CATALYTIC PROFICIENCY: the Unusual Case of OMP Decarboxylase
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Arginine Enzymatic Deprivation and Diet Restriction for Cancer Treatment
Brazilian Journal of Pharmaceutical Sciences Review http://dx.doi.org/10.1590/s2175-97902017000300200 Arginine enzymatic deprivation and diet restriction for cancer treatment Wissam Zam* Al-Andalus University for Medical Sciences, Faculty of Pharmacy, Analytical and Food Chemistry, Tartous, Syrian Arab Republic Recent findings in amino acid metabolism and the differences between normal, healthy cells and neoplastic cells have revealed that targeting single amino acid metabolic enzymes in cancer therapy is a promising strategy for the development of novel therapeutic agents. Arginine is derived from dietary protein intake, body protein breakdown, or endogenous de novo arginine production and several studies have revealed disturbances in its synthesis and metabolism which could enhance or inhibit tumor cell growth. Consequently, there has been an increased interest in the arginine-depleting enzymes and dietary deprivation of arginine and its precursors as a potential antineoplastic therapy. This review outlines the most recent advances in targeting arginine metabolic pathways in cancer therapy and the different chemo- and radio-therapeutic approaches to be co-applied. Key words: Arginine-depleting enzyme/antineoplastic therapy. Dietary deprivation. INTRODUCTION variety of human cancer cells have been found to be auxotrophic for arginine, depletion of which results in Certain cancers may be auxotrophic for a particular cell death (Tytell, Neuman, 1960; Kraemer, 1964; Dillon amino acid, and amino acid deprivation is one method to et al., 2004). Arginine can be degraded by three enzymes: treat these tumors. The strategy of enzymatic degradation arginase, arginine decarboxylase and arginine deiminase of amino acids to deprive malignant cells of important (ADI). Both arginine decarboxylase and ADI are not nutrients is an established component of induction therapy expressed in mammalian cells (Morris, 2007; Miyazaki of several tumor cells. -
Current IUBMB Recommendations on Enzyme Nomenclature and Kinetics$
Perspectives in Science (2014) 1,74–87 Available online at www.sciencedirect.com www.elsevier.com/locate/pisc REVIEW Current IUBMB recommendations on enzyme nomenclature and kinetics$ Athel Cornish-Bowden CNRS-BIP, 31 chemin Joseph-Aiguier, B.P. 71, 13402 Marseille Cedex 20, France Received 9 July 2013; accepted 6 November 2013; Available online 27 March 2014 KEYWORDS Abstract Enzyme kinetics; The International Union of Biochemistry (IUB, now IUBMB) prepared recommendations for Rate of reaction; describing the kinetic behaviour of enzymes in 1981. Despite the more than 30 years that have Enzyme passed since these have not subsequently been revised, though in various respects they do not nomenclature; adequately cover current needs. The IUBMB is also responsible for recommendations on the Enzyme classification naming and classification of enzymes. In contrast to the case of kinetics, these recommenda- tions are kept continuously up to date. & 2014 The Author. Published by Elsevier GmbH. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/). Contents Introduction...................................................................75 Kinetics introduction...........................................................75 Introduction to enzyme nomenclature ................................................76 Basic definitions ................................................................76 Rates of consumption and formation .................................................76 Rate of reaction .............................................................76 -
Collection of Information on Enzymes a Great Deal of Additional Information on the European Union Is Available on the Internet
European Commission Collection of information on enzymes A great deal of additional information on the European Union is available on the Internet. It can be accessed through the Europa server (http://europa.eu.int). Luxembourg: Office for Official Publications of the European Communities, 2002 ISBN 92-894-4218-2 © European Communities, 2002 Reproduction is authorised provided the source is acknowledged. Final Report „Collection of Information on Enzymes“ Contract No B4-3040/2000/278245/MAR/E2 in co-operation between the Federal Environment Agency Austria Spittelauer Lände 5, A-1090 Vienna, http://www.ubavie.gv.at and the Inter-University Research Center for Technology, Work and Culture (IFF/IFZ) Schlögelgasse 2, A-8010 Graz, http://www.ifz.tu-graz.ac.at PROJECT TEAM (VIENNA / GRAZ) Werner Aberer c Maria Hahn a Manfred Klade b Uli Seebacher b Armin Spök (Co-ordinator Graz) b Karoline Wallner a Helmut Witzani (Co-ordinator Vienna) a a Austrian Federal Environmental Agency (UBA), Vienna b Inter-University Research Center for Technology, Work, and Culture - IFF/IFZ, Graz c University of Graz, Department of Dermatology, Division of Environmental Dermatology, Graz Executive Summary 5 EXECUTIVE SUMMARY Technical Aspects of Enzymes (Chapter 3) Application of enzymes (Section 3.2) Enzymes are applied in various areas of application, the most important ones are technical use, manufacturing of food and feedstuff, cosmetics, medicinal products and as tools for re- search and development. Enzymatic processes - usually carried out under mild conditions - are often replacing steps in traditional chemical processes which were carried out under harsh industrial environments (temperature, pressures, pH, chemicals). Technical enzymes are applied in detergents, for pulp and paper applications, in textile manufacturing, leather industry, for fuel production and for the production of pharmaceuticals and chiral substances in the chemical industry. -
The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota. -
(12) Patent Application Publication (10) Pub. No.: US 2009/0292100 A1 Fiene Et Al
US 20090292100A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2009/0292100 A1 Fiene et al. (43) Pub. Date: Nov. 26, 2009 (54) PROCESS FOR PREPARING (86). PCT No.: PCT/EP07/57646 PENTAMETHYLENE 1.5-DIISOCYANATE S371 (c)(1), (75) Inventors: Martin Fiene, Niederkirchen (DE): (2), (4) Date: Jan. 9, 2009 (DE);Eckhard Wolfgang Stroefer, Siegel, Mannheim (30) Foreign ApplicationO O Priority Data Limburgerhof (DE); Stephan Aug. 1, 2006 (EP) .................................. O61182.56.4 Freyer, Neustadt (DE); Oskar Zelder, Speyer (DE); Gerhard Publication Classification Schulz, Bad Duerkheim (DE) (51) Int. Cl. Correspondence Address: CSG 18/00 (2006.01) OBLON, SPIVAK, MCCLELLAND MAIER & CD7C 263/2 (2006.01) NEUSTADT, L.L.P. CI2P I3/00 (2006.01) 194O DUKE STREET CD7C 263/10 (2006.01) ALEXANDRIA, VA 22314 (US) (52) U.S. Cl. ........... 528/85; 560/348; 435/128; 560/347; 560/355 (73) Assignee: BASFSE, LUDWIGSHAFEN (DE) (57) ABSTRACT (21) Appl. No.: 12/373,088 The present invention relates to a process for preparing pen tamethylene 1,5-diisocyanate, to pentamethylene 1,5-diiso (22) PCT Filed: Jul. 25, 2007 cyanate prepared in this way and to the use thereof. US 2009/0292100 A1 Nov. 26, 2009 PROCESS FOR PREPARING ene diisocyanates, especially pentamethylene 1,4-diisocyan PENTAMETHYLENE 1.5-DIISOCYANATE ate. Depending on its preparation, this proportion may be up to several % by weight. 0014. The pentamethylene 1,5-diisocyanate prepared in 0001. The present invention relates to a process for pre accordance with the invention has, in contrast, a proportion of paring pentamethylene 1,5-diisocyanate, to pentamethylene the branched pentamethylene diisocyanate isomers of in each 1.5-diisocyanate prepared in this way and to the use thereof. -
Metalloenzymes: Native Co-Factor Or Experimental Artifact? Marcy Hernick* Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
nalytic A al & B y i tr o s c i h e Hernick, Biochem Anal Biochem 2012, 1:6 m m e Biochemistry & i h s c t r o DOI: 10.4172/2161-1009.1000e120 i y B ISSN: 2161-1009 Analytical Biochemistry Editorial Open Access Metalloenzymes: Native Co-factor or Experimental Artifact? Marcy Hernick* Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA There has been much interest in the biochemical characterization metallohydrolases. Superoxide dismutase (SOD) is an example of a of metalloenzymes, owing in part to past successes in targeting metalloenzyme that utilizes Mn2+, Fe2+, or Mn/Fe as native co-factors metalloenzymes for the development of therapeutic agents. It is across different species [16-20]. (Note: The cited references offer just a estimated that ~10% of approved drugs target metalloenzymes, [1] such small sampling of the research examining SOD co-factor preferences). as carbonic anhydrase, matrix metalloprotesases, and angiotensin- These detailed studies on SOD reinforce the important contributions converting enzyme [2-5]. Inhibitors of metalloenzymes typically that metal ion availability and experimental conditions have on contain a metal-binding group that targets the catalytic metal ion, identifying the native co-factor(s) preferences of metalloenzymes. and therefore, inhibitor affinity is affected by changes to the catalytic In addition to metalloenzymes that prefer a single co-factor as metal ion. Consequently, the development of therapeutically effective described above, there are also increasing numbers of cambialistic inhibitors requires that the biologically relevant form(s) of the enzyme enzymes that can utilize multiple co-factors in vivo has been identified. -
Supplementary Informations SI2. Supplementary Table 1
Supplementary Informations SI2. Supplementary Table 1. M9, soil, and rhizosphere media composition. LB in Compound Name Exchange Reaction LB in soil LBin M9 rhizosphere H2O EX_cpd00001_e0 -15 -15 -10 O2 EX_cpd00007_e0 -15 -15 -10 Phosphate EX_cpd00009_e0 -15 -15 -10 CO2 EX_cpd00011_e0 -15 -15 0 Ammonia EX_cpd00013_e0 -7.5 -7.5 -10 L-glutamate EX_cpd00023_e0 0 -0.0283302 0 D-glucose EX_cpd00027_e0 -0.61972444 -0.04098397 0 Mn2 EX_cpd00030_e0 -15 -15 -10 Glycine EX_cpd00033_e0 -0.0068175 -0.00693094 0 Zn2 EX_cpd00034_e0 -15 -15 -10 L-alanine EX_cpd00035_e0 -0.02780553 -0.00823049 0 Succinate EX_cpd00036_e0 -0.0056245 -0.12240603 0 L-lysine EX_cpd00039_e0 0 -10 0 L-aspartate EX_cpd00041_e0 0 -0.03205557 0 Sulfate EX_cpd00048_e0 -15 -15 -10 L-arginine EX_cpd00051_e0 -0.0068175 -0.00948672 0 L-serine EX_cpd00054_e0 0 -0.01004986 0 Cu2+ EX_cpd00058_e0 -15 -15 -10 Ca2+ EX_cpd00063_e0 -15 -100 -10 L-ornithine EX_cpd00064_e0 -0.0068175 -0.00831712 0 H+ EX_cpd00067_e0 -15 -15 -10 L-tyrosine EX_cpd00069_e0 -0.0068175 -0.00233919 0 Sucrose EX_cpd00076_e0 0 -0.02049199 0 L-cysteine EX_cpd00084_e0 -0.0068175 0 0 Cl- EX_cpd00099_e0 -15 -15 -10 Glycerol EX_cpd00100_e0 0 0 -10 Biotin EX_cpd00104_e0 -15 -15 0 D-ribose EX_cpd00105_e0 -0.01862144 0 0 L-leucine EX_cpd00107_e0 -0.03596182 -0.00303228 0 D-galactose EX_cpd00108_e0 -0.25290619 -0.18317325 0 L-histidine EX_cpd00119_e0 -0.0068175 -0.00506825 0 L-proline EX_cpd00129_e0 -0.01102953 0 0 L-malate EX_cpd00130_e0 -0.03649016 -0.79413596 0 D-mannose EX_cpd00138_e0 -0.2540567 -0.05436649 0 Co2 EX_cpd00149_e0 -
NIH Public Access Author Manuscript Curr Opin Chem Biol
NIH Public Access Author Manuscript Curr Opin Chem Biol. Author manuscript; available in PMC 2010 October 1. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Curr Opin Chem Biol. 2009 October ; 13(4): 468±476. doi:10.1016/j.cbpa.2009.06.023. Pyridoxal 5'-Phosphate: Electrophilic Catalyst Extraordinaire John P. Richard†,*, Tina L. Amyes†, Juan Crugeiras#, and Ana Rios# †Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA. #Departamento de Química Física, Facultad de Química, Universidad de Santiago, 15782 Santiago de Compostela, Spain. Abstract Studies of nonenzymatic electrophilic catalysis of carbon deprotonation of glycine show that pyridoxal 5'-phosphate (PLP) strongly enhances the carbon acidity of α-amino acids, but that this is not the overriding mechanistic imperative for cofactor catalysis. Although the fully protonated PLP-glycine iminium ion adduct exhibits an extraordinary low α-imino carbon acidity (pKa = 6), the more weakly acidic zwitterionic iminium ion adduct (pKa = 17) is selected for use in enzymatic reactions. The similar α-imino carbon acidities of the iminium ion adducts of glycine with 5'- deoxypyridoxal and with phenylglyoxylate shows that the cofactor pyridine nitrogen plays a relatively minor role in carbanion stabilization. The 5'-phosphodianion group of PLP likely plays an important role in catalysis by providing up to 12 kcal/mol of binding energy that may be utilized for transition state stabilization. Introduction Scientists prize the rush of adrenalin that comes with making an original discovery, or with bringing order to seemingly disconnected experimental observations. Snell and Braunstein must have received tremendous satisfaction from their independent discovery, more than sixty years ago, that heating pyridoxal 5'-phosphate (PLP) with an amino acid yields the products of transamination of the amino acid [1]. -
Fmicb-07-01854
Temporal Metagenomic and Metabolomic Characterization of Fresh Perennial Ryegrass Degradation by Rumen Bacteria Mayorga, O. L., Kingston-Smith, A. H., Kim, E. J., Allison, G. G., Wilkinson, T. J., Hegarty, M. J., Theodorou, M. K., Newbold, C. J., & Huws, S. A. (2016). Temporal Metagenomic and Metabolomic Characterization of Fresh Perennial Ryegrass Degradation by Rumen Bacteria. Frontiers in Microbiology, 7, 1854. https://doi.org/10.3389/fmicb.2016.01854 Published in: Frontiers in Microbiology Document Version: Publisher's PDF, also known as Version of record Queen's University Belfast - Research Portal: Link to publication record in Queen's University Belfast Research Portal Publisher rights Copyright 2017 the authors. This is an open access article published under a Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. General rights Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws. If you discover content in the Research Portal that you believe breaches copyright or violates any law, please contact [email protected]. Download date:07. -
Expression of Manganese Superoxide Dismutase in Ovine Kidney Cortex During Development
003 I-3998/94/350 1-004 1 $03.00/0 PEDIATRIC RESEARCH Vol. 35, No. 1, 1994 Copyright O 1993 International Pediatric Research Foundation, Inc. Printed in U.S.A. Expression of Manganese Superoxide Dismutase in Ovine Kidney Cortex during Development G. M. R. CARBONE, D. K. ST. CLAIR, Y. ANNE XU, AND J. C. ROSE Department of Physiology and Pharmacology, Perinatal Research Laboratories, Bowman Gray School of Medicine of Wake Forest University, Winston-Salem.North Carolina 27157[G.M.R.C.,J.C.R.], and Graduate Center for Toxicology, University of Kentucky, Lexington, Kentucky 40506-0054 [D.K.St.C.,Y.A.X.] ABSTRACT. Manganese superoxide dismutase (MnSOD) Recent data indicate that the activity of antioxidant enzymes is one of the main antioxidant enzymes in mammalian is developmentally regulated in the kidney as it is in the lung. tissue. Previous studies have shown that the activity of MnSOD activity has been shown to increase in guinea pig and MnSOD increases in the rat kidney during development. rat kidney from fetal to the adult period (2, 7). In addition, To define further the developmental change in MnSOD MnSOD has been also detected by immunohistochemistry in activity and better understand some of the steps involved kidney cortex and medulla in the Syrian hamster and the staining in the control of MnSOD expression during kidney devel- increases progressively during development (8). opment, we measured MnSOD messenger RNA and en- Therefore, to understand better the mechanisms of MnSOD zyme activity in the ovine kidney cortex during fetal life, expression in the developing kidney, we measured MnSOD in the newborn period, and in adults. -
Unravelling the Mechanism of Fdc1, a Novel Prfmn Dependent Decarboxylase
Unravelling the Mechanism of Fdc1, a Novel prFMN Dependent Decarboxylase A thesis submitted to the University of Manchester for the degree of Doctor in Philosophy (PhD) in the Faculty of Science and Engineering School of Chemistry Samuel S. Bailey 2018 Table of Contents 1 Abstract and Preface 0 1.1 Abstract 0 1.2 Declaration 1 1.3 Copyright Statement 1 1.4 Acknowledgments 2 1.5 Preface to Journal Format 3 2 Introduction 5 2.1 Project Outline 5 2.2 Biofuels 5 2.2.1 Second generation biofuels 6 2.3 Flavoenzymes 7 2.3.1 Covalent Modifications of Flavins 9 2.3.2 The Reactions of Flavin with Oxygen 10 2.4 Diels-Alderases: [4+2] Cycloaddition in Natural Product Biosynthesis 12 2.4.1 Artificial Diels-Alderases 13 2.4.2 Natural Diels-Alderases 13 2.5 The Role of Substrate Strain in Enzymatic Catalysis 14 2.5.1 Substrate Strain in Chelatases 15 2.5.2 Substrate Strain in Lysozyme 15 2.5.3 Substrate Strain in Human Transketolase 16 2.6 Enzymatic Decarboxylation 18 2.6.1 Cofactor Independent Decarboxylases 18 2.6.2 Thiamine Pyrophosphate (TPP) Dependent Decarboxylases 20 2.6.3 Pyridoxal 5’-phosphate (PLP) Dependent Decarboxylases 20 2.6.4 Flavin dependent decarboxylases 21 2.7 The UbiX/UbiD and Pad/Fdc systems 22 2.7.1 UbiX is responsible for the synthesis of a novel flavin cofactor 23 2.7.2 Fdc1 uses prFMN for decarboxylation 26 2.7.3 The structure of A. niger Fdc1 27 2.7.4 Proposed Mechanism of Decarboxylation by Fdc1 27 2.8 Other UbiD enzymes 29 1 2.8.1 The UbiD Superfamily 29 2.8.2 Common themes among the UbiD superfamily 31 2.9 Unravelling the -
Development Perspective of Bioelectrocatalysis-Based Biosensors
sensors Review Development Perspective of Bioelectrocatalysis-Based Biosensors , Taiki Adachi, Yuki Kitazumi, Osamu Shirai and Kenji Kano * y Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan; [email protected] (T.A.); [email protected] (Y.K.); [email protected] (O.S.) * Correspondence: [email protected] Present address: Center for Advanced Science and Innovation, Kyoto University, Gokasho, Uji, y Kyoto 611-0011, Japan. Received: 19 July 2020; Accepted: 25 August 2020; Published: 26 August 2020 Abstract: Bioelectrocatalysis provides the intrinsic catalytic functions of redox enzymes to nonspecific electrode reactions and is the most important and basic concept for electrochemical biosensors. This review starts by describing fundamental characteristics of bioelectrocatalytic reactions in mediated and direct electron transfer types from a theoretical viewpoint and summarizes amperometric biosensors based on multi-enzymatic cascades and for multianalyte detection. The review also introduces prospective aspects of two new concepts of biosensors: mass-transfer-controlled (pseudo)steady-state amperometry at microelectrodes with enhanced enzymatic activity without calibration curves and potentiometric coulometry at enzyme/mediator-immobilized biosensors for absolute determination. Keywords: current–potential curve; multi-enzymatic cascades; multianalyte detection; mass-transfer-controlled amperometric response; potentiometric coulometry 1. Introduction Electron transfer reactions such as photosynthesis, respiration and metabolisms play an important role in all living things. A huge variety of redox enzymes catalyze the oxidation and reduction of couples of two inherent substrates. Usually, the electrons are transferred between the two substrates through a cofactor(s) that is covalently or non-covalently bound to the redox enzymes.