Supplemental Table 1. Complete List of the 392 EC1 Homologs
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Human Sulfite Oxidase R160Q: Identification of the Mutation in a Sulfite Oxidase-Deficient Patient and Expression and Characterization of the Mutant Enzyme
Proc. Natl. Acad. Sci. USA Vol. 95, pp. 6394–6398, May 1998 Medical Sciences Human sulfite oxidase R160Q: Identification of the mutation in a sulfite oxidase-deficient patient and expression and characterization of the mutant enzyme ROBERT M. GARRETT*†,JEAN L. JOHNSON*, TYLER N. GRAF*, ANNETTE FEIGENBAUM‡, AND K. V. RAJAGOPALAN*§ *Department of Biochemistry, Duke University Medical Center, Durham, NC 27710; and ‡Department of Genetics, The Hospital for Sick Children and University of Toronto, 555 University Avenue, Toronto, ON, Canada M5G 1X8 Edited by Irwin Fridovich, Duke University Medical Center, Durham, NC, and approved March 19, 1998 (received for review February 17, 1998) ABSTRACT Sulfite oxidase catalyzes the terminal reac- tion in the degradation of sulfur amino acids. Genetic defi- ciency of sulfite oxidase results in neurological abnormalities and often leads to death at an early age. The mutation in the sulfite oxidase gene responsible for sulfite oxidase deficiency in a 5-year-old girl was identified by sequence analysis of cDNA obtained from fibroblast mRNA to be a guanine to adenine transition at nucleotide 479 resulting in the amino acid substitution of Arg-160 to Gln. Recombinant protein containing the R160Q mutation was expressed in Escherichia coli, purified, and characterized. The mutant protein con- tained its full complement of molybdenum and heme, but exhibited 2% of native activity under standard assay condi- tions. Absorption spectroscopy of the isolated molybdenum domains of native sulfite oxidase and of the R160Q mutant showed significant differences in the 480- and 350-nm absorp- tion bands, suggestive of altered geometry at the molybdenum center. -
Enzymes Handling/Processing
Enzymes Handling/Processing 1 Identification of Petitioned Substance 2 3 This Technical Report addresses enzymes used in used in food processing (handling), which are 4 traditionally derived from various biological sources that include microorganisms (i.e., fungi and 5 bacteria), plants, and animals. Approximately 19 enzyme types are used in organic food processing, from 6 at least 72 different sources (e.g., strains of bacteria) (ETA, 2004). In this Technical Report, information is 7 provided about animal, microbial, and plant-derived enzymes generally, and more detailed information 8 is presented for at least one model enzyme in each group. 9 10 Enzymes Derived from Animal Sources: 11 Commonly used animal-derived enzymes include animal lipase, bovine liver catalase, egg white 12 lysozyme, pancreatin, pepsin, rennet, and trypsin. The model enzyme is rennet. Additional details are 13 also provided for egg white lysozyme. 14 15 Chemical Name: Trade Name: 16 Rennet (animal-derived) Rennet 17 18 Other Names: CAS Number: 19 Bovine rennet 9001-98-3 20 Rennin 25 21 Chymosin 26 Other Codes: 22 Prorennin 27 Enzyme Commission number: 3.4.23.4 23 Rennase 28 24 29 30 31 Chemical Name: CAS Number: 32 Peptidoglycan N-acetylmuramoylhydrolase 9001-63-2 33 34 Other Name: Other Codes: 35 Muramidase Enzyme Commission number: 3.2.1.17 36 37 Trade Name: 38 Egg white lysozyme 39 40 Enzymes Derived from Plant Sources: 41 Commonly used plant-derived enzymes include bromelain, papain, chinitase, plant-derived phytases, and 42 ficin. The model enzyme is bromelain. -
Resolving Electron Transport Pathways in the Selenate Respiring Bacterium Thauera Selenatis
RESOLVING ELECTRON TRANSPORT PATHWAYS IN THE SELENATE RESPIRING BACTERIUM THAUERA SELENATIS. Submitted by Elisabeth Clare Lowe To the University of Exeter as a thesis for the degree of Doctor of Philosophy in Biological Sciences, July 2008. This thesis is available for Library use on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. I certify that all material in this thesis which is not my own work has been identified and that no material has previously been submitted and approved for the award of a degree by this or any other University. Elisabeth Clare Lowe Acknowledgements I would like to thank Clive Butler for all his help, support, encouragement and enthusiasm, especially during the move to Exeter and my last few months in the lab. Thanks to Ian Singleton for help and enthusiasm during my time in Newcastle. I also owe huge thanks to everyone in Team Butler, past and present, Carys Watts for helping me get started and all the help with the Thauera preps, Auntie Helen for being brilliant, Jim Leaver for rugby, beer, tea-offs and 30 hour growth curves and Lizzy Dridge for being a great friend and scientific team member, in and out of the lab. Thanks also to everyone in M3013 at the start of my PhD and everyone in the Biocat at the end, for lots of help, borrowing of equipment and most importantly, tea. Thanks to AFP for help, tea breaks and motivation, especially during the writing period. Thank you to everyone who has been generous with their time and equipment, namely Prof. -
Selenium Reduction by Shigella Fergusonii Strain Tb42616 and Pantoea Vagans Strain Ewb32213-2 in Bioreactor Systems
University of Kentucky UKnowledge Theses and Dissertations--Civil Engineering Civil Engineering 2019 BIOLOGICAL SELENIUM CONTROL: SELENIUM REDUCTION BY SHIGELLA FERGUSONII STRAIN TB42616 AND PANTOEA VAGANS STRAIN EWB32213-2 IN BIOREACTOR SYSTEMS Yuxia Ji University of Kentucky, [email protected] Author ORCID Identifier: https://orcid.org/0000-0002-4866-4856 Digital Object Identifier: https://doi.org/10.13023/etd.2019.393 Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Ji, Yuxia, "BIOLOGICAL SELENIUM CONTROL: SELENIUM REDUCTION BY SHIGELLA FERGUSONII STRAIN TB42616 AND PANTOEA VAGANS STRAIN EWB32213-2 IN BIOREACTOR SYSTEMS" (2019). Theses and Dissertations--Civil Engineering. 91. https://uknowledge.uky.edu/ce_etds/91 This Doctoral Dissertation is brought to you for free and open access by the Civil Engineering at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Civil Engineering by an authorized administrator of UKnowledge. For more information, please contact [email protected]. STUDENT AGREEMENT: I represent that my thesis or dissertation and abstract are my original work. Proper attribution has been given to all outside sources. I understand that I am solely responsible for obtaining any needed copyright permissions. I have obtained needed written permission statement(s) from the owner(s) of each third-party copyrighted matter to be included in my work, allowing electronic distribution (if such use is not permitted by the fair use doctrine) which will be submitted to UKnowledge as Additional File. I hereby grant to The University of Kentucky and its agents the irrevocable, non-exclusive, and royalty-free license to archive and make accessible my work in whole or in part in all forms of media, now or hereafter known. -
A Web Tool for Hydrogenase Classification and Analysis Dan Søndergaard1, Christian N
www.nature.com/scientificreports OPEN HydDB: A web tool for hydrogenase classification and analysis Dan Søndergaard1, Christian N. S. Pedersen1 & Chris Greening2,3 H2 metabolism is proposed to be the most ancient and diverse mechanism of energy-conservation. The Received: 24 June 2016 metalloenzymes mediating this metabolism, hydrogenases, are encoded by over 60 microbial phyla Accepted: 09 September 2016 and are present in all major ecosystems. We developed a classification system and web tool, HydDB, Published: 27 September 2016 for the structural and functional analysis of these enzymes. We show that hydrogenase function can be predicted by primary sequence alone using an expanded classification scheme (comprising 29 [NiFe], 8 [FeFe], and 1 [Fe] hydrogenase classes) that defines 11 new classes with distinct biological functions. Using this scheme, we built a web tool that rapidly and reliably classifies hydrogenase primary sequences using a combination of k-nearest neighbors’ algorithms and CDD referencing. Demonstrating its capacity, the tool reliably predicted hydrogenase content and function in 12 newly-sequenced bacteria, archaea, and eukaryotes. HydDB provides the capacity to browse the amino acid sequences of 3248 annotated hydrogenase catalytic subunits and also contains a detailed repository of physiological, biochemical, and structural information about the 38 hydrogenase classes defined here. The database and classifier are freely and publicly available at http://services.birc.au.dk/hyddb/ Microorganisms conserve energy by metabolizing H2. Oxidation of this high-energy fuel yields electrons that can be used for respiration and carbon-fixation. This diffusible gas is also produced in diverse fermentation and 1 anaerobic respiratory processes . H2 metabolism contributes to the growth and survival of microorganisms across the three domains of life, including chemotrophs and phototrophs, lithotrophs and heterotrophs, aerobes and 1,2 anaerobes, mesophiles and extremophiles alike . -
Table S4. List of Enzymes Directly Involved in the Anti-Oxidant Defense Response
Table S4. List of Enzymes directly involved in the anti-oxidant defense response. Gene Name Gene Symbol Classification/Pathway 6-phosphogluconate dehydrogenase 6PGD NADPH regeneration/Pentose Phosphate Glucose-6-phosphate dehydrogenase G6PD NADPH regeneration/Pentose Phosphate Isocitrate Dehydrogenase 1 IDH1 NADPH regeneration/Krebs Isocitrate Dehydrogenase 2 IDH2 NADPH regeneration/Krebs Malic Enzyme 1 ME1 NADPH regeneration/Krebs Methylenetetrahydrofolate dehydrogenase 1 MTHFD1 NADPH regeneration/Folate Methylenetetrahydrofolate dehydrogenase 2 MTHFD2 NADPH regeneration/Folate Nicotinamide Nucleotide Transhydrogenase NNT NADPH regeneration/NAD Catalase CAT Antioxidants/Catalses/free radical detoxification Glutamate-cysteine ligase catalytic subunit GCLC Antioxidants/Glutathione synthesis Glutamate-cysteine ligase modifier subunit GCLM Antioxidants/Glutathione synthesis Glutathione peroxidase1 GPx1 Antioxidants/Glutathione Peroxidases/free radical detoxification Glutathione peroxidase2 GPx2 Antioxidants/Glutathione Peroxidases/free radical detoxification Glutathione peroxidase3 GPx3 Antioxidants/Glutathione Peroxidases/free radical detoxification Glutathione peroxidase4 GPx4 Antioxidants/Glutathione Peroxidases/free radical detoxification Glutathione peroxidase5 GPx5 Antioxidants/Glutathione Peroxidases/free radical detoxification Glutathione peroxidase6 GPx6 Antioxidants/Glutathione Peroxidases/free radical detoxification Glutathione peroxidase7 GPx7 Antioxidants/Glutathione Peroxidases/free radical detoxification Glutathione S-transferase -
Sulfite Dehydrogenases in Organotrophic Bacteria : Enzymes
Sulfite dehydrogenases in organotrophic bacteria: enzymes, genes and regulation. Dissertation zur Erlangung des akademischen Grades des Doktors der Naturwissenschaften (Dr. rer. nat.) an der Universität Konstanz Fachbereich Biologie vorgelegt von Sabine Lehmann Tag der mündlichen Prüfung: 10. April 2013 1. Referent: Prof. Dr. Bernhard Schink 2. Referent: Prof. Dr. Andrew W. B. Johnston So eine Arbeit wird eigentlich nie fertig, man muss sie für fertig erklären, wenn man nach Zeit und Umständen das möglichste getan hat. (Johann Wolfgang von Goethe, Italienische Reise, 1787) DANKSAGUNG An dieser Stelle möchte ich mich herzlich bei folgenden Personen bedanken: . Prof. Dr. Alasdair M. Cook (Universität Konstanz, Deutschland), der mir dieses Thema und seine Laboratorien zur Verfügung stellte, . Prof. Dr. Bernhard Schink (Universität Konstanz, Deutschland), für seine spontane und engagierte Übernahme der Betreuung, . Prof. Dr. Andrew W. B. Johnston (University of East Anglia, UK), für seine herzliche und bereitwillige Aufnahme in seiner Arbeitsgruppe, seiner engagierten Unter- stützung, sowie für die Übernahme des Koreferates, . Prof. Dr. Frithjof C. Küpper (University of Aberdeen, UK), für seine große Hilfsbereitschaft bei der vorliegenden Arbeit und geplanter Manuskripte, als auch für die mentale Unterstützung während der letzten Jahre! Desweiteren möchte ich herzlichst Dr. David Schleheck für die Übernahme des Koreferates der mündlichen Prüfung sowie Prof. Dr. Alexander Bürkle, für die Übernahme des Prüfungsvorsitzes sowie für seine vielen hilfreichen Ratschläge danken! Ein herzliches Dankeschön geht an alle beteiligten Arbeitsgruppen der Universität Konstanz, der UEA und des SAMS, ganz besonders möchte ich dabei folgenden Personen danken: . Dr. David Schleheck und Karin Denger, für die kritische Durchsicht dieser Arbeit, der durch und durch sehr engagierten Hilfsbereitschaft bei Problemen, den zahlreichen wissenschaftlichen Diskussionen und für die aufbauenden Worte, . -
Annotation Guidelines for Experimental Procedures
Annotation Guidelines for Experimental Procedures Developed By Mohammed Alliheedi Robert Mercer Version 1 April 14th, 2018 1- Introduction and background information What is rhetorical move? A rhetorical move can be defined as a text fragment that conveys a distinct communicative goal, in other words, a sentence that implies an author’s specific purpose to readers. What are the types of rhetorical moves? There are several types of rhetorical moves. However, we are interested in 4 rhetorical moves that are common in the method section of a scientific article that follows the Introduction Methods Results and Discussion (IMRaD) structure. 1- Description of a method: It is concerned with a sentence(s) that describes experimental events (e.g., “Beads with bound proteins were washed six times (for 10 min under rotation at 4°C) with pulldown buffer and proteins harvested in SDS-sample buffer, separated by SDS-PAGE, and analyzed by autoradiography.” (Ester & Uetz, 2008)). 2- Appeal to authority: It is concerned with a sentence(s) that discusses the use of standard methods, protocols, and procedures. There are two types of this move: - A reference to a well-established “standard” method (e.g., the use of a method like “PCR” or “electrophoresis”). - A reference to a method that was previously described in the literature (e.g., “Protein was determined using fluorescamine assay [41].” (Larsen, Frandesn and Treiman, 2001)). 3- Source of materials: It is concerned with a sentence(s) that lists the source of biological materials that are used in the experiment (e.g., “All microalgal strains used in this study are available at the Elizabeth Aidar Microalgae Culture Collection, Department of Marine Biology, Federal Fluminense University, Brazil.” (Larsen, Frandesn and Treiman, 2001)). -
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 -
Amino Acid Disorders
471 Review Article on Inborn Errors of Metabolism Page 1 of 10 Amino acid disorders Ermal Aliu1, Shibani Kanungo2, Georgianne L. Arnold1 1Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; 2Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, MI, USA Contributions: (I) Conception and design: S Kanungo, GL Arnold; (II) Administrative support: S Kanungo; (III) Provision of study materials or patients: None; (IV) Collection and assembly of data: E Aliu, GL Arnold; (V) Data analysis and interpretation: None; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors. Correspondence to: Georgianne L. Arnold, MD. UPMC Children’s Hospital of Pittsburgh, 4401 Penn Avenue, Suite 1200, Pittsburgh, PA 15224, USA. Email: [email protected]. Abstract: Amino acids serve as key building blocks and as an energy source for cell repair, survival, regeneration and growth. Each amino acid has an amino group, a carboxylic acid, and a unique carbon structure. Human utilize 21 different amino acids; most of these can be synthesized endogenously, but 9 are “essential” in that they must be ingested in the diet. In addition to their role as building blocks of protein, amino acids are key energy source (ketogenic, glucogenic or both), are building blocks of Kreb’s (aka TCA) cycle intermediates and other metabolites, and recycled as needed. A metabolic defect in the metabolism of tyrosine (homogentisic acid oxidase deficiency) historically defined Archibald Garrod as key architect in linking biochemistry, genetics and medicine and creation of the term ‘Inborn Error of Metabolism’ (IEM). The key concept of a single gene defect leading to a single enzyme dysfunction, leading to “intoxication” with a precursor in the metabolic pathway was vital to linking genetics and metabolic disorders and developing screening and treatment approaches as described in other chapters in this issue. -
Investigation of the Redox Centres of Periplasmic Selenate Reductase
Investigation of the redox centres of periplasmic selenate reductase from Thauera selenatis by EPR spectroscopy Elizabeth J Dridge, Carys A Watts, Brian J Jepson, Kirsty Line, Joanne M Santini, David J Richardson, Clive S Butler To cite this version: Elizabeth J Dridge, Carys A Watts, Brian J Jepson, Kirsty Line, Joanne M Santini, et al.. Investigation of the redox centres of periplasmic selenate reductase from Thauera selenatis by EPR spectroscopy. Biochemical Journal, Portland Press, 2007, 408 (1), pp.19-28. 10.1042/BJ20070669. hal-00478807 HAL Id: hal-00478807 https://hal.archives-ouvertes.fr/hal-00478807 Submitted on 30 Apr 2010 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. Biochemical Journal Immediate Publication. Published on 10 Aug 2007 as manuscript BJ20070669 1 Investigation of the redox centres of selenate reductase from Thauera selenatis by electron paramagnetic resonance spectroscopy Elizabeth J. DRIDGE1,2†, Carys A. WATTS2†, Brian J.N. JEPSON3, Kirsty LINE1, Joanne M. SANTINI4, David J. RICHARDSON3 and Clive S. BUTLER1* 1School of -
Molybdenum Cofactor and Sulfite Oxidase Deficiency Jochen Reiss* Institute of Human Genetics, University Medicine Göttingen, Germany
ics: O om pe ol n b A a c t c e e M s s Reiss, Metabolomics (Los Angel) 2016, 6:3 Metabolomics: Open Access DOI: 10.4172/2153-0769.1000184 ISSN: 2153-0769 Research Article Open Access Molybdenum Cofactor and Sulfite Oxidase Deficiency Jochen Reiss* Institute of Human Genetics, University Medicine Göttingen, Germany Abstract A universal molybdenum-containing cofactor is necessary for the activity of all eukaryotic molybdoenzymes. In humans four such enzymes are known: Sulfite oxidase, xanthine oxidoreductase, aldehyde oxidase and a mitochondrial amidoxime reducing component. Of these, sulfite oxidase is the most important and clinically relevant one. Mutations in the genes MOCS1, MOCS2 or GPHN - all encoding cofactor biosynthesis proteins - lead to molybdenum cofactor deficiency type A, B or C, respectively. All three types plus mutations in the SUOX gene responsible for isolated sulfite oxidase deficiency lead to progressive neurological disease which untreated in most cases leads to death in early childhood. Currently, only for type A of the cofactor deficiency an experimental treatment is available. Introduction combination with SUOX deficiency. Elevated xanthine and lowered uric acid concentrations in the urine are used to differentiate this Isolated sulfite oxidase deficiency (MIM#606887) is an autosomal combined form from the isolated SUOX deficiency. Rarely and only in recessive inherited disease caused by mutations in the sulfite oxidase cases of isolated XOR deficiency xanthine stones have been described (SUOX) gene [1]. Sulfite oxidase is localized in the mitochondrial as a cause of renal failure. Otherwise, isolated XOR deficiency often intermembrane space, where it catalyzes the oxidation of sulfite to goes unnoticed.