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https://www.readbyqxmd.com/read/28911222/a-ratiometric-fluorescent-probe-for-imaging-of-pantetheinase-in-living-cells
#1
Yiming Hu, Hongyu Li, Wen Shi, Huimin Ma
Pantetheinase, which catalyzes the cleavage of pantetheine to pantothenic acid (vitamin B5) and cysteamine, is involved in the regulation of oxidative stress, pantothenate recycling and cell migration. However, further elucidating the cellular function of this enzyme is largely limited by the lack of a suitable fluorescence imaging probe. By conjugating pantothenic acid with cresyl violet, herein we develop a new fluorescence probe CV-PA for the assay of pantetheinase. The probe not only possesses long analytical wavelengths but also displays linear ratiometric (I628/582 nm) fluorescence response to pantetheinase in the range of 5-400 ng/mL with a detection limit of 4...
September 15, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28719588/structures-of-carboxylic-acid-reductase-reveal-domain-dynamics-underlying-catalysis
#2
Deepankar Gahloth, Mark S Dunstan, Daniela Quaglia, Evaldas Klumbys, Michael P Lockhart-Cairns, Andrew M Hill, Sasha R Derrington, Nigel S Scrutton, Nicholas J Turner, David Leys
Carboxylic acid reductase (CAR) catalyzes the ATP- and NADPH-dependent reduction of carboxylic acids to the corresponding aldehydes. The enzyme is related to the nonribosomal peptide synthetases, consisting of an adenylation domain fused via a peptidyl carrier protein (PCP) to a reductase termination domain. Crystal structures of the CAR adenylation-PCP didomain demonstrate that large-scale domain motions occur between the adenylation and thiolation states. Crystal structures of the PCP-reductase didomain reveal that phosphopantetheine binding alters the orientation of a key Asp, resulting in a productive orientation of the bound nicotinamide...
September 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28576495/metabolic-pathway-catalyzed-by-vanin-1-pantetheinase-plays-a-suppressive-role-in-influenza-virus-replication-in-human-alveolar-epithelial-a549-cells
#3
Nobuko Yamashita, Masato Yashiro, Hirohito Ogawa, Hikaru Namba, Nobuyuki Nosaka, Yousuke Fujii, Tsuneo Morishima, Hirokazu Tsukahara, Masao Yamada
Our previous analysis of gene expression profiles in the peripheral blood from patients with influenza A (H1N1) pdm09 pneumonia revealed elevated transcription levels of the vanin-1 (vascular non-inflammatory molecule 1, VNN1) gene, which encodes an epithelial ectoenzyme with pantetheinase activity involved in recycling coenzyme A. Here, to elucidate the role of VNN1 in influenza A virus (IAV) H1N1 infection, we investigated the change of VNN1 expression in the context of IAV infection and the effects of its related substances, i...
August 5, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28484029/polyketide-mimetics-yield-structural-and-mechanistic-insights-into-product-template-domain-function-in-nonreducing-polyketide-synthases
#4
Jesus F Barajas, Gaurav Shakya, Gabriel Moreno, Heriberto Rivera, David R Jackson, Caitlyn L Topper, Anna L Vagstad, James J La Clair, Craig A Townsend, Michael D Burkart, Shiou-Chuan Tsai
Product template (PT) domains from fungal nonreducing polyketide synthases (NR-PKSs) are responsible for controlling the aldol cyclizations of poly-β-ketone intermediates assembled during the catalytic cycle. Our ability to understand the high regioselective control that PT domains exert is hindered by the inaccessibility of intrinsically unstable poly-β-ketones for in vitro studies. We describe here the crystallographic application of "atom replacement" mimetics in which isoxazole rings linked by thioethers mimic the alternating sites of carbonyls in the poly-β-ketone intermediates...
May 23, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28451251/substrate-selectivity-of-an-isolated-enoyl-reductase-catalytic-domain-from-an-iterative-highly-reducing-fungal-polyketide-synthase-reveals-key-components-of-programming
#5
Douglas M Roberts, Christoph Bartel, Alan Scott, David Ivison, Thomas J Simpson, Russell J Cox
A cis-acting enoyl reductase (ER) catalytic domain was isolated from a fungal highly reducing iterative polyketide synthase (HR-iPKS) for the first time and studied in vitro. The ER from the squalestatin tetraketide synthase forms a discrete dimeric protein in solution. The ER shows broad substrate selectivity, reducing enoyl species including both natural and unnatural substrates. Pantetheine-bound substrate thiolesters reacted much faster than the corresponding SNAC thiolesters. The unnatural substrates included Z-olefins, 2-ethyl olefins and pentaketides...
February 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28448444/role-of-the-vanins-myeloperoxidase-axis-in-colorectal-carcinogenesis
#6
REVIEW
Francesco Mariani, Luca Roncucci
The presence of chronic inflammation in the colonic mucosa leads to an increased risk of cancer. Among proteins involved in the regulation of mucosal inflammation and that may contribute both to structural damage of the intestinal mucosa and to intestinal carcinogenesis, there are myeloperoxidase (MPO) and vanins. The infiltration of colonic mucosa by neutrophils may promote carcinogenesis through MPO, a key enzyme contained in the lysosomes of neutrophils that regulates local inflammation and the generation of reactive oxygen species (ROS) and mutagenic species...
April 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28208756/homocysteine-editing-thioester-chemistry-coenzyme-a-and-the-origin-of-coded-peptide-synthesis-%C3%A2
#7
REVIEW
Hieronim Jakubowski
Aminoacyl-tRNA synthetases (AARSs) have evolved "quality control" mechanisms which prevent tRNA aminoacylation with non-protein amino acids, such as homocysteine, homoserine, and ornithine, and thus their access to the Genetic Code. Of the ten AARSs that possess editing function, five edit homocysteine: Class I MetRS, ValRS, IleRS, LeuRS, and Class II LysRS. Studies of their editing function reveal that catalytic modules of these AARSs have a thiol-binding site that confers the ability to catalyze the aminoacylation of coenzyme A, pantetheine, and other thiols...
February 9, 2017: Life
https://www.readbyqxmd.com/read/27676316/validation-of-coabc-as-a-bactericidal-target-in-the-coenzyme-a-pathway-of-mycobacterium-tuberculosis
#8
Joanna C Evans, Carolina Trujillo, Zhe Wang, Hyungjin Eoh, Sabine Ehrt, Dirk Schnappinger, Helena I M Boshoff, Kyu Y Rhee, Clifton E Barry, Valerie Mizrahi
Mycobacterium tuberculosis relies on its own ability to biosynthesize coenzyme A to meet the needs of the myriad enzymatic reactions that depend on this cofactor for activity. As such, the essential pantothenate and coenzyme A biosynthesis pathways have attracted attention as targets for tuberculosis drug development. To identify the optimal step for coenzyme A pathway disruption in M. tuberculosis, we constructed and characterized a panel of conditional knockdown mutants in coenzyme A pathway genes. Here, we report that silencing of coaBC was bactericidal in vitro, whereas silencing of panB, panC, or coaE was bacteriostatic over the same time course...
December 9, 2016: ACS Infectious Diseases
https://www.readbyqxmd.com/read/27160974/structural-and-biochemical-characterisation-of-archaeoglobus-fulgidus-esterase-reveals-a-bound-coa-molecule-in-the-vicinity-of-the-active-site
#9
Christopher Sayer, William Finnigan, Michail N Isupov, Mark Levisson, Servé W M Kengen, John van der Oost, Nicholas J Harmer, Jennifer A Littlechild
A new carboxyl esterase, AF-Est2, from the hyperthermophilic archaeon Archaeoglobus fulgidus has been cloned, over-expressed in Escherichia coli and biochemically and structurally characterized. The enzyme has high activity towards short- to medium-chain p-nitrophenyl carboxylic esters with optimal activity towards the valerate ester. The AF-Est2 has good solvent and pH stability and is very thermostable, showing no loss of activity after incubation for 30 min at 80 °C. The 1.4 Å resolution crystal structure of AF-Est2 reveals Coenzyme A (CoA) bound in the vicinity of the active site...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27130242/facilitating-unambiguous-nmr-assignments-and-enabling-higher-probe-density-through-selective-labeling-of-all-methyl-containing-amino-acids
#10
Andrew Proudfoot, Andreas O Frank, Fiorella Ruggiu, Mulugeta Mamo, Andreas Lingel
The deuteration of proteins and selective labeling of side chain methyl groups has greatly enhanced the molecular weight range of proteins and protein complexes which can be studied using solution NMR spectroscopy. Protocols for the selective labeling of all six methyl group containing amino acids individually are available, however to date, only a maximum of five amino acids have been labeled simultaneously. Here, we describe a new methodology for the simultaneous, selective labeling of all six methyl containing amino acids using the 115 kDa homohexameric enzyme CoaD from E...
May 2016: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/27041211/transition-of-phosphopantetheine-adenylyltransferase-from-catalytic-to-allosteric-state-is-characterized-by-ternary-complex-formation-in-pseudomonas-aeruginosa
#11
Rakesh Chatterjee, Abhisek Mondal, Abhishek Basu, Saumen Datta
BACKGROUND: Phosphopantetheine adenylyltransferase (PPAT) is a rate limiting enzyme which catalyzes the conversion of ATP and pantetheine to dephosphocoenzyme and pyrophosphate. The enzyme is allosteric in nature and regulated by Coenzyme A (CoA) through feedback inhibition. So far, several structures have been solved to decipher the catalytic mechanism of this enzyme. METHODS: To address catalytic and inhibitory mechanisms of PPAT, structural insights from single crystal X-ray diffraction method were primarily used, followed by biophysical and biochemical analysis...
July 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/26932716/genetic-and-pharmacological-inhibition-of-vanin-1-activity-in-animal-models-of-type-2-diabetes
#12
Janna A van Diepen, Patrick A Jansen, Dov B Ballak, Anneke Hijmans, Floris P J T Rutjes, Cees J Tack, Mihai G Netea, Joost Schalkwijk, Rinke Stienstra
Vanins are enzymes that convert pantetheine to pantothenic acid (vitamin B5). Insights into the function of vanins have evolved lately, indicating vanin-1 to play a role in inflammation, oxidative stress and cell migration. Moreover, vanin-1 has recently gained attention as a novel modulator of hepatic glucose and lipid metabolism. In the present study, we investigated the role of vanin-1 in the development of hepatic steatosis and insulin resistance in animal models of obesity and diabetes. In addition, we evaluated the potency of RR6, a novel pharmacological vanin-1 inhibitor, as an anti-diabetic drug...
March 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/26888486/determination-of-thiol-metabolites-in-human-urine-by-stable-isotope-labeling-in-combination-with-pseudo-targeted-mass-spectrometry-analysis
#13
Ping Liu, Chu-Bo Qi, Quan-Fei Zhu, Bi-Feng Yuan, Yu-Qi Feng
Precursor ion scan and multiple reaction monitoring scan (MRM) are two typical scan modes in mass spectrometry analysis. Here, we developed a strategy by combining stable isotope labeling (IL) with liquid chromatography-mass spectrometry (LC-MS) under double precursor ion scan (DPI) and MRM for analysis of thiols in 5 types of human cancer urine. Firstly, the IL-LC-DPI-MS method was applied for non-targeted profiling of thiols from cancer samples. Compared to traditional full scan mode, the DPI method significantly improved identification selectivity and accuracy...
February 18, 2016: Scientific Reports
https://www.readbyqxmd.com/read/26863427/epimerase-and-reductase-activities-of-polyketide-synthase-ketoreductase-domains-utilize-the-same-conserved-tyrosine-and-serine-residues
#14
Xinqiang Xie, Ashish Garg, Adrian T Keatinge-Clay, Chaitan Khosla, David E Cane
The role of the conserved active site tyrosine and serine residues in epimerization catalyzed by polyketide synthase ketoreductase (PKS KR) domains has been investigated. Both mutant and wild-type forms of epimerase-active KR domains, including the intrinsically redox-inactive EryKR3° and PicKR3° as well as redox-inactive mutants of EryKR1, were incubated with [2-(2)H]-(2R,3S)-2-methyl-3-hydroxypentanoyl-SACP ([2-(2)H]-2) and 0.05 equiv of NADP(+) in the presence of the redox-active, epimerase-inactive EryKR6 domain...
March 1, 2016: Biochemistry
https://www.readbyqxmd.com/read/26762462/synthetic-cycle-of-the-initiation-module-of-a-formylating-nonribosomal-peptide-synthetase
#15
Janice M Reimer, Martin N Aloise, Paul M Harrison, T Martin Schmeing
Nonribosomal peptide synthetases (NRPSs) are very large proteins that produce small peptide molecules with wide-ranging biological activities, including environmentally friendly chemicals and many widely used therapeutics. NRPSs are macromolecular machines, with modular assembly-line logic, a complex catalytic cycle, moving parts and many active sites. In addition to the core domains required to link the substrates, they often include specialized tailoring domains, which introduce chemical modifications and allow the product to access a large expanse of chemical space...
January 14, 2016: Nature
https://www.readbyqxmd.com/read/26762461/structures-of-two-distinct-conformations-of-holo-non-ribosomal-peptide-synthetases
#16
Eric J Drake, Bradley R Miller, Ce Shi, Jeffrey T Tarrasch, Jesse A Sundlov, C Leigh Allen, Georgios Skiniotis, Courtney C Aldrich, Andrew M Gulick
Many important natural products are produced by multidomain non-ribosomal peptide synthetases (NRPSs). During synthesis, intermediates are covalently bound to integrated carrier domains and transported to neighbouring catalytic domains in an assembly line fashion. Understanding the structural basis for catalysis with non-ribosomal peptide synthetases will facilitate bioengineering to create novel products. Here we describe the structures of two different holo-non-ribosomal peptide synthetase modules, each revealing a distinct step in the catalytic cycle...
January 14, 2016: Nature
https://www.readbyqxmd.com/read/26709023/wine-metabolomics-reveals-new-sulfonated-products-in-bottled-white-wines-promoted-by-small-amounts-of-oxygen
#17
Panagiotis Arapitsas, Maurizio Ugliano, Daniele Perenzoni, Andrea Angeli, Paolo Pangrazzi, Fulvio Mattivi
The impact of minute amounts of oxygen in the headspace on the post-bottling development of wine is generally considered to be very important, since oxygen can either damage or improve the quality of wine. This project aimed to gain new experimental evidence about the chemistry of the interaction between wine and oxygen. The experimental design included 216 bottles of 12 different white wines produced from 6 different cultivars (Inzolia, Muller Thurgau, Chardonnay, Grillo, Traminer and Pinot gris). Half of them were bottled using the standard industrial process with inert headspace and the other half without inert gas and with extra headspace...
January 15, 2016: Journal of Chromatography. A
https://www.readbyqxmd.com/read/26669854/a-unique-gcn5-related-glucosamine-n-acetyltransferase-region-exist-in-the-fungal-multi-domain-glycoside-hydrolase-family-3-%C3%AE-n-acetylglucosaminidase
#18
Zhen Qin, Yibei Xiao, Xinbin Yang, Jeroen R Mesters, Shaoqing Yang, Zhengqiang Jiang
Glycoside hydrolase (GH) family 3 β-N-acetylglucosaminidases widely exist in the filamentous fungi, which may play a key role in chitin metabolism of fungi. A multi-domain GH family 3 β-N-acetylglucosaminidase from Rhizomucor miehei (RmNag), exhibiting a potential N-acetyltransferase region, has been recently reported to show great potential in industrial applications. In this study, the crystal structure of RmNag was determined at 2.80 Å resolution. The three-dimensional structure of RmNag showed four distinctive domains, which belong to two distinguishable functional regions--a GH family 3 β-N-acetylglucosaminidase region (N-terminal) and a N-acetyltransferase region (C-terminal)...
December 16, 2015: Scientific Reports
https://www.readbyqxmd.com/read/26549544/influence-of-vanin-1-and-catalytic-products-in-liver-during-normal-and-oxidative-stress-conditions
#19
Daniel W Ferreira, Philippe Naquet, Jose E Manautou
In liver, cysteamine in all probability represents a "low-capacity, high-affinity" scavenger of ROS. The available body of evidence suggests that reduced cysteamine and oxidized cystamine exist in equilibrium and that this ratio acts as an active redox sensor within the cell much like GSH. During normal liver homeostasis cysteamine's antioxidant properties are evident. Highly metabolic and/or pro-oxidative conditions, such as in mice treated with peroxisome proliferators, shift this equilibrium to favor the oxidized form...
2015: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/26527136/structures-of-yeast-peroxisomal-%C3%AE-3-%C3%AE-2-enoyl-coa-isomerase-complexed-with-acyl-coa-substrate-analogues-the-importance-of-hydrogen-bond-networks-for-the-reactivity-of-the-catalytic-base-and-the-oxyanion-hole
#20
Goodluck U Onwukwe, M Kristian Koski, Petri Pihko, Werner Schmitz, Rik K Wierenga
Δ(3),Δ(2)-Enoyl-CoA isomerases (ECIs) catalyze the shift of a double bond from 3Z- or 3E-enoyl-CoA to 2E-enoyl-CoA. ECIs are members of the crotonase superfamily. The crotonase framework is used by many enzymes to catalyze a wide range of reactions on acyl-CoA thioesters. The thioester O atom is bound in a conserved oxyanion hole. Here, the mode of binding of acyl-CoA substrate analogues to peroxisomal Saccharomyces cerevisiae ECI (ScECI2) is described. The best defined part of the bound acyl-CoA molecules is the 3',5'-diphosphate-adenosine moiety, which interacts with residues of loop 1 and loop 2, whereas the pantetheine part is the least well defined...
November 2015: Acta Crystallographica. Section D, Biological Crystallography
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