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Decarboxylation

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https://www.readbyqxmd.com/read/28102965/isotope-probing-of-the-udp-apiose-udp-xylose-synthase-reaction-evidence-of-a-mechanism-via-a-coupled-oxidation-and-aldol-cleavage
#1
Thomas Eixelsberger, Doroteja Horvat, Alexander Gutmann, Hansjörg Weber, Bernd Nidetzky
The C-branched sugar d-apiose (Api) is essential for plant cell-wall development. An enzyme-catalyzed decarboxylation/pyranoside ring-contraction reaction leads from UDP-α-d-glucuronic acid (UDP-GlcA) to the Api precursor UDP-α-d-apiose (UDP-Api). We examined the mechanism of UDP-Api/UDP-α-d-xylose synthase (UAXS) with site-selectively (2) H-labeled and deoxygenated substrates. The analogue UDP-2-deoxy-GlcA, which prevents C-2/C-3 aldol cleavage as the plausible initiating step of pyranoside-to-furanoside conversion, did not give the corresponding Api product...
January 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28102357/a-single-identified-glomerulus-in-the-zebrafish-olfactory-bulb-carries-the-high-affinity-response-to-death-associated-odor-cadaverine
#2
Milan Dieris, Gaurav Ahuja, Venkatesh Krishna, Sigrun I Korsching
The death-associated odor cadaverine, generated by bacteria-mediated decarboxylation of lysine, has been described as the principal activator of a particular olfactory receptor in zebrafish, TAAR13c. Low concentrations of cadaverine activated mainly TAAR13c-expressing olfactory sensory neurons, suggesting TAAR13c as an important element of the neuronal processing pathway linking cadaverine stimulation to a strongly aversive innate behavioral response. Here, we characterized the initial steps of this neuronal pathway...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28101806/purification-and-characterization-of-glutamate-decarboxylase-from-enterococcus-raffinosus-tccc11660
#3
Chuanyou Chang, Jun Zhang, Shenxi Ma, Lin Wang, Depei Wang, Jian Zhang, Qiang Gao
Glutamate decarboxylase (GAD) is the sole enzyme that synthesizes γ-aminobutyric acid through the irreversible decarboxylation of L-glutamate. In this study, the purification and characterization of an unreported GAD from a novel strain of Enterococcus raffinosus TCCC11660 were investigated. The native GAD from E. raffinosus TCCC11660 was purified 32.3-fold with a recovery rate of 8.3%, using ultrafiltration and ammonium sulfate precipitation, followed by ion-exchange and size-exclusion chromatography. The apparent molecular weight of purified GAD, as determined by SDS-PAGE and size-exclusion chromatography was 55 and 110 kDa, respectively, suggesting that GAD exists as a dimer of identical subunits in solution...
January 18, 2017: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28100850/molecular-characteristic-and-physiological-role-of-dopa-decarboxylase
#4
Joanna Guenter, Robert Lenartowski
The enzyme DOPA decarboxylase (aromatic-L-amino-acid decarboxylase, DDC) plays an important role in the dopaminergic system and participates in the uptake and decarboxylation of amine precursors in the peripheral tissues. Apart from catecholamines, DDC catalyses the biosynthesis of serotonin and trace amines. It has been shown that the DDC amino acid sequence is highly evolutionarily conserved across many species. The activity of holoenzyme is regulated by stimulation/blockade of membrane receptors, phosphorylation of serine residues, and DDC interaction with regulatory proteins...
December 31, 2016: Postȩpy Higieny i Medycyny Doświadczalnej
https://www.readbyqxmd.com/read/28098952/solving-the-puzzle-of-one-carbon-loss-in-ripostatin-biosynthesis
#5
Chengzhang Fu, David Auerbach, Yanyan Li, Ullrich Scheid, Eva Luxenburger, Ronald Garcia, Herbert Irschik, Rolf Müller
Ripostatin is a promising antibiotic that inhibits RNA polymerase by binding to a novel binding site. In this study, the characterization of the biosynthetic gene cluster of ripostatin, which is a peculiar polyketide synthase (PKS) hybrid cluster encoding cis- and trans-acyltransferase PKS genes, is reported. Moreover, an unprecedented mechanism for phenyl acetic acid formation and loading as a starter unit was discovered. This phenyl-C2 unit is derived from phenylpyruvate (phenyl-C3) and the mechanism described herein explains the mysterious loss of one carbon atom in ripostatin biosynthesis from the phenyl-C3 precursor...
January 18, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28098230/molecular-mechanism-of-the-allosteric-regulation-of-the-%C3%AE-%C3%AE-heterodimer-of-human-nad-dependent-isocitrate-dehydrogenase
#6
Tengfei Ma, Yingjie Peng, Wei Huang, Jianping Ding
Human NAD-dependent isocitrate dehydrogenase catalyzes the decarboxylation of isocitrate (ICT) into α-ketoglutarate in the Krebs cycle. It exists as the α2βγ heterotetramer composed of the αβ and αγ heterodimers. Previously, we have demonstrated biochemically that the α2βγ heterotetramer and αγ heterodimer can be allosterically activated by citrate (CIT) and ADP. In this work, we report the crystal structures of the αγ heterodimer with the γ subunit bound without or with different activators...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28095457/lysine-decarboxylase-with-an-enhanced-affinity-for-pyridoxal-5-phosphate-by-disulfide-bond-mediated-spatial-reconstitution
#7
Hye-Young Sagong, Kyung-Jin Kim
Lysine decarboxylase (LDC) catalyzes the decarboxylation of l-lysine to produce cadaverine, an important industrial platform chemical for bio-based polyamides. However, due to high flexibility at the pyridoxal 5-phosphate (PLP) binding site, use of the enzyme for cadaverine production requires continuous supplement of large amounts of PLP. In order to develop an LDC enzyme from Selenomonas ruminantium (SrLDC) with an enhanced affinity for PLP, we introduced an internal disulfide bond between Ala225 and Thr302 residues with a desire to retain the PLP binding site in a closed conformation...
2017: PloS One
https://www.readbyqxmd.com/read/28092273/in-vivo-testing-of-extracorporeal-membrane-ventilators-ila-activve%C3%A2-vs-prototype-i-lung%C3%A2
#8
Sabine Kischkel, Stefan Bergt, Beate Brock, Johan von Grönheim, Anne Herbst, Marc-Jonas Epping, Georg Matheis, Esther Novosel, Joerg Schneider, Philipp Warnke, Andreas Podbielski, Jan P Roesner, Peter I Lelkes, Brigitte Vollmar
A side-by-side comparison of the decarboxylation efficacy of two pump-driven veno-venous extracorporeal lung assist devices, i.e. a first prototype of the new miniaturized ambulatory extracorporeal membrane ventilator, I-lung® versus the commercial system iLA-activve® over a period of 72 hours in a large animal model.Fifteen German Landrace pigs were anesthetized and underwent mechanical hypoventilation to induce severe hypercapnia. Decarboxylation was accomplished by either the I-lung® or the iLA-activve® via a double lumen catheter in the jugular vein...
January 4, 2017: ASAIO Journal: a Peer-reviewed Journal of the American Society for Artificial Internal Organs
https://www.readbyqxmd.com/read/28089246/identification-and-characterization-of-l-lysine-decarboxylase-from-huperzia-serrata-and-its-role-in-the-metabolic-pathway-of-lycopodium-alkaloid
#9
Baofu Xu, Lei Lei, Xiaocen Zhu, Yiqing Zhou, Youli Xiao
Lysine decarboxylation is the first biosynthetic step of Huperzine A (HupA). Six cDNAs encoding lysine decarboxylases (LDCs) were cloned from Huperzia serrata by degenerate PCR and rapid amplification of cDNA ends (RACE). One HsLDC isoform was functionally characterized as lysine decarboxylase. The HsLDC exhibited greatest catalytic efficiency (kcat/Km, 2.11 s(-1) mM(-1)) toward L-lysine in vitro among all reported plant-LDCs. Moreover, transient expression of the HsLDC in tobacco leaves specifically increased cadaverine content from zero to 0...
January 12, 2017: Phytochemistry
https://www.readbyqxmd.com/read/28079957/palladium-catalyzed-remote-aryldifluoroalkylation-of-alkenyl-aldehydes
#10
Xingliang Nie, Cungui Cheng, Gangguo Zhu
A palladium-catalyzed three-component reaction between fluoroalkyl bromides, arylboronic acids, and alkenyl aldehydes has been developed and provides facile access to 5-, 6-, or 7-difluoroalkylated ketones under very mild reaction conditions. The resultant products can be smoothly converted into CF2 -containing tetrahydronaphthalenes by a novel silver-catalyzed intramolecular decarboxylative cyclization of 5-aryl-2,2-difluoropentanoic acids.
January 12, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28078753/photoredox-catalysed-decarboxylative-alkylation-of-n-heteroarenes-with-n-acyloxy-phthalimides
#11
Yao Fu, Wan-Min Cheng, Rui Shang, Ming-Chen Fu
An iridium-photoredox catalyst in combination with either a stoichiometric amount of Brønsted acid or a catalytic amount of Lewis acid is capable of catalysing regioselective alkylation of N-heteroarenes with N-(acyloxy)phthalimides at room temperature under irradiation. A broad range of N-heteroarenes can be alkylated using a variety of secondary, tertiary, and quaternary carboxylates. Mechanistic studies suggest that an Ir(II)/Ir(III) redox catalytic cycle is responsible for the observed reactivity.
January 12, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28077628/the-creatininase-homolog-mfte-from-mycobacterium-smegmatis-catalyzes-a-peptide-cleavage-reaction-in-the-biosynthesis-of-a-novel-ripp
#12
Nathan A Bruender, Vahe Bandarian
Most ribosomally-synthesized and post-translationally modified peptide (RiPP) natural products are processed by tailoring enzymes to create complex natural products that are still recognizably peptide-based. However, some tailoring enzymes dismantle the peptide en route to synthesis of small molecules. The biosynthesis of a small-molecule natural product of as yet unknown structure, mycofactocin, is thought to be synthesized in this way, via the mft gene cluster found in many strains of Mycobacteria. This cluster harbors at least six genes, which appear to be conserved across species...
January 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28075068/binding-and-processing-of-%C3%AE-lactam-antibiotics-by-the-transpeptidase-ldtmt2-from-mycobacterium-tuberculosis
#13
Eva Maria Steiner, Gunter Schneider, Robert Schnell
β-lactam antibiotics represent a novel direction in the chemotherapy of tuberculosis that brings the peptidoglycan layer of the complex mycobacterial cell wall in focus as therapeutic target. Peptidoglycan stability in Mycobacterium tuberculosis especially during infection relies on the non-conventional peptide cross-links formed by L,D-transpeptidases. These enzymes are known to be inhibited by β-lactams, primarily carbapenems, leading to a stable covalent modification at the enzyme active site. A panel of sixteen β-lactams antibiotics was characterized by inhibition kinetics, mass spectrometry and x-ray crystallography to identify efficient compounds and study their action on the essential transpeptidase LdtMt2 ...
January 11, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28075062/specific-arabidopsis-thaliana-malic-enzyme-isoforms-can-provide-anaplerotic-pyruvate-carboxylation-function-in-saccharomyces-cerevisiae
#14
Mariana Beatriz Badia, Robert Mans, Alicia V Lis, Marcos Ariel Tronconi, Cintia Lucía Arias, Verónica Graciela Maurino, Carlos Santiago Andreo, María Fabiana Drincovich, Antonius J A van Maris, Mariel Claudia Gerrard Wheeler
NAD(P)-malic enzyme (NAD(P)-ME) catalyzes the reversible oxidative decarboxylation of malate to pyruvate, CO2 and NAD(P)H and is present as a multigene family in Arabidopsis. The carboxylation reaction catalyzed by purified recombinant A. thaliana NADP-ME proteins is faster than those reported for other animal or plant isoforms. In contrast, no carboxylation activity could be detected in vitro for the NAD-dependent counterparts. In order to further investigate their putative carboxylating role in vivo, Arabidopsis NAD(P)-ME isoforms, as well as the NADP-ME2del2 (with a decreased ability to carboxylate pyruvate) and NADP-ME2R115A (lacking fumarate activation) versions, were functionally expressed in the cytosol of pyruvate carboxylase negative (Pyc(-) ) Saccharomyces cerevisiae strains...
January 11, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28067512/substituent-and-solvent-effects-on-the-stability-of-n-heterocyclic-carbene-complexes-with-co2
#15
Derek M Denning, Daniel Edward Falvey
Carbon dioxide forms covalent complexes with N-heterocyclic carbenes. These complexes are of interest in catalysis as well as for their potential use in various carbon capture and storage strategies. A previous report showed that the stability one such complex, N,N-dimethylimidazolium-2-carboxylate, was remarkably sensitive to solvent polarity. Polar environments lead to a kinetically stronger, shorter, and more polar bond between the carbene and CO2. The current study shows that this solvent effect is general across a wide range of NHC complexes with CO2...
January 9, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28064497/palladium-catalyzed-decarboxylative-allylation-wittig-reaction-substrate-controlled-synthesis-of-c-vinyl-glycosides
#16
Wei-Lin Leng, Hongze Liao, Hui Yao, Zi-En Ang, Shaohua Xiang, Xue-Wei Liu
A palladium-catalyzed one-pot Tsuji-Trost type decarboxylative allylation/Wittig reaction has been developed to synthesize C-vinyl glycosides. Screening of various aldehydes led to formation of β,(E)-selective C-vinyl glycosides with pyridyl group containing aldehydes and β,(Z)-selective C-vinyl glycosides with nonpyridyl aldehydes. A plausible mechanism is proposed based on the coordination effect of the aldehydes.
January 8, 2017: Organic Letters
https://www.readbyqxmd.com/read/28062647/on-the-effect-of-alkaline-ph-and-cofactor-availability-in-the-conformational-and-oligomeric-state-of-escherichia-coli-glutamate-decarboxylase
#17
F Giovannercole, C Mérigoux, C Zamparelli, D Verzili, G Grassini, M Buckle, P Vachette, D De Biase
Escherichia coli glutamate decarboxylase (EcGad) is a homohexameric pyridoxal 5'-phosphate (PLP)-dependent enzyme. It is the structural component of the major acid resistance system that protects E. coli from strong acid stress (pH < 3), typically encountered in the mammalian gastrointestinal tract. In fact EcGad consumes one proton/catalytic cycle while yielding γ-aminobutyrate and carbon dioxide from the decarboxylation of l-glutamate. Two isoforms of Gad occur in E. coli (GadA and GadB) that are 99% identical in sequence...
January 5, 2017: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/28062376/a-biotin-enrichment-strategy-identifies-novel-carbonylated-amino-acids-in-proteins-from-human-plasma
#18
Jesper F Havelund, Katarzyna Wojdyla, Michael J Davies, Ole N Jensen, Ian Max Møller, Adelina Rogowska-Wrzesinska
: Protein carbonylation is an irreversible protein oxidation correlated with oxidative stress, various diseases and ageing. Here we describe a peptide-centric approach for identification and characterisation of up to 14 different types of carbonylated amino acids in proteins. The modified residues are derivatised with biotin-hydrazide, enriched and characterised by tandem mass spectrometry. The strength of the method lies in an improved elution of biotinylated peptides from monomeric avidin resin using hot water (95°C) and increased sensitivity achieved by reduction of analyte losses during sample preparation and chromatography...
January 3, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28061857/coordinated-regulation-of-acid-resistance-in-escherichia-coli
#19
Patricia Aquino, Brent Honda, Suma Jaini, Anna Lyubetskaya, Krutika Hosur, Joanna G Chiu, Iriny Ekladious, Dongjian Hu, Lin Jin, Marianna K Sayeg, Arion I Stettner, Julia Wang, Brandon G Wong, Winnie S Wong, Stephen L Alexander, Cong Ba, Seth I Bensussen, David B Bernstein, Dana Braff, Susie Cha, Daniel I Cheng, Jang Hwan Cho, Kenny Chou, James Chuang, Daniel E Gastler, Daniel J Grasso, John S Greifenberger, Chen Guo, Anna K Hawes, Divya V Israni, Saloni R Jain, Jessica Kim, Junyu Lei, Hao Li, David Li, Qian Li, Christopher P Mancuso, Ning Mao, Salwa F Masud, Cari L Meisel, Jing Mi, Christine S Nykyforchyn, Minhee Park, Hannah M Peterson, Alfred K Ramirez, Daniel S Reynolds, Nae Gyune Rim, Jared C Saffie, Hang Su, Wendell R Su, Yaqing Su, Meng Sun, Meghan M Thommes, Tao Tu, Nitinun Varongchayakul, Tyler E Wagner, Benjamin H Weinberg, Rouhui Yang, Anastasia Yaroslavsky, Christine Yoon, Yanyu Zhao, Alicia J Zollinger, Anne M Stringer, John W Foster, Joseph Wade, Sahadaven Raman, Natasha Broude, Wilson W Wong, James E Galagan
BACKGROUND: Enteric Escherichia coli survives the highly acidic environment of the stomach through multiple acid resistance (AR) mechanisms. The most effective system, AR2, decarboxylates externally-derived glutamate to remove cytoplasmic protons and excrete GABA. The first described system, AR1, does not require an external amino acid. Its mechanism has not been determined. The regulation of the multiple AR systems and their coordination with broader cellular metabolism has not been fully explored...
January 6, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28059413/convenient-synthesis-of-6-alkyl-phenanthridines-and-1-alkyl-isoquinolines-via-silver-catalyzed-oxidative-radical-decarboxylation
#20
Qian Yao, Xin Zhou, Xiuli Zhang, Cong Wang, Peng Wang, Ming Li
A convenient and efficient protocol for the synthesis of 6-alkyl phenanthridines and 1-alkyl isoquinolines has been developed. The reaction relies on the coupling of 2-isocyanobiphenyls and vinyl isonitriles with alkyl radicals formed by the silver-catalyzed decarboxylation of stoichiometric aliphatic carboxylic acids, and affords diverse phenanthridine and isoquinoline derivatives under mild reaction conditions. The experiment of β-scission of cyclobutylcarbinyl radicals is used to shed light on the reaction mechanism...
January 6, 2017: Organic & Biomolecular Chemistry
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