Enzyme Catalysed Tandem Reactions Abstract 1 Introduction
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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. -
Measuring Phenol Oxidase and Peroxidase Activities with Pyrogallol, L-DOPA, and ABTS: Effect of Assay Conditions and Soil Type
UC Irvine UC Irvine Previously Published Works Title Measuring phenol oxidase and peroxidase activities with pyrogallol, l-DOPA, and ABTS: Effect of assay conditions and soil type Permalink https://escholarship.org/uc/item/3nw4m85r Authors Bach, CE Warnock, DD Van Horn, DJ et al. Publication Date 2013-12-01 DOI 10.1016/j.soilbio.2013.08.022 Peer reviewed eScholarship.org Powered by the California Digital Library University of California SBB5589_grabs ■ 10 September 2013 ■ 1/1 Soil Biology & Biochemistry xxx (2013) 1 Contents lists available at ScienceDirect Soil Biology & Biochemistry journal homepage: www.elsevier.com/locate/soilbio 1 2 3 4 Highlights 5 6 We tested whether pH and redox potential affect three common oxidase substrates. 7 Pyrogallol and ABTS were useless under alkaline conditions for different reasons. 8 L-DOPA appears to be stable for use across a broad range of pH. 9 Autoclaved and combusted soils cannot be used as negative controls. 10 Current “oxidase” methods measure a soil property more so than enzyme activity. 11 12 0038-0717/$ e see front matter Ó 2013 Published by Elsevier Ltd. http://dx.doi.org/10.1016/j.soilbio.2013.08.022 Please cite this article in press as: Bach, C.E., et al., Measuring phenol oxidase and peroxidase activities with pyrogallol, L-DOPA, and ABTS: Effect of assay conditions and soil type, Soil Biology & Biochemistry (2013), http://dx.doi.org/10.1016/j.soilbio.2013.08.022 SBB5589_proof ■ 10 September 2013 ■ 1/9 Soil Biology & Biochemistry xxx (2013) 1e9 Contents lists available at ScienceDirect Soil Biology & Biochemistry journal homepage: www.elsevier.com/locate/soilbio 1 56 2 Measuring phenol oxidase and peroxidase activities with pyrogallol, 57 3 58 4 L-DOPA, and ABTS: Effect of assay conditions and soil type 59 5 60 6 a b b c 61 Q5 Christopher E. -
Oxidative Power: Tools for Assessing LPMO Activity on Cellulose
biomolecules Review Oxidative Power: Tools for Assessing LPMO Activity on Cellulose Federica Calderaro 1,2,* , Loes E. Bevers 1 and Marco A. van den Berg 1 1 DSM Biotechnology Center, 2613 AX Delft, The Netherlands; [email protected] (L.E.B.); [email protected] (M.A.v.d.B.) 2 Molecular Enzymolog y Group, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands * Correspondence: [email protected]; Tel.: +31-6-36028569 Abstract: Lytic polysaccharide monooxygenases (LPMOs) have sparked a lot of research regarding their fascinating mode-of-action. Particularly, their boosting effect on top of the well-known cel- lulolytic enzymes in lignocellulosic hydrolysis makes them industrially relevant targets. As more characteristics of LPMO and its key role have been elucidated, the need for fast and reliable methods to assess its activity have become clear. Several aspects such as its co-substrates, electron donors, inhibiting factors, and the inhomogeneity of lignocellulose had to be considered during experimental design and data interpretation, as they can impact and often hamper outcomes. This review provides an overview of the currently available methods to measure LPMO activity, including their potential and limitations, and it is illustrated with practical examples. Keywords: lytic polysaccharide monooxygenase; enzyme assay; cellulose; lignocellulosic biomass; chromatography; enzyme kinetics Citation: Calderaro, F.; Bevers, L.E.; van den Berg, M.A. Oxidative Power: Tools for Assessing LPMO Activity 1. Introduction on Cellulose. Biomolecules 2021, 11, Until recently, the enzymatic conversion of recalcitrant polysaccharidic materials such 1098. https://doi.org/10.3390/ as chitin or cellulose was thought to solely depend on the activity of hydrolytic enzymes. -
Molecular Analysis of the Aldolase B Gene in Patients with Hereditary
1of8 J Med Genet: first published as 10.1136/jmg.39.9.e56 on 1 September 2002. Downloaded from ONLINE MUTATION REPORT Molecular analysis of the aldolase B gene in patients with hereditary fructose intolerance from Spain J C Sánchez-Gutiérrez, T Benlloch, M A Leal, B Samper, I García-Ripoll, J E Felíu ............................................................................................................................. J Med Genet 2002;39:e56 (http://www.jmedgenet.com/cgi/content/full/39/9/e56) ereditary fructose intolerance (HFI) is an autosomal resident in the following regions: Madrid (11 families), Anda- recessive metabolic disorder caused by aldolase (fructo- lusia (4), Galicia (3), Estremadura (1), Valencia (1), and Hsediphosphate aldolase, EC 4.1.2.13) B deficiency.1 The Spanish possessions in North Africa (1). HFI diagnosis was B isoform of aldolase is critical for the metabolism of based on enzymatic studies (deficient aldolase B activity in exogenous fructose by the liver, kidney, and intestine, since it hepatic biopsies from 16 patients) or clinical symptoms (six can use fructose-1-phosphate as substrate at physiological patients). Another six subjects were suspected to suffer from concentrations, unlike aldolases A and C. Affected subjects HFI on the basis of dietary intolerance with episodes sugges- suffer abdominal pain, vomiting, and hypoglycaemia after the tive of hypoglycaemia and occurrence of the disease in their ingestion of fructose, sucrose, or sorbitol. Continued ingestion first degree relatives. of noxious sugars causes hepatic and renal injury, which eventually leads to liver cirrhosis and sometimes death, Reagents particularly in small infants.1 Treatment consists of strict Thermostable DNA polymerase, deoxynucleotides, and gen- elimination of fructose, sucrose, and sorbitol from the diet eral PCR products were from Biotools (Madrid, Spain). -
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Research Article Glutathione Transferase P Plays a Critical Role in the Development of Lung Carcinogenesis following Exposure to Tobacco-Related Carcinogens and Urethane Kenneth J. Ritchie,1 Colin J. Henderson,1 Xiu Jun Wang,1 Olga Vassieva,1 Dianne Carrie,1 Peter B. Farmer,2 Margaret Gaskell,2 Kevin Park,3 and C. Roland Wolf1 1Cancer Research UK Molecular Pharmacology Unit, Biomedical Research Centre, Ninewells Hospital and Medical School, Dundee, United Kingdom; 2Cancer Biomarkers and Prevention Group, Biocentre, University of Leicester, Leicester, United Kingdom;and 3Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, United Kingdom Abstract family of dimeric enzymes (EC 2.5.1.18;GST a, A, k, u, j, ~, n, and N) Human cancer is controlled by a complex interaction between identified on the basis of their amino acid sequence and substrate genetic and environmental factors. Such environmental specificity (4). GSTs are regarded as being important detoxification factors are well defined for smoking-induced lung cancer; enzymes due to their capacity to catalyze the addition of reduced however, the roles of specific genes have still to be elucidated. glutathione (GSH) to reactive electrophiles produced by cyto- Glutathione transferase P (GSTP) catalyzes the detoxification chrome P450 metabolism. As a consequence, there has been a of electrophilic diol epoxides produced by the metabolism of significant interest in elucidating the relationship between GSTP polycyclic aromatic hydrocarbons such as benzo[a]pyrene function and resistance to cancer chemotherapeutic agents and the development of cancer (5–7). In a genetic approach to study GST (BaP), a common constituent of tobacco smoke. Activity- altering polymorphisms in Gstp have therefore been speculated functions, we have generated mice nulled at the Gstp gene locus to be potential risk modifiers in lung cancer development. -
Insights Into the Oxidative Degradation of Cellulose by a Copper Metalloenzyme That Exploits Biomass Components
Insights into the oxidative degradation of cellulose by a copper metalloenzyme that exploits biomass components R. Jason Quinlana,1, Matt D. Sweeneya,1, Leila Lo Leggiob, Harm Ottenb, Jens-Christian N. Poulsenb, Katja Salomon Johansenc,2, Kristian B. R. M. Kroghc, Christian Isak Jørgensenc, Morten Tovborgc, Annika Anthonsenc, Theodora Tryfonad, Clive P. Walterc, Paul Dupreed, Feng Xua, Gideon J. Daviese, and Paul H. Waltone aNovozymes, Inc., Davis, CA 95618; bDepartment of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark; cNovozymes A/S, DK-2880 Bagsværd, Denmark; dDepartment of Biochemistry, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QW, United Kingdom; and eDepartment of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom Edited* by Diter von Wettstein, Washington State University, Pullman, WA, and approved August 2, 2011 (received for review April 13, 2011) The enzymatic degradation of recalcitrant plant biomass is one lysis. From this work, it was suggested that GH61s act directly on of the key industrial challenges of the 21st century. Accordingly, cellulose rendering it more accessible to traditional cellulase there is a continuing drive to discover new routes to promote action (11). Moreover, recent genomic sequencing of the brown polysaccharide degradation. Perhaps the most promising approach rot fungi Postia placenta showed a number of GH61 genes in this involves the application of “cellulase-enhancing factors,” such as organism (13–15), indicating the widespread nature of this those from the glycoside hydrolase (CAZy) GH61 family. Here we family of enzymes in cellulose degradation. As such, GH61s show that GH61 enzymes are a unique family of copper-depen- likely hold major potential for industrial decomposition of dent oxidases. -
Evaluation of Oxidative Enzymes in Leaf Tissue from Intact Cotton Plants Exposed to Different Oxygen Concentrations
EVALUATION OF OXIDATIVE ENZYMES IN LEAF TISSUE FROM INTACT COTTON PLANTS EXPOSED TO DIFFERENT OXYGEN CONCENTRATIONS by Joyce Geraldine Foster Dissertation submitted to the Graduate Faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Biochemistry and Nutrition APPROVED: J. L. Hess, Chairman L. B. Barnett R. D. Brown, Jr. 't. M. Grego2'y L. D. Moore R. R. Schmidt March,1979 Blacksburg, Virginia ACKNOWLEDGMENTS My deepest appreciation is extended to my advisor, Dr. John L. Hess, whose assistance, optimism, and con- stant encouragement during this project made even the darkest hours seem bright. A heartfelt thank you goes to my committee members, Dr. L. B. Barnett, Dr. R. D. Brown, Jr., Dr. E. M. Gregory, Dr. L. D. Moore, and Dr. R. R. Schmidt, for their support and guida~ce throughout the degree program and especially during Dr. Hess' sabba- tical. I especially wish to acknowledge for arranging extended use of growth chambers and instru- ments for monitoring environmental conditions and tissue properties and particularly for his invaluable technical advice. Special thanks are express2d to Dr. E. M. Gregory for his constant assistance with experimental design 2nd maintenance of equipment. The follJwing people who so generously made their instruments available during the course of this project are also grc. l:efully acknowledged: Dr. E. M. Gregory, I Dr. R. D. Brown, Jr• I I and Dr. R. R. Schmidt. I am also grateful to ii , and the personnel of the Virginia Polytechnic Institute and State University soils testing lab for their assistance in the identification of optimal culture condi- tions for cotton in controlled environments; to and personnel of the Virginia Polytechnic Institute and State University statistics consulting center for as- sistance with statistical analysis of data; to for competent technical assistance; to , and all the fellows in the department for moving untold numbers of compressed gas cylinders; and to and for typing this dissertation. -
Gut Bacterial Tyrosine Decarboxylases Restrict the Bioavailability Of
bioRxiv preprint doi: https://doi.org/10.1101/356246; this version posted August 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Title: Gut bacterial tyrosine decarboxylases restrict the bioavailability of levodopa, the primary treatment in Parkinson’s disease Authors: Sebastiaan P. van Kessel1, Alexandra K. Frye1, Ahmed O. El-Gendy1,2, Maria Castejon1, Ali Keshavarzian3, Gertjan van Dijk4, Sahar El Aidy1*† Affiliations: 1 Department of Molecular Immunology and Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands. 2 Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt 3 Division of Digestive Disease and Nutrition, Section of Gastroenterology, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois. 4 Department of Behavioral Neuroscience, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands. * Corresponding author. Email: [email protected] † Present address: Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands. P:+31(0)503632201. 1 bioRxiv preprint doi: https://doi.org/10.1101/356246; this version posted August 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Summary Human gut bacteria play a critical role in the regulation of immune and metabolic systems, as well as in the function of the nervous system. The microbiota senses its environment and responds by releasing metabolites, some of which are key regulators of human health and disease. -
Isolation and Characterization of a Mutant Liver Aldolase in Adult Hereditary Fructose Intolerance
Isolation and characterization of a mutant liver aldolase in adult hereditary fructose intolerance. Identification of the enzyme variant by radioassay in tissue biopsy specimens Timothy M. Cox, … , Michael Camilleri, Arthur H. Burghes J Clin Invest. 1983;72(1):201-213. https://doi.org/10.1172/JCI110958. Hereditary fructose intolerance (HFI) is a metabolic disorder caused by enzymic deficiency of aldolase B, a genetically distinct cytosolic isoenzyme expressed exclusively in liver, kidney, and intestine. The molecular basis of this enzyme defect has been investigated in three affected individuals from a nonconsanguineous kindred, in whom fructose-l- phosphate aldolase activities in liver or intestinal biopsy samples were reduced to 2-6% of mean control values. To identify a putative enzyme mutant in tissue extracts, aldolase B was purified from human liver by affinity chromatography and monospecific antibodies were prepared from antiserum raised in sheep. Immunodiffusion gels showed a single precipitin line common to pure enzyme and extracts of normal liver and intestine, but no reaction with extracts of brain, muscle, or HFI liver. However, weak positive staining for aldolase in hepatocyte and enterocyte cytosol was demonstrated by indirect immunofluorescence of HFI tissues. This was abolished by pretreatment with pure enzyme protein. Accordingly, a specific radioimmunoassay (detection limit 7.5 ng) was established to quantify immunoreactive aldolase B in human biopsy specimens. Extracts of tissue from affected patients gave 10-25% immunoreactive enzyme in control samples; immunoreactive aldolase in intestinal extracts from four heterozygotes was reduced (to 55%) when compared with seven samples from normal control subjects (P < 0.05). In extracts of HFI tissues, there was a sevenfold reduction in apparent absolute specific […] Find the latest version: https://jci.me/110958/pdf Isolation and Characterization of a Mutant Liver Aldolase in Adult Hereditary Fructose Intolerance IDENTIFICATION OF THE ENZYME VARIANT BY RADIOASSAY IN TISSUE BIOPSY SPECIMENS TIMOTHY M. -
Structure and Ligands Interactions of Citrus Tryptophan Decarboxylase by Molecular Modeling and Docking Simulations
Communication Structure and Ligands Interactions of Citrus Tryptophan Decarboxylase by Molecular Modeling and Docking Simulations Angelo Facchiano 1,*, Domenico Pignone 2, Luigi Servillo 3, Domenico Castaldo 4 and Luigi De Masi 5,* 1 Consiglio Nazionale delle Ricerche (CNR), Istituto di Scienze dell’Alimentazione (ISA), 83100 Avellino, Italy; [email protected] 2 CNR, Istituto di Bioscienze e BioRisorse (IBBR), 70126 Bari, Italy; [email protected] 3 Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Napoli, Italy; [email protected] 4 Stazione Sperimentale per le Industrie delle Essenze e dei Derivati dagli Agrumi (SSEA), Azienda Speciale della Camera di Commercio di Reggio Calabria, 89125 Reggio Calabria, Italy; [email protected] 5 CNR, IBBR, 80055 Portici, Italy; [email protected] * Correspondence: [email protected] (A.F.); [email protected] (L.D.M.). Received: 29 December 2019; Accepted: 22 March 2019; Published: 26 March 2019 Abstract: In a previous work, we in silico annotated protein sequences of Citrus genus plants as putative tryptophan decarboxylase (pTDC). Here, we investigated the structural properties of Citrus pTDCs by using the TDC sequence of Catharanthus roseus as an experimentally annotated reference to carry out comparative modeling and substrate docking analyses. The functional annotation as TDC was verified by combining 3D molecular modeling and docking simulations, evidencing the peculiarities and the structural similarities with C. roseus TDC. Docking with L-tryptophan as a ligand showed specificity of pTDC for this substrate. These combined results confirm our previous in silico annotation of the examined protein sequences of Citrus as TDC and provide support for TDC activity in this plant genus. -
No Temperature Acclimation of Soil Extracellular Enzymes to Experimental Warming in an Alpine Grassland Ecosystem on the Tibetan Plateau
Biogeochemistry DOI 10.1007/s10533-013-9844-2 No temperature acclimation of soil extracellular enzymes to experimental warming in an alpine grassland ecosystem on the Tibetan Plateau Xin Jing • Yonghui Wang • Haegeun Chung • Zhaorong Mi • Shiping Wang • Hui Zeng • Jin-Sheng He Received: 12 September 2012 / Accepted: 28 March 2013 Ó Springer Science+Business Media Dordrecht 2013 Abstract Alpine grassland soils store large amounts Tibetan Plateau. A free air-temperature enhancement of soil organic carbon (SOC) and are susceptible to system was set up in May 2006. We measured soil rising air temperature. Soil extracellular enzymes microbial biomass, nutrient availability and the activity catalyze the rate-limiting step in SOC decomposition of five extracellular enzymes in 2009 and 2010. The Q10 and their catalysis, production and degradation rates are of each enzyme was calculated using a simple first-order regulated by temperature. Therefore, the responses of exponential equation. We found that warming had no these enzymes to warming could have a profound significant effects on soil microbial biomass C, the labile impact on carbon cycling in the alpine grassland C or N content, or nutrient availability. Significant ecosystems. This study was conducted to measure the differences in the activity of most extracellular enzymes responses of soil extracellular enzyme activity and among sampling dates were found, with typically higher temperature sensitivity (Q10) to experimental warming enzyme activity during the warm period of the year. The in samples from an alpine grassland ecosystem on the effects of warming on the activity of the five extracel- lular enzymes at 20 °C were not significant. -
Screening Method to Evaluate Amino Acid-Decarboxylase Activity of Bacteria Present in Spanish Artisanal Ripened Cheeses
foods Article Screening Method to Evaluate Amino Acid-Decarboxylase Activity of Bacteria Present in Spanish Artisanal Ripened Cheeses Diana Espinosa-Pesqueira, Artur X. Roig-Sagués * and M. Manuela Hernández-Herrero CIRTTA—Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Travessera dels Turons S/N, 08193 Barcelona, Spain; [email protected] (D.E.-P.); [email protected] (M.M.H.-H.) * Correspondence: [email protected]; Tel.: +34-935-812-582 Received: 13 September 2018; Accepted: 31 October 2018; Published: 6 November 2018 Abstract: A qualitative microplate screening method, using both low nitrogen (LND) and low glucose (LGD) decarboxylase broths, was used to evaluate the biogenic amine (BA) forming capacity of bacteria present in two types of Spanish ripened cheeses, some of them treated by high hydrostatic pressure. BA formation in decarboxylase broths was later confirmed by High Performance Liquid Chromatography (HPLC). An optimal cut off between 10–25 mg/L with a sensitivity of 84% and a specificity of 92% was obtained when detecting putrescine (PU), tyramine (TY) and cadaverine (CA) formation capability, although these broths showed less capacity detecting histamine forming bacteria. TY forming bacteria were the most frequent among the isolated BA forming strains showing a strong production capability (exceeding 100 mg/L), followed by CA and PU formers. Lactococcus, Lactobacillus, Enterococcus and Leuconostoc groups were found as the main TY producers, and some strains were also able to produce diamines at a level above 100 mg/L, and probably ruled the BA formation during ripening. Enterobacteriaceae and Staphylococcus spp., as well as some Bacillus spp.