Modern Biocatalysis: Advances Towards Synthetic Biological Systems

Total Page:16

File Type:pdf, Size:1020Kb

Modern Biocatalysis: Advances Towards Synthetic Biological Systems Modern Biocatalysis Advances Towards Synthetic Biological Systems Catalysis Series Series editors: Bert Klein Gebbink, Utrecht University, The Netherlands Jose Rodriguez, Brookhaven National Laboratory, USA Titles in the series: 1: Carbons and Carbon Supported Catalysts in Hydroprocessing 2: Chiral Sulfur Ligands: Asymmetric Catalysis 3: Recent Developments in Asymmetric Organocatalysis 4: Catalysis in the Refining of Fischer–Tropsch Syncrude 5: Organocatalytic Enantioselective Conjugate Addition Reactions: A Powerful Tool for the Stereocontrolled Synthesis of Complex Molecules 6: N-Heterocyclic Carbenes: From Laboratory Curiosities to Efficient Synthetic Tools 7: P-Stereogenic Ligands in Enantioselective Catalysis 8: Chemistry of the Morita–Baylis–Hillman Reaction 9: Proton-Coupled Electron Transfer: A Carrefour of Chemical Reactivity Traditions 10: Asymmetric Domino Reactions 11: C–H and C–X Bond Functionalization: Transition Metal Mediation 12: Metal Organic Frameworks as Heterogeneous Catalysts 13: Environmental Catalysis Over Gold-Based Materials 14: Computational Catalysis 15: Catalysis in Ionic Liquids: From Catalyst Synthesis to Application 16: Economic Synthesis of Heterocycles: Zinc, Iron, Copper, Cobalt, Manganese and Nickel Catalysts 17: Metal Nanoparticles for Catalysis: Advances and Applications 18: Heterogeneous Gold Catalysts and Catalysis 19: Conjugated Linoleic Acids and Conjugated Vegetable Oils 20: Enantioselective Multicatalysed Tandem Reactions 21: New Trends in Cross-Coupling: Theory and Applications 22: Atomically-Precise Methods for Synthesis of Solid Catalysts 23: Nanostructured Carbon Materials for Catalysis 24: Heterocycles from Double-Functionalized Arenes: Transition Metal Catalyzed Coupling Reactions 25: Asymmetric Functionalization of C–H Bonds 26: Enantioselective Nickel-catalysed Transformations 27: N-Heterocyclic Carbenes: From Laboratory Curiosities to Efficient Synthetic Tools, 2nd edition 28: Zeolites in Catalysis: Properties and Applications 29: Biocatalysis: An Industrial Perspective 30: Dienamine Catalysis for Organic Synthesis 31: Metal-free Functionalized Carbons in Catalysis: Synthesis, Characterization and Applications 32: Modern Biocatalysis: Advances Towards Synthetic Biological Systems How to obtain future titles on publication: A standing order plan is available for this series. A standing order will bring delivery of each new volume immediately on publication. For further information please contact: Book Sales Department, Royal Society of Chemistry, Thomas Graham House, Science Park, Milton Road, Cambridge, CB4 0WF, UK Telephone: þ44 (0)1223 420066, Fax: þ44 (0)1223 420247 Email: [email protected] Visit our website at www.rsc.org/books Modern Biocatalysis Advances Towards Synthetic Biological Systems Edited by Gavin Williams North Carolina State University, USA Email: [email protected] and Me´lanie Hall University of Graz, Austria Email: [email protected] Catalysis Series No. 32 Print ISBN: 978-1-78262-726-5 PDF ISBN: 978-1-78801-045-0 EPUB ISBN: 978-1-78801-453-3 ISSN: 1757-6725 A catalogue record for this book is available from the British Library r The Royal Society of Chemistry 2018 All rights reserved Apart from fair dealing for the purposes of research for non-commercial purposes or for private study, criticism or review, as permitted under the Copyright, Designs and Patents Act 1988 and the Copyright and Related Rights Regulations 2003, this publication may not be reproduced, stored or transmitted, in any form or by any means, without the prior permission in writing of The Royal Society of Chemistry or the copyright owner, or in the case of reproduction in accordance with the terms of licences issued by the Copyright Licensing Agency in the UK, or in accordance with the terms of the licences issued by the appropriate Reproduction Rights Organization outside the UK. Enquiries concerning reproduction outside the terms stated here should be sent to The Royal Society of Chemistry at the address printed on this page. Whilst this material has been produced with all due care, The Royal Society of Chemistry cannot be held responsible or liable for its accuracy and completeness, nor for any consequences arising from any errors or the use of the information contained in this publication. The publication of advertisements does not constitute any endorsement by The Royal Society of Chemistry or Authors of any products advertised. The views and opinions advanced by contributors do not necessarily reflect those of The Royal Society of Chemistry which shall not be liable for any resulting loss or damage arising as a result of reliance upon this material. The Royal Society of Chemistry is a charity, registered in England and Wales, Number 207890, and a company incorporated in England by Royal Charter (Registered No. RC000524), registered office: Burlington House, Piccadilly, London W1J 0BA, UK, Telephone: þ44 (0) 207 4378 6556. For further information see our web site at www.rsc.org Printed in the United Kingdom by CPI Group (UK) Ltd, Croydon, CR0 4YY, UK Preface Biocatalysis—the use of enzymes for chemical transformations—has a long history in providing mankind with all sorts of molecules. While early processes almost exclusively relied on naturally occurring whole-cell sys- tems, the implementation of molecular biology-based methods has rendered the manipulation of isolated enzymes routine work. This in turn has led to improved knowledge about enzymatic mechanisms and boosted enzyme- orientated research in multiple areas. The past years have seen impressive advances leading to sophisticated tools and innovative techniques for the design and development of bio-based processes for the production of (fine) chemicals. The synergy between synthetic biology and biocatalysis is now strongly emerging as an important trend for future sustainable processes and we felt the need to merge these two complementary branches, which have been evolving mainly concurrently. Excellent books are available for chemists wishing to implement natural catalysts in synthetic processes, while recent books on synthetic biology focus on bottom-up creation of new modular parts, circuit design, and chassis engineering but are not enzyme centric. Specialized and focused reviews in prominent journals on the development of robust and efficient biosynthetic routes are becoming more frequent, but a unifying platform was still missing. This book includes a number of contributions to document the current merging of traditional biocatalysis with more syn- thetic biology-based approaches, and keeps enzymes as the central protagonists. The book is organized into five sections. In Section I, Accessing New Enzymes, several contributions exemplify the technical diversity at hand to identify new enzymes, which largely benefits from ever-improving compu- tational power. In Section II, Understanding and Engineering Enzymes,we gathered experts to highlight how modifying protein sequence and structure Catalysis Series No. 32 Modern Biocatalysis: Advances Towards Synthetic Biological Systems Edited by Gavin Williams and Me´lanie Hall r The Royal Society of Chemistry 2018 Published by the Royal Society of Chemistry, www.rsc.org vii viii Preface in silico and in vivo is fundamental to obtaining crucial catalytic insights used to tailor enzyme properties. In Section III, Enzymes from Secondary Metabolism, several contributions highlight the remarkable ability of enzymes in secondary metabolism to construct complex natural products from simple small molecule building blocks. Approaches to engineer and optimize these pathways are also described. Section IV, Biocatalysis for Modern Synthesis, focuses on elaborate enzyme-based processes developed for the synthesis of fine chemicals. Importantly, multi-step reactions now combine various types of (bio)catalysts and are particularly well suited for the cost-effective generation of enantiopure molecules of high value. Finally, Section V, Applied Biocatalysis, reflects the technological input required to implement natural or engineered enzymes in industrial settings, and finishes with an opening on the promising use of enzymes in remediation, according to which biodegradation processes might witness a restored interest. We hope that readers will find this book helpful to connect all areas that biocatalysis—and synthetic biology—as progressive field now encompasses, and to identify current and emerging trends towards the development of efficient synthetic biological systems in a broad sense. We thereby hope to trigger mutual inspiration for the currently unfolding generation of hybrid chemists/biologists who are committed to render current and upcoming synthetic processes more sustainable. Tools exist, let’s use them! Me´lanie Hall (Graz, Austria) Gavin Williams (Raleigh, USA) Contents Section I: Accessing New Enzymes Chapter 1 Genome Mining for Enzyme Discovery 3 Anne Zaparucha, Ve´ronique de Berardinis and Carine Vaxelaire-Vergne 1.1 Introduction 3 1.2 Text-based Searches Using Enzyme Name 5 1.3 Sequence-driven Approaches 7 1.3.1 Probe Technology Based on PCR Primer Design 7 1.3.2 Pairwise Sequence Alignment-based Strategy 8 1.3.3 Signature-/Key Motif-based Strategy 15 1.4 3D Structure-guided Approach 18 1.4.1 Exploring 3D Structures of Proteins 19 1.4.2 Active Site Topology/Constellation-guided Strategy 19 1.5 Conclusion 22 References 23 Chapter 2 Exploiting Natural Diversity for Industrial Enzymatic Applications 28 Yasuhisa Asano and Richard Metzner 2.1 Introduction 28 2.2 Screening Enzymes
Recommended publications
  • Mice Carrying a Human GLUD2 Gene Recapitulate Aspects of Human Transcriptome and Metabolome Development
    Mice carrying a human GLUD2 gene recapitulate aspects of human transcriptome and metabolome development Qian Lia,b,1, Song Guoa,1, Xi Jianga, Jaroslaw Brykc,2, Ronald Naumannd, Wolfgang Enardc,3, Masaru Tomitae, Masahiro Sugimotoe, Philipp Khaitovicha,c,f,4, and Svante Pääboc,4 aChinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China; bUniversity of Chinese Academy of Sciences, 100049 Beijing, China; cMax Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; dMax Planck Institute of Molecular Cell Biology and Genetics, D-01307 Dresden, Germany; eInstitute for Advanced Biosciences, Keio University, 997-0035 Tsuruoka, Yamagata, Japan; and fSkolkovo Institute for Science and Technology, 143025 Skolkovo, Russia Edited by Joshua M. Akey, University of Washington, Seattle, WA, and accepted by the Editorial Board April 1, 2016 (received for review September 28, 2015) Whereas all mammals have one glutamate dehydrogenase gene metabolic flux from glucose and glutamine to lipids by way of the (GLUD1), humans and apes carry an additional gene (GLUD2), TCA cycle (12). which encodes an enzyme with distinct biochemical properties. To investigate the physiological role the GLUD2 gene may We inserted a bacterial artificial chromosome containing the human play in human and ape brains, we generated mice transgenic for GLUD2. GLUD2 gene into mice and analyzed the resulting changes in the a genomic region containing human We compared effects transcriptome and metabolome during postnatal brain development. on gene expression and metabolism during postnatal development Effects were most pronounced early postnatally, and predominantly of the frontal cortex of the brain in these mice and their wild-type genes involved in neuronal development were affected.
    [Show full text]
  • O O2 Enzymes Available from Sigma Enzymes Available from Sigma
    COO 2.7.1.15 Ribokinase OXIDOREDUCTASES CONH2 COO 2.7.1.16 Ribulokinase 1.1.1.1 Alcohol dehydrogenase BLOOD GROUP + O O + O O 1.1.1.3 Homoserine dehydrogenase HYALURONIC ACID DERMATAN ALGINATES O-ANTIGENS STARCH GLYCOGEN CH COO N COO 2.7.1.17 Xylulokinase P GLYCOPROTEINS SUBSTANCES 2 OH N + COO 1.1.1.8 Glycerol-3-phosphate dehydrogenase Ribose -O - P - O - P - O- Adenosine(P) Ribose - O - P - O - P - O -Adenosine NICOTINATE 2.7.1.19 Phosphoribulokinase GANGLIOSIDES PEPTIDO- CH OH CH OH N 1 + COO 1.1.1.9 D-Xylulose reductase 2 2 NH .2.1 2.7.1.24 Dephospho-CoA kinase O CHITIN CHONDROITIN PECTIN INULIN CELLULOSE O O NH O O O O Ribose- P 2.4 N N RP 1.1.1.10 l-Xylulose reductase MUCINS GLYCAN 6.3.5.1 2.7.7.18 2.7.1.25 Adenylylsulfate kinase CH2OH HO Indoleacetate Indoxyl + 1.1.1.14 l-Iditol dehydrogenase L O O O Desamino-NAD Nicotinate- Quinolinate- A 2.7.1.28 Triokinase O O 1.1.1.132 HO (Auxin) NAD(P) 6.3.1.5 2.4.2.19 1.1.1.19 Glucuronate reductase CHOH - 2.4.1.68 CH3 OH OH OH nucleotide 2.7.1.30 Glycerol kinase Y - COO nucleotide 2.7.1.31 Glycerate kinase 1.1.1.21 Aldehyde reductase AcNH CHOH COO 6.3.2.7-10 2.4.1.69 O 1.2.3.7 2.4.2.19 R OPPT OH OH + 1.1.1.22 UDPglucose dehydrogenase 2.4.99.7 HO O OPPU HO 2.7.1.32 Choline kinase S CH2OH 6.3.2.13 OH OPPU CH HO CH2CH(NH3)COO HO CH CH NH HO CH2CH2NHCOCH3 CH O CH CH NHCOCH COO 1.1.1.23 Histidinol dehydrogenase OPC 2.4.1.17 3 2.4.1.29 CH CHO 2 2 2 3 2 2 3 O 2.7.1.33 Pantothenate kinase CH3CH NHAC OH OH OH LACTOSE 2 COO 1.1.1.25 Shikimate dehydrogenase A HO HO OPPG CH OH 2.7.1.34 Pantetheine kinase UDP- TDP-Rhamnose 2 NH NH NH NH N M 2.7.1.36 Mevalonate kinase 1.1.1.27 Lactate dehydrogenase HO COO- GDP- 2.4.1.21 O NH NH 4.1.1.28 2.3.1.5 2.1.1.4 1.1.1.29 Glycerate dehydrogenase C UDP-N-Ac-Muramate Iduronate OH 2.4.1.1 2.4.1.11 HO 5-Hydroxy- 5-Hydroxytryptamine N-Acetyl-serotonin N-Acetyl-5-O-methyl-serotonin Quinolinate 2.7.1.39 Homoserine kinase Mannuronate CH3 etc.
    [Show full text]
  • Michigan State University
    ..____ LIEMRY Michigan State University ———— OVERDUE FINES: 25¢ per day per ite- RETURNING LIBRARY MATERIALS: Place in book return to remove charge from c1 rcuht1on records BRAIN IRON'IN THE RAT: DISTRIBUTION, SEX DIFFERENCES, AND EFFECTS OF SEX HORMONES By Joanna Marie Hill A DISSERTATION Submitted to Michigan State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Department of Zoology 1981 ABSTRACT BRAIN IRON IN THE RAT: DISTRIBUTION, SEX DIFFERENCES, AND EFFECTS OF SEX HORMONES By Joanna Marie Hill Although the brain contains relatively large amounts of iron, and iron deficiency alters behavior, little is known about those factors which affect brain iron or the role of n J .r iron in the brain. Sex hormones are responsible for sex r’ ’7 differences in many aspects of iron metabolism throughout ,l' .3 I the body. 6// The purposes of this study were to: (l) localize iron deposits in the rat brain; (2) determine if a sex difference exists in brain iron stores; (3) determine the effects on brain iron levels of natural events in which sex hormones fluctuate (e.g. estrous cycle and pregnancy); and (4) determine if exogenous estrogen alters the effects of ovari- ectomy and castration on brain iron levels. Brain iron was localized by histochemical methods and direct measurement of iron concentrations of high-iron areas (pooled globus pallidus and substantia nigra) and lower iron areas (cortex) of the brain, as well as the serum and liver were made by spectr0photometry. This study has determined that brain iron: is unevenly distributed in the rat brain; occurs in different cellular and extracellular compartments in different parts of the Joanna Marie Hill brain; and increases with age.
    [Show full text]
  • Natural Product Biosyntheses in Cyanobacteria: a Treasure Trove of Unique Enzymes
    Natural product biosyntheses in cyanobacteria: A treasure trove of unique enzymes Jan-Christoph Kehr, Douglas Gatte Picchi and Elke Dittmann* Review Open Access Address: Beilstein J. Org. Chem. 2011, 7, 1622–1635. University of Potsdam, Institute for Biochemistry and Biology, doi:10.3762/bjoc.7.191 Karl-Liebknecht-Str. 24/25, 14476 Potsdam-Golm, Germany Received: 22 July 2011 Email: Accepted: 19 September 2011 Jan-Christoph Kehr - [email protected]; Douglas Gatte Picchi - Published: 05 December 2011 [email protected]; Elke Dittmann* - [email protected] This article is part of the Thematic Series "Biosynthesis and function of * Corresponding author secondary metabolites". Keywords: Guest Editor: J. S. Dickschat cyanobacteria; natural products; NRPS; PKS; ribosomal peptides © 2011 Kehr et al; licensee Beilstein-Institut. License and terms: see end of document. Abstract Cyanobacteria are prolific producers of natural products. Investigations into the biochemistry responsible for the formation of these compounds have revealed fascinating mechanisms that are not, or only rarely, found in other microorganisms. In this article, we survey the biosynthetic pathways of cyanobacteria isolated from freshwater, marine and terrestrial habitats. We especially empha- size modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) pathways and highlight the unique enzyme mechanisms that were elucidated or can be anticipated for the individual products. We further include ribosomal natural products and UV-absorbing pigments from cyanobacteria. Mechanistic insights obtained from the biochemical studies of cyanobacterial pathways can inspire the development of concepts for the design of bioactive compounds by synthetic-biology approaches in the future. Introduction The role of cyanobacteria in natural product research Cyanobacteria flourish in diverse ecosystems and play an enor- [2] (Figure 1).
    [Show full text]
  • Production of Monatin and Monatin Precursors Herstellung Von Monatin Und Monatinvorläufer Production De Monatine Et Précurseurs De Monatine
    (19) TZZ ¥Z Z_T (11) EP 2 302 067 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12P 13/04 (2006.01) C12N 9/88 (2006.01) 05.03.2014 Bulletin 2014/10 C12N 9/10 (2006.01) C12N 1/21 (2006.01) (21) Application number: 10009952.2 (22) Date of filing: 21.10.2004 (54) Production of monatin and monatin precursors Herstellung von Monatin und Monatinvorläufer Production de monatine et précurseurs de monatine (84) Designated Contracting States: • Sanchez-Riera, Fernando A. AT BE BG CH CY CZ DE DK EE ES FI FR GB GR Eden Prairie, MN 55346 (US) HU IE IT LI LU MC NL PL PT RO SE SI SK TR • Cameron, Douglas C. Plymouth, MN 55447 (US) (30) Priority: 21.10.2003 US 513406 P • Desouza, Mervyn L. Plymouth, MN 55441 (US) (43) Date of publication of application: • Rosazza, Jack 30.03.2011 Bulletin 2011/13 Iowa City, IA 55240 (US) • Gort, Steven J. (62) Document number(s) of the earlier application(s) in Brooklyn Center, MN 55429 (US) accordance with Art. 76 EPC: • Abraham, Timothy W. 04795689.1 / 1 678 313 Minnetonka, MN 55345 (US) (73) Proprietor: Cargill, Incorporated (74) Representative: Wibbelmann, Jobst Wayzata, MN 55391-5624 (US) Wuesthoff & Wuesthoff Patent- und Rechtsanwälte (72) Inventors: Schweigerstrasse 2 • McFarlan, Sara C. 81541 München (DE) St.Paul, MN 55116 (US) • Hicks, Paula M. (56) References cited: Bend, Oregon 97702 (US) WO-A-03/056026 WO-A-2005/016022 • Zidwick, Mary Jo WO-A-2005/020721 WO-A2-03/091396 Wayzata, MN 55391 (US) WO-A2-2005/014839 Note: Within nine months of the publication of the mention of the grant of the European patent in the European Patent Bulletin, any person may give notice to the European Patent Office of opposition to that patent, in accordance with the Implementing Regulations.
    [Show full text]
  • WO 2017/123676 A9 20 July 2017 (20.07.2017) P O P C T
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) CORRECTED VERSION (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2017/123676 A9 20 July 2017 (20.07.2017) P O P C T (51) International Patent Classification: 16 November 2016 (16. 11.2016) US C12N 9/78 (2006.0 1) C12N 1/00 (2006.0 1) 15/379,445 14 December 20 16 ( 14. 12.20 16) us A61K 35/74 (2015.01) C12N 15/52 (2006.01) 62/434,406 14 December 2016 (14. 12.2016) us A61K 35/741 (2015.01) C12N 15/74 (2006.01) 62/439,820 28 December 2016 (28. 12.2016) us C07K 14/195 (2006.01) 62/439,871 28 December 2016 (28. 12.2016) us PCT/US201 6/069052 (21) International Application Number: 28 December 2016 (28. 12.2016) us PCT/US20 17/0 13074 62/443,639 6 January 2017 (06.01.2017) us (22) International Filing Date: PCT/US201 7/013072 11 January 2017 ( 11.01 .2017) 11 January 2017 ( 11.01 .2017) us (25) Filing Language: English Applicant: SYNLOGIC, INC. [US/US]; 130 Brookline Street, #201, Cambridge, MA 02139 (US). (26) Publication Language: English (72) Inventors: FALB, Dean; 180 Lake Street, Sherborn, MA (30) Priority Data: 01770 (US). KOTULA, Jonathan, W.; 345 Washington 62/277,413 11 January 2016 ( 11.01.2016) US Street, Somerville, MA 02143 (US). ISABELLA, Vin¬ 62/277,450 11 January 2016 ( 11.01.2016) us cent, M.; 465 Putnam Avenue, Unit 1, Cambridge, MA 62/277,455 11 January 2016 ( 11.01.2016) us 02139 (US).
    [Show full text]
  • All Enzymes in BRENDA™ the Comprehensive Enzyme Information System
    All enzymes in BRENDA™ The Comprehensive Enzyme Information System http://www.brenda-enzymes.org/index.php4?page=information/all_enzymes.php4 1.1.1.1 alcohol dehydrogenase 1.1.1.B1 D-arabitol-phosphate dehydrogenase 1.1.1.2 alcohol dehydrogenase (NADP+) 1.1.1.B3 (S)-specific secondary alcohol dehydrogenase 1.1.1.3 homoserine dehydrogenase 1.1.1.B4 (R)-specific secondary alcohol dehydrogenase 1.1.1.4 (R,R)-butanediol dehydrogenase 1.1.1.5 acetoin dehydrogenase 1.1.1.B5 NADP-retinol dehydrogenase 1.1.1.6 glycerol dehydrogenase 1.1.1.7 propanediol-phosphate dehydrogenase 1.1.1.8 glycerol-3-phosphate dehydrogenase (NAD+) 1.1.1.9 D-xylulose reductase 1.1.1.10 L-xylulose reductase 1.1.1.11 D-arabinitol 4-dehydrogenase 1.1.1.12 L-arabinitol 4-dehydrogenase 1.1.1.13 L-arabinitol 2-dehydrogenase 1.1.1.14 L-iditol 2-dehydrogenase 1.1.1.15 D-iditol 2-dehydrogenase 1.1.1.16 galactitol 2-dehydrogenase 1.1.1.17 mannitol-1-phosphate 5-dehydrogenase 1.1.1.18 inositol 2-dehydrogenase 1.1.1.19 glucuronate reductase 1.1.1.20 glucuronolactone reductase 1.1.1.21 aldehyde reductase 1.1.1.22 UDP-glucose 6-dehydrogenase 1.1.1.23 histidinol dehydrogenase 1.1.1.24 quinate dehydrogenase 1.1.1.25 shikimate dehydrogenase 1.1.1.26 glyoxylate reductase 1.1.1.27 L-lactate dehydrogenase 1.1.1.28 D-lactate dehydrogenase 1.1.1.29 glycerate dehydrogenase 1.1.1.30 3-hydroxybutyrate dehydrogenase 1.1.1.31 3-hydroxyisobutyrate dehydrogenase 1.1.1.32 mevaldate reductase 1.1.1.33 mevaldate reductase (NADPH) 1.1.1.34 hydroxymethylglutaryl-CoA reductase (NADPH) 1.1.1.35 3-hydroxyacyl-CoA
    [Show full text]
  • Open Full Article
    BIOLOGIA PLANTARUM (PRAHA) 33 (5):395-407, 1991 Proposed Enzymes of Auxin Biosynthesis and Their Regulation II. Tryptophan Dehydrogenase Activity in Plants. M. KUT/~t~EK and SULTANA TERZIIVANOVA-DIMOVA* Institute of Experimental Botany, Czechoslovak Academy of Sciences, Ke dvoru 15, 166 30 Praha 6, Czechoslovakia *Institute of Plant Physiology "M. Popov", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria Abstract. In pea, maize and tomato plants a hitherto undescribed L-tryptophan dehydrogenase activity (TDH) has been detected. This enzyme catalyzes the reversible formation of indolepyruvic acid (IPyA) from L-tryptophan (L-trp). TDH and L-glutamate dehydrogenase (GDH), related enzymes in their mode of action, could be separated by gel chromatography. Enzymatic activity of TDH was sustained by both pyridine coenzymes NAD/NADP. With pea TDH the coenzyme NAD displays, at optimum pH 8.5 and at room temperature, only about 40-70 % of the activity of NADP. The amination of IPyA is catalysed more actively than the deamination of L-trp. L-trp/IPyA, L-glu/ketoglutarate, L-ala/pyruvate reacted as dehydrogenase substrates; L-phe/phenylpyruvate, D-trp and D-phe did not react with pea enzyme extracts. A considerable similarity between the active centres of TDH and GDH has been found using inhibitors: absence of heavy metals, presence of a carbonyl group, indispensibility of bivalent ions for the enzyme activity. Pea TDH and GDH were distinctly inhibited by sodium azide. For the activity of TDH the presence of SH groups is less important than for GDH. The TDH activity in the investigated plants was lower than the GDH activity.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2005/0112260 A1 Abraham Et Al
    US 2005O112260A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2005/0112260 A1 Abraham et al. (43) Pub. Date: May 26, 2005 (54) MONATIN TABLETOPSWEETENER (21) Appl. No.: 10/903,582 COMPOSITIONS AND METHODS OF MAKING SAME (22) Filed: Aug. 2, 2004 (75) Inventors: Timothy W. Abraham, Minnetonka, Related U.S. Application Data MN (US); Douglas C. Cameron, Plymouth, MN (US); Melanie J. (60) Provisional application No. 60/492,014, filed on Aug. Goulson, Dayton, MN (US); Paula M. 1, 2003. Hicks, Eden Prairie, MN (US); Michael O O G. Lindley, Crowthorne (GB); Sara C. Publication Classification McFarlan, St.Paul, MN (US); James 7 R. Millis, Plymouth, MN (US); John s - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A: Rosazza, Iowa City, IA (US); Lishan ( 2) O O - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - /5 Zhao, Carlsbad, CA (US); David P. Weiner, Del Mar, CA (US) (57) ABSTRACT Correspondence Address: The present invention relates to novel Sweetener composi CARGILL, INCORPORATED tions comprising monatin and methods for making Such LAW/24 compositions. The present invention also relates to Sweet 15407 MCGINTY ROAD WEST ener compositions comprising Specific monatin Stereoiso WAYZATA, MN 55391 (US) mers, Specific blends of monatin Stereoisomers, and/or monatin produced via a biosynthetic pathway in Vivo (e.g., (73) Assignee: Cargill, Inc. inside cells) or in vitro. -- re Tryptophan Indole-3-lactic
    [Show full text]
  • Crystal Structure of L-Tryptophan Dehydrogenase
    Photon Factory Activity Report 2018 #36 (2019) AR-NE3A/2017G010 Crystal structure of L-tryptophan dehydrogenase Taisuke Wakamatsu 1, *, Haruhiko Sakuraba 2, *, Megumi Kitamura 1, Yuichi Hakumai1, Kenji Fukui 3, Kouhei Ohnishi 4, Makoto Ashiuchi 1, and Toshihisa Ohshima 5 1 Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Kochi, Japan 2 Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Kagawa, Japan 3 Department of Biochemistry, Osaka Medical College, Osaka, Japan 4 Research Institute of Molecular Genetics, Kochi University, Kochi, Japan 5 Department of Biomedical Engineering, Osaka Institute of Technology, Osaka, Japan 1 Introduction preferred substrate, whereas phenylpyruvate, the 2-oxo NAD(P)-dependent L-amino acid dehydrogenases (EC analog of L-Phe, was inert as a substrate. Despite these 1.4.1.x) catalyze reversible oxidative deamination of L- interesting observations, there exists no structural amino acids to their corresponding 2-oxo acids and information on TrpDH. Thus, we employed X-ray ammonia in the presence of NAD(P). So far, more than crystallography to solve the apo-structure of NpTrpDH, fifteen types of L-amino acid dehydrogenases have been identified from various organisms and characterized 2 Experiment extensively. In particular, detailed structure and function Data were collected under cryo conditions at the analyses of L-Glu/L-Leu/L-Phe dehydrogenases have led to Beamline AR-NE3A at Photon Factory in Japan. The the elucidation of their catalytic mechanisms. crystal structure of LeuDH from Sporosarcina Consequently, several L-amino acid dehydrogenases have psychrophila (SpLeuDH, PDB ID: 3VPX, amino acid been successfully used for the syntheses for chiral amino sequence identity: 49%) was applied as a search model, acids and their analogs, for developing biosensors for L- and the program PHENIX was used for molecular amino acids.
    [Show full text]
  • Targeting Glutamine Addiction in Gliomas
    cancers Review Targeting Glutamine Addiction in Gliomas Marta Obara-Michlewska and Monika Szeliga * Department of Neurotoxicology, Mossakowski Medical Research Centre, Polish Academy of Sciences, 5 Pawi´nskiegoStreet, 02-106 Warsaw, Poland; [email protected] * Correspondence: [email protected]; Tel.: +48-22-608-6416 Received: 20 December 2019; Accepted: 27 January 2020; Published: 29 January 2020 Abstract: The most common malignant brain tumors are those of astrocytic origin, gliomas, with the most aggressive glioblastoma (WHO grade IV) among them. Despite efforts, medicine has not made progress in terms of the prognosis and life expectancy of glioma patients. Behind the malignant phenotype of gliomas lies multiple genetic mutations leading to reprogramming of their metabolism, which gives those highly proliferating cells an advantage over healthy ones. The so-called glutamine addiction is a metabolic adaptation that supplements oxidative glycolysis in order to secure neoplastic cells with nutrients and energy in unfavorable conditions of hypoxia. The present review aims at presenting the research and clinical attempts targeting the different metabolic pathways involved in glutamine metabolism in gliomas. A brief description of the biochemistry of glutamine transport, synthesis, and glutaminolysis, etc. will forego a detailed comparison of the therapeutic strategies undertaken to inhibit glutamine utilization by gliomas. Keywords: glioma; glutamine; glutamate; glutaminase; glutamine synthetase; glutamate dehydrogenase; therapy 1. Introduction The metabolism of neoplasms has evolved to meet the demands of their high proliferative activity and growth in adverse conditions of hypoxia, nutrient shortage, and immunological pressure of the host. The reprogrammed metabolism of neoplasms, eventually adapting them to specific growth requirements and conditions, involves addiction to glucose (the Warburg effect, oxidative glycolysis) and/or glutamine.
    [Show full text]
  • Springer Handbook of Enzymes
    Dietmar Schomburg Ida Schomburg (Eds.) Springer Handbook of Enzymes Alphabetical Name Index 1 23 © Springer-Verlag Berlin Heidelberg New York 2010 This work is subject to copyright. All rights reserved, whether in whole or part of the material con- cerned, specifically the right of translation, printing and reprinting, reproduction and storage in data- bases. The publisher cannot assume any legal responsibility for given data. Commercial distribution is only permitted with the publishers written consent. Springer Handbook of Enzymes, Vols. 1–39 + Supplements 1–7, Name Index 2.4.1.60 abequosyltransferase, Vol. 31, p. 468 2.7.1.157 N-acetylgalactosamine kinase, Vol. S2, p. 268 4.2.3.18 abietadiene synthase, Vol. S7,p.276 3.1.6.12 N-acetylgalactosamine-4-sulfatase, Vol. 11, p. 300 1.14.13.93 (+)-abscisic acid 8’-hydroxylase, Vol. S1, p. 602 3.1.6.4 N-acetylgalactosamine-6-sulfatase, Vol. 11, p. 267 1.2.3.14 abscisic-aldehyde oxidase, Vol. S1, p. 176 3.2.1.49 a-N-acetylgalactosaminidase, Vol. 13,p.10 1.2.1.10 acetaldehyde dehydrogenase (acetylating), Vol. 20, 3.2.1.53 b-N-acetylgalactosaminidase, Vol. 13,p.91 p. 115 2.4.99.3 a-N-acetylgalactosaminide a-2,6-sialyltransferase, 3.5.1.63 4-acetamidobutyrate deacetylase, Vol. 14,p.528 Vol. 33,p.335 3.5.1.51 4-acetamidobutyryl-CoA deacetylase, Vol. 14, 2.4.1.147 acetylgalactosaminyl-O-glycosyl-glycoprotein b- p. 482 1,3-N-acetylglucosaminyltransferase, Vol. 32, 3.5.1.29 2-(acetamidomethylene)succinate hydrolase, p. 287 Vol.
    [Show full text]