Action of Multiple Rice -Glucosidases on Abscisic Acid Glucose Ester
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United States Patent (19) 11, 3,708,396 Mitsuhashi Et Al
United States Patent (19) 11, 3,708,396 Mitsuhashi et al. (45) Jan. 2, 1973 54 PROCESS FOR PRODUCING 3,492,203 1/1970 Mitsuhashi............................. 195/31 MALTTOL 3,565,765 2/1971 Heady et al.................. .......... 195/31 75) Inventors: Masakazu Mitsuhashi, Okayama-shi, 3,535,123 10/1970 Heady.................................... 195/31 Okayama; Mamoru Hirao, Akaiwa 2,004,135 6/1935 Rothrock.......................... 260/635 C gun, Okayama; Kaname Sugimoto, OTHER PUBLICATIONS Okayama-shi, Okayama, all of Japan Abdullah et al., Mechanism of Carbohydrase Action, Vol.43, 1966. 73) : Assignee: Hayashibara Company, Okayama, Hou, E. F., Chem. Abs., Vol. 69, 1968, 53049d. Japan Kjolberg et al., Biochem. J. p. 258-262, Vol. 86, 1963. 22 Filed: Jan. 8, 1969 Lee et al., Arch Biochem. Biophys, Vol. 1 16, p. (21) Appl. No.:789,912 162-167, 1966. Payur, J. H., Starch, Chem. and Tech., Vol. 1, p. 166, 30 Foreign Application Priority Data 1965. Jan. 23, 1968 Japan.................................. 43/3862 Primary Examiner-A. Louis Monacell July 1, 1968 Japan................................. 43148921 Assistant Examiner-Gary M. Nath July 1 1, 1968 Japan................................. 43148922 Attorney-Browdy and Neimark 52 U.S. Cl.............. 195/31 R, 260/635 C, 99/141 R 5 Int. Cl................................................ C13d 1100 57 ABSTRACT 58) Field of Search............. 195/31; 99/141; 127/37; A process for producing maltitol from a starch slurry 260/635 C which comprises hydrolyzing the starch slurry with beta-amylase and alpha-1,6-glucosidase to produce a 56 References Cited high maltose containing product and catalytically hydrogenating the maltose with Raney nickel after ad UNITED STATES PATENTS justing the pH of the maltose product with calcium 2,868,847 111959 Boyers................................. -
The Architecture of the Protein Domain Universe
The architecture of the protein domain universe Nikolay V. Dokholyan Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC 27599 ABSTRACT Understanding the design of the universe of protein structures may provide insights into protein evolution. We study the architecture of the protein domain universe, which has been found to poses peculiar scale-free properties (Dokholyan et al., Proc. Natl. Acad. Sci. USA 99: 14132-14136 (2002)). We examine the origin of these scale-free properties of the graph of protein domain structures (PDUG) and determine that that the PDUG is not modular, i.e. it does not consist of modules with uniform properties. Instead, we find the PDUG to be self-similar at all scales. We further characterize the PDUG architecture by studying the properties of the hub nodes that are responsible for the scale-free connectivity of the PDUG. We introduce a measure of the betweenness centrality of protein domains in the PDUG and find a power-law distribution of the betweenness centrality values. The scale-free distribution of hubs in the protein universe suggests that a set of specific statistical mechanics models, such as the self-organized criticality model, can potentially identify the principal driving forces of molecular evolution. We also find a gatekeeper protein domain, removal of which partitions the largest cluster into two large sub- clusters. We suggest that the loss of such gatekeeper protein domains in the course of evolution is responsible for the creation of new fold families. INTRODUCTION The principles of molecular evolution remain elusive despite fundamental breakthroughs on the theoretical front 1-5 and a growing amount of genomic and proteomic data, over 23,000 solved protein structures 6 and protein functional annotations 7-9. -
Structure and Function of a Glycoside Hydrolase Family 8 Endoxylanase from Teredinibacter Turnerae
This is a repository copy of Structure and function of a glycoside hydrolase family 8 endoxylanase from Teredinibacter turnerae. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/137106/ Version: Published Version Article: Fowler, Claire A, Hemsworth, Glyn R orcid.org/0000-0002-8226-1380, Cuskin, Fiona et al. (5 more authors) (2018) Structure and function of a glycoside hydrolase family 8 endoxylanase from Teredinibacter turnerae. Acta crystallographica. Section D, Structural biology. pp. 946-955. ISSN 2059-7983 https://doi.org/10.1107/S2059798318009737 Reuse This article is distributed under the terms of the Creative Commons Attribution (CC BY) licence. This licence allows you to distribute, remix, tweak, and build upon the work, even commercially, as long as you credit the authors for the original work. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ research papers Structure and function of a glycoside hydrolase family 8 endoxylanase from Teredinibacter turnerae ISSN 2059-7983 Claire A. Fowler,a Glyn R. Hemsworth,b Fiona Cuskin,c Sam Hart,a Johan Turkenburg,a Harry J. Gilbert,d Paul H. Waltone and Gideon J. Daviesa* aYork Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England, b Received 20 March 2018 School of Molecular and Cellular Biology, The Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, c Accepted 9 July 2018 England, School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne NE1 7RU, England, dInstitute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, England, and eDepartment of Chemistry, The University of York, York YO10 5DD, England. -
Supplementary Table S1. Table 1. List of Bacterial Strains Used in This Study Suppl
Supplementary Material Supplementary Tables: Supplementary Table S1. Table 1. List of bacterial strains used in this study Supplementary Table S2. List of plasmids used in this study Supplementary Table 3. List of primers used for mutagenesis of P. intermedia Supplementary Table 4. List of primers used for qRT-PCR analysis in P. intermedia Supplementary Table 5. List of the most highly upregulated genes in P. intermedia OxyR mutant Supplementary Table 6. List of the most highly downregulated genes in P. intermedia OxyR mutant Supplementary Table 7. List of the most highly upregulated genes in P. intermedia grown in iron-deplete conditions Supplementary Table 8. List of the most highly downregulated genes in P. intermedia grown in iron-deplete conditions Supplementary Figures: Supplementary Figure 1. Comparison of the genomic loci encoding OxyR in Prevotella species. Supplementary Figure 2. Distribution of SOD and glutathione peroxidase genes within the genus Prevotella. Supplementary Table S1. Bacterial strains Strain Description Source or reference P. intermedia V3147 Wild type OMA14 isolated from the (1) periodontal pocket of a Japanese patient with periodontitis V3203 OMA14 PIOMA14_I_0073(oxyR)::ermF This study E. coli XL-1 Blue Host strain for cloning Stratagene S17-1 RP-4-2-Tc::Mu aph::Tn7 recA, Smr (2) 1 Supplementary Table S2. Plasmids Plasmid Relevant property Source or reference pUC118 Takara pBSSK pNDR-Dual Clonetech pTCB Apr Tcr, E. coli-Bacteroides shuttle vector (3) plasmid pKD954 Contains the Porpyromonas gulae catalase (4) -
Review Article Pullulanase: Role in Starch Hydrolysis and Potential Industrial Applications
Hindawi Publishing Corporation Enzyme Research Volume 2012, Article ID 921362, 14 pages doi:10.1155/2012/921362 Review Article Pullulanase: Role in Starch Hydrolysis and Potential Industrial Applications Siew Ling Hii,1 Joo Shun Tan,2 Tau Chuan Ling,3 and Arbakariya Bin Ariff4 1 Department of Chemical Engineering, Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, 53300 Kuala Lumpur, Malaysia 2 Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia 3 Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia 4 Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia Correspondence should be addressed to Arbakariya Bin Ariff, [email protected] Received 26 March 2012; Revised 12 June 2012; Accepted 12 June 2012 Academic Editor: Joaquim Cabral Copyright © 2012 Siew Ling Hii et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The use of pullulanase (EC 3.2.1.41) has recently been the subject of increased applications in starch-based industries especially those aimed for glucose production. Pullulanase, an important debranching enzyme, has been widely utilised to hydrolyse the α-1,6 glucosidic linkages in starch, amylopectin, pullulan, and related oligosaccharides, which enables a complete and efficient conversion of the branched polysaccharides into small fermentable sugars during saccharification process. The industrial manufacturing of glucose involves two successive enzymatic steps: liquefaction, carried out after gelatinisation by the action of α- amylase; saccharification, which results in further transformation of maltodextrins into glucose. -
Mannoside Recognition and Degradation by Bacteria Simon Ladeveze, Elisabeth Laville, Jordane Despres, Pascale Mosoni, Gabrielle Veronese
Mannoside recognition and degradation by bacteria Simon Ladeveze, Elisabeth Laville, Jordane Despres, Pascale Mosoni, Gabrielle Veronese To cite this version: Simon Ladeveze, Elisabeth Laville, Jordane Despres, Pascale Mosoni, Gabrielle Veronese. Mannoside recognition and degradation by bacteria. Biological Reviews, Wiley, 2016, 10.1111/brv.12316. hal- 01602393 HAL Id: hal-01602393 https://hal.archives-ouvertes.fr/hal-01602393 Submitted on 26 May 2020 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. Biol. Rev. (2016), pp. 000–000. 1 doi: 10.1111/brv.12316 Mannoside recognition and degradation by bacteria Simon Ladeveze` 1, Elisabeth Laville1, Jordane Despres2, Pascale Mosoni2 and Gabrielle Potocki-Veron´ ese` 1∗ 1LISBP, Universit´e de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France 2INRA, UR454 Microbiologie, F-63122, Saint-Gen`es Champanelle, France ABSTRACT Mannosides constitute a vast group of glycans widely distributed in nature. Produced by almost all organisms, these carbohydrates are involved in numerous cellular processes, such as cell structuration, protein maturation and signalling, mediation of protein–protein interactions and cell recognition. The ubiquitous presence of mannosides in the environment means they are a reliable source of carbon and energy for bacteria, which have developed complex strategies to harvest them. -
Structure of Human Endo-Α-1,2-Mannosidase (MANEA), an Antiviral Host- Glycosylation Target
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.30.179523; this version posted July 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 CLASSIFICATION: Biological Sciences / Physical Sciences (Chemistry) TITLE: Structure of human endo-α-1,2-mannosidase (MANEA), an antiviral host- glycosylation target AUTHORS: Łukasz F. Sobala1, Pearl Z Fernandes2, Zalihe Hakki2, Andrew J Thompson1, Jonathon D Howe3, Michelle Hill3, Nicole Zitzmann3, Scott Davies4, Zania Stamataki4, Terry D. Butters3, Dominic S. Alonzi3, Spencer J Williams2,*, Gideon J Davies1,* AFFILIATIONS: 1. Department of Chemistry, University of York, YO10 5DD, United Kingdom. 2. School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia. 3. Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road Oxford OX1 3QU, United Kingdom. 4. Institute for Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom. CORRESPONDING AUTHOR: [email protected], ORCID 0000-0001-6341-4364 [email protected] ORCID 0000-0002-7343-776X bioRxiv preprint doi: https://doi.org/10.1101/2020.06.30.179523; this version posted July 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. -
Cmse 520 Biomolecular Structure, Function And
CMSE 520 BIOMOLECULAR STRUCTURE, FUNCTION AND DYNAMICS (Computational Structural Biology) OUTLINE Review: Molecular biology Proteins: structure, conformation and function(5 lectures) Generalized coordinates, Phi, psi angles, DNA/RNA: structure and function (3 lectures) Structural and functional databases (PDB, SCOP, CATH, Functional domain database, gene ontology) Use scripting languages (e.g. python) to cross refernce between these databases: starting from sequence to find the function Relationship between sequence, structure and function Molecular Modeling, homology modeling Conservation, CONSURF Relationship between function and dynamics Confromational changes in proteins (structural changes due to ligation, hinge motions, allosteric changes in proteins and consecutive function change) Molecular Dynamics Monte Carlo Protein-protein interaction: recognition, structural matching, docking PPI databases: DIP, BIND, MINT, etc... References: CURRENT PROTOCOLS IN BIOINFORMATICS (e-book) (http://www.mrw.interscience.wiley.com/cp/cpbi/articles/bi0101/frame.html) Andreas D. Baxevanis, Daniel B. Davison, Roderic D.M. Page, Gregory A. Petsko, Lincoln D. Stein, and Gary D. Stormo (eds.) 2003 John Wiley & Sons, Inc. INTRODUCTION TO PROTEIN STRUCTURE Branden C & Tooze, 2nd ed. 1999, Garland Publishing COMPUTER SIMULATION OF BIOMOLECULAR SYSTEMS Van Gusteren, Weiner, Wilkinson Internet sources Ref: Department of Energy Rapid growth in experimental technologies Human Genome Projects Two major goals 1. DNA mapping 2. DNA sequencing Rapid growth in experimental technologies z Microrarray technologies – serial gene expression patterns and mutations z Time-resolved optical, rapid mixing techniques - folding & function mechanisms (Æ ns) z Techniques for probing single molecule mechanics (AFM, STM) (Æ pN) Æ more accurate models/data for computer-aided studies Weiss, S. (1999). Fluorescence spectroscopy of single molecules. -
Structural and Functional Studies of Glycoside Hydrolase Family 12 Enzymes from Trichoderma Reesei and Other Cellulolytic Microorganisms
Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 819 Structural and Functional Studies of Glycoside Hydrolase Family 12 Enzymes from Trichoderma reesei and other Cellulolytic Microorganisms BY MATS SANDGREN ACTA UNIVERSITATIS UPSALIENSIS UPPSALA 2003 Dissertation for the Degree of Doctor of Philosophy in Molecular Biology presented at Uppsala University in 2003. ABSTRACT Sandgren, M. 2003. Structural and functional studies of glycoside hydrolase family 12 enzymes from Trichoderma reesei and other cellulolytic microorganisms. Acta Universitatis Upsaliensis. Comprehensive Summaries of Uppsala Dissertations from the faculty of Science and Technology 819. 68 pp. Uppsala. ISBN 91-554-5562-X Cellulose is the most abundant organic compound on earth. A wide range of highly specialized microorganisms, have evolved that utilize cellulose as carbon and energy source. Enzymes called cellulases, produced by these cellulolytic organisms, perform the major part of cellulose degradation. In this study the three-dimensional structure of four homologous glycoside hydrolase family 12 cellulases will be presented, three fungal enzymes; Humicola grisea Cel12A, Hypocrea schweinitzii Cel12A, Trichoderma reesei Cel12A, and one bacterial; Streptomyces sp. 11AG8 Cel12A. The structural and biochemical information gathered from these and 15 other GH family 12 homologues has been used for the design of variants of these enzymes. These variants have biochemically been characterized, and thereby the positions and the types of mutations have been identified responsible for the biochemical differences between the homologous enzymes, e.g., thermal stability and activity. The three-dimensional structures of two T. reesei Cel12A variants, where the mutations have significant impact on the stability or the activity of the enzyme have been determined. -
Glycoside Hydrolase Stabilization of Transition State Charge: New Directions for Inhibitor Design† Cite This: Chem
Chemical Science View Article Online EDGE ARTICLE View Journal | View Issue Glycoside hydrolase stabilization of transition state charge: new directions for inhibitor design† Cite this: Chem. Sci., 2020, 11, 10488 a a a b All publication charges for this article Weiwu Ren, ‡ Marco Farren-Dai, Natalia Sannikova, Katarzyna Swiderek,´ have been paid for by the Royal Society Yang Wang, ‡a Oluwafemi Akintola, a Robert Britton, *a Vicent Moliner *b of Chemistry and Andrew J. Bennet *a Carbasugars are structural mimics of naturally occurring carbohydrates that can interact with and inhibit enzymes involved in carbohydrate processing. In particular, carbasugars have attracted attention as inhibitors of glycoside hydrolases (GHs) and as therapeutic leads in several disease areas. However, it is unclear how the carbasugars are recognized and processed by GHs. Here, we report the synthesis of three carbasugar isotopologues and provide a detailed transition state (TS) analysis for the formation of the initial GH-carbasugar covalent intermediate, as well as for hydrolysis of this intermediate, using a combination of experimentally measured kinetic isotope effects and hybrid QM/MM calculations. We find that the a-galactosidase from Thermotoga maritima effectively stabilizes TS charge development on Creative Commons Attribution-NonCommercial 3.0 Unported Licence. a remote C5-allylic center acting in concert with the reacting carbasugar, and catalysis proceeds via an exploded, or loose, SN2 transition state with no discrete enzyme-bound cationic intermediate. We conclude that, in complement to what we know about the TS structures of enzyme-natural substrate Received 10th August 2020 complexes, knowledge of the TS structures of enzymes reacting with non-natural carbasugar substrates Accepted 16th September 2020 shows that GHs can stabilize a wider range of positively charged TS structures than previously thought. -
Microbial Beta Glucosidase Enzymes: Recent Advances in Biomass Conversation for Biofuels Application
biomolecules Review Microbial Beta Glucosidase Enzymes: Recent Advances in Biomass Conversation for Biofuels Application 1, , 2 3 1 4, Neha Srivastava * y, Rishabh Rathour , Sonam Jha , Karan Pandey , Manish Srivastava y, Vijay Kumar Thakur 5,* , Rakesh Singh Sengar 6, Vijai K. Gupta 7,* , Pranab Behari Mazumder 8, Ahamad Faiz Khan 2 and Pradeep Kumar Mishra 1,* 1 Department of Chemical Engineering and Technology, IIT (BHU), Varanasi 221005, India; [email protected] 2 Department of Bioengineering, Integral University, Lucknow 226026, India; [email protected] (R.R.); [email protected] (A.F.K.) 3 Department of Botany, Banaras Hindu University, Varanasi 221005, India; [email protected] 4 Department of Physics and Astrophysics, University of Delhi, Delhi 110007, India; [email protected] 5 Enhanced Composites and Structures Center, School of Aerospace, Transport and Manufacturing, Cranfield University, Bedfordshire MK43 0AL, UK 6 Department of Agriculture Biotechnology, College of Agriculture, Sardar Vallabhbhai Patel, University of Agriculture and Technology, Meerut 250110, U.P., India; [email protected] 7 Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, Tallinn University of Technology, 12618 Tallinn, Estonia 8 Department of Biotechnology, Assam University, Silchar 788011, India; [email protected] * Correspondence: [email protected] (N.S.); vijay.Kumar@cranfield.ac.uk (V.K.T.); [email protected] (V.K.G.); [email protected] (P.K.M.); Tel.: +372-567-11014 (V.K.G.); Fax: +372-620-4401 (V.K.G.) These authors have equal contribution. y Received: 29 March 2019; Accepted: 28 May 2019; Published: 6 June 2019 Abstract: The biomass to biofuels production process is green, sustainable, and an advanced technique to resolve the current environmental issues generated from fossil fuels. -
Catalytic Properties, Functional Attributes and Industrial Applications of B-Glucosidases
3 Biotech (2016) 6:3 DOI 10.1007/s13205-015-0328-z ORIGINAL ARTICLE Catalytic properties, functional attributes and industrial applications of b-glucosidases 1 2 3 Gopal Singh • A. K. Verma • Vinod Kumar Received: 20 April 2015 / Accepted: 19 June 2015 / Published online: 31 December 2015 Ó The Author(s) 2015. This article is published with open access at Springerlink.com Abstract b-Glucosidases are diverse group of enzymes with biochemical characterization of such enzymes is with great functional importance to biological systems. presented for the better understanding and efficient use of These are grouped in multiple glycoside hydrolase families diverse b-glucosidases. based on their catalytic and sequence characteristics. Most studies carried out on b-glucosidases are focused on their Keywords b-Glucosidases Á Glycoside hydrolase Á industrial applications rather than their endogenous func- Cellulosome Á Glucosides Á Cellulase tion in the target organisms. b-Glucosidases performed many functions in bacteria as they are components of large complexes called cellulosomes and are responsible for the Introduction hydrolysis of short chain oligosaccharides and cellobiose. In plants, b-glucosidases are involved in processes like b-Glucosidases (b-D-glucopyrranoside glucohydrolase) formation of required intermediates for cell wall lignifi- [E.C.3.2.1.21] are the enzymes which hydrolyze the gly- cation, degradation of endosperm’s cell wall during ger- cosidic bond of a carbohydrate moiety to release nonre- mination and in plant defense against biotic stresses. ducing terminal glycosyl residues, glycoside and Mammalian b-glucosidases are thought to play roles in oligosaccharides (Bhatia et al. 2002; Morant et al.