Coenzymes and Prosthetic Groups Nomenclature
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A New Mode of B Binding and the Direct Participation of A
Research Article 997 A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase Naoki Shibata1, Jun Masuda1, Takamasa Tobimatsu2, Tetsuo Toraya2*, Kyoko Suto1, Yukio Morimoto1 and Noritake Yasuoka1* Background: Diol dehydratase is an enzyme that catalyzes the adenosylcobalamin Addresses: 1Department of Life Science, Himeji (coenzyme B ) dependent conversion of 1,2-diols to the corresponding Institute of Technology, 1475-2 Kanaji, Kamigori, 12 Ako-gun, Hyogo 678-1297, Japan and 2Department aldehydes. The reaction initiated by homolytic cleavage of the cobalt–carbon bond of Bioscience and Biotechnology, Faculty of α β γ of the coenzyme proceeds by a radical mechanism. The enzyme is an 2 2 2 Engineering, Okayama University, Tsushima-Naka, heterooligomer and has an absolute requirement for a potassium ion for catalytic Okayama 700-8530, Japan. activity. The crystal structure analysis of a diol dehydratase–cyanocobalamin *Corresponding authors. complex was carried out in order to help understand the mechanism of action of E-mail: [email protected] this enzyme. [email protected] Results: The three-dimensional structure of diol dehydratase in complex with Key words: B12 enzyme, diol dehydratase, radicals, cyanocobalamin was determined at 2.2 Å resolution. The enzyme exists as a reaction mechanism, TIM barrel αβγ dimer of heterotrimers ( )2. The cobalamin molecule is bound between the Received: 16 March 1999 α and β subunits in the ‘base-on’ mode, that is, 5,6-dimethylbenzimidazole of Revisions requested: 7 April 1999 the nucleotide moiety coordinates to the cobalt atom in the lower axial position. -
The Influence of Vitamin B12on the Content, Distribution and in Vivo
The Influence of Vitamin B12on the Content, Distribution and in Vivo Synthesis of Thiamine Pyrophosphate, Flavin Adenine Dinucleotide and Pyridine Nucleotides in Rat Liver1 URMILA MARFATIA, D. V. REGE, H. P. TIPNIS ANDA. SREENIVASAN Department of Chemical Technology, University of Bombay, Matunga, Bombay Apart from the well-known interrelation (FAD) and pyridine nucleotides (PN), and ships among the B vitamins, there is rea to their in vivo synthesis from the corre son to believe that folie acid and vitamin sponding administered vitamins, in the rat Downloaded from Bu may influence the functioning of other liver. Data on the distribution of these vitamins as cofactors. Thus, dietary folie cofactors in liver cells of the normal rat acid has been known to determine rat are available in the works of Goethart ('52) liver stores of coenzyme A (CoA) and and Dianzani and Dianzani Mor ('57) on adenotriphosphate (ATP) (Popp and Tot TPP, of Carruthers and Suntzeff ('54) and ter, '52; Totter, '53); a decrease in liver Dianzani ('55) on pyridine nucleotides DPN is also caused by aminopterin2 (PN) and of Schneider and Hogeboom jn.nutrition.org (Strength et al., '54). The in vivo incor (Schneider, '56) on FAD. poration of nitcotinamide into pyridino- nucleotides in rat liver is affected in a EXPERIMENTAL deficiency of vitamin B«(Nadkarni et al., Young, male Wistar rats weighing ap '57). Low blood level of citrovorum factor proximately 100 gm each were used. The by guest on April 19, 2011 in the hyperthyroid, vitamin Bi2-deficient animals, housed individually in raised rat is corrected by administration of vita mesh-bottom cages, were initially depleted min B«(Pfander et al., '52). -
Chemistry and Functions of Proteins
TVER STATE MEDICAL UNIVERSITY BIOCHEMISTRY DEPARTMENT CHEMISTRY AND FUNCTIONS OF PROTEINS ILLUSTRATED BIOCHEMISTRY Schemes, formulas, terms and algorithm of preparation The manual for making notes of lectures and preparation for classes Tver, 2018 AMINO ACIDS -amino acids -These are organic acids with at least a minimum of one of its hydrogen atoms in the carbon chains substituted by an amino group.( Show the radical, amino and carboxyl groups) NH2 R | C – H | COOH Proteinogenous and Nonproteinogenous Amino acids - Major proteinogenous (standard) amino acids. (Give the names of each amino acid) R R 1 H – 2 CH3 – 12 HO – CH2 – (CH3)2 CH – 3 CH3 – CH – (CH3)2 CH – CH2 – 4 13 | CH3 – CH2 – CH – OH 5 | CH 3 6 14 HS – CH2 – HOOC – CH2 – 15 CH3 – S – CH2 – CH2 – 7 HOOC – CH2 – CH2 – NH2 | – C – H - | COOH 8 16 NH2 – CO – CH2 – 9 NH2 – CO – CH2 – CH2 – 17 10 NH2 – (CH2)3 – CH2 – 18 NH2 – C – NH – (CH2)3 – CH2 – 11 || NH 19 20 СООН NH -Glycine -Arginine Alanine -Serine -Valine -Threonine Leucine -Cysteine Isoleucine -Methionine Aspartic acid -Phenylalanine Glutamic acid -Tyrosine Asparagine -Tryptophan Glutamine -Histidine Lysine -Proline •Rare proteinogenous (standard) amino acids. ( Derivatives of lysine, proline and tyrosine) NH2 | H2N – CH2 – CH – (CH2)2 – CH | | OH COOH •Nonproteinogenous amino acids. (Name and show them) NH2 NH2 | | H2N – (CH2)3 – CH HS – (CH2)2 – CH | | COOH COOH NH2 | NH2 – C – HN – (CH2)3 – CH || | O COOH Ornithine Homocysteine Citrulline 2 CLASSIFICATION OF PROTEINOGENOUS (STANDARD) AMINO ACIDS Amino acids are classified by: *The structure of the radical (show); - aliphatic amino acids -monoaminodicarboxylic amino acids -amides of amino acids -diaminomonocarboxylic amino acids -hydroxy amino acids -sulfur-containing amino acids -cyclic (aromatic and heterolytic) amino acids *the polarity of the radical (show); -Non-polar (hydrophobic –Ala, Val, Leu, Ile, Trp, Pro.) -Polar (hydrophilic). -
Chapter 7. "Coenzymes and Vitamins" Reading Assignment
Chapter 7. "Coenzymes and Vitamins" Reading Assignment: pp. 192-202, 207-208, 212-214 Problem Assignment: 3, 4, & 7 I. Introduction Many complex metabolic reactions cannot be carried out using only the chemical mechanisms available to the side-chains of the 20 standard amino acids. To perform these reactions, enzymes must rely on other chemical species known broadly as cofactors that bind to the active site and assist in the reaction mechanism. An enzyme lacking its cofactor is referred to as an apoenzyme whereas the enzyme with its cofactor is referred to as a holoenzyme. Cofactors are subdivided into essential ions and organic molecules known as coenzymes (Fig. 7.1). Essential ions, commonly metal ions, may participate in substrate binding or directly in the catalytic mechanism. Coenzymes typically act as group transfer agents, carrying electrons and chemical groups such as acyl groups, methyl groups, etc., depending on the coenzyme. Many of the coenzymes are derived from vitamins which are essential for metabolism, growth, and development. We will use this chapter to introduce all of the vitamins and coenzymes. In a few cases--NAD+, FAD, coenzyme A--the mechanisms of action will be covered. For the remainder of the water-soluble vitamins, discussion of function will be delayed until we encounter them in metabolism. We also will discuss the biochemistry of the fat-soluble vitamins here. II. Inorganic cation cofactors Many enzymes require metal cations for activity. Metal-activated enzymes require or are stimulated by cations such as K+, Ca2+, or Mg2+. Often the metal ion is not tightly bound and may even be carried into the active site attached to a substrate, as occurs in the case of kinases whose actual substrate is a magnesium-ATP complex. -
Roles of Vitamin Metabolizing Genes in Multidrug-Resistant Plasmids of Superbugs
bioRxiv preprint doi: https://doi.org/10.1101/285403; this version posted March 20, 2018. 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 4.0 International license. Roles of Vitamin Metabolizing Genes in Multidrug-Resistant Plasmids of Superbugs Asit Kumar Chakraborty, Genetic Engineering Laboratory, Department of Biotechnology & Biochemistry, Oriental Institute of Science & Technology, Vidyasagar University, Midnapore 721102, West Bengal, India. Abstract Superbug crisis has rocked this world with million deaths due to failure of potent antibiotics. Thousands mdr genes with hundreds of mutant isomers are generated. Small integrons and R-plasmids have combined with F'-plasmids creating a space for >10-20 of mdr genes that inactivate antibiotics in different mechanisms. Mdr genes are created to save bacteria from antibiotics because gut microbiota synthesize >20 vitamins and complex bio-molecules needed for >30000 biochemical reactions of human metabolosome. In other words, mdr gene creation is protected from both sides, intestinal luminal cells and gut bacteria in a tight symbiotic signalling system. We have proposed, to avert the crisis all vitamin metabolizing genes will be acquired in MDR- plasmids if we continue oral antibiotics therapy. Therefore, we have checked the plasmid databases and have detected thiamine, riboflavin, folate, cobalamine and biotin metabolizing enzymes in MDR plasmids. Thus vit genes may mobilise recently into MDR-plasmids and are likely essential for gut microbiota protection. Analysis found that cob and thi genes are abundant and likely very essential than other vit genes. -
ATP Structure and Function
ATP: Universal Currency of Cellular Energy All living things including plants, animals, birds, insects, humans need energy for the proper functioning of cells, tissues and other organ systems. As we are aware that green plants, obtain their energy from the sunlight, and animals get their energy by feeding on these plants. Energy acts as a source of fuel. We, humans, gain energy from the food we eat, but how are the energy produced and stored in our body. A living cell cannot store significant amounts of free energy. Excess free energy would result in an increase of heat in the cell, which would result in excessive thermal motion that could damage and then destroy the cell. Rather, a cell must be able to handle that energy in a way that enables the cell to store energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the “energy currency” of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell. How? It functions similarly to a rechargeable battery. When ATP is broken down, usually by the removal of its terminal phosphate group, energy is released. The energy is used to do work by the cell, usually by the released phosphate binding to another molecule, activating it. For example, in the mechanical work of muscle contraction, ATP supplies the energy to move the contractile muscle proteins. Recall the active transport work of the sodium-potassium pump in cell membranes. -
Bioenergetics, ATP & Enzymes
Bioenergetics, ATP & Enzymes Some Important Compounds Involved in Energy Transfer and Metabolism Bioenergetics can be defined as all the energy transfer mechanisms occurring within living organisms. Energy transfer is necessary because energy cannot be created and it cannot be destroyed (1st law of thermodynamics). Organisms can acquire energy from chemicals (chemotrophs) or they can acquire it from light (phototrophs), but they cannot make it. Thermal energy (heat) from the environment can influence the rate of chemical reactions, but is not generally considered an energy source organisms can “capture” and put to specific uses. Metabolism, all the chemical reactions occurring within living organisms, is linked to bioenergetics because catabolic reactions release energy (are exergonic) and anabolic reactions require energy (are endergonic). Various types of high-energy compounds can “donate” the energy required to drive endergonic reactions, but the most commonly used energy source within cells is adenosine triphosphate (ATP), a type of coenzyme. When this molecule is catabolized (broken down), the energy released can be used to drive a wide variety of synthesis reactions. Endergonic reactions required for the synthesis of nucleic acids (DNA and RNA) are exceptions because all the nucleotides incorporated into these molecules are initially high-energy molecules as described below. The nitrogenous base here is adenine, the sugar is the pentose monosaccharide ribose and there are three phosphate groups attached. The sugar and the base form a molecule called a nucleoside, and the number of phosphate groups bound to the nucleoside is variable; thus alternative forms of this molecule occur as adenosine monophosphate (AMP) and adenosine diphosphate (ADP). -
Unit –V CITRIC ACID CYCLE
M.Sc. Botany Semester-II (2018-20) MBOTCC-7: Physiology & Biochemistry Unit –V CITRIC ACID CYCLE Nitu Bharti Assistant Professor Department of Botany CITRIC ACID CYCLE Cellular respiration occurs in three major stages. In the first,organic fuel molecules— glucose, fatty acids, and some amino acids—are oxidized to yield two-carbon fragments in the form of the acetyl group of acetyl-coenzyme A (acetyl-CoA). In the second stage, the acetyl groups are oxidized to CO2 in the citric acid cycle, and much of the energy of these oxidations is conserved in the reduced electron carriers NADH and FADH2. In the third stage of respiration, these reduced coenzymes are themselves oxidized, giving up + protons (H ) and electrons. The electrons are transferred to O2 via a series of electron- carrying molecules known as the respiratory chain, resulting in the formation of water (H2O). Fig: Catabolism of proteins, fats, and carbohydrates in the three stages of cellular respiration. Stage 1: oxidation of fatty acids, glucose, andsome amino acids yields acetyl-CoA. Stage 2: oxidation of acetyl groups in the citric acid cycle includes four steps in which electrons are abstracted. Stage 3:electrons carried by NADH and FADH2 are funneled into a chain of mitochondrial (or, in bacteria, plasma membrane-bound) electron carriers—the respiratory chain—ultimately reducing O2 to H2O. This electron flow drives the production of ATP. Production of Acetyl-CoA (Activated Acetate) Pyruvate, the product of glycolysis, is transported into the mitochondrial matrix by the mitochondrial pyruvate carrier. Pyruvate is converted to acetyl-CoA, the starting material for the citric acid cycle, by the pyruvate dehydrogenase complex. -
Catalysis of Peroxide Reduction by Fast Reacting Protein Thiols Focus Review †,‡ †,‡ ‡,§ ‡,§ ∥ Ari Zeida, Madia Trujillo, Gerardo Ferrer-Sueta, Ana Denicola, Darío A
Review Cite This: Chem. Rev. 2019, 119, 10829−10855 pubs.acs.org/CR Catalysis of Peroxide Reduction by Fast Reacting Protein Thiols Focus Review †,‡ †,‡ ‡,§ ‡,§ ∥ Ari Zeida, Madia Trujillo, Gerardo Ferrer-Sueta, Ana Denicola, Darío A. Estrin, and Rafael Radi*,†,‡ † ‡ § Departamento de Bioquímica, Centro de Investigaciones Biomedicaś (CEINBIO), Facultad de Medicina, and Laboratorio de Fisicoquímica Biologica,́ Facultad de Ciencias, Universidad de la Republica,́ 11800 Montevideo, Uruguay ∥ Departamento de Química Inorganica,́ Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 2160 Buenos Aires, Argentina ABSTRACT: Life on Earth evolved in the presence of hydrogen peroxide, and other peroxides also emerged before and with the rise of aerobic metabolism. They were considered only as toxic byproducts for many years. Nowadays, peroxides are also regarded as metabolic products that play essential physiological cellular roles. Organisms have developed efficient mechanisms to metabolize peroxides, mostly based on two kinds of redox chemistry, catalases/peroxidases that depend on the heme prosthetic group to afford peroxide reduction and thiol-based peroxidases that support their redox activities on specialized fast reacting cysteine/selenocysteine (Cys/Sec) residues. Among the last group, glutathione peroxidases (GPxs) and peroxiredoxins (Prxs) are the most widespread and abundant families, and they are the leitmotif of this review. After presenting the properties and roles of different peroxides in biology, we discuss the chemical mechanisms of peroxide reduction by low molecular weight thiols, Prxs, GPxs, and other thiol-based peroxidases. Special attention is paid to the catalytic properties of Prxs and also to the importance and comparative outlook of the properties of Sec and its role in GPxs. -
Characterisation, Classification and Conformational Variability Of
Characterisation, Classification and Conformational Variability of Organic Enzyme Cofactors Julia D. Fischer European Bioinformatics Institute Clare Hall College University of Cambridge A thesis submitted for the degree of Doctor of Philosophy 11 April 2011 This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation does not exceed the word limit of 60,000 words. Acknowledgements I would like to thank all the members of the Thornton research group for their constant interest in my work, their continuous willingness to answer my academic questions, and for their company during my time at the EBI. This includes Saumya Kumar, Sergio Martinez Cuesta, Matthias Ziehm, Dr. Daniela Wieser, Dr. Xun Li, Dr. Irene Pa- patheodorou, Dr. Pedro Ballester, Dr. Abdullah Kahraman, Dr. Rafael Najmanovich, Dr. Tjaart de Beer, Dr. Syed Asad Rahman, Dr. Nicholas Furnham, Dr. Roman Laskowski and Dr. Gemma Holli- day. Special thanks to Asad for allowing me to use early development versions of his SMSD software and for help and advice with the KEGG API installation, to Roman for knowing where to find all kinds of data, to Dani for help with R scripts, to Nick for letting me use his E.C. tree program, to Tjaart for python advice and especially to Gemma for her constant advice and feedback on my work in all aspects, in particular the chemistry side. Most importantly, I would like to thank Prof. Janet Thornton for giving me the chance to work on this project, for all the time she spent in meetings with me and reading my work, for sharing her seemingly limitless knowledge and enthusiasm about the fascinating world of enzymes, and for being such an experienced and motivational advisor. -
The S Tudy of Apo-Enzyme/Prosthetic Groups and Their Applications in Chemical Analysis
THE S TUDY OF APO-ENZYME/PROSTHETIC GROUPS AND THEIR APPLICATIONS IN CHEMICAL ANALYSIS by Dongxuan Shen A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Chemistry) in The University of Michigan 2009 Doctoral Committee: Professor Mark E. Meyerhoff, Chair Associate Professor Shuichi Takayama Associate Professor Nils G. Walter Assistant Professor Kristina I. Håkansson © Dongxuan Shen 2009 ACKNOWLEDGEMENTS First of all, I would like to thank my advisor, Dr. Mark E. Meyerhoff, for his teaching and guidance, his patience, his continuous support and encouragement throughout my dissertation work. His enthusiasm toward scientific research and his truth-seeking attitude will be a lifetime example for myself in pursuing future careers. I would also like to thank Dr. Hakansson, Dr. Takayama, and Dr. Walter for their service on my doctoral committee, especially Dr. Walter for the discussion and suggestions with synthetic PQQ work in Chapter 4. Special thanks go to my collaborators at Berry & Associates. Without their expertise in the organic synthesis, one of my PQQ projects would be impossible to advance. I want to thank specifically Dr. Jack Hodges for the preparation of PQQ derivatives and collaboration on the project described in Chapter 4. I also feel indebted to my past and present group members. I want to give special thanks to Dr. Hyoungsik Yim for his encouragement, support, and his help with starting my thesis research; Dr. Jeremy Mitchell-Koch, and Dr. Stacey Buchanan for their help during my rotation research; Dr. Sangyeul Huang for his helpful discussions with my organic synthesis work; Dr. -
The Biosynthesis of the Molybdenum Cofactor in Escherichia Coli and Its Connection to Fes Cluster Assembly and the Thiolation of Trna
Hindawi Publishing Corporation Advances in Biology Volume 2014, Article ID 808569, 21 pages http://dx.doi.org/10.1155/2014/808569 Review Article The Biosynthesis of the Molybdenum Cofactor in Escherichia coli and Its Connection to FeS Cluster Assembly and the Thiolation of tRNA Silke Leimkühler Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany Correspondence should be addressed to Silke Leimkuhler;¨ [email protected] Received 16 January 2014; Accepted 28 March 2014; Published 29 April 2014 Academic Editor: Paul Rosch¨ Copyright © 2014 Silke Leimkuhler.¨ 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 thiolation of biomolecules is a complex process that involves the activation of sulfur. The L-cysteine desulfurase IscS is the main sulfur mobilizing protein in Escherichia coli that provides the sulfur from L-cysteine to several important biomolecules in the cell such as iron sulfur (FeS) clusters, molybdopterin (MPT), thiamine, and thionucleosides of tRNA. Various proteins mediate the transfer of sulfur from IscS to various biomolecules using different interaction partners. A direct connection between the sulfur- containing molecules FeS clusters, thiolated tRNA, and the molybdenum cofactor (Moco) has been identified. The first step of Moco biosynthesis involves the conversion of 5 GTP to cyclic pyranopterin monophosphate (cPMP), a reaction catalyzed by a FeS cluster containing protein. Formed cPMP is further converted to MPT by insertion of two sulfur atoms. The sulfur for this reaction is provided by the L-cysteine desulfurase IscS in addition to the involvement of the TusA protein.