Anthranilate Synthase and Chorismate Mutase Activities In
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Part One Amino Acids As Building Blocks
Part One Amino Acids as Building Blocks Amino Acids, Peptides and Proteins in Organic Chemistry. Vol.3 – Building Blocks, Catalysis and Coupling Chemistry. Edited by Andrew B. Hughes Copyright Ó 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim ISBN: 978-3-527-32102-5 j3 1 Amino Acid Biosynthesis Emily J. Parker and Andrew J. Pratt 1.1 Introduction The ribosomal synthesis of proteins utilizes a family of 20 a-amino acids that are universally coded by the translation machinery; in addition, two further a-amino acids, selenocysteine and pyrrolysine, are now believed to be incorporated into proteins via ribosomal synthesis in some organisms. More than 300 other amino acid residues have been identified in proteins, but most are of restricted distribution and produced via post-translational modification of the ubiquitous protein amino acids [1]. The ribosomally encoded a-amino acids described here ultimately derive from a-keto acids by a process corresponding to reductive amination. The most important biosynthetic distinction relates to whether appropriate carbon skeletons are pre-existing in basic metabolism or whether they have to be synthesized de novo and this division underpins the structure of this chapter. There are a small number of a-keto acids ubiquitously found in core metabolism, notably pyruvate (and a related 3-phosphoglycerate derivative from glycolysis), together with two components of the tricarboxylic acid cycle (TCA), oxaloacetate and a-ketoglutarate (a-KG). These building blocks ultimately provide the carbon skeletons for unbranched a-amino acids of three, four, and five carbons, respectively. a-Amino acids with shorter (glycine) or longer (lysine and pyrrolysine) straight chains are made by alternative pathways depending on the available raw materials. -
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. -
Production of Muconic Acid in Plants T ⁎ Aymerick Eudesa,B, , Roland Berthomieua,C, Zhangying Haoa,B, Nanxia Zhaoa,D, ⁎ Veronica Teixeira Benitesa,E, Edward E.K
Metabolic Engineering 46 (2018) 13–19 Contents lists available at ScienceDirect Metabolic Engineering journal homepage: www.elsevier.com/locate/meteng Production of muconic acid in plants T ⁎ Aymerick Eudesa,b, , Roland Berthomieua,c, Zhangying Haoa,b, Nanxia Zhaoa,d, ⁎ Veronica Teixeira Benitesa,e, Edward E.K. Baidooa,e, Dominique Loquéa,b,f,g, a Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA b Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA c Ecole Polytechnique, Université Paris-Saclay, Palaiseau 91120, France d Department of Bioengineering, Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, USA e Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA f Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA g Université Lyon 1, INSA de Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 rue Raphaël Dubois, F-69622, Villeurbanne, France ARTICLE INFO ABSTRACT Keywords: Muconic acid (MA) is a dicarboxylic acid used for the production of industrially relevant chemicals such as Muconic acid adipic acid, terephthalic acid, and caprolactam. Because the synthesis of these polymer precursors generates Salicylic acid toxic intermediates by utilizing petroleum-derived chemicals and corrosive catalysts, the development of al- Catechol ternative strategies for the bio-based production of MA has garnered significant interest. Plants produce organic Shikimate carbon skeletons by harvesting carbon dioxide and energy from the sun, and therefore represent advantageous Plastid hosts for engineered metabolic pathways towards the manufacturing of chemicals. -
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). -
Exploring the Chemistry and Evolution of the Isomerases
Exploring the chemistry and evolution of the isomerases Sergio Martínez Cuestaa, Syed Asad Rahmana, and Janet M. Thorntona,1 aEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom Edited by Gregory A. Petsko, Weill Cornell Medical College, New York, NY, and approved January 12, 2016 (received for review May 14, 2015) Isomerization reactions are fundamental in biology, and isomers identifier serves as a bridge between biochemical data and ge- usually differ in their biological role and pharmacological effects. nomic sequences allowing the assignment of enzymatic activity to In this study, we have cataloged the isomerization reactions known genes and proteins in the functional annotation of genomes. to occur in biology using a combination of manual and computa- Isomerases represent one of the six EC classes and are subdivided tional approaches. This method provides a robust basis for compar- into six subclasses, 17 sub-subclasses, and 245 EC numbers cor- A ison and clustering of the reactions into classes. Comparing our responding to around 300 biochemical reactions (Fig. 1 ). results with the Enzyme Commission (EC) classification, the standard Although the catalytic mechanisms of isomerases have already approach to represent enzyme function on the basis of the overall been partially investigated (3, 12, 13), with the flood of new data, an integrated overview of the chemistry of isomerization in bi- chemistry of the catalyzed reaction, expands our understanding of ology is timely. This study combines manual examination of the the biochemistry of isomerization. The grouping of reactions in- chemistry and structures of isomerases with recent developments volving stereoisomerism is straightforward with two distinct types cis-trans in the automatic search and comparison of reactions. -
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. -
Genetic Characterisaton of Rhodococcus Rhodochrous ATCC
The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town Genetic characterization of Rhodococcus rhodochrous ATCC BAA-870 with emphasis on nitrile hydrolysing enzymes n ow Joni Frederick A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy in the Departmentty of of MolecularCape and T Cell Biology, Universitysi of Cape Town er UnivSupervisor: Professor B. T. Sewell Co-supervisor: Professor D. Brady February 2013 Keywords Nitrile hydrolysis Biocatalysis Rhodococcus rhodochrous ATCC BAA-870 Genome sequencing Nitrilase Nitrile hydratase n ow ty of Cape T si er Univ ii Keywords Abstract Rhodococcus rhodochrous ATCC BAA-870 (BAA-870) had previously been isolated on selective media for enrichment of nitrile hydrolysing bacteria. The organism was found to have a wide substrate range, with activity against aliphatics, aromatics, and aryl aliphatics, and enantioselectivity towards beta substituted nitriles and beta amino nitriles, compounds that have potential applications in the pharmaceutical industry. This makes R. rhodochrous ATCC BAA-870 potentially a versatile biocatalyst for the synthesis of a broad range of compounds with amide and carboxylic acid groups that can be derived from structurally related nitrile precursors. The selectivity of biocatalysts allows for high product yields and better atom economyn than non- selective chemical methods of performing this reaction, suchow as acid or base hydrolysis. -
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). -
Crystal Structure of Chorismate Synthase: a Novel FMN-Binding Protein Fold and Functional Insights
doi:10.1016/j.jmb.2003.12.072 J. Mol. Biol. (2004) 336, 903–915 Crystal Structure of Chorismate Synthase: A Novel FMN-binding Protein Fold and Functional Insights Hyung Jun Ahn, Hye-Jin Yoon, Byung Il Lee and Se Won Suh* Department of Chemistry Chorismate synthase catalyzes the conversion of 5-enolpyruvylshikimate College of Natural Sciences 3-phosphate to chorismate in the shikimate pathway, which represents Seoul National University an attractive target for discovering antimicrobial agents and herbicides. Seoul 151-0742, South Korea Chorismate serves as a common precursor for the synthesis of aromatic amino acids and many aromatic compounds in microorganisms and plants. Chorismate synthase requires reduced FMN as a cofactor but the catalyzed reaction involves no net redox change. Here, we have deter- mined the crystal structure of chorismate synthase from Helicobacter pylori in both FMN-bound and FMN-free forms. It is a tetrameric enzyme, with each monomer possessing a novel “b-a-b sandwich fold”. Highly con- served regions, including several flexible loops, cluster together around the bound FMN to form the active site. The unique FMN-binding site is formed largely by a single subunit, with a small contribution from a neighboring subunit. The isoalloxazine ring of the bound FMN is signifi- cantly non-planar. Our structure illuminates the essential functional roles played by the cofactor. q 2004 Elsevier Ltd. All rights reserved. Keywords: aroC; chorismate synthase; FMN-binding protein; Helicobacter *Corresponding author pylori; shikimate -
Structure of Isochorismate Synthase in Complex with Magnesium
short communications Acta Crystallographica Section D Biological Structure of isochorismate synthase in complex Crystallography with magnesium ISSN 0907-4449 James F. Parsons,a* Katherine M. The electron carrier menaquinone is one of many important bacterial Shia and Jane E. Ladnera,b metabolites that are derived from the key intermediate chorismic acid. MenF, the first enzyme in the menaquinone pathway, catalyzes the isomerization of chorismate to isochorismate. Here, an improved structure of MenF in a new a Center for Advanced Research in crystal form is presented. The structure, solved at 2.0 A˚ resolution in complex Biotechnology, University of Maryland Biotechnology Institute, USA, and bNational with magnesium, reveals a well defined closed active site. Existing evidence Institute of Standards and Technology, USA suggests that the mechanism of the reaction catalyzed by MenF involves nucleophilic attack of a water molecule on the chorismate ring. The structure reveals a well defined water molecule located in an appropriate position for Correspondence e-mail: activation by Lys190 and attack on the substrate. [email protected] Received 23 January 2008 Accepted 26 February 2008 1. Introduction The menaquinone-specific isochorismate synthase (MenF) from Escherichia coli is a chorismate-utilizing enzyme that catalyzes the formation of isochorismate for use in menaquinone biosynthesis PDB References: apo-MenF, 3bzm, r3bzmsf; MenF–Mg2+ complex, 3bzn, r3bznsf. (Fig. 1; Daruwala et al., 1997). Menaquinone is an electron carrier that is essential for anaerobic electron transport in bacteria. Isochorismate is also an intermediate in the biosynthesis of sidero- phores such as the iron chelator enterobactin. The E. coli genome encodes a second isochorismate synthase, EntC, which is involved in this pathway (Buss et al., 2001).