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Kuttenlochner W, Beller P, Kaysser L, Groll M. Deciphering the SAM- and metal-dependent mechanism of O-methyltransferases in cystargolide and belactosin biosynthesis: A structure-activity relationship study. J Biol Chem 2024; 300:107646. [PMID: 39121999 PMCID: PMC11408123 DOI: 10.1016/j.jbc.2024.107646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/18/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
Cystargolides and belactosins are natural products with a distinct dipeptide structure and an electrophilic β-lactone warhead. They are known to inhibit proteases such as the proteasome or caseinolytic protease P, highlighting their potential in treating cancers and neurodegenerative diseases. Recent genetic analyses have shown homology between the biosynthetic pathways of the two inhibitors. Here, we characterize the O-methyltransferases BelI and CysG, which catalyze the initial step of β-lactone formation. Employing techniques such as crystallography, computational analysis, mutagenesis, and activity assays, we identified a His-His-Asp (HHD) motif in the active sites of the two enzymes, which is crucial for binding a catalytically active calcium ion. Our findings thus elucidate a conserved divalent metal-dependent mechanism in both biosynthetic pathways that distinguish BelI and CysG from previously characterized O-methyltransferases.
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Affiliation(s)
- Wolfgang Kuttenlochner
- Department of Bioscience, Center for Protein Assemblies (CPA), TUM School of Natural Sciences, Technical University of Munich, Garching, Germany.
| | - Patrick Beller
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Leonard Kaysser
- Department of Pharmaceutical Biology, Institute for Drug Discovery, University of Leipzig, Leipzig, Germany
| | - Michael Groll
- Department of Bioscience, Center for Protein Assemblies (CPA), TUM School of Natural Sciences, Technical University of Munich, Garching, Germany.
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2
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Poudel PB, Dhakal D, Lee JC, Sohng JK. Functional characterization of a naphthalene-O-methyltransferase from Nocardia sp. CS682. Enzyme Microb Technol 2024; 172:110351. [PMID: 37939423 DOI: 10.1016/j.enzmictec.2023.110351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/10/2023]
Abstract
Methylation plays important roles in biosynthesis, metabolism, signal transduction, detoxification, protein sorting and repair, and nucleic acid processing. Generally the methyltransferases transfer methyl groups in various natural products using S-adenosyl methionine (SAM) as a cofactor. In this study, we examined and functionally characterized ThnM3 (enzyme), by testing various substrates with different chemical structures. Among the tested substrates, 1,8-dihydroxynaphthalene was the best substrate for methylation. Whole-cell biotransformation was performed using the enzyme in engineered Escherichia coli to produce 8-methoxynaphthalene-1-ol, and 1,8-dimethoxynaphthalene derivatives of 1,8-dihydroxynaphthalene. The products were confirmed using high-performance liquid chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopic analyses. Therefore, this study is the first to amplify, express the thnM3 (gene), and functionally characterize theThnM3, which exhibits the regioselective modifications of 1,8-dihydroxynaphthalene.
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Affiliation(s)
- Purna Bahadur Poudel
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, South Korea
| | - Dipesh Dhakal
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, South Korea
| | - Jong Cheol Lee
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, South Korea
| | - Jae Kyung Sohng
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, South Korea; Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, South Korea.
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3
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Huang S, Ji H, Zheng J. Structural and computational insights into the regioselectivity of SpnK involved in rhamnose methylation of spinosyn. Int J Biol Macromol 2023; 253:126763. [PMID: 37703985 DOI: 10.1016/j.ijbiomac.2023.126763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023]
Abstract
Rhamnose methylation of spinosyn critical for insecticidal activity is orchestrated by substrate specificity of three S-adenosyl-L-methionine (SAM) dependent methyltransferases (MTs). Previous in vitro enzymatic assays indicate that 3'-O-MT SpnK accepts the rhamnosylated aglycone (RAGL) and 2'-O-methylated RAGL as substrates, but does not tolerate the presence of a methoxy moiety at the O-4' position of the rhamnose unit. Here we solved the crystal structures of apo and ligand-bound SpnK, and used molecular dynamic (MD) simulations to decipher the molecular basis of substrate specificity. SpnK assembles into a tetramer, with each set of three monomers forming an integrated substrate binding pocket. The MD simulations of SpnK complexed with RAGL or 2'-O-methylated RAGL revealed that the 4'-hydroxyl of the rhamnose unit formed a hydrogen bond with a conserved Asp299 of the catalytic center, which is disrupted in structures of SpnK complexed with 4'-O-methylated RAGL or 2',4'-di-O-methylated RAGL. Comparison with SpnI methylating the C2'-hydroxyl of RAGL reveals a correlation between a DLQT/DLWT motif and the selectivity of rhamnose O-MTs. Together, our structural and computational results revealed the structural basis of substrate specificity of rhamnose O-MTs and would potentially help the engineering of spinosyn derivatives.
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Affiliation(s)
- Shuxin Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huining Ji
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.
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4
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Abdelraheem E, Thair B, Varela RF, Jockmann E, Popadić D, Hailes HC, Ward JM, Iribarren AM, Lewkowicz ES, Andexer JN, Hagedoorn P, Hanefeld U. Methyltransferases: Functions and Applications. Chembiochem 2022; 23:e202200212. [PMID: 35691829 PMCID: PMC9539859 DOI: 10.1002/cbic.202200212] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/10/2022] [Indexed: 11/25/2022]
Abstract
In this review the current state-of-the-art of S-adenosylmethionine (SAM)-dependent methyltransferases and SAM are evaluated. Their structural classification and diversity is introduced and key mechanistic aspects presented which are then detailed further. Then, catalytic SAM as a target for drugs, and approaches to utilise SAM as a cofactor in synthesis are introduced with different supply and regeneration approaches evaluated. The use of SAM analogues are also described. Finally O-, N-, C- and S-MTs, their synthetic applications and potential for compound diversification is given.
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Affiliation(s)
- Eman Abdelraheem
- BiocatalysisDepartment of BiotechnologyDelft University of TechnologyVan der Maasweg 92629 HZDelft (TheNetherlands
| | - Benjamin Thair
- Department of ChemistryUniversity College London20 Gordon StreetLondonWC1H 0AJUK
| | - Romina Fernández Varela
- Laboratorio de Biotransformaciones y Química de Ácidos NucleicosUniversidad Nacional de QuilmesRoque S. Peña 352B1876BXDBernalArgentina
| | - Emely Jockmann
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstr. 2579104FreiburgGermany
| | - Désirée Popadić
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstr. 2579104FreiburgGermany
| | - Helen C. Hailes
- Department of ChemistryUniversity College London20 Gordon StreetLondonWC1H 0AJUK
| | - John M. Ward
- Department of Biochemical EngineeringBernard Katz BuildingUniversity College LondonLondonWC1E 6BTUK
| | - Adolfo M. Iribarren
- Laboratorio de Biotransformaciones y Química de Ácidos NucleicosUniversidad Nacional de QuilmesRoque S. Peña 352B1876BXDBernalArgentina
| | - Elizabeth S. Lewkowicz
- Laboratorio de Biotransformaciones y Química de Ácidos NucleicosUniversidad Nacional de QuilmesRoque S. Peña 352B1876BXDBernalArgentina
| | - Jennifer N. Andexer
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstr. 2579104FreiburgGermany
| | - Peter‐Leon Hagedoorn
- BiocatalysisDepartment of BiotechnologyDelft University of TechnologyVan der Maasweg 92629 HZDelft (TheNetherlands
| | - Ulf Hanefeld
- BiocatalysisDepartment of BiotechnologyDelft University of TechnologyVan der Maasweg 92629 HZDelft (TheNetherlands
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Poudel PB, Pandey RP, Dhakal D, Kim TS, Nguyen TTH, Jung HJ, Shin HJ, Timalsina B, Sohng JK. Functional Characterization of a Regiospecific Sugar- O-Methyltransferase from Nocardia. Appl Environ Microbiol 2022; 88:e0075422. [PMID: 35703553 PMCID: PMC9275233 DOI: 10.1128/aem.00754-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022] Open
Abstract
Methyltransferases transfer a methyl group to a diverse group of natural products, thus providing structural diversity, stability, and altered pharmacological properties to the molecules. A limited number of regiospecific sugar-O-methyltransferases are functionally characterized. Thus, discovery of such an enzyme could solve the difficulties of biological production of methoxy derivatives of glycosylated molecules. In the current study, a regiospecific sugar-O-methyltransferase, ThnM1, belonging to the biosynthetic gene cluster (BGC) of 1-(α-L-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene produced by Nocardia sp. strain CS682, was analyzed and functionally characterized. ThnM1 demonstrated promiscuity to diverse chemical structures such as rhamnose-containing anthraquinones and flavonoids with regiospecific methylation at the 2'-hydroxyl group of the sugar moiety. Compared with other compounds, anthraquinone rhamnosides were found to be the preferred substrates for methylation. Thus, the enzyme was further employed for whole-cell biotransformation using engineered Escherichia coli to produce a methoxy-rhamnosyl derivative of quinizarin, an anthraquinone derivative. The structure of the newly generated derivative from Escherichia coli fermentation was elucidated by liquid chromatography-mass spectrometry and nuclear magnetic resonance spectroscopic analyses and identified as quinizarin-4-O-α-l-2-O-methylrhamnoside (QRM). Further, the biological impact of methylation was studied by comparing the cytotoxicity of QRM with that of quinizarin against the U87MG, SNU-1, and A375SM cancer cell lines. IMPORTANCE ThnM1 is a putative sugar-O-methyltransferase produced by the Nocardia sp. strain CS682 and is encoded by a gene belonging to the biosynthetic gene cluster (BGC) of 1-(α-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene. We demonstrated that ThnM1 is a promiscuous enzyme with regiospecific activity at the 2'-OH of rhamnose. As regiospecific methylation of sugars by chemical synthesis is a challenging step, ThnM1 may fill the gap in the potential diversification of natural products by methylating the rhamnose moiety attached to them.
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Affiliation(s)
- Purna Bahadur Poudel
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Ramesh Prasad Pandey
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Dipesh Dhakal
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Tae-Su Kim
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Trang Thi Huyen Nguyen
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Hye Jin Jung
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
- Department of Biotechnology and Pharmaceutical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Hee Jeong Shin
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Binod Timalsina
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, Republic of Korea
| | - Jae Kyung Sohng
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
- Department of Biotechnology and Pharmaceutical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
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6
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Enzymatic characterization of three human RNA adenosine methyltransferases reveals diverse substrate affinities and reaction optima. J Biol Chem 2021; 296:100270. [PMID: 33428944 PMCID: PMC7948815 DOI: 10.1016/j.jbc.2021.100270] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 11/22/2022] Open
Abstract
RNA methylations of varied RNA species (mRNA, tRNA, rRNA, non-coding RNA) generate a range of modified nucleotides, including N6-methyladenosine. Here we study the enzymology of three human RNA methyltransferases that methylate the adenosine amino group in diverse contexts, when it is: the first transcribed nucleotide after the mRNA cap (PCIF1), at position 1832 of 18S rRNA (MettL5-Trm112 complex), and within a hairpin in the 3′ UTR of the S-adenosyl-l-methionine synthetase (MettL16). Among these three enzymes, the catalytic efficiency ranges from PCIF1, with the fastest turnover rate of >230 h−1 μM−1 on mRNA cap analog, down to MettL16, which has the lowest rate of ∼3 h−1 μM−1 acting on an RNA hairpin. Both PCIF1 and MettL5 have a binding affinity (Km) of ∼1 μM or less for both substrates of SAM and RNA, whereas MettL16 has significantly lower binding affinities for both (Km >0.4 mM for SAM and ∼10 μM for RNA). The three enzymes are active over a wide pH range (∼5.4–9.4) and have different preferences for ionic strength. Sodium chloride at 200 mM markedly diminished methylation activity of MettL5-Trm112 complex, whereas MettL16 had higher activity in the range of 200 to 500 mM NaCl. Zinc ion inhibited activities of all three enzymes. Together, these results illustrate the diversity of RNA adenosine methyltransferases in their enzymatic mechanisms and substrate specificities and underline the need for assay optimization in their study.
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Speciale I, Laugieri ME, Noel E, Lin S, Lowary TL, Molinaro A, Duncan GA, Agarkova IV, Garozzo D, Tonetti MG, Van Etten JL, De Castro C. Chlorovirus PBCV-1 protein A064R has three of the transferase activities necessary to synthesize its capsid protein N-linked glycans. Proc Natl Acad Sci U S A 2020; 117:28735-28742. [PMID: 33139538 PMCID: PMC7682578 DOI: 10.1073/pnas.2016626117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Paramecium bursaria chlorella virus-1 (PBCV-1) is a large double-stranded DNA (dsDNA) virus that infects the unicellular green alga Chlorella variabilis NC64A. Unlike many other viruses, PBCV-1 encodes most, if not all, of the enzymes involved in the synthesis of the glycans attached to its major capsid protein. Importantly, these glycans differ from those reported from the three domains of life in terms of structure and asparagine location in the sequon of the protein. Previous data collected from 20 PBCV-1 spontaneous mutants (or antigenic variants) suggested that the a064r gene encodes a glycosyltransferase (GT) with three domains, each with a different function. Here, we demonstrate that: domain 1 is a β-l-rhamnosyltransferase; domain 2 is an α-l-rhamnosyltransferase resembling only bacterial proteins of unknown function, and domain 3 is a methyltransferase that methylates the C-2 hydroxyl group of the terminal α-l-rhamnose (Rha) unit. We also establish that methylation of the C-3 hydroxyl group of the terminal α-l-Rha is achieved by another virus-encoded protein A061L, which requires an O-2 methylated substrate. This study, thus, identifies two of the glycosyltransferase activities involved in the synthesis of the N-glycan of the viral major capsid protein in PBCV-1 and establishes that a single protein A064R possesses the three activities needed to synthetize the 2-OMe-α-l-Rha-(1→2)-β-l-Rha fragment. Remarkably, this fragment can be attached to any xylose unit.
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Affiliation(s)
- Immacolata Speciale
- Department of Chemical Sciences, University of Napoli Federico II, 80126 Napoli, Italy
- Department of Agricultural Sciences, University of Napoli Federico II, 80055 Portici NA, Italy
| | - Maria Elena Laugieri
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, 16132 Genova, Italy
| | - Eric Noel
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588-0118
| | - Sicheng Lin
- Department of Chemistry, University of Alberta, Gunning-Lemieux Chemistry Centre, Edmonton, AB T6G 2G2 , Canada
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Gunning-Lemieux Chemistry Centre, Edmonton, AB T6G 2G2 , Canada
- Institute of Biological Chemistry, Academia Sinica, Nangang, 11529 Taipei, Taiwan
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli Federico II, 80126 Napoli, Italy
| | - Garry A Duncan
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900
| | - Irina V Agarkova
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583-0722
| | - Domenico Garozzo
- CNR, Institute for Polymers, Composites and Biomaterials, 95126 Catania, Italy
| | - Michela G Tonetti
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, 16132 Genova, Italy;
| | - James L Van Etten
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900;
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583-0722
| | - Cristina De Castro
- Department of Agricultural Sciences, University of Napoli Federico II, 80055 Portici NA, Italy;
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Wang R, Zhang L, Chen Y, Zhang S, Zhuang T, Wang L, Xu M, Zhang N, Liu S. Elevated non-essential metals and the disordered metabolism of essential metals are associated to abnormal pregnancy with spontaneous abortion. ENVIRONMENT INTERNATIONAL 2020; 144:106061. [PMID: 32890886 DOI: 10.1016/j.envint.2020.106061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/10/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Spontaneous abortion is a considerable threat to the physiology and mental health of the mother. The etiology of spontaneous abortion is multifactorial with complicated mechanisms, of which overexposure to non-essential metals (especially heavy metals) has been proposed to be associated with adverse birth outcomes. However, significant knowledge gaps remain to be filled in, such as the deleterious profile of non-essential metals and their interplay with essential metals in abnormal pregnancy. Under this setting, we aimed to address these challenges by conducting a cross-sectional study on 56 patients with spontaneous abortion in the 1st trimester, by comparing to 55 healthy pregnant women in 1st the trimester and 41 non-pregnant healthy women. Overexposure to a few non-essential metals, such as arsenic (As), antimony (Sb) and bismuth (Bi), was found in patients with spontaneous abortion, and likewise, some essential elements, such as magnesium (Mg), copper (Cu), vanadium (V), strontium (Sr) and tin (Sn), were also found to be elevated under spontaneous abortion. Further evidence of abnormal pregnancy was induced by a reduced level of internal hormones necessary for normal gestation, such as estradiol (E2) and progesterone (PRGE) in women with spontaneous abortion. Lactate dehydrogenase (LDH) and thyroid-stimulating hormone (TSH) levels were slightly increased in patients with spontaneous abortion. Comprehensive correlation analyses were carried out to identify the crucial factors that result in abortion. Our data stratified the important variables in decreasing order: PRGE, As, Mg, Sb, Sr, Sn, Bi and pregnant times in the progress of spontaneous abortion. Moreover, labyrinthine associations were uncovered between PRGE, non-essential metals and essential elements in causing spontaneous abortion. Therefore, our combined data unveiled the likely synergistic implications of elevated non-essential metals and the disordered metabolism of essential metals in abnormal pregnancy.
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Affiliation(s)
- Ruixia Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Le Zhang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Yongjiu Chen
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Shuping Zhang
- The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Taifeng Zhuang
- Department of Neonatal Intensive Care Unit (NICU), Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Li Wang
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Ming Xu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Na Zhang
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China.
| | - Sijin Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
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9
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Torres MDT, Pedron CN, Higashikuni Y, Kramer RM, Cardoso MH, Oshiro KGN, Franco OL, Silva Junior PI, Silva FD, Oliveira Junior VX, Lu TK, de la Fuente-Nunez C. Structure-function-guided exploration of the antimicrobial peptide polybia-CP identifies activity determinants and generates synthetic therapeutic candidates. Commun Biol 2018; 1:221. [PMID: 30534613 PMCID: PMC6286318 DOI: 10.1038/s42003-018-0224-2] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 10/18/2018] [Indexed: 12/20/2022] Open
Abstract
Antimicrobial peptides (AMPs) constitute promising alternatives to classical antibiotics for the treatment of drug-resistant infections, which are a rapidly emerging global health challenge. However, our understanding of the structure-function relationships of AMPs is limited, and we are just beginning to rationally engineer peptides in order to develop them as therapeutics. Here, we leverage a physicochemical-guided peptide design strategy to identify specific functional hotspots in the wasp-derived AMP polybia-CP and turn this toxic peptide into a viable antimicrobial. Helical fraction, hydrophobicity, and hydrophobic moment are identified as key structural and physicochemical determinants of antimicrobial activity, utilized in combination with rational engineering to generate synthetic AMPs with therapeutic activity in a mouse model. We demonstrate that, by tuning these physicochemical parameters, it is possible to design nontoxic synthetic peptides with enhanced sub-micromolar antimicrobial potency in vitro and anti-infective activity in vivo. We present a physicochemical-guided rational design strategy to generate peptide antibiotics.
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Affiliation(s)
- Marcelo D. T. Torres
- Synthetic Biology Group, MIT Synthetic Biology Center; The Center for Microbiome Informatics and Therapeutics; Research Laboratory of Electronics, Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP 09210580 Brazil
| | - Cibele N. Pedron
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP 09210580 Brazil
| | - Yasutomi Higashikuni
- Synthetic Biology Group, MIT Synthetic Biology Center; The Center for Microbiome Informatics and Therapeutics; Research Laboratory of Electronics, Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Robin M. Kramer
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Marlon H. Cardoso
- Programa de Pós-Gradução em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, DF 70297400 Brazil
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, DF 71966700 Brazil
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS 79117010 Brazil
| | - Karen G. N. Oshiro
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS 79117010 Brazil
| | - Octávio L. Franco
- Programa de Pós-Gradução em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, DF 70297400 Brazil
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, DF 71966700 Brazil
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS 79117010 Brazil
| | - Pedro I. Silva Junior
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, SP 05503900 Brazil
| | - Fernanda D. Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP 09210580 Brazil
| | - Vani X. Oliveira Junior
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP 09210580 Brazil
| | - Timothy K. Lu
- Synthetic Biology Group, MIT Synthetic Biology Center; The Center for Microbiome Informatics and Therapeutics; Research Laboratory of Electronics, Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Cesar de la Fuente-Nunez
- Synthetic Biology Group, MIT Synthetic Biology Center; The Center for Microbiome Informatics and Therapeutics; Research Laboratory of Electronics, Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
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10
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Darsandhari S, Dhakal D, Shrestha B, Parajuli P, Seo JH, Kim TS, Sohng JK. Characterization of regioselective flavonoid O- methyltransferase from the Streptomyces sp. KCTC 0041BP. Enzyme Microb Technol 2018; 113:29-36. [DOI: 10.1016/j.enzmictec.2018.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/05/2018] [Accepted: 02/20/2018] [Indexed: 12/22/2022]
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11
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A structural appraisal of sterol carrier protein 2. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:565-577. [DOI: 10.1016/j.bbapap.2017.03.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/03/2017] [Accepted: 03/07/2017] [Indexed: 11/19/2022]
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12
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Bernard SM, Akey DL, Tripathi A, Park SR, Konwerski JR, Anzai Y, Li S, Kato F, Sherman DH, Smith JL. Structural basis of substrate specificity and regiochemistry in the MycF/TylF family of sugar O-methyltransferases. ACS Chem Biol 2015; 10:1340-51. [PMID: 25692963 DOI: 10.1021/cb5009348] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Sugar moieties in natural products are frequently modified by O-methylation. In the biosynthesis of the macrolide antibiotic mycinamicin, methylation of a 6'-deoxyallose substituent occurs in a stepwise manner first at the 2'- and then the 3'-hydroxyl groups to produce the mycinose moiety in the final product. The timing and placement of the O-methylations impact final stage C-H functionalization reactions mediated by the P450 monooxygenase MycG. The structural basis of pathway ordering and substrate specificity is unknown. A series of crystal structures of MycF, the 3'-O-methyltransferase, including the free enzyme and complexes with S-adenosyl homocysteine (SAH), substrate, product, and unnatural substrates, show that SAM binding induces substantial ordering that creates the binding site for the natural substrate, and a bound metal ion positions the substrate for catalysis. A single amino acid substitution relaxed the 2'-methoxy specificity but retained regiospecificity. The engineered variant produced a new mycinamicin analog, demonstrating the utility of structural information to facilitate bioengineering approaches for the chemoenzymatic synthesis of complex small molecules containing modified sugars. Using the MycF substrate complex and the modeled substrate complex of a 4'-specific homologue, active site residues were identified that correlate with the 3' or 4' specificity of MycF family members and define the protein and substrate features that direct the regiochemistry of methyltransfer. This classification scheme will be useful in the annotation of new secondary metabolite pathways that utilize this family of enzymes.
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Affiliation(s)
- Steffen M. Bernard
- Chemical
Biology Doctoral Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David L. Akey
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ashootosh Tripathi
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sung Ryeol Park
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jamie R. Konwerski
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yojiro Anzai
- Faculty
of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Shengying Li
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fumio Kato
- Faculty
of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - David H. Sherman
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Departments of Medicinal Chemistry, Chemistry, and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Janet L. Smith
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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13
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Structure and mechanism of an antibiotics-synthesizing 3-hydroxykynurenine C-methyltransferase. Sci Rep 2015; 5:10100. [PMID: 25960001 PMCID: PMC4426599 DOI: 10.1038/srep10100] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/27/2015] [Indexed: 12/15/2022] Open
Abstract
Streptosporangium sibiricum SibL catalyzes the methyl transfer from S-adenosylmethionine (SAM) to 3-hydroxykynurenine (3-HK) to produce S-adenosylhomocysteine (SAH) and 3-hydroxy-4-methyl-kynurenine for sibiromycin biosynthesis. Here, we present the crystal structures of apo-form Ss-SibL, Ss-SibL/SAH binary complex and Ss-SibL/SAH/3-HK ternary complex. Ss-SibL is a homodimer. Each subunit comprises a helical N-terminal domain and a Rossmann-fold C-terminal domain. SAM (or SAH) binding alone results in domain movements, suggesting a two-step catalytic cycle. Analyses of the enzyme-ligand interactions and further mutant studies support a mechanism in which Tyr134 serves as the principal base in the transferase reaction of methyl group from SAM to 3-HK.
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14
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15
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Zou XW, Liu YC, Hsu NS, Huang CJ, Lyu SY, Chan HC, Chang CY, Yeh HW, Lin KH, Wu CJ, Tsai MD, Li TL. Structure and mechanism of a nonhaem-iron SAM-dependent C-methyltransferase and its engineering to a hydratase and an O-methyltransferase. ACTA ACUST UNITED AC 2014; 70:1549-60. [PMID: 24914966 DOI: 10.1107/s1399004714005239] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/06/2014] [Indexed: 12/16/2022]
Abstract
In biological systems, methylation is most commonly performed by methyltransferases (MTs) using the electrophilic methyl source S-adenosyl-L-methionine (SAM) via the S(N)2 mechanism. (2S,3S)-β-Methylphenylalanine, a nonproteinogenic amino acid, is a building unit of the glycopeptide antibiotic mannopeptimycin. The gene product of mppJ from the mannopeptimycin-biosynthetic gene cluster is the MT that methylates the benzylic C atom of phenylpyruvate (Ppy) to give βMePpy. Although the benzylic C atom of Ppy is acidic, how its nucleophilicity is further enhanced to become an acceptor for C-methylation has not conclusively been determined. Here, a structural approach is used to address the mechanism of MppJ and to engineer it for new functions. The purified MppJ displays a turquoise colour, implying the presence of a metal ion. The crystal structures reveal MppJ to be the first ferric ion SAM-dependent MT. An additional four structures of binary and ternary complexes illustrate the molecular mechanism for the metal ion-dependent methyltransfer reaction. Overall, MppJ has a nonhaem iron centre that bind, orients and activates the α-ketoacid substrate and has developed a sandwiched bi-water device to avoid the formation of the unwanted reactive oxo-iron(IV) species during the C-methylation reaction. This discovery further prompted the conversion of the MT into a structurally/functionally unrelated new enzyme. Through stepwise mutagenesis and manipulation of coordination chemistry, MppJ was engineered to perform both Lewis acid-assisted hydration and/or O-methyltransfer reactions to give stereospecific new compounds. This process was validated by six crystal structures. The results reported in this study will facilitate the development and design of new biocatalysts for difficult-to-synthesize biochemicals.
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Affiliation(s)
- Xiao-Wei Zou
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Chen Liu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ning-Shian Hsu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | | | - Syue-Yi Lyu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsiu-Chien Chan
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chin-Yuan Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsien-Wei Yeh
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chang-Jer Wu
- Department of Food Science, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Ming-Daw Tsai
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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16
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Akey DL, Brown WC, Dutta S, Konwerski J, Jose J, Jurkiw TJ, DelProposto J, Ogata CM, Skiniotis G, Kuhn RJ, Smith JL. Flavivirus NS1 structures reveal surfaces for associations with membranes and the immune system. Science 2014; 343:881-5. [PMID: 24505133 PMCID: PMC4263348 DOI: 10.1126/science.1247749] [Citation(s) in RCA: 296] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Flaviviruses, the human pathogens responsible for dengue fever, West Nile fever, tick-borne encephalitis, and yellow fever, are endemic in tropical and temperate parts of the world. The flavivirus nonstructural protein 1 (NS1) functions in genome replication as an intracellular dimer and in immune system evasion as a secreted hexamer. We report crystal structures for full-length, glycosylated NS1 from West Nile and dengue viruses. The NS1 hexamer in crystal structures is similar to a solution hexamer visualized by single-particle electron microscopy. Recombinant NS1 binds to lipid bilayers and remodels large liposomes into lipoprotein nanoparticles. The NS1 structures reveal distinct domains for membrane association of the dimer and interactions with the immune system and are a basis for elucidating the molecular mechanism of NS1 function.
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Affiliation(s)
- David L. Akey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - W. Clay Brown
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Somnath Dutta
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jamie Konwerski
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joyce Jose
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Thomas J. Jurkiw
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - James DelProposto
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Craig M. Ogata
- GM/CA@APS, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Georgios Skiniotis
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Richard J. Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - Janet L. Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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17
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Singh S, Chang A, Helmich KE, Bingman CA, Wrobel RL, Beebe ET, Makino SI, Aceti DJ, Dyer K, Hura GL, Sunkara M, Morris AJ, Phillips GN, Thorson JS. Structural and functional characterization of CalS11, a TDP-rhamnose 3'-O-methyltransferase involved in calicheamicin biosynthesis. ACS Chem Biol 2013; 8:1632-9. [PMID: 23662776 PMCID: PMC3875630 DOI: 10.1021/cb400068k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sugar methyltransferases (MTs) are an important class of tailoring enzymes that catalyze the transfer of a methyl group from S-adenosyl-l-methionine to sugar-based N-, C- and O-nucleophiles. While sugar N- and C-MTs involved in natural product biosynthesis have been found to act on sugar nucleotide substrates prior to a subsequent glycosyltransferase reaction, corresponding sugar O-methylation reactions studied thus far occur after the glycosyltransfer reaction. Herein we report the first in vitro characterization using (1)H-(13)C-gHSQC with isotopically labeled substrates and the X-ray structure determination at 1.55 Å resolution of the TDP-3'-O-rhamnose-methyltransferase CalS11 from Micromonospora echinospora. This study highlights a unique NMR-based methyltransferase assay, implicates CalS11 to be a metal- and general acid/base-dependent O-methyltransferase, and as a first crystal structure for a TDP-hexose-O-methyltransferase, presents a new template for mechanistic studies and/or engineering.
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Affiliation(s)
- Shanteri Singh
- Center for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, 789 South Limestone Street, Lexington, KY 40536-0596, USA
| | - Aram Chang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kate E. Helmich
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Russel L. Wrobel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Emily T. Beebe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Shin-Ichi Makino
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - David J. Aceti
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kevin Dyer
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720, USA
| | - Greg L. Hura
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720, USA
| | - Manjula Sunkara
- Division of Cardiovascular Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Andrew J. Morris
- Division of Cardiovascular Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - George N. Phillips
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, USA
| | - Jon S. Thorson
- Center for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, 789 South Limestone Street, Lexington, KY 40536-0596, USA
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18
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Liscombe DK, Louie GV, Noel JP. Architectures, mechanisms and molecular evolution of natural product methyltransferases. Nat Prod Rep 2012; 29:1238-50. [PMID: 22850796 DOI: 10.1039/c2np20029e] [Citation(s) in RCA: 212] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The addition of a methyl moiety to a small chemical is a common transformation in the biosynthesis of natural products across all three domains of life. These methylation reactions are most often catalysed by S-adenosyl-L-methionine (SAM)-dependent methyltransferases (MTs). MTs are categorized based on the electron-rich, methyl accepting atom, usually O, N, C, or S. SAM-dependent natural product MTs (NPMTs) are responsible for the modification of a wide array of structurally distinct substrates, including signalling and host defense compounds, pigments, prosthetic groups, cofactors, cell membrane and cell wall components, and xenobiotics. Most notably, methylation modulates the bioavailability, bioactivity, and reactivity of acceptor molecules, and thus exerts a central role on the functional output of many metabolic pathways. Our current understanding of the structural enzymology of NPMTs groups these phylogenetically diverse enzymes into two MT-superfamily fold classes (class I and class III). Structural biology has also shed light on the catalytic mechanisms and molecular bases for substrate specificity for over fifty NPMTs. These biophysical-based approaches have contributed to our understanding of NPMT evolution, demonstrating how a widespread protein fold evolved to accommodate chemically diverse methyl acceptors and to catalyse disparate mechanisms suited to the physiochemical properties of the target substrates. This evolutionary diversity suggests that NPMTs may serve as starting points for generating new biocatalysts.
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Affiliation(s)
- David K Liscombe
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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19
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Singh S, Phillips GN, Thorson JS. The structural biology of enzymes involved in natural product glycosylation. Nat Prod Rep 2012; 29:1201-37. [PMID: 22688446 DOI: 10.1039/c2np20039b] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The glycosylation of microbial natural products often dramatically influences the biological and/or pharmacological activities of the parental metabolite. Over the past decade, crystal structures of several enzymes involved in the biosynthesis and attachment of novel sugars found appended to natural products have emerged. In many cases, these studies have paved the way to a better understanding of the corresponding enzyme mechanism of action and have served as a starting point for engineering variant enzymes to facilitate to production of differentially-glycosylated natural products. This review specifically summarizes the structural studies of bacterial enzymes involved in biosynthesis of novel sugar nucleotides.
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Affiliation(s)
- Shanteri Singh
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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20
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Lyskowski A, Tengg M, Steinkellner G, Schwab H, Gruber-Khadjawi M, Gruber K. Crystallization of the novel S-adenosyl-L-methionine-dependent C-methyltransferase CouO from Streptomyces rishiriensis and preliminary diffraction data analysis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:698-700. [PMID: 22684074 PMCID: PMC3370914 DOI: 10.1107/s1744309112017137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 04/18/2012] [Indexed: 11/10/2022]
Abstract
Recombinant Q9F8T9 protein from Streptomyces rishiriensis (CouO), an S-adenosyl-L-methionine-dependent C-methyltransferase, has been successfully cloned, expressed and purified. CouO was crystallized from a single condition in the Morpheus crystallization screen. A vitrified crystal diffracted to 2.05 Å resolution and belonged to space group P2(1), with unit-cell parameters a = 33.02, b = 82.87, c = 76.77 Å, β = 96.93°.
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Affiliation(s)
- Andrzej Lyskowski
- AAustrian Centre of Industrial Biotechnology, GmbH, Petersgasse 14, 8010 Graz, Austria.
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