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Zhao F, Moriwaki Y, Noguchi T, Shimizu K, Kuzuyama T, Terada T. QM/MM Study of the Catalytic Mechanism and Substrate Specificity of the Aromatic Substrate C-Methyltransferase Fur6. Biochemistry 2024; 63:806-814. [PMID: 38422553 DOI: 10.1021/acs.biochem.3c00556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
In the field of medical chemistry and other organic chemistry, introducing a methyl group into a designed position has been difficult to achieve. However, owing to the vigorous developments in the field of enzymology, methyltransferases are considered potential tools for addressing this problem. Within the methyltransferase family, Fur6 catalyzes the methylation of C3 of 1,2,4,5,7-pentahydroxynaphthalene (PHN) using S-adenosyl-l-methionine (SAM) as the methyl donor. Here, we report the catalytic mechanism and substrate specificity of Fur6 based on computational studies. Our molecular dynamics (MD) simulation studies reveal the reactive form of PHN and its interactions with the enzyme. Our hybrid quantum mechanics/molecular mechanics (QM/MM) calculations suggest the reaction pathway of the methyl transfer step in which the energy barrier is 8.6 kcal mol-1. Our free-energy calculations with a polarizable continuum model (PCM) indicate that the final deprotonation step of the methylated intermediate occurs after it is ejected into the water solvent from the active center pocket of Fur6. Additionally, our studies on the protonation states, the highest occupied molecular orbital (HOMOs), and the energy barriers of the methylation reaction for the analogs of PHN demonstrate the mechanism of the specificity to PHN. Our study provides valuable insights into Fur6 chemistry, contributing to a deeper understanding of molecular mechanisms and offering an opportunity to engineer the enzyme to achieve high yields of the desired product(s).
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Affiliation(s)
- Fan Zhao
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yoshitaka Moriwaki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Graduate School of Agricultural and Life Sciences and Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohiro Noguchi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kentaro Shimizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohisa Kuzuyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Graduate School of Agricultural and Life Sciences and Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tohru Terada
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Graduate School of Agricultural and Life Sciences and Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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2
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Menke MJ, Schneider P, Badenhorst CPS, Kunzendorf A, Heinz F, Dörr M, Hayes MA, Bornscheuer UT. A Universal, Continuous Assay for SAM-dependent Methyltransferases. Angew Chem Int Ed Engl 2023; 62:e202313912. [PMID: 37917964 DOI: 10.1002/anie.202313912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/04/2023]
Abstract
Enzyme-catalyzed late-stage functionalization (LSF), such as methylation of drug molecules and lead structures, enables direct access to more potent active pharmaceutical ingredients (API). S-adenosyl-l-methionine-dependent methyltransferases (MTs) can play a key role in the development of new APIs, as they catalyze the chemo- and regioselective methylation of O-, N-, S- and C-atoms, being superior to traditional chemical routes. To identify suitable MTs, we developed a continuous fluorescence-based, high-throughput assay for SAM-dependent methyltransferases, which facilitates screening using E. coli cell lysates. This assay involves two enzymatic steps for the conversion of S-adenosyl-l-homocysteine into H2 S to result in a selective fluorescence readout via reduction of an azidocoumarin sulfide probe. Investigation of two O-MTs and an N-MT confirmed that this assay is suitable for the determination of methyltransferase activity in E. coli cell lysates.
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Affiliation(s)
- Marian J Menke
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Pascal Schneider
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Christoffel P S Badenhorst
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Andreas Kunzendorf
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Florian Heinz
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Mark Dörr
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Martin A Hayes
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Uwe T Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
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3
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Müller M, Germer P, Andexer JN. Biocatalytic One-Carbon Transfer – A Review. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/s-0040-1719884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
AbstractThis review provides an overview of different C1 building blocks as substrates of enzymes, or part of their cofactors, and the resulting functionalized products. There is an emphasis on the broad range of possibilities of biocatalytic one-carbon extensions with C1 sources of different oxidation states. The identification of uncommon biosynthetic strategies, many of which might serve as templates for synthetic or biotechnological applications, towards one-carbon extensions is supported by recent genomic and metabolomic progress and hence we refer principally to literature spanning from 2014 to 2020.1 Introduction2 Methane, Methanol, and Methylamine3 Glycine4 Nitromethane5 SAM and SAM Ylide6 Other C1 Building Blocks7 Formaldehyde and Glyoxylate as Formaldehyde Equivalents8 Cyanide9 Formic Acid10 Formyl-CoA and Oxalyl-CoA11 Carbon Monoxide12 Carbon Dioxide13 Conclusions
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4
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Li C, Crack JC, Newton‐Payne S, Murphy ARJ, Chen X, Pinchbeck BJ, Zhou S, Williams BT, Peng M, Zhang X, Chen Y, Le Brun NE, Todd JD, Zhang Y. Mechanistic insights into the key marine dimethylsulfoniopropionate synthesis enzyme DsyB/DSYB. MLIFE 2022; 1:114-130. [PMID: 38817677 PMCID: PMC10989797 DOI: 10.1002/mlf2.12030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 06/01/2024]
Abstract
Marine algae and bacteria produce approximately eight billion tonnes of the organosulfur molecule dimethylsulfoniopropionate (DMSP) in Earth's surface oceans annually. DMSP is an antistress compound and, once released into the environment, a major nutrient, signaling molecule, and source of climate-active gases. The methionine transamination pathway for DMSP synthesis is used by most known DMSP-producing algae and bacteria. The S-directed S-adenosylmethionine (SAM)-dependent 4-methylthio-2-hydroxybutyrate (MTHB) S-methyltransferase, encoded by the dsyB/DSYB gene, is the key enzyme of this pathway, generating S-adenosylhomocysteine (SAH) and 4-dimethylsulfonio-2-hydroxybutyrate (DMSHB). DsyB/DSYB, present in most haptophyte and dinoflagellate algae with the highest known intracellular DMSP concentrations, is shown to be far more abundant and transcribed in marine environments than any other known S-methyltransferase gene in DMSP synthesis pathways. Furthermore, we demonstrate in vitro activity of the bacterial DsyB enzyme from Nisaea denitrificans and provide its crystal structure in complex with SAM and SAH-MTHB, which together provide the first important mechanistic insights into a DMSP synthesis enzyme. Structural and mutational analyses imply that DsyB adopts a proximity and desolvation mechanism for the methyl transfer reaction. Sequence analysis suggests that this mechanism may be common to all bacterial DsyB enzymes and also, importantly, eukaryotic DSYB enzymes from e.g., algae that are the major DMSP producers in Earth's surface oceans.
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Affiliation(s)
- Chun‐Yang Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life SciencesOcean University of ChinaQingdaoChina
- State Key Laboratory of Microbial TechnologyMarine Biotechnology Research Center, Shandong UniversityQingdaoChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoShandongChina
| | - Jason C. Crack
- School of Chemistry, Centre for Molecular and Structural BiochemistryUniversity of East Anglia, Norwich Research ParkNorwichUK
| | | | | | - Xiu‐Lan Chen
- State Key Laboratory of Microbial TechnologyMarine Biotechnology Research Center, Shandong UniversityQingdaoChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoShandongChina
| | | | - Shun Zhou
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life SciencesOcean University of ChinaQingdaoChina
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | | | - Ming Peng
- State Key Laboratory of Microbial TechnologyMarine Biotechnology Research Center, Shandong UniversityQingdaoChina
| | - Xiao‐Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Yin Chen
- School of Life SciencesUniversity of WarwickCoventryUK
| | - Nick E. Le Brun
- School of Chemistry, Centre for Molecular and Structural BiochemistryUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - Jonathan D. Todd
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life SciencesOcean University of ChinaQingdaoChina
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Yu‐Zhong Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life SciencesOcean University of ChinaQingdaoChina
- State Key Laboratory of Microbial TechnologyMarine Biotechnology Research Center, Shandong UniversityQingdaoChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoShandongChina
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5
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Song S, Chen A, Zhu J, Yan Z, An Q, Zhou J, Liao H, Yu Y. Structure basis of the caffeic acid O-methyltransferase from Ligusiticum chuanxiong to understand its selective mechanism. Int J Biol Macromol 2022; 194:317-330. [PMID: 34838855 DOI: 10.1016/j.ijbiomac.2021.11.135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/05/2021] [Accepted: 11/20/2021] [Indexed: 02/08/2023]
Abstract
Caffeic acid O-methyltransferase from Ligusticum chuanxiong (LcCOMT) showed strict regiospecificity despite a relative degree of preference. Compared with caffeic acid, methyl caffeate was the preferential substrate by its low Km and high Kcat. In this study, we obtained the SAM binary (1.80 Å) and SAH binary (1.95 Å) complex LcCOMT crystal structures, and established the ternary complex structure with methyl caffeate by molecular docking. The active site of LcCOMT included phenolic substrate pocket, SAM/SAH ligand pocket and conserved catalytic residues as well. The regiospecificity of LcCOMT that permitted only 3-hydroxyl group to be methylated arise from the interactions between the active site and the phenyl ring. However, the propanoid tail governed the relative preference of LcCOMT. The ester group in methyl caffeate stabilized the anionic intermediate caused by His268-Asp269 pair, whereas caffeic acid was unable to stabilize the anionic intermediate due to the adjacent carboxylate anion in the propanoid tail. Ser183 residue formed an additional hydrogen bond with SAH and its role was identified by S183A mutation. Ile318 residue might be a potential site for determination of substrate preference, and its mutation led to the change of tertiary conformation. The results supported the selective mechanism of LcCOMT.
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Affiliation(s)
- Simin Song
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Anqi Chen
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Jianquan Zhu
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Zicheng Yan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Qiuju An
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China
| | - Jiayu Zhou
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China.
| | - Hai Liao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China.
| | - Yamei Yu
- Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China.
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6
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Liao L, Zhou Y, Peng T, Guo Y, Zhao Y, Zeng Z. Crystal structure of a S-adenosyl-L-methionine-dependent O-methyltransferase-like enzyme from Aspergillus flavus. Proteins 2020; 89:185-192. [PMID: 32875607 DOI: 10.1002/prot.26004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 08/05/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
Abstract
S-adenosyl-L-methionine (SAM)-dependent methyltransferases (MTases) are widely distributed among almost all organisms and often characterized with conserved Rossmann fold, TIM barrel, and D×G×G×G motif. However, some MTases show no methyltransferase activity. In the present study, the crystal structure of LepI, one MTase-like enzyme isolated from A. flavus that catalyzes pericyclic reactions, was investigated to determine its structure-function relationship. The overall structure of LepI in complex with the SAM mimic S-adenosyl-L-homocysteine (SAH) (PDB ID: 6IV7) indicated that LepI is a tetramer in solution. The residues His133, Arg197, Arg295, and Asp296 located near the active site can form hydrogen bonds with the substrate, thus participating in catalytic reactions. The binding of SAH in LepI is almost identical to that in other resolved MTases; however, the location of catalytic residues differs significantly. Phylogenetic trials suggest that LepI proteins share a common ancestor in plants and algae, which may explain the conserved SAM-binding site. However, the accelerated evolution of A. flavus has introduced both functional and structural changes in LepI. More importantly, the residue Arg295, which is unique to LepI, might be a key determinant for the altered enzymatic behavior. Collectively, the differences in the composition of catalytic residues, as well as the unique tetrameric form of LepI, define its unique enzymatic behavior. The present work provides an additional understanding of the structure-function relationship of MTases and MTase-like enzymes.
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Affiliation(s)
- Lijing Liao
- Shandong Provincial Key Laboratory of Microbial Engineering, College of Bioengineering, Qilu University of Technology, Jinan, China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yuanze Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ting Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yan Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yucheng Zhao
- Department of Resources Science of Traditional Chinese Medicines and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, P. R. China
| | - Zhixiong Zeng
- Shandong Provincial Key Laboratory of Microbial Engineering, College of Bioengineering, Qilu University of Technology, Jinan, China
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7
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Guo X, Crnovcic I, Chang CY, Luo J, Lohman JR, Papinski M, Bechthold A, Horsman GP, Shen B. PokMT1 from the Polyketomycin Biosynthetic Machinery of Streptomyces diastatochromogenes Tü6028 Belongs to the Emerging Family of C-Methyltransferases That Act on CoA-Activated Aromatic Substrates. Biochemistry 2018; 57:1003-1011. [PMID: 29341603 DOI: 10.1021/acs.biochem.7b01219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Recent biochemical characterizations of the MdpB2 CoA ligase and MdpB1 C-methyltransferase (C-MT) from the maduropeptin (MDP, 2) biosynthetic machinery revealed unusual pathway logic involving C-methylation occurring on a CoA-activated aromatic substrate. Here we confirmed this pathway logic for the biosynthesis of polyketomycin (POK, 3). Biochemical characterization unambiguously established that PokM3 and PokMT1 catalyze the sequential conversion of 6-methylsalicylic acid (6-MSA, 4) to form 3,6-dimethylsalicylyl-CoA (3,6-DMSA-CoA, 6), which serves as the direct precursor for the 3,6-dimethylsalicylic acid (3,6-DMSA) moiety in the biosynthesis of 3. PokMT1 catalyzes the C-methylation of 6-methylsalicylyl-CoA (6-MSA-CoA, 5) with a kcat of 1.9 min-1 and a Km of 2.2 ± 0.1 μM, representing the most proficient C-MT characterized to date. Bioinformatics analysis of MTs from natural product biosynthetic machineries demonstrated that PokMT1 and MdpB1 belong to a phylogenetic clade of C-MTs that preferably act on aromatic acids. Significantly, this clade includes the structurally characterized enzyme SibL, which catalyzes C-methylation of 3-hydroxykynurenine in its free acid form, using two conserved tyrosine residues for catalysis. A homology model and site-directed mutagenesis suggested that PokMT1 also employs this unusual arrangement of tyrosine residues to coordinate C-methylation but revealed a large cavity capable of accommodating the CoA moiety tethered to 5. CoA activation of the aromatic acid substrate may represent a general strategy that could be exploited to improve catalytic efficiency. This study sets the stage to further investigate and exploit the catalytic utility of this emerging family of C-MTs in biocatalysis and synthetic biology.
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Affiliation(s)
- Xun Guo
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Ivana Crnovcic
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Chin-Yuan Chang
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Jun Luo
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Jeremy R Lohman
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Monica Papinski
- Department of Chemistry and Biochemistry, Wilfrid Laurier University , Waterloo, ON N2L 3C5, Canada
| | - Andreas Bechthold
- Institute for Pharmaceutical Sciences, Pharmaceutical Biology and Biotechnology, University of Freiburg , Stefan-Meier-Strasse 19, 79104 Freiburg, Germany
| | - Geoffrey P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University , Waterloo, ON N2L 3C5, Canada
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States.,Department of Molecular Medicine, The Scripps Research Institute , Jupiter, Florida 33458, United States.,Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute , Jupiter, Florida 33458, United States
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8
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Bai L, Wagner T, Xu T, Hu X, Ermler U, Shima S. A Water-Bridged H-Bonding Network Contributes to the Catalysis of the SAM-Dependent C-Methyltransferase HcgC. Angew Chem Int Ed Engl 2017; 56:10806-10809. [DOI: 10.1002/anie.201705605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Indexed: 01/31/2023]
Affiliation(s)
- Liping Bai
- Max-Planck-Institut für terrestrische Mikrobiologie; Karl-von-Frisch-Straße 10 35043 Marburg Germany
| | - Tristan Wagner
- Max-Planck-Institut für terrestrische Mikrobiologie; Karl-von-Frisch-Straße 10 35043 Marburg Germany
| | - Tao Xu
- Institute of Chemical Science and Engineering; Ecole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305; 1015 Lausanne Switzerland
| | - Xile Hu
- Institute of Chemical Science and Engineering; Ecole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305; 1015 Lausanne Switzerland
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik; Max-von-Laue-Straße 3 60438 Frankfurt/Main Germany
| | - Seigo Shima
- Max-Planck-Institut für terrestrische Mikrobiologie; Karl-von-Frisch-Straße 10 35043 Marburg Germany
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9
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Bai L, Wagner T, Xu T, Hu X, Ermler U, Shima S. A Water-Bridged H-Bonding Network Contributes to the Catalysis of the SAM-Dependent C-Methyltransferase HcgC. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705605] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Liping Bai
- Max-Planck-Institut für terrestrische Mikrobiologie; Karl-von-Frisch-Straße 10 35043 Marburg Germany
| | - Tristan Wagner
- Max-Planck-Institut für terrestrische Mikrobiologie; Karl-von-Frisch-Straße 10 35043 Marburg Germany
| | - Tao Xu
- Institute of Chemical Science and Engineering; Ecole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305; 1015 Lausanne Switzerland
| | - Xile Hu
- Institute of Chemical Science and Engineering; Ecole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305; 1015 Lausanne Switzerland
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik; Max-von-Laue-Straße 3 60438 Frankfurt/Main Germany
| | - Seigo Shima
- Max-Planck-Institut für terrestrische Mikrobiologie; Karl-von-Frisch-Straße 10 35043 Marburg Germany
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10
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Sadler JC, Chung CWH, Mosley JE, Burley GA, Humphreys LD. Structural and Functional Basis of C-Methylation of Coumarin Scaffolds by NovO. ACS Chem Biol 2017; 12:374-379. [PMID: 28068060 DOI: 10.1021/acschembio.6b01053] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
C-methylation of aromatic small molecules by C-methyltransferases (C-MTs) is an important biological transformation that involves C-C bond formation using S-adenosyl-l-methionine (SAM) as the methyl donor. Here, two advances in the mechanistic understanding of C-methylation of the 8-position of coumarin substrates catalyzed by the C-MT NovO from Streptomyces spheroides are described. First, a crystal structure of NovO reveals the Arg116-Asn117 and His120-Arg121 motifs are essential for coumarin substrate binding. Second, the active-site His120 is responsible for deprotonation of the phenolic 7-hydroxyl group on the coumarin substrate, activating the rate-determining methyl transfer step from SAM. This work expands our mechanistic knowledge of C-MTs, which could be used in the downstream development of engineered biocatalysts for small molecule C-alkylations.
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Affiliation(s)
- Joanna C. Sadler
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
- WestCHEM,
Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, United Kingdom
| | - Chun-wa H. Chung
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
| | - Julie E. Mosley
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
| | - Glenn A. Burley
- WestCHEM,
Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, United Kingdom
| | - Luke D. Humphreys
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
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11
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Gutmann A, Schiller M, Gruber-Khadjawi M, Nidetzky B. An ortho C-methylation/O-glycosylation motif on a hydroxy-coumarin scaffold, selectively installed by biocatalysis. Org Biomol Chem 2017; 15:7917-7924. [DOI: 10.1039/c7ob01513e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To achieve near quantitative dual modification of the hydroxy-coumarin scaffold, the C-methylation had to occur strictly before the O-glucosylation.
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Affiliation(s)
- Alexander Gutmann
- Institute of Biotechnology and Biochemical Engineering
- Graz University of Technology
- NAWI Graz
- 8010 Graz
- Austria
| | - Margaretha Schiller
- Institute of Biotechnology and Biochemical Engineering
- Graz University of Technology
- NAWI Graz
- 8010 Graz
- Austria
| | - Mandana Gruber-Khadjawi
- Austrian Centre of Industrial Biotechnology
- 8010 Graz
- Austria
- Institute of Organic Chemistry
- Graz University of Technology
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering
- Graz University of Technology
- NAWI Graz
- 8010 Graz
- Austria
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12
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de Paul N. Nziko V, Scheiner S. Effects of Angular Deformation on the Energetics of the S N2 Reaction. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | - Steve Scheiner
- Department of Chemistry and Biochemistry; Utah State University; 84322-0300 Logan UT USA
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13
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Tengg M, Stecher H, Offner L, Plasch K, Anderl F, Weber H, Schwab H, Gruber-Khadjawi M. Methyltransferases: Green Catalysts for Friedel-Crafts Alkylations. ChemCatChem 2016. [DOI: 10.1002/cctc.201501306] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Martin Tengg
- ACIB, Austrian Centre of Industrial Biotechnology GmbH; Petersgasse 14 8010 Graz Austria
- Institute of Molecular Biotechnology; Graz University of Technology; Petersgasse 14 8010 Graz Austria
| | - Harald Stecher
- ACIB, Austrian Centre of Industrial Biotechnology GmbH; Petersgasse 14 8010 Graz Austria
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
| | - Lisa Offner
- ACIB, Austrian Centre of Industrial Biotechnology GmbH; Petersgasse 14 8010 Graz Austria
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
| | - Katharina Plasch
- ACIB, Austrian Centre of Industrial Biotechnology GmbH; Petersgasse 14 8010 Graz Austria
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
| | - Felix Anderl
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
| | - Hansjörg Weber
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
| | - Helmut Schwab
- ACIB, Austrian Centre of Industrial Biotechnology GmbH; Petersgasse 14 8010 Graz Austria
- Institute of Molecular Biotechnology; Graz University of Technology; Petersgasse 14 8010 Graz Austria
| | - Mandana Gruber-Khadjawi
- ACIB, Austrian Centre of Industrial Biotechnology GmbH; Petersgasse 14 8010 Graz Austria
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
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