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https://www.readbyqxmd.com/read/28644475/post-translational-modification-of-ribosomally-synthesized-peptides-by-a-radical-sam-epimerase-in-bacillus-subtilis
#1
Alhosna Benjdia, Alain Guillot, Pauline Ruffié, Jérôme Leprince, Olivier Berteau
Ribosomally synthesized peptides are built out of L-amino acids, whereas D-amino acids are generally the hallmark of non-ribosomal synthetic processes. Here we show that the model bacterium Bacillus subtilis is able to produce a novel type of ribosomally synthesized and post-translationally modified peptide that contains D-amino acids, and which we propose to call epipeptides. We demonstrate that a two [4Fe-4S]-cluster radical S-adenosyl-L-methionine (SAM) enzyme converts L-amino acids into their D-counterparts by catalysing Cα-hydrogen-atom abstraction and using a critical cysteine residue as the hydrogen-atom donor...
July 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28643349/a-qm-mm-study-of-the-catalytic-mechanism-of-sam-methyltransferase-rlmn-from-escherichia-coli
#2
Chenxiao Zhao, Lihua Dong, Yongjun Liu
RlmN is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the C2 methylation of adenosine 2503 (A2503) in 23S rRNA and adenosine 37 (A37) in several Escherichia coli transfer RNAs (tRNA). The catalytic reaction of RlmN is distinctly different from that of typical SAM-dependent methyltransferases that employs an SN 2 mechanism, but follows a ping-pong mechanism which involves the intermediate methylation of a conserved cysteine residue. Recently, the x-ray structure of a key intermediate in the RlmN reaction has been reported, allowing us to perform combined quantum mechanics and molecular mechanics (QM/MM) calculations to delineate the reaction details of RlmN at atomic level...
June 23, 2017: Proteins
https://www.readbyqxmd.com/read/28640310/spectroscopic-evidence-for-cofactor-substrate-interaction-in-the-radical-sam-enzyme-tyw1
#3
Velavan Kathirvelu, Phanélie Perche-Letuvée, Jean-Marc Latour, Mohamed Atta, Farhad Forouhar, Serge Gambarelli, Ricardo Garcia-Serres
TYW1 is a metalloenzyme involved in the modifications of guanosine 37 of Phe-tRNA of Eukaryota and Archaea. It catalyzes the second step of Wybutosine biosynthesis, which consists of the formation of the tricyclic compound imG-14 from m(1)G using pyruvate and SAM (S-adenosyl-methionine) as co-substrates. Two [4Fe-4S] clusters are needed in the catalytic process. One effects the reductive binding of SAM, which initiates the radical reaction that inserts a C-C moiety into m(1)G. The other [4Fe-4S] cluster binds the pyruvate molecule that provides the C-C motif...
June 22, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28617585/solution-phase-photochemical-nanopatterning-enabled-by-high-refractive-index-beam-pen-arrays
#4
Zhuang Xie, Pavlo Gordiichuk, Qing-Yuan Lin, Brian Meckes, Peng-Cheng Chen, Lin Sun, Jingshan S Du, Jinghan Zhu, Yuan Liu, Vinayak P Dravid, Chad A Mirkin
A high-throughput, solution-based, scanning-probe photochemical nanopatterning approach, which does not require the use of probes with subwavelength apertures, is reported. Specifically, pyramid arrays made from high-refractive-index polymeric materials were constructed and studied as patterning tools in a conventional liquid-phase beam pen lithography experiment. Two versions of the arrays were explored with either metal-coated or metal-free tips. Importantly, light can be channeled through both types of tips and the appropriate solution phase (e...
June 15, 2017: ACS Nano
https://www.readbyqxmd.com/read/28615450/cellular-requirements-for-iron-sulfur-cluster-insertion-into-the-antiviral-radical-sam-protein-viperin
#5
Arunkumar S Upadhyay, Oliver Stehling, Christakis Panayiotou, Ralf Rösser, Roland Lill, Anna K Överby
Viperin (RSAD2) is an interferon-stimulated antiviral protein that belongs to the radical S-adenosyl methionine (SAM) enzyme family. Viperin's iron-sulfur (Fe/S) cluster is critical for its antiviral activity against many different viruses. CIA1 (CIAO1), an essential component of the cytosolic iron-sulfur protein assembly (CIA) machinery, is crucial for Fe/S cluster insertion into viperin and hence for viperin's antiviral activity. In the CIA pathway, CIA1 cooperates with CIA2A, CIA2B, and MMS19 targeting factors to form various complexes that mediate the dedicated maturation of specific Fe/S recipient proteins...
June 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28607080/structural-studies-of-viperin-an-antiviral-radical-sam-enzyme
#6
Michael K Fenwick, Yue Li, Peter Cresswell, Yorgo Modis, Steven E Ealick
Viperin is an IFN-inducible radical S-adenosylmethionine (SAM) enzyme that inhibits viral replication. We determined crystal structures of an anaerobically prepared fragment of mouse viperin (residues 45-362) complexed with S-adenosylhomocysteine (SAH) or 5'-deoxyadenosine (5'-dAdo) and l-methionine (l-Met). Viperin contains a partial (βα)6-barrel fold with a disordered N-terminal extension (residues 45-74) and a partially ordered C-terminal extension (residues 285-362) that bridges the partial barrel to form an overall closed barrel structure...
June 12, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28585831/characterization-of-self-assembled-monolayers-on-a-ruthenium-surface
#7
A Shaheen, J M Sturm, R Ricciardi, J Huskens, C J Lee, F Bijkerk
We have modified and stabilized the ruthenium surface by depositing a self-assembled monolayer (SAM) of 1-hexadecanethiol on a polycrystalline ruthenium thin film. The growth mechanism, dynamics, and stability of these monolayers were studied. SAMs, deposited under ambient conditions, on piranha-cleaned and piranha + H2SO4 cleaned substrates were compared to monolayers formed on H-radical-cleaned Ru surfaces. We found that alkanethiols on H-radical-cleaned Ru formed densely packed monolayers that remained stable when kept in a nitrogen atmosphere...
June 12, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28579687/therapeutic-ultrasound-and-prostate-cancer
#8
REVIEW
Karthik M Sundaram, Sam S Chang, David F Penson, Sandeep Arora
Therapeutic ultrasound approaches including high-intensity focused ultrasound (HIFU) are emerging as popular minimally invasive alternative treatments for localized, low-to-intermediate risk prostate cancer. FDA approval was recently granted for two ultrasound-guided HIFU devices. Clinical trials for devices using MRI guidance are ongoing. The current level of evidence for whole-gland ultrasound ablation suggests that its clinical efficacy and adverse event rates including erectile dysfunction and urinary incontinence are similar to current definitive therapies such as radical prostatectomy and external-beam radiotherapy...
June 2017: Seminars in Interventional Radiology
https://www.readbyqxmd.com/read/28553520/watasemycin-biosynthesis-in-streptomyces-venezuelae-thiazoline-c-methylation-by-a-type-b-radical-sam-methylase-homologue
#9
Yuki Inahashi, Shanshan Zhou, Maureen J Bibb, Lijiang Song, Mahmoud M Al-Bassam, Mervyn J Bibb, Gregory L Challis
2-Hydroxyphenylthiazolines are a family of iron-chelating nonribosomal peptide natural products that function as virulence-conferring siderophores in various Gram-negative bacteria. They have also been reported as metabolites of Gram-positive Streptomyces species. Transcriptional analyses of Streptomyces venezuelae ATCC 10712 revealed that its genome contains a putative 2-hydroxyphenylthiazoline biosynthetic gene cluster. Heterologous expression of the gene cluster in Streptomyces coelicolor M1152 showed that the mono- and dimethylated derivatives, thiazostatin and watasemycin, respectively, of the 2-hydroxyphenylthiazoline enantiopyochelin are two of its metabolic products...
April 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28533006/association-between-preoperative-albumin-levels-and-length-of-stay-after-radical-cystectomy
#10
Rohan G Bhalla, Li Wang, Sam S Chang, Mark D Tyson
PURPOSE: Using contemporary population-based epidemiologic data, we measured the relationship between preoperative serum albumin level and hospital length of stay (LOS) after cystectomy and urinary diversion. MATERIALS & METHODS: Data was acquired from the 2014-2015 National Surgical Quality Improvement Program (NSQIP) database. We identified 1,582 adult patients who underwent a cystectomy between January 1st 2014 and December 31st 2015 and had a documented preoperative serum albumin level...
May 19, 2017: Journal of Urology
https://www.readbyqxmd.com/read/28505894/re-the-prognostic-significance-of-the-early-postoperative-neutrophil-to-lymphocyte-ratio-in-patients-with-urothelial-carcinoma%C3%A2-of%C3%A2-the%C3%A2-bladder-undergoing-radical-cystectomy
#11
https://www.readbyqxmd.com/read/28487403/cluster-assembly-in-nitrogenase
#12
REVIEW
Nathaniel S Sickerman, Lee A Rettberg, Chi Chung Lee, Yilin Hu, Markus W Ribbe
The versatile enzyme system nitrogenase accomplishes the challenging reduction of N2and other substrates through the use of two main metalloclusters. For molybdenum nitrogenase, the catalytic component NifDK contains the [Fe8S7]-core P-cluster and a [MoFe7S9C-homocitrate] cofactor called the M-cluster. These chemically unprecedented metalloclusters play a critical role in the reduction of N2, and both originate from [Fe4S4] clusters produced by the actions of NifS and NifU. Maturation of P-cluster begins with a pair of these [Fe4S4] clusters on NifDK called the P*-cluster...
May 9, 2017: Essays in Biochemistry
https://www.readbyqxmd.com/read/28476884/insights-into-catalysis-of-lysine-tryptophan-bond-in-bacterial-peptides-by-a-spasm-domain-radical-sam-peptide-cyclase
#13
Alhosna Benjdia, Laure Decamps, Alain Guillot, Xavier Kubiak, Pauline Ruffie, Corine Sandstrom, Olivier Berteau
Radical SAM enzymes are emerging as a major superfamily of biological catalysts involved in the biosynthesis of the broad family of bioactive peptides called ribosomally synthesized and post-translationally-modified peptides (RiPPs). These enzymes have been shown to catalyze unconventional reactions such as methyl transfer to electrophilic carbon atoms, sulfur to Cα-atom thioether bonds or carbon-carbon bond formation. Recently, a novel radical SAM enzyme catalyzing the formation of a lysine-tryptophan bond has been identified in Streptococcus thermophilus and a reaction mechanism has been proposed...
May 5, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28455341/lack-of-methylated-hopanoids-renders-the-cyanobacterium-nostoc-punctiforme-sensitive-to-osmotic-and-ph-stress
#14
Tamsyn J Garby, Emily D Matys, Sarah E Ongley, Anya Salih, Anthony W D Larkum, Malcolm R Walter, Roger E Summons, Brett A Neilan
To investigate the function of 2-methylhopanoids in modern cyanobacteria, the hpnP gene coding for the radical SAM methylase protein that acts on the C2 position of hopanoids, was deleted from the filamentous cyanobacterium Nostoc punctiforme ATCC 29133S. The resulting ΔhpnP mutant lacked all 2-methylhopanoids, but was found to produce much higher levels of two bacteriohopanepentol isomers compared to the wild type. Growth rates of ΔhpnP mutant cultures were not significantly different from those of the wild type under standard growth conditions...
April 28, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28451191/construction-of-an-octosyl-acid-backbone-catalyzed-by-a-radical-s-adenosylmethionine-enzyme-and-a-phosphatase-in-the-biosynthesis-of-high-carbon-sugar-nucleoside-antibiotics
#15
Nisha He, Pan Wu, Yongxing Lei, Baofu Xu, Xiaochen Zhu, Gudan Xu, Yaojie Gao, Jianzhao Qi, Zixin Deng, Gongli Tang, Wenqing Chen, Youli Xiao
Unique bicyclic octosyl uronic acid nucleosides include ezomycin, malayamycin, and octosyl acid (OA). They are structurally characterized by OA, an unusual 8-carbon furanosyl nucleoside core proposed to be the precursor to polyoxin and nikkomycin. Despite the well-known bioactivity of these nucleoside antibiotics, the biosynthesis of OA has not been elucidated yet. Here we report the two pivotal enzymatic steps in the polyoxin biosynthetic pathway leading to the identification of OA as a key intermediate. Our data suggest that this intermediate is formed via a free radical reaction catalyzed by the radical S-adenosylmethionine (SAM) enzyme, PolH, and using 3'-enolpyruvyl uridine 5'-monophosphate (3'-EUMP) as a substrate...
January 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28443932/nucleoside-linked-shunt-products-in-the-reaction-catalyzed-by-the-class-c-radical-s-adenosylmethionine-methyltransferase-nosn
#16
Wei Ding, Yujie Wu, Xinjian Ji, Haocheng Qianzhu, Fener Chen, Zixin Deng, Yi Yu, Qi Zhang
NosN is a class C radical S-adenosylmethionine (SAM) methyltransferase (RSMT) involved in the biosynthesis of nosiheptide, a clinically interesting thiopeptide antibiotic produced by Streptomyces actuosus. NosN employs an unprecedented catalytic mechanism, in which SAM is converted to 5'-methylthioadenosine (MTA) as a direct methyl donor. In this study, we report identification of several nucleoside-linked shunt products in the NosN-catalyzed reaction. Comparative analysis of NosN and the class A RSMT RlmN and further density functional theory (DFT) calculations reveal important mechanistic insights into the catalyses of the two types of enzymes, showing that the radical intermediates generated by similar pathways can have very diverse reactivities...
May 4, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28383907/substrate-dependent-cleavage-site-selection-by-unconventional-radical-s-adenosylmethionine-enzymes-in-diphthamide-biosynthesis
#17
Min Dong, Masaki Horitani, Boris Dzikovski, Jack H Freed, Steven E Ealick, Brian M Hoffman, Hening Lin
S-Adenosylmethionine (SAM) has a sulfonium ion with three distinct C-S bonds. Conventional radical SAM enzymes use a [4Fe-4S] cluster to cleave homolytically the C5',adenosine-S bond of SAM to generate a 5'-deoxyadenosyl radical, which catalyzes various downstream chemical reactions. Radical SAM enzymes involved in diphthamide biosynthesis, such as Pyrococcus horikoshii Dph2 (PhDph2) and yeast Dph1-Dph2 instead cleave the Cγ,Met-S bond of methionine to generate a 3-amino-3-carboxylpropyl radical. We here show radical SAM enzymes can be tuned to cleave the third C-S bond to the sulfonium sulfur by changing the structure of SAM...
April 13, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28366513/cost-of-new-technologies-in-prostate-cancer-treatment-systematic-review-of-costs-and-cost-effectiveness-of-robotic-assisted-laparoscopic-prostatectomy-intensity-modulated-radiotherapy-and-proton-beam-therapy
#18
REVIEW
Florian Rudolf Schroeck, Bruce L Jacobs, Sam B Bhayani, Paul L Nguyen, David Penson, Jim Hu
CONTEXT: Some of the high costs of robot-assisted radical prostatectomy (RARP), intensity-modulated radiotherapy (IMRT), and proton beam therapy may be offset by better outcomes or less resource use during the treatment episode. OBJECTIVE: To systematically review the literature to identify the key economic trade-offs implicit in a particular treatment choice for prostate cancer. EVIDENCE ACQUISITION: We systematically reviewed the literature according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) statement and protocol...
March 30, 2017: European Urology
https://www.readbyqxmd.com/read/28361051/on-the-role-of-additional-4fe-4s-clusters-with-a-free-coordination-site-in-radical-sam-enzymes
#19
REVIEW
Etienne Mulliez, Victor Duarte, Simon Arragain, Marc Fontecave, Mohamed Atta
The canonical CysXXXCysXXCys motif is the hallmark of the Radical-SAM superfamily. This motif is responsible for the ligation of a [4Fe-4S] cluster containing a free coordination site available for SAM binding. The five enzymes MoaA, TYW1, MiaB, RimO and LipA contain in addition a second [4Fe-4S] cluster itself bound to three other cysteines and thus also displaying a potentially free coordination site. This review article summarizes recent important achievements obtained on these five enzymes with the main focus to delineate the role of this additional [4Fe-4S] cluster in catalysis...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28346939/a-b12-dependent-radical-sam-enzyme-involved-in-oxetanocin-a-biosynthesis
#20
Jennifer Bridwell-Rabb, Aoshu Zhong, He G Sun, Catherine L Drennan, Hung-Wen Liu
Oxetanocin A (OXT-A) is a potent antitumour, antiviral and antibacterial compound. Biosynthesis of OXT-A has been linked to a plasmid-borne Bacillus megaterium gene cluster that contains four genes: oxsA, oxsB, oxrA and oxrB. Here we show that both the oxsA and oxsB genes are required for the production of OXT-A. Biochemical analysis of the encoded proteins, a cobalamin (Cbl)-dependent S-adenosylmethionine (AdoMet) radical enzyme, OxsB, and an HD-domain phosphohydrolase, OxsA, reveals that OXT-A is derived from a 2'-deoxyadenosine phosphate in an OxsB-catalysed ring contraction reaction initiated by hydrogen atom abstraction from C2'...
April 20, 2017: Nature
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