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Peter M H Kroneck

Publications and source records attributed to Peter M H Kroneck.

At least 19 recordsLinked to original sources
PubMed2007

Respiratory transformation of nitrous oxide (N2O) to dinitrogen by Bacteria and Archaea.

N2O is a potent greenhouse gas and stratospheric reactant that has been steadily on the rise since the beginning of industrialization. It is an obligatory inorganic metabolite of denitrifying bacteria, and some production of N2O is also found in nitrifying and methanotrophic bacteria. We focus this review on the respiratory aspect of N2O transformation catalysed by the multicopper enzyme nitrous oxide reductase (N2OR) that provides the bacterial cell with an electron sink for anaerobic growth. Two types of Cu centres discovered in N2OR were both novel structures among the Cu proteins: the mixed-valent dinuclear Cu(A) species at the electron entry site of the enzyme, and the tetranuclear Cu(Z) centre as the first catalytically active Cu-sulfur complex known. Several accessory proteins function as Cu chaperone and ABC transporter systems for the biogenesis of the catalytic centre. We describe here the paradigm of Z-type N2OR, whose characteristics have been studied in most detail in the genera Pseudomonas and Paracoccus. Sequenced bacterial genomes now provide an invaluable additional source of information. New strains harbouring nos genes and capability of N2O utilization are being uncovered. This reveals previously unknown relationships and allows pattern recognition and predictions. The core nos genes, nosZDFYL, share a common phylogeny. Most principal taxonomic lineages follow the same biochemical and genetic pattern and share the Z-type enzyme. A modified N2OR is found in Wolinella succinogenes, and circumstantial evidence also indicates for certain Archaea another type of N2OR. The current picture supports the view of evolution of N2O respiration prior to the separation of the domains Bacteria and Archaea. Lateral nos gene transfer from an epsilon-proteobacterium as donor is suggested for Magnetospirillum magnetotacticum and Dechloromonas aromatica. In a few cases, nos gene clusters are plasmid borne. Inorganic N2O metabolism is associated with a diversity of physiological traits and biochemically challenging metabolic modes or habitats, including halorespiration, diazotrophy, symbiosis, pathogenicity, psychrophily, thermophily, extreme halophily and the marine habitat down to the greatest depth. Components for N2O respiration cover topologically the periplasm and the inner and outer membranes. The Sec and Tat translocons share the task of exporting Nos components to their functional sites. Electron donation to N2OR follows pathways with modifications depending on the host organism. A short chronology of the field is also presented.

Amino Acid Sequence↗
PubMed2006

Expression and purification of the soluble isoform of human receptor for advanced glycation end products (sRAGE) from Pichia pastoris.

RAGE is a multi-ligand receptor involved in various human diseases including diabetes, cancer or Alzheimer's disease. Engagement of RAGE by its ligands triggers activation of key cellular signalling pathways such as the MAP kinase and NF-kappaB pathways. Whereas the main isoform of RAGE is a transmembrane receptor with both extra- and intracellular domains, a secreted soluble isoform (sRAGE), corresponding to the extracellular part only, has the ability to block RAGE signalling and suppress cellular activation. Administration of sRAGE to animal models of cancer or multiple sclerosis blocked successfully tumour growth and the course of the autoimmune disease. These findings demonstrate that sRAGE may have a potential as therapeutic. We present here a fast and simple purification protocol of sRAGE from the yeast Pichia pastoris. The identity of the protein was confirmed by mass spectrometry and Western blot. The protein was N-glycosylated and 95-98% pure as judged by SDS-PAGE.

Amino Acid Sequence↗
PubMed2006

Reaction mechanism of the iron-sulfur flavoenzyme adenosine-5'-phosphosulfate reductase based on the structural characterization of different enzymatic states.

The iron-sulfur flavoenzyme adenosine-5'-phosphosulfate (APS) reductase catalyzes a key reaction of the global sulfur cycle by reversibly transforming APS to sulfite and AMP. The structures of the dissimilatory enzyme from Archaeoglobus fulgidus in the reduced state (FAD(red)) and in the sulfite adduct state (FAD-sulfite-AMP) have been recently elucidated at 1.6 and 2.5 A resolution, respectively. Here we present new structural features of the enzyme trapped in four different catalytically relevant states that provide us with a detailed picture of its reaction cycle. In the oxidized state (FAD(ox)), the isoalloxazine moiety of the FAD cofactor exhibits a similarly bent conformation as observed in the structure of the reduced enzyme. In the APS-bound state (FAD(ox)-APS), the substrate APS is embedded into a 17 A long substrate channel in such a way that the isoalloxazine ring is pushed toward the channel bottom, thereby producing a compressed enzyme-substrate complex. A clamp formed by residues ArgA317 and LeuA278 to fix the adenine ring and the curved APS conformation appear to be key factors to hold APS in a strained conformation. This energy-rich state is relaxed during the attack of APS on the reduced FAD. A relaxed FAD-sulfite adduct is observed in the structure of the FAD-sulfite state. Finally, a FAD-sulfite-AMP1 state with AMP within van der Waals distance of the sulfite adduct could be characterized. This structure documents how adjacent negative charges are stabilized by the protein matrix which is crucial for forming APS from AMP and sulfite in the reverse reaction.

Adenosine Monophosphate↗
PubMed2005

Electron spin relaxation of copper(II) complexes in glassy solution between 10 and 120 K.

The temperature dependence, between 10 and 120 K, of electron spin-lattice relaxation at X-band was analyzed for a series of eight pyrrolate-imine complexes and for ten other copper(II) complexes with varying ligands and geometry including copper-containing prion octarepeat domain and S100 type proteins. The geometry of the CuN4 coordination sphere for pyrrolate-imine complexes with R=H, methyl, n-butyl, diphenylmethyl, benzyl, 2-adamantyl, 1-adamantyl, and tert-butyl has been shown to range from planar to pseudo-tetrahedral. The fit to the recovery curves was better for a distribution of values of T1 than for a single time constant. Distributions of relaxation times may be characteristic of Cu(II) in glassy solution. Long-pulse saturation recovery and inversion recovery measurements were performed. The temperature dependence of spin-lattice relaxation rates was analyzed in terms of contributions from the direct process, the Raman process, and local modes. It was necessary to include more than one process to fit the experimental data. There was a small contribution from the direct process at low temperature. The Raman process was the dominant contribution to relaxation between about 20 and 60 K. Debye temperatures were between 80 and 120 K. For samples with similar Debye temperatures the coefficient of the Raman process tended to increase as gz increased, as expected if modulation of spin-orbit coupling is a major factor in relaxation rates. Above about 60 K local modes with energies in the range of 260-360 K (180-250 cm-1) dominated the relaxation. For molecules with similar geometry, relaxation rates were faster for more flexible molecules than for more rigid ones. Relaxation rates for the copper protein samples were similar to rates for small molecules with comparable coordination spheres. At each temperature studied the range of relaxation rates was less than an order of magnitude. The spread was smaller between 20 and 60 K where the Raman process dominates, than at higher temperatures where local modes dominate the relaxation. Spin echo dephasing time constants, Tm, were calculated from two-pulse spin echo decays. Near 10 K Tm was dominated by proton spins in the surroundings. As temperature was increased motion and spin-lattice relaxation made increasing contributions to Tm. Near 100 K spin-lattice relaxation dominated Tm.

Copper↗
PubMed2005

NosX function connects to nitrous oxide (N2O) reduction by affecting the Cu(Z) center of NosZ and its activity in vivo.

The effect of loss of the 34-kDa periplasmic NosX protein on the properties of N2O reductase was investigated with an N2O-respiration negative, double mutant of the paralogous genes nosX and nirX of Paracoccus denitrificans. In spite of absence of whole-cell N2O-reducing activity, the purified reductase was catalytically active, which attributes NosX a physiological role in sustaining the reaction cycle. N2O reductase exhibited the spectroscopic features of Cu(A) and the redox-inert, paramagnetic state, Cu(Z)*, of the catalytic center. Cu(Z)*, hitherto considered the result of spontaneous reaction of the reductase with dioxygen, attains cellular significance.

Bacterial Proteins↗
PubMed2005

Purification, crystallization and preliminary X-ray diffraction studies on human Ca2+-binding protein S100B.

S100B, a Ca2+-binding protein, acts intracellularly as a Ca2+-signalling protein but is also secreted to the extracellular space, acting in a cytokine-like manner through its receptor RAGE. Recombinant human S100B has been purified and crystallized in the Ca2+-bound state. Size-exclusion chromatography indicates that S100B can exist as a dimer and as a multimer in solution. Crystals of S100B diffract to 1.9 A and belong to space group P2(1), with unit-cell parameters a = 63.4, b = 81.6, c = 71.5 A, alpha = 90, beta = 107, gamma = 90 degrees. Preliminary analysis of the X-ray data indicate that there are four homodimers per asymmetric unit.

Calcium↗
PubMed2005

Crystallization and preliminary X-ray analysis of the tungsten-dependent acetylene hydratase from Pelobacter acetylenicus.

Acetylene hydratase is a tungsten-containing hydroxylase that converts acetylene to acetaldehyde in a unique reaction that requires a strong reductant. The subsequent disproportionation of acetaldehyde yields acetate and ethanol. Crystals of the tungsten/iron-sulfur protein acetylene hydratase from Pelobacter acetylenicus strain WoAcy 1 (DSM 3246) were grown by the vapour-diffusion method in an N2/H2 atmosphere using polyethylene glycol as precipitant. Growth of crystals suitable for X-ray analysis strictly depended on the presence of Ti(III) citrate or dithionite as reducing agents.

Amino Acid Sequence↗
PubMed2005

Novel bacterial molybdenum and tungsten enzymes: three-dimensional structure, spectroscopy, and reaction mechanism.

The molybdenum enzymes 4-hydroxybenzoyl-CoA reductase and pyrogallol-phloroglucinol transhydroxylase and the tungsten enzyme acetylene hydratase catalyze reductive dehydroxylation reactions, i.e., transhydroxylation between phenolic residues and the addition of water to a triple bond. Such activities are unusual for this class of enzymes, which carry either a mononuclear Mo or W center. Crystallization and subsequent structural analysis by high-resolution X-ray crystallography has helped to resolve the reaction centers of these enzymes to a degree that allows us to understand the interaction of the enzyme and the respective substrate(s) in detail, and to develop a concept for the respective reaction mechanism, at least in two cases.

Bacteria, Anaerobic↗
PubMed2004

Crystal structure of pyrogallol-phloroglucinol transhydroxylase, an Mo enzyme capable of intermolecular hydroxyl transfer between phenols.

The Mo enzyme transhydroxylase from the anaerobic microorganism Pelobacter acidigallici catalyzes the conversion of pyrogallol to phloroglucinol. Such trihydroxybenzenes and their derivatives represent important building blocks of plant polymers. None of the transferred hydroxyl groups originates from water during transhydroxylation; instead a cosubstrate, such as 1,2,3,5-tetrahydroxybenzene, is used in a reaction without apparent electron transfer. Here, we report on the crystal structure of the enzyme in the reduced Mo(IV) state, which we solved by single anomalous-diffraction technique. It represents the largest structure (1,149 amino acid residues per molecule, 12 independent molecules per unit cell), which has been solved so far by single anomalous-diffraction technique. Tranhydroxylase is a heterodimer, with the active Mo-molybdopterin guanine dinucleotide (MGD)(2) site in the alpha-subunit, and three [4Fe-4S] centers in the beta-subunit. The latter subunit carries a seven-stranded, mainly antiparallel beta-barrel domain. We propose a scheme for the transhydroxylation reaction based on 3D structures of complexes of the enzyme with various polyphenols serving either as substrate or inhibitor.

Bacteria, Anaerobic↗
PubMed2004

The unprecedented nos gene cluster of Wolinella succinogenes encodes a novel respiratory electron transfer pathway to cytochrome c nitrous oxide reductase.

The -proteobacterium Wolinella succinogenes grows anaerobically by respiratory nitrite ammonification but not by denitrification. Nevertheless, it is capable of N(2)O reduction to N(2). Recently, the genome sequence of W. succinogenes revealed a nos gene cluster with intriguing features encoding a new type of N(2)O reductase. The predicted enzyme is similar to other N(2)O reductases exhibiting conservation of all residues ligating the two multinuclear copper centers but carries an unprecedented C-terminal monoheme cytochrome c domain. Notably, the N(2)O reductase pre-protein is synthesized with a Sec-dependent signal peptide, rather than the usually observed twin-arginine signal sequence, implying that the copper and heme cofactors are both incorporated in the periplasm. The nos gene cluster further consists of four adjacent open reading frames which are predicted to encode two monoheme c-type cytochromes as well as homologs of NapG and NapH. The latter proteins are thought to function in quinol oxidation coupled to cytochrome c reduction in electron transport to periplasmic nitrate reductase. While the accessory genes nosD, -F, -Y and -L are present in W. succinogenes, homologs of nosR and nosX are absent from the genome. We hypothesize that the nos gene cluster of W. succinogenes encodes a complete electron transport chain catalyzing N(2)O reduction by menaquinol, a pathway which might also be relevant to other bacteria.

Amino Acid Sequence↗
PubMed2004

Tissue- and age-dependent differences in the complexation of cadmium and zinc in the cadmium/zinc hyperaccumulator Thlaspi caerulescens (Ganges ecotype) revealed by x-ray absorption spectroscopy.

Extended x-ray absorption fine structure measurements were performed on frozen hydrated samples of the cadmium (Cd)/zinc (Zn) hyperaccumulator Thlaspi caerulescens (Ganges ecotype) after 6 months of Zn(2+) treatment with and without addition of Cd(2+). Ligands depended on the metal and the function and age of the plant tissue. In mature and senescent leaves, oxygen ligands dominated. This result combined with earlier knowledge about metal compartmentation indicates that the plants prefer to detoxify hyperaccumulated metals by pumping them into vacuoles rather than to synthesize metal specific ligands. In young and mature tissues (leaves, petioles, and stems), a higher percentage of Cd was bound by sulfur (S) ligands (e.g. phytochelatins) than in senescent tissues. This may indicate that young tissues require strong ligands for metal detoxification in addition to the detoxification by sequestration in the epidermal vacuoles. Alternatively, it may reflect the known smaller proportion of epidermal metal sequestration in younger tissues, combined with a constant and high proportion of S ligands in the mesophyll. In stems, a higher proportion of Cd was coordinated by S ligands and of Zn by histidine, compared with leaves of the same age. This may suggest that metals are transported as stable complexes or that the vacuolar oxygen coordination of the metals is, like in leaves, mainly found in the epidermis. The epidermis constitutes a larger percentage of the total volume in leaves than in stems and petioles. Zn-S interaction was never observed, confirming earlier results that S ligands are not involved in Zn resistance of hyperaccumulator plants.

Cadmium↗
PubMed2004

Structural basis of denitrification.

Denitrification represents an important part of the biogeochemical cycle of the essential element nitrogen. It constitutes the predominant pathway of the reductive dissimilation of nitrate in the environment. Via four enzymatic reactions, nitrate is transformed stepwise to nitrite (NO2-), nitric oxide (NO), and nitrous oxide (N2O), to finally yield dinitrogen gas (N2). All steps within this metabolic pathway are catalyzed by complex multi-site metalloenzymes with unique spectroscopic and structural features. In recent years, high-resolution crystal structures have become available for these enzymes with the exception of the structure for NO reductase.

Animals↗
PubMed2003

Allosteric control of internal electron transfer in cytochrome cd1 nitrite reductase.

Cytochrome cd1 nitrite reductase is a bifunctional multiheme enzyme catalyzing the one-electron reduction of nitrite to nitric oxide and the four-electron reduction of dioxygen to water. Kinetics and thermodynamics of the internal electron transfer process in the Pseudomonas stutzeri enzyme have been studied and found to be dominated by pronounced interactions between the c and the d1 hemes. The interactions are expressed both in dramatic changes in the internal electron-transfer rates between these sites and in marked cooperativity in their electron affinity. The results constitute a prime example of intraprotein control of the electron-transfer rates by allosteric interactions.

Allosteric Site↗
PubMed2002

Mechanism of the six-electron reduction of nitrite to ammonia by cytochrome c nitrite reductase.

Cytochrome c nitrite reductase catalyzes the six-electron reduction of nitrite to ammonia without the release of potential reaction intermediates, such as NO or hydroxylamine. On the basis of the crystallographic observation of reaction intermediates and of density functional calculations, we present a working hypothesis for the reaction mechanism of this multiheme enzyme which carries a novel lysine-coordinated heme group (Fe-Lys). It is proposed that nitrite reduction starts with a heterolytic cleavage of the N-O bond which is facilitated by a pronounced back-bonding interaction of nitrite coordinated through nitrogen to the reduced (Fe(II)) but not the oxidized (Fe(III)) active site iron. This step leads to the formation of an [FeNO](6) species and a water molecule and is further facilitated by a hydrogen bonding network that induces an electronic asymmetry in the nitrite molecule that weakens one N-O bond and strengthens the other. Subsequently, two rapid one-electron reductions lead to an [FeNO](8) form and, by protonation, to an Fe(II)-HNO adduct. Hereafter, hydroxylamine will be formed by a consecutive two-electron two-proton step which is dehydrated in the final two-electron reduction step to give ammonia and an additional water molecule. A single electron reduction of the active site closes the catalytic cycle.

Ammonia↗
PubMed2002

Kinetics and efficiency of excitation energy transfer from chlorophylls, their heavy metal-substituted derivatives, and pheophytins to singlet oxygen.

Time-resolved measurements of the singlet oxygen infrared (1269 nm) luminescence were used to follow the kinetics and efficiency of excitation energy transfer (EET) between chlorophyll (Chl) derivatives and oxygen in acetone. The studied pigments were Mg-Chl a and b and their heavy metal (Cu(2+) and Zn(2+))-substituted analogues, as well as pheophytin (Pheo) a and b. The efficiency of EET from chlorophyll to oxygen was highly dependent on the central ion in the pigment. Cu-Chl a and Cu-Chl b had the lowest efficiencies of singlet oxygen production, while Pheo a had a higher one, and Zn-Chl a had a similar one compared to Mg-Chl a. Also the side chain (position C-7, i.e. Chl a vs. Chl b) influenced the efficiency of singlet oxygen formation. In the case of square-planar complexes like Cu-Chl and Pheo, EET was more efficient in the Chl a derivatives than in those of Chl b; the opposite effect was observed in the case of the five- or six-coordinated Mg-Chl and Zn-Chl. As for the lifetime of the Chl triplet state, the most striking difference to Mg-Chl again was found in the case of Cu-Chls, which had much shorter lifetimes. Furthermore, the central ion in Chl affected the physical quenching of singlet oxygen: its efficiency was decreasing from Mg-Chl through Zn-Chl over Cu-Chl to Pheo. The results are discussed in the context of the oxidative stress accompanying heavy metal-induced stress in plants.

Chlorophyll↗