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Bare A, Thomas J, Etoroma D, Lee SG. Functional analysis of phosphoethanolamine N-methyltransferase in plants and parasites: Essential S-adenosylmethionine-dependent methyltransferase in choline and phospholipid metabolism. Methods Enzymol 2023; 680:101-137. [PMID: 36710008 DOI: 10.1016/bs.mie.2022.08.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Phospholipids play an essential role as a barrier between cell content and the extracellular environment and regulate various cell signaling processes. Phosphatidylcholine (PtdCho) is one of the most abundant phospholipids in plant, animal, and some prokaryote cell membranes. In plants and some parasites, the biosynthesis of PtdCho begins with the amino acid serine, followed mainly through a phosphoethanolamine N-methyltransferase (PMT)-mediated biosynthetic pathway to phosphocholine (pCho). Because the PMT-mediated pathway, referred to as the phosphobase methylation pathway, produces a series of important primary and specialized metabolites for plant development and stress response, understanding the PMT enzyme is a key aspect of engineering plants with improved stress tolerance and fortified nutrients. Importantly, given the very limited phylogenetic distribution of PMTs, functional analysis and the identification of inhibitors targeting PMTs have potential and positive impacts in humans and in veterinary and agricultural fields. Here, we describe detailed basic knowledge and practical research methods to enable the systematic study of the biochemical and biophysical functions of PMT. The research methods described in this chapter are also applicable to the studies of other ubiquitous S-adenosyl-l-methionine (SAM)-dependent methyltransferases in all kingdoms.
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Affiliation(s)
- Alex Bare
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC, United States
| | - Jaime Thomas
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Daniel Etoroma
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC, United States
| | - Soon Goo Lee
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC, United States.
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2
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Lemfack MC, Brandt W, Krüger K, Gurowietz A, Djifack J, Jung JP, Hopf M, Noack H, Junker B, von Reuß S, Piechulla B. Reaction mechanism of the farnesyl pyrophosphate C-methyltransferase towards the biosynthesis of pre-sodorifen pyrophosphate by Serratia plymuthica 4Rx13. Sci Rep 2021; 11:3182. [PMID: 33542330 PMCID: PMC7862628 DOI: 10.1038/s41598-021-82521-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/18/2021] [Indexed: 11/25/2022] Open
Abstract
Classical terpenoid biosynthesis involves the cyclization of the linear prenyl pyrophosphate precursors geranyl-, farnesyl-, or geranylgeranyl pyrophosphate (GPP, FPP, GGPP) and their isomers, to produce a huge number of natural compounds. Recently, it was shown for the first time that the biosynthesis of the unique homo-sesquiterpene sodorifen by Serratia plymuthica 4Rx13 involves a methylated and cyclized intermediate as the substrate of the sodorifen synthase. To further support the proposed biosynthetic pathway, we now identified the cyclic prenyl pyrophosphate intermediate pre-sodorifen pyrophosphate (PSPP). Its absolute configuration (6R,7S,9S) was determined by comparison of calculated and experimental CD-spectra of its hydrolysis product and matches with those predicted by semi-empirical quantum calculations of the reaction mechanism. In silico modeling of the reaction mechanism of the FPP C-methyltransferase (FPPMT) revealed a SN2 mechanism for the methyl transfer followed by a cyclization cascade. The cyclization of FPP to PSPP is guided by a catalytic dyad of H191 and Y39 and involves an unprecedented cyclopropyl intermediate. W46, W306, F56, and L239 form the hydrophobic binding pocket and E42 and H45 complex a magnesium cation that interacts with the diphosphate moiety of FPP. Six additional amino acids turned out to be essential for product formation and the importance of these amino acids was subsequently confirmed by site-directed mutagenesis. Our results reveal the reaction mechanism involved in methyltransferase-catalyzed cyclization and demonstrate that this coupling of C-methylation and cyclization of FPP by the FPPMT represents an alternative route of terpene biosynthesis that could increase the terpenoid diversity and structural space.
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Affiliation(s)
- Marie Chantal Lemfack
- Institute of Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany.
| | - Wolfgang Brandt
- Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany.
| | - Katja Krüger
- Institute of Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany.,Department of Internal Medicine I, University Hospital RWTH Aachen, 52074, Aachen, Germany
| | - Alexandra Gurowietz
- Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany.,Institute of Biology, Martin-Luther-Universität Halle-Wittenberg, Weinberg 10, 06120, Halle (Saale), Germany
| | - Jacky Djifack
- Institute of Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany.,PIMAN Consultants, 12 Rue Barthelemy Danjou, 92100, Boulogne-Billancourt, France
| | - Jan-Philip Jung
- Institute of Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - Marius Hopf
- Institute of Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany.,Duale Hochschule Gera-Eisenach, Weg der Freundschaft 4, 07546, Gera, Germany
| | - Heiko Noack
- Institute of Pharmacy/Biosynthesis of Active Substances, Hoher Weg 8, 06120, Halle (Saale), Germany
| | - Björn Junker
- Institute of Pharmacy/Biosynthesis of Active Substances, Hoher Weg 8, 06120, Halle (Saale), Germany
| | - Stephan von Reuß
- Laboratory of Bioanalytical Chemistry, Institute of Chemistry, University of Neuchatel, Avenue de Bellevaux 51, 2000, Neuchâtel, Switzerland
| | - Birgit Piechulla
- Institute of Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
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3
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Lee SG, Chung MS, DeMarsilis AJ, Holland CK, Jaswaney RV, Jiang C, Kroboth JHP, Kulshrestha K, Marcelo RZW, Meyyappa VM, Nelson GB, Patel JK, Petronio AJ, Powers SK, Qin PR, Ramachandran M, Rayapati D, Rincon JA, Rocha A, Ferreira JGRN, Steinbrecher MK, Yao K, Zhang EJ, Zou AJ, Gang M, Sparks M, Cascella B, Cruz W, Jez JM. Structural and biochemical analysis of phosphoethanolamine methyltransferase from the pine wilt nematode Bursaphelenchus xylophilus. Mol Biochem Parasitol 2020; 238:111291. [PMID: 32479776 DOI: 10.1016/j.molbiopara.2020.111291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/11/2020] [Accepted: 05/15/2020] [Indexed: 11/28/2022]
Abstract
In free-living and parasitic nematodes, the methylation of phosphoethanolamine to phosphocholine provides a key metabolite to sustain phospholipid biosynthesis for growth and development. Because the phosphoethanolamine methyltransferases (PMT) of nematodes are essential for normal growth and development, these enzymes are potential targets of inhibitor design. The pine wilt nematode (Bursaphelenchus xylophilus) causes extensive damage to trees used for lumber and paper in Asia. As a first step toward testing BxPMT1 as a potential nematicide target, we determined the 2.05 Å resolution x-ray crystal structure of the enzyme as a dead-end complex with phosphoethanolamine and S-adenosylhomocysteine. The three-dimensional structure of BxPMT1 served as a template for site-directed mutagenesis to probe the contribution of active site residues to catalysis and phosphoethanolamine binding using steady-state kinetic analysis. Biochemical analysis of the mutants identifies key residues on the β1d-α6 loop (W123F, M126I, and Y127F) and β1e-α7 loop (S155A, S160A, H170A, T178V, and Y180F) that form the phosphobase binding site and suggest that Tyr127 facilitates the methylation reaction in BxPMT1.
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Affiliation(s)
- Soon Goo Lee
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Michelle S Chung
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Antea J DeMarsilis
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Cynthia K Holland
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Rohit V Jaswaney
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Cherry Jiang
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Jakob H P Kroboth
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Kevin Kulshrestha
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Raymundo Z W Marcelo
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Vidhya M Meyyappa
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Grant B Nelson
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Janki K Patel
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Alex J Petronio
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Samantha K Powers
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Peter R Qin
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Mythili Ramachandran
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Divya Rayapati
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - John A Rincon
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Andreia Rocha
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | | | - Micah K Steinbrecher
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Kaisen Yao
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Eric J Zhang
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Angela J Zou
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Margery Gang
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Melanie Sparks
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Barrie Cascella
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Wilhelm Cruz
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, United States.
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4
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Lang DE, Morris JS, Rowley M, Torres MA, Maksimovich VA, Facchini PJ, Ng KKS. Structure-function studies of tetrahydroprotoberberine N-methyltransferase reveal the molecular basis of stereoselective substrate recognition. J Biol Chem 2019; 294:14482-14498. [PMID: 31395658 DOI: 10.1074/jbc.ra119.009214] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/01/2019] [Indexed: 12/18/2022] Open
Abstract
Benzylisoquinoline alkaloids (BIAs) are a structurally diverse class of plant-specialized metabolites that have been particularly well-studied in the order Ranunculales. The N-methyltransferases (NMTs) in BIA biosynthesis can be divided into three groups according to substrate specificity and amino acid sequence. Here, we report the first crystal structures of enzyme complexes from the tetrahydroprotoberberine NMT (TNMT) subclass, specifically for GfTNMT from the yellow horned poppy (Glaucium flavum). GfTNMT was co-crystallized with the cofactor S-adenosyl-l-methionine (d min = 1.6 Å), the product S-adenosyl-l-homocysteine (d min = 1.8 Å), or in complex with S-adenosyl-l-homocysteine and (S)-cis-N-methylstylopine (d min = 1.8 Å). These structures reveal for the first time how a mostly hydrophobic L-shaped substrate recognition pocket selects for the (S)-cis configuration of the two central six-membered rings in protoberberine BIA compounds. Mutagenesis studies confirm and functionally define the roles of several highly-conserved residues within and near the GfTNMT-active site. The substrate specificity of TNMT enzymes appears to arise from the arrangement of subgroup-specific stereospecific recognition elements relative to catalytic elements that are more widely-conserved among all BIA NMTs. The binding mode of protoberberine compounds to GfTNMT appears to be similar to coclaurine NMT, with the isoquinoline rings buried deepest in the binding pocket. This binding mode differs from that of pavine NMT, in which the benzyl ring is bound more deeply than the isoquinoline rings. The insights into substrate recognition and catalysis provided here form a sound basis for the rational engineering of NMT enzymes for chemoenzymatic synthesis and metabolic engineering.
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Affiliation(s)
- Dean E Lang
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Jeremy S Morris
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Michael Rowley
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Miguel A Torres
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
| | - Vook A Maksimovich
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Kenneth K S Ng
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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5
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Santatiwongchai J, Gleeson D, Gleeson MP. Theoretical Evaluation of the Reaction Mechanism of Serine Hydroxymethyltransferase. J Phys Chem B 2019; 123:407-418. [PMID: 30522268 DOI: 10.1021/acs.jpcb.8b10196] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate (PLP)-dependent enzyme that catalyzes the reversible conversion of serine and tetrahydrofolate (THF) to glycine and 5,10-methylene THF. SHMT is a folate pathway enzyme and is therefore of considerable medical interest due to its role as an important intervention point for antimalarial, anticancer, and antibacterial treatments. Despite considerable experimental effort, the precise reaction mechanism of SHMT remains unclear. In this study, we explore the mechanism of SHMT to determine the roles of active site residues and the nature and the sequence of chemical steps. Molecular dynamics (MD) methods were employed to generate a suitable starting structure which then underwent analysis using hybrid quantum mechanical/molecular mechanical (QM/MM) simulations. The QM region consisted of 12 key residues, two substrates, and explicit solvent. Our results show that the catalytic reaction proceeds according to a retro-aldol synthetic process with His129 acting as the general base in the reaction. The rate-determining step involves the cleavage of the PLP-serine aldimine Cα-Cβ bond and the formation of formaldehyde in line with experimental evidence. The pyridyl ring of the PLP-serine aldimine substrate exists in deprotonated form, being stabilized directly by Asp208 via a strong H-bond, as well as through interactions with Arg371, Lys237, and His211, and with the surrounding protein which was electrostatically embedded. This knowledge has the potential to impact the design and development of new inhibitors.
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Affiliation(s)
- Jirapat Santatiwongchai
- Department of Chemistry, Faculty of Science , Kasetsart University , Bangkok 10900 , Thailand
| | - Duangkamol Gleeson
- Department of Chemistry, Faculty of Science , King Mongkut's Institute of Technology Ladkrabang , Bangkok 10520 , Thailand
| | - M Paul Gleeson
- Department of Chemistry, Faculty of Science , Kasetsart University , Bangkok 10900 , Thailand.,Department of Biomedical Engineering, Faculty of Engineering , King Mongkut's Institute of Technology Ladkrabang , Bangkok 10520 , Thailand
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6
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Hörberg J, Saenz-Mendez P, Eriksson LA. QM/MM Studies of Dph5 - A Promiscuous Methyltransferase in the Eukaryotic Biosynthetic Pathway of Diphthamide. J Chem Inf Model 2018; 58:1406-1414. [PMID: 29927239 DOI: 10.1021/acs.jcim.8b00217] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Eukaryotic diphthine synthase, Dph5, is a promiscuous methyltransferase that catalyzes an extraordinary N, O-tetramethylation of 2-(3-carboxy-3-aminopropyl)-l-histidine (ACP) to yield diphthine methyl ester (DTM). These are intermediates in the biosynthesis of the post-translationally modified histidine residue diphthamide (DTA), a unique and essential residue part of the eukaryotic elongation factor 2 (eEF2). Herein, the promiscuity of Saccharomyces cerevisiae Dph5 has been studied with in silico approaches, including homology modeling to provide the structure of Dph5, protein-protein docking and molecular dynamics to construct the Dph5-eEF2 complex, and quantum mechanics/molecular mechanics (QM/MM) calculations to outline a plausible mechanism. The calculations show that the methylation of ACP follows a typical SN2 mechanism, initiating with a complete methylation (trimethylation) at the N-position, followed by the single O-methylation. For each of the three N-methylation reactions, our calculations support a stepwise mechanism, which first involve proton transfer through a bridging water to a conserved aspartate residue D165, followed by a methyl transfer. Once fully methylated, the trimethyl amino group forms a weak electrostatic interaction with D165, which allows the carboxylate group of diphthine to attain the right orientation for the final methylation step to be accomplished.
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Affiliation(s)
- Johanna Hörberg
- Department of Chemistry and Molecular Biology , University of Gothenburg , 405 30 Göteborg , Sweden
| | - Patricia Saenz-Mendez
- Computational Chemistry and Biology Group, Facultad de Química , Universidad de la República , 11800 Montevideo , Uruguay
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology , University of Gothenburg , 405 30 Göteborg , Sweden
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7
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Lee SG, Jez JM. Conformational changes in the di-domain structure of Arabidopsis phosphoethanolamine methyltransferase leads to active-site formation. J Biol Chem 2017; 292:21690-21702. [PMID: 29084845 DOI: 10.1074/jbc.ra117.000106] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/20/2017] [Indexed: 01/05/2023] Open
Abstract
Phosphocholine (pCho) is a precursor for phosphatidylcholine and osmoprotectants in plants. In plants, de novo synthesis of pCho relies on the phosphobase methylation pathway. Phosphoethanolamine methyltransferase (PMT) catalyzes the triple methylation of phosphoethanolamine (pEA) to pCho. The plant PMTs are di-domain methyltransferases that divide the methylation of pEA in one domain from subsequent methylations in the second domain. To understand the molecular basis of this architecture, we examined the biochemical properties of three Arabidopsis thaliana PMTs (AtPMT1-3) and determined the X-ray crystal structures of AtPMT1 and AtPMT2. Although each isoform synthesizes pCho from pEA, their physiological roles differ with AtPMT1 essential for normal growth and salt tolerance, whereas AtPMT2 and AtPMT3 overlap functionally. The structures of AtPMT1 and AtPMT2 reveal unique features in each methyltransferase domain, including active sites that use different chemical mechanisms for phosphobase methylation. These structures also show how rearrangements in both the active sites and the di-domain linker form catalytically competent active sites and provide insight on the evolution of the PMTs in plants, nematodes, and apicomplexans. Connecting conformational changes with catalysis in modular enzymes, like the PMT, provides new insights on interdomain communication in biosynthetic systems.
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Affiliation(s)
- Soon Goo Lee
- From the Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Joseph M Jez
- From the Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
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8
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Shandilya A, Hoda N, Khan S, Jameel E, Kumar J, Jayaram B. De novo lead optimization of triazine derivatives identifies potent antimalarials. J Mol Graph Model 2017; 71:96-103. [DOI: 10.1016/j.jmgm.2016.10.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/11/2016] [Accepted: 10/14/2016] [Indexed: 11/27/2022]
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9
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Torres MA, Hoffarth E, Eugenio L, Savtchouk J, Chen X, Morris JS, Facchini PJ, Ng KKS. Structural and Functional Studies of Pavine N-Methyltransferase from Thalictrum flavum Reveal Novel Insights into Substrate Recognition and Catalytic Mechanism. J Biol Chem 2016; 291:23403-23415. [PMID: 27573242 DOI: 10.1074/jbc.m116.747261] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Indexed: 11/06/2022] Open
Abstract
Benzylisoquinoline alkaloids (BIAs) are produced in a wide variety of plants and include many common analgesic, antitussive, and anticancer compounds. Several members of a distinct family of S-adenosylmethionine (SAM)-dependent N-methyltransferases (NMTs) play critical roles in BIA biosynthesis, but the molecular basis of substrate recognition and catalysis is not known for NMTs involved in BIA metabolism. To address this issue, the crystal structure of pavine NMT from Thalictrum flavum was solved using selenomethionine-substituted protein (dmin = 2.8 Å). Additional structures were determined for the native protein (dmin = 2.0 Å) as well as binary complexes with SAM (dmin = 2.3 Å) or the reaction product S-adenosylhomocysteine (dmin = 1.6 Å). The structure of a complex with S-adenosylhomocysteine and two molecules of tetrahydropapaverine (THP; one as the S conformer and a second in the R configuration) (dmin = 1.8 Å) revealed key features of substrate recognition. Pavine NMT converted racemic THP to laudanosine, but the enzyme showed a preference for (±)-pavine and (S)-reticuline as substrates. These structures suggest the involvement of highly conserved residues at the active site. Mutagenesis of three residues near the methyl group of SAM and the nitrogen atom of the alkaloid acceptor decreased enzyme activity without disrupting the structure of the protein. The binding site for THP provides a framework for understanding substrate specificity among numerous NMTs involved in the biosynthesis of BIAs and other specialized metabolites. This information will facilitate metabolic engineering efforts aimed at producing medicinally important compounds in heterologous systems, such as yeast.
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Affiliation(s)
- Miguel A Torres
- From the Department of Biological Sciences and.,Alberta Glycomics Centre, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Elesha Hoffarth
- From the Department of Biological Sciences and.,Alberta Glycomics Centre, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Luiz Eugenio
- From the Department of Biological Sciences and.,Alberta Glycomics Centre, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Julia Savtchouk
- From the Department of Biological Sciences and.,Alberta Glycomics Centre, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Xue Chen
- From the Department of Biological Sciences and
| | | | | | - Kenneth K-S Ng
- From the Department of Biological Sciences and .,Alberta Glycomics Centre, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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10
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Park YH, Shi YP, Liang B, Medriano CAD, Jeon YH, Torres E, Uppal K, Slutsker L, Jones DP. High-resolution metabolomics to discover potential parasite-specific biomarkers in a Plasmodium falciparum erythrocytic stage culture system. Malar J 2015; 14:122. [PMID: 25889340 PMCID: PMC4377044 DOI: 10.1186/s12936-015-0651-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/16/2015] [Indexed: 12/27/2022] Open
Abstract
Background Current available malaria diagnostic methods each have some limitations to meet the need for real-time and large-scale screening of asymptomatic and low density malaria infection at community level. It was proposed that malaria parasite-specific low molecular-weight metabolites could be used as biomarkers for the development of a malaria diagnostic tool aimed to address this diagnostic challenge. In this study, high resolution metabolomics (HRM) was employed to identify malaria parasite-specific metabolites in Plasmodium falciparum in vitro culture samples. Methods Supernatants were collected at 12 hours interval from 3% haematocrit in vitro 48-hour time-course asynchronized culture system of P. falciparum. Liquid chromatography coupled with high resolution mass spectrometry was applied to discover potential parasite-specific metabolites in the cell culture supernatant. A metabolome-wide association study was performed to extract metabolites using Manhattan plot with false discovery rate (FDR) and hierarchical cluster analysis. The significant metabolites based on FDR cutoff were annotated using Metlin database. Standard curves were created using corresponding chemical compounds to accurately quantify potential Plasmodium-specific metabolites in culture supernatants. Results The number of significant metabolite features was 1025 in the supernatant of the Plasmodium infected culture based on Manhattan plot with FDR q=0.05. A two way hierarchical cluster analysis showed a clear segregation of the metabolic profile of parasite infected supernatant from non-infected supernatant at four time points during the 48 hour culture. Among the 1025 annotated metabolites, the intensities of four molecules were significantly increased with culture time suggesting a positive association between the quantity of these molecules and level of parasitaemia: i) 3-methylindole, a mosquito attractant, ii) succinylacetone, a haem biosynthesis inhibitor, iii) S-methyl-L-thiocitrulline, a nitric oxide synthase inhibitor, and iv) O-arachidonoyl glycidol, a fatty acid amide hydrolase inhibitor, The highest concentrations of 3-methylindole and succinylacetone were 178 ± 18.7 pmoles at 36 hours and 157±30.5 pmoles at 48 hours respectively in parasite infected supernatant. Conclusion HRM with bioinformatics identified four potential parasite-specific metabolite biomarkers using in vitro culture supernatants. Further study in malaria infected human is needed to determine presence of the molecules and its relationship with parasite densities. Electronic supplementary material The online version of this article (doi:10.1186/s12936-015-0651-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Youngja H Park
- Dept of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA. .,College of Pharmacy, Korea University, Sejong City, South Korea.
| | - Ya Ping Shi
- Malaria Branch, Division of Parasitic Diseases and Malaria (DPDM), Centers for Disease Control and Prevention (CDC), Atlanta, USA.
| | - Bill Liang
- Dept of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | | | - Young Ho Jeon
- College of Pharmacy, Korea University, Sejong City, South Korea.
| | - Eucaris Torres
- Malaria Branch, Division of Parasitic Diseases and Malaria (DPDM), Centers for Disease Control and Prevention (CDC), Atlanta, USA.
| | - Karan Uppal
- Dept of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Laurence Slutsker
- Malaria Branch, Division of Parasitic Diseases and Malaria (DPDM), Centers for Disease Control and Prevention (CDC), Atlanta, USA.
| | - Dean P Jones
- Dept of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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Garg A, Lukk T, Kumar V, Choi JY, Augagneur Y, Voelker DR, Nair S, Ben Mamoun C. Structure, function and inhibition of the phosphoethanolamine methyltransferases of the human malaria parasites Plasmodium vivax and Plasmodium knowlesi. Sci Rep 2015; 5:9064. [PMID: 25761669 PMCID: PMC4357015 DOI: 10.1038/srep09064] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/03/2015] [Indexed: 11/09/2022] Open
Abstract
Phosphoethanolamine methyltransferases (PMTs) catalyze the three-step methylation of phosphoethanolamine to form phosphocholine, a critical step in the synthesis of phosphatidylcholine in a select number of eukaryotes including human malaria parasites, nematodes and plants. Genetic studies in the malaria parasite Plasmodium falciparum have shown that the methyltransferase PfPMT plays a critical function in parasite development and differentiation. The presence of PMT orthologs in other malaria parasites that infect humans and their absence in mammals make them ideal targets for the development of selective antimalarials with broad specificity against different Plasmodium species. Here we describe the X-ray structures and biochemical properties of PMT orthologs from Plasmodium vivax and Plasmodium knowlesi and show that both enzymes are inhibited by amodiaquine and NSC158011, two drugs with potent antimalarial activity. Metabolic studies in a yeast mutant that relies on PkPMT or PvPMT for survival demonstrated that these compounds inhibit phosphatidylcholine biosynthesis from ethanolamine. Our structural and functional data provide insights into the mechanism of catalysis and inhibition of PMT enzymes and set the stage for a better design of more specific and selective antimalarial drugs.
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Affiliation(s)
- Aprajita Garg
- Department of Internal Medicine, Yale University School of Medicine, New Haven CT, 06520 USA
| | - Tiit Lukk
- 1] Department of Biochemistry, University of Illinois at Urbana-Champaign [2] Cornell High Energy Synchrotron Source, Cornell University
| | - Vidya Kumar
- Department of Internal Medicine, Yale University School of Medicine, New Haven CT, 06520 USA
| | - Jae-Yeon Choi
- Basic Science Section, Department of Medicine, National Jewish Health, Denver, Colorado 80206
| | - Yoann Augagneur
- Department of Internal Medicine, Yale University School of Medicine, New Haven CT, 06520 USA
| | - Dennis R Voelker
- Basic Science Section, Department of Medicine, National Jewish Health, Denver, Colorado 80206
| | - Satish Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign
| | - Choukri Ben Mamoun
- Department of Internal Medicine, Yale University School of Medicine, New Haven CT, 06520 USA
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