Academic literature on the topic 'Coenzyme enzyme complex'
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Journal articles on the topic "Coenzyme enzyme complex"
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Tsai, C. Stan, and D. J. Senior. "Dual coenzyme activities of high-Km aldehyde dehydrogenase from rat liver mitochondria." Biochemistry and Cell Biology 68, no. 4 (April 1, 1990): 751–57. http://dx.doi.org/10.1139/o90-108.
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Various kinetic approaches were carried out to investigate kinetic attributes for the dual coenzyme activities of mitochondrial aldehyde dehydrogenase from rat liver. The enzyme catalyses NAD+- and NADP+-dependent oxidations of ethanal by an ordered bi-bi mechanism with NAD(P)+ as the first reactant bound and NAD(P)H as the last product released. The two coenzymes presumably interact with the kinetically identical site. NAD+ forms the dynamic binary complex with the enzyme, while the enzyme-NAD(P)H complex formation is associated with conformation change(s). A stopped-flow burst of NAD(P)H formation, followed by a slower steady-state turnover, suggests that either the deacylation or the release of NAD(P)H is rate limiting. Although NADP+ is reduced by a faster burst rate, NAD+ is slightly favored as the coenzyme by virtue of its marginally faster turnover rate.Key words: aldehyde dehydrogenase, coenzyme preference.
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Speranza, Giovanna, Wolfgang Buckel, and Bernard T. Golding. "CoenzymeB12-dependent enzymatic dehydration of 1,2-diols: simple reaction, complex mechanism!" Journal of Porphyrins and Phthalocyanines 08, no. 03 (March 2004): 290–300. http://dx.doi.org/10.1142/s1088424604000271.
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The conversion of glycerol to acrolein is an undesirable event in whisky production, caused by infection of the broth with Klebsiella pneumoniae. This organism uses glycerol dehydratase to transform glycerol into 3-hydroxypropanal, which affords acrolein on distillation. The enzyme requires adenosylcobalamin (coenzyme B12) as cofactor and a monovalent cation (e.g. K+). Diol dehydratase is a similar enzyme that converts 1,2-diols ( C2- C4) including glycerol into an aldehyde and water. The subtle stereochemical features of these enzymes are exemplified by propane-1,2-diol: both enantiomers are substrates but different hydrogen and oxygen atoms are abstracted. The mechanism of action of the dehydratases has been elucidated by protein crystallography and ab initio molecular orbital calculations, aided by stereochemical and model studies. The 5'-deoxyadenosyl (adenosyl) radical from homolysis of the coenzyme's Co - C σ-bond abstracts a specific hydrogen atom from C -1 of diol substrate giving a substrate radical that rearranges to a product radical by 1,2-shift of hydroxyl from C -2 to C -1. The rearrangement mechanism involves an acid-base 'push-pull' in which migration of OH is facilitated by partial protonation by Hisα143, synergistically assisted by partial deprotonation of the non-migrating ( C -1) OH by the carboxylate of Gluα170. The active site K+ion holds the two hydroxyl groups in the correct conformation, whilst not significantly contributing to catalysis. Recently, diol dehydratases not dependent on coenzyme B12have been discovered. These enzymes utilize the same kind of diol radical chemistry as the coenzyme B12-dependent enzymes and they also use the adenosyl radical as initiator, but this is generated from S-adenosylmethionine.
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Ehebauer, Matthias, Madhan Anandhakrishnan, Michael Zimmermann, Elke Noens, Arjen Jakobi, Carsten Sachse, Uwe Sauer, and Matthias Wilmanns. "AccD1 And AccA1 from M. tuberculosis form A dodecameric MCC-type holo complex." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C429. http://dx.doi.org/10.1107/s2053273314095709.
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Mycobacteria have an unusual redundancy of six putative carboxyltransferase genes that form high-molecular weight holo acyl coenzyme A carboxylase complexes with a complementary set of three biotin carboxylase genes. Most of these enzyme complexes use small fatty acid coenzyme A esters as substrate, to allow their extension by one methylene group via a carboxybiotin-mediated α-carboxylation reaction. Redundant occurrence of these complexes was assumed to be related to highly complex enzymatic requirements in lipid biosynthesis, as the mycobacterial thick cell wall comprises unusual very long chain fatty acids, including mycolic acid. We have solved two high-resolution crystal structures of the 350 kDa hexameric assemblies of two different acyl coenzyme A carboxylase hexameric assemblies, AccD5 and AccD6 [1; Anandhakrishnan et al., unpublished], and characterized these enzyme complexes functionally. In a second step we investigated the acyl coenzyme A carboxylase complex AccD1-AccA1 from Mycobacteria tuberculosis with hitherto unknown function. By using a metabolomics approach we found that AccD1-AccA1 is involved in branched amino acid catabolism, which was not investigated in mycobacteria before [Ehebauer et al, unpublished. Using an in vitro assay, we show that the enzyme complex uses methylcrotonyl coenzyme A as substrate]. We determined the overall architecture of the 700 kDa AccD1-AccA1 complex to be formed from three layers of a central AccD1 hexameric ring, flanked by two distal tiers composed of three AccA1 subunits each. Our electron microscopy data match the overall dimensions of a methylcrotonyl coenzyme A holo complex with known structure and thus support our functional findings. Our data suggest a unique functional role of the AccD1-AccA1 complex within the Mycobacterium tuberculosis acyl coenzyme A carboxylase interactome. Ultimately, it is our goal to solve this and related structures of ACCase holo complexes by high-resolution crystallography as well. The abstract is dedicated to Louis Delbaere with whom I shared time during my PhD at the University of Basel, Switzerland.
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Teixido, Francisco, Dolores De Arriaga, Félix Busto, and Joaquin Soler. "Cytoplasmic malate dehydrogenase from Phycomyces blakesleeanus: Kinetics and mechanism." Canadian Journal of Biochemistry and Cell Biology 63, no. 10 (October 1, 1985): 1097–105. http://dx.doi.org/10.1139/o85-137.
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The kinetics and reaction mechanism of cytoplasmic malate dehydrogenase (L-malate:NAD+ oxidoreductase, EC 1.1.1.37) from mycelium of Phycomyces blakesleeanus NRRL 1555 (−) in 0.1 M potassium phosphate buffer (pH 7.5) at 30 °C have been investigated. The initial rate and product inhibition studies were consistent with an ordered bi-bi mechanism that involved more than one kinetically significant ternary complex and also with the coenzyme binding first. The dissociation of the coenzyme from the enzyme–coenzyme complex appeared to be the slowest step in either direction of the reaction. The kinetic and rate constants for the individual steps of the reaction were determined.
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Kang, Lin-Woo, Sandra B. Gabelli, Mario A. Bianchet, Wen Lian Xu, Maurice J. Bessman, and L. Mario Amzel. "Structure of a Coenzyme A Pyrophosphatase from Deinococcus radiodurans: a Member of the Nudix Family." Journal of Bacteriology 185, no. 14 (July 15, 2003): 4110–18. http://dx.doi.org/10.1128/jb.185.14.4110-4118.2003.
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ABSTRACT Gene Dr1184 from Deinococcus radiodurans codes for a Nudix enzyme (DR-CoAse) that hydrolyzes the pyrophosphate moiety of coenzyme A (CoA). Nudix enzymes with the same specificity have been found in yeast, humans, and mice. The three-dimensional structure of DR-CoAse, the first of a Nudix hydrolase with this specificity, reveals that this enzyme contains, in addition to the fold observed in other Nudix enzymes, insertions that are characteristic of a CoA-hydrolyzing Nudix subfamily. The structure of the complex of the enzyme with Mg2+, its activating cation, reveals the position of the catalytic site. A helix, part of the N-terminal insertion, partially occludes the binding site and has to change its position to permit substrate binding. Comparison of the structure of DR-CoAse to those of other Nudix enzymes, together with the location in the structure of the sequence characteristic of CoAses, suggests a mode of binding of the substrate to the enzyme that is compatible with all available data.
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Bell, E. T., C. LiMuti, C. L. Renz, and J. E. Bell. "Negative co-operativity in glutamate dehydrogenase. Involvement of the 2-position in glutamate in the induction of conformational changes." Biochemical Journal 225, no. 1 (January 1, 1985): 209–17. http://dx.doi.org/10.1042/bj2250209.
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The 2-position substituent on substrates or substrate analogues for glutamate dehydrogenase is shown to be intimately involved in the induction of conformational changes between subunits in the hexamer by coenzyme. These conformational changes are associated with the negative co-operativity exhibited by this enzyme. 2-Oxoglutarate and L-2-hydroxyglutarate induce indications of co-operativity similar to those induced by the substrate of oxidative deamination, glutamate, in kinetic studies. Glutarate (2-position CH2) does not. A comparison of the effects of L-2-hydroxyglutarate and D-2-hydroxyglutarate or D-glutamate indicates that the 2-position substituent must be in the L-configuration for these conformational changes to be triggered. In addition, glutarate and L-glutamate in ternary enzyme-NAD(P)H-substrate complexes induce very different coenzyme fluorescence properties, showing that glutamate induces a different conformation of the enzyme-coenzyme complex from that induced by glutarate. Although glutamate and glutarate both tighten the binding of reduced coenzyme to the active site, the effect is much greater with glutamate, and the binding is described by two dissociation constants when glutamate is present. The data suggest that the two carboxy groups on the substrate are required to allow synergistic binding of coenzyme and substrate to the active site, but that interactions between the 2-position on the substrate and the enzyme trigger the conformational changes that result in subunit-subunit interactions and in the catalytic co-operativity exhibited by this enzyme.
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Friedmann, Silke, Astrid Steindorf, Birgit E. Alber, and Georg Fuchs. "Properties of Succinyl-Coenzyme A:l-Malate Coenzyme A Transferase and Its Role in the Autotrophic 3-Hydroxypropionate Cycle of Chloroflexus aurantiacus." Journal of Bacteriology 188, no. 7 (April 1, 2006): 2646–55. http://dx.doi.org/10.1128/jb.188.7.2646-2655.2006.
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ABSTRACT The 3-hydroxypropionate cycle has been proposed to operate as the autotrophic CO2 fixation pathway in the phototrophic bacterium Chloroflexus aurantiacus. In this pathway, acetyl coenzyme A (acetyl-CoA) and two bicarbonate molecules are converted to malate. Acetyl-CoA is regenerated from malyl-CoA by l-malyl-CoA lyase. The enzyme forming malyl-CoA, succinyl-CoA:l-malate coenzyme A transferase, was purified. Based on the N-terminal amino acid sequence of its two subunits, the corresponding genes were identified on a gene cluster which also contains the gene for l-malyl-CoA lyase, the subsequent enzyme in the pathway. Both enzymes were severalfold up-regulated under autotrophic conditions, which is in line with their proposed function in CO2 fixation. The two CoA transferase genes were cloned and heterologously expressed in Escherichia coli, and the recombinant enzyme was purified and studied. Succinyl-CoA:l-malate CoA transferase forms a large (αβ)n complex consisting of 46- and 44-kDa subunits and catalyzes the reversible reaction succinyl-CoA + l-malate → succinate + l-malyl-CoA. It is specific for succinyl-CoA as the CoA donor but accepts l-citramalate instead of l-malate as the CoA acceptor; the corresponding d-stereoisomers are not accepted. The enzyme is a member of the class III of the CoA transferase family. The demonstration of the missing CoA transferase closes the last gap in the proposed 3-hydroxypropionate cycle.
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Leskovac, Vladimir, Svetlana Trivic, and Draginja Pericin. "Isomerization of an enzyme-coenzyme complex in yeast alcohol dehydrogenase-catalysed reactions." Journal of the Serbian Chemical Society 68, no. 2 (2003): 77–84. http://dx.doi.org/10.2298/jsc0302077l.
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In this work, all the rate constants in the kinetic mechanism of the yeast alcohol dehydrogenase-catalyzed oxidation of ethanol by NAD+, at pH 7.0, 25 ?C, have been estimated. The determination of the individual rate constants was achieved by fitting the reaction progress curves to the experimental data, using the procedures of the FITSIM and KINSIM software package of Carl Frieden. This work is the first report in the literature showing the internal equilibrium constants for the isomerization of the enzyme-NAD+ complex in yeast alcohol dehydrogenase-catalyzed reactions.
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Winberg, J. O., and J. S. McKinley-McKee. "Drosophila melanogaster alcohol dehydrogenase: product-inhibition studies." Biochemical Journal 301, no. 3 (August 1, 1994): 901–9. http://dx.doi.org/10.1042/bj3010901.
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The Drosophila melanogaster alleloenzymes AdhS and AdhF have been studied with respect to product inhibition by using the two substrate couples propan-2-ol/acetone and ethanol/acetaldehyde together with the coenzyme couple NAD+/NADH. With both substrate couples the reaction was consistent with an ordered Bi Bi mechanism. The substrates added to the enzyme in a compulsory order, with coenzyme as the leading substrate, to give two interconverting ternary complexes. The second ternary complex broke down with release of products in an obligatory order, with the aldehyde/ketone leaving first. Both the acetaldehyde and acetone products formed binary complexes with the enzyme that affected NAD+ binding. However, only an enzyme-acetone complex seemed to affect NADH binding and hence the reverse reaction. The inhibitory pattern with acetaldehyde as product was also affected by the formation of a ternary enzyme-NAD(+)-acetaldehyde complex, which broke down to acetic acid and NADH. The product-inhibition pattern shown in the present work is different from that published for Drosophila Adh previously and this discrepancy can not be explained by the use of different variants of Drosophila Adh.
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Stiborová, Marie, and Sylva Leblová. "Mechanism of action of heavy metals, S-triazine herbicides and nitrates on alcohol dehydrogenase from rape." Collection of Czechoslovak Chemical Communications 51, no. 8 (1986): 1781–88. http://dx.doi.org/10.1135/cccc19861781.
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Heavy metals (Pb2+, Cu2+, Cd2+, and Zn2+) inhibited alcohol dehydrogenase (ADH) of rape (EC 1.1.1.1.); Pb2+ and Cd2+ ions affected the imidazole ring of histidine, Cu2+ and Zn2+ ions interacted with the sulphydryl groups of cysteine in the molecule of the enzyme. The coenzyme protected ADH from inactivation by Pb2+ and Cd2+, but did not protect it from Cu2+ and Zn2+. Ethanol in a ternary complex ADH-NAD+ -ethanol was a strong protecting agent from Pb2+ and Cd2+ ions. Nitrates inhibited rape ADH toward any substrate. Sulphates and fluorides had no effect. The S-triazine herbicides studied proved strong inhibitors of rape ADH (their Ki's corresponded to concentrations of the order 10-4 mol 1-1), occupying the binding site for the coenzyme. The herbicides interacted with the metallic component of the enzyme, to which the nicotinamide part of the coenzyme is bound.
Dissertations / Theses on the topic "Coenzyme enzyme complex"
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Goulas, Philippe. "Etude de déshydrogénases a NAD(P) : Utilisation en synthèse organique." Université Louis Pasteur (Strasbourg) (1971-2008), 1986. http://www.theses.fr/1986STR13005.
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Etude des problèmes liés à l'utilisation des déshydrogénases a NAD(P) en synthèse organique. Etude, à l'aide d'analogues structuraux du NAD(P), de la 6-phosphogluconate déshydrogénase de Candida Utilis et de l'oestradiol déshydrogénase de placenta humain. Synthese d'un complexe covalent NAD-alcool déshydrogénase du foie de cheval, catalytiquement actif. Purification de la carnitine déshydrogénase de Pseudomonas Putida et la mise en oeuvre pour la synthèse stéréospécifique de la l-carnitine. Mise au point d'une électrode à enzyme spécifique de la l-carnitine
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Li, Bo. "Chaîne respiratoire et pore de transition de perméabilité mitochondriale dans la cardioprotection." Phd thesis, Université Claude Bernard - Lyon I, 2009. http://tel.archives-ouvertes.fr/tel-00609514.
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Le pore de transition de perméabilité mitochondriale (PTPm) joue un rôle majeur dans la mort cellulaire et dans la cardioprotection. Notre hypothèse est que le complexe I de la chaîne respiratoire est impliqué dans la régulation de l'ouverture du PTPm. Sur des mitochondries isolées de cœurs des rongeurs, nous avons pu démontrer que le PTPm est désensibilisé par la cyclosporine A, un inhibiteur de la cyclophiline D (CyP-D), et cet effet est largement amplifié en présence de la roténone, un inhibiteur du complexe I. Ces résultats ont été confirmés chez la souris CyP-D déficiente. L'étude de plusieurs types cellulaires a aussi confirmé l'effet de la roténone dans la régulation du PTPm. Ainsi, nous avons pu montrer que le flux d'électrons travers le complexe I est capable de réagir sur un site de régulation du PTPm cardiaque masqué par la CyP-D. De plus, les analogues de l'ubiquinone, élément de la chaîne respiratoire impliqué dans le transfert d'électrons entre les complexes I, II et III, modulent la susceptibilité du PTPm vis-à-vis du Ca2+. Par ailleurs, dans un modèle de cœur isolé du rat, le postconditionnement par le perindoprilate, un inhibiteur de l'enzyme de conversion, diminue la taille de l'infarctus après l'ischémie-reperfusion d'une façon NO-dépendant. L'ensemble de nos résultats ouvre de nouvelles perspectives thérapeutiques dans la cardioprotection et montre l'importance du complexe I et de la CyP-D comme cibles moléculaires incontournables dans la cardioprotection
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Rapolu, Chaitanya. "Inhibition of Cysteine Protease by Platinum (II) Diamine Complexes." TopSCHOLAR®, 2011. http://digitalcommons.wku.edu/theses/1137.
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Chemotherapy is the first line of treatment used in cancer. Chemotherapy drugs such as cisplatin, carboplatin and oxaliplatin are used in treatment. Cisplatin enters the cell through copper transporter CTR1 by passive diffusion and bind to DNA and proteins. Cisplatin is found to inhibit several enzymes targeting cysteine, histidine and methionine residues, which are expected to be responsible for its anticancer activity. A better understanding of how the size and shape and leaving ligands of platinum complexes affect cysteine protease, papain enzyme are studied. This could give new ways to optimize anticancer activity. The activity of papain enzyme was measured on UV-Visible spectroscopy. The inhibition profile of papain with different platinum (II) complexes, and with different combinations was studied.
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Hajj, Chehade Mahmoud. "Élucidation du rôle de nouveaux acteurs de la biosynthèse de Q8 chez Escherichia coli et caractérisation du complexe protéique de biosynthèse de Q8." Thesis, Université Grenoble Alpes (ComUE), 2015. http://www.theses.fr/2015GREAV010/document.
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Le coenzyme Q est une molécule lipophile rédox rencontrée chez les eucaryotes et chez la plupart des procaryotes. La structure de Q correspond à une benzoquinone substituée par une chaîne polyisoprényle dont la longueur varie selon les organismes. Q joue le rôle de transporteur d'électrons dans les chaînes respiratoires d'où provient la plupart de l'énergie de la cellule. La biosynthèse de Q chez la bactérie Escherichia coli comporte huit étapes et implique au moins neuf protéines (UbiA-UbiH et UbiX). Trois réactions d'hydroxylation sont nécessaires pour la biosynthèse de Q8 en conditions aérobies. Alors que les protéines UbiH et UbiF présentent des homologies de séquence avec des monooxygénases à flavine connues pour catalyser des réactions d'hydroxylation, UbiB qui a été proposée comme étant la troisième hydroxylase, présente uniquement une homologie de séquence avec des kinases. Nous rapportons dans ce travail que la protéine VisC, renommée UbiI, catalyse la réaction d'hydroxylation auparavant attribuée à UbiB. Nous avons également identifié deux nouvelles protéines (YigP et YqiC, renommées respectivement UbiJ et UbiK) importantes pour le métabolisme de Q chez Escherichia coli puisque leur mutation diminue fortement le contenu en Q des souches mutantes. Ces protéines interagissent avec la plupart des protéines connues pour participer à la biosynthèse de Q ce qui implique l'existence d'un complexe de biosynthèse de Q. En utilisant des approches biochimiques et protéomiques, nous avons pu mettre en évidence un complexe impliquant plusieurs protéines Ubi et notamment UbiJ et UbiK. Ces deux protéines semblent avoir un rôle dans l'assemblage et/ou la stabilisation de ce complexe multiprotéique. Enfin, nous nous sommes intéressés à la biosynthèse de Q dans des conditions de cultures anaérobies. Nos résultats montrent l'existence « d'hydroxylases anaérobies », inconnues à ce jour, qui remplaçent les hydroxylases aérobies UbiH, UbiI et UbiF. Grâce à une approche phylogénétique, nous identifions un gène important pour la biosynthèse de Q uniquement en conditions anaérobies suggérant une réorganisation de la biosynthèse de Q entre ces deux environnements fréquemment rencontrés par E. coli. L'ensemble de nos résultats a permis d'améliorer notre connaissance de la voie de biosynthèse procaryote de Q grâce à la découverte de nouveaux gènes impliqués dans ce processus et grâce à l'identification de la fonction moléculaire de certaines protéinesUbiquinone (Q) is a lipophilic compound that plays an important role in electron and proton transport in the respiratory chains of Escherichia coli. Besides this important role in energy production, Q also functions as a membrane soluble antioxidant. The biosynthesis of Q8 requires eight reactions and involves at least nine proteins (UbiA-UbiH and UbiX) in Escherichia coli. Three of these reactions are hydroxylations resulting in the introduction of a hydroxyl group on carbon atoms at position 1, 5 and 6 of the aromatic ring. The C1 and C6 hydroxylation are well characterized whereas the C5 hydroxylation has been proposed to involve UbiB, a protein kinase without any sequence homology with monooxygenase. In this work, by genetic and biochemical methods we provide evidence that VisC which we renamed UbiI, displays sequence homology with monooxygenases and catalyzes the C5 hydroxylation, not UbiB. We have identified two new genes, yqiC and yigP (renammed UbiJ and UbiK) which are required only for Q8 biosynthesis in aerobic conditions. The exact role of the corresponding proteins, renamed UbiJ and UbiK, remains unknown. These proteins are able to interact with other Ubi proteins to be able to produce Q supporting the protein complex hypothesis. Our progress on the characterization of an Ubi-complex regrouping several Ubi proteins suggest that UbiJ and UbiK may fulfill functions related to the Ubi-complex stability. Mutants affected in hydroxylation steps are deficient for Q8 in aerobic conditions but recover a wild type Q8 content when grown in anaerobic conditions. This intriguing observation supports the existence of an alternative hydroxylation system independent from dioxygen which has not been characterized so far. By phylogenetic studies, we have identified a new gene in which the deletion affect the biosynthesis of Q only in anaerobic conditions suggesting a reorganization of Q biosynthesis in these two conditions. Our results has improved our knowledge of the prokaryotic Q biosynthetic pathway through the discovery of new genes involved in this process and through the identification of the molecular function of some proteins
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Zimmerman, Joshua R. "Model complexes for nickel containing enzymes: Carbon monoxide dehydrogenase/ acetyl coenzyme a synthase and nickel superoxide dismutase." Diss., Wichita State University, 2009. http://hdl.handle.net/10057/2555.
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Carbon Monoxide Dehydrogenase / Acetyl CoA Synthase (CODH/ACS) is a bifunctional enzyme that catalyzes the reduction of CO₂ to CO and the assembly of Acetyl CoA. The A-cluster active site, which catalyzes the Acetyl CoA synthesis, contains a Fe-S cubane bridged by a cysteine thiolate to a dinuclear Ni(µ-S)₂Ni cluster (Fig. 1). The proximal nickel, Nip, has S₃X coordination, while the distal nickel, Nid, has N₂S₂ coordination. This project focuses on the synthesis of model complexes for the asymmetric dinuclear metal center in order to understand the electronic characteristics of this cluster and investigate the feasibility of proposed intermediates. The initial target compound is shown in Figure 2. We have developed an efficient method for synthesizing metal complexes with mixed N/S coordination through the use of 2-2'-dithiodibenzaldehyde, DTDB. Symmetric nickel complexes with NS₃ coordination have previously been synthesized using DTDB and various bidentate NS ligands. Herein we present our results upon incorporating N,N-dimethylethylenediamine into this methodology.Thesis (Ph.D.)--Wichita State University, College of Liberal Arts and Sciences, Dept. of Chemistry
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Fatih, Mustapha. "Contribution à la connaissance du chemin réactionnel des Glycéraldéhyde-3-phosphate déshydrogénases phosphorylantes : structures cristallines de complexes ternaires (enzyme mutée + cofacteur + substrat)." Nancy 1, 2000. http://docnum.univ-lorraine.fr/public/SCD_T_2000_0074_FATIH.pdf.
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Ces travaux concernent l'étude cristallographique de complexes ternaires de la Glycéraldéhyde-3-phosphate déshydrogénase phosphorylante de B. Stearothermophilus. Cette enzyme catalyse la phosphorylation oxydative du Glycéraldéhyde-3-phosphate en présence d'un cofacteur, le NAD, et de phosphate inorganique. Pour fixer les groupements phosphates de ces deux substrats, l'enzyme possède deux sites de reconnaissance anionique, dénommés respectivement Pi et Ps. Cependant, la façon dont ces deux sites contribuent à la fixation des deux groupements phosphate reste encore soumise à controverse et différents modèles ont été proposés. Afin de tester la validité des ces modèles, il semblait essentiel de pouvoir disposer d'évidences structurales directes. Deux mutants ont été étudiés : le mutant C149A, inactif et le mutant C149S, très faiblement actif. Des cristaux de ces deux mutants ont été obtenus dans des conditions originales, exemptes de tout anion. Ces nouvelles conditions de cristallisation ont conduit à de nouveaux empilements cristallins. L'analyse des structures des complexes binaires met en évidence des sites Pi libres de tout anion. Par contre, les sites Ps sont occupés par un anion sulfate issu probablement de la purification. Ceci montre que le site Ps a une meilleure affinité que le site Pi vis-à-vis des anions. Ce résultat a été confirmé par l'analyse des acides aminés impliqués dans la formation des sites Pi et Ps et par le fait que le potentiel électrostatique local est plus important au niveau du site Ps qu'au niveau site Pi. Les complexes ternaires que nous avons obtenus constituent la première structure tridimensionnelle d'une GAPDH en complexe avec son substrat physiologique. L'analyse de ces complexes a permis d'apporter des informations quant aux interactions enzyme-substrat. Nous montrons sans ambigüité que dans les deux complexes obtenus, le groupement phosphate du G3P est localisé dans le site Ps. De même, les facteurs moléculaires responsables de la stéréosélectivité vis-à-vis du D-G3P ont pu être élucidés. Cependant, le débat reste ouvert concernant, d'une part, la contribution de la boucle 205-210 à la catalyse et d'autre part, la conséquence de la formation de la liaison covalente entre l'enzyme et le substrat sur le positionnement des intermédiaires réactionnels dans le site actif.
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Matranga, Christian B. "Understanding Assembly of AGO2 RISC: the RNAi enzyme: a Dissertation." eScholarship@UMMS, 2007. https://escholarship.umassmed.edu/gsbs_diss/347.
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In 1990, Richard Jorgensen’s lab initiated a study to test if they could create a more vivid color petunia (Napoli et al. 1990). Their plan was to transform plants with the chalcone synthase transgene––the predicted rate limiting factor in the production of purple pigmentation. Much to their surprise, the transgenic plants, as well as their progeny, displayed a great reduction in pigmentation. This loss of endogenous function was termed “cosuppression” and it was thought that sequence-specific repression resulted from over-expression of the homologous transgene sequence. In 1998, Andrew Fire and Craig Mello described a phenomenon in which double stranded RNA (dsRNA) can trigger silencing of cognate sequences when injected into the nematode, Caenorhabditis elegans (Fire et al. 1998). This data explained observations seen years earlier by other worm researchers, and suggested that repression of pigmentation in plants was caused by a dsRNA-intermediate (Guo and Kemphues 1995; Napoli et al. 1990). The phenomenon––which soon after was coined RNA interference (RNAi)––was soon discovered to be a post-transcriptional surveillance system in plants and animals to remove foreign nucleic acids.
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Porter-Goff, Mary Elizabeth. "The Role of the MRN Complex in the S-Phase DNA Damage Checkpoint: A Dissertation." eScholarship@UMMS, 2009. https://escholarship.umassmed.edu/gsbs_diss/405.
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The main focus of my work has been the role of the MRN in the S-phase DNA damage checkpoint. The MRN plays many roles in cellular metabolism; some are checkpoint dependent and some are checkpoint independent. The multiple roles in cellular metabolism complicate study of the role of the MRN in the checkpoint. MRN mutations in budding yeast and mammals may display separation of function. Mechanistically, MRN, along with its cofactor Ctp1, is involved in 5’ resection to create single stranded DNA that is required for both signaling and homologous recombination. However, it is unclear if resection is essential for all of the cellular functions of MRN. Therefore I have made mutations to mimic those in budding yeast and mammals. I found that several alleles of rad32, as well as ctp1Δ, are defective in double-strand break repair and most other functions of the complex but maintain an intact S-phase DNA damage checkpoint. Thus, the MRN S-phase checkpoint role is separate from its Ctp1- and resection-dependent role in double-strand break repair. This observation leads me to conclude that other functions of MRN, possibly its role in replication fork metabolism, are required for S-phase DNA damage checkpoint function.
One of the potential roles of Rad32 and the rest of the MRN complex is in sister chromatid exchange. The genetic requirements of sister chromatid exchange have been examined using unequal sister chromatid assays which only are able to assay exchanges that are illegitimate and produce changes in the genome. Most sister chromatid exchange must be equal to maintain genomic integrity and thus far there is no good assay for equal sister chromatid exchange. Yeast cells expressing the human equilibrative nucleoside transporter 1 (hENT1) and the herpes simplex virus thymidine kinase (tk) are able to incorporate exogenous thymidine into their DNA. This strain makes it possible for the fission yeast DNA to be labeled with halogenated thymidine analogs. This strain is being used to design an assay that will label one sister with BrdU and then DNA combing will be used to see equal sister chromatid exchange.
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Erturk, Hasdemir Deniz. "Regulation of the NF-кB Precursor relish by the Drosophila I-кB Kinase Complex: A Dissertation." eScholarship@UMMS, 2008. https://escholarship.umassmed.edu/gsbs_diss/376.
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The innate immune system is the first line of defense against infectious agents. It is essential for protection against pathogens and stimulation of long-term adaptive immune responses. Therefore, deciphering the mechanisms of the innate immune system is crucial for understanding the integrated systems of host defense against microbial infections, which is conserved from insects to humans.
Despite lacking a conventional adaptive immune system, insects can mount a robust immune response against a wide array of microbial pathogens. These innate immune mechanisms have been widely studied in Drosophila melanogaster, because of the model system’s powerful genetic, genomic and molecular tools. The Drosophila immunity relies on cellular and humoral innate immune responses to fight pathogens. The hallmark of the Drosophilahumoral immune response is the rapid induction of antimicrobial peptide genes in the fat body, the homolog of the mammalian liver. Expression of these antimicrobial peptide genes is controlled by two distinct immune signaling pathways, the Toll pathway and the IMD (immune deficiency) pathway.
The Toll pathway is activated by fungal and Gram-positive bacterial infections, whereas the IMD pathway responds to Gram-negative bacteria. Both pathways culminate in activation of the Rel/NF-кB transcription factors DIF (Dorsal-related immunity factor), Dorsal and Relish, which in turn translocate to the nucleus to induce the antimicrobial peptide genes. DIF and Dorsal are activated by the Toll pathway and control induction of antimicrobial peptide genes such as Drosomycin. The NF-кB precursor Relish, which is composed of an N-terminal Rel homology domain and a C-terminal IкB-like domain, is activated by the IMD pathway and initiates transcription of antimicrobial peptide genes such as Diptericin. Although many components of the Drosophila immune signaling pathways have been identified, the detailed mechanisms of signal trans
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Zhang, Lin. "Co-immobilisation du complexe (2,2'-bipyridyl) (pentaméthylcyclopentadiényl)-rhodium et de déshydrogénases NAD-dépendantes pour l’électrosynthèse enzymatique énantiosélective." Thesis, Université de Lorraine, 2016. http://www.theses.fr/2016LORR0283/document.
Full textAbstract:
Dans ce travail, nous avons développé différentes méthodes pour la co-immobilisation sur des électrodes poreuses de carbone de déshydrogénases NAD-dépendantes avec le complexe (2,2'-bipyridyle)(pentaméthylcyclopentadiényl)-rhodium ([Cp*Rh(bpy)Cl]+) pour des applications de synthèse électroenzymatique d’alcools et de sucres chiraux. L'objectif était d'éviter la dégradation de l'activité enzymatique provenant de l'interaction entre les groupes fonctionnels de surface de l'enzyme (-SH, -NH2) et le complexe [Cp*Rh(bpy)Cl]+, et également de permettre le recyclage des catalyseurs. L’électrogreffage de sels de diazonium a été utilisé pour introduire des fonctions alcène et/ou azoture sur une surface de carbone (carbone vitreux plan, feutre de carbone poreux ou couches de nanotubes de carbone). La chimie click « thiol-ène » a été utilisée pour lier de manière covalente une D-sorbitol déshydrogénase modifiée par un tag cystéine (soit 1 ou 2 fragments cystéine à l'extrémité N-terminale de la chaîne polypeptidique) à des électrodes de carbone. Ensuite, la réaction de cyclo-addition de Huisgen alcyne-azoture a été utilisée pour lier le complexe [Cp*Rh(bpy)Cl]+ à l’électrode. Ensuite la co-immobilisation des enzymes redox (D-sorbitol et galactitol déshydrogénases) avec le complexe [Cp*Rh(bpy)Cl]+ a été testée par l'encapsulation des protéines dans une couche de gel de silice, à l'intérieur d'un feutre de carbone poreux préalablement fonctionnalisé par le complexe de rhodium. Le catalyseur est alors stable pendant plusieurs semaines pour la réaction de régénération de NADH, mais cette architecture d'électrode conduit à l'inhibition de l'activité enzymatique, probablement causée par un microenvironnement local (augmentation du pH et de la concentration du produit). La combinaison des chimies clicks « thiol-ène » et cyclo-addition de Huisgen a ensuite été étudiée pour l'immobilisation séquentielle de [Cp*Rh(bpy)Cl]+ et d’une D-sorbitol déshydrogénase porteuse d’un tag cystéine, sur une électrode poreuse bi-fonctionnalisée par les groupes azoture et alcène. Enfin, compte tenu de la différence de durée de vie des enzymes et du complexe [Cp*Rh(bpy)Cl]+ et de la nécessité d'améliorer la séparation de ces éléments du système bioélectrochimique, l’assemblage optimal a été obtenu en associant une couche poreuse de silice dans laquelle est immobilisée l’enzyme avec un papier de nanotubes de carbone fonctionnalisé par le complexe de rhodium. Le catalyseur [Cp*Rh(bpy)Cl]+ pour la régénération de NADH peut être réutilisé successivement avec plusieurs couches de protéines. Ce système optimal a finalement été appliqué à la conversion bioélectrochimique du D-fructose en D-sorbitolIn this work we developed methods for the co-immobilization of NAD-dependent dehydrogenases and the (2,2'-bipyridyl) (pentamethylcyclopentadienyl)-rhodium complex ([Cp*Rh(bpy)Cl]+) on porous carbon electrodes for application in the electroenzymatic synthesis of chiral alcohols and sugars. The goal was to avoid the degradation of the enzymatic activity coming from the interaction of functional groups from the enzyme surface (eg.-SH, -NH2) with [Cp*Rh(bpy)Cl]+ and to promote the recyclability of the catalyst. Diazonium electrografting was used to introduce alkene and azide groups on a carbon surface (flat glassy carbon, porous carbon felt or carbon nanotubes layers). Thiol-ene click chemistry was applied to bind a D-sorbitol dehydrogenase with cysteine tags (either 1 or 2 cysteine moieties at the N terminus of the polypeptide chain) onto carbon electrodes. Azide-alkyne Huisgen cyclo-addition reaction was used to bind an alkyne-modified [Cp*Rh(bpy)Cl]+. Then co-immobilization of the redox enzymes (D-sorbitol and galactitol dehydrogenase) with the complex [Cp*Rh(bpy)Cl]+ was tested by encapsulation of the proteins in a silica gel layer, inside a rhodium-functionalized porous carbon felt. The immobilized [Cp*Rh(bpy)Cl]+ was stable over weeks for NADH regeneration, but this electrode architecture led to the inhibition of the enzymatic activity, possibly because of the local environment (increase of pH and product accumulation in the porous electrode). The combination of ‘thiol-ene’ and Huisgen cyclo-addition was then investigated for sequential immobilization of [Cp*Rh(bpy)Cl]+ and cysteine-tagged D-sorbitol dehydrogenase on an azide-alkene bi-functionalized electrode. Finally, considering the different lifetime of enzymes and [Cp*Rh(bpy)Cl]+ catalyst, and the need for a better separation of these elements from the bioelectrochemical system, the best configuration was achieved by associating a porous silica layer with the immobilized enzyme with a bucky paper of carbon nanotubes functionalized with [Cp*Rh(bpy)Cl]+. The reusability of this functionalized electrode was proved and the designed bioelectrode was successfully applied to a bioelectrochemical conversion of D-fructose to D-sorbitol
Books on the topic "Coenzyme enzyme complex"
Book chapters on the topic "Coenzyme enzyme complex"
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Frey, Perry A., and Adrian D. Hegeman. "Oxidases and Oxygenases." In Enzymatic Reaction Mechanisms. Oxford University Press, 2007. http://dx.doi.org/10.1093/oso/9780195122589.003.0021.
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An oxidase catalyzes the oxidation of a substrate by O2 without incorporating an oxygen atom into the product. A monooxygenase catalyzes oxidation by O2 with incorporation of one oxygen atom into the product, and oxidation by a dioxygenase proceeds with incorporation of both atoms of O2 into the product. These reactions generally require an organic or metallic coenzyme, with few exceptions, notably urate oxidase. Mechanisms of action of phenylalanine hydroxylase, galactose oxidase, and ascorbate oxidase are provided in chapter 4 in connection with the introduction of metallic coenzymes. In this chapter, we present cases of well-studied coenzyme and metal-dependent oxidases and oxygenases, and we consider one example of an oxidase that does not require a cofactor. Biochemical diversity may be a characteristic of oxidases, which include flavoproteins, heme proteins, copper proteins, and quinoproteins. The actions of copper and topaquinone-dependent amine oxidases are presented in chapter 3, and in chapter 4, two copper-dependent oxidases are discussed. In this chapter, we discuss flavin-dependent oxidases, a mononuclear iron oxidase, and a cofactor-independent oxidase. Flavin-dependent oxidases catalyze the reaction of O2 with an alcohol or amine to produce the corresponding carbonyl compound and H2O2. Examples include glucose oxidase, which produces gluconolactone and H2O2 from glucose and O2 according to. A D-Amino acid oxidase (EC 1.4.3.3) catalyzes a formally similar reaction to produce an α-keto acid from the corresponding α-D-amino acid. The oxidation of an amino acid by an oxidase produces ammonium ion in addition to hydrogen peroxide and the ketoacid, and so it is formally more complex. It proceeds in the three phases described in, the reduction of FAD to FADH2 by the amino acid, hydrolysis of the resultant α-iminoacid to the corresponding α-ketoacid and NH4, and oxidation of FADH2 by O2 to form H2O2. D-Amino acid oxidase is a thoroughly studied example of a flavoprotein oxidase. The enzyme is a 84-kDa homodimer containing one molecule of FAD per subunit. The mechanisms of the hydrolysis of imines and of the oxidation of dihydroflavins are discussed in chapters 1 and 3.
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Frey, Perry A., and Adrian D. Hegeman. "Decarboxylation and Carboxylation." In Enzymatic Reaction Mechanisms. Oxford University Press, 2007. http://dx.doi.org/10.1093/oso/9780195122589.003.0012.
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Decarboxylation is an essential process in catabolic metabolism of essentially all nutrients that serve as sources of energy in biological cells and organisms. The most widely known biological process leading to decarboxylation is the metabolism of glucose, in which all of the carbon in the molecule is oxidized to carbon dioxide by way of the glycolytic pathway, the pyruvate dehydrogenase complex, and the tricarboxylic acid cycle. The decarboxylation steps take place in thiamine pyrophosphate (TPP)–dependent α-ketoacid dehydrogenase complexes and isocitrate dehydrogenase. The latter enzyme does not require a coenzyme, other than the cosubstrate NAD+. Many other decarboxylations require coenzymes such as pyridoxal-5'-phosphate (PLP) or a pyruvoyl moiety in the peptide chain. Biological carboxylation is the essential process in the fixation of carbon dioxide by plants and of bicarbonate by animals, plants, and bacteria. Carboxylation by enzymes requires the action of biotin or a divalent metal cofactor, and it requires ATP when the carboxylating agent is the bicarbonate ion. The most prevalent enzymatic carboxylation is that of ribulose bisphosphate carboxylase (rubisco), which is responsible for carbon dioxide fixation in plants. The basic chemistry of decarboxylation is illustrated by mechanisms A to D in fig. 8-1. The mechanisms all require some means of accommodation for the electrons from the cleavage of the bond linking the carboxylate group to the α-carbon. In mechanism A, an electron sink at the β-carbon provides a haven for two electrons. Acetoacetate decarboxylase functions by this mechanism (see chap. 1), as well as PLP- and TPP-dependent decarboxylases (see chap. 3). In mechanism B, a leaving group at the β-carbon departs with two electrons. Mevalonate-5-diphosphate decarboxylate functions by mechanism B and is discussed in a later section. In mechanism C, a leaving group replaces the α-carbon and departs with a pair of electrons. A biological example is formate dehydrogenase, in which the leaving group is a hydride that is transferred to NAD+. In mechanism D, a free radical center is created adjacent to the α-carbon and potentiates the homolytic scission of the bond to the carboxylate group. Mechanism D requires secondary electron transfer processes to create the radical center and quench the formyl radical.
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Gore, Michael G., and Stephen P. Bottomley. "Stopped-flow fluorescence spectroscopy." In Spectrophotometry and Spectrofluorimetry. Oxford University Press, 2000. http://dx.doi.org/10.1093/oso/9780199638130.003.0013.
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Biochemical reactions, such as substrate or coenzyme binding to enzymes are usually completed in no more than 50-100 ms and thus require rapid reaction techniques such as stopped-flow instrumentation for their study. Fortunately, many such reactions can be followed by changes in the absorption properties of the substrate, product or coenzyme, and examples of these have been described in Chapters 1, 7 and 8. An alternative possibility is that during the reaction there is a change in the fluorescence properties of the substrate, coenzyme or the protein itself. Some reactions, particularly those involving the oxidation/ reduction of coenzymes, involve both changes in absorption and changes in fluorescence emission intensity. In many cases, the fluorescence properties of the ligand or protein itself may change when a complex is formed, even in the absence of a full catalytic reaction occurring, e.g. the protein fluorescence emission of most pyridine or flavin nucleotide-dependent dehydrogenases is quenched when NAD(P)H or FADH (respectively) binds to them, due to resonance energy transfer from the aromatic amino acids of the protein to the coenzyme. Conversely, the fluorescence emission from the reduced-coenzymes is usually enhanced on formation of the complex with these enzymes (1-3). The principles behind both fluorescence and stopped-flow techniques have been described in preceding chapters (2 and 8, respectively) and therefore readers should familiarize themselves with these chapters for some of the background information. In this chapter, we discuss the use of stopped-flow fluorescence spectroscopy and its application to a number of biochemical problems. A typical stopped-flow system is assembled from modular components of a conventional spectrophotometer/fluorimeter, a device permitting rapid mixing of the components of a reaction and a data recording system with a fast response. Commercially available instruments offer facilities for the observation of changes in absorption and/or fluorescence emission after rapid mixing of the reagents. These measurements can often be made simultaneously due to the different optical requirements of the two spectroscopic techniques. Figure 1 gives a generalized diagram of the geometry of a stopped-flow system able to simultaneously measure changes in absorption and fluorescence intensity of a reaction.
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Jordan, Robert B. "Bioinorganic Systems." In Reaction Mechanisms of Inorganic and Organometallic Systems. Oxford University Press, 2007. http://dx.doi.org/10.1093/oso/9780195301007.003.0010.
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The field of bioinorganic chemistry has grown tremendously in the past 25 years. Much of the work is concerned with establishing the coordination site, ligand geometry and metal oxidation state in biologically active systems. The field also extends to the preparation and characterization of simpler model complexes that mimic the spectroscopic properties and perhaps some of the reactivity of the biological system. Much of this characterization work must precede meaningful mechanistic studies. Williams has provided an interesting overview of metal ions in biology from an inorganic perspective. There are several early review series and specialized journals devoted to the subject, and a recent issue of Chemical Reviews is devoted to the area. There also are several books covering general aspects of the subject. The field is so large and the systems are so individualistic that it is necessary, for the purposes of a text such as this, to choose a few sample systems as illustrative of the mechanistic achievements and problems. Studies of bioinorganic systems inevitably use some terminology from biochemistry which may be unfamiliar to an inorganic chemist. The examples in this Chapter are all metalloenzymes which catalyze some process. Clearly they contain a metal, but there are other components of an enzyme, and terms used to describe these are summarized as follows: An apoenzyme is a polypeptide whose composition, peptide sequence and structure depend on the biological source of the metalloenzyme. Typically, the molar mass of the polypeptide is in the range of 1.5-5xl05 daltons. The polypeptide is folded into coils and sheets whose shape is determined by electrostatics and hydrogen bonding. These terms designate the same type of component, but one or the other is used more commonly for a particular system. This is a nonprotein component which binds to the apoenzyme to produce the active catalyst. It is not covalently bonded to the apoenzyme and can be removed by relatively mild denaturation of the polypeptide. Common bioinorganic examples are coenzyme B12, discussed in Section 8.3, and Zn(II) in carbonic anhydrase, discussed in Section 8.4. A prosthetic group is analogous to a coenzyme except that a prosthetic group is believed to be covalently bonded to the apoenzyme.
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H. Al-Shekaili, Hilal, Clara van Karnebeek, and Blair R. Leavitt. "Vitamin B6 and Related Inborn Errors of Metabolism." In B-Complex Vitamins - Sources, Intakes and Novel Applications [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.99751.
Full textAbstract:
Vitamin B6 (vitB6) is a generic term that comprises six interconvertible pyridine compounds. These vitB6 compounds (also called vitamers) are pyridoxine (PN), pyridoxamine (PM), pyridoxal (PL) and their 5′-phosphorylated forms pyridoxine 5′-phosphate (PNP), pyridoxamine 5′-phosphate (PMP) and pyridoxal 5′-phosphate (PLP). VitB6 is an essential nutrient for all living organisms, but only microorganisms and plants can carry out de novo synthesis of this vitamin. Other organisms obtain vitB6 from dietary sources and interconvert its different forms according to their needs via a biochemical pathway known as the salvage pathway. PLP is the biologically active form of vitB6 which is important for maintaining the biochemical homeostasis of the body. In the human body, PLP serves as a cofactor for more than 140 enzymatic reactions, mainly associated with synthesis, degradation and interconversion of amino acids and neurotransmitter metabolism. PLP-dependent enzymes are also involved in various physiological processes, including biologically active amine biosynthesis, lipid metabolism, heme synthesis, nucleic acid synthesis, protein and polyamine synthesis and several other metabolic pathways. PLP is an important vitamer for normal brain function since it is required as a coenzyme for the synthesis of several neurotransmitters including D-serine, D-aspartate, L-glutamate, glycine, γ-aminobutyric acid (GABA), serotonin, epinephrine, norepinephrine, histamine and dopamine. Intracellular levels of PLP are tightly regulated and conditions that disrupt this homeostatic regulation can cause disease. In humans, genetic and dietary (intake of high doses of vitB6) conditions leading to increase in PLP levels is known to cause motor and sensory neuropathies. Deficiency of PLP in the cell is also implicated in several diseases, the most notable example of which are the vitB6-dependent epileptic encephalopathies. VitB6-dependent epileptic encephalopathies (B6EEs) are a clinically and genetically heterogeneous group of rare inherited metabolic disorders. These debilitating conditions are characterized by recurrent seizures in the prenatal, neonatal, or postnatal period, which are typically resistant to conventional anticonvulsant treatment but are well-controlled by the administration of PN or PLP. In addition to seizures, children affected with B6EEs may also suffer from developmental and/or intellectual disabilities, along with structural brain abnormalities. Five main types of B6EEs are known to date, these are: PN-dependent epilepsy due to ALDH7A1 (antiquitin) deficiency (PDE-ALDH7A1) (MIM: 266100), hyperprolinemia type 2 (MIM: 239500), PLP-dependent epilepsy due to PNPO deficiency (MIM: 610090), hypophosphatasia (MIM: 241500) and PLPBP deficiency (MIM: 617290). This chapter provides a review of vitB6 and its different vitamers, their absorption and metabolic pathways in the human body, the diverse physiological roles of vitB6, PLP homeostasis and its importance for human health. Finally, the chapter reviews the inherited neurological disorders affecting PLP homeostasis with a special focus on vitB6-dependent epileptic encephalopathies (B6EEs), their different subtypes, the pathophysiological mechanism underlying each type, clinical and biochemical features and current treatment strategies.