Nonredox nickel enzymes.
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ABSTRACT:
SUBMITTER: Maroney MJ
PROVIDER: S-EPMC5675112 | biostudies-literature | 2014 Apr
REPOSITORIES: biostudies-literature
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Project description:A thorough comprehension of the mechanism behind organic electrooxidation is crucial for the development of efficient energy conversion technology. Here, we find that trivalent nickel is capable of oxidizing organics through a nucleophilic attack and electron transfer via a nonredox process. This nonredox trivalent nickel exhibits exceptional kinetic efficiency in oxidizing organics that possess the highest occupied molecular orbital energy levels ranging from -7.4 to -6 eV (vs. Vacuum level) and the dual local softness values of nucleophilic atoms in nucleophilic functional groups, such as hydroxyls (methanol, ethanol, benzyl alcohol), carbonyls (formamide, urea, formaldehyde, glucose, and N-acetyl glucosamine), and aminos (benzylamine), ranging from -0.65 to -0.15. The rapid electrooxidation kinetics can be attributed to the isoenergetic channels created by the nucleophilic attack and the nonredox electron transfer via the unoccupied eg orbitals of trivalent nickel (t2g6eg1). Our findings are valuable in identifying kinetically fast organic electrooxidation on nonredox catalysts for efficient energy conversions.
| S-EPMC10693638 | biostudies-literature
Project description:Nickel enzymes, present in archaea, bacteria, plants, and primitive eukaryotes are divided into redox and nonredox enzymes and play key functions in diverse metabolic processes, such as energy metabolism and virulence. They catalyze various reactions by using active sites of diverse complexities, such as mononuclear nickel in Ni-superoxide dismutase, glyoxylase I and acireductone dioxygenase, dinuclear nickel in urease, heteronuclear metalloclusters in [NiFe]-carbon monoxide dehydrogenase, acetyl-CoA decarbonylase/synthase and [NiFe]-hydrogenase, and even more complex cofactors in methyl-CoM reductase and lactate racemase. The presence of metalloenzymes in a cell necessitates a tight regulation of metal homeostasis, in order to maintain the appropriate intracellular concentration of nickel while avoiding its toxicity. As well, the biosynthesis and insertion of nickel active sites often require specific and elaborated maturation pathways, allowing the correct metal to be delivered and incorporated into the target enzyme. In this review, the phylogenetic distribution of nickel enzymes will be briefly described. Their tridimensional structures as well as the complexity of their active sites will be discussed. In view of the latest findings on these enzymes, a special focus will be put on the biosynthesis of their active sites and nickel activation of apo-enzymes.
| S-EPMC7184782 | biostudies-literature
Project description:The nickel-pincer nucleotide (NPN) cofactor is a modified pyridinium mononucleotide that tri-coordinates nickel and is crucial for the activity of certain racemases and epimerases. LarB, LarC, and LarE are responsible for NPN synthesis, with the cofactor subsequently installed into LarA homologs. Hurdles for investigating the functional properties of such proteins arise from the difficulty of obtaining the active, NPN cofactor-loaded enzymes and in assaying their diverse reactivities. Here, we show that when the Lactiplantibacillus plantarum lar genes are cloned into the Duet expression system and cultured in Escherichia coli, they confer lactate racemase activity to the cells. By replacing L. plantarum larA with related genes from other microorganisms, this system allows for the generation of active LarA homologs. Furthermore, the Duet system enables the functional testing of LarB, LarC, and LarE homologs from other microorganisms. In addition to applying the Duet expression system for synthesis of active, NPN cofactor-containing enzymes in E. coli, we demonstrate that circular dichroism spectroscopy provides a broadly applicable means of assaying these enzymes. By selecting a wavelength of high molar ellipticity and low absorbance for a given 2-hydroxy acid substrate enantiomer, the conversion of one enantiomer/epimer into the other can be monitored for LarA homologs without the need for any coupling enzymes or reagents. The methods discussed here further our abilities to investigate the unique activities of Lar proteins.ImportanceEnzymes containing the nickel-pincer nucleotide (NPN) cofactor are prevalent in a wide range of microorganisms and catalyze various critical biochemical reactions, yet they remain underexplored due, in part, to limitations in current research methodologies. The two significant advancements described here, the heterologous production of active NPN-cofactor containing enzymes in Escherichia coli and the use of a circular dichroism-based assay to monitor enzyme activities, expand our capacity to analyze these enzymes. Such additional detailed characterization will deepen our understanding of the diverse chemistry catalyzed by the NPN cofactor and potentially uncover novel roles for this organometallic species in microbial metabolism.
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Project description:Significance: Nicotinamide adenine dinucleotide (NAD+) spans diverse roles in biology, serving as both an important redox cofactor in metabolism and a substrate for signaling enzymes that regulate protein post-translational modifications (PTMs). Critical Issues: Although the interactions between these different roles of NAD+ (and its reduced form NADH) have been considered, little attention has been paid to the role of compartmentation in these processes. Specifically, the role of NAD+ in metabolism is compartment specific (e.g., mitochondrial vs. cytosolic), affording a very different redox landscape for PTM-modulating enzymes such as sirtuins and poly(ADP-ribose) polymerases in different cell compartments. In addition, the orders of magnitude differences in expression levels between NAD+-dependent enzymes are often not considered when assuming the effects of bulk changes in NAD+ levels on their relative activities. Recent Advances: In this review, we discuss the metabolic, nonmetabolic, redox, and enzyme substrate roles of cellular NAD+, and the recent discoveries regarding the interplay between these roles in different cell compartments. Future Directions: Therapeutic implications for the compartmentation and manipulation of NAD+ biology are discussed. Antioxid. Redox Signal. 31, 623-642.
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Project description:Sulfur is present in several nucleosides within tRNAs. In particular, thiolation of the universally conserved methyl-uridine at position 54 stabilizes tRNAs from thermophilic bacteria and hyperthermophilic archaea and is required for growth at high temperature. The simple nonredox substitution of the C2-uridine carbonyl oxygen by sulfur is catalyzed by tRNA thiouridine synthetases called TtuA. Spectroscopic, enzymatic, and structural studies indicate that TtuA carries a catalytically essential [4Fe-4S] cluster and requires ATP for activity. A series of crystal structures shows that (i) the cluster is ligated by only three cysteines that are fully conserved, allowing the fourth unique iron to bind a small ligand, such as exogenous sulfide, and (ii) the ATP binding site, localized thanks to a protein-bound AMP molecule, a reaction product, is adjacent to the cluster. A mechanism for tRNA sulfuration is suggested, in which the unique iron of the catalytic cluster serves to bind exogenous sulfide, thus acting as a sulfur carrier.
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Project description:Genomics of macroalgal-polysaccharide degrading marine bacteria
| PRJEB53743 | ENA
Project description:Fibrinolytic enzymes from food fermenting bacteria
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Project description:The effect of nanomaterials (NMs) is less understood in light of the implemented and existing methodologies for regular chemicals. To understand the mode of action of NMs is one of the alternatives to improve predictions and environmental risk assessment (ERA). In the present work the high-throughput gene expression tool (4x44K microarray for Enchytraeus crypticus) was used to investigate the mechanisms activated by Ni exposure. Ni nanoparticles (Ni-NPs) were investigated together with Ni-salt (NiNO3). Testing was done based on reproduction effect concentrations (EC20, EC50) using 3 and 7 days exposure periods.
2017-06-13 | GSE69793 | GEO
Project description:Purification of valuable engineered proteins and enzymes can be laborious, costly, and generating large amount of chemical waste. Whilst enzyme immobilization can enhance recycling and reuse of enzymes, conventional methods for immobilizing engineered enzymes from purified samples are also inefficient with multiple-step protocols, regarding both the carrier preparation and enzyme binding. Nickel ferrite magnetic nanoparticles (NiFe2O4 MNPs) offer distinct advantages in both purification and immobilization of enzymes. In this work, we demonstrate the preparation of NiFe2O4 MNPs via a one-step solvothermal synthesis and their use in direct enzyme binding from cell lysates. These NiFe2O4 MNPs have showed an average diameter of 8.9 ± 1.7 nm from TEM analysis and a magnetization at saturation (Ms) value of 53.0 emu g-1 from SQUID measurement. The nickel binding sites of the MNP surface allow direct binding of three his-tagged enzymes, D-phenylglycine aminotransferase (D-PhgAT), Halomonas elongata ω-transaminase (HeωT), and glucose dehydrogenase from Bacillus subtilis (BsGDH). It was found that the enzymatic activities of all immobilized samples directly prepared from cell lysates were comparable to those prepared from the conventional immobilization method using purified enzymes. Remarkably, D-PhgAT supported on NiFe2O4 MNPs also showed similar activity to the purified free enzyme. By comparing on both carrier preparation and enzyme immobilization protocols, use of NiFe2O4 MNPs for direct enzyme immobilization from cell lysate can significantly reduce the number of steps, time, and use of chemicals. Therefore, NiFe2O4 MNPs can offer considerable advantages for use in both enzyme immobilization and protein purification in pharmaceutical and other chemical industries.
| S-EPMC10700653 | biostudies-literature
Project description:The first nickel bis-boryl complexes cis-[Ni( i Pr2ImMe)2(Bcat)2], cis-[Ni( i Pr2ImMe)2(Bpin)2] and cis-[Ni( i Pr2ImMe)2(Beg)2] are reported, which were prepared via the reaction of a source of [Ni( i Pr2ImMe)2] with the diboron(4) compounds B2cat2, B2pin2 and B2eg2 ( i Pr2ImMe = 1,3-di-iso-propyl-4,5-dimethylimidazolin-2-ylidene; B2cat2 = bis(catecholato)diboron; B2pin2 = bis(pinacolato)diboron; B2eg2 = bis(ethylene glycolato)diboron). X-ray diffraction and DFT calculations strongly suggest that a delocalized, multicenter bonding scheme dictates the bonding situation of the NiB2 moiety in these square planar complexes, reminiscent of the bonding situation of "non-classical" H2 complexes. [Ni( i Pr2ImMe)2] also efficiently catalyzes the diboration of alkynes using B2cat2 as the boron source under mild conditions. In contrast to the known platinum-catalyzed diboration, the nickel system follows a different mechanistic pathway, which not only provides the 1,2-borylation product in excellent yields, but also provides an efficient approach to other products such as C-C coupled borylation products or rare tetra-borylated compounds. The mechanism of the nickel-catalyzed alkyne borylation was examined by means of stoichiometric reactions and DFT calculations. Oxidative addition of the diboron reagent to nickel is not dominant; the first steps of the catalytic cycle are coordination of the alkyne to [Ni( i Pr2ImMe)2] and subsequent borylation at the coordinated and, thus, activated alkyne to yield complexes of the type [Ni(NHC)2(η2-cis-(Bcat)(R)C[double bond, length as m-dash]C(R)(Bcat))], exemplified by the isolation and structural characterization of [Ni( i Pr2ImMe)2(η2-cis-(Bcat)(Me)C[double bond, length as m-dash]C(Me)(Bcat))] and [Ni( i Pr2ImMe)2(η2-cis-(Bcat)(H7C3)C[double bond, length as m-dash]C(C3H7)(Bcat))].
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