Read by QxMD icon Read


Julia K Lewis, Nathan A Bruender, Vahe Bandarian
7-Carboxy-7-deazaguanine (CDG) is a common intermediate in the biosynthesis of 7-deazapurine-containing natural products. The biosynthesis of CDG from GTP requires three enzymes: GTP cyclohydrolase I, 6-carboxy-5,6,7,8-tetrahydropterin (CPH4 ) synthase, and CDG synthase (QueE). QueE is a member of the radical S-adenosyl-l-methionine (SAM) superfamily and catalyzes the SAM-dependent radical-mediated ring contraction of CPH4 to generate CDG. This chapter focuses on methods to reconstitute the activity of QueE in vitro...
2018: Methods in Enzymology
Smaranda Bodea, Emily P Balskus
Anaerobic choline deamination catalyzed by the glycyl radical enzyme choline trimethylamine-lyase (CutC) has emerged as a major route for trimethylamine (TMA) production within anaerobic environments, including the human gut. The association of this microbial metabolite and its downstream products with diseases such as atherosclerosis and chronic kidney disease has driven the need for a better molecular understanding of TMA-generating enzymes. Our previous work has shown that generating the critical, glycine-centered radical species on CutC requires posttranslational modification by an S-adenosyl-l-methionine (SAM)-dependent radical-activating protein (CutD) harboring an oxygen-sensitive [4Fe-4S] cofactor...
2018: Methods in Enzymology
Haoran Pang, Kenichi Yokoyama
MoaA is one of the founding members of the radical S-adenosyl-L -methionine (SAM) superfamily, and together with the second enzyme, MoaC, catalyzes the construction of the pyranopterin backbone structure of the molybdenum cofactor (Moco). However, the exact functions of both MoaA and MoaC had remained ambiguous for more than 2 decades. Recently, their functions were finally elucidated through successful characterization of the MoaA product as 3',8-cyclo-7,8-dihydro-GTP (3',8-cH2 GTP), which was shown to be converted to cyclic pyranopterin monophosphate (cPMP) by MoaC...
2018: Methods in Enzymology
Kylie D Allen, Robert H White
Methanogenic archaea represent a source of unique and fascinating anaerobic biochemistry that includes the involvement of many radical S-adenosyl-l-methionine (SAM) enzymes, some of which have well-established functions, while the majority have currently unknown or only partially understood functions. Here, we describe our strategy for the identification of the radical SAM enzyme that catalyzes the two methylation reactions in methanopterin biosynthesis in Methanocaldococcus jannaschii. Additionally, we describe the similar strategy carried out for the identification of the two radical SAM enzymes required for the biosynthesis of the 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F0 ) moiety of coenzyme F420 in M...
2018: Methods in Enzymology
Wen Zhu, Ana M Martins, Judith P Klinman
PqqE is the first enzyme in the biosynthetic pathway of the redox cofactor pyrroloquinoline quinone (PQQ), catalyzing the formation of a carbon-carbon bond in the precursor peptide PqqA. PqqE is a radical S-adenosyl-l-methionine (SAM) (RS) enzyme, a family of enzymes that use the reductive cleavage of a [4Fe-4S] cluster-bound SAM molecule to generate a 5'-deoxyadenosyl radical. This radical is then used to initiate an array of reactions that otherwise would be unlikely to occur. PqqE is a founding member of a subset family of RS enzymes that, additionally to the SAM [4Fe-4S] cluster, have a SPASM domain containing additional, auxiliary Fe-S clusters...
2018: Methods in Enzymology
Julia D Cramer, Joseph T Jarrett
Biotin synthase (BioB) catalyzes the oxidative insertion of a sulfur atom between the C6 methylene and the C9 methyl positions in dethiobiotin. The enzyme couples oxidation of each carbon position to reduction of the S-adenosyl-l-methionine (SAM) sulfonium center, generating 5'-deoxyadenosine and l-methionine, products that are characteristic of enzymes from the radical SAM superfamily. In bacteria, biotin biosynthesis is tightly regulated by the dual-function BirA repressor/holocarboxylase synthetase, resulting in very low levels of all biotin biosynthetic enzymes such that activity-based purification of BioB from the native organism is virtually impossible...
2018: Methods in Enzymology
Lee Rettberg, Kazuki Tanifuji, Andrew Jasniewski, Markus Walter Ribbe, Yilin Hu
Nitrogenase is the only known enzymatic system that converts atmospheric dinitrogen (N2 ) into bioavailable ammonia (NH3 ). The active-site cofactor responsible for this reactivity is a [(R-homocitrate)MoFe7 S9 C] cluster that is designated as the M-cluster. This important cofactor is assembled stepwise from a pair of [Fe4 S4 ] clusters that become fused into a [Fe8 S9 C] core before additional refinements take place to complete the biosynthesis. NifB, a member of the radical S-adenosyl-l-methionine (SAM) superfamily, facilitates the conversion of the [Fe4 S4 ] clusters (called the K-cluster) to the [Fe8 S9 C] core (called the L-cluster)...
2018: Methods in Enzymology
Amanda S Byer, Elizabeth C McDaniel, Stella Impano, William E Broderick, Joan B Broderick
The radical SAM enzyme superfamily is large and diverse, with ever-increasing numbers of examples of characterized reactions. This chapter focuses on the methodology we have developed over the last 25 years for working with these enzymes, with the specific examples discussed being the pyruvate formate-lyase activating enzyme (PFL-AE) and lysine 2,3-aminomutase (LAM). Both enzymes are purified from overexpressing Escherichia coli, but differ in that PFL-AE is expressed without an affinity tag and does not require iron-sulfur cluster reconstitution, while LAM purification is carried out through use of a His6 affinity tag and the enzyme benefits from cluster reconstitution...
2018: Methods in Enzymology
Anthony P Young, Vahe Bandarian
Transfer RNA is extensively modified by the actions of a variety of enzymes. The radical S-adenosyl-l-methionine enzyme TYW1 modifies tRNAPhe forming the characteristic tricyclic ring via the condensation of carbons 2 and 3 of pyruvate. This chapter details methods that are required for studies of TYW1.
2018: Methods in Enzymology
Ji Hye Shin, Chang Wook Park, Gyesoon Yoon, Sun Mi Hong, Kwan Yong Choi
Nicotinamide N-methyl transferase (NNMT) transfers a methyl group from S-adenosyl-L-methionine (SAM) to nicotinamide (NAM), producing 1-methylnicotinamide (1MNA). NNMT has been implicated in several cancer types and recently in metabolism, but its role in autophagy regulation has not yet been investigated. In this study, we determined that NNMT negatively regulated autophagy at the stage of ULK1 activation through protein phosphatase 2A (PP2A) activity. Specifically, NNMT knockdown increased PP2A methylation and subsequently enhanced phosphatase activity...
August 10, 2018: Oncogenesis
Susan C Wang
Covering: 2011 to 2018This highlight summarizes the investigation of cobalamin (Cbl)- and radical S-adenosyl-l-methionine (SAM)-dependent enzymes found in natural product biosynthesis to date and suggests some possibilities for the future. Though some mechanistic aspects are apparently shared, the overall diversity of this family's functions and abilities is significant and may be tailored to the specific substrate and/or reaction being catalyzed. A little over a year ago, the first crystal structure of a Cbl- and radical SAM-dependent enzyme was solved, providing the first insight into what may be the shared scaffolding of these enzymes...
August 6, 2018: Natural Product Reports
Vnira Rakhimovna Akhmetova, Rozalia Akramovna Galimova, Nail Salavatovich Akhmadiev, Albina Midkhatovna Galimova, Ravil Akhmetzyanovich Khisamutdinov, Galiya Maratovna Nurtdinova, Eduard Feliksovich Agletdinov, Valery Alekseevich Kataev
Purpose: This research is devoted to designing the synthesis of sulfanyl-substituted 3,5-dimethylisoxazoles, which contain structural analogues of the SAM drug in the molecule. SAM (S-adenosyl-L-methionine), formed in the biosynthetic process, is used as an effective hepatoprotective drug. Complexation and hepatoprotective properties of the combinatorial series of bis(isoxazolylsulfanyl)ethane have been studied. Methods: Bis(isoxazol-4-ylmethylsulfanyl)alkanes were synthesized using the one-pot method. The structures of compounds were established by one-dimensional (1 H,13 C) and two-dimensional (COSY, HCQS, HMBC) NMR spectroscopy, mass-spectrometry and X-ray diffraction...
June 2018: Advanced Pharmaceutical Bulletin
Wen-Bing Jin, Sheng Wu, Xiao-Hong Jian, Hua Yuan, Gong-Li Tang
Cyclopropanation of unactivated olefinic bonds via addition of a reactive one-carbon species is well developed in synthetic chemistry, whereas natural cyclopropane biosynthesis employing this strategy is very limited. Here, we identify a two-component cyclopropanase system, composed of a HemN-like radical S-adenosyl-L-methionine (SAM) enzyme C10P and a methyltransferase C10Q, catalyzes chemically challenging cyclopropanation in the antitumor antibiotic CC-1065 biosynthesis. C10P uses its [4Fe-4S] cluster for reductive cleavage of the first SAM to yield a highly reactive 5'-deoxyadenosyl radical, which abstracts a hydrogen from the second SAM to produce a SAM methylene radical that adds to an sp2 -hybridized carbon of substrate to form a SAM-substrate adduct...
July 17, 2018: Nature Communications
Shusuke Sato, Fumitaka Kudo, Tomohisa Kuzuyama, Friedrich Hammerschmidt, Tadashi Eguchi
Fom3, a cobalamin-dependent radical S-adenosyl-l-methionine (SAM) methyltransferase, catalyzes C-methylation at the C2 position of cytidylylated 2-hydroxyethylphosphonate (HEP-CMP) to afford cytidylylated 2-hydroxypropylphosphonate (HPP-CMP) in fosfomycin biosynthesis. In this study, the Fom3 reaction product HPP-CMP was reanalyzed by chiral ligand exchange chromatography to confirm its stereochemistry. The Fom3 methylation product was found to be ( S)-HPP-CMP only, indicating that the stereochemistry of the C-methylation catalyzed by Fom3 is ( S)-selective...
July 12, 2018: Biochemistry
William M Kincannon, Nathan A Bruender, Vahe Bandarian
Sporulation killing factor (SKF) is a ribosomally synthesized and post-translationally modified peptide (RiPP) produced by Bacillus. SKF contains a thioether cross-link between the α-carbon at position 40 and the thiol of Cys32, introduced by a member of the radical S-adenosyl-l-methionine (SAM) superfamily, SkfB. Radical SAM enzymes employ a 4Fe-4S cluster to bind and reductively cleave SAM to generate a 5'-deoxyadenosyl radical. SkfB utilizes this radical intermediate to abstract the α-H atom at Met40 to initiate cross-linking...
July 24, 2018: Biochemistry
Amanda S Byer, Hao Yang, Elizabeth C McDaniel, Venkatesan Kathiresan, Stella Impano, Adrien Pagnier, Hope Watts, Carly Denler, Anna L Vagstad, Jörn Piel, Kaitlin S Duschene, Eric M Shepard, Thomas P Shields, Lincoln G Scott, Edward A Lilla, Kenichi Yokoyama, William E Broderick, Brian M Hoffman, Joan B Broderick
Radical S-adenosyl-l-methionine (SAM) enzymes comprise a vast superfamily catalyzing diverse reactions essential to all life through homolytic SAM cleavage to liberate the highly reactive 5'-deoxyadenosyl radical (5'-dAdo·). Our recent observation of a catalytically competent organometallic intermediate Ω that forms during reaction of the radical SAM (RS) enzyme pyruvate formate-lyase activating-enzyme (PFL-AE) was therefore quite surprising, and led to the question of its broad relevance in the superfamily...
July 18, 2018: Journal of the American Chemical Society
Hesitha Abeysundera, Ramandeep Gill
This paper describes a patient who presented with mania with psychotic features in the context of concomitant use of S-adenosyl-L-methionine (SAMe) and selective serotonin reuptake inhibitor (SSRI). The aim of this case report is to provide medical practitioners with a greater awareness of the possibility of a psychotic episode and/or mania manifesting with concurrent use of SAMe and SSRI.
June 27, 2018: BMJ Case Reports
Anthony S Gizzi, Tyler L Grove, Jamie J Arnold, Joyce Jose, Rohit K Jangra, Scott J Garforth, Quan Du, Sean M Cahill, Natalya G Dulyaninova, James D Love, Kartik Chandran, Anne R Bresnick, Craig E Cameron, Steven C Almo
Viral infections continue to represent major challenges to public health, and an enhanced mechanistic understanding of the processes that contribute to viral life cycles is necessary for the development of new therapeutic strategies 1 . Viperin, a member of the radical S-adenosyl-L-methionine (SAM) superfamily of enzymes, is an interferon-inducible protein implicated in the inhibition of replication of a broad range of RNA and DNA viruses, including dengue virus, West Nile virus, hepatitis C virus, influenza A virus, rabies virus 2 and HIV3,4 ...
June 2018: Nature
Milda Mickute, Milda Nainyte, Lina Vasiliauskaite, Alexandra Plotnikova, Viktoras Masevicius, Saulius Klimašauskas, Giedrius Vilkaitis
S-adenosyl-L-methionine-dependent 2'-O-methylati-on of the 3'-terminal nucleotide plays important roles in biogenesis of eukaryotic small non-coding RNAs, such as siRNAs, miRNAs and Piwi-interacting RNAs (piRNAs). Here we demonstrate that, in contrast to Mg2+/Mn2+-dependent plant and bacterial homologues, the Drosophila DmHen1 and human HsHEN1 piRNA methyltransferases require cobalt cations for their enzymatic activity in vitro. We also show for the first time the capacity of the animal Hen1 to catalyse the transfer of a variety of extended chemical groups from synthetic analogues of the AdoMet cofactor onto a wide range (22-80 nt) of single-stranded RNAs permitting their 3'-terminal functionalization and labelling...
June 13, 2018: Nucleic Acids Research
Stephanie Oerum, Martine Roovers, Robert P Rambo, Jola Kopec, Henry J Bailey, Fiona Fitzpatrick, Joseph A Newman, William G Newman, Albert Amberger, Johannes Zschocke, Louis Droogmans, Udo Oppermann, Wyatt W Yue
Mitochondrial tRNAs are transcribed as long polycistronic transcripts of precursor tRNAs and undergo posttranscriptional modifications such as endonucleolytic processing and methylation required for their correct structure and function. Among them, 5'-end processing and purine 9 N1-methylation of mitochondrial tRNA are catalysed by two proteinaceous complexes with overlapping subunit composition. The Mg2+-dependent ribonuclease P complex for 5'-end cleavage comprises the methyltransferase domain-containing protein TRMT10C/MRPP1, short-chain oxidoreductase HSD17B10/MRPP2, and metallonuclease KIAA0391/MRPP3...
June 7, 2018: Journal of Biological Chemistry
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"