Purification and partial characterization of the extradiol dioxygenase, 2′-carboxy-2,3-dihydroxybiphenyl 1,2-dioxygenase,in the fluorene degradation pathway from Rhodococcus sp. strain DFA3

Type II extradiol dioxygenase, 2′-carboxy-2,3-dihydroxybiphenyl 1,2-dioxygenase (FlnD1D2) involved in the fluorene degradation pathway of Rhodococcus sp. DFA3 was purified to homogeneity from a heterologously expressing Escherichia coli. Gel filtration chromatography and SDS-PAGE suggested that FlnD1D2 is an α₄β₄ heterooctamer and that the molecular masses of these subunits are 30 and 9.9 kDa, respectively. The optimum pH and temperature for enzyme activity were 8.0 and 30 °C, respectively. Assessment of metal ion effects suggested that exogenously supplied Fe²⁺ increases enzyme activity 3.2-fold. FlnD1D2 catalyzed meta-cleavage of 2′-carboxy-2,3-dihydroxybiphenyl homologous compounds, but not single-ring catecholic compounds. The K_m and k_cat/K_m values of FlnD1D2 for 2,3-dihidroxybiphenyl were 97.2 μM and 1.5 × 10^?2 μM^?1sec^?1, and for 2,2′,3-trihydroxybiphenyl, they were 168.0 μM and 0.5 × 10^?2 μM^?1sec^?1, respectively. A phylogenetic tree of the large and small subunits of type II extradiol dioxygenases suggested that FlnD1D2 constitutes a novel subgroup among heterooligomeric type II extradiol dioxygenases.     

Degradation of 4′-dimethylaminoazobenzene-2-carboxylic acid by Pseudomonas stutzeri

4-Dimethylaminoazobenzene-2-carboxylic acid (DMBC) was utilized as a necessary carbon and nitrogen source by Pseudomonas stutzeri IAM 12097. o-Aminobenzoic acid (o-ABA), N,N-dimethyl-p-phenylenediamine (DMPA) and cathecol were identified as intermediates of DMBC degradation. DMBC was degraded at a concentration below 70 mol dm^–3. The ability to utilize DMBC in P. stutzeri was lost spontaneously to some extent. When P. stutzeri was cured of plasmid DNA (approximately 8 MDal) by treatment with mitomycin C, acridine orange, and chloramphenicol, DMBC was not utilized by the resultant strain. These facts suggest that the degradative ability on DMBC in P. stutzeri is controlled by plasmid DNA. Correspondence to: C. Yatome     

M?ssbauer and EPR spectroscopy of protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa.

Protocatechuate 3,4-dioxygenase (EC 1.13.11.3) from Pseudomonas aeruginosa has been investigated by EPR and M?ssbauer spectroscopy. Low temperature M?ssbauer data on the native enzyme (Fe3+, S = 5/2) yields a hyperfine field Hsat=-525 kG at the nucleus. This observation is inconsistent with earlier suggestions, based on EPR data of a rubredoxin-like ligand environment around the iron, i.e. a tetrahedral sulfur coordination. Likewise, the dithionite-reduced enzyme has M?ssbauer parameters unlike those of reduced rubredoxin. We conclude that the iron atoms are in a previously unrecognized environment. The ternary complex of the enzyme with 3,4-dihydroxyphenylpropionate and O2 yields EPR signals at g = 6.7 and g = 5.3; these signals result from an excited state Kramers doublet. The kinetics of the disappearance of these signals parallels product formation and the decay of the ternary complex as observed in the optical spectrum. The M?ssbauer and EPR data on the ternary complex establish the iron atoms to be a high-spin ferric state characterized by a large and negative zero-field splitting, D = approximately -2 cm-1.     

Purification and biochemical characterization of a detergent stable α-amylase from Pseudomonas stutzeri AS22

This study reports the purification and biochemical characterization of a novel maltotetraose-forming-α-amylase from Pseudomonas stutzeri AS22, designated PSA. The P. stutzeri α-amylase (PSA) was purified from the culture supernatant to homogeneity by Sepharose mono Q anion exchange chromatography, ultrafiltration and Sephadex G-100 gel filtration, with a 37.32-fold increase in specific activity, and 31% recovery. PSA showed a molecular weight of approximately 57 kDa by SDS-PAGE. The N-terminal amino acid sequence of the first 7 amino acids was DQAGKSP. This enzyme exhibited maximum activity at pH 8.0 and 55°C, performed stably over a broad range of pH 5.0 ≈ 12.0, but rapidly lost activity above 50°C. Both potato starch and Ca²⁺ ions have a protective effect on the thermal stability of PSA. The enzyme activity was inhibited by Hg²⁺, Mn²⁺, Cd²⁺, Cu²⁺, and Co²⁺, and enhanced by Ba²⁺. PSA belonged to the EDTA-sensitive α-amylase. The purified enzyme showed high stability towards surfactants (Tween 20, Tween 80 and Triton X-100), and oxidizing agents, such as sodium per borate and H₂O₂. In addition, PSA showed excellent compatibility with a wide range of commercial solid and liquid detergents at 30°C, suggesting potential application in the detergent industry. Maltotetraose was the specific end product obtained after hydrolysis of starch by the enzyme for an extended period of time, and was not further degraded.     

Synthesis of purine and pyrimidine 2′-deoxynucleosides from a 1,2-dithio sugar precursor

9-(2-S-Ethyl-2-thio- and α-D-mannofuranosyl)adenine (8α and 8β) were synthesized from ethyl 3,5,6-tri-O-acetyl-2-S-ethyl-1,2-dithio-α-D-mannofuranoside (1) by bromination followed by coupling of the resultant bromide (2) with 6-benzamido-(chloromercuri)purine. The 2-chloro analogues (10α and 10β) of 8α and 8β were obtained by way of a fusion reaction between 1,3,5,6-tetra-O-acetyl-2-S- ethyl-2-thio-α-D-mannofuranose (5) and 2,6-dichloropurine. Fusion of the bromide 2 with 2,4-bis(trimethylsilyloxy)pyrimidine and its 5-methyl derivative led to 1-(2-S- ethyl-2-thio-β-D-mannofuranosyl)uracil (16) and its thymine analogue (15). The action of Raney nickel led to rapid dechlorination of 10α and 10β, and all of the 2′-thio-nucleosides underwent desulfurization to give the corresponding 2′-deoxynucleosides. Sequential periodate oxidation-borohydride reduction converted the hexofuranosyl nucleosides into their pentofuranosyl analogues. Thus prepared were 9-(2-deoxy-α-and β-D-arabino-hexofuranosyl)adenine (11α and 11β) and their 2-deoxy-D-threo-pentofuranosyl counterparts (6α and 2′-deoxy-3′-epiadenosine, 6β), and 1-(2-deoxy- β-D-arabino-hexofuranosyl)-thymine (17) and -uracil (18) and their 2-deoxy-D-threo-pentofuranosyl counterparts (3′-epithymidine, 21, and 2′-deoxy-3′-epiuridine, 20). Detailed n.m.r.-spectral correlations are described for the series, and various derivatives of the nucleosides are reported.     

Lipid A with 2,3-diamino-2,3-dideoxy-glucose in lipopolysaccharides from slow-growing members of Rhizobiaceae and from “Pseudomonas carboxydovorans”

Lipid A's from two Bradyrhizobium species and from the phylogenetically closely related species Pseudomonas carboxydovorans were found to contain 2,3-diamino-2,3-dideoxy-glucose as lipid A backbone sugar. In contrast, three representatives of the genus Rhizobium, as well as the phylogenetically related species Agrobacterium tumefaciens, contain solely glucosamine as lipid A backbone sugar. These findings suppor independent studies on the phylogenetical relatedness based on 16S rRNA-data of the genus Bradyrhizobium with Pseudomonas carboxydovorans and Rhodopseudomonas palustris, which form a tight phylogenetical cluster and which all contain the 2,3-diamino-2,3-dideoxy-glucose-containing lipid A. The relatedness of these species to the glucosamine-containing species of the genus Rhizobium and to Agrobacterium tumefaciens is rather distant as documented by 16S rRNA studies.Abbreviations LPS lipopolysaccharide - KDO 2-keto-3-deoxyoctonic acid - GalA galacturonic acid - ld-heptose l-glycero-d-manno-heptose - dd-heptose d-glycero-d-manno-heptose - DOC sodium deoxycholate - PAGE polyacrylamide gel electrophoresis - DAG 2,3-diamino-2,3-dideoxy-glucose     

Deep sequencing of microRNAs from hickory reveals an extensive degradation and 3′ end modification

The degradation and 3′ end modification of plant microRNAs (miRNAs) may play crucial roles in regulating miRNA function and stability. However, the mechanism as to how the degradation and the modification are processed are still poorly characterized. Here, we report a survey of miRNA degradation and 3′ modification from two hickory floral differentiation stages through deep sequencing. We constructed two small RNA (sRNA) libraries from two hickory floral differentiation stages and obtained a large number of truncated miRNAs and miRNAs with 3′ end modifications. The presence of so many truncated miRNAs suggests a mechanism degrading through both ends simultaneously. Further analysis reveals that the truncation from the 3′ end has higher probability than from the 5′ end. Single- or double-nucleotide additions to the 3′ end have been observed in many families. We found that the addition of adenine base to the 3′ end is the most common event, accounting for more than 50 % of all miRNA 3′ end modification in the two sRNA libraries. Uridine addition is the second popular modification. These observations suggest that the 3′ end modification of miRNAs preferentially selects adenine and uridine in the hickory plant. Furthermore, we observed that expression of either truncated miRNA or isomiR associates with mature miRNAs. Altogether, our study provides more information regarding the degradation and 3′ end modification of miRNAs in plants.     

Biological Activity and Phosphorylation of 2′-Azido-2′-Deoxyuridine and 2′-Azido-2′-Deoxycytidlne

Abstract

2′-Azido-2′-deoxyuridine and 2′-azido-2′-deoxycytidine were evaluated for their inhibitory activity against ribonucleotide reductase and for subsequent cell growth inhibition. Their mono-and di-phosphates were synthesized and their inhibitory activities against the reductase were also determined in a permeabilized cell system, along with the two nucleosides. The results of the present study identify the first phosphorylation step involved in the conversion of the two azidonucleosides to the corresponding diphosphates to be rate-limiting in the overall activation.     

New syntheses of 2′-C-methylnucleosides starting from d-glucose and d-ribose

Effective general methods have been developed for the synthesis of 2′-C-methylnucleosides starting from d-glucose and d-ribose. 3-O-benzyl-1,2-O-isopropylidene-3-C-methyl-α-d-allofuranose was prepared in 5 steps from d-glucose and converted into 1,2,3-tri-O-acetyl-2-C-methyl-5-O-p-methylbenzoyl-d-ribofuranose (5), the starting compound for nucleoside synthesis. Compound 5 was also synthesised from 2-C-hydroxymethyl-2,3-O-isopropylidene-5-O-trityl-d-ribofuranose, prepared in 3 steps from d-ribose. Condensation of 5 with the bis-trimethylsilyl derivatives of uracil, N⁴-benzoylcytosine, and N⁶-benzoyladenine in the presence of F₃CSO₃OSiMe₃ followed by removal of the protecting acyl groups yielded the corresponding 2′-C-methylnucleosides.     

Carbonic anhydrase inhibitors. Inhibition and homology modeling studies of the fungal β-carbonic anhydrase from Candida albicans with sulfonamides

The β-carbonic anhydrase (CA, EC 4.2.1.1) from the fungal pathogen Candida albicans (Nce103) is involved in a CO₂ sensing pathway critical for the pathogen life cycle and amenable to drug design studies. Herein we report an inhibition study of Nce103 with a library of sulfonamides and one sulfamate, showing that Nce103, similarly to the related enzyme from Cryptococcus neoformans Can2, is inhibited by these compounds with K_Is in the range of 132 nM–7.6 μM. The best Nce103 inhibitors were acetazolamide, methazolamide, bromosulfanilamide, and 4-hydroxymethylbenzenesulfonamide (K_Is < 500 nM). A homology model was generated for Nce103 based on the crystal structure of Can2. The model shows that compounds with zinc-binding groups incorporating less polar moieties and compact scaffolds generate stronger Nce103 inhibitors, whereas highly polar zinc-binding groups and bulkier compounds appear more promising for the specific inhibition of Can2. Such compounds may be useful for the design of antifungal agents possessing a new mechanism of action.     

Fold-recognition and comparative modeling of human α2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni

Background  

The 3-D structure of none of the eukaryotic sialyltransferases (SiaTs) has been determined so far. Sequence alignment algorithms such as BLAST and PSI-BLAST could not detect a homolog of these enzymes from the protein databank. SiaTs, thus, belong to the hard/medium target category in the CASP experiments. The objective of the current work is to model the 3-D structures of human SiaTs which transfer the sialic acid in α2,3-linkage viz., ST3Gal I, II, III, IV, V, and VI, using fold-recognition and comparative modeling methods. The pair-wise sequence similarity among these six enzymes ranges from 41 to 63%.     

Synthesis of 3- and 2′-fucosyl-lactose and 3,2′-difucosyl-lactose from partially benzylated lactose derivatives

O-β-d-Galactopyranosyl-(1→4)-O-[α-l-fucopyranosyl-(1→3)]-d-glucose has been synthesised by reaction of benzyl 2,6-di-O-benzyl-4-O-(2,3,4,6-tetra-O-benzyl-β-d-galactopyranosyl)-β-d-glucopyranoside with 2,3,4-tri-O-benzyl-α-l-fucopyranosyl bromide in the presence of mercuric bromide, followed by hydrogenolysis. Benzylation of benzyl 3′,4′-O-isopropylidene-β-lactoside, via tributylstannylation, in the presence of tetrabutylammonium bromide or N-methylimidazole, gave benzyl 2,6-di-O-benzyl-4-O-(6-O-benzyl-3,4-O-isopropylidene-β-d-galactopyranosyl)-β-d-glucopyranoside (6). α-Fucosylation of 6 in the presence of tetraethylammonium bromide provided either benzyl 2,6-di-O-benzyl-4-O-[6-O-benzyl-3,4-O-isopropylidene-2-O-(2,3,4-tri-O-benzyl-α-l-fucopyransoyl)-β-d- galactopyranosyl]-β-d-glucopyranoside (13, 73%) or a mixture of 13 (42%) and benzyl 2,6-di-O-benzyl-4-O-[6-O-benzyl-3,4,-O-isopropylidene-2-O-(2,3,4-tri-O-benzyl-α-l-fucopyranosyl)-β-d- galactopyranosyl-3-O-(2,3,4-tri-O-benzyl-α-l-fucopyranosyl)-β-d-glucopyranoside (16, 34%). α-Fucosylation of 13 in the presence of mercuric bromide and 2,6-di-tert-butyl-4-methylpyridine gave 16 (73%). Hydrogenolysis and acid hydrolysis of 13 and 16 afforded O-α-l-fucopyranosyl-(1→2)-O-β-d-galactopyranosyl-(1→4)-d-glucose and O-α-l-fucopyranosyl-(1→2)-O-β-d-galactopyranosyl-(1→4)-O-[α-l-fucopyranosyl-(1→3)]-d-glucose, respectively.     

1,2-Diol and Hydrazide Phosphoramidites for Solid-Phase Synthesis and Chemoselective Ligation of 2′-Modified Oligonucleotides

Abstract

The preparation of two novel 2′-O-alkyl phosphoramidites bearing 1,2-diol and hydrazide functions for a chemoselective ligation is described. The former amidite was used to obtain 2′-modified oligodeoxyribonucleotides, which can be later oxidised by NaIO₄ to generate 2′-aldehyde oligonucleotides. These were successfully conjugated to acceptor molecules. The latter amidite also showed good coupling yields, but the hydrazide function was demonstrated to be labile under basic deprotection conditions.     

2′-Fluoro-modified phosphorothioate oligonucleotide can cause rapid degradation of P54nrb and PSF

Synthetic oligonucleotides are used to regulate gene expression through different mechanisms. Chemical modifications of the backbone of the nucleic acid and/or of the 2′ moiety of the ribose can increase nuclease stability and/or binding affinity of oligonucleotides to target molecules. Here we report that transfection of 2′-F-modified phosphorothioate oligonucleotides into cells can reduce the levels of P54nrb and PSF proteins through proteasome-mediated degradation. Such deleterious effects of 2′-F-modified oligonucleotides were observed in different cell types from different species, and were independent of oligonucleotide sequence, positions of the 2′-F-modified nucleotides in the oligonucleotides, method of delivery or mechanism of action of the oligonucleotides. Four 2′-F-modified nucleotides were sufficient to cause the protein reduction. P54nrb and PSF belong to Drosophila behavior/human splicing (DBHS) family. The third member of the family, PSPC1, was also reduced by the 2′-F-modified oligonucleotides. Preferential association of 2′-F-modified oligonucleotides with P54nrb was observed, which is partially responsible for the protein reduction. Consistent with the role of DBHS proteins in double-strand DNA break (DSB) repair, elevated DSBs were observed in cells treated with 2′-F-modified oligonucleotides, which contributed to severe impairment in cell proliferation. These results suggest that oligonucleotides with 2′-F modifications can cause non-specific loss of cellular protein(s).     

Isolation of 2′-Hydroxy-4′-methoxy propiophenone from Tribolium castaneum and T confusum

The copper binding properties were influenced by growth phase of cells, pH and concentration of copper in reaction mixtures. The efficiency of copper absorption increased with growth time and was largest at the mid-logarithmic growth phase. The time course of copper absorption was biphasic, that copper rapidly bound to cell surface for initial few minutes after addition of copper and then the copper was slowly transported into cells. The copper binding to the cell surface depended on the molecular form of copper complex in the reaction mixture and the ligand residue to copper on the cell surface. Double reciprocal plots of absorption velocity of copper vs. copper concentration gave straight lines at low concentration between 0.01 to 0.1 mm. The apparent affinity of copper to the cells of stationary growth phase was the same as that of logarithmic growth phase, that is, the Km values were about 0.01 mm. On the other hand, at high concentration of copper between 0.1 to 5.0 mm the apparent affinity decreased but the absorption velocity of copper remarkably increased. Zinc sulfate most strongly inhibited the copper absorption in this test. It was assumed that zinc competitively bound to the copper binding sites of cell surface.     

Acyl Coenzyme A Synthetase from Pseudomonas fragi Catalyzes the Synthesis of Adenosine 5′-Polyphosphates and Dinucleoside Polyphosphates

Acyl coenzyme A (CoA) synthetase (EC 6.2.1.8) from Pseudomonas fragi catalyzes the synthesis of adenosine 5′-tetraphosphate (p₄A) and adenosine 5′-pentaphosphate (p₅A) from ATP and tri- or tetrapolyphosphate, respectively. dATP, adenosine-5′-O-[γ-thiotriphosphate] (ATPγS), adenosine(5′)tetraphospho(5′)adenosine (Ap₄A), and adenosine(5′)pentaphospho(5′)adenosine (Ap₅A) are also substrates of the reaction yielding p₄(d)A in the presence of tripolyphosphate (P₃). UTP, CTP, and AMP are not substrates of the reaction. The K_m values for ATP and P₃ are 0.015 and 1.3 mM, respectively. Maximum velocity was obtained in the presence of MgCl₂ or CoCl₂ equimolecular with the sum of ATP and P₃. The relative rates of synthesis of p₄A with divalent cations were Mg = Co > Mn = Zn >> Ca. In the pH range used, maximum and minimum activities were measured at pH values of 5.5 and 8.2, respectively; the opposite was observed for the synthesis of palmitoyl-CoA, with maximum activity in the alkaline range. The relative rates of synthesis of palmitoyl-CoA and p₄A are around 10 (at pH 5.5) and around 200 (at pH 8.2). The synthesis of p₄A is inhibited by CoA, and the inhibitory effect of CoA can be counteracted by fatty acids. To a lesser extent, the enzyme catalyzes the synthesis also of Ap₄A (from ATP), Ap₅A (from p₄A), and adenosine(5′)tetraphospho(5′)nucleoside (Ap₄N) from adequate adenylyl donors (ATP, ATPγS, or octanoyl-AMP) and adequate adenylyl acceptors (nucleoside triphosphates).Dinucleoside polyphosphates have been detected in a wide variety of eukaryotic and prokaryotic organisms (13). In higher organisms, their concentrations are generally on the order of 0.01 to 1 μM. Human blood platelets and chromaffin cells of bovine adrenal medulla contain diadenosine polyphosphates located in the dense bodies (10, 26, 35) and chromaffin granules (32, 38), respectively, where they may reach higher local concentrations. The occurrence of dinucleoside polyphosphates has been described for lower eukaryotic (Saccharomyces cerevisiae, Dictyostelium discoideum, and Physarum polycephalum) and for prokaryotic (Salmonella typhimurium, Escherichia coli, and Clostridium acetobutylicum) organisms (13).Dinucleoside tetraphosphates participate in the control of purine nucleotide metabolism (36), where Ap₄A is an activator of both the IMP-GMP-specific cytosolic 5′-nucleotidase (EC 3.1.3.5) and AMP deaminase (EC 3.5.4.6) (K_a, micromolar range) and Gp₄G is an activator of GMP reductase (EC 1.6.6.8) (K_a, nanomolar range) (36). As the concentration of dinucleoside polyphosphates increases under unfavorable environmental conditions, they have been implicated in the cellular response to stress (31). A role of Ap₄A in DNA synthesis has been proposed elsewhere (14). Dinucleoside polyphosphates are also transition state analogs of some kinases (37). More recently, the dinucleoside triphosphatase activity of a putative tumor suppressor gene product has been described (3).The nucleoside 5′-polyphosphates (p_nN) are another family of related compounds, p₄A has been detected in rabbit and horse muscle (41), rat liver (44), S. cerevisiae spores (19), and chromaffin granules (38). As p₄A is a very strong inhibitor (K_i, nanomolar range) of asymmetrical dinucleoside tetraphosphatase (EC 3.6.1.17) (22), changes in the level of p₄A could affect the concentration and physiological roles of Ap₄A. Other enzymes known to be inhibited (K_i, micromolar range) by p₄N are guanylate cyclase (EC 4.6.1.2) (p₄A and p₄G) (18) and phosphodiesterase I (EC 3.1.4.1) (p₄G) (9). Effects of p₄A on the tone of the vascular system, mediated by P₂ receptors, have also been described elsewhere (21).The cellular level of dinucleoside polyphosphates results from their rate of degradation and synthesis. The following specific enzymes, implicated in the cleavage of dinucleoside polyphosphates, have been described (see reference 15 for a review): asymmetrical dinucleoside tetraphosphatase (EC 3.6.1.17), symmetrical dinucleoside tetraphosphatase (EC 3.6.1.41), dinucleoside tetraphosphate phosphorylase (EC 2.7.7.53), and dinucleoside triphosphatase (EC 3.6.1.29). In addition, there are other unspecific enzymes able to catalyze the hydrolysis of dinucleoside polyphosphates like E. coli 5′-nucleotidase (34) and phosphodiesterase I (9, 15, 26).This paper deals with the synthesis of (di)nucleoside polyphosphates. It has been known since 1966 that some aminoacyl tRNA synthetases (30, 45) catalyze the synthesis of Ap₄A through reactions 1 and 2: reaction 1 reaction 2 The possibility that other enzymes (mainly synthetases and some transferases) which catalyze the formation of AMP, via nucleotidyl-containing intermediates and by releasing PP_i, could catalyze the synthesis of dinucleoside polyphosphates was later raised (17). Luciferase (EC 1.13.12.7), considered as an oxidoreductase, catalyzes the synthesis of Ap₄A with ATP as substrate and luciferin as an essential activator (27, 40): reaction 3 reaction 4 Acetyl-CoA synthetase (EC 6.2.1.1) from S. cerevisiae also catalyzes the synthesis of p₄A and p₅A, from ATP and P₃ and P₄, respectively (16). In the reactions catalyzed by luciferase and acetyl-CoA synthetase, ATP is a very good substrate for the formation of the E · X-AMP complex (X = the appropriate acyl residue), whereas any NTP (or even P₃) is an acceptor (particularly in the case of luciferase) of the AMP moiety of the complex, provided that it has an intact terminal pyrophosphate (27, 40).Here we show that acyl-CoA synthetase from Pseudomonas fragi catalyzes the synthesis of p₄A, p₅A, Ap₄A, Ap₅A, and a variety of Ap₄Ns. In our view, these findings widen the knowledge of the mechanisms of synthesis of (di)nucleoside polyphosphates in prokaryotes and, by extrapolation, also in eukaryotes.     

Functional characterization, homology modeling and docking studies of β-glucosidase responsible for bioactivation of cyanogenic hydroxynitrile glucosides from Leucaena leucocephala (subabul)

Glycosyl hydrolase family 1 β-glucosidases are important enzymes that serve many diverse functions in plants including defense, whereby hydrolyzing the defensive compounds such as hydroxynitrile glucosides. A hydroxynitrile glucoside cleaving β-glucosidase gene (Llbglu1) was isolated from Leucaena leucocephala, cloned into pET-28a (+) and expressed in E. coli BL21 (DE3) cells. The recombinant enzyme was purified by Ni–NTA affinity chromatography. The optimal temperature and pH for this β-glucosidase were found to be 45 °C and 4.8, respectively. The purified Llbglu1 enzyme hydrolyzed the synthetic glycosides, pNPGlucoside (pNPGlc) and pNPGalactoside (pNPGal). Also, the enzyme hydrolyzed amygdalin, a hydroxynitrile glycoside and a few of the tested flavonoid and isoflavonoid glucosides. The kinetic parameters K _m and V _max were found to be 38.59 μM and 0.8237 μM/mg/min for pNPGlc, whereas for pNPGal the values were observed as 1845 μM and 0.1037 μM/mg/min. In the present study, a three dimensional (3D) model of the Llbglu1 was built by MODELLER software to find out the substrate binding sites and the quality of the model was examined using the program PROCHEK. Docking studies indicated that conserved active site residues are Glu 199, Glu 413, His 153, Asn 198, Val 270, Asn 340, and Trp 462. Docking of rhodiocyanoside A with the modeled Llbglu1 resulted in a binding with free energy change (ΔG) of ?5.52 kcal/mol on which basis rhodiocyanoside A could be considered as a potential substrate.     

Enzymatic synthesis of 2′-ara and 2′-deoxy analogues of c-di-GMP

The substrate specificity of recombinant full-length diguanylate cyclase (DGC) of Thermotoga maritima with mutant allosteric site was investigated. It has been originally shown that the enzyme could use GTP closest analogues – 2′-deoxyguanosine-5′-triphosphate (dGTP) and 9-β-D-arabinofuranosyl-guanine-5′-triphosphate (araGTP) as the substrates. The first demonstrations of an enzymatic synthesis of bis-(3′-5′)-cyclic dimeric deoxyguanosine monophosphate (c-di-dGMP) and the previously unknown bis-(3′-5′)-cyclic dimeric araguanosine monophosphate (c-di-araGMP) using DGC of T. maritima in the form of inclusion bodies have been provided.