Towards a Halophenol Dehalogenase from Iodotyrosine Deiodinase Via Computational Design
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Diversity and Mechanisms of Bacterial Dehalogenation Reactions High Number of Halogen Substituents
O.B. Janssen, T. Bosma and G.J. Poelarends Diversity and Mechanisms of 8acterial Dehalogenation Reactions Abstract Halogenated aliphatic compounds occur widespread as environmental pollutants. Since many of these compounds are xenobiotics and show large dif ferences in degradability which can be correlated to critical steps in catabolic pathways, they are suitable for studies on the evolution of dehalogenating pathways. We have investigated the degradation of 1,2-dichloroethane and 1,3- dichloropropene in detail. For both compounds, the initial step is hydrolytic dehalogenation. The 1,2-dichloroethane and 1,3-dichloropropene dehalogenases we re found to belong to different groups of identical enzymes detected in bac teria isolated from various sites. Genetic analysis and adaptation experiments indicated th at the 1,2-dichloroethane degradation pathway may be of recent evolutionary origin. The large-scale use of 1,3-dichloropropene in agriculture may have contributed to the distribution of genes encoding hydrolytic dehalogenases in the environment. Introduction The biodegradation of synthetic chlorinated chemicals that enter the environ ment is dependent on the capacity of microbial enzymes to recognize these xenobiotic molecules and cleave or labilize carbon-halogen bonds (Janssen et al., 1994). Microbiological studies have led to the isolation of a range of organisms that degrade halogenated aliphatic compounds and use them as a carbon source for growth, and a several dehalogenating enzymes that directly act on carbon halogen bonds have now been identified (Leisinger and Bader 1993; Janssen et al., 1994; Fetzner and Lingens, 1994). In a few cases, the carbon-halogen bond is not directly cleaved but labilized by introduction of other functional groups (Ensley, 1991). -
Light-Emitting Dehalogenases: Reconstruction of Multifunctional
Research Article Cite This: ACS Catal. 2019, 9, 4810−4823 pubs.acs.org/acscatalysis Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts Radka Chaloupkova,† Veronika Liskova,† Martin Toul,† Klara Markova,† Eva Sebestova,† Lenka Hernychova,‡ Martin Marek,† Gaspar P. Pinto,†,∥ Daniel Pluskal,† Jitka Waterman,§ Zbynek Prokop,†,∥ and Jiri Damborsky*,†,∥ † Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic ‡ Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic § Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom ∥ International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic *S Supporting Information ABSTRACT: To obtain structural insights into the emergence of biological functions from catalytically promiscuous enzymes, we reconstructed an ancestor of catalytically distinct, but evolutionarily related, haloalkane dehalogenases (EC 3.8.1.5) and Renilla luciferase (EC 1.13.12.5). This ancestor has both hydrolase and monooxygenase activities. Its crystal structure solved to 1.39 Å resolution revealed the presence of a catalytic pentad conserved in both dehalogenase and luciferase descend- ants and a molecular oxygen bound in between two residues typically stabilizing a halogen anion. The differences in the conformational dynamics of the specificity-determining cap domains between the ancestral and descendant enzymes were accessed by molecular dynamics and hydrogen−deuterium exchange mass spectrometry. Stopped-flow analysis revealed that the alkyl enzyme intermediate formed in the luciferase-catalyzed reaction is trapped by blockage of a hydrolytic reaction step. -
Biotransformation of Halogenated Compounds by Lyophilized Cells Of
Biotransformation of halogenated compounds by lyophilized cells of Rhodococcus erythropolis in a continuous solid-gas biofilter Benjamin Erable, Thierry Maugard, Isabelle Goubet, Sylvain Lamare, Marie Dominique Legoy To cite this version: Benjamin Erable, Thierry Maugard, Isabelle Goubet, Sylvain Lamare, Marie Dominique Legoy. Biotransformation of halogenated compounds by lyophilized cells of Rhodococcus erythropolis in a continuous solid-gas biofilter. Process Biochemistry, Elsevier, 2005, vol. 40, pp.45-51. 10.1016/j.procbio.2003.11.031. hal-00782060 HAL Id: hal-00782060 https://hal.archives-ouvertes.fr/hal-00782060 Submitted on 29 Jan 2013 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Open Archive Toulouse Archive Ouverte ( OATAO ) OATAO is an open access repository that collects the work of Toulouse researchers and makes it freely available over the web where possible. This is an author-deposited version published in: http://oatao.univ-toulouse.fr/ Eprints ID: 7878 To link to this article : DOI:10.1016/j.procbio.2003.11.031 URL: http://dx.doi.org/10.1016/j.procbio.2003.11.031 To cite this version: Erable, Benjamin and Maugard, Thierry and Goubet, Isabelle and Lamare, Sylvain and Legoy, Marie Dominique Biotransformation of halogenated compounds by lyophilized cells of Rhodococcus erythropolis in a continuous solid–gas biofilter. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Oxidative Stress and Antioxidant Status in Hypo- and Hyperthyroidism
Chapter 8 Oxidative Stress and Antioxidant Status in Hypo- and Hyperthyroidism Mirela Petrulea, Adriana Muresan and Ileana Duncea Additional information is available at the end of the chapter http://dx.doi.org/10.5772/51018 1. Introduction Thyroid hormones are involved in the regulation of basal metabolic state and in oxidative metabolism [1]. They can cause many changes in the number and activity of mitochondrial respiratory chain components. This may result in the increased generation of reactive oxygen species (ROS) [2,3]. Oxidative stress is a general term used to describe a state of damage caused by ROS [4]. ROS have a high reactivity potential, therefore they are toxic and can lead to oxidative damage in cellular macromolecules such as proteins, lipids and DNA [5]. In fact, the cell contains a variety of substances capable of scavenging the free radicals, protecting them from harmful effects. Among the enzymatic antioxidants, are glutathione reductase (GR), glutathione peroxydase (GPx), catalase (CAT), superoxide dismutase (SOD), while the non-enzymatic antioxidants are glutathione (GSH), vitamin E, vitamin C, β- carotene, and flavonoids [6]. When ROS generation exceeds the antioxidant capacity of cells, oxidative stress develops [7]. Life means a continuous struggle for energy, which is required to fight against entropy. The most effective way to obtain energy is oxidation. Oxidative processes predominantly occur in mitochondria [8]. On the other hand, mitochondria are the favorite targets of thyroid hormones. During thyroid hormone synthesis, there is a constant production of oxygenated water, which is absolutely indispensable for iodine intrafollicular oxidation in the presence of thyroid peroxidase. In recent years, the possible correlation between impaired thyroid gland function and reactive oxygen species has been increasingly taken into consideration [9]. -
ABSTRACT Title of Dissertation: Insight Into the Structure And
ABSTRACT Title of dissertation: Insight into the Structure and Mechanism of Iodotyrosine Deiodinase, the First Mammalian Member of the NADH Oxidase / Flavin Reductase Superfamily James Ambrose Watson, Jr. Doctor of Philosophy, 2006 Dissertation directed by: Professor Steven E. Rokita Department of Chemistry and Biochemistry Iodotyrosine deiodinase (IYD) has remained poorly characterized for nearly 50 years in spite of its function as an iodine salvage pathway and its role in regulation of mammalian basal metabolism. IYD catalyzes the reductive deiodination of both mono- and diiodotyrosine, the iodinated side-products of thyroid hormone production. The Rokita lab previously purified IYD from porcine thyroids and identified a putative dehalogenase gene. The work in this dissertation confirms the identity of the gene that encodes IYD -1 -1 through expression in HEK293 cells (KM = 4.4 ± 1.7 µM and Vmax = 12 ± 1 nmol hr µg ) and, furthermore, identifies IYD as the first mammalian member of the NADH oxidase/flavin reductase superfamily, a protein fold previously found only in bacteria. In addition, a three- dimensional model of the NADH oxidase/flavin reductase domain of IYD was constructed based on the x-ray crystal structure coordinates (Protein Data Bank code 1ICR) of the minor nitroreductase from Escherichia coli. The model also predicts structural features of IYD, including interactions between the flavin bound to IYD and one of three conserved cysteines. To investigate the role of the NADH oxidase/flavin reductase domain plays in electron transfer, two truncation mutants were generated: IYD-NR (residues 81-285) and IYD-∆TM (residues 34-285) encoding transmembrane-domain deleted IYD. -
Characterization of Hydrolytic Dehalogenases
CHARACTERIZATION OF HYDROLYTIC DEHALOGENASES: SUBSTRATE SPECIFICITY AND CARBON ISOTOPE FRACTIONATION A thesis submitted in conformity with the requirements for the degree of Master of Science. Graduate Department of Cell and Systems Biology University of Toronto © Copyright by Christopher Tran (2013) ABSTRACT: Characterization of Hydrolytic Dehalogenases: Substrate Specificity and Carbon Isotope Fractionation: Christopher Tran, 2013, M.Sc., Department of Cell and Systems Biology, University of Toronto The first project is focused on kinetic analysis of two enzymes: Rsc1362 (Ralstonia solanacearum GMI1000) and PA0810 (Pseudomonas aeruginosa PA01). Rsc1362 had a kcat of 504±66 min-1 and a KM of 0.06±0.02 mM, PA0810 had a kcat of 2.6±0.6 min-1 and a KM of 0.44±0.2 mM. A lack of environmental conteXt for a chloroacetate dehalogenase was noted in Pseudomonas aeruginosa PA01. The second project focuses on kinetic and stable isotope fractionation of 1,2- dichloroethane by DhlA (Xanthobacter autotrophicus GJ10), and Jann2620 (Jannaschia CCS1). Although both enzymes had different kinetics (DhlA: KM = 4.8±0.6 mM and kcat = 133±8 min-1, Jann2620: KM = 25.9±2.3 mM and kcat = ~1.7 min-1), they fractionated similarly (ε values of -33.9‰ and -32.9‰ for DhlA and Jann2620, respectively). As calculated AKIE values were similar to the eXpected values of an abiotic reaction, it was determined that neither enzyme masks the intrinsic fractionation. ii Table of Contents ABSTRACT: ............................................................................................................................... -
Iodotyrosine Deiodinase from Selected Phyla Engineered for Bacterial Expression
ABSTRACT Title of Document: IODOTYROSINE DEIODINASE FROM SELECTED PHYLA ENGINEERED FOR BACTERIAL EXPRESSION Jennifer Marilyn Buss Doctor of Philosophy, 2012 Directed By: Professor Steven E. Rokita Department of Chemistry and Biochemistry Iodide is a well known halogen necessary for development. The majority of iodide processing in biological systems occurs in the thyroid gland. Iodide salvage is essential to thyroid hormone metabolism and metabolic regulation. The DEHAL1 gene product iodotyrosine deiodinase (IYD) is responsible for deiodination of the mono- and diiodotyrosine byproducts of thyroid hormone synthesis (triiodothyronine and thyroxine, T3 and T4, respectively). IYD is a membrane-bound flavoprotein comprised of three domains with the catalytic domain belonging to the NADPH oxidase/flavin reductase structural superfamily. This enzyme required engineering for expression of soluble protein in E. coli and was characterized using CD spectra, kinetic rate constants, binding constants of substrates, and crystal structure. Analysis of the crystal structure of IYD indicates a dimer with an active site comprising of both monomers and orienting the C-I bond of iodotyrosine substrate stacking above the N5 of the flavin mononucleotide (FMN) required for activity. The crystal structure also identifies an active site lid that distinguishes IYD from other proteins in the NADPH oxidase/flavin reductase superfamily. Three amino acids (E153, Y157, and K178) on the active site lid form hydrogen bonding and electrostatic contacts with the zwitterionic portion of the substrate. Mutation to any of these three amino acids significantly decreases substrate-binding affinity and enzymatic activity. Homologous sequences of IYD were identified in other organisms and four sequences as representatives from their phyla were expressed in E. -
Repositioning the Catalytic Triad Aspartic Acid of Haloalkane Dehalogenase: Effects on Stability, Kinetics, and Structure
2 Repositioning the Catalytic Triad Aspartic Acid of Haloalkane Dehalogenase: Effects on Stability, Kinetics, and Structure Geja H. Krooshof, Edwin M. Kwant, Jiří Damborský, Jaroslav Koča, and Dick B. Janssen Biochemistry 36, 9571–9580 (1997) Chapter 2 Repositioning the Catalytic Triad Aspartic Acid of Haloalkane Dehalogenase: Effects on Stability, Kinetics, and Structure Haloalkane dehalogenase (DhlA) catalyzes the hydrolysis of haloalkanes via an alkyl– enzyme intermediate. The covalent intermediate, which is formed by nucleophilic substitution with Asp124, is hydrolyzed by a water molecule that is activated by His289. The role of Asp260, which is the third member of the catalytic triad, was studied by site-directed mutagenesis. Mutation of Asp260 to asparagine resulted in a catalytically inactive D260N mutant, which demonstrates that the triad acid Asp260 is essential for dehalogenase activity. Furthermore, Asp260 has an important structural role, since the D260N enzyme accumulated mainly in inclusion bodies during expression, and neither substrate nor product could bind in the active site cavity. Activity for brominated substrates was restored to D260N by replacing Asn148 with an aspartic or glutamic acid. Both double mutants D260N+N148D and D260N+N148E had a 10-fold reduced kcat and 40-fold higher Km values for 1,2-dibromoethane compared to the wild-type enzyme. Pre-steady-state kinetic analysis of the D260N+N148E double mutant showed that the decrease in kcat was mainly caused by a 220-fold reduction of the rate of carbon–bromine bond cleavage and a 10-fold decrease in the rate of hydrolysis of the alkyl–enzyme intermediate. On the other hand, bromide was released 12-fold faster and via a different pathway than in the wild-type enzyme. -
University of Groningen Bacterial Growth on Halogenated
University of Groningen Bacterial Growth on Halogenated Aliphatic Hydrocarbons Janssen, Dick B.; Oppentocht, Jantien E.; Poelarends, Gerrit J. Published in: EPRINTS-BOOK-TITLE IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2003 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Janssen, D. B., Oppentocht, J. E., & Poelarends, G. J. (2003). Bacterial Growth on Halogenated Aliphatic Hydrocarbons: Genetics and Biochemistry. In EPRINTS-BOOK-TITLE Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 12-11-2019 Chapter 7 BACTERIAL GROWTH ON HALOGENATED ALIPHATIC HYDROCARBONS: GENETICS AND BIOCHEMISTRY DICK B. JANSSEN, JANTIEN E. OPPENTOCHT AND GERRIT J. POELARENDS Biochemical Laboratory, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands 1. INTRODUCTION Many synthetically produced halogenated aliphatic compounds are xenobiotic chemicals in the sense that they do not naturally occur on earth at biologically significant concentrations. -
Effects of Inorganic Iodide on the Intermediary Carbohydrate Metabolism of Surviving Sheep Thyroid Slices
EFFECTS OF INORGANIC IODIDE ON THE INTERMEDIARY CARBOHYDRATE METABOLISM OF SURVIVING SHEEP THYROID SLICES William L. Green, Sidney H. Ingbar J Clin Invest. 1963;42(11):1802-1815. https://doi.org/10.1172/JCI104865. Research Article Find the latest version: https://jci.me/104865/pdf Journal of Clinical Investigation Vol. 42, No. 11, 1963 EFFECTS OF INORGANIC IODIDE ON THE INTERMEDIARY CARBOHYDRATE METABOLISM OF SURVIVING SHEEP THYROID SLICES * By WILLIAM L. GREEN t AND SIDNEY H. INGBAR t (From the Thorndike Memorial Laboratory and Second and Fourth [Harvard] Medical Services, Boston City Hospital, and the Department of Medicine, Harvard Medical School, Boston, Mass.; and the Department of Medicine, Seton Hall College of Medicine, Jersey City, N. J.) (Submitted for publication April 2, 1963; accepted July 31, 1963) The rate of hormone formation by the thyroid changes in the rate of hormone formation in- in vivo is greatly influenced by acute alterations duced by varying the availability of iodide to thy- in the concentration of inorganic iodide in the roid slices in vitro are associated with, or can be extracellular fluid. In the rat (1-3) and in man ascribed to, alterations of intermediary metabolism (4, 5), increasing concentrations of iodide in the within the thyroid. A preliminary report of these plasma are associated with increased thyroidal studies has appeared (17). uptake of iodine until a critical concentration of iodide is reached. Beyond this range, the forma- METHODS tion of hormone declines. A similar relationship Preparation of slices. Thyroid glands were obtained between extracellular iodide concentration and from freshly killed sheep and were brought from the organic iodinations occurs in vitro in slices of abattoir to the laboratory packed in ice. -
Štítná Žláza
Thyroid gland • Glandula thyroidea (15 - 20 g, frontal side of trachea under thyroid cartilage • Two lobes connected by thyroidal isthmus, lobus pyramidalis • Strong vascularization • Round follicles (acini) with one layer of follicular cells (T3/T4) • Cavity filled with colloid • Capillaries with fenestrations • Parafollicular (C-) cells (calcitonin) • From day 29 of gravidity (Tg), T4 – 11th week Follicles are the basic functional units of thyroid gland Iodine and hormone secretion – general view • NIS (Na+/I- symporter) • PDS (pendrin) • TPO (thyroidal peroxidase) • TG homodimers and their iodation – MIT and DIT • DUOX1 and 2 – together with TPO oxidation of iodide and transportation to TG structure • TPO - connection DIT+DIT (T4) or DIT+MIT (T3) • Pinocytosis and phagolysosomes • Deiodation of MIT and DIT – DEHAL1 (iodotyrosine dehalogenase) • Other proteins (TSHR) • Transcriptional factors (TTF-1, TTF-2, PAX8, HNF-3) Dietary iodine - Bioavailability of organic and inorganic I - ECF + Ery, saliva, gastric juice - breast milk - I- filtered with passive reabsorption 60 – 70 % Clinical relevance - loss through stool (10 – 20 mg/day) - Endemic goiter - Endemic cretinism - Highest daily intake in Japan (several mg) - In many countries on decrease – eating habits Iodine fate in follicular cells NIS DEHAL1 - Concentration of I in follicular cells -MIT and DIT, iodine recyclation - - - - Transport of other ions (TcO4 , ClO4 , SCN ) – clinical significance - Salivary glands, mammary gland, choroid plexus, gastric IYD mucosa, cytotrophoblast,