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Adam Frankel, Jennifer I Brown
Protein arginine N-methyltransferase (PRMT) kinetic parameters have been catalogued over the past fifteen years for eight of the nine mammalian enzyme family members. Like the majority of methyltransferases, these enzymes employ the highly ubiquitous cofactor S-adenosyl-l-methionine as a co-substrate to methylate arginine residues in peptidic substrates with an approximately 4-μM median KM . The median values for PRMT turnover number (kcat ) and catalytic efficiency (kcat /KM ) are 0.0051 s-1 and 708 M-1  s-1 , respectively...
October 17, 2018: Biochimica et biophysica acta. Proteins and proteomics
Tsehai A J Grell, Benjamin N Bell, Chi Nguyen, Daniel P Dowling, Nathan A Bruender, Vahe Bandarian, Catherine L Drennan
7-carboxy-7-deazaguanine synthase, QueE, catalyzes the radical mediated ring contraction of 6-carboxy-5,6,7,8-tetrahydropterin, forming the characteristic pyrrolopyrimidine core of all 7-deazaguanine natural products. QueE is a member of the S-adenosyl-L-methionine (AdoMet) radical enzyme superfamily, which harnesses the reactivity of radical intermediates to perform challenging chemical reactions. Members of the AdoMet radical enzyme superfamily utilize a canonical binding motif, a CX3 CXφC motif, to bind a [4Fe-4S] cluster and a partial (β/α)6 TIM barrel fold for the arrangement of AdoMet and substrates for catalysis...
October 19, 2018: Protein Science: a Publication of the Protein Society
Yan Li, Wenhe Zhong, Ann Zhufang Koay, Hui Qi Ng, Xiaoying Koh-Stenta, Qianhui Nah, Siau Hoi Lim, Andreas Larsson, Julien Lescar, Jeffrey Hill, Peter C Dedon, CongBao Kang
Bacterial tRNA (guanine37 -N1 )-methyltransferase (TrmD) is an important antibacterial target due to its essential role in translation. TrmD has two domains connected with a flexible linker. The N-terminal domain (NTD) of TrmD contains the S-adenosyl-L-methionine (SAM) cofactor binding site and the C-terminal domain is critical for tRNA binding. Here we report the backbone NMR resonance assignments for NTD of Pseudomonas aeruginosa TrmD. Its secondary structure was determined based on the assigned resonances...
October 8, 2018: Biomolecular NMR Assignments
Xiao Liu, Chenghua Wei, Jing Luo, Yiping Wu, Xiaoyu Guo, Ye Ying, Ying Wen, Haifeng Yang
A photoelectrochemical (PEC) method is described for the determination of the activity of M.SssI methyltransferase (MTase). The assay relies on enzyme-linkage reactions and a DNA intercalator Ru(bpy)2 (dppz)2+ (where bpy is 2,2'-bipyridine, and dppz is dipyrido[3,2-a:2',3'-c]phenazine) which both serves as a PEC signal. The PEC electrode was obtained by immobilizing 5'-amino modified DNA strands (containing the methylation recognition site 5'-CCGG-3') on a polyethylenimine (PEI) coated ITO/SnO2 electrode with glutaraldehyde as crosslinking agent...
October 5, 2018: Mikrochimica Acta
Lindsey M Walker, William MacLeod Kincannon, Vahe Bandarian, Sean J Elliott
Enzymes in the S-adenosyl-L-methionine (AdoMet) radical enzyme superfamily are metalloenzymes that catalyze wide variety of complex radical-mediated transformations with the aid of a [4Fe-4S] cluster, which is required for activation of AdoMet to generate 5'-deoadenosyl radical to initiate the catalytic cycle. In addition to this cluster, some enzymes share an additional domain, SPASM domain, that houses auxiliary FeS clusters whose functional significance is not clearly understood. The AdoMet radical enzyme Tte118, which catalyzes a thioether crosslink in a cysteine rich peptide (SCIFF), has two auxiliary [4Fe-4S] clusters within a SPASM domain which are required for enzymatic activity but not for the generation of the 5'-deoxyadenosyl radical intermediate...
October 1, 2018: Biochemistry
Ewa Wunsch, Joanna Raszeja-Wyszomirska, Olivier Barbier, Malgorzata Milkiewicz, Marcin Krawczyk, Piotr Milkiewicz
BACKGROUND AND AIMS: Chronic liver disease induces an acquired deficiency of S-adenosyl-L-methionine (SAMe) leading to impairment of detoxifying processes in the liver. Ursodeoxycholic acid (UDCA) represents the standard treatment in primary biliary cholangitis (PBC). As both compounds exert their hepatoprotective effects by different mechanisms, it is conceivable that when used together their effect might be additive. The aim of this study was to analyse the effect of SAMe supplementation on liver biochemistry and health-related quality of life (HRQoL) in patients with PBC, treated with UDCA...
September 2018: Journal of Gastrointestinal and Liver Diseases: JGLD
Lizhi Tao, Troy A Stich, Corey J Fugate, Joseph T Jarrett, R David Britt
Biotin (vitamin B7 ) is an enzyme cofactor required by organisms from all branches of life but synthesized only in microbes and plants. In the final step of biotin biosynthesis, a radical S-adenosyl-l-methionine (SAM) enzyme, biotin synthase (BioB), converts the substrate dethiobiotin to biotin through the stepwise formation of two C-S bonds. Previous electron paramagnetic resonance (EPR) spectroscopic studies identified a semistable intermediate in the formation of the first C-S bond as 9-mercaptodethiobiotin linked to a paramagnetic [2Fe-2S] cluster through one of its bridging sulfides...
September 28, 2018: Journal of the American Chemical Society
Derek M Gagnon, Troy A Stich, Angad P Mehta, Sameh H Abdelwahed, Tadhg P Begley, R David Britt
Organisms that perform the de novo biosynthesis of cobalamin (vitamin B12) do so via unique pathways depending on the presence of oxygen in the environment. The anaerobic biosynthesis pathway of 5,6-dimethylbenzimidazole, the so-called "lower ligand" to the cobalt center, has been recently identified. This process begins with the conversion of 5-aminoimidazole ribotide (AIR) to 5-hydroxybenzimidazole (HBI) by the radical S-adenosyl-l-methionine (SAM) enzyme BzaF, also known as HBI synthase. In this work we report the characterization of a radical intermediate in the reaction of BzaF using electron paramagnetic resonance spectroscopy...
September 27, 2018: Journal of the American Chemical Society
Yajun Tao, Jun Wang, Jun Miao, Jie Chen, Shujun Wu, Jinyan Zhu, Dongping Zhang, Houwen Gu, Huan Cui, Shuangyue Shi, Mingyue Xu, Youli Yao, Zhiyun Gong, Zefeng Yang, Minghong Gu, Yong Zhou, Guohua Liang
Polyamines, including putrescine (Put), spermidine (Spd), and spermine (Spm), play essential roles in a wide variety of prokaryotic and eukaryotic organisms. Rice (Oryza sativa) contains four putative spermidine/spermine synthase (SPMS)-encoding genes (OsSPMS1, OsSPMS2, OsSPMS3, and OsACAULIS5), but none have been functionally characterized. In this study, we used a reverse genetic strategy to investigate the biological function of OsSPMS1. We generated several homozygous RNA interference (RNAi) and overexpression (OE) lines of OsSPMS1...
September 6, 2018: Plant Physiology
Lital Estrella Weil, Yulia Shmidov, Margarita Kublanovsky, David Morgenstern, Michal Feldman, Ronit Bitton, Dan Levy
Signaling via lysine methylation by protein lysine methyltransferases (PKMTs), has been linked to diverse biological and disease processes. The mono-methyltransferase SETD6 (SET-domain-containing protein 6) is a member of the PKMT family and was previously shown to regulate essential cellular processes such as the NF-κB, WNT and the oxidative stress pathways. However, on the biochemical level, little is known about the enzymatic mode of action of SETD6. Here we provide evidence that SETD6 forms high-molecular-weight structures...
October 19, 2018: Journal of Molecular Biology
Ekaterina Yu Bezsudnova, Tatiana N Stekhanova, Anna V Popinako, Tatiana V Rakitina, Alena Yu Nikolaeva, Konstantin M Boyko, Vladimir O Popov
Substrate and reaction promiscuity is a remarkable property of some enzymes and facilitates the adaptation to new metabolic demands in the evolutionary process. Substrate promiscuity is also a basis for protein engineering for biocatalysis. However, molecular principles of enzyme promiscuity are not well understood. Even for the widely studied PLP-dependent transaminases of class III, the reliable prediction of the biocatalytically important amine transaminase activity is still difficult if the desired activity is unrelated to the natural activity...
September 3, 2018: Applied Microbiology and Biotechnology
David Mischoulon, Mark Hyman Rapaport
Depression remains difficult to manage, despite the many registered treatments available. For many depressed individuals, particularly those who have not responded to and/or had adverse effects from standard therapies, herbal and natural medications represent a potentially valuable alternative. This chapter will review several natural remedies used in the treatment of depression. Specific remedies covered include St. John's wort (SJW), S-adenosyl-L-methionine (SAMe), omega-3 fatty acids, rhodiola, and others...
August 24, 2018: Handbook of Experimental Pharmacology
Yu Zhao, Yu-Feng Mao, Yi-Shuang Tang, Ming-Zhu Ni, Qiao-Hong Liu, Yan Wang, Qin Feng, Jing-Hua Peng, Yi-Yang Hu
AIM: To elucidate tongue coating microbiota and metabolic differences in chronic hepatitis B (CHB) patients with yellow or white tongue coatings. METHODS: Tongue coating samples were collected from 53 CHB patients (28 CHB yellow tongue coating patients and 25 CHB white tongue coating patients) and 22 healthy controls. Microbial DNA was extracted from the tongue samples, and the bacterial 16S ribosomal RNA gene V3 region was amplified from all samples and sequenced with the Ion Torrent PGM™ sequencing platform according to the standard protocols...
August 14, 2018: World Journal of Gastroenterology: WJG
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
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