Exploring the Chemistry and Evolution of the Isomerases
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Regulation of the Tyrosine Kinase Itk by the Peptidyl-Prolyl Isomerase Cyclophilin A
Regulation of the tyrosine kinase Itk by the peptidyl-prolyl isomerase cyclophilin A Kristine N. Brazin, Robert J. Mallis, D. Bruce Fulton, and Amy H. Andreotti* Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011 Edited by Owen N. Witte, University of California, Los Angeles, CA, and approved December 14, 2001 (received for review October 5, 2001) Interleukin-2 tyrosine kinase (Itk) is a nonreceptor protein tyrosine ulation of the cis and trans conformers. The majority of folded kinase of the Tec family that participates in the intracellular proteins for which three-dimensional structural information has signaling events leading to T cell activation. Tec family members been gathered contain trans prolyl imide bonds. The cis con- contain the conserved SH3, SH2, and catalytic domains common to formation occurs at a frequency of Ϸ6% in folded proteins (17), many kinase families, but they are distinguished by unique se- and a small subset of proteins are conformationally heteroge- quences outside of this region. The mechanism by which Itk and neous with respect to cis͞trans isomerization (18–21). Further- related Tec kinases are regulated is not well understood. Our more, the activation energy for interconversion between cis and studies indicate that Itk catalytic activity is inhibited by the peptidyl trans proline is high (Ϸ20 kcal͞mol) leading to slow intercon- prolyl isomerase activity of cyclophilin A (CypA). NMR structural version rates (22). This barrier is a rate-limiting step in protein studies combined with mutational analysis show that a proline- folding and may serve to kinetically isolate two functionally and dependent conformational switch within the Itk SH2 domain reg- conformationally distinct molecules. -
Part I Principles of Enzyme Catalysis
j1 Part I Principles of Enzyme Catalysis Enzyme Catalysis in Organic Synthesis, Third Edition. Edited by Karlheinz Drauz, Harald Groger,€ and Oliver May. Ó 2012 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2012 by Wiley-VCH Verlag GmbH & Co. KGaA. j3 1 Introduction – Principles and Historical Landmarks of Enzyme Catalysis in Organic Synthesis Harald Gr€oger and Yasuhisa Asano 1.1 General Remarks Enzyme catalysis in organic synthesis – behind this term stands a technology that today is widely recognized as a first choice opportunity in the preparation of a wide range of chemical compounds. Notably, this is true not only for academic syntheses but also for industrial-scale applications [1]. For numerous molecules the synthetic routes based on enzyme catalysis have turned out to be competitive (and often superior!) compared with classic chemicalaswellaschemocatalyticsynthetic approaches. Thus, enzymatic catalysis is increasingly recognized by organic chemists in both academia and industry as an attractive synthetic tool besides the traditional organic disciplines such as classic synthesis, metal catalysis, and organocatalysis [2]. By means of enzymes a broad range of transformations relevant in organic chemistry can be catalyzed, including, for example, redox reactions, carbon–carbon bond forming reactions, and hydrolytic reactions. Nonetheless, for a long time enzyme catalysis was not realized as a first choice option in organic synthesis. Organic chemists did not use enzymes as catalysts for their envisioned syntheses because of observed (or assumed) disadvantages such as narrow substrate range, limited stability of enzymes under organic reaction conditions, low efficiency when using wild-type strains, and diluted substrate and product solutions, thus leading to non-satisfactory volumetric productivities. -
Pin1 Inhibitors: Towards Understanding the Enzymatic
Pin1 Inhibitors: Towards Understanding the Enzymatic Mechanism Guoyan Xu Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University In the partial fulfillment of the requirement for the degree of Doctor of Philosophy In Chemistry Felicia A Etzkorn, Chair David G. I. Kingston Neal Castagnoli Paul R. Carlier Brian E. Hanson May 6, 2010 Blacksburg, Virginia Keywords: Pin1, anti-cancer drug target, transition-state analogues, ketoamides, ketones, reduced amides, PPIase assay, inhibition Pin1 Inhibitors: Towards Understanding the Enzymatic Mechanism Guoyan Xu Abstract An important role of Pin1 is to catalyze the cis-trans isomerization of pSer/Thr- Pro bonds; as such, it plays an important role in many cellular events through the effects of conformational change on the function of its biological substrates, including Cdc25, c- Jun, and p53. The expression of Pin1 correlates with cyclin D1 levels, which contributes to cancer cell transformation. Overexpression of Pin1 promotes tumor growth, while its inhibition causes tumor cell apoptosis. Because Pin1 is overexpressed in many human cancer tissues, including breast, prostate, and lung cancer tissues, it plays an important role in oncogenesis, making its study vital for the development of anti-cancer agents. Many inhibitors have been discovered for Pin1, including 1) several classes of designed inhibitors such as alkene isosteres, non-peptidic, small molecular Pin1 inhibitors, and indanyl ketones, and 2) several natural products such as juglone, pepticinnamin E analogues, PiB and its derivatives obtained from a library screen. These Pin1 inhibitors show promise in the development of novel diagnostic and therapeutic anticancer drugs due to their ability to block cell cycle progression. -
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 -
Genomic Analyses of Unique Carbohydrate and Phytohormone Metabolism in the Macroalga Gracilariopsis Lemaneiformis (Rhodophyta)
Sun et al. BMC Plant Biology (2018) 18:94 https://doi.org/10.1186/s12870-018-1309-2 RESEARCH ARTICLE Open Access Genomic analyses of unique carbohydrate and phytohormone metabolism in the macroalga Gracilariopsis lemaneiformis (Rhodophyta) Xue Sun1, Jun Wu2, Guangce Wang3, Yani Kang1,2, Hong Sain Ooi4, Tingting Shen2, Fangjun Wang1, Rui Yang1, Nianjun Xu1* and Xiaodong Zhao2* Abstract Background: Red algae are economically valuable for food and in industry. However, their genomic information is limited, and the genomic data of only a few species of red algae have been sequenced and deposited recently. In this study, we annotated a draft genome of the macroalga Gracilariopsis lemaneiformis (Gracilariales, Rhodophyta). Results: The entire 88.98 Mb genome of Gp. lemaneiformis 981 was generated from 13,825 scaffolds (≥500 bp) with an N50 length of 30,590 bp, accounting for approximately 91% of this algal genome. A total of 38.73 Mb of scaffold sequences were repetitive, and 9281 protein-coding genes were predicted. A phylogenomic analysis of 20 genomes revealed the relationship among the Chromalveolata, Rhodophyta, Chlorophyta and higher plants. Homology analysis indicated phylogenetic proximity between Gp. lemaneiformis and Chondrus crispus. The number of enzymes related to the metabolism of carbohydrates, including agar, glycoside hydrolases, glycosyltransferases, was abundant. In addition, signaling pathways associated with phytohormones such as auxin, salicylic acid and jasmonates are reported for the first time for this alga. Conclusion: We sequenced and analyzed a draft genome of the red alga Gp. lemaneiformis, and revealed its carbohydrate metabolism and phytohormone signaling characteristics. This work will be helpful in research on the functional and comparative genomics of the order Gracilariales and will enrich the genomic information on marine algae. -
ENZYMES: Catalysis, Kinetics and Mechanisms N
ENZYMES: Catalysis, Kinetics and Mechanisms N. S. Punekar ENZYMES: Catalysis, Kinetics and Mechanisms N. S. Punekar Department of Biosciences & Bioengineering Indian Institute of Technology Bombay Mumbai, Maharashtra, India ISBN 978-981-13-0784-3 ISBN 978-981-13-0785-0 (eBook) https://doi.org/10.1007/978-981-13-0785-0 Library of Congress Control Number: 2018947307 # Springer Nature Singapore Pte Ltd. 2018 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Printed on acid-free paper This Springer imprint is published by the registered company Springer Nature Singapore Pte Ltd. -
Role of Protein Repair Enzymes in Oxidative Stress Survival And
Shome et al. Annals of Microbiology (2020) 70:55 Annals of Microbiology https://doi.org/10.1186/s13213-020-01597-2 REVIEW ARTICLE Open Access Role of protein repair enzymes in oxidative stress survival and virulence of Salmonella Arijit Shome1* , Ratanti Sarkhel1, Shekhar Apoorva1, Sonu Sukumaran Nair2, Tapan Kumar Singh Chauhan1, Sanjeev Kumar Bhure1 and Manish Mahawar1 Abstract Purpose: Proteins are the principal biomolecules in bacteria that are affected by the oxidants produced by the phagocytic cells. Most of the protein damage is irreparable though few unfolded proteins and covalently modified amino acids can be repaired by chaperones and repair enzymes respectively. This study reviews the three protein repair enzymes, protein L-isoaspartyl O-methyl transferase (PIMT), peptidyl proline cis-trans isomerase (PPIase), and methionine sulfoxide reductase (MSR). Methods: Published articles regarding protein repair enzymes were collected from Google Scholar and PubMed. The information obtained from the research articles was analyzed and categorized into general information about the enzyme, mechanism of action, and role played by the enzymes in bacteria. Special emphasis was given to the importance of these enzymes in Salmonella Typhimurium. Results: Protein repair is the direct and energetically preferred way of replenishing the cellular protein pool without translational synthesis. Under the oxidative stress mounted by the host during the infection, protein repair becomes very crucial for the survival of the bacterial pathogens. Only a few covalent modifications of amino acids are reversible by the protein repair enzymes, and they are highly specific in activity. Deletion mutants of these enzymes in different bacteria revealed their importance in the virulence and oxidative stress survival. -
Coordinated Slowing of Metabolism in Enteric Bacteria Under Nitrogen
Coordinated Slowing of Metabolism in Enteric Bacteria under Nitrogen Limitation: A Perspective Ned S. Wingreen NEC Research Institute, 4 Independence Way Princeton, New Jersey 08540 and Department of Physics, University of California Berkeley, CA 94720 Sydney Kustu Department of Plant Biology, Molecular and Cell Biology University of California, Berkeley, CA 94720 Abstract It is natural to ask how bacteria coordinate metabolism when depletion of an essential nutrient limits their growth, and they must slow their entire rate of biosyn- thesis. A major nutrient with a fluctuating abundance is nitrogen. The growth rate of enteric bacteria under nitrogen-limiting conditions is known to correlate with the internal concentration of free glutamine, the glutamine pool. Here we compare the patterns of utilization of L-glutamine and L-glutamate, the two central inter- mediates of nitrogen metabolism. Monomeric precursors of all of the cell’s macro- molecules – proteins, nucleic acids, and surface polymers – require the amide group of glutamine at the first dedicated step of biosynthesis. This is the case even though only a minority (∼12%) of total cell nitrogen derives from glutamine. In contrast, the amino group of glutamate, which provides the remainder of cell nitrogen, is arXiv:physics/0110037v1 [physics.bio-ph] 12 Oct 2001 generally required late in biosynthetic pathways, e.g. in transaminase reactions for amino acid synthesis. We propose that the pattern of glutamine dependence coor- dinates the decrease in biosynthesis under conditions of nitrogen limitation. Hence, the glutamine pool plays a global regulatory role in the cell. 1 INTRODUCTION Enteric bacteria are notable for their varying environment. -
Letters to Nature
letters to nature Received 7 July; accepted 21 September 1998. 26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the re®nement of macromolecules. Acta Crystallogr. A 48, 912±916 (1992). 1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli signal peptidases. Protein Sci. 6, 1129±1138 (1997). and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073±12080 2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement (1983). for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274±280 (1993). 28. Kraulis, P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. 3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader J. Appl. Crystallogr. 24, 946±950 (1991). peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935±3941 29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and (1995). the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281±296 (1991). 4. Allsop, A. E. et al.inAnti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationships 30. Meritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505± (eds Bently, P. H. & O'Hanlon, P. J.) 61±72 (R. Soc. Chem., Cambridge, 1997). -
Physcomitrium Patens Infection by Colletotrichum Gloeosporioides: Understanding the Fungal–Bryophyte Interaction by Microscopy, Phenomics and RNA Sequencing
Journal of Fungi Article Physcomitrium patens Infection by Colletotrichum gloeosporioides: Understanding the Fungal–Bryophyte Interaction by Microscopy, Phenomics and RNA Sequencing Adriana Otero-Blanca 1 , Yordanis Pérez-Llano 1 , Guillermo Reboledo-Blanco 2, Verónica Lira-Ruan 1 , Daniel Padilla-Chacon 3, Jorge Luis Folch-Mallol 4 , María del Rayo Sánchez-Carbente 4 , Inés Ponce De León 2 and Ramón Alberto Batista-García 1,* 1 Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico; [email protected] (A.O.-B.); [email protected] (Y.P.-L.); [email protected] (V.L.-R.) 2 Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo 11600, Uruguay; [email protected] (G.R.-B.); [email protected] (I.P.D.L.) 3 Consejo Nacional de Ciencia y Tecnología (CONACyT), Colegio de Postgraduados de México, Campus Montecillo, Texcoco 56230, Mexico; [email protected] 4 Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico; [email protected] (J.L.F.-M.); [email protected] (M.d.R.S.-C.) Citation: Otero-Blanca, A.; * Correspondence: [email protected] or [email protected]; Tel.: +52-777-3297020 Pérez-Llano, Y.; Reboledo-Blanco, G.; Lira-Ruan, V.; Padilla-Chacon, D.; Abstract: Anthracnose caused by the hemibiotroph fungus Colletotrichum gloeosporioides is a dev- Folch-Mallol, J.L.; Sánchez-Carbente, astating plant disease with an extensive impact on plant productivity. The process of colonization M.d.R.; Ponce De León, I.; and disease progression of C. -
(10) Patent No.: US 8119385 B2
US008119385B2 (12) United States Patent (10) Patent No.: US 8,119,385 B2 Mathur et al. (45) Date of Patent: Feb. 21, 2012 (54) NUCLEICACIDS AND PROTEINS AND (52) U.S. Cl. ........................................ 435/212:530/350 METHODS FOR MAKING AND USING THEMI (58) Field of Classification Search ........................ None (75) Inventors: Eric J. Mathur, San Diego, CA (US); See application file for complete search history. Cathy Chang, San Diego, CA (US) (56) References Cited (73) Assignee: BP Corporation North America Inc., Houston, TX (US) OTHER PUBLICATIONS c Mount, Bioinformatics, Cold Spring Harbor Press, Cold Spring Har (*) Notice: Subject to any disclaimer, the term of this bor New York, 2001, pp. 382-393.* patent is extended or adjusted under 35 Spencer et al., “Whole-Genome Sequence Variation among Multiple U.S.C. 154(b) by 689 days. Isolates of Pseudomonas aeruginosa” J. Bacteriol. (2003) 185: 1316 1325. (21) Appl. No.: 11/817,403 Database Sequence GenBank Accession No. BZ569932 Dec. 17. 1-1. 2002. (22) PCT Fled: Mar. 3, 2006 Omiecinski et al., “Epoxide Hydrolase-Polymorphism and role in (86). PCT No.: PCT/US2OO6/OOT642 toxicology” Toxicol. Lett. (2000) 1.12: 365-370. S371 (c)(1), * cited by examiner (2), (4) Date: May 7, 2008 Primary Examiner — James Martinell (87) PCT Pub. No.: WO2006/096527 (74) Attorney, Agent, or Firm — Kalim S. Fuzail PCT Pub. Date: Sep. 14, 2006 (57) ABSTRACT (65) Prior Publication Data The invention provides polypeptides, including enzymes, structural proteins and binding proteins, polynucleotides US 201O/OO11456A1 Jan. 14, 2010 encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides. -
Amino Acid Residue. Chorismate Mutase by Variation of a Single
Modulation of the allosteric equilibrium of yeast chorismate mutase by variation of a single amino acid residue. R Graf, Y Dubaquié and G H Braus J. Bacteriol. 1995, 177(6):1645. Downloaded from Updated information and services can be found at: http://jb.asm.org/content/177/6/1645 These include: CONTENT ALERTS Receive: RSS Feeds, eTOCs, free email alerts (when new articles cite this article), more» http://jb.asm.org/ on March 22, 2013 by guest Information about commercial reprint orders: http://journals.asm.org/site/misc/reprints.xhtml To subscribe to to another ASM Journal go to: http://journals.asm.org/site/subscriptions/ JOURNAL OF BACTERIOLOGY, Mar. 1995, p. 1645–1648 Vol. 177, No. 6 0021-9193/95/$04.0010 Copyright q 1995, American Society for Microbiology Modulation of the Allosteric Equilibrium of Yeast Chorismate Mutase by Variation of a Single Amino Acid Residue RONEY GRAF,† YVES DUBAQUIE´,‡ AND GERHARD H. BRAUS* Institut fu¨r Mikrobiologie, Biochemie & Genetik, Friedrich-Alexander Universita¨t Erlangen-Nu¨rnberg, D-91058 Erlangen, Germany Received 26 September 1994/Accepted 11 January 1995 Chorismate mutase (EC 5.4.99.5) from the yeast Saccharomyces cerevisiae is an allosteric enzyme which can be locked in its active R (relaxed) state by a single threonine-to-isoleucine exchange at position 226. Seven new replacements of residue 226 reveal that this position is able to direct the enzyme’s allosteric equilibrium, without interfering with the catalytic constant or the affinity for the activator. Downloaded from Chorismate is the last common precursor of the amino acids amino acid 226 of yeast chorismate mutase to glycine and tyrosine, phenylalanine, and tryptophan and an important in- alanine (small), aspartate and arginine (charged), serine (hy- termediate in the biosynthesis of other aromatic compounds in drophilic, similar to the wild-type threonine), cysteine (sulfur fungi, bacteria, and plants (9).