Identification, Characterization and Application of Novel (R)-Selective Amine Transaminases
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
The Role of Protein Crystallography in Defining the Mechanisms of Biogenesis and Catalysis in Copper Amine Oxidase
Int. J. Mol. Sci. 2012, 13, 5375-5405; doi:10.3390/ijms13055375 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Review The Role of Protein Crystallography in Defining the Mechanisms of Biogenesis and Catalysis in Copper Amine Oxidase Valerie J. Klema and Carrie M. Wilmot * Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-612-624-2406; Fax: +1-612-624-5121. Received: 6 April 2012; in revised form: 22 April 2012 / Accepted: 26 April 2012 / Published: 3 May 2012 Abstract: Copper amine oxidases (CAOs) are a ubiquitous group of enzymes that catalyze the conversion of primary amines to aldehydes coupled to the reduction of O2 to H2O2. These enzymes utilize a wide range of substrates from methylamine to polypeptides. Changes in CAO activity are correlated with a variety of human diseases, including diabetes mellitus, Alzheimer’s disease, and inflammatory disorders. CAOs contain a cofactor, 2,4,5-trihydroxyphenylalanine quinone (TPQ), that is required for catalytic activity and synthesized through the post-translational modification of a tyrosine residue within the CAO polypeptide. TPQ generation is a self-processing event only requiring the addition of oxygen and Cu(II) to the apoCAO. Thus, the CAO active site supports two very different reactions: TPQ synthesis, and the two electron oxidation of primary amines. Crystal structures are available from bacterial through to human sources, and have given insight into substrate preference, stereospecificity, and structural changes during biogenesis and catalysis. -
C1 Assimilation in Obligate Methylotrophs and Restricted Facultative Methylotrophs by JOHN COLBY* and LEONARD J
Biochem. J. (1975) 148, 513-520 513 Printed in Great Britain Enzymological Aspects ofthe Pathways for Trimethylamine Oxidation and C1 Assimilation in Obligate Methylotrophs and Restricted Facultative Methylotrophs By JOHN COLBY* and LEONARD J. ZATMAN Department ofMicrobiology, University ofReading, Reading RG1 5AQ, U.K. (Received8 January 1975) 1. Extracts of trimethylamine-grown W6A and W3A1 (type M restricted facultative methylotrophs) contain trimethylamine dehydrogenase whereas similar extracts of Bacillus PM6 and Bacillus S2A1 (type L restricted facultative methylotrophs) contain trimethylamine mono-oxygenase and trimethylamine N-oxide demethylase but no trimethylamine dehydrogenase. 2. Extracts oftherestricted facultatives and ofthe obligate methylotroph C2A1 contain hexulose phosphate synthase-hexulose phosphate isomerase activity; hydroxypyruvate reductase was not detected. 3. Neither the restricted facultatives nor the obligates 4B6 and C2A1 contain all the enzymes ofthe hexulose phos- phatecycleofformaldehyde assimilation as originallyproposed byKemp & Quayle (1967). 4. Organisms PM6 and S2A1 lack transaldolase and use a modified cycle involving sedoheptulose 1,7-diphosphate and sedoheptulose diphosphatase. 5. The obligates 4B6 and C2A1, and the type M organisms W6A and W3A1, use a different modification of the assimilatory hexulose phosphate cycle involving the Entner-Doudoroff-pathway enzymes phosphogluconate dehydratase and phospho-2-keto-3-deoxygluconate aldolase. Thelackoffructosediphosphatealdolaseandhexosediphosphataseintheseorganismsmay -
Yeast Genome Gazetteer P35-65
gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal -
Novel Amine Dehydrogenase from Leucine Dehydrogenase 19
DEVELOPMENT OF AN AMINE DEHYDROGENASE A Dissertation Presented to The Academic Faculty by Michael J. Abrahamson In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the School of Chemical and Biomolecular Engineering Georgia Institute of Technology December 2012 DEVELOPMENT OF AN AMINE DEHYDROGENASE Approved by: Dr. Andreas S. Bommarius, Advisor Dr. Jeffrey Skolnick School of Chemical & Biomolecular School of Biology Engineering Georgia Institute of Technology Georgia Institute of Technology Dr. Christopher W. Jones Dr. John W. Wong School of Chemical & Biomolecular Biocatalysis Center of Emphasis Engineering Chemical Research & Development Georgia Institute of Technology Pfizer Global Research & Development Dr. Yoshiaki Kawajiri School of Chemical & Biomolecular Engineering Georgia Institute of Technology Date Approved: August 13, 2012 To my parents, Joseph & Deborah ACKNOWLEDGEMENTS First and foremost, I would like to thank my parents Joseph and Deborah. Your guidance and unconditional support has been invaluable to my success throughout college. The encouragement from my entire family has been so helpful throughout graduate school. I would also like to thank my advisor, Prof. Andreas Bommarius for his direction, instruction, and patience over the last five years. Your input and optimism has kept me ‘plowing ahead’ and has been instrumental in my scientific development. I would like to thank my committee members; Prof. Christopher Jones, Prof. Yoshiaki Kawajiri, Prof. Jeffrey Skolnick, and Dr. John W. Wong. Thank you all for your time, encouragement, and support. All of the members of the Bommarius lab, past and present, have made my graduate career not only productive, but enjoyable. We have shared many great and unforgettable moments. -
Pyruvate Carboxylase and Phosphoenolpyruvate Carboxykinase Activity in Leukocytes and Fibroblasts from a Patient with Pyruvate Carboxylase Deficiency
Pediat. Res. 13: 3843 (1979) Citrate synthase lymphocytes fibroblasts phosphoenol pyruvate carboxykinase lactic acidosis pyruvate carboxylase pyruvate carboxylase deficiency Pyruvate Carboxylase and Phosphoenolpyruvate Carboxykinase Activity in Leukocytes and Fibroblasts from a Patient with Pyruvate Carboxylase Deficiency Division of Genetics and Departmenr of Pediatrics, Universiy of Oregon Health Sciences Center, Porrland, Oregon; and Department of Biochemistry, School of Medicine, Case Western Reserve Universi!,., Cleveland, Ohio, USA Summary complex (PDC) (7, 13, 32, 35), and PEPCK (14, 17,40). With the exception of PDC which catalyzes the first step in the Krebs cycle, Normal values are given for the activities of pyruvate carbox- the enzymes are necessary for gluconeogenesis in mammalian ylase (E.C. 6.4.1.1), mitochondrial phosphoenolpyruvate carboxy- renal cortex and liver. In addition to its gluconeogenic role. base (E.C. 4.1.1.32, PEPCK), and citrate synthase (E.C. 4.1.3.7) pyruvate carboxylase is required for the adequate operation of the in fibroblasts, lymphocytes, and leukocytes. Also given are values Krebs cycle because of its role in the replenishment of four-carbon for these enzymes in the leukocytes and fibroblasts from a severely Krebs cycle intermediates. Both the kitochondrial and cytosolic mentally and developmentally retarded patient with proximal renal forms of PEPCK are present in human liver. tubular acidosis and hepatic, cerebral, and renal cortical pyruvate Fructose 1,6-bisphosphatase (28) and PDC deficiency (7) have carboxylase deficiency. In normals, virtually all of the mitochon- been diagnosed in leukocytes and, although there are references drial PEPCK and pyruvate carboxylase activity was present in the to the presence of pyruvate carboxylase in fibroblasts (3. -
Glutamate-Secretion-In-Cancer-Cell
Biochemical and Biophysical Research Communications 495 (2018) 761e767 Contents lists available at ScienceDirect Biochemical and Biophysical Research Communications journal homepage: www.elsevier.com/locate/ybbrc Glutamate production from ammonia via glutamate dehydrogenase 2 activity supports cancer cell proliferation under glutamine depletion * Yukiko Takeuchi a, Yasumune Nakayama b, c, Eiichiro Fukusaki b, Yasuhiro Irino a, d, a The Integrated Center for Mass Spectrometry, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Kobe 650-0017, Japan b Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan c Department of Applied Microbial Technology, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan d Division of Evidence-based Laboratory Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Kobe 650-0017, Japan article info abstract Article history: Cancer cells rapidly consume glutamine as a carbon and nitrogen source to support proliferation, but the Received 9 November 2017 cell number continues to increase exponentially after glutamine is nearly depleted from the medium. In Accepted 13 November 2017 contrast, cell proliferation rates are strongly depressed when cells are cultured in glutamine-free me- Available online 14 November 2017 dium. How cancer cells survive in response to nutrient limitation and cellular stress remains poorly understood. In addition, rapid glutamine catabolism yields ammonia, which is a potentially toxic Keywords: metabolite that is secreted into the extracellular space. Here, we show that ammonia can be utilized for Ammonia glutamate production, leading to cell proliferation under glutamine-depleted conditions. -
The PEP–Pyruvate–Oxaloacetate Node As the Switch Point for Carbon flux Distribution in Bacteria
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by RERO DOC Digital Library FEMS Microbiology Reviews 29 (2005) 765–794 www.fems-microbiology.org The PEP–pyruvate–oxaloacetate node as the switch point for carbon flux distribution in bacteria Uwe Sauer a, Bernhard J. Eikmanns b,* a Institute of Biotechnology, ETH Zu¨rich, 8093 Zu¨rich, Switzerland b Department of Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany Received 18 August 2004; received in revised form 27 October 2004; accepted 1 November 2004 First published online 28 November 2004 We dedicate this paper to Rudolf K. Thauer, Director of the Max-Planck-Institute for Terrestrial Microbiology in Marburg, Germany, on the occasion of his 65th birthday Abstract In many organisms, metabolite interconversion at the phosphoenolpyruvate (PEP)–pyruvate–oxaloacetate node involves a struc- turally entangled set of reactions that interconnects the major pathways of carbon metabolism and thus, is responsible for the dis- tribution of the carbon flux among catabolism, anabolism and energy supply of the cell. While sugar catabolism proceeds mainly via oxidative or non-oxidative decarboxylation of pyruvate to acetyl-CoA, anaplerosis and the initial steps of gluconeogenesis are accomplished by C3- (PEP- and/or pyruvate-) carboxylation and C4- (oxaloacetate- and/or malate-) decarboxylation, respectively. In contrast to the relatively uniform central metabolic pathways in bacteria, the set of enzymes at the PEP–pyruvate–oxaloacetate node represents a surprising diversity of reactions. Variable combinations are used in different bacteria and the question of the sig- nificance of all these reactions for growth and for biotechnological fermentation processes arises. -
University of London Thesis
REFERENCE ONLY UNIVERSITY OF LONDON THESIS Degree Year^^0^ Name of Author C O P Y R IG H T This is a thesis accepted for a Higher Degree of the University of London. It is an unpublished typescript and the copyright is held by the author. All persons consulting the thesis must read and abide by the Copyright Declaration below. COPYRIGHT DECLARATION I recognise that the copyright of the above-described thesis rests with the author and that no quotation from it or information derived from it may be published without the prior written consent of the author. LOANS Theses may not be lent to individuals, but the Senate House Library may lend a copy to approved libraries within the United Kingdom, for consultation solely on the premises of those libraries. Application should be made to: Inter-Library Loans, Senate House Library, Senate House, Malet Street, London WC1E 7HU. REPRODUCTION University of London theses may not be reproduced without explicit written permission from the Senate House Library. Enquiries should be addressed to the Theses Section of the Library. Regulations concerning reproduction vary according to the date of acceptance of the thesis and are listed below as guidelines. A. Before 1962. Permission granted only upon the prior written consent of the author. (The Senate House Library will provide addresses where possible). B. 1962- 1974. In many cases the author has agreed to permit copying upon completion of a Copyright Declaration. C. 1975 - 1988. Most theses may be copied upon completion of a Copyright Declaration. D. 1989 onwards. Most theses may be copied. -
Identification, Characterization and Site-Saturation Mutagenesis of a Thermostable
Identication, Characterization and Site-Saturation Mutagenesis of a Thermostable ω-Transaminase From Chloroexi Bacterium Chen Wang Nanjing Tech University Kexin Tang Nanjing Tech University Ya Dai Nanjing Tech University Honghua Jia ( [email protected] ) Nanjing Tech University https://orcid.org/0000-0002-3824-7768 Yan Li Nanjing Tech University Zhen Gao Nanjing Tech University Bin Wu Nanjing Tech University Research Keywords: ω-Transaminase,Chloroexibacterium, Characterization,Substrate specicity, Site- saturationmutagenesis Posted Date: March 17th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-296936/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Identification, characterization and site-saturation mutagenesis of a thermostable ω-transaminase from Chloroflexi bacterium Chen Wang, Kexin Tang, Ya Dai, Honghua Jia*, Yan Li*, Zhen Gao, Bin Wu College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China Correspondent authors: [email protected]; [email protected] Abstract In present study, we have mined a ω-transaminase (ω-TA) from Chloroflexi bacterium from genome database by using an ω-TA sequence ATA117 Arrmut11 from Arthrobacter sp. KNK168 and an amine transaminase from Aspergillus terreus as templates in a BLASTP search and motif sequence alignment. The protein sequence of the ω-TA from C. bacterium shows 38% sequence identity to ATA117 Arrmut11. The gene sequence of the ω-TA was inserted into pRSF-Duet1 and functionally expressed in E. coli BL21(DE3). Results showed that the recombinant ω-TA has a specific activity of 1.19 U/mg at pH 8.5, 40 °C. The substrate acceptability test showed that ω-TA has significant reactivity to aromatic amino donors and amino receptors. -
1 Here Are the Quiz 4 Questions You Will Answer Online Using the Quiz
Chemistry 6720, quiz 4 handout Here are the quiz 4 questions you will answer online using the quiz tool in canvas instructure. Some of the questions deal with citric acid cycle enzymes that use mechanistic strategies covered in the lectures. Since we did not cover all of those specific enzymes in lecture, be sure to review the citric acid cycle ahead of taking the quiz online so you can answer the appropriate questions regarding mechanistic strategies/themes for the enzymes. In doing so, practice drawing mechanisms for each enzyme of the citric acid cycle. You will probably need to look up the mechanisms for isocitrate dehydrogenase, aconitase, succinate dehydrogenase, and succinyl-CoA synthetase in a general biochemistry text. I will not be asking specific details of the mechanisms for those 4 enzymes, but you will still need to be generally familiar with how they operate to answer a few of the questions below. You do not need to know the chemistry of FAD reduction for the quiz. Be sure to note the quiz deadline in canvas to be sure you get your answers submitted by the deadline. 1. Shown at the right is a Fischer projection for D-glucose. Use the strategy described in the lecture to assign the configurations (R or S) of the chiral centers at C2, C3, C4, and C5. 2. Using the structures shown to the right, assign the methyl groups of isopropanol, and the hydrogens at C2 and C3 of succinate, as either ProR or ProS. Use the strategy covered in lecture to guide you in making the assignments. -
Potential Pharmacological Applications of Enzymes Associated with Bacterial Metabolism of Aromatic Compounds
Vol. 9(1), pp. 1-13, January 2017 DOI: 10.5897/JMA2015.0354 Article Number: BD2460762280 ISSN 2141-2308 Journal of Microbiology and Antimicrobials Copyright © 2017 Author(s) retain the copyright of this article http://www.academicjournals.org/JMA Review Potential pharmacological applications of enzymes associated with bacterial metabolism of aromatic compounds Ranjith N. Kumavath1*, Debmalya Barh2, Vasco Azevedo3 and Alan Prem Kumar 4,5,6,7** 1Department of Genomic Sciences, School of Biological Sciences, Central University of Kerala, P.O. Central University, Kasaragod- 671314, India. 2Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, PurbaMedinipur, West Bengal 721172, India. 3 Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais. MG, Brazil 4 Cancer Science Institute of Singapore, National University of Singapore, Singapore 5Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore. 6Curtin Medical School, Faculty of Health Sciences, Curtin University, Perth, Western Australia. 7 Department of Biological Sciences, University of North Texas, Denton, TX, USA. Received 30 September, 2015; Accepted 3 January, 2016 Many purple anoxygenic bacteria contribute significantly to the catabolic and anabolic processes in the oxic/anoxic zones of several ecosystems. However, these bacteria are incapable of degrading the benzenoid ring during the biotransformation of aromatic hydrocarbons. The key enzymes in the aromatic -
Kobe University Repository : Kernel
Kobe University Repository : Kernel タイトル Glutamate production from ammonia via glutamate dehydrogenase 2 Title activity supports cancer cell proliferation under glutamine depletion 著者 Takeuchi, Yukiko / Nakayama, Yasumune / Fukusaki, Eiichiro / Irino, Author(s) Yasuhiro 掲載誌・巻号・ページ Biochemical and Biophysical Research Communications,495(1):761- Citation 767 刊行日 2018-01-01 Issue date 資源タイプ Journal Article / 学術雑誌論文 Resource Type 版区分 author Resource Version © 2017 Elsevier. This manuscript version is made available under the 権利 CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc- Rights nd/4.0/ DOI 10.1016/j.bbrc.2017.11.088 JaLCDOI URL http://www.lib.kobe-u.ac.jp/handle_kernel/90005457 PDF issue: 2021-10-11 Glutamate production from ammonia via glutamate dehydrogenase 2 activity supports cancer cell proliferation under glutamine depletion Yukiko Takeuchia, Yasumune Nakayamab, c, Eiichiro Fukusakib and Yasuhiro Irinoa, d aThe Integrated Center for Mass Spectrometry, Kobe University Graduate School of Medicine, 7- 5-1 Kusunoki-cho, Kobe 650-0017, Japan bDepartment of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada- oka, Suita, Osaka 565-0871, Japan cDepartment of Applied Microbial Technology, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan dDivision of Evidence-based Laboratory Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Kobe 650-0017, Japan Address for correspondence: Yasuhiro Irino, PhD. Assistant Professor, Division of Evidence-based Laboratory Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan Tel.: +81-78-382-5846; Fax: +81-78-382-5859; E-mail: [email protected] 1 Abstract Cancer cells rapidly consume glutamine as a carbon and nitrogen source to support proliferation, but the cell number continues to increase exponentially after glutamine is nearly depleted from the medium.