1,721,031 research outputs found
The structure-based reaction mechanism of urease, a nickel dependent enzyme: tale of a long debate
Full text linkThis review is an attempt to retrace the chronicle that starts from the discovery of the role of nickel as the essential metal ion in urease for the enzymatic catalysis of urea, a key step in the biogeochemical cycle of nitrogen on Earth, to the most recent progress in understanding the chemistry of this historical enzyme. Data and facts are presented through the magnifying lenses of the authors, using their best judgment to filter and elaborate on the many facets of the research carried out on this metalloenzyme over the years. The tale is divided in chapters that discuss and describe the results obtained in the subsequent leaps in the knowledge that led from the discovery of a biological role for Ni to the most recent advancements in the comprehension of the relationship between the structure and function of urease. This review is intended not only to focus on the bioinorganic chemistry of this beautiful metal-based catalysis, but also, and maybe primarily, to evoke inspiration and motivation to further explore the realm of bio-based coordination chemistry
Correction to: The structure-based reaction mechanism of urease, a nickel dependent enzyme: tale of a long debate (JBIC Journal of Biological Inorganic Chemistry, (2020), 25, 6, (829-845), 10.1007/s00775-020-01808-w)
No full texterrors in Schemes 3 and 6. In particular, the protonation state of the base B in Scheme 3 (lower right panel) and the bridging hydroxide in Scheme 6 (lower left panel) have been corrected. The correct schemes are shown below upon request of the authors
Nickel import and export in the human pathogen Helicobacter pylori, perspectives from molecular modelling
No full textThe uptake of essential metal ions and the ability to extrude them when their excess causes toxicity are crucial processes for all living beings. Nickel is a virulence factor for several human pathogens and in particular for the human gastric pathogen Helicobacter pylori because of its crucial role in the catalytic activity of two Ni-dependent enzymes, urease and hydrogenase. H. pylori requires efficient uptake mechanisms to import Ni(II) because of its scarcity in the human body, but the molecular details of Ni(II) homeostasis are not fully known. Here we offer a structural framework for the machinery of Ni(II) import/export in H. pylori, obtained through comparative modelling and macromolecular docking. The model structures reported in this perspective are initial steps towards the understanding of these processes at the molecular level and in the direction to exploit them to eradicate infections caused by this family of pathogens. The differences between the structural models obtained by using both the recently released neural network-based approach implemented in AlphaFold2 and a more classical user-driven modelling procedure are also discussed
Correction to: The model structure of the copper-dependent ammonia Monooxygenase (JBIC Journal of Biological Inorganic Chemistry, (2020), 25, 7, (995-1007), 10.1007/s00775-020-01820-0)
No full textIn the original article published, the authors missed to acknowledging an article published by Liew et al. (Mutagenesis of the hydrocarbon monooxygenase indicates a metal centre in subunit-C, and not subunit-B, is essential for copper- containing membrane monooxygenase activity, Microbiology 2014, 160, 1267–1277). “Thus far, however, the crystal structures have not fully established the location and composition of the pMMO active site [48], but all evidence points to either the CuB or the CuC site for this role. It is the opinion of the authors of the present study that the latter, with its labile water-bound position, should more logically constitute the enzyme active metal site. This conclusion is strongly supported by site-directed mutagenesis studies on the copper-dependent hydrocarbon monooxygenase (HMO) from Mycobacterium NBB4 which provided the first evidence that the C site was essential for activity, whereas mutations in the B site impaired, but did not eliminate, activity (E. F. Liew, D. Tong, N. V. Coleman, A. J. Holmes, Microbiology 2014, 160, 1267–1277)”
The model structure of the copper-dependent ammonia monooxygenase
Full text linkAbstract: Ammonia monooxygenase is a copper-dependent membrane-bound enzyme that catalyzes the first step of nitrification in ammonia-oxidizing bacteria to convert ammonia to hydroxylamine, through the reductive insertion of a dioxygen-derived O atom in an N–H bond. This reaction is analogous to that carried out by particulate methane monooxygenase, which catalyzes the conversion of methane to methanol. The enzymatic activity of ammonia monooxygenase must be modulated to reduce the release of nitrogen-based soil nutrients for crop production into the atmosphere or underground waters, a phenomenon known to significantly decrease the efficiency of primary production as well as increase air and water pollution. The structure of ammonia monooxygenase is not available, rendering the rational design of enzyme inhibitors impossible. This study describes a successful attempt to build a structural model of ammonia monooxygenase, and its accessory proteins AmoD and AmoE, from Nitrosomonas europaea, taking advantage of the high sequence similarity with particulate methane monooxygenase and the homologous PmoD protein, for which crystal structures are instead available. The results obtained not only provide the structural details of the proteins ternary and quaternary structures, but also suggest a location for the copper-containing active site for both ammonia and methane monooxygenases, as well as support a proposed structure of a CuA-analogue dinuclear copper site in AmoD and PmoD. Graphic abstract: [Figure not available: see fulltext.
Dynamic characterization and substrate binding of cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase-an enzyme used in bioremediation.
No full textIn recent years, techniques involving the use oforganisms to remove or neutralize pollutants from contaminatedsites have attracted great attention. The aim of bioremediationis to use naturally occurring organisms to degradedangerous substances to less toxic or non toxic molecules.The gram-negative bacterium Pandoraea pnomenusa strainB-356 (Pp) has been found to be able to transform a persistentclass of organic pollutant compounds, namely the biphenyland polychlorinated biphenyls (PCBs). A key enzyme in thePCB catabolic pathway is NAD-dependent cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (BphB), for whichthe crystal structure from Pp has been crystallized in apo-,NAD-bound and biphenyldiol-/NAD-bound forms. The substratebinding loop structure has not been completely resolvedto date in the former two bound states. Here we report theresults of the first extensive molecular dynamics simulationson the three different states of PpBphB. This allowed an indepth characterization of the mechanism of ligand uptake andbinding, including unraveling of the gating mechanism. Oursimulations give a deep insight into several dynamic featuresof the enzyme that were not captured by crystal structure
Determination and Kinetic Characterization of a New Potential Inhibitor for AmsI Protein Tyrosine Phosphatase from the Apple Pathogen Erwinia amylovora
Full text linkErwinia amylovora is a Gram-negative bacterium, responsible for the fire blight disease in Rosaceae plants. Its virulence is correlated with the production of an exopolysaccharide (EPS) called amylovoran, which protects the bacterium from the surrounding environment and helps its diffusion inside the host. Amylovoran biosynthesis relies on the expression of twelve genes clustered in the ams operon. One of these genes, amsI, encodes for a Low Molecular Weight Protein Tyrosine Phosphatase (LMW-PTP) called EaAmsI, which plays a key role in the regulation of the EPS production pathway. For this reason, EaAmsI was chosen in this work as a target for the development of new antibacterial agents against E. amylovora. To achieve this aim, a set of programs (DOCK6, OpenEye FRED) was selected to perform a virtual screening using a database of ca. 700 molecules. The six best-scoring compounds identified were tested in in vitro assays. A complete inhibition kinetic characterization carried out on the most promising molecule (n-Heptyl β-D-glucopyranoside, N7G) showed an inhibition constant of 7.8 ± 0.6 μM. This study represents an initial step towards the development of new EaAmsI inhibitors able to act as antibacterial agents against E. amylovora infections
Structure-based computational study of the catalytic and inhibition mechanisms of urease
No full textAbstract The viability of different mechanisms of catalysis and inhibition of the nickel-containing enzyme urease was explored using the available highresolution structures of the enzyme isolated from Bacillus pasteurii in the native form and inhibited with several substrates. The structures and charge distribution of urea, its catalytic transition state, and three enzyme inhibitors were calculated using ab initio and density functional theory methods. The DOCK program suite was employed to determine families of structures of urease complexes characterized by docking energy scores indicative of their relative stability according to steric and electrostatic criteria. Adjustment of the parameters used by DOCK, in order to account for the presence of the metal ion in the active site, resulted in the calculation of best energy structures for the nickel-bound inhibitors β-mercaptoethanol, acetohydroxamic acid, and diamidophosphoric acid. These calculated structures are, in good agreement with the experimentally determined structures, and provide hints on the reactivity and mobility of the inhibitors in the active site. The same docking protocol was applied to the substrate urea and its catalytic transition state, in order to shed light onto the possible catalytic steps occurring at the binuclear nickel active site. These calculations suggest that the most viable pathway for urea hydrolysis involve a nucleophilic attack by the bridging, and not the terminal, nickel-bound hydroxide onto a urea molecule, with active site residues playing important roles in orienting and activating the substrate, and stabilizing the catalytic transition state
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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