1
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Dong D, Xia M, Wang S, Fang P, Liu W. Structural Basis of Substrate Recognition by the Postmitosane Modification Enzyme MitM in Mitomycin Biosynthesis. Biochemistry 2024. [PMID: 39141610 DOI: 10.1021/acs.biochem.4c00330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Mitomycins make up a class of natural molecules produced by Streptomyces with strong antibacterial and antitumor activities. MitM is a key postmitosane modification enzyme involved in mitomycin biosynthesis in Streptomyces caespitosus. This protein was previously suggested to catalyze the aziridinium methylation of mitomycin A and the mitomycin intermediate 9a-demethyl-mitomycin A as an N-methyltransferase. The structural basis for MitM to recognize cofactor S-adenosyl-l-methionine (SAM) and substrate mitomycin A is unknown. Here, we determined the crystal structures of apo-MitM and MitM-mitomycin A-S-adenosylhomocysteine (SAH) ternary complexes with resolutions of 2.23 and 2.80 Å, respectively. We found that MitM adopts a class I SAM-dependent methyltransferase fold and forms a homodimer in solution. Conformational changes in a series of residues involved in the formation of active pockets assist MitM in binding SAH and mitomycin A. In particular, the 28ALGAASLGE36 loop changes most significantly. When mitomycin A binds, the bending direction of this loop is reversed, changing the entrance of the active site from open to closed. This study provides structural insights into MitM's involvement in the postmitosane stage of mitomycin biosynthesis and provides a template for the engineering of methyltransferases.
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Affiliation(s)
- Danna Dong
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
| | - Mingyu Xia
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Sili Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Pengfei Fang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China
| | - Wen Liu
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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2
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Li Z, Jiao Y, Ling J, Zhao J, Yang Y, Mao Z, Zhou K, Wang W, Xie B, Li Y. Characterization of a methyltransferase for iterative N-methylation at the leucinostatin termini in Purpureocillium lilacinum. Commun Biol 2024; 7:757. [PMID: 38909167 PMCID: PMC11193748 DOI: 10.1038/s42003-024-06467-0] [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: 08/20/2023] [Accepted: 06/18/2024] [Indexed: 06/24/2024] Open
Abstract
N-methyltransferase (NMT)-catalyzed methylation at the termini of nonribosomal peptides (NRPs) has rarely been reported. Here, we discover a fungal NMT LcsG for the iterative terminal N-methylation of a family of NRPs, leucinostatins. Gene deletion results suggest that LcsG is essential for leucinostatins methylation. Results from in vitro assays and HRESI-MS-MS analysis reveal the methylation sites as NH2, NHCH3 and N(CH3)2 in the C-terminus of various leucinostatins. LcsG catalysis yields new lipopeptides, some of which demonstrate effective antibiotic properties against the human pathogen Cryptococcus neoformans and the plant pathogen Phytophthora infestans. Multiple sequence alignments and site-directed mutagenesis of LcsG indicate the presence of a highly conserved SAM-binding pocket, along with two possible active site residues (D368 and D395). Molecular dynamics simulations show that the targeted N can dock between these two residues. Thus, this study suggests a method for increasing the variety of natural bioactivity of NPRs and a possible catalytic mechanism underlying the N-methylation of NRPs.
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Affiliation(s)
- Zixin Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
- Microbial Processes and Interactions (MiPI), TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium
| | - Yang Jiao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Jian Ling
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Jianlong Zhao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Yuhong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Zhenchuan Mao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Kaixiang Zhou
- Center for Advanced Materials Research, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, 519087, China
| | - Wenzhao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Bingyan Xie
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
| | - Yan Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
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3
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Daniel-Ivad P, Ryan KS. Structure of methyltransferase RedM that forms the dimethylpyrrolinium of the bisindole reductasporine. J Biol Chem 2024; 300:105520. [PMID: 38042494 PMCID: PMC10784701 DOI: 10.1016/j.jbc.2023.105520] [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: 08/08/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 12/04/2023] Open
Abstract
Bisindoles are biologically active natural products that arise from the oxidative dimerization of two molecules of l-tryptophan. In bacterial bisindole pathways, a core set of transformations is followed by the action of diverse tailoring enzymes that catalyze reactions that lead to diverse bisindole products. Among bisindoles, reductasporine is distinct due to its dimethylpyrrolinium structure. Its previously reported biosynthetic gene cluster encodes two unique tailoring enzymes, the imine reductase RedE and the dimethyltransferase RedM, which were shown to produce reductasporine from a common bisindole intermediate in recombinant E. coli. To gain more insight into the unique tailoring enzymes in reductasporine assembly, we reconstituted the biosynthetic pathway to reductasporine in vitro and then solved the 1.7 Å resolution structure of RedM. Our work reveals RedM adopts a variety of conformational changes with distinct open and closed conformations, and site-directed mutagenesis alongside sequence analysis identifies important active site residues. Finally, our work sets the stage for understanding how RedM evolved to react with a pyrrolinium scaffold and may enable the development of new dimethyltransferase catalysts.
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Affiliation(s)
- Phillip Daniel-Ivad
- Department of Chemistry, The University of British Columbia, Vancouver, Canada
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia, Vancouver, Canada.
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4
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Zhao Y, Liu X, Xiao Z, Zhou J, Song X, Wang X, Hu L, Wang Y, Sun P, Wang W, He X, Lin S, Deng Z, Pan L, Jiang M. O-methyltransferase-like enzyme catalyzed diazo installation in polyketide biosynthesis. Nat Commun 2023; 14:5372. [PMID: 37666836 PMCID: PMC10477347 DOI: 10.1038/s41467-023-41062-7] [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: 12/20/2022] [Accepted: 08/17/2023] [Indexed: 09/06/2023] Open
Abstract
Diazo compounds are rare natural products possessing various biological activities. Kinamycin and lomaiviticin, two diazo natural products featured by the diazobenzofluorene core, exhibit exceptional potency as chemotherapeutic agents. Despite the extensive studies on their biosynthetic gene clusters and the assembly of their polyketide scaffolds, the formation of the characteristic diazo group remains elusive. L-Glutamylhydrazine was recently shown to be the hydrazine donor in kinamycin biosynthesis, however, the mechanism for the installation of the hydrazine group onto the kinamycin scaffold is still unclear. Here we describe an O-methyltransferase-like protein, AlpH, which is responsible for the hydrazine incorporation in kinamycin biosynthesis. AlpH catalyses a unique SAM-independent coupling of L-glutamylhydrazine and polyketide intermediate via a rare Mannich reaction in polyketide biosynthesis. Our discovery expands the catalytic diversity of O-methyltransferase-like enzymes and lays a strong foundation for the discovery and development of novel diazo natural products through genome mining and synthetic biology.
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Affiliation(s)
- Yuchun Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, P. R. China
| | - Xiangyang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, P. R. China
| | - Zhihong Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, P. R. China
| | - Jie Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, P. R. China
| | - Xingyu Song
- Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, 200438, Shanghai, China
| | - Xiaozheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, P. R. China
| | - Lijun Hu
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Center for Bioactive Natural Molecules and Innovative Drugs Research, Jinan University, 510632, Guangzhou, P. R. China
| | - Ying Wang
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Center for Bioactive Natural Molecules and Innovative Drugs Research, Jinan University, 510632, Guangzhou, P. R. China
| | - Peng Sun
- School of Pharmacy, Second Military Medical University, 325 Guo-He Road, 200433, Shanghai, P. R. China
| | - Wenning Wang
- Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, 200438, Shanghai, China
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, P. R. China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, P. R. China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, P. R. China
| | - Lifeng Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Ming Jiang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, P. R. China.
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5
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Pal P, Wessely SML, Townsend CA. Normal and Aberrant Methyltransferase Activities Give Insights into the Final Steps of Dynemicin A Biosynthesis. J Am Chem Soc 2023; 145:12935-12947. [PMID: 37276497 PMCID: PMC10985829 DOI: 10.1021/jacs.3c04393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The naturally occurring enediynes are notable for their complex structures, potent DNA cleaving ability, and emerging usefulness in cancer chemotherapy. They can be classified into three distinct structural families, but all are thought to originate from a common linear C15-heptaene. Dynemicin A (DYN) is the paradigm member of anthraquinone-fused enediynes, one of the three main classes and exceptional among them for derivation of both its enediyne and anthraquinone portions from this same early biosynthetic building block. Evidence is growing about how two structurally dissimilar, but biosynthetically related, intermediates combine in two heterodimerization reactions to create a nitrogen-containing C30-coupled product. We report here deletions of two genes that encode biosynthetic proteins that are annotated as S-adenosylmethionine (SAM)-dependent methyltransferases. While one, DynO6, is indeed the required O-methyltransferase implicated long ago in the first studies of DYN biosynthesis, the other, DynA5, functions in an unanticipated manner in the post-heterodimerization events that complete the biosynthesis of DYN. Despite its removal from the genome of Micromonospora chersina, the ΔdynA5 strain retains the ability to synthesize DYN, albeit in reduced titers, accompanied by two unusual co-metabolites. We link the appearance of these unexpected structures to a substantial and contradictory body of other recent experimental data to advance a biogenetic rationale for the downstream steps that lead to the final formation of DYN. A sequence of product-forming transformations that is in line with new and existing experimental results is proposed and supported by a model reaction that also encompasses the formation of the crucial epoxide essential for the activation of DYN for DNA cleavage.
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Affiliation(s)
- Paramita Pal
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Serena M L Wessely
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
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6
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Huber EM, Kreling L, Heinrich AK, Dünnebacke M, Pöthig A, Bode HB, Groll M. A set of closely related methyltransferases for site-specific tailoring of anthraquinone pigments. Structure 2023; 31:573-583.e5. [PMID: 36963398 DOI: 10.1016/j.str.2023.03.001] [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: 11/28/2022] [Revised: 02/01/2023] [Accepted: 02/28/2023] [Indexed: 03/26/2023]
Abstract
Modification of the polyketide anthraquinone AQ-256 in the entomopathogenic Photorhabdus luminescens involves several O-methylations, but the biosynthetic gene cluster antA-I lacks corresponding tailoring enzymes. We here describe the identification of five putative, highly homologous O-methyltransferases encoded in the genome of P. luminescens. Activity assays in vitro and deletion experiments in vivo revealed that three of them account for anthraquinone tailoring by producing three monomethylated and two dimethylated species of AQ-256. X-ray structures of all five enzymes indicate high structural and mechanistic similarity. As confirmed by structure-based mutagenesis, a conserved histidine at the active site likely functions as a general base for substrate deprotonation and subsequent methyl transfer in all enzymes. Eight complex structures with AQ-256 as well as mono- and dimethylated derivatives confirm the substrate specificity patterns found in vitro and visualize how single amino acid differences in the active-site pockets impact substrate orientation and govern site-specific methylation.
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Affiliation(s)
- Eva M Huber
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Chair of Biochemistry, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany.
| | - Lukas Kreling
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Antje K Heinrich
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Maximilian Dünnebacke
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Chair of Biochemistry, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Alexander Pöthig
- Technical University of Munich, TUM School of Natural Sciences, Department of Chemistry, Catalysis Research Center, Chair of Inorganic and Metal-Organic Chemistry, Ernst-Otto-Fischer-Str. 1, 85748 Garching, Germany
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Chemical Biology, Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, 35043 Marburg, Germany; Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany.
| | - Michael Groll
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Chair of Biochemistry, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany.
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7
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Chen X, Johnson RM, Li B. A Permissive Amide N-Methyltransferase for Dithiolopyrrolones. ACS Catal 2023; 13:1899-1905. [PMID: 38106463 PMCID: PMC10720983 DOI: 10.1021/acscatal.2c05439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Amide N-methylation is important for the activity and permeability of bioactive compounds but can be challenging to perform selectively. The broad-spectrum antimicrobial natural products thiolutin and holomycin differ only by an N-methyl group at the endocyclic amide of thiolutin, but only thiolutin exhibits antifungal activity. The enzyme responsible for amide N--methylation in thiolutin biosynthesis has remained elusive. Here, we identified and characterized the amide N-methyltransferase DtpM that is encoded >400 kb outside of the thiolutin gene cluster. DtpM catalyzes efficient conversion of holomycin to thiolutin, exhibits broad substrate scope toward dithiolopyrrolones, and has high thermal stability. In addition, sequence similarity network analysis suggests DtpM is more closely related to phenol O-methyltransferases than some amide methyltransferases. This study expands the limited examples of amide N-methyltransferases and may facilitate chemoenzymatic synthesis of diverse dithiolopyrrolone compounds as potential therapeutics.
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Affiliation(s)
- Xiaoyan Chen
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Rachel M Johnson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Bo Li
- Department of Chemistry, and Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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8
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Unusual Post-Translational Modifications in the Biosynthesis of Lasso Peptides. Int J Mol Sci 2022; 23:ijms23137231. [PMID: 35806232 PMCID: PMC9266682 DOI: 10.3390/ijms23137231] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022] Open
Abstract
Lasso peptides are a subclass of ribosomally synthesized and post-translationally modified peptides (RiPPs) and feature the threaded, lariat knot-like topology. The basic post-translational modifications (PTMs) of lasso peptide contain two steps, including the leader peptide removal of the ribosome-derived linear precursor peptide by an ATP-dependent cysteine protease, and the macrolactam cyclization by an ATP-dependent macrolactam synthetase. Recently, advanced bioinformatic tools combined with genome mining have paved the way to uncover a rapidly growing number of lasso peptides as well as a series of PTMs other than the general class-defining processes. Despite abundant reviews focusing on lasso peptide discoveries, structures, properties, and physiological functionalities, few summaries concerned their unique PTMs. In this review, we summarized all the unique PTMs of lasso peptides uncovered to date, shedding light on the related investigations in the future.
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9
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Xue Y, Liang Y, Zhang W, Geng C, Feng D, Huang X, Dong S, Zhang Y, Sun J, Qi F, Lu X. Characterization and Structural Analysis of Emodin- O-Methyltransferase from Aspergillus terreus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5728-5737. [PMID: 35475366 DOI: 10.1021/acs.jafc.2c01281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
All O-methylated derivatives of emodin, including physcion, questin, and 1-O-methylemodin, show potential antifungal activities. Notably, emodin and questin are two pivotal intermediates of geodin biosynthesis in Aspergillus terreus. Although most of the geodin biosynthetic steps have been investigated, the key O-methyltransferase (OMT) responsible for the O-methylation of emodin to generate questin has remained unidentified. Herein, through phylogenetic tree analysis and in vitro biochemical assays, the long-sought class II emodin-O-methyltransferase GedA has been functionally characterized. Additionally, the catalytic mechanism and key residues at the catalytic site of GedA were elucidated by enzyme-substrate-methyl donor analogue ternary complex crystal structure determination and site-directed mutagenesis. As we demonstrate, GedA adopts a typical general acid/base (E446/H373)-mediated transmethylation mechanism. In particular, residue D374 is also crucial for efficient catalysis through blocking the formation of intramolecular hydrogen bonds in emodin. This study will facilitate future engineering of GedA for the production of physcion or other site-specific O-methylated anthraquinone derivatives with potential applications as biopesticides.
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Affiliation(s)
- Yingying Xue
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | - Yajing Liang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Energy Institute, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
| | - Wei Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Energy Institute, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ce Geng
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Energy Institute, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
| | - Dandan Feng
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Energy Institute, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
| | - Xuenian Huang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Energy Institute, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sheng Dong
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Energy Institute, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
| | - Yingfang Zhang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | - Jia Sun
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | - Feifei Qi
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Energy Institute, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
| | - Xuefeng Lu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Energy Institute, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Marine Biology and Biotechnology Laboratory, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266101, China
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10
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Qiu S, Xu D, Xu M, Zhou H, Sun N, Zhang L, Zhao M, He J, Ran T, Sun B, Wang W. Crystal structures of PigF, an O-methyltransferase involved in the prodigiosin synthetic pathway, reveal an induced-fit substrate-recognition mechanism. IUCRJ 2022; 9:316-327. [PMID: 35371495 PMCID: PMC8895007 DOI: 10.1107/s2052252521011696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/04/2021] [Indexed: 06/14/2023]
Abstract
Prodigiosin, a red linear tripyrrole pigment, is a typical secondary metabolite with numerous biological functions, such as anticancer, antibacterial and immunosuppressant activities, and is synthesized through a bifurcated biosynthesis pathway from 4-methoxy-2,2'-bipyrrole-5-carbaldehyde (MBC) and 2-methyl-3-n-amylpyrrole (MAP). The last step in the biosynthetic pathway of MBC is catalysed by PigF, which transfers a methyl group to 4-hydroxy-2,20-bipyrrole-5-carbaldehyde (HBC) to form the final product MBC. However, the catalytic mechanism of PigF is still elusive. In this study, crystal structures of apo PigF and S-adenosylhomocysteine (SAH)-bound PigF were determined. PigF forms a homodimer and each monomer consists of two domains: a C-terminal catalytic domain and an N-terminal dimerization domain. Apo PigF adopts an open conformation, while the structure of the complex with the product SAH adopts a closed conformation. The binding of SAH induces dramatic conformational changes of PigF, suggesting an induced-fit substrate-binding mechanism. Further structural comparison suggests that this induced-fit substrate-recognition mechanism may generally exist in O-methyltransferases. Docking and mutation studies identified three key residues (His98, His247 and Asp248) that are crucial for enzyme activity. The essential function of His247 and Asp248 and structure analysis suggests that both residues are involved in activation of the HBC substrate of PigF. The invariance of Asp248 in PigF further confirmed its essential role. The invariance and essential role of His98 in PigF suggests that it is involved in correctly positioning the substrate. This study provides new insight into the catalytic mechanism of PigF, reveals an induced-fit substrate-recognition model for PigF and broadens the understanding of O-methyltransferases.
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Affiliation(s)
- Shenshen Qiu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Dongqing Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Mengxue Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
| | - Huan Zhou
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
| | - Ning Sun
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Li Zhang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Mengmeng Zhao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Jianhua He
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
| | - Tingting Ran
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Bo Sun
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
| | - Weiwu Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
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11
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Sun Q, Huang M, Wei Y. Diversity of the reaction mechanisms of SAM-dependent enzymes. Acta Pharm Sin B 2021; 11:632-650. [PMID: 33777672 PMCID: PMC7982431 DOI: 10.1016/j.apsb.2020.08.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/30/2020] [Accepted: 08/08/2020] [Indexed: 02/08/2023] Open
Abstract
S-adenosylmethionine (SAM) is ubiquitous in living organisms and is of great significance in metabolism as a cofactor of various enzymes. Methyltransferases (MTases), a major group of SAM-dependent enzymes, catalyze methyl transfer from SAM to C, O, N, and S atoms in small-molecule secondary metabolites and macromolecules, including proteins and nucleic acids. MTases have long been a hot topic in biomedical research because of their crucial role in epigenetic regulation of macromolecules and biosynthesis of natural products with prolific pharmacological moieties. However, another group of SAM-dependent enzymes, sharing similar core domains with MTases, can catalyze nonmethylation reactions and have multiple functions. Herein, we mainly describe the nonmethylation reactions of SAM-dependent enzymes in biosynthesis. First, we compare the structural and mechanistic similarities and distinctions between SAM-dependent MTases and the non-methylating SAM-dependent enzymes. Second, we summarize the reactions catalyzed by these enzymes and explore the mechanisms. Finally, we discuss the structural conservation and catalytical diversity of class I-like non-methylating SAM-dependent enzymes and propose a possibility in enzymes evolution, suggesting future perspectives for enzyme-mediated chemistry and biotechnology, which will help the development of new methods for drug synthesis.
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12
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Abstract
An ongoing challenge in chemical research is to design catalysts that select the outcomes of the reactions of complex molecules. Chemists rely on organo- or transition metal catalysts to control stereo-, regio-, and periselectivity (selectivity among possible pericyclic reactions). Nature achieves these types of selectivity with a variety of enzymes such as the recently discovered pericyclases – a family of enzymes that catalyze pericyclic reactions.1 To date, the majority of characterized enzymatic pericyclic reactions are cycloadditions and it has been difficult to rationalize how observed selectivities are achieved.2-13 We report here the discovery of two homologous groups of pericyclases that catalyze distinct reactions: one group catalyzes an Alder-ene reaction, previously unknown in biology; the second catalyzes a stereoselective hetero-Diels–Alder reaction. Guided by computational studies, we rationalized the observed differences in reactivities and designed mutants that reverse periselectivities from Alder-ene to hetero-Diels–Alder and vice versa. A combination of in vitro biochemical characterizations, computational studies, enzyme co-crystal structures, and mutational studies provide a picture of how high regio- and periselectivities are achieved in nearly identical active sites.
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13
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Kong L, Wang Q, Yang W, Shen J, Li Y, Zheng X, Wang L, Chu Y, Deng Z, Chooi YH, You D. Three Recently Diverging Duplicated Methyltransferases Exhibit Substrate-Dependent Regioselectivity Essential for Xantholipin Biosynthesis. ACS Chem Biol 2020; 15:2107-2115. [PMID: 32649177 DOI: 10.1021/acschembio.0c00296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Polycyclic xanthones are characterized by highly oxygenated, angular hexacyclic frameworks and exhibit diverse biological activities. Although many of them have been isolated and chemically synthesized, the detailed biosynthetic machinery awaits discovery. Recently, xanthone construction in the xantholipin (1) pathway was shown to involve cryptic demethoxylation. This suggested a rationale for the existence of three O-methyltransferase (OMT) genes in the gene cluster, although there are only two O-methyl groups in the structure of 1. Here, in vivo and in vitro analysis have been used to show that the three paralogous OMTs, XanM1-M3, introduce individual methyl groups at specific points in the biosynthetic pathway. Each OMT can to some extent take over the role of the other OMTs, although they exhibit highly substrate-dependent regiospecificity. In addition, phylogenetic analysis suggests their evolution from a common ancestor. Four putative ancestral proteins were constructed, and one of them performed all the functions of XanM1-M3, while the others possessed more limited catalytic functions. The results suggest that a promiscuous common ancestor may have been able to catalyze all three reactions prior to gene duplication and functional divergence. The characterization of XanM1-M3 expands the enzyme inventory for polycyclic xanthone biosynthesis and suggests novel directed evolution approaches to diversifying natural product pathways.
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Affiliation(s)
- Lingxin Kong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Qing Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Weinan Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jufang Shen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yan Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xiaoqing Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Lu Wang
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610052, China
| | - Yiwen Chu
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610052, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yit-Heng Chooi
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
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14
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Yue R, Li M, Wang Y, Guan Y, Zhang J, Yan Z, Liu F, Lu F, Zhang H. Insight into enzyme-catalyzed aziridine formation mechanism in ficellomycin biosynthesis. Eur J Med Chem 2020; 204:112639. [PMID: 32712437 DOI: 10.1016/j.ejmech.2020.112639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 11/17/2022]
Abstract
Ficellomycin is an aziridine-containing antibiotic, produced by Streptomyces ficellus. Based on the newly identified ficellomycin gene cluster and the assigned functions of its genes, a possible pathway for aziridine ring formation in ficellomycin was proposed, which is a complex process involving at least 3 enzymatic steps. To obtain support for the proposed mechanism, the targeted genes encoding sulfate adenylyltransferase, adenylsulfate kinase, and a putative sulfotransferase were respectively disrupted and the subsequent analysis of their fermentation products revealed that all the three genes were involved in aziridine formation. To further confirm the mechanism, the key gene encoding a putative sulfotransferase was over expressed in Escherichia coli Rosseta (DE3). Enzyme assays indicated that the expressed sulfotransferase could specifically transfer a sulfo group from 3'-phosphoadenosine-5'-phosphosulfate (PAPS) onto the hydroxyl group of (R)-(-)-2-pyrrolidinemethanol. This introduces a good leaving group in the form of the sulfated hydroxyl moiety, which is then converted into an aziridine ring through an intramolecular nucleophilic attack by the adjacent secondary amine. The sulfation/intramolecular cyclization reaction sequence maybe a general strategy for aziridine biosynthesis in microorganisms. Discovery of this mechanism revealed an enzyme-catalyzed route for the synthesis of aziridine-containing reagents and provided an important insight into the functional diversity of sulfotransferases.
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Affiliation(s)
- Rong Yue
- Key Laboratory of Industrial Fermentation Microbiology, College of Bioengineering, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Meng Li
- Key Laboratory of Industrial Fermentation Microbiology, College of Bioengineering, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Yue Wang
- Key Laboratory of Industrial Fermentation Microbiology, College of Bioengineering, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Ying Guan
- Key Laboratory of Industrial Fermentation Microbiology, College of Bioengineering, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Jing Zhang
- Key Laboratory of Industrial Fermentation Microbiology, College of Bioengineering, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Zhongli Yan
- Key Laboratory of Industrial Fermentation Microbiology, College of Bioengineering, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology, College of Bioengineering, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, College of Bioengineering, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Huitu Zhang
- Key Laboratory of Industrial Fermentation Microbiology, College of Bioengineering, Tianjin University of Science & Technology, Tianjin, 300457, PR China.
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15
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Sun Q, Hu Y, Gu Y, Huang J, He J, Luo L, Yang Y, Yin S, Dou C, Wang T, Fu X, He L, Qi S, Zhu X, Yang S, Wei X, Cheng W. Deciphering the regulatory and catalytic mechanisms of an unusual SAM-dependent enzyme. Signal Transduct Target Ther 2019; 4:17. [PMID: 31149354 PMCID: PMC6533283 DOI: 10.1038/s41392-019-0052-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 04/28/2019] [Accepted: 05/07/2019] [Indexed: 02/05/2023] Open
Abstract
S-adenosyl-1-methionine (SAM)-dependent enzymes regulate various disease-related behaviors in all organisms. Recently, the leporin biosynthesis enzyme LepI, a SAM-dependent enzyme, was reported to catalyze pericyclic reactions in leporin biosynthesis; however, the mechanisms underlying LepI activation and catalysis remain unclear. This study aimed to investigate the molecular mechanisms of LepI. Here, we reported crystal structures of LepI bound to SAM/5'-deoxy-5'-(methylthio) adenosine (MTA), S-adenosyl-homocysteine (SAH), and SAM/substrate states. Structural and biochemical analysis revealed that MTA or SAH inhibited the enzyme activities, whereas SAM activated the enzyme. The analysis of the substrate-bound structure of LepI demonstrated that this enzymatic retro-Claisen rearrangement was primarily driven by three critical polar residues His133, Arg197, Arg295 around the active site and assisted by SAM with unclear mechanism. The present studies indicate that the unique mechanisms underlying regulatory and catalysis of the unusual SAM-dependent enzyme LepI, not only strengthening current understanding of the fundamentally biochemical catalysis, but also providing novel insights into the design of SAM-dependent enzyme-specific small molecules.
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Affiliation(s)
- Qiu Sun
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Yuehong Hu
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Yijun Gu
- Shanghai Synchrotron Radiation Facility, Zhangjiang Lab, Zhangheng Road 239, Pudong District, Shanghai, 201203 China
| | - Jiangkun Huang
- Department of Medicinal Chemistry, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041 China
| | - Jun He
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Lan Luo
- Department of Medicinal Chemistry, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041 China
| | - Yi Yang
- West China School of Public Health, Sichuan University, Chengdu, 610041 China
| | - Shuo Yin
- West China School of Public Health, Sichuan University, Chengdu, 610041 China
| | - Chao Dou
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Tianqi Wang
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Xianghui Fu
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Ling He
- Department of Medicinal Chemistry, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041 China
| | - Shiqian Qi
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Xiaofeng Zhu
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Shengyong Yang
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Xiawei Wei
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
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16
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Chang M, Zhou Y, Wang H, Liu Z, Zhang Y, Feng Y. Crystal structure of the multifunctional SAM-dependent enzyme LepI provides insights into its catalytic mechanism. Biochem Biophys Res Commun 2019; 515:255-260. [PMID: 31101338 DOI: 10.1016/j.bbrc.2019.05.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 05/03/2019] [Indexed: 01/13/2023]
Abstract
Pericyclic reactions are among the most powerful synthetic transformations widely applied in the synthesis of multiple regioselective and stereoselective carbon-carbon bonds. LepI is a recently identified S-adenosyl-l-methionine (SAM)-dependent enzyme, which could catalyze dehydration, Diels-Alder reaction, and the retro-Claisen rearrangement reactions. However, the mechanism underlying these reactions by LepI remains elusive. Here we report the structure of LepI in complex with SAM as its co-factor, which adopts a typical class I methyltransferase fold. Docking studies are performed to investigate the binding modes of various substrates/products and provide insights into the catalytic mechanism of the multiple reactions catalyzed by LepI. Our study suggests that the dehydration reaction may start from the deprotonation of the hydroxyl group on the pyridone ring of the substrate by LepIH133, during which R295 and D296 play important roles in substrate binding and stabilizing the reaction intermediate. The stereoselective dehydration is accomplished through the trans-conformer of the leaving alcohol group which is trapped by nearby residues. The pericyclic reactions following dehydration are facilitated by the hydrophobic and hydrophilic interactions in the binding pocket. H133 and R295, two residues not conserved in other methyltransferases, might account for the unique activity of LepI among the SAM-dependent methyltransferase family. Together, this study provides important structural insights into the unique reactions catalyzed by LepI and will shed light on the knowledge of mechanisms of pericyclic reactions.
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Affiliation(s)
- Min Chang
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Yu Zhou
- National Institute of Biological Sciences, Beijing, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, PR China
| | - Hao Wang
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Zihe Liu
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Yi Zhang
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Yue Feng
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China.
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17
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Wang X, Wang C, Duan L, Zhang L, Liu H, Xu YM, Liu Q, Mao T, Zhang W, Chen M, Lin M, Gunatilaka AAL, Xu Y, Molnár I. Rational Reprogramming of O-Methylation Regioselectivity for Combinatorial Biosynthetic Tailoring of Benzenediol Lactone Scaffolds. J Am Chem Soc 2019; 141:4355-4364. [PMID: 30767524 PMCID: PMC6416077 DOI: 10.1021/jacs.8b12967] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Indexed: 11/28/2022]
Abstract
O-Methylation modulates the pharmacokinetic and pharmacodynamic (PK/PD) properties of small-molecule natural products, affecting their bioavailability, stability, and binding to targets. Diversity-oriented combinatorial biosynthesis of new chemical entities for drug discovery and optimization of known bioactive scaffolds during drug development both demand efficient O-methyltransferase (OMT) biocatalysts with considerable substrate promiscuity and tunable regioselectivity that can be deployed in a scalable and sustainable manner. Here we demonstrate efficient total biosynthetic and biocatalytic platforms that use a pair of fungal OMTs with orthogonal regiospecificity to produce unnatural O-methylated benzenediol lactone polyketides. We show that rational, structure-guided active-site cavity engineering can reprogram the regioselectivity of these enzymes. We also characterize the interplay of engineered regioselectivity with substrate plasticity. These findings will guide combinatorial biosynthetic tailoring of unnatural products toward the generation of diverse chemical matter for drug discovery and the PK/PD optimization of bioactive scaffolds for drug development.
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Affiliation(s)
- Xiaojing Wang
- Biotechnology
Research Institute, Chinese Academy of Agricultural
Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
- Southwest
Center for Natural Products Research, University
of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United
States
- State
Key Laboratory of Plant Physiology and Biochemistry, Department of
Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100193, P.R. China
| | - Chen Wang
- Biotechnology
Research Institute, Chinese Academy of Agricultural
Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
- Southwest
Center for Natural Products Research, University
of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United
States
| | - Lixin Duan
- Southwest
Center for Natural Products Research, University
of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United
States
- Guangzhou
University of Chinese Medicine, 232 Waihuan East Road, Guangzhou University
City, Panyu District, Guangzhou 510006, P.R. China
| | - Liwen Zhang
- Biotechnology
Research Institute, Chinese Academy of Agricultural
Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Hang Liu
- Biotechnology
Research Institute, Chinese Academy of Agricultural
Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
- Southwest
Center for Natural Products Research, University
of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United
States
| | - Ya-ming Xu
- Southwest
Center for Natural Products Research, University
of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United
States
| | - Qingpei Liu
- Southwest
Center for Natural Products Research, University
of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United
States
- Key
Laboratory of Environment Correlative Dietology, College of Food Science
and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Tonglin Mao
- State
Key Laboratory of Plant Physiology and Biochemistry, Department of
Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100193, P.R. China
| | - Wei Zhang
- Biotechnology
Research Institute, Chinese Academy of Agricultural
Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Ming Chen
- Biotechnology
Research Institute, Chinese Academy of Agricultural
Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Min Lin
- Biotechnology
Research Institute, Chinese Academy of Agricultural
Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
| | - A. A. Leslie Gunatilaka
- Southwest
Center for Natural Products Research, University
of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United
States
| | - Yuquan Xu
- Biotechnology
Research Institute, Chinese Academy of Agricultural
Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
| | - István Molnár
- Southwest
Center for Natural Products Research, University
of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United
States
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18
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Newmister SA, Romminger S, Schmidt JJ, Williams RM, Smith JL, Berlinck RGS, Sherman DH. Unveiling sequential late-stage methyltransferase reactions in the meleagrin/oxaline biosynthetic pathway. Org Biomol Chem 2019; 16:6450-6459. [PMID: 30141817 DOI: 10.1039/c8ob01565a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Antimicrobial and anti-proliferative meleagrin and oxaline are roquefortine C-derived alkaloids produced by fungi of the genus Penicillium. Tandem O-methylations complete the biosynthesis of oxaline from glandicoline B through meleagrin. Currently, little is known about the role of these methylation patterns in the bioactivity profile of meleagrin and oxaline. To establish the structural and mechanistic basis of methylation in these pathways, crystal structures were determined for two late-stage methyltransferases in the oxaline and meleagrin gene clusters from Penicillium oxalicum and Penicillium chrysogenum. The homologous enzymes OxaG and RoqN were shown to catalyze penultimate hydroxylamine O-methylation to generate meleagrin in vitro. Crystal structures of these enzymes in the presence of methyl donor S-adenosylmethionine revealed an open active site, which lacks an apparent base indicating that catalysis is driven by proximity effects. OxaC was shown to methylate meleagrin to form oxaline in vitro, the terminal pathway product. Crystal structures of OxaC in a pseudo-Michaelis complex containing sinefungin and meleagrin, and in a product complex containing S-adenosyl-homocysteine and oxaline, reveal key active site residues with His313 serving as a base that is activated by Glu369. These data provide structural insights into the enzymatic methylation of these alkaloids that include a rare hydroxylamine oxygen acceptor, and can be used to guide future efforts towards selective derivatization and structural diversification and establishing the role of methylation in bioactivity.
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Affiliation(s)
- Sean A Newmister
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.
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19
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Discovery and characterization of a novel C-terminal peptide carboxyl methyltransferase in a lassomycin-like lasso peptide biosynthetic pathway. Appl Microbiol Biotechnol 2019; 103:2649-2664. [DOI: 10.1007/s00253-019-09645-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/02/2019] [Accepted: 01/10/2019] [Indexed: 12/28/2022]
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20
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Jiang J, Guiza Beltran D, Schacht A, Wright S, Zhang L, Du L. Functional and Structural Analysis of Phenazine O-Methyltransferase LaPhzM from Lysobacter antibioticus OH13 and One-Pot Enzymatic Synthesis of the Antibiotic Myxin. ACS Chem Biol 2018; 13:1003-1012. [PMID: 29510028 DOI: 10.1021/acschembio.8b00062] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Myxin is a well-known antibiotic that had been used for decades. It belongs to the phenazine natural products that exhibit various biological activities, which are often dictated by the decorating groups on the heteroaromatic three-ring system. The three rings of myxin carry a number of decorations, including an unusual aromatic N5, N10-dioxide. We previously showed that phenazine 1,6-dicarboxylic acid (PDC) is the direct precursor of myxin, and two redox enzymes (LaPhzS and LaPhzNO1) catalyze the decarboxylative hydroxylation and aromatic N-oxidations of PDC to produce iodinin (1.6-dihydroxy- N5, N10-dioxide phenazine). In this work, we identified the LaPhzM gene from Lysobacter antibioticus OH13 and demonstrated that LaPhzM encodes a SAM-dependent O-methyltransferase converting iodinin to myxin. The results further showed that LaPhzM is responsible for both monomethoxy and dimethoxy formation in all phenazine compounds isolated from strain OH13. LaPhzM exhibits relaxed substrate selectivity, catalyzing O-methylation of phenazines with non-, mono-, or di- N-oxide. In addition, we demonstrated a one-pot biosynthesis of myxin by in vitro reconstitution of the three phenazine-ring decorating enzymes. Finally, we determined the X-ray crystal structure of LaPhzM with a bound cofactor at 1.4 Å resolution. The structure provided molecular insights into the activity and selectivity of the first characterized phenazine O-methyltransferase. These results will facilitate future exploitation of the thousands of phenazines as new antibiotics through metabolic engineering and chemoenzymatic syntheses.
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Affiliation(s)
- Jiasong Jiang
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | | | | | - Stephen Wright
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | | | - Liangcheng Du
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
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21
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Crystal structure of Rv2258c from Mycobacterium tuberculosis H37Rv, an S -adenosyl- l -methionine-dependent methyltransferase. J Struct Biol 2016; 193:172-180. [DOI: 10.1016/j.jsb.2016.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 01/05/2016] [Indexed: 11/21/2022]
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22
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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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Singh S, Nandurkar NS, Thorson JS. Characterization of the calicheamicin orsellinate C2-O-methyltransferase CalO6. Chembiochem 2015; 15:1418-21. [PMID: 24978950 DOI: 10.1002/cbic.201402119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Indexed: 11/09/2022]
Abstract
Although bacterial iterative type I polyketide synthases are now known to participate in the biosynthesis of a small set of diverse natural products, the subsequent downstream modification of the resulting polyketide products is poorly understood. We report the functional characterization of the putative orsellinic acid C2-O-methyltransferase, which is involved in calicheamicin biosynthesis. This study suggests that C2-O-methylation precedes C3-hydroxylation/methylation and C5-iodination and requires a coenzyme A- or acyl carrier protein-bound substrate.
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Affiliation(s)
- Shanteri Singh
- Center for Pharmaceutical Research and Innovation, Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536 (USA).
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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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25
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Liu S, Ran T, Shen X, Xu L, Wang W, Xu D. Expression, crystallization and preliminary crystallographic data analysis of PigF, an O-methyltransferase from the prodigiosin-synthetic pathway in Serratia. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:898-901. [PMID: 22869117 DOI: 10.1107/s1744309112024001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 05/25/2012] [Indexed: 11/10/2022]
Abstract
Prodigiosin, which is a member of the prodiginines, is a red linear tripyrrole compound. A gene cluster for the biosynthesis of prodigiosin has been identified in Serratia and most genes in the cluster have been functionally assigned. A bifurcated biosynthetic pathway for prodigiosin has previously been determined. The last step in the biosynthetic pathway of 4-methoxy-2,2'-bipyrrole-5-carbaldehyde (MBC) is catalyzed by PigF, which transfers a methyl group to 4-hydroxy-2,2'-bipyrrole-5-carbaldehyde (HBC) to form the terminal product MBC, but its catalytic mechanism is not known. To elucidate its mechanism, recombinant PigF was purified and crystallized. The crystals belonged to space group P2(1), with unit-cell parameters a = 69.4, b = 52.4, c = 279.2 Å, β = 96.8°. The native crystals may contain six molecules in the asymmetric unit, with a V(M) of 2.17 Å(3) Da(-1) and a solvent content of 43.43%. A full data set was collected at 2.6 Å resolution using synchrotron radiation on beamline BL17U of Shanghai Synchrotron Radiation Facility (SSRF), People's Republic of China. Molecular replacement was unsuccessful. To solve the structure of PigF by experimental phasing, selenomethionine-derivativized protein crystals were prepared from a condition with 0.01 M spermidine as an additive. One crystal diffracted to 1.9 Å resolution and a full data set was collected on beamline BL17U at SSRF. The crystal belonged to space group P2(1), with unit-cell parameters a = 69.0, b = 52.9, c = 93.4 Å, β = 97.3°. Heavy-atom substructure determination and phasing by SAD clearly showed that the crystal contains two molecules in the asymmetric unit, with a V(M) of 2.19 Å(3) Da(-1) and a solvent content of 43.82%.
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Affiliation(s)
- Shaowei Liu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
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