1
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Benjdia A, Berteau O. B 12-dependent radical SAM enzymes: Ever expanding structural and mechanistic diversity. Curr Opin Struct Biol 2023; 83:102725. [PMID: 37931378 DOI: 10.1016/j.sbi.2023.102725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/26/2023] [Accepted: 10/03/2023] [Indexed: 11/08/2023]
Abstract
In the last decade, B12-dependent radical SAM enzymes have emerged as central biocatalysts in the biosynthesis of a myriad of natural products. Notably, these enzymes have been shown to catalyze carbon-carbon bond formation on unactivated carbon atoms leading to unusual methylations. Recently, structural studies have revealed unprecedented insights into the complex chemistry catalyzed by these enzymes. In this review, we cover recent advances in our understanding of B12-dependent radical SAM enzymes from a mechanistic and structural perspective. We discuss the unanticipated diversity of these enzymes which suggests evolutionary links between various biosynthetic and metabolic pathways from antibiotic to RiPP and methane biosynthesis.
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Affiliation(s)
- Alhosna Benjdia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, 78350, Jouy-en-Josas, France.
| | - Olivier Berteau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, 78350, Jouy-en-Josas, France.
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2
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Ciccone MM, Lepera ME, Guaricci AI, Forleo C, Cafiero C, Colella M, Palmirotta R, Santacroce L. Might Gut Microbiota Be a Target for a Personalized Therapeutic Approach in Patients Affected by Atherosclerosis Disease? J Pers Med 2023; 13:1360. [PMID: 37763128 PMCID: PMC10532785 DOI: 10.3390/jpm13091360] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
In recent years, the increasing number of studies on the relationship between the gut microbiota and atherosclerosis have led to significant interest in this subject. The gut microbiota, its metabolites (metabolome), such as TMAO, and gut dysbiosis play an important role in the development of atherosclerosis. Furthermore, inflammation, originating from the intestinal tract, adds yet another mechanism by which the human ecosystem is disrupted, resulting in the manifestation of metabolic diseases and, by extension, cardiovascular diseases. The scientific community must understand and elucidate these mechanisms in depth, to gain a better understanding of the relationship between atherosclerosis and the gut microbiome and to promote the development of new therapeutic targets in the coming years. This review aims to present the knowledge acquired so far, to trigger others to further investigate this intriguing topic.
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Affiliation(s)
- Marco Matteo Ciccone
- Cardiology Unit, Interdisciplinary Department of Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (M.M.C.); (M.E.L.); (A.I.G.); (C.F.)
| | - Mario Erminio Lepera
- Cardiology Unit, Interdisciplinary Department of Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (M.M.C.); (M.E.L.); (A.I.G.); (C.F.)
| | - Andrea Igoren Guaricci
- Cardiology Unit, Interdisciplinary Department of Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (M.M.C.); (M.E.L.); (A.I.G.); (C.F.)
| | - Cinzia Forleo
- Cardiology Unit, Interdisciplinary Department of Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (M.M.C.); (M.E.L.); (A.I.G.); (C.F.)
| | - Concetta Cafiero
- Area of Molecular Pathology, Anatomic Pathology Unit, Fabrizio Spaziani Hospital, 03100 Frosinone, Italy;
| | - Marica Colella
- Interdisciplinary Department of Medicine, Section of Microbiology and Virology, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (M.C.); (L.S.)
| | - Raffele Palmirotta
- Interdisciplinary Department of Medicine, Section of Microbiology and Virology, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (M.C.); (L.S.)
| | - Luigi Santacroce
- Interdisciplinary Department of Medicine, Section of Microbiology and Virology, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (M.C.); (L.S.)
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3
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Kudo F, Minato A, Sato S, Nagano N, Maruyama C, Hamano Y, Hashimoto J, Kozone I, Shin-Ya K, Eguchi T. Mechanism of S-Adenosyl-l-methionine C-Methylation by Cobalamin-dependent Radical S-Adenosyl-l-methionine Methylase in 1-Amino-2-methylcyclopropanecarboxylic Acid Biosynthesis. Org Lett 2022; 24:8975-8979. [PMID: 36458844 DOI: 10.1021/acs.orglett.2c03555] [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: 12/05/2022]
Abstract
The radical S-adenosyl-l-methionine (SAM) methylase Orf29 catalyzes the C-methylation of SAM in the biosynthesis of 1-amino-2-methylcyclopropanecarboxylic acid. Here, we determined that the methylation product is (4″R)-4″-methyl-SAM. Furthermore, we found that the 5'-deoxyadenosyl radical generated by Orf29 abstracts the pro-R hydrogen atom from the C-4″ position of SAM to generate the radical intermediate, which reacts with methylcobalamin to give (4″R)-4″-methyl-SAM. Consequently, the Orf29-catalyzed C-methylation was confirmed to proceed with retention of configuration.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Tokyo 152-8551, Japan
| | - Atsushi Minato
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Tokyo 152-8551, Japan
| | - Shusuke Sato
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Tokyo 152-8551, Japan
| | - Nayuta Nagano
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Tokyo 152-8551, Japan
| | - Chitose Maruyama
- Department of Bioscience, Fukui Prefectural University, 4-1-1 Yoshida-Gun, Fukui 910-1195, Japan
| | - Yoshimitsu Hamano
- Department of Bioscience, Fukui Prefectural University, 4-1-1 Yoshida-Gun, Fukui 910-1195, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Tokyo 152-8551, Japan
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4
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Lichstrahl MS, Townsend CA, Sinner EK. Stereochemical course of cobalamin-dependent radical SAM methylation by TokK and ThnK. RSC Chem Biol 2022; 3:1028-1034. [PMID: 36042702 PMCID: PMC9358933 DOI: 10.1039/d2cb00113f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/06/2022] [Indexed: 11/21/2022] Open
Abstract
Complex carbapenems are important clinical antibiotics for difficult-to-treat infections. An essential step in the biosyntheses of these natural products is stereospecific methylation at C6 and subsequent alkylations by cobalamin-dependent radical SAM methylases such as TokK and ThnK. We have prepared isotopically labeled substrates in a stereospecific manner and found that both homologous enzymes selectively abstract the 6-pro-S hydrogen, followed by methyl transfer to the opposite face to give the (6R)-methyl carbapenam product proceeding, therefore, by inversion of absolute configuration at C6. These data clarify an unexpected ambiguity in the recently solved substrate-bound crystal structure of TokK and have led to a stereochemically complete mechanistic proposal for both TokK and ThnK.
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Affiliation(s)
- Michael S Lichstrahl
- Department of Chemistry, The Johns Hopkins University 3400 N Charles St Baltimore Maryland USA
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University 3400 N Charles St Baltimore Maryland USA
| | - Erica K Sinner
- Department of Chemistry, The Johns Hopkins University 3400 N Charles St Baltimore Maryland USA
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5
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Characterization of the cobalamin-dependent radical S-adenosyl-l-methionine enzyme C-methyltransferase Fom3 in fosfomycin biosynthesis. Methods Enzymol 2022; 669:45-70. [PMID: 35644180 DOI: 10.1016/bs.mie.2021.11.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fosfomycin is a clinically used broad-spectrum antibiotic that has the structure of an oxirane ring with a phosphonic acid substituent and a methyl substituent. In nature, fosfomycin is produced by Streptomyces spp. and Pseudomonas sp., but biosynthesis of fosfomycin significantly differs between the two bacteria, especially in the incorporation mechanism of the methyl group. It has been proposed that the cobalamin-dependent radical S-adenosyl-l-methionine (SAM) enzyme Fom3 is responsible for the methyl-transfer reaction in Streptomyces fosfomycin biosynthesis. In this chapter, we describe the experimental methods to characterize Fom3. We performed the methylation reaction with the purified recombinant Fom3, revealing that Fom3 recognizes a cytidylylated 2-hydroxyethylphosphonate as a substrate and catalyzes stereoselective methylation of the sp3 carbon at the C2 position to afford cytidylylated (S)-2-hydroxypropylphosphonate. Reaction analysis using deuterium-labeled substrates showed that the 5'-deoxyadenosyl radical generated by reductive cleavage of SAM stereoselectively abstracts the pro-R hydrogen atom of the CH bond at the C2 position of cytidylylated 2-hydroxyethylphosphonate. Therefore, the C-methylation reaction catalyzed by Fom3 proceeds with inversion of the configuration at the C2 position. Experimental methods to elucidate the chemical structures of the substrate and products and the stereochemical course in the Fom3-catalyzed reaction could give information to progress investigation of cobalamin-dependent radical SAM C-methyltransferases.
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6
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Ulrich EC, Drennan CL. The Atypical Cobalamin-Dependent S-Adenosyl-l-Methionine Nonradical Methylase TsrM and Its Radical Counterparts. J Am Chem Soc 2022; 144:5673-5684. [PMID: 35344653 PMCID: PMC8992657 DOI: 10.1021/jacs.1c12064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 12/29/2022]
Abstract
Cobalamin (Cbl)-dependent S-adenosyl-l-methionine (AdoMet) radical methylases are known for their use of a dual cofactor system to perform challenging radical methylation reactions at unactivated carbon and phosphorus centers. These enzymes are part of a larger subgroup of Cbl-dependent AdoMet radical enzymes that also perform difficult ring contractions and radical rearrangements. This subgroup is a largely untapped reservoir of diverse chemistry that requires steady efforts in biochemical and structural characterization to reveal its complexity. In this Perspective, we highlight the significant efforts over many years to elucidate the function, mechanism, and structure of TsrM, an unexpected nonradical methylase in this subgroup. We also discuss recent achievements in characterizing radical methylase subgroup members that exemplify how key tools in mechanistic enzymology are valuable time and again. Finally, we identify recent enzyme activity studies that have made use of bioinformatic analyses to expand our definition of the subgroup. Additional breakthroughs in radical (and nonradical) enzymatic chemistry and challenging transformations from the unexplored space of this subgroup are undoubtedly on the horizon.
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Affiliation(s)
- Emily C. Ulrich
- Department
of Biology and Department of Chemistry, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Catherine L. Drennan
- Department
of Biology and Department of Chemistry, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- Howard
Hughes Medical Institute, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
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7
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Sinner E, Marous DR, Townsend CA. Evolution of Methods for the Study of Cobalamin-Dependent Radical SAM Enzymes. ACS BIO & MED CHEM AU 2022; 2:4-10. [PMID: 35341020 PMCID: PMC8950095 DOI: 10.1021/acsbiomedchemau.1c00032] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While bioinformatic evidence of cobalamin-dependent radical S-adenosylmethionine (SAM) enzymes has existed since the naming of the radical SAM superfamily in 2001, none were biochemically characterized until 2011. In the past decade, the field has flourished as methodological advances have facilitated study of the subfamily. Because of the ingenuity and perseverance of researchers in this field, we now have functional, mechanistic, and structural insight into how this class of enzymes harnesses the power of both the cobalamin and radical SAM cofactors to achieve catalysis. All of the early characterized enzymes in this subfamily were methylases, but the activity of these enzymes has recently been expanded beyond methylation. We anticipate that the characterized functions of these enzymes will become both better understood and increasingly diverse with continued study.
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Affiliation(s)
- Erica
K. Sinner
- Department
of Chemistry, Johns Hopkins University, 3400 N Charles St., Baltimore, Maryland 21218, United States
| | - Daniel R. Marous
- Department
of Chemistry, Wittenberg University, 200 W Ward St., Springfield, Ohio 45504, United States
| | - Craig A. Townsend
- Department
of Chemistry, Johns Hopkins University, 3400 N Charles St., Baltimore, Maryland 21218, United States
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8
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McLaughlin M, Pallitsch K, Wallner G, van der Donk WA, Hammerschmidt F. Overall Retention of Methyl Stereochemistry during B 12-Dependent Radical SAM Methyl Transfer in Fosfomycin Biosynthesis. Biochemistry 2021; 60:1587-1596. [PMID: 33942609 PMCID: PMC8158854 DOI: 10.1021/acs.biochem.1c00113] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/24/2021] [Indexed: 11/30/2022]
Abstract
Methylcobalamin-dependent radical S-adenosylmethionine (SAM) enzymes methylate non-nucleophilic atoms in a range of substrates. The mechanism of the methyl transfer from cobalt to the receiving atom is still mostly unresolved. Here we determine the stereochemical course of this process at the methyl group during the biosynthesis of the clinically used antibiotic fosfomycin. In vitro reaction of the methyltransferase Fom3 using SAM labeled with 1H, 2H, and 3H in a stereochemically defined manner, followed by chemoenzymatic conversion of the Fom3 product to acetate and subsequent stereochemical analysis, shows that the overall reaction occurs with retention of configuration. This outcome is consistent with a double-inversion process, first in the SN2 reaction of cob(I)alamin with SAM to form methylcobalamin and again in a radical transfer of the methyl group from methylcobalamin to the substrate. The methods developed during this study allow high-yield in situ generation of labeled SAM and recombinant expression and purification of the malate synthase needed for chiral methyl analysis. These methods facilitate the broader use of in vitro chiral methyl analysis techniques to investigate the mechanisms of other novel enzymes.
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Affiliation(s)
- Martin
I. McLaughlin
- Department
of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | | | - Gabriele Wallner
- Institute
of Inorganic Chemistry, University of Vienna, Vienna 1090, Austria
| | - Wilfred A. van der Donk
- Department
of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Howard
Hughes Medical Institute, University of
Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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9
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Zhong A, Lee YH, Liu YN, Liu HW. Biosynthesis of Oxetanocin-A Includes a B 12-Dependent Radical SAM Enzyme That Can Catalyze both Oxidative Ring Contraction and the Demethylation of SAM. Biochemistry 2021; 60:537-546. [PMID: 33560833 PMCID: PMC7904626 DOI: 10.1021/acs.biochem.0c00915] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oxetanocin-A is an antitumor, antiviral, and antibacterial nucleoside. It is biosynthesized via the oxidative ring contraction of a purine nucleoside co-opted from primary metabolism. This reaction is catalyzed by a B12-dependent radical S-adenosyl-l-methionine (SAM) enzyme, OxsB, and a phosphohydrolase, OxsA. Previous experiments showed that the product of the OxsB/OxsA-catalyzed reaction is an oxetane aldehyde produced alongside an uncharacterized byproduct. Experiments reported herein reveal that OxsB/OxsA complex formation is crucial for the ring contraction reaction and that reduction of the aldehyde intermediate is catalyzed by a nonspecific dehydrogenase from the general cellular pool. In addition, the byproduct is identified as a 1,3-thiazinane adduct between the aldehyde and l-homocysteine. While homocysteine was never included in the OxsB/OxsA assays, the data suggest that it can be generated from SAM via S-adenosyl-l-homocysteine (SAH). Further study revealed that conversion of SAM to SAH is facilitated by OxsB; however, the subsequent conversion of SAH to homocysteine is due to protein contaminants that co-purify with OxsA. Nevertheless, the observed demethylation of SAM to SAH suggests possible methyltransferase activity of OxsB, and substrate methylation was indeed detected in the OxsB-catalyzed reaction. This work is significant because it not only completes the description of the oxetanocin-A biosynthetic pathway but also suggests that OxsB may be capable of methyltransferase activity.
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Affiliation(s)
- Aoshu Zhong
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA
| | - Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Yung-nan Liu
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA
| | - Hung-wen Liu
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
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10
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Shiraishi T, Kuzuyama T. Biosynthetic pathways and enzymes involved in the production of phosphonic acid natural products. Biosci Biotechnol Biochem 2021; 85:42-52. [PMID: 33577658 DOI: 10.1093/bbb/zbaa052] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/04/2020] [Indexed: 02/07/2023]
Abstract
Phosphonates are organophosphorus compounds possessing a characteristic C-P bond in which phosphorus is directly bonded to carbon. As phosphonates mimic the phosphates and carboxylates of biological molecules to potentially inhibit metabolic enzymes, they could be lead compounds for the development of a variety of drugs. Fosfomycin (FM) is a representative phosphonate natural product that is widely used as an antibacterial drug. Here, we review the biosynthesis of FM, which includes a recent breakthrough to find a missing link in the biosynthetic pathway that had been a mystery for a quarter-century. In addition, we describe the genome mining of phosphonate natural products using the biosynthetic gene encoding an enzyme that catalyzes C-P bond formation. We also introduce the chemoenzymatic synthesis of phosphonate derivatives. These studies expand the repertoires of phosphonates and the related biosynthetic machinery. This review mainly covers the years 2012-2020.
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Affiliation(s)
- Taro Shiraishi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Tomohisa Kuzuyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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11
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Vitamin B 12-dependent biosynthesis ties amplified 2-methylhopanoid production during oceanic anoxic events to nitrification. Proc Natl Acad Sci U S A 2020; 117:32996-33004. [PMID: 33318211 DOI: 10.1073/pnas.2012357117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacterial hopanoid lipids are ubiquitous in the geologic record and serve as biomarkers for reconstructing Earth's climatic and biogeochemical evolution. Specifically, the abundance of 2-methylhopanoids deposited during Mesozoic ocean anoxic events (OAEs) and other intervals has been interpreted to reflect proliferation of nitrogen-fixing marine cyanobacteria. However, there currently is no conclusive evidence for 2-methylhopanoid production by extant marine cyanobacteria. As an alternative explanation, here we report 2-methylhopanoid production by bacteria of the genus Nitrobacter, cosmopolitan nitrite oxidizers that inhabit nutrient-rich freshwater, brackish, and marine environments. The model organism Nitrobacter vulgaris produced only trace amounts of 2-methylhopanoids when grown in minimal medium or with added methionine, the presumed biosynthetic methyl donor. Supplementation of cultures with cobalamin (vitamin B12) increased nitrite oxidation rates and stimulated a 33-fold increase of 2-methylhopanoid abundance, indicating that the biosynthetic reaction mechanism is cobalamin dependent. Because Nitrobacter spp. cannot synthesize cobalamin, we postulate that they acquire it from organisms inhabiting a shared ecological niche-for example, ammonia-oxidizing archaea. We propose that during nutrient-rich conditions, cobalamin-based mutualism intensifies upper water column nitrification, thus promoting 2-methylhopanoid deposition. In contrast, anoxia underlying oligotrophic surface ocean conditions in restricted basins would prompt shoaling of anaerobic ammonium oxidation, leading to low observed 2-methylhopanoid abundances. The first scenario is consistent with hypotheses of enhanced nutrient loading during OAEs, while the second is consistent with the sedimentary record of Pliocene-Pleistocene Mediterranean sapropel events. We thus hypothesize that nitrogen cycling in the Pliocene-Pleistocene Mediterranean resembled modern, highly stratified basins, whereas no modern analog exists for OAEs.
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12
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Sun SQ, Chen SL. An Unprecedented Ring-Contraction Mechanism in Cobalamin-Dependent Radical S-Adenosylmethionine Enzymes. J Phys Chem Lett 2020; 11:6812-6818. [PMID: 32787210 DOI: 10.1021/acs.jpclett.0c01725] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A unique member of the family of cobalamin (Cbl)-dependent radical S-adenosylmethionine (SAM) enzymes, OxsB, catalyzes the ring constriction of deoxyadenosine triphosphate (dATP) to the base oxetane aldehyde phosphate, a crucial precursor for oxetanocin A (OXT-A), which is an antitumor, antiviral, and antibacterial compound. This enzyme reveals a new catalytic function for this big family that is different from the common methylation. On the basis of density functional theory calculations, a mechanism has been proposed to mainly include that the generation of 5'-deoxyadenosine radical, a hydrogen transfer forming 2'-dATP radical, and a Cbl-catalyzed ring contraction of the deoxyribose in 2'-dATP radical. The ring contraction is a concerted rearrangement step accompanied by an electron transfer from the deoxyribose hydroxyl oxygen to CoIII without any ring-opening intermediate. CoIICbl has been ruled out as an active state. Other mechanistic characteristics are also revealed. This unprecedented non-methylation mechanism provides a new catalytic repertoire for the family of radical SAM enzymes, representing a new class of ring-contraction enzymes.
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Affiliation(s)
- Shuo-Qi Sun
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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13
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Wang Y, Begley TP. Mechanistic Studies on CysS - A Vitamin B 12-Dependent Radical SAM Methyltransferase Involved in the Biosynthesis of the tert-Butyl Group of Cystobactamid. J Am Chem Soc 2020; 142:9944-9954. [PMID: 32374991 DOI: 10.1021/jacs.9b06454] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Cobalamin (Cbl)-dependent radical S-adenosylmethionine (SAM) methyltransferases catalyze methylation reactions at non-nucleophilic centers in a wide range of substrates. CysS is a Cbl-dependent radical SAM methyltransferase involved in cystobactamid biosynthesis. This enzyme catalyzes the sequential methylation of a methoxy group to form ethoxy, i-propoxy, s-butoxy, and t-butoxy groups on a p-aminobenzoate peptidyl carrier protein thioester intermediate. This biosynthetic strategy enables the host myxobacterium to biosynthesize a combinatorial antibiotic library of 25 cystobactamid analogues. In this Article, we describe three experiments to elucidate how CysS uses Cbl, SAM, and a [4Fe-4S] cluster to catalyze iterative methylation reactions: a cyclopropylcarbinyl rearrangement was used to trap the substrate radical and to estimate the rate of the radical substitution reaction involved in the methyl transfer; a bromoethoxy analogue was used to explore the active site topography; and deuterium isotope effects on the hydrogen atom abstraction by the adenosyl radical were used to investigate the kinetic significance of the hydrogen atom abstraction. On the basis of these experiments, a revised mechanism for CysS is proposed.
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Affiliation(s)
- Yuanyou Wang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Tadhg P Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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14
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Wang SC. Cobalamin-dependent radical S-adenosyl-l-methionine enzymes in natural product biosynthesis. Nat Prod Rep 2019; 35:707-720. [PMID: 30079906 DOI: 10.1039/c7np00059f] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Covering: 2011 to 2018 This highlight summarizes the investigation of cobalamin (Cbl)- and radical S-adenosyl-l-methionine (SAM)-dependent enzymes found in natural product biosynthesis to date and suggests some possibilities for the future. Though some mechanistic aspects are apparently shared, the overall diversity of this family's functions and abilities is significant and may be tailored to the specific substrate and/or reaction being catalyzed. A little over a year ago, the first crystal structure of a Cbl- and radical SAM-dependent enzyme was solved, providing the first insight into what may be the shared scaffolding of these enzymes.
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Affiliation(s)
- Susan C Wang
- Case Western Reserve University School of Medicine, Department of Biochemistry, USA.
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15
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Radle MI, Miller DV, Laremore TN, Booker SJ. Methanogenesis marker protein 10 (Mmp10) from Methanosarcina acetivorans is a radical S-adenosylmethionine methylase that unexpectedly requires cobalamin. J Biol Chem 2019; 294:11712-11725. [PMID: 31113866 DOI: 10.1074/jbc.ra119.007609] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/10/2019] [Indexed: 11/06/2022] Open
Abstract
Methyl coenzyme M reductase (MCR) catalyzes the last step in the biological production of methane by methanogenic archaea, as well as the first step in the anaerobic oxidation of methane to methanol by methanotrophic archaea. MCR contains a number of unique post-translational modifications in its α subunit, including thioglycine, 1-N-methylhistidine, S-methylcysteine, 5-C-(S)-methylarginine, and 2-C-(S)-methylglutamine. Recently, genes responsible for the thioglycine and methylarginine modifications have been identified in bioinformatics studies and in vivo complementation of select mutants; however, none of these reactions has been verified in vitro Herein, we purified and biochemically characterized the radical S-adenosylmethionine (SAM) protein MaMmp10, the product of the methanogenesis marker protein 10 gene in the methane-producing archaea Methanosarcina acetivorans Using an array of approaches, including kinetic assays, LC-MS-based quantification, and MALDI TOF-TOF MS analyses, we found that MaMmp10 catalyzes the methylation of the equivalent of Arg285 in a peptide substrate surrogate, but only in the presence of cobalamin. We noted that the methyl group derives from SAM, with cobalamin acting as an intermediate carrier, and that MaMmp10 contains a C-terminal cobalamin-binding domain. Given that Mmp10 has not been annotated as a cobalamin-binding protein, these findings suggest that cobalamin-dependent radical SAM proteins are more prevalent than previously thought.
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Affiliation(s)
- Matthew I Radle
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Danielle V Miller
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Tatiana N Laremore
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Squire J Booker
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802 .,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802.,Howard Hughes Medical Institute, Pennsylvania State University, University Park, Pennsylvania 16802
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Biocatalytic hydrogen atom transfer: an invigorating approach to free-radical reactions. Curr Opin Chem Biol 2018; 49:16-24. [PMID: 30269010 DOI: 10.1016/j.cbpa.2018.09.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 09/02/2018] [Indexed: 10/28/2022]
Abstract
Initiating and terminating free-radical reactionis via hydrogen atom transfer (HAT) is an attractive means of avoiding substrate prefunctionalization. Small molecule catalysts and reagents, however, struggle to execute this fundamental step with useful levels of diastereoselectivity and enantioselectivity. In contrast, nature often carries out HAT with exquisite levels of selectivity for even electronically unactivated carbon-hydrogen bonds. By understanding how enzymes exploit and control this fundamental step, new strategies can be developed to address several long-standing challenges in free-radical reactions. This review will cover recent discoveries in biocatalysis that exploit a HAT mechanism to either initiate or terminate novel one-electron reactions.
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Wang B, Blaszczyk A, Knox HL, Zhou S, Blaesi EJ, Krebs C, Wang RX, Booker SJ. Stereochemical and Mechanistic Investigation of the Reaction Catalyzed by Fom3 from Streptomyces fradiae, a Cobalamin-Dependent Radical S-Adenosylmethionine Methylase. Biochemistry 2018; 57:4972-4984. [PMID: 30036047 PMCID: PMC6554712 DOI: 10.1021/acs.biochem.8b00693] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Fom3, a cobalamin-dependent radical S-adenosylmethionine (SAM) methylase, has recently been shown to catalyze the methylation of carbon 2″ of cytidylyl-2-hydroxyethylphosphonate (HEP-CMP) to form cytidylyl-2-hydroxypropylphosphonate (HPP-CMP) during the biosynthesis of fosfomycin, a broad-spectrum antibiotic. It has been hypothesized that a 5'-deoxyadenosyl 5'-radical (5'-dA•) generated from the reductive cleavage of SAM abstracts a hydrogen atom from HEP-CMP to prime the substrate for addition of a methyl group from methylcobalamin (MeCbl); however, the mechanistic details of this reaction remain elusive. Moreover, it has been reported that Fom3 catalyzes the methylation of HEP-CMP to give a mixture of the ( S)-HPP and ( R)-HPP stereoisomers, which is rare for an enzyme-catalyzed reaction. Herein, we describe a detailed biochemical investigation of a Fom3 that is purified with 1 equiv of its cobalamin cofactor bound, which is almost exclusively in the form of MeCbl. Electron paramagnetic resonance and Mössbauer spectroscopies confirm that Fom3 contains one [4Fe-4S] cluster. Using deuterated enantiomers of HEP-CMP, we demonstrate that the 5'-dA• generated by Fom3 abstracts the C2″- pro-R hydrogen of HEP-CMP and that methyl addition takes place with inversion of configuration to yield solely ( S)-HPP-CMP. Fom3 also sluggishly converts cytidylyl-ethylphosphonate to the corresponding methylated product but more readily acts on cytidylyl-2-fluoroethylphosphonate, which exhibits a lower C2″ homolytic bond-dissociation energy. Our studies suggest a mechanism in which the substrate C2″ radical, generated upon hydrogen atom abstraction by the 5'-dA•, directly attacks MeCbl to transfer a methyl radical (CH3•) rather than a methyl cation (CH3+), directly forming cob(II)alamin in the process.
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Affiliation(s)
- Bo Wang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Anthony Blaszczyk
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Hayley L. Knox
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Shengbin Zhou
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Elizabeth J. Blaesi
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Roy X. Wang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Squire J. Booker
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Howard Hughes Medical Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Sato S, Miyanaga A, Kim SY, Kuzuyama T, Kudo F, Eguchi T. Biochemical and Structural Analysis of FomD That Catalyzes the Hydrolysis of Cytidylyl ( S)-2-Hydroxypropylphosphonate in Fosfomycin Biosynthesis. Biochemistry 2018; 57:4858-4866. [PMID: 30010320 DOI: 10.1021/acs.biochem.8b00690] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In fosfomycin biosynthesis, the hydrolysis of cytidylyl ( S)-2-hydroxypropylphosphonate [( S)-HPP-CMP] to afford ( S)-HPP is the only uncharacterized step. Because FomD is an uncharacterized protein with a DUF402 domain that is encoded in the fosfomycin biosynthetic gene cluster, FomD was hypothesized to be responsible for this reaction. In this study, FomD was found to hydrolyze ( S)-HPP-CMP to give ( S)-HPP and CMP efficiently in the presence of Mn2+ or Co2+. FomD also hydrolyzed cytidylyl 2-hydroxyethylphosphonate (HEP-CMP), which is a biosynthetic intermediate before C-methylation. The kcat/ KM value of FomD with ( S)-HPP-CMP was 10-fold greater than that with HEP-CMP, suggesting that FomD hydrolyzes ( S)-HPP-CMP rather than HEP-CMP in bacteria. The crystal structure of FomD showed that this protein adopts a barrel-like fold, which consists of a large twisted antiparallel β-sheet. This is a key structural feature of the DUF402 domain-containing proteins. Two metal cations are located between the FomD barrel and the two α-helices at the C-terminus and serve to presumably activate the phosphonate group of substrates for hydrolysis. Docking simulations with ( S)-HPP-CMP suggested that the methyl group at the C2 position of the HPP moiety is recognized by a hydrophobic interaction with Trp68. Further mutational analysis suggested that a conserved Tyr107 among the DUF402 domain family of proteins activates a water molecule to promote nucleophilic attack on the phosphorus atom of the phosphonate moiety. These findings provide mechanistic insights into the FomD reaction and lead to a complete understanding of the fosfomycin biosynthetic pathway in Streptomyces.
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Affiliation(s)
- Shusuke Sato
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1 O-okayama , Meguro-ku, Tokyo 152-8551 , Japan
| | - Akimasa Miyanaga
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1 O-okayama , Meguro-ku, Tokyo 152-8551 , Japan
| | | | | | - Fumitaka Kudo
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1 O-okayama , Meguro-ku, Tokyo 152-8551 , Japan
| | - Tadashi Eguchi
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1 O-okayama , Meguro-ku, Tokyo 152-8551 , Japan
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Iterative Methylations Resulting in the Biosynthesis of the t-Butyl Group Catalyzed by a B 12-Dependent Radical SAM Enzyme in Cystobactamid Biosynthesis. Methods Enzymol 2018; 606:199-216. [PMID: 30097093 DOI: 10.1016/bs.mie.2018.05.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
B12-dependent radical SAM enzymes that can perform methylations on sp3 carbon centers are important for functional diversity and regulation of biological activity in several nonribosomal peptides. Detailed studies on these enzymes are hindered by the complexity of the substrates and low levels of expression of active enzymes. CysS can catalyze iterative methylations of a methoxybenzene moiety during the biosynthesis of the cystobactamids. Here, we describe the overexpression, purification, substrate identification, and mechanism of this enzyme.
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Abstract
The Natural Product Reports themed issue on ‘Metalloenzymes in natural product biosynthetic pathways’ is introduced by the Guest Editors, Katherine Ryan and Catherine Drennan.
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Affiliation(s)
- Katherine S Ryan
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, BC, CanadaV6T 1Z1.
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