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https://www.readbyqxmd.com/read/29626512/substrate-bound-structures-of-a-ketoreductase-from-amphotericin-modular-polyketide-synthase
#1
Chenguang Liu, Meijuan Yuan, Xu Xu, Lei Wang, Adrian T Keatinge-Clay, Zixin Deng, Shuangjun Lin, Jianting Zheng
Ketoreductase (KR) domains of modular polyketide synthases (PKSs) control the stereochemistry of C2 methyl and C3 hydroxyl substituents of polyketide intermediates. To understand the molecular basis of stereocontrol exerted by KRs, the crystal structure of a KR from the second module of the amphotericin PKS (AmpKR2) complexed with NADP+ and 2-methyl-3-oxopentanoyl-pantetheine was solved. This first ternary structure provides direct evidence to the hypothesis that a substrate enters into the active site of an A-type KR from the side opposite the coenzyme to generate an L-hydroxyl substituent...
April 4, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29498517/fragment-based-drug-discovery-of-inhibitors-of-phosphopantetheine-adenylyltransferase-from-gram-negative-bacteria
#2
Robert J Moreau, Colin K Skepper, Brent A Appleton, Anke Blechschmidt, Carl J Balibar, Bret M Benton, Joseph E Drumm, Brian Y Feng, Mei Geng, Cindy Li, Mika K Lindvall, Andreas Lingel, Yipin Lu, Mulugeta Mamo, Wosenu Mergo, Valery Polyakov, Thomas M Smith, Kenneth Takeoka, Kyoko Uehara, Lisha Wang, Jun-Rong Wei, Andrew H Weiss, Lili Xie, Wenjian Xu, Qiong Zhang, Javier de Vicente
The discovery and development of new antibiotics capable of curing infections due to multidrug-resistant and pandrug-resistant Gram-negative bacteria are a major challenge with fundamental importance to our global healthcare system. Part of our broad program at Novartis to address this urgent, unmet need includes the search for new agents that inhibit novel bacterial targets. Here we report the discovery and hit-to-lead optimization of new inhibitors of phosphopantetheine adenylyltransferase (PPAT) from Gram-negative bacteria...
April 26, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29437374/stereospecificity-of-enoylreductase-domains-from-modular-polyketide-synthases
#3
Luyun Zhang, Junjie Ji, Meijuan Yuan, Yuanyuan Feng, Lei Wang, Zixin Deng, Linquan Bai, Jianting Zheng
An enoylreductase (ER) domain of a polyketide synthase module recruiting a methylmalonate extender unit sets the C2 methyl branch to either the S or R configuration during processing of a polyketide intermediate carried by an acyl carrier protein (ACP) domain. In the present study, pantetheine- and ACP-bound trans-2-methylcrotonyl substrate surrogates were used to scrutinize the stereospecificity of the ER domains. The pantetheine-bound thioester was reduced to mixtures of both 2 R and 2 S products, whereas the expected 2 S epimer was almost exclusively generated when the cognate ACP-bound substrate surrogate was utilized...
April 20, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29372902/crystal-structure-of-cytoplasmic-acetoacetyl-coa-thiolase-from-saccharomyces-cerevisiae
#4
Pengfei Zhou, Zhongliang Zhu, Muhammad Hidayatullah Khan, Peiyi Zheng, Maikun Teng, Liwen Niu
Thiolases are vital enzymes which participate in both degradative and biosynthetic pathways. Biosynthetic thiolases catalyze carbon-carbon bond formation by a Claisen condensation reaction. The cytoplasmic acetoacetyl-CoA thiolase from Saccharomyces cerevisiae, ERG10, catalyses carbon-carbon bond formation in the mevalonate pathway. The structure of a S. cerevisiae biosynthetic thiolase has not previously been reported. Here, crystal structures of apo ERG10 and its Cys91Ala variant were solved at resolutions of 2...
January 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29352172/hemoglobin-catalyzes-coa-degradation-and-thiol-addition-to-flavonoids
#5
Toshiki Nagakubo, Takuto Kumano, Yoshiteru Hashimoto, Michihiko Kobayashi
In the presence of CoA, cell-free extracts prepared from porcine liver was found to convert 7,8-dihydroxyflavone (DHF) to a pantetheine conjugate, which was a novel flavonoid. We purified a 7,8-DHF-converting enzyme from the extracts, and identified it as hemoglobin (Hb). The purified Hb showed the following two activities: (i) degradation of CoA into pantetheine through hydrolytic cleavage to yield pantetheine and 3'-phospho-adenosine-5'-diphosphate (ADP) independently of heme, and (ii) addition of a thiol (e...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29332383/developing-pantetheinase-resistant-pantothenamide-antibacterials-structural-modification-impacts-on-pank-interaction-and-mode-of-action
#6
Leanne Barnard, Konrad J Mostert, Willem A L van Otterlo, Erick Strauss
Pantothenamides (PanAms) are analogues of pantothenate, the biosynthetic precursor of coenzyme A (CoA), and show potent antimicrobial activity against several bacteria and the malaria parasite in vitro. However, pantetheinase enzymes that normally degrade pantetheine in human serum also act on the PanAms, thereby reducing their potency. In this study, we designed analogues of the known antibacterial PanAm N-heptylpantothenamide (N7-Pan) to be resistant to pantetheinase by using three complementary structural modification strategies...
January 23, 2018: ACS Infectious Diseases
https://www.readbyqxmd.com/read/29172027/an-enhanced-chemoenzymatic-method-for-loading-substrates-onto-carrier-protein-domains
#7
Tiia Kittilä, Max J Cryle
Non-ribosomal peptide synthetase (NRPS) machineries produce many medically relevant peptides that cannot be easily accessed by chemical synthesis. Thus, understanding NRPS mechanism is of crucial importance to allow efficient redesign of these machineries to produce new compounds. During NRPS-mediated synthesis, substrates are covalently attached to peptidyl carrier proteins (PCPs), and studies of NRPSs are impeded by difficulties in producing PCPs loaded with substrates. Different approaches to load substrates onto PCP domains have been described, but all suffer from difficulties in either the complexity of chemical synthesis or low enzymatic efficiency...
November 24, 2017: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
https://www.readbyqxmd.com/read/29099125/formation-and-structure-of-the-ferryl-fe-double-bond-length-as-m-dash-o-intermediate-in-the-non-haem-iron-halogenase-syrb2-classical-and-qm-mm-modelling-agree
#8
G Rugg, H M Senn
To rationalise mechanistically the intriguing regio- and chemoselectivity patterns for different substrates of the non-haem iron/2-oxoglutarate dependent halogenase SyrB2, it is crucial to elucidate the structure of the pivotal [FeIV [double bond, length as m-dash]O] intermediate. We have approached the problem by a combination of classical and QM/MM modelling. We present complete atomistic models of SyrB2 in complex with its native substrate l-threonine as well as l-α-amino butyric acid and l-norvaline (all conjugated to the pantetheine tether), constructed by molecular docking and extensive MD simulations...
November 15, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28911222/ratiometric-fluorescent-probe-for-imaging-of-pantetheinase-in-living-cells
#9
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...
October 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28719588/structures-of-carboxylic-acid-reductase-reveal-domain-dynamics-underlying-catalysis
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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...
May 10, 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
#18
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
#19
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
#20
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
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