-binding domain 2 show various conformations in structure. The XoGluRS structure could provide useful information to develop a new pesticide against Xoo and bacterial blight.

RNA polymerase (RNAP) plays a crucial role in gene expression in all organisms. It is a multiprotein complex that produces primary transcript RNA. Generally, the basal transcription apparatus in archaea is simpler than the eukaryotic RNA polymerase II counterpart. To understand the structure and function of archaeal RNAP, theTON-0309gene encoding DNA-directed RNA polymerase subunit L (ToRNAP_L) fromThermococcus onnurineusNA1 was cloned and the protein was overexpressed inEscherichia coli, purified and crystallized. The purified protein was crystallized using the hanging-drop vapour-diffusion method and the crystal diffracted to 2.10 Å resolution. The crystal belonged to the hexagonal space groupP6122, with unit-cell parametersa=b= 42.3,c= 211.2 Å. One molecule was present in the asymmetric unit, with a correspondingVMof 2.5 Å3 Da−1and a solvent content of 50.0%.