27 results on '"Andreas Dietl"'
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2. Neodymium as Metal Cofactor for Biological Methanol Oxidation: Structure and Kinetics of an XoxF1-Type Methanol Dehydrogenase
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Rob A. Schmitz, Nunzia Picone, Helena Singer, Andreas Dietl, Kerstin-Anikó Seifert, Arjan Pol, Mike S. M. Jetten, Thomas R. M. Barends, Lena J. Daumann, and Huub J. M. Op den Camp
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Microbiology ,QR1-502 - Abstract
Lanthanides comprise a group of 15 elements with atomic numbers 57 to 71 that are essential in a variety of high-tech devices, such as mobile phones, but were considered biologically inert for a long time. The biological relevance of lanthanides became evident when the acidophilic methanotroph Methylacidiphilum fumariolicum
- Published
- 2021
- Full Text
- View/download PDF
3. Dynamics in an unusual acyl carrier protein (ACP) from a ladderane lipid-synthesizing organism
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Andreas Dietl and Thomas R. M. Barends
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Stereochemistry ,Amino Acid Motifs ,Sequence (biology) ,Molecular Dynamics Simulation ,010402 general chemistry ,Thioester ,01 natural sciences ,Biochemistry ,Cofactor ,Anaerobic Ammonia Oxidation ,03 medical and health sciences ,Bacterial Proteins ,Structural Biology ,Lipid biosynthesis ,Acyl Carrier Protein ,Ladderane ,Molecular Biology ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,biology ,Planctomycetes ,Protein dynamics ,Lipid Metabolism ,0104 chemical sciences ,Acyl carrier protein ,chemistry ,Helix ,biology.protein ,lipids (amino acids, peptides, and proteins) - Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria express a distinct acyl carrier protein implicated in the biosynthesis of the highly unusual "ladderane" lipids these organisms produce. This "anammox-specific" ACP, or amxACP, shows several unique features such as a conserved FF motif and an unusual sequence in the functionally important helix III. Investigation of the protein's structure and dynamics, both in the crystal by ensemble refinement and by MD simulations reveal that helix III adopts a rare six-residue-long 310 -helical conformation that confers a large degree of conformational and positional variability on this part of the protein. This way of introducing structural flexibility by using the inherent properties of 310 -helices appears unique among ACPs. Moreover, the structure suggests a role for the FF motif in shielding the thioester linkage between the protein's prosthetic group and its acyl cargo from hydrolysis. This article is protected by copyright. All rights reserved.
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- 2022
4. Living on hydrazine: Metabolic protein complexes from an anaerobic ammonium oxidizer
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Lea Dietrich, Tadeo Moreno Chicano, Naomi M. Almeida, Mohd Akram, Mike Jetten, Laura van Niftrik, Andreas Dietl, Boran Kartal, Thomas R.M. Barends, and Kristian Parey
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Biophysics - Published
- 2023
5. A nitric oxide–binding heterodimeric cytochrome c complex from the anammox bacterium Kuenenia stuttgartiensis binds to hydrazine synthase
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Mike S. M. Jetten, Andreas Dietl, Andreas Menzel, Joachim Reimann, Boran Kartal, Wouter Versantvoort, Thomas R. M. Barends, and Mohd Akram
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0301 basic medicine ,Enzyme complex ,030102 biochemistry & molecular biology ,ATP synthase ,biology ,Stereochemistry ,Nitric oxide binding ,Cytochrome c ,Protein subunit ,Cell Biology ,Biochemistry ,Electron transport chain ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,chemistry ,Anammox ,Ecological Microbiology ,biology.protein ,Molecular Biology ,Heme - Abstract
Contains fulltext : 209065.pdf (Publisher’s version ) (Open Access) Anaerobic ammonium oxidation (anammox) is a microbial process responsible for significant nitrogen loss from the oceans and other ecosystems. The redox reactions at the heart of anammox are catalyzed by large multiheme enzyme complexes that rely on small cytochrome c proteins for electron shuttling. Among the most highly abundant of these cytochromes is a unique heterodimeric complex composed of class I and class II c-type cytochrome called NaxLS, which has distinctive biochemical and spectroscopic properties. Here, we present the 1.7 Å resolution crystal structure of this complex from the anammox organism Kuenenia stuttgartiensis (KsNaxLS). The structure reveals that the heme irons in each subunit exhibit a rare His/Cys ligation, which, as we show by substitution, causes the observed unusual spectral properties. Unlike its individual subunits, the KsNaxLS complex binds nitric oxide (NO) only at the distal heme side, forming 6cNO adducts. This is likely due to steric immobilization of the proximal heme binding motifs upon complex formation, a finding that may be of functional relevance, since NO is an intermediate in the central anammox metabolism. Pulldown experiments with K. stuttgartiensis cell-free extract showed that the KsNaxLS complex binds specifically to one of the central anammox enzyme complexes, hydrazine synthase, which uses NO as one of its substrates. It is therefore possible that the KsNaxLS complex plays a role in binding the volatile NO to retain it in the cell for transfer to hydrazine synthase. Alternatively, we propose that KsNaxLS may shuttle electrons to this enzyme complex. 22 september 2019
- Published
- 2019
6. Specificity of Small
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Mohd, Akram, Josephine, Bock, Andreas, Dietl, and Thomas R M, Barends
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Article - Abstract
Anaerobic ammonium oxidation (anammox) is a bacterial process in which ammonium and nitrite are combined into dinitrogen gas and water, yielding energy for the cell. This process relies on a series of redox reactions catalyzed by a set of enzymes, with electrons being shuttled to and from these enzymes, likely by small cytochrome c proteins. For this system to work productively, these electron carriers require a degree of specificity toward the various possible redox partners they encounter in the cell. Here, we compare two cytochrome c proteins from the anammox model organism Kuenenia stuttgartiensis. We show that they are highly homologous, are expressed at comparable levels, share the same fold, and display highly similar redox potentials, yet one of them accepts electrons from the metabolic enzyme hydroxylamine oxidase (HAO) efficiently, whereas the other does not. An analysis of the crystal structures supplemented by Monte Carlo simulations of the transient redox interactions suggests that this difference is at least partly due to the electrostatic field surrounding the proteins, illustrating one way in which the electron carriers in anammox could attain the required specificity. Moreover, the simulations suggest a different “outlet” for electrons on HAO than has traditionally been assumed.
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- 2021
7. Purification of the key enzyme complexes of the anammox pathway from <scp>DEMON</scp> sludge
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Mohd Akram, Thomas R. M. Barends, Andreas Dietl, and Melanie J. I. Müller
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Nitrogen ,Hydrazine ,Biophysics ,Crystallography, X-Ray ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Anaerobic Ammonia Oxidation ,Biomaterials ,chemistry.chemical_compound ,Bioreactors ,Bacterial Proteins ,Multienzyme Complexes ,Ammonium Compounds ,Ammonium ,Ladderane ,Nitrosomonas ,Nitrite ,Hydroxylamine Oxidoreductase ,Nitrites ,Phylogeny ,Bacteria ,Sewage ,biology ,010405 organic chemistry ,Organic Chemistry ,General Medicine ,biology.organism_classification ,6. Clean water ,0104 chemical sciences ,Kinetics ,Hydrazines ,chemistry ,Anammox ,Sewage treatment ,Oxidoreductases ,Oxidation-Reduction - Abstract
Anaerobic Ammonium Oxidation ("anammox") is a bacterial process in which nitrite and ammonium are converted into nitrogen gas and water, yielding energy for the cell. Anammox is an important branch of the global biological nitrogen cycle, being responsible for up to 50% of the yearly nitrogen removal from the oceans. Strikingly, the anammox process uniquely relies on the extremely reactive and toxic compound hydrazine as a free intermediate. Given its global importance and biochemical novelty, there is considerable interest in the enzymes at the heart of the anammox pathway. Unfortunately, obtaining these enzymes in sufficiently large amounts for biochemical and structural studies is problematic, given the slow growth of pure cultures of anammox bacteria when high cell densities are required. However, the anammox process is being applied in wastewater treatment to remove nitrogenous waste in processes like DEamMONification (DEMON). In plants using such processes, which rely on a combination of aerobic ammonia-oxidizers and anammox organisms, kilogram amounts of anammox bacteria-containing sludge are readily available. Here, we report a protein isolation protocol starting from anammox cells present in DEMON sludge from a wastewater treatment plan that readily yields pure preparations of key anammox proteins in the tens of milligrams, including hydrazine synthase HZS and hydrazine dehydrogenase (HDH), as well as hydroxylamine oxidoreductase (HAO). HDH and HAO were active and of sufficient quality for biochemical studies and for HAO, the crystal structure could be determined. The method presented here provides a viable way to obtain materials for the study of proteins not only from the central anammox metabolism but also for the study of other exciting aspects of anammox bacteria, such as for example, their unusual ladderane lipids.
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- 2021
8. Neodymium as Metal Cofactor for Biological Methanol Oxidation: Structure and Kinetics of an XoxF1-Type Methanol Dehydrogenase
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Andreas Dietl, Kerstin-Anikó Seifert, Rob A. Schmitz, Helena Singer, Thomas R. M. Barends, Nunzia Picone, Lena J. Daumann, Huub J. M. Op den Camp, Arjan Pol, and Mike S. M. Jetten
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Lanthanide ,Methanotroph ,Praseodymium ,Inorganic chemistry ,chemistry.chemical_element ,methanol dehydrogenase ,Crystallography, X-Ray ,Lanthanoid Series Elements ,Microbiology ,chemistry.chemical_compound ,methanotrophs ,Bacterial Proteins ,Verrucomicrobia ,Virology ,Lanthanum ,Methylacidiphilum fumariolicum ,lanthanides ,Methylacidimicrobium ,Ecosystem ,Phylogeny ,Neodymium ,PQQ ,Methanol dehydrogenase ,Methanol ,QR1-502 ,Alcohol Oxidoreductases ,Kinetics ,Cerium ,chemistry ,Ecological Microbiology ,Methane ,Oxidation-Reduction ,Research Article - Abstract
The methane-oxidizing bacterium Methylacidimicrobium thermophilum AP8 thrives in acidic geothermal ecosystems that are characterized by high degassing of methane (CH4), H2, H2S, and by relatively high lanthanide concentrations. Lanthanides (atomic numbers 57 to 71) are essential in a variety of high-tech devices, including mobile phones. Remarkably, the same elements are actively taken up by methanotrophs/methylotrophs in a range of environments, since their XoxF-type methanol dehydrogenases require lanthanides as a metal cofactor. Lanthanide-dependent enzymes seem to prefer the lighter lanthanides (lanthanum, cerium, praseodymium, and neodymium), as slower methanotrophic/methylotrophic growth is observed in medium supplemented with only heavier lanthanides. Here, we purified XoxF1 from the thermoacidophilic methanotroph Methylacidimicrobium thermophilum AP8, which was grown in medium supplemented with neodymium as the sole lanthanide. The neodymium occupancy of the enzyme is 94.5% ± 2.0%, and through X-ray crystallography, we reveal that the structure of the active site shows interesting differences from the active sites of other methanol dehydrogenases, such as an additional aspartate residue in close proximity to the lanthanide. Nd-XoxF1 oxidizes methanol at a maximum rate of metabolism (Vmax) of 0.15 ± 0.01 μmol · min-1 · mg protein-1 and an affinity constant (Km) of 1.4 ± 0.6 μM. The structural analysis of this neodymium-containing XoxF1-type methanol dehydrogenase will expand our knowledge in the exciting new field of lanthanide biochemistry. IMPORTANCE Lanthanides comprise a group of 15 elements with atomic numbers 57 to 71 that are essential in a variety of high-tech devices, such as mobile phones, but were considered biologically inert for a long time. The biological relevance of lanthanides became evident when the acidophilic methanotroph Methylacidiphilum fumariolicum SolV, isolated from a volcanic mud pot, could only grow when lanthanides were supplied to the growth medium. We expanded knowledge in the exciting and rapidly developing field of lanthanide biochemistry by the purification and characterization of a neodymium-containing methanol dehydrogenase from a thermoacidophilic methanotroph.
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- 2021
9. Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex
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Guylaine H. L. Nuijten, Naomi M. de Almeida, Mike S. M. Jetten, Kerstin-Anikó Seifert, Thomas R. M. Barends, Andreas Dietl, Mohd Akram, Joachim Reimann, Tadeo Moreno Chicano, L. Dietrich, Elisabeth Hartmann, Daniel Leopoldus, Laura van Niftrik, F. Leidreiter, Ilme Schlichting, Boran Kartal, Kristian Parey, Melanie Mueller, and Ricardo M. Sanchez
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Microbiology (medical) ,Multiprotein complex ,Immunology ,Crystallography, X-Ray ,Applied Microbiology and Biotechnology ,Microbiology ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Bacterial Proteins ,Catalytic Domain ,Genetics ,Nitrite ,Nitrites ,030304 developmental biology ,X-ray crystallography ,chemistry.chemical_classification ,0303 health sciences ,Nitrates ,biology ,Bacteria ,Cryoelectron Microscopy ,Active site ,Cell Biology ,Electron acceptor ,Comammox ,Electron transport chain ,Kinetics ,chemistry ,Nitrite oxidoreductase ,Anammox ,Multiprotein Complexes ,Ecological Microbiology ,biology.protein ,Biophysics ,Cryoelectron tomography ,Oxidoreductases ,Oxidation-Reduction ,030217 neurology & neurosurgery - Abstract
Nitrate is an abundant nutrient and electron acceptor throughout Earth’s biosphere. Virtually all nitrate in nature is produced by the oxidation of nitrite by the nitrite oxidoreductase (NXR) multiprotein complex. NXR is a crucial enzyme in the global biological nitrogen cycle, and is found in nitrite-oxidizing bacteria (including comammox organisms), which generate the bulk of the nitrate in the environment, and in anaerobic ammonium-oxidizing (anammox) bacteria which produce half of the dinitrogen gas in our atmosphere. However, despite its central role in biology and decades of intense study, no structural information on NXR is available. Here, we present a structural and biochemical analysis of the NXR from the anammox bacterium Kuenenia stuttgartiensis, integrating X-ray crystallography, cryo-electron tomography, helical reconstruction cryo-electron microscopy, interaction and reconstitution studies and enzyme kinetics. We find that NXR catalyses both nitrite oxidation and nitrate reduction, and show that in the cell, NXR is arranged in tubules several hundred nanometres long. We reveal the tubule architecture and show that tubule formation is induced by a previously unidentified, haem-containing subunit, NXR-T. The results also reveal unexpected features in the active site of the enzyme, an unusual cofactor coordination in the protein’s electron transport chain, and elucidate the electron transfer pathways within the complex., The oxidoreductase (NXR) multiprotein complex is a key enzyme in the nitrogen cycle. A detailed structural and biochemical characterization of NXR from the anammox bacterium Kuenenia stuttgartiensis shows that this complex is a filament-forming protein that catalysers both nitrite oxidation and nitrate reduction, and elucidates the mechanisms governing complex assembly and function.
- Published
- 2021
10. Structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV and the phylogeny of the aminotransferase pathway
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Tom Berben, Andreas Dietl, Rob A. Schmitz, Melanie J. I. Müller, Thomas R. M. Barends, and Huub J. M. Op den Camp
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Methanotroph ,Lysine ,Biophysics ,Biochemistry ,Research Communications ,03 medical and health sciences ,Bacterial Proteins ,Protein Domains ,Verrucomicrobia ,X-Ray Diffraction ,Structural Biology ,Phylogenetics ,Catalytic Domain ,Genetics ,Methylacidiphilum fumariolicum ,Gene ,Hydro-Lyases ,Phylogeny ,Transaminases ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,ATP synthase ,biology ,030302 biochemistry & molecular biology ,Containment of Biohazards ,Condensed Matter Physics ,4-hydroxy-tetrahydrodipicolinate synthase ,Enzyme ,chemistry ,Ecological Microbiology ,biology.protein ,Protein Multimerization ,Allosteric Site ,Genome, Bacterial - Abstract
The enzyme 4-hydroxy-tetrahydrodipicolinate synthase (DapA) is involved in the production of lysine and precursor molecules for peptidoglycan synthesis. In a multistep reaction, DapA converts pyruvate and L-aspartate-4-semialdehyde to 4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid. In many organisms, lysine binds allosterically to DapA, causing negative feedback, thus making the enzyme an important regulatory component of the pathway. Here, the 2.1 Å resolution crystal structure of DapA from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV is reported. The enzyme crystallized as a contaminant of a protein preparation from native biomass. Genome analysis reveals that M. fumariolicum SolV utilizes the recently discovered aminotransferase pathway for lysine biosynthesis. Phylogenetic analyses of the genes involved in this pathway shed new light on the distribution of this pathway across the three domains of life.
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- 2020
11. A Peltier-cooled microscope stage for protein crystal post-crystallization treatment
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Christian Kieser, Thomas R. M. Barends, and Andreas Dietl
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0301 basic medicine ,Diffraction ,Materials science ,Microscope ,Hydrazine ,macromolecular substances ,010403 inorganic & nuclear chemistry ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,Mosaicity ,0104 chemical sciences ,law.invention ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,Betaine ,Chemical engineering ,chemistry ,law ,Thermoelectric effect ,Crystallization ,Protein crystallization - Abstract
Crystals of the multi-enzyme complex hydrazine synthase showed severe diffuse scattering and high mosaicity. Improved diffraction quality was achieved by soaking the crystals in highly concentrated betaine solutions at reduced temperatures. To enable this, a Peltier-cooled microscope stage was developed for the slow cooling of protein crystals immersed in cryoprotectants or other soaking solutions. Both the construction of the stage and its successful application to hydrazine synthase crystals are described.
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- 2017
12. A nitric oxide-binding heterodimeric cytochrome
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Mohd, Akram, Joachim, Reimann, Andreas, Dietl, Andreas, Menzel, Wouter, Versantvoort, Boran, Kartal, Mike S M, Jetten, and Thomas R M, Barends
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Carbon Monoxide ,Binding Sites ,Bacteria ,Amino Acid Motifs ,Cytochromes c ,Molecular Dynamics Simulation ,Crystallography, X-Ray ,Nitric Oxide ,Protein Structure, Tertiary ,Protein Subunits ,Bacterial Proteins ,Mutagenesis ,Protein Structure and Folding ,Oxidoreductases ,Dimerization ,Oxidation-Reduction - Abstract
Anaerobic ammonium oxidation (anammox) is a microbial process responsible for significant nitrogen loss from the oceans and other ecosystems. The redox reactions at the heart of anammox are catalyzed by large multiheme enzyme complexes that rely on small cytochrome c proteins for electron shuttling. Among the most highly abundant of these cytochromes is a unique heterodimeric complex composed of class I and class II c-type cytochromes called NaxLS, which has distinctive biochemical and spectroscopic properties. Here, we present the 1.7 Å resolution crystal structure of this complex from the anammox organism Kuenenia stuttgartiensis (KsNaxLS). The structure reveals that the heme irons in each subunit exhibit a rare His/Cys ligation, which, as we show by substitution, causes the observed unusual spectral properties. Unlike its individual subunits, the KsNaxLS complex binds nitric oxide (NO) only at the distal heme side, forming 6cNO adducts. This is likely due to steric immobilization of the proximal heme-binding motifs upon complex formation, a finding that may be of functional relevance, because NO is an intermediate in the central anammox metabolism. Pulldown experiments with K. stuttgartiensis cell-free extract showed that the KsNaxLS complex binds specifically to one of the central anammox enzyme complexes, hydrazine synthase, which uses NO as one of its substrates. It is therefore possible that the KsNaxLS complex plays a role in binding the volatile NO to retain it in the cell for transfer to hydrazine synthase. Alternatively, we propose that KsNaxLS may shuttle electrons to this enzyme complex.
- Published
- 2019
13. A 192-heme electron transfer network in the hydrazine dehydrogenase complex
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Joachim Reimann, Kristian Parey, Simone Prinz, Mike S. M. Jetten, Christina Ferousi, Ulrike Mersdorf, Mohd Akram, N.M. de Almeida, Andreas Dietl, Boran Kartal, Jan T. Keltjens, Wouter J. Maalcke, and Thomas R. M. Barends
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Reactive intermediate ,Hydrazine ,chemistry.chemical_element ,Dehydrogenase ,Heme ,010402 general chemistry ,Photochemistry ,Crystallography, X-Ray ,01 natural sciences ,Biochemistry ,Electron Transport ,03 medical and health sciences ,Electron transfer ,chemistry.chemical_compound ,Bacterial Proteins ,Oxidoreductase ,Catalytic Domain ,ddc:570 ,Gram-Negative Bacteria ,Ammonium ,Protein Structure, Quaternary ,Research Articles ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Multidisciplinary ,Binding Sites ,Chemistry ,Cryoelectron Microscopy ,SciAdv r-articles ,Nitrogen ,0104 chemical sciences ,3. Good health ,Anammox ,Ecological Microbiology ,Oxidoreductases ,Research Article - Abstract
A protein complex key to the global nitrogen cycle has an unprecedented electron transport network of 192 heme groups., Anaerobic ammonium oxidation (anammox) is a major process in the biogeochemical nitrogen cycle in which nitrite and ammonium are converted to dinitrogen gas and water through the highly reactive intermediate hydrazine. So far, it is unknown how anammox organisms convert the toxic hydrazine into nitrogen and harvest the extremely low potential electrons (−750 mV) released in this process. We report the crystal structure and cryo electron microscopy structures of the responsible enzyme, hydrazine dehydrogenase, which is a 1.7 MDa multiprotein complex containing an extended electron transfer network of 192 heme groups spanning the entire complex. This unique molecular arrangement suggests a way in which the protein stores and releases the electrons obtained from hydrazine conversion, the final step in the globally important anammox process.
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- 2019
14. A 60-heme reductase complex from an anammox bacterium shows an extended electron transfer pathway
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Thomas R. M. Barends, Boran Kartal, Christina Ferousi, Wouter J. Maalcke, Andreas Dietl, and Mike S. M. Jetten
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chemistry.chemical_classification ,Models, Molecular ,0303 health sciences ,Gram-Negative Anaerobic Bacteria ,Protein family ,Bacteria ,Stereochemistry ,Protein subunit ,030302 biochemistry & molecular biology ,Oxidative phosphorylation ,Electron Transport ,03 medical and health sciences ,chemistry.chemical_compound ,Electron transfer ,chemistry ,Bacterial Proteins ,Structural Biology ,Oxidoreductase ,Covalent bond ,Ecological Microbiology ,Oxidoreductases ,Hydroxylamine Oxidoreductase ,Heme ,030304 developmental biology - Abstract
The hydroxylamine oxidoreductase/hydrazine dehydrogenase (HAO/HDH) protein family constitutes an important group of octaheme cytochromes c (OCCs). The majority of these proteins form homotrimers, with their subunits being covalently attached to each other via a rare cross-link between the catalytic heme moiety and a conserved tyrosine residue in an adjacent subunit. This covalent cross-link has been proposed to modulate the active-site heme towards oxidative catalysis by distorting the heme plane. In this study, the crystal structure of a stable complex of an HAO homologue (KsHAOr) with its diheme cytochrome c redox partner (KsDH) from the anammox bacterium Kuenenia stuttgartiensis was determined. KsHAOr lacks the tyrosine cross-link and is therefore tuned to reductive catalysis. The molecular model of the KsHAOr–KsDH complex at 2.6 Å resolution shows a heterododecameric (α6β6) assembly, which was also shown to be the oligomeric state in solution by analytical ultracentrifugation and multi-angle static light scattering. The 60-heme-containing protein complex reveals a unique extended electron transfer pathway and provides deeper insights into catalysis and electron transfer in reductive OCCs.
- Published
- 2019
15. Characterization of Anammox Hydrazine Dehydrogenase, a Key N-2-producing Enzyme in the Global Nitrogen Cycle
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Mike S. M. Jetten, Nardy Kip, Thomas R. M. Barends, Ulrike Mersdorf, Joachim Reimann, Simon de Vries, Andreas Dietl, Boran Kartal, Jan T. Keltjens, Julea N. Butt, and Wouter J. Maalcke
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0301 basic medicine ,Nitrogen ,030106 microbiology ,Hydrazine ,Dehydrogenase ,Biochemistry ,Catalysis ,03 medical and health sciences ,chemistry.chemical_compound ,Hydroxylamine ,Bacterial Proteins ,Oxidoreductase ,Ammonium Compounds ,Enzyme kinetics ,Molecular Biology ,Hydroxylamine Oxidoreductase ,Heme ,GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries) ,chemistry.chemical_classification ,Cell Biology ,Planctomycetales ,030104 developmental biology ,Hydrazines ,chemistry ,Anammox ,Ecological Microbiology ,Enzymology ,Oxidoreductases ,Oxidation-Reduction - Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria derive their energy for growth from the oxidation of ammonium with nitrite as the electron acceptor. N2, the end product of this metabolism, is produced from the oxidation of the intermediate, hydrazine (N2H4). Previously, we identified N2-producing hydrazine dehydrogenase (KsHDH) from the anammox organism Kuenenia stuttgartiensis as the gene product of kustc0694 and determined some of its catalytic properties. In the genome of K. stuttgartiensis, kustc0694 is one out of ten paralogs related to octaheme hydroxylamine (NH2OH) oxidoreductase (HAO). Here, we characterized KsHDH as a covalently cross-linked homotrimeric octaheme protein as found for HAO and HAOrelated hydroxylamine-oxidizing enzyme kustc1061 (KsHOX) from K. stuttgartiensis. Interestingly, the HDH trimers formed octamers in solution, each octamer harbouring an amazing 192 c-type heme moieties. While HAO and KsHOX are capable of hydrazine oxidation as well, KsHDH was highly specific for this activity. To understand this specificity, we performed detailed amino acid sequence analyses and investigated the catalytic and spectroscopic (electronic absorbance, EPR) properties of KsHDH in comparison with the well-defined HAO and HOX. We conclude that HDH specificity is most likely derived from structural changes around the catalytic heme 4 (“P460”) and of the electron-wiring circuit comprising seven His/His-ligated c-type hemes in each subunit. These nuances make HDH a globally prominent N2-producing enzyme, next to nitrous oxide (N2O) reductase from denitrifying microorganisms.
- Published
- 2016
16. An unexpected reactivity of the P460cofactor in hydroxylamine oxidoreductase
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Andreas Dietl, Thomas R. M. Barends, and Wouter J. Maalcke
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Models, Molecular ,Ethylene Glycol ,Stereochemistry ,Haem peroxidase ,Heme ,Crystallography, X-Ray ,Cofactor ,chemistry.chemical_compound ,Cryoprotective Agents ,Hydroxylamine ,Structural Biology ,Oxidoreductase ,Ammonium Compounds ,polycyclic compounds ,Organic chemistry ,Hydroxylamine Oxidoreductase ,chemistry.chemical_classification ,Binding Sites ,Bacteria ,biology ,Ligand ,digestive, oral, and skin physiology ,General Medicine ,chemistry ,Covalent bond ,Ecological Microbiology ,biology.protein ,Oxidoreductases ,Oxidation-Reduction - Abstract
Hydroxylamine oxidoreductases (HAOs) contain a unique haem cofactor called P460that consists of a profoundly ruffledc-type haem with two covalent bonds between the haem porphyrin and a conserved tyrosine. This cofactor is exceptional in that it abstracts electrons from a ligand bound to the haem iron, whereas other haems involved in redox chemistry usually inject electrons into their ligands. The effects of the tyrosine cross-links and of the haem ruffling on the chemistry of this cofactor have been investigated theoretically but are not yet clear. A new crystal structure of an HAO fromCandidatusKuenenia stuttgartiensis, a model organism for anaerobic ammonium oxidation, now shows that its P460cofactor has yet another unexpected reactivity: when ethylene glycol was used as a cryoprotectant, the 1.8 Å resolution electron-density maps showed additional density which could be interpreted as an ethylene glycol molecule covalently bound to the C16atom of the haem ring, opposite the covalent links to the conserved tyrosine. Possible causes for this unexpected reactivity are discussed.
- Published
- 2015
17. Front Cover: Similar but Not the Same: First Kinetic and Structural Analyses of a Methanol Dehydrogenase Containing a Europium Ion in the Active Site (ChemBioChem 11/2018)
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Thomas R. M. Barends, Carmen Hogendoorn, Arjan Pol, Andreas Dietl, Henning Lumpe, Huub J. M. Op den Camp, Lena J. Daumann, and Bérénice Jahn
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Lanthanide ,Methanol dehydrogenase ,biology ,Organic Chemistry ,Inorganic chemistry ,chemistry.chemical_element ,Active site ,Kinetic energy ,Biochemistry ,Europium ion ,Front cover ,chemistry ,biology.protein ,Molecular Medicine ,Europium ,Molecular Biology - Published
- 2018
18. The inner workings of the hydrazine synthase multiprotein complex
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Simon de Vries, Andreas Dietl, Andreas Menzel, Mike S. M. Jetten, Christina Ferousi, Jan T. Keltjens, Wouter J. Maalcke, Thomas R. M. Barends, and Boran Kartal
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Models, Molecular ,Multiprotein complex ,Hydrazine ,Inorganic chemistry ,Reactive intermediate ,Hydroxylamine ,Crystallography, X-Ray ,Nitric Oxide ,Redox ,chemistry.chemical_compound ,Ammonia ,Multienzyme Complexes ,Catalytic Domain ,Metalloproteins ,Multidisciplinary ,Bacteria ,biology ,Active site ,Combinatorial chemistry ,Hydrazines ,chemistry ,Anammox ,Ecological Microbiology ,biology.protein ,Protein Multimerization - Abstract
Anaerobic ammonium oxidation (anammox) has a major role in the Earth's nitrogen cycle and is used in energy-efficient wastewater treatment. This bacterial process combines nitrite and ammonium to form dinitrogen (N2) gas, and has been estimated to synthesize up to 50% of the dinitrogen gas emitted into our atmosphere from the oceans. Strikingly, the anammox process relies on the highly unusual, extremely reactive intermediate hydrazine, a compound also used as a rocket fuel because of its high reducing power. So far, the enzymatic mechanism by which hydrazine is synthesized is unknown. Here we report the 2.7 Å resolution crystal structure, as well as biophysical and spectroscopic studies, of a hydrazine synthase multiprotein complex isolated from the anammox organism Kuenenia stuttgartiensis. The structure shows an elongated dimer of heterotrimers, each of which has two unique c-type haem-containing active sites, as well as an interaction point for a redox partner. Furthermore, a system of tunnels connects these active sites. The crystal structure implies a two-step mechanism for hydrazine synthesis: a three-electron reduction of nitric oxide to hydroxylamine at the active site of the γ-subunit and its subsequent condensation with ammonia, yielding hydrazine in the active centre of the α-subunit. Our results provide the first, to our knowledge, detailed structural insight into the mechanism of biological hydrazine synthesis, which is of major significance for our understanding of the conversion of nitrogenous compounds in nature.
- Published
- 2015
19. 1H, 13C, and 15N chemical shift assignments of the phosphotyrosine binding domain 2 (PTB2) of human FE65
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Klemens Wild, Andreas Dietl, and Bernd Simon
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chemistry.chemical_classification ,Phosphotyrosine binding ,Scaffold protein ,biology ,Biochemistry ,Cellular signal transduction ,Amino acid ,Protein–protein interaction ,chemistry ,Structural Biology ,Amyloid precursor protein ,biology.protein ,Phosphotyrosine-binding domain - Abstract
Phosphotyrosine binding domains (PTB) are protein–protein interaction domains that play important roles in various cellular signal transduction pathways. The second phosphotyrosine binding domain (PTB2) of the human scaffolding protein FE65 interacts with the C-terminal part of the Amyloid Precursor Protein (APP) involved in Alzheimer’s disease. The structure of PTB2 in complex with a 32 amino acid fragment of APP has been solved previously by X-ray crystallography. Here, we report the NMR spectral assignments of the free FE65 PTB2. This provides the basis for further investigation of the interactions of PTB2 with peptides and small organic ligands with the aim of disrupting the PTB2-APP interaction.
- Published
- 2013
20. Structural insights into biological hydrazine synthesis
- Author
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Frauke Baymann, Andreas Dietl, Mike S. M. Jetten, Joachim Reimann, Christina Ferousi, Wouter J. Maalcke, Thomas R. M. Barends, Boran Kartal, and Jan T. Keltjens
- Subjects
chemistry.chemical_compound ,chemistry ,Chemical engineering ,Ecological Microbiology ,Hydrazine ,Biophysics ,Organic chemistry ,Cell Biology ,GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries) ,Biochemistry - Abstract
Contains fulltext : 163338.pdf (Publisher’s version ) (Closed access)
- Published
- 2016
21. Structural basis of biological NO generation by octaheme oxidoreductases
- Author
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Boran Kartal, Sophie J. Marritt, Julea N. Butt, Wouter J. Maalcke, Andreas Dietl, Thomas R. M. Barends, Mike S. M. Jetten, and Jan T. Keltjens
- Subjects
010402 general chemistry ,Crystallography, X-Ray ,Nitric Oxide ,01 natural sciences ,Biochemistry ,03 medical and health sciences ,chemistry.chemical_compound ,Structure-Activity Relationship ,Protein structure ,Hydroxylamine ,Bacterial Proteins ,Oxidoreductase ,Ammonia ,Nitrosomonas europaea ,Enzyme kinetics ,Molecular Biology ,Hydroxylamine Oxidoreductase ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,biology ,Cell Biology ,respiratory system ,biology.organism_classification ,0104 chemical sciences ,Protein Structure, Tertiary ,Planctomycetales ,Hydrazines ,chemistry ,Anammox ,Ecological Microbiology ,Enzymology ,Oxidoreductases ,human activities ,Oxidation-Reduction ,Bacteria - Abstract
Nitric oxide is an important molecule in all domains of life with significant biological functions in both pro- and eukaryotes. Anaerobic ammonium-oxidizing (anammox) bacteria that contribute substantially to the release of fixed nitrogen into the atmosphere use the oxidizing power of NO to activate inert ammonium into hydrazine (N2H4). Here, we describe an enzyme from the anammox bacterium Kuenenia stuttgartiensis that uses a novel pathway to make NO from hydroxylamine. This new enzyme is related to octaheme hydroxylamine oxidoreductase, a key protein in aerobic ammonium-oxidizing bacteria. By a multiphasic approach including the determination of the crystal structure of the K. stuttgartiensis enzyme at 1.8 Å resolution and refinement and reassessment of the hydroxylamine oxidoreductase structure from Nitrosomonas europaea, both in the presence and absence of their substrates, we propose a model for NO formation by the K. stuttgartiensis enzyme. Our results expand the understanding of the functions that the widespread family of octaheme proteins have.
- Published
- 2014
- Full Text
- View/download PDF
22. Rare earth metals are essential for methanotrophic life in volcanic mudpots
- Author
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Huub J. M. Op den Camp, Ahmad F. Khadem, Thomas R. M. Barends, Jelle Eygensteyn, Mike S. M. Jetten, Arjan Pol, and Andreas Dietl
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PQQ Cofactor ,Volcanic Eruptions ,Crystallography, X-Ray ,Microbiology ,Cofactor ,03 medical and health sciences ,chemistry.chemical_compound ,Pyrroloquinoline quinone ,Bacterial Proteins ,Verrucomicrobia ,Oxidoreductase ,Methylacidiphilum fumariolicum ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,biology ,Methanol dehydrogenase ,030306 microbiology ,biology.organism_classification ,Amino acid ,Alcohol Oxidoreductases ,Enzyme ,Methylobacterium ,chemistry ,Biochemistry ,Ecological Microbiology ,biology.protein ,Metals, Rare Earth ,Methane - Abstract
Summary Growth of Methylacidiphilum fumariolicum SolV, an extremely acidophilic methanotrophic microbe isolated from an Italian volcanic mudpot, is shown to be strictly dependent on the presence of lanthanides, a group of rare earth elements (REEs) such as lanthanum (Ln), cerium (Ce), praseodymium (Pr) and neodymium (Nd). After fractionation of the bacterial cells and crystallization of the methanol dehydrogenase (MDH), it was shown that lanthanides were essential as cofactor in a homodimeric MDH comparable with one of the MDHs of Methylobacterium extorquens AM1. We hypothesize that the lanthanides provide superior catalytic properties to pyrroloquinoline quinone (PQQ)-dependent MDH, which is a key enzyme for both methanotrophs and methylotrophs. Thus far, all isolated MxaF-type MDHs contain calcium as a catalytic cofactor. The gene encoding the MDH of strain SolV was identified to be a xoxF-ortholog, phylogenetically closely related to mxaF. Analysis of the protein structure and alignment of amino acids showed potential REE-binding motifs in XoxF enzymes of many methylotrophs, suggesting that these may also be lanthanide-dependent MDHs. Our findings will have major environmental implications as metagenome studies showed (lanthanide-containing) XoxF-type MDH is much more prominent in nature than MxaF-type enzymes.
- Published
- 2014
23. Optically active transition metal compounds 112. Synthesis of chiral carbonylnitrosylcobalt complexes with bidentate PP∗, PN∗ and NN∗ ligands
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Andreas Dietl, Bernhard Nuber, Henri Brunner, and Peter Faustmann
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Denticity ,Chemistry ,Stereochemistry ,Ligand ,Organic Chemistry ,Diastereomer ,chemistry.chemical_element ,Crystal structure ,Biochemistry ,Triphos ,Inorganic Chemistry ,chemistry.chemical_compound ,Crystallography ,Transition metal ,Materials Chemistry ,Physical and Theoretical Chemistry ,Chirality (chemistry) ,Cobalt - Abstract
The substitution of two carbonyl groups in Co(CO)3(NO) by optically active unsymmetrical bidentate ligands LL∗ yields pairs of diastereomers Co(CO)(NO)(LL∗), which differ only in the configuration at the Co atom. LL∗ can be a bisphosphane, trisphosphane, phosphaneimine or pyridineimine. For the complexes 2 ( LL ∗ = ( S,S)-norphos ), 3 ( LL ∗ = ( R )-1,2,4- triphos ) and 4 ( LL ∗ = ( R )-1,2,5- triphos ) the diastereomer ratios of 45:55 (2a:2b), 83:17 (3a:3b) and 63:37 (4a:4b) respectively indicate an optical induction from the ligand to the metal configuration during the synthesis. By crystallization it is possible to separate the diastereomers of 1 ( LL ∗ = ( R )- prophos ), 2 and 3, 1a and 3a are obtained as pure diastereomers, 2a as an enriched sample (2a:2b 73:27). The crystal structures and absolute configurations of (SCo, RC)-1a and (SCo, RC)-3a were determined by X-ray analysis. In 3a the cobalt center is configurationally stable at room temperature, whereas 1a epimerizes in benzene-d6 at 35°C with a half-life of τ 1 2 = 141 min and 2a in CDCl3 at 24°C with τ 1 2 = 160 min .
- Published
- 1997
24. Efficacy of cultured epithelial autografts in pediatric burns and reconstructive surgery
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Andreas Dietl, Martin Meuli, Rita Gobet, Stefan Altermatt, Claudia Meuli-Simmen, Messod Benathan, and Michael Raghunath
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Male ,Scar Excision ,medicine.medical_specialty ,Reconstructive surgery ,Adolescent ,medicine.medical_treatment ,Scars ,Transplantation, Autologous ,Epithelium ,Cicatrix ,medicine ,Humans ,In patient ,Child ,Cells, Cultured ,Mechanical instability ,business.industry ,Dermabrasion ,Skin Transplantation ,Surgery ,Transplantation ,Plastic surgery ,surgical procedures, operative ,Child, Preschool ,Female ,medicine.symptom ,Burns ,business - Abstract
Background . Cultured epithelial autografts are regularly used in burn patients, but they have not been tested in patients undergoing reconstructive surgery. The aim of this study was to analyze and compare the efficacy of cultured grafts in both burn and reconstructive surgery patients. Methods . In six children with severe and massive burns, full-thickness areas were grafted with cultured grafts. In another six children with hypertrophic or hyperpigmented scars, or both, cultured grafts were used to cover defects resulting from scar excision or deep dermabrasion. Results . In burn surgery the final cover rate averaged 60% (range, 0% to 100%). The functional and cosmetic results were good and at least equivalent to results after conventional grafting. Fragility, infection, and, in particular, mechanical instability of cultured grafts during the first weeks after transplantation were, the main problems encountered. In reconstructive surgery the final cover rate was 100% in all patients. The functional and cosmetic results were very good and considered better than those obtained by using conventional grafting techniques. No major management problems were encountered. Conclusions . In massively burned children, cultured epithelial autografts represent an effective additional and potentially lifesaving method to conventional grafting. Questions remain regarding the use of this technique to treat less severe burns. For resurfacing-type scar revisions, cultured epithelial autografts yield excellent results that appear to be superior to those of conventional techniques.
- Published
- 1997
25. ¹H, ¹³C, and ¹⁵N chemical shift assignments of the phosphotyrosine binding domain 2 (PTB2) of human FE65
- Author
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Andreas, Dietl, Klemens, Wild, and Bernd, Simon
- Subjects
Carbon Isotopes ,Nitrogen Isotopes ,Molecular Sequence Data ,Humans ,Nuclear Proteins ,Nerve Tissue Proteins ,Amino Acid Sequence ,Phosphotyrosine ,Nuclear Magnetic Resonance, Biomolecular ,Sequence Alignment ,Protein Structure, Secondary ,Hydrogen ,Protein Structure, Tertiary - Abstract
Phosphotyrosine binding domains (PTB) are protein-protein interaction domains that play important roles in various cellular signal transduction pathways. The second phosphotyrosine binding domain (PTB2) of the human scaffolding protein FE65 interacts with the C-terminal part of the Amyloid Precursor Protein (APP) involved in Alzheimer's disease. The structure of PTB2 in complex with a 32 amino acid fragment of APP has been solved previously by X-ray crystallography. Here, we report the NMR spectral assignments of the free FE65 PTB2. This provides the basis for further investigation of the interactions of PTB2 with peptides and small organic ligands with the aim of disrupting the PTB2-APP interaction.
- Published
- 2012
26. Phosphorylation of LRP1 regulates the interaction with Fe65
- Author
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Andreas Dietl, Irmgard Sinning, Klemens Wild, Wilfried Klug, and Bernd Simon
- Subjects
LRP1B ,Amino Acid Motifs ,Biophysics ,Nerve Tissue Proteins ,Biology ,Biochemistry ,Protein–protein interaction ,Amyloid beta-Protein Precursor ,Fe65 ,Structural Biology ,Alzheimer Disease ,Phosphotyrosine binding domain (PTB) ,mental disorders ,Genetics ,Amyloid precursor protein ,Humans ,Phosphorylation ,Amyloid precursor protein (APP) ,Protein kinase A ,Molecular Biology ,Ternary complex ,P3 peptide ,Nuclear Proteins ,Cell Biology ,Cell biology ,Protein Structure, Tertiary ,Multiprotein Complexes ,biology.protein ,LDL receptor-related protein 1 (LRP1) ,NPXY ,Amyloid precursor protein secretase ,Low Density Lipoprotein Receptor-Related Protein-1 ,Proto-oncogene tyrosine-protein kinase Src - Abstract
Neuronal Fe65 is a central adapter for the intracellular protein network of Alzheimer’s disease related amyloid precursor protein (APP). It contains a unique tandem array of phosphotyrosine-binding (PTB) domains that recognize NPXY internalization motifs present in the intracellular domains of APP (AICD) and the low-density lipoprotein receptor-related protein LRP1 (LICD). The ternary APP/Fe65/LRP1 complex is an important mediator of APP processing and affects β-amyloid peptide production. Here we dissect by biochemical and biophysical methods the direct interactions within the ternary complex and reveal a phosphorylation-dependent insulin receptor substrate (IRS-) like interaction of the distal NPVY 4507 motif of LICD with Fe65-PTB1. Structured summary of protein interactions APP-AICD and FE65 bind by nuclear magnetic resonance ( View interaction ) Src phosphorylates LRP1-LICD by protein kinase assay ( View interaction ) LRP1-LICD physically interacts with FE65 and APP-AICD by pull down ( View interaction ) FE65-PTB1 and LRP1-LICD bind by nuclear magnetic resonance ( View interaction ) LRP1-LICD binds to FE65-PTB1 by pull down ( View interaction ) APP-AICD binds to FE65-PTB2 by pull down ( View interaction )
- Published
- 2011
27. Urinary oxalate and glycolate excretion in healthy infants and children
- Author
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Andreas Dietl, Ernst Leumann, and A. Matasovic
- Subjects
Molar ,Adolescent ,Oxalate oxidase ,Urinary system ,Oxalic acid ,Urine ,Oxalate ,Excretion ,Random Allocation ,chemistry.chemical_compound ,Animal science ,Reference Values ,Humans ,Medicine ,Child ,Hyperoxaluria ,Oxalates ,Creatinine ,business.industry ,Oxalic Acid ,Infant, Newborn ,Infant ,Glycolates ,Biochemistry ,chemistry ,Nephrology ,Child, Preschool ,Pediatrics, Perinatology and Child Health ,business ,Aluminum - Abstract
The molar ratios of oxalate and glycolate over creatinine were determined in single urine samples of 26 infants and 27 children aged 1-5 years. In 135 children aged 5-16 years, two urine specimens were collected, one before breakfast and one at noon. Oxalate was determined by oxalate oxidase, and glycolate was measured by a colorimetric method (improved chromatotropic acid--sulphuric acid assay after prior purification by cation and anion exchanger). Both ratios (expressed in mmol/mol creatinine and analysed on a log-normal basis) were highest in infants 0-6 months old [mean oxalate 147 (95% confidence interval: 60-360), mean glycolate 175 (72-425)]. The mean oxalate ratio was 72 mmol/mol (29-174) at the age of 7-24 months, 44 (19-101) at the age of 2-5 years and 22 (12-40) in adolescents aged 16 years. Molar glycolate ratios were higher, but disclosed the same pattern. Oxalate and glycolate ratios in fasting urines did not differ significantly from those in noon samples (except glycolate in the oldest age group). Oxalate ratios correlated well with glycolate ratios in children up to 5 years of age only. Random urine samples are thus suitable for screening. However, interpretation of data requires use of age-specific reference values that are based on comparable methods.
- Published
- 1990
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