1
|
Shomar H, Bokinsky G. Harnessing iron‑sulfur enzymes for synthetic biology. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119718. [PMID: 38574823 DOI: 10.1016/j.bbamcr.2024.119718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
Reactions catalysed by iron-sulfur (Fe-S) enzymes appear in a variety of biosynthetic pathways that produce valuable natural products. Harnessing these biosynthetic pathways by expression in microbial cell factories grown on an industrial scale would yield enormous economic and environmental benefits. However, Fe-S enzymes often become bottlenecks that limits the productivity of engineered pathways. As a consequence, achieving the production metrics required for industrial application remains a distant goal for Fe-S enzyme-dependent pathways. Here, we identify and review three core challenges in harnessing Fe-S enzyme activity, which all stem from the properties of Fe-S clusters: 1) limited Fe-S cluster supply within the host cell, 2) Fe-S cluster instability, and 3) lack of specialized reducing cofactor proteins often required for Fe-S enzyme activity, such as enzyme-specific flavodoxins and ferredoxins. We highlight successful methods developed for a variety of Fe-S enzymes and electron carriers for overcoming these difficulties. We use heterologous nitrogenase expression as a grand case study demonstrating how each of these challenges can be addressed. We predict that recent breakthroughs in protein structure prediction and design will prove well-suited to addressing each of these challenges. A reliable toolkit for harnessing Fe-S enzymes in engineered metabolic pathways will accelerate the development of industry-ready Fe-S enzyme-dependent biosynthesis pathways.
Collapse
Affiliation(s)
- Helena Shomar
- Institut Pasteur, université Paris Cité, Inserm U1284, Diversité moléculaire des microbes (Molecular Diversity of Microbes lab), 75015 Paris, France
| | - Gregory Bokinsky
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
| |
Collapse
|
2
|
Abstract
Covering: from 2000 up to the very early part of 2023S-Adenosyl-L-methionine (SAM) is a naturally occurring trialkyl sulfonium molecule that is typically associated with biological methyltransfer reactions. However, SAM is also known to donate methylene, aminocarboxypropyl, adenosyl and amino moieties during natural product biosynthetic reactions. The reaction scope is further expanded as SAM itself can be modified prior to the group transfer such that a SAM-derived carboxymethyl or aminopropyl moiety can also be transferred. Moreover, the sulfonium cation in SAM has itself been found to be critical for several other enzymatic transformations. Thus, while many SAM-dependent enzymes are characterized by a methyltransferase fold, not all of them are necessarily methyltransferases. Furthermore, other SAM-dependent enzymes do not possess such a structural feature suggesting diversification along different evolutionary lineages. Despite the biological versatility of SAM, it nevertheless parallels the chemistry of sulfonium compounds used in organic synthesis. The question thus becomes how enzymes catalyze distinct transformations via subtle differences in their active sites. This review summarizes recent advances in the discovery of novel SAM utilizing enzymes that rely on Lewis acid/base chemistry as opposed to radical mechanisms of catalysis. The examples are categorized based on the presence of a methyltransferase fold and the role played by SAM within the context of known sulfonium chemistry.
Collapse
Affiliation(s)
- Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Daan Ren
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Byungsun Jeon
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
3
|
Cheng B, Huang J, Duan Y, Liu W. Association of Radical Chemistry with LanD Flavoprotein Activity for C-Terminal Macrocyclization of a Ribosomal Peptide by Formation of an Unsaturated Thioether Residue. Angew Chem Int Ed Engl 2023; 62:e202308733. [PMID: 37431841 DOI: 10.1002/anie.202308733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/12/2023]
Abstract
LanD flavoproteins catalyze oxidative decarboxylation of the C-terminal Cys residue of a peptide to produce an enethiol. This enethiol is highly reactive and can be coupled with an upstream dehydroamino acid through Michael addition to form S-[2-aminovinyl](3-methyl)cysteine, an unsaturated thioether residue known to be characteristic of an array of C-terminally macrocyclized, ribosomally synthesized and posttranslationally modified peptides (RiPPs). Based on a two-stage bioinformatics mining of posttranslational modifications (PTMs) related to C-terminal Cys processing, we report herein that LanD activity can couple with radical S-adenosylmethionine chemistry to provide a new unsaturated thioether residue, S-[2-aminovinyl]-3-carbamoylcysteine, by conjugating the resultant enethiol with Cβ of the Asn residue in the C-terminal NxxC motif of a peptide for macrocyclization. This study furthers our understanding of the variety of PTMs involved in creating the structure diversity of macrocyclic RiPPs.
Collapse
Affiliation(s)
- Botao Cheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Jiwu Huang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Yuting Duan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| |
Collapse
|
4
|
Booker SJ, Lloyd CT. Twenty Years of Radical SAM! The Genesis of the Superfamily. ACS BIO & MED CHEM AU 2022; 2:538-547. [PMID: 37101427 PMCID: PMC10114671 DOI: 10.1021/acsbiomedchemau.2c00078] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Indexed: 12/10/2022]
Affiliation(s)
- Squire J Booker
- Departments of Chemistry, and of Biochemistry and Molecular Biology, and the Howard Hughes Medical Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Cody T Lloyd
- Departments of Chemistry, and of Biochemistry and Molecular Biology, and the Howard Hughes Medical Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
5
|
Wang S, Cheng Y, Wang X, Yang Q, Liu W. Tracing of Acyl Carrier Protein-channeled Mitomycin Intermediates in Streptomyces caespitosus Facilitates Characterization of the Biosynthetic Steps for AHBA-GlcN Formation and Processing. J Am Chem Soc 2022; 144:14945-14956. [PMID: 35943208 DOI: 10.1021/jacs.2c06969] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mitomycins are a family of naturally occurring, potent alkylating agents in which the C member has been clinically used for cancer chemotherapy for over 5 decades. In Streptomyces caespitosus, mitomycins are derived from an N-glycoside composed of a 3-amino-5-hydroxybenzoic acid (AHBA) unit and a d-glucosamine (GlcN) unit; however, how this N-glycoside is formed and rearranged to a mitosane, for example, the compact polycyclic ring system of mitomycin C, remains elusive. Benefiting from the development of a method used to trace the mitomycin intermediates that accumulate on an acyl carrier protein (ACP), we here dissect the enzymatic steps for AHBA-GlcN formation and processing to underlie the mitosane structure. Following the N-glycosylation of AHBA with activated N-acetyl-GlcN, deacetylation occurs on ACP to provide AHBA-GlcN. Then, the sugar portion of this N-glycoside is transformed into a linear aminodiol that terminates with an epoxyethane, yielding an ACP-channeled intermediate that is ready for mitosane formation through crosslinking between the AHBA and linearized sugar units. This transformation is unusual and relies on the functional association of a dihydronicotinamide adenine dinucleotide (phosphate)-dependent protein with a radical S-adenosyl-l-methionine protein. Characterization of these ACP-based enzymatic steps for AHBA-GlcN formation and processing sheds light on the poorly understood biosynthetic pathway of mitomycins.
Collapse
Affiliation(s)
- Sili Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yiyuan Cheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xiaofeng Wang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China
| | - Qian Yang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| |
Collapse
|
6
|
Knox HL, Booker SJ. Structural characterization of cobalamin-dependent radical S-adenosylmethionine methylases. Methods Enzymol 2022; 669:3-27. [PMID: 35644177 DOI: 10.1016/bs.mie.2021.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cobalamin-dependent radical S-adenosylmethionine (SAM) methylases catalyze key steps in the biosynthesis of numerous biomolecules, including protein cofactors, antibiotics, herbicides, and other natural products, but have remained a relatively understudied subclass of radical SAM enzymes due to their inherent insolubility upon overproduction in Escherichia coli. These enzymes contain two cofactors: a [4Fe-4S] cluster that is ligated by three cysteine residues, and a cobalamin cofactor typically bound by residues in the N-terminal portion of the enzyme. Recent advances in the expression and purification of these enzymes in their active states and with both cofactors present has allowed for more detailed biochemical studies as well as structure determination by X-ray crystallography. Herein, we use KsTsrM and TokK to highlight methods for the structural characterization of cobalamin-dependent radical SAM (RS) enzymes and describe recent advances in in the overproduction and purification of these enzymes.
Collapse
Affiliation(s)
- Hayley L Knox
- The Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Squire J Booker
- The Department of Chemistry, The Pennsylvania State University, University Park, PA, United States; The Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States; The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, United States.
| |
Collapse
|
7
|
Unusual structures and unknown roles of FeS clusters in metalloenzymes seen from a resonance Raman spectroscopic perspective. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214287] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
8
|
Biochemical Approaches to Probe the Role of the Auxiliary Iron-Sulfur Cluster of Lipoyl Synthase from Mycobacterium Tuberculosis. Methods Mol Biol 2021. [PMID: 34292556 DOI: 10.1007/978-1-0716-1605-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Lipoic acid is an essential sulfur-containing cofactor used by several multienzyme complexes involved in energy metabolism and the breakdown of certain amino acids. It is composed of n-octanoic acid with sulfur atoms appended at C6 and C8. Lipoic acid is biosynthesized de novo in its cofactor form, in which it is covalently bound in an amide linkage to a target lysyl residue on a lipoyl carrier protein (LCP). The n-octanoyl moiety of the cofactor is derived from type 2 fatty acid biosynthesis and is transferred to an LCP to afford an octanoyllysyl amino acid. Next, lipoyl synthase (LipA in bacteria) catalyzes the attachment of the two sulfur atoms to afford the intact cofactor. LipA is a radical S-adenosylmethionine (SAM) enzyme that contains two [4Fe-4S] clusters. One [4Fe-4S] cluster is used to facilitate a reductive cleavage of SAM to render the highly oxidizing 5'-deoxyadenosyl 5'-radical needed to abstract C6 and C8 hydrogen atoms to allow for sulfur attachment. By contrast, the second cluster is the sulfur source, necessitating its destruction during turnover. In Escherichia coli, this auxiliary cluster can be restored after each turnover by NfuA or IscU, which are two iron-sulfur cluster carrier proteins that are implicated in iron-sulfur cluster biogenesis. In this chapter, we describe methods for purifying and characterizing LipA and NfuA from Mycobacterium tuberculosis, a human pathogen for which endogenously synthesized lipoic acid is essential. These studies provide the foundation for assessing lipoic acid biosynthesis as a potential target for the design of novel antituberculosis agents.
Collapse
|
9
|
Ye Y, Fu H, Hyster TK. Activation modes in biocatalytic radical cyclization reactions. J Ind Microbiol Biotechnol 2021; 48:kuab021. [PMID: 33674826 PMCID: PMC8210684 DOI: 10.1093/jimb/kuab021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/26/2021] [Indexed: 12/17/2022]
Abstract
Radical cyclizations are essential reactions in the biosynthesis of secondary metabolites and the chemical synthesis of societally valuable molecules. In this review, we highlight the general mechanisms utilized in biocatalytic radical cyclizations. We specifically highlight cytochrome P450 monooxygenases (P450s) involved in the biosynthesis of mycocyclosin and vancomycin, nonheme iron- and α-ketoglutarate-dependent dioxygenases (Fe/αKGDs) used in the biosynthesis of kainic acid, scopolamine, and isopenicillin N, and radical S-adenosylmethionine (SAM) enzymes that facilitate the biosynthesis of oxetanocin A, menaquinone, and F420. Beyond natural mechanisms, we also examine repurposed flavin-dependent "ene"-reductases (ERED) for non-natural radical cyclization. Overall, these general mechanisms underscore the opportunity for enzymes to augment and enhance the synthesis of complex molecules using radical mechanisms.
Collapse
Affiliation(s)
- Yuxuan Ye
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Haigen Fu
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Todd K Hyster
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| |
Collapse
|
10
|
Mordhorst S, Andexer JN. Round, round we go - strategies for enzymatic cofactor regeneration. Nat Prod Rep 2020; 37:1316-1333. [PMID: 32582886 DOI: 10.1039/d0np00004c] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: up to the beginning of 2020Enzymes depending on cofactors are essential in many biosynthetic pathways of natural products. They are often involved in key steps: catalytic conversions that are difficult to achieve purely with synthetic organic chemistry. Hence, cofactor-dependent enzymes have great potential for biocatalysis, on the condition that a corresponding cofactor regeneration system is available. For some cofactors, these regeneration systems require multiple steps; such complex enzyme cascades/multi-enzyme systems are (still) challenging for in vitro biocatalysis. Further, artificial cofactor analogues have been synthesised that are more stable, show an altered reaction range, or act as inhibitors. The development of bio-orthogonal systems that can be used for the production of modified natural products in vivo is an ongoing challenge. In light of the recent progress in this field, this review aims to provide an overview of general strategies involving enzyme cofactors, cofactor analogues, and regeneration systems; highlighting the current possibilities for application of enzymes using some of the most common cofactors.
Collapse
Affiliation(s)
- Silja Mordhorst
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | | |
Collapse
|
11
|
Jungen S, Chen P. Alkyl Radical Generation by an Intramolecular Homolytic Substitution Reaction between Iron(II) and Trialkylsulfonium Groups. Chemistry 2018; 24:11008-11020. [PMID: 29768681 DOI: 10.1002/chem.201801952] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/15/2018] [Indexed: 11/08/2022]
Abstract
Intramolecular, homolytic substitution reactions between iron(II) species and various trialkylsulfonium groups were directly observed in the gas phase upon collision-induced dissociation. In spite of the notoriously low reduction potential of trialkylsulfonium species and the mismatched oxidation potential of iron(II), the reactions proceed at moderate collision energies, forming an alkyl radical as well as a thioether coordinated to the iron. In contrast to classical homolytic substitutions, the attacking radical is a "metalloradical", namely iron(II) that is oxidized to iron(III) during the reaction. With this process we demonstrate that the conceptually analogous, putative radical generation step in radical S-adenosyl methionine (SAM) enzymes is possible and plausible. Further, we show that this kind of reaction only occurs in constrained systems with a defined geometry. Combining experimental measurements with DFT studies and NBO analyses allowed us to gain insights into the reactivity and transition states of these systems. Based on our findings, we challenge the notion of a collinear transition state in the radical generation step of radical SAM enzymes and propose it to be bent instead.
Collapse
Affiliation(s)
- Stefan Jungen
- Laboratorium für Organische Chemie, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Peter Chen
- Laboratorium für Organische Chemie, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| |
Collapse
|
12
|
Maio N, Rouault TA. Mammalian Fe-S proteins: definition of a consensus motif recognized by the co-chaperone HSC20. Metallomics 2017; 8:1032-1046. [PMID: 27714045 DOI: 10.1039/c6mt00167j] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Iron-sulfur (Fe-S) clusters are inorganic cofactors that are fundamental to several biological processes in all three kingdoms of life. In most organisms, Fe-S clusters are initially assembled on a scaffold protein, ISCU, and subsequently transferred to target proteins or to intermediate carriers by a dedicated chaperone/co-chaperone system. The delivery of assembled Fe-S clusters to recipient proteins is a crucial step in the biogenesis of Fe-S proteins, and, in mammals, it relies on the activity of a multiprotein transfer complex that contains the chaperone HSPA9, the co-chaperone HSC20 and the scaffold ISCU. How the transfer complex efficiently engages recipient Fe-S target proteins involves specific protein interactions that are not fully understood. This mini review focuses on recent insights into the molecular mechanism of amino acid motif recognition and discrimination by the co-chaperone HSC20, which guides Fe-S cluster delivery.
Collapse
Affiliation(s)
- N Maio
- Molecular Medicine Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, 20892 Bethesda, MD, USA.
| | - T A Rouault
- Molecular Medicine Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, 20892 Bethesda, MD, USA.
| |
Collapse
|
13
|
Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part I. [4Fe-4S] + [2Fe-2S] iron-sulfur proteins. J Struct Biol 2017; 200:1-19. [DOI: 10.1016/j.jsb.2017.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/25/2017] [Indexed: 01/08/2023]
|
14
|
Abstract
Oxidative cyclizations are important transformations that occur widely during natural product biosynthesis. The transformations from acyclic precursors to cyclized products can afford morphed scaffolds, structural rigidity, and biological activities. Some of the most dramatic structural alterations in natural product biosynthesis occur through oxidative cyclization. In this Review, we examine the different strategies used by nature to create new intra(inter)molecular bonds via redox chemistry. This Review will cover both oxidation- and reduction-enabled cyclization mechanisms, with an emphasis on the former. Radical cyclizations catalyzed by P450, nonheme iron, α-KG-dependent oxygenases, and radical SAM enzymes are discussed to illustrate the use of molecular oxygen and S-adenosylmethionine to forge new bonds at unactivated sites via one-electron manifolds. Nonradical cyclizations catalyzed by flavin-dependent monooxygenases and NAD(P)H-dependent reductases are covered to show the use of two-electron manifolds in initiating cyclization reactions. The oxidative installations of epoxides and halogens into acyclic scaffolds to drive subsequent cyclizations are separately discussed as examples of "disappearing" reactive handles. Last, oxidative rearrangement of rings systems, including contractions and expansions, will be covered.
Collapse
Affiliation(s)
- Man-Cheng Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Yi Zou
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA 94305
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| |
Collapse
|
15
|
Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
16
|
Sommer-Kamann C, Fries A, Mordhorst S, Andexer JN, Müller M. Asymmetric C-Alkylation by the S
-Adenosylmethionine-Dependent Methyltransferase SgvM. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609375] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Christina Sommer-Kamann
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Alexander Fries
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Silja Mordhorst
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Jennifer N. Andexer
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Michael Müller
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
| |
Collapse
|
17
|
Sommer-Kamann C, Fries A, Mordhorst S, Andexer JN, Müller M. Asymmetric C-Alkylation by the S-Adenosylmethionine-Dependent Methyltransferase SgvM. Angew Chem Int Ed Engl 2017; 56:4033-4036. [PMID: 28247461 DOI: 10.1002/anie.201609375] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 11/13/2016] [Indexed: 11/06/2022]
Abstract
S-Adenosylmethionine-dependent methyltransferases (MTs) play a decisive role in the biosynthesis of natural products and in epigenetic processes. MTs catalyze the methylation of heteroatoms and even of carbon atoms, which, in many cases, is a challenging reaction in conventional synthesis. However, C-MTs are often highly substrate-specific. Herein, we show that SgvM from Streptomyces griseoviridis features an extended substrate scope with respect to the nucleophile as well as the electrophile. Aside from its physiological substrate 4-methyl-2-oxovalerate, SgvM catalyzes the (di)methylation of pyruvate, 2-oxobutyrate, 2-oxovalerate, and phenylpyruvate at the β-carbon atom. Chiral-phase HPLC analysis revealed that the methylation of 2-oxovalerate occurs with R selectivity while the ethylation of 2-oxobutyrate with S-adenosylethionine results in the S enantiomer of 3-methyl-2-oxovalerate. Thus SgvM could be a valuable tool for asymmetric biocatalytic C-alkylation reactions.
Collapse
Affiliation(s)
- Christina Sommer-Kamann
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Alexander Fries
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Silja Mordhorst
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Jennifer N Andexer
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Michael Müller
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| |
Collapse
|
18
|
Khaliullin B, Aggarwal P, Bubas M, Eaton GR, Eaton SS, Latham JA. Mycofactocin biosynthesis: modification of the peptide MftA by the radical S-adenosylmethionine protein MftC. FEBS Lett 2016; 590:2538-48. [DOI: 10.1002/1873-3468.12249] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/01/2016] [Accepted: 06/05/2016] [Indexed: 02/04/2023]
Affiliation(s)
- Bulat Khaliullin
- Department of Chemistry and Biochemistry; University of Denver; CO USA
| | - Priyanka Aggarwal
- Department of Chemistry and Biochemistry; University of Denver; CO USA
| | - Michael Bubas
- Department of Chemistry and Biochemistry; University of Denver; CO USA
| | - Gareth R. Eaton
- Department of Chemistry and Biochemistry; University of Denver; CO USA
| | - Sandra S. Eaton
- Department of Chemistry and Biochemistry; University of Denver; CO USA
| | - John A. Latham
- Department of Chemistry and Biochemistry; University of Denver; CO USA
| |
Collapse
|
19
|
Abstract
Radical S-adenosylmethionine (SAM) enzymes catalyze an astonishing array of complex and chemically challenging reactions across all domains of life. Of approximately 114,000 of these enzymes, 8 are known to be present in humans: MOCS1, molybdenum cofactor biosynthesis; LIAS, lipoic acid biosynthesis; CDK5RAP1, 2-methylthio-N(6)-isopentenyladenosine biosynthesis; CDKAL1, methylthio-N(6)-threonylcarbamoyladenosine biosynthesis; TYW1, wybutosine biosynthesis; ELP3, 5-methoxycarbonylmethyl uridine; and RSAD1 and viperin, both of unknown function. Aberrations in the genes encoding these proteins result in a variety of diseases. In this review, we summarize the biochemical characterization of these 8 radical S-adenosylmethionine enzymes and, in the context of human health, describe the deleterious effects that result from such genetic mutations.
Collapse
Affiliation(s)
- Bradley J Landgraf
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Erin L McCarthy
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Squire J Booker
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802.,The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, Pennsylvania 16802;
| |
Collapse
|
20
|
Blaszczyk AJ, Silakov A, Zhang B, Maiocco SJ, Lanz ND, Kelly WL, Elliott SJ, Krebs C, Booker SJ. Spectroscopic and Electrochemical Characterization of the Iron-Sulfur and Cobalamin Cofactors of TsrM, an Unusual Radical S-Adenosylmethionine Methylase. J Am Chem Soc 2016; 138:3416-26. [PMID: 26841310 DOI: 10.1021/jacs.5b12592] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
TsrM, an annotated radical S-adenosylmethionine (SAM) enzyme, catalyzes the methylation of carbon 2 of the indole ring of L-tryptophan. Its reaction is the first step in the biosynthesis of the unique quinaldic acid moiety of thiostrepton A, a thiopeptide antibiotic. The appended methyl group derives from SAM; however, the enzyme also requires cobalamin and iron-sulfur cluster cofactors for turnover. In this work we report the overproduction and purification of TsrM and the characterization of its metallocofactors by UV-visible, electron paramagnetic resonance, hyperfine sublevel correlation (HYSCORE), and Mössbauer spectroscopies as well as protein-film electrochemistry (PFE). The enzyme contains 1 equiv of its cobalamin cofactor in its as-isolated state and can be reconstituted with iron and sulfide to contain one [4Fe-4S] cluster with a site-differentiated Fe(2+)/Fe(3+) pair. Our spectroscopic studies suggest that TsrM binds cobalamin in an uncharacteristic five-coordinate base-off/His-off conformation, whereby the dimethylbenzimidazole group is replaced by a non-nitrogenous ligand, which is likely a water molecule. Electrochemical analysis of the protein by PFE indicates a one-electron redox feature with a midpoint potential of -550 mV, which is assigned to a [4Fe-4S](2+)/[4Fe-4S](+) redox couple. Analysis of TsrM by Mössbauer and HYSCORE spectroscopies suggests that SAM does not bind to the unique iron site of the cluster in the same manner as in other radical SAM (RS) enzymes, yet its binding still perturbs the electronic configuration of both the Fe/S cluster and the cob(II)alamin cofactors. These biophysical studies suggest that TsrM is an atypical RS enzyme, consistent with its reported inability to catalyze formation of a 5'-deoxyadenosyl 5'-radical.
Collapse
Affiliation(s)
| | | | | | - Stephanie J Maiocco
- Department of Chemistry, Boston University , 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | | | - Wendy L Kelly
- School of Chemistry and Biochemistry and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Sean J Elliott
- Department of Chemistry, Boston University , 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | | | | |
Collapse
|
21
|
Lanz ND, Booker SJ. Auxiliary iron-sulfur cofactors in radical SAM enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1316-34. [PMID: 25597998 DOI: 10.1016/j.bbamcr.2015.01.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/15/2014] [Accepted: 01/06/2015] [Indexed: 11/19/2022]
Abstract
A vast number of enzymes are now known to belong to a superfamily known as radical SAM, which all contain a [4Fe-4S] cluster ligated by three cysteine residues. The remaining, unligated, iron ion of the cluster binds in contact with the α-amino and α-carboxylate groups of S-adenosyl-l-methionine (SAM). This binding mode facilitates inner-sphere electron transfer from the reduced form of the cluster into the sulfur atom of SAM, resulting in a reductive cleavage of SAM to methionine and a 5'-deoxyadenosyl radical. The 5'-deoxyadenosyl radical then abstracts a target substrate hydrogen atom, initiating a wide variety of radical-based transformations. A subset of radical SAM enzymes contains one or more additional iron-sulfur clusters that are required for the reactions they catalyze. However, outside of a subset of sulfur insertion reactions, very little is known about the roles of these additional clusters. This review will highlight the most recent advances in the identification and characterization of radical SAM enzymes that harbor auxiliary iron-sulfur clusters. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
Collapse
Affiliation(s)
- Nicholas D Lanz
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States; Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States.
| |
Collapse
|
22
|
Wang J, Woldring RP, Román-Meléndez GD, McClain AM, Alzua BR, Marsh ENG. Recent advances in radical SAM enzymology: new structures and mechanisms. ACS Chem Biol 2014; 9:1929-38. [PMID: 25009947 PMCID: PMC4168785 DOI: 10.1021/cb5004674] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
The radical S-adenosylmethionine
(SAM) superfamily of enzymes catalyzes
an amazingly diverse variety of reactions ranging from simple hydrogen
abstraction to complicated multistep rearrangements and insertions.
The reactions they catalyze are important for a broad range of biological
functions, including cofactor and natural product biosynthesis, DNA
repair, and tRNA modification. Generally conserved features of the
radical SAM superfamily include a CX3CX2C motif
that binds an [Fe4S4] cluster essential for
the reductive cleavage of SAM. Here, we review recent advances in
our understanding of the structure and mechanisms of these enzymes
that, in some cases, have overturned widely accepted mechanisms.
Collapse
Affiliation(s)
- Jiarui Wang
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Rory P. Woldring
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Alan M. McClain
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brian R. Alzua
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - E. Neil G. Marsh
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
23
|
Brown LJ, Baranowski M, Wang Y, Schrey AK, Lenz T, Taverna SD, Cole PA, Sefkow M. Using S-adenosyl-L-homocysteine capture compounds to characterize S-adenosyl-L-methionine and S-adenosyl-L-homocysteine binding proteins. Anal Biochem 2014; 467:14-21. [PMID: 25172130 DOI: 10.1016/j.ab.2014.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 08/12/2014] [Accepted: 08/14/2014] [Indexed: 11/18/2022]
Abstract
S-Adenosyl-l-methionine (SAM) is recognized as an important cofactor in a variety of biochemical reactions. As more proteins and pathways that require SAM are discovered, it is important to establish a method to quickly identify and characterize SAM binding proteins. The affinity of S-adenosyl-l-homocysteine (SAH) for SAM binding proteins was used to design two SAH-derived capture compounds (CCs). We demonstrate interactions of the proteins COMT and SAHH with SAH-CC with biotin used in conjunction with streptavidin-horseradish peroxidase. After demonstrating SAH-dependent photo-crosslinking of the CC to these proteins, we used a CC labeled with a fluorescein tag to measure binding affinity via fluorescence anisotropy. We then used this approach to show and characterize binding of SAM to the PR domain of PRDM2, a lysine methyltransferase with putative tumor suppressor activity. We calculated the Kd values for COMT, SAHH, and PRDM2 (24.1 ± 2.2 μM, 6.0 ± 2.9 μM, and 10.06 ± 2.87 μM, respectively) and found them to be close to previously established Kd values of other SAM binding proteins. Here, we present new methods to discover and characterize SAM and SAH binding proteins using fluorescent CCs.
Collapse
Affiliation(s)
- Lindsey J Brown
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Yun Wang
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Thomas Lenz
- Caprotec Bioanalytics, 12489 Berlin, Germany
| | - Sean D Taverna
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Philip A Cole
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | | |
Collapse
|
24
|
Hiratsuka T, Suzuki H, Kariya R, Seo T, Minami A, Oikawa H. Biosynthesis of the Structurally Unique Polycyclopropanated Polyketide-Nucleoside Hybrid Jawsamycin (FR-900848). Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
25
|
Hiratsuka T, Suzuki H, Kariya R, Seo T, Minami A, Oikawa H. Biosynthesis of the Structurally Unique Polycyclopropanated Polyketide-Nucleoside Hybrid Jawsamycin (FR-900848). Angew Chem Int Ed Engl 2014; 53:5423-6. [DOI: 10.1002/anie.201402623] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Indexed: 02/06/2023]
|
26
|
Driesener RC, Duffus BR, Shepard EM, Bruzas IR, Duschene KS, Coleman NJR, Marrison APG, Salvadori E, Kay CWM, Peters JW, Broderick JB, Roach PL. Biochemical and kinetic characterization of radical S-adenosyl-L-methionine enzyme HydG. Biochemistry 2013; 52:8696-707. [PMID: 24206022 DOI: 10.1021/bi401143s] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The radical S-adenosyl-L-methionine (AdoMet) enzyme HydG is one of three maturase enzymes involved in [FeFe]-hydrogenase H-cluster assembly. It catalyzes L-tyrosine cleavage to yield the H-cluster cyanide and carbon monoxide ligands as well as p-cresol. Clostridium acetobutylicum HydG contains the conserved CX3CX2C motif coordinating the AdoMet binding [4Fe-4S] cluster and a C-terminal CX2CX22C motif proposed to coordinate a second [4Fe-4S] cluster. To improve our understanding of the roles of each of these iron-sulfur clusters in catalysis, we have generated HydG variants lacking either the N- or C-terminal cluster and examined these using spectroscopic and kinetic methods. We have used iron analyses, UV-visible spectroscopy, and electron paramagnetic resonance (EPR) spectroscopy of an N-terminal C96/100/103A triple HydG mutant that cannot coordinate the radical AdoMet cluster to unambiguously show that the C-terminal cysteine motif coordinates an auxiliary [4Fe-4S] cluster. Spectroscopic comparison with a C-terminally truncated HydG (ΔCTD) harboring only the N-terminal cluster demonstrates that both clusters have similar UV-visible and EPR spectral properties, but that AdoMet binding and cleavage occur only at the N-terminal radical AdoMet cluster. To elucidate which steps in the catalytic cycle of HydG require the auxiliary [4Fe-4S] cluster, we compared the Michaelis-Menten constants for AdoMet and L-tyrosine for reconstituted wild-type, C386S, and ΔCTD HydG and demonstrate that these C-terminal modifications do not affect the affinity for AdoMet but that the affinity for L-tyrosine is drastically reduced compared to that of wild-type HydG. Further detailed kinetic characterization of these HydG mutants demonstrates that the C-terminal cluster and residues are not essential for L-tyrosine cleavage to p-cresol but are necessary for conversion of a tyrosine-derived intermediate to cyanide and CO.
Collapse
Affiliation(s)
- Rebecca C Driesener
- Chemistry, Faculty of Natural and Engineering Sciences, University of Southampton , Highfield SO17 1BJ, U.K
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Yosca TH, Rittle J, Krest CM, Onderko EL, Silakov A, Calixto JC, Behan RK, Green MT. Iron(IV)hydroxide pK(a) and the role of thiolate ligation in C-H bond activation by cytochrome P450. Science 2013; 342:825-9. [PMID: 24233717 PMCID: PMC4299822 DOI: 10.1126/science.1244373] [Citation(s) in RCA: 242] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Cytochrome P450 enzymes activate oxygen at heme iron centers to oxidize relatively inert substrate carbon-hydrogen bonds. Cysteine thiolate coordination to iron is posited to increase the pK(a) (where K(a) is the acid dissociation constant) of compound II, an iron(IV)hydroxide complex, correspondingly lowering the one-electron reduction potential of compound I, the active catalytic intermediate, and decreasing the driving force for deleterious auto-oxidation of tyrosine and tryptophan residues in the enzyme's framework. Here, we report on the preparation of an iron(IV)hydroxide complex in a P450 enzyme (CYP158) in ≥90% yield. Using rapid mixing technologies in conjunction with Mössbauer, ultraviolet/visible, and x-ray absorption spectroscopies, we determine a pK(a) value for this compound of 11.9. Marcus theory analysis indicates that this elevated pK(a) results in a >10,000-fold reduction in the rate constant for oxidations of the protein framework, making these processes noncompetitive with substrate oxidation.
Collapse
Affiliation(s)
- Timothy H Yosca
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Landgraf BJ, Arcinas AJ, Lee KH, Booker SJ. Identification of an intermediate methyl carrier in the radical S-adenosylmethionine methylthiotransferases RimO and MiaB. J Am Chem Soc 2013; 135:15404-15416. [PMID: 23991893 PMCID: PMC4023531 DOI: 10.1021/ja4048448] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
RimO and MiaB are radical S-adenosylmethionine (SAM) enzymes that catalyze the attachment of methylthio (-SCH3) groups to macromolecular substrates. RimO attaches a methylthio group at C3 of aspartate 89 of protein S12, a component of the 30S subunit of the bacterial ribosome. MiaB attaches a methylthio group at C2 of N(6)-(isopentenyl)adenosine, found at nucleotide 37 in several prokaryotic tRNAs. These two enzymes are prototypical members of a subclass of radical SAM enzymes called methylthiotransferases (MTTases). It had been assumed that the sequence of steps in MTTase reactions involves initial sulfur insertion into the organic substrate followed by capping of the inserted sulfur atom with a SAM-derived methyl group. In this work, however, we show that both RimO and MiaB from Thermotoga maritima catalyze methyl transfer from SAM to an acid/base labile acceptor on the protein in the absence of their respective macromolecular substrates. Consistent with the assignment of the acceptor as an iron-sulfur cluster, denaturation of the SAM-treated protein with acid results in production of methanethiol. When RimO or MiaB is first incubated with SAM in the absence of substrate and reductant and then incubated with excess S-adenosyl-l-[methyl-d3]methionine in the presence of substrate and reductant, production of the unlabeled product precedes production of the deuterated product, showing that the methylated species is chemically and kinetically competent to be an intermediate.
Collapse
Affiliation(s)
- Bradley J. Landgraf
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Arthur J. Arcinas
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Kyung-Hoon Lee
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Squire J. Booker
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| |
Collapse
|
29
|
Challand MR, Salvadori E, Driesener RC, Kay CWM, Roach PL, Spencer J. Cysteine methylation controls radical generation in the Cfr radical AdoMet rRNA methyltransferase. PLoS One 2013; 8:e67979. [PMID: 23861844 PMCID: PMC3702613 DOI: 10.1371/journal.pone.0067979] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/23/2013] [Indexed: 11/18/2022] Open
Abstract
The 'radical S-adenosyl-L-methionine (AdoMet)' enzyme Cfr methylates adenosine 2503 of the 23S rRNA in the peptidyltransferase centre (P-site) of the bacterial ribosome. This modification protects host bacteria, notably methicillin-resistant Staphylococcus aureus (MRSA), from numerous antibiotics, including agents (e.g. linezolid, retapamulin) that were developed to treat such organisms. Cfr contains a single [4Fe-4S] cluster that binds two separate molecules of AdoMet during the reaction cycle. These are used sequentially to first methylate a cysteine residue, Cys338; and subsequently generate an oxidative radical intermediate that facilitates methyl transfer to the unreactive C8 (and/or C2) carbon centres of adenosine 2503. How the Cfr active site, with its single [4Fe-4S] cluster, catalyses these two distinct activities that each utilise AdoMet as a substrate remains to be established. Here, we use absorbance and electron paramagnetic resonance (EPR) spectroscopy to investigate the interactions of AdoMet with the [4Fe-4S] clusters of wild-type Cfr and a Cys338 Ala mutant, which is unable to accept a methyl group. Cfr binds AdoMet with high (∼ 10 µM) affinity notwithstanding the absence of the RNA cosubstrate. In wild-type Cfr, where Cys338 is methylated, AdoMet binding leads to rapid oxidation of the [4Fe-4S] cluster and production of 5'-deoxyadenosine (DOA). In contrast, while Cys338 Ala Cfr binds AdoMet with equivalent affinity, oxidation of the [4Fe-4S] cluster is not observed. Our results indicate that the presence of a methyl group on Cfr Cys338 is a key determinant of the activity of the enzyme towards AdoMet, thus enabling a single active site to support two distinct modes of AdoMet cleavage.
Collapse
Affiliation(s)
- Martin R. Challand
- School of Cellular and Molecular Medicine, University of Bristol Medical Sciences Building, Bristol, United Kingdom
| | - Enrico Salvadori
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
- London Centre for Nanotechnology, University College London, London, United Kingdom
| | | | - Christopher W. M. Kay
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
- London Centre for Nanotechnology, University College London, London, United Kingdom
- * E-mail: (CWMK); (PLR); (JS)
| | - Peter L. Roach
- Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Highfield, Southampton, United Kingdom
- * E-mail: (CWMK); (PLR); (JS)
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol Medical Sciences Building, Bristol, United Kingdom
- * E-mail: (CWMK); (PLR); (JS)
| |
Collapse
|
30
|
|
31
|
Grove TL, Livada J, Schwalm EL, Green MT, Booker SJ, Silakov A. A substrate radical intermediate in catalysis by the antibiotic resistance protein Cfr. Nat Chem Biol 2013; 9:422-7. [PMID: 23644479 PMCID: PMC3897224 DOI: 10.1038/nchembio.1251] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 04/02/2013] [Indexed: 01/08/2023]
Abstract
Cfr-dependent methylation of C8 of adenosine 2503 (A2503) in 23S rRNA confers bacterial resistance to an array of clinically important antibiotics that target the large subunit of the ribosome, including the synthetic oxazolidinone antibiotic linezolid. The key element of the proposed mechanism for Cfr, a radical S-adenosylmethionine (SAM) enzyme, is the addition of a methylene radical — generated by hydrogen-atom abstraction from the methyl group of an S-methylated cysteine residue (mCys) — onto C8 of A2503 to form a protein – nucleic acid cross-linked species containing an unpaired electron. Herein we use continuous-wave and pulsed electron paramagnetic resonance (EPR) techniques to provide direct spectroscopic evidence for this intermediate, showing a spin-delocalized radical with maximum spin density at N7 of the adenine ring. In addition, we use rapid-freeze quench EPR to show that the radical forms and decays with rate constants that are consistent with the rate of formation of the methylated product.
Collapse
Affiliation(s)
- Tyler L Grove
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA
| | | | | | | | | | | |
Collapse
|
32
|
Grove TL, Ahlum JH, Qin RM, Lanz ND, Radle MI, Krebs C, Booker SJ. Further characterization of Cys-type and Ser-type anaerobic sulfatase maturating enzymes suggests a commonality in the mechanism of catalysis. Biochemistry 2013; 52:2874-87. [PMID: 23477283 DOI: 10.1021/bi400136u] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The anaerobic sulfatase-maturating enzyme from Clostridium perfringens (anSMEcpe) catalyzes the two-electron oxidation of a cysteinyl residue on a cognate protein to a formylglycyl residue (FGly) using a mechanism that involves organic radicals. The FGly residue plays a unique role as a cofactor in a class of enzymes termed arylsulfatases, which catalyze the hydrolysis of various organosulfate monoesters. anSMEcpe has been shown to be a member of the radical S-adenosylmethionine (SAM) family of enzymes, [4Fe-4S] cluster-requiring proteins that use a 5'-deoxyadenosyl 5'-radical (5'-dA(•)) generated from a reductive cleavage of SAM to initiate radical-based catalysis. Herein, we show that anSMEcpe contains in addition to the [4Fe-4S] cluster harbored by all radical SAM (RS) enzymes, two additional [4Fe-4S] clusters, similar to the radical SAM protein AtsB, which catalyzes the two-electron oxidation of a seryl residue to a FGly residue. We show by size-exclusion chromatography that both AtsB and anSMEcpe are monomeric proteins, and site-directed mutagenesis studies of AtsB reveal that individual Cys → Ala substitutions at seven conserved positions result in an insoluble protein, consistent with those residues acting as ligands to the two additional [4Fe-4S] clusters. Ala substitutions at an additional conserved Cys residue (C291 in AtsB and C276 in anSMEcpe) afford proteins that display intermediate behavior. These proteins exhibit reduced solubility and drastically reduced activity, behavior that is conspicuously similar to that of a critical Cys residue in BtrN, another radical SAM dehydrogenase [Grove, T. L., et al. (2010) Biochemistry 49, 3783-3785]. We also show that wild-type anSMEcpe acts on peptides containing other oxidizable amino acids at the target position. Moreover, we show that the enzyme will convert threonyl peptides to the corresponding ketone product, and also allo-threonyl peptides, but with a significantly reduced efficiency, suggesting that the pro-S hydrogen atom of the normal cysteinyl substrate is stereoselectively removed during turnover. Lastly, we show that the electron generated during catalysis by AtsB and anSMEcpe can be utilized for multiple turnovers, albeit through a reduced flavodoxin-mediated pathway.
Collapse
Affiliation(s)
- Tyler L Grove
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | | | | | | | | | | | | |
Collapse
|
33
|
Hamed RB, Gomez-Castellanos JR, Henry L, Ducho C, McDonough MA, Schofield CJ. The enzymes of β-lactam biosynthesis. Nat Prod Rep 2013; 30:21-107. [DOI: 10.1039/c2np20065a] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
34
|
Lanz ND, Booker SJ. Identification and function of auxiliary iron-sulfur clusters in radical SAM enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1196-212. [PMID: 22846545 DOI: 10.1016/j.bbapap.2012.07.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 07/16/2012] [Accepted: 07/17/2012] [Indexed: 11/27/2022]
Abstract
Radical SAM (RS) enzymes use a 5'-deoxyadenosyl 5'-radical generated from a reductive cleavage of S-adenosyl-l-methionine to catalyze over 40 distinct reaction types. A distinguishing feature of these enzymes is a [4Fe-4S] cluster to which each of three iron ions is ligated by three cysteinyl residues most often located in a Cx(3)Cx(2)C motif. The α-amino and α-carboxylate groups of SAM anchor the molecule to the remaining iron ion, which presumably facilitates its reductive cleavage. A subset of RS enzymes contains additional iron-sulfur clusters, - which we term auxiliary clusters - most of which have unidentified functions. Enzymes in this subset are involved in cofactor biosynthesis and maturation, post-transcriptional and post-translational modification, enzyme activation, and antibiotic biosynthesis. The additional clusters in these enzymes have been proposed to function in sulfur donation, electron transfer, and substrate anchoring. This review will highlight evidence supporting the presence of multiple iron-sulfur clusters in these enzymes as well as their predicted roles in catalysis. This article is part of a special issue entitled: Radical SAM enzymes and radical enzymology.
Collapse
Affiliation(s)
- Nicholas D Lanz
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | | |
Collapse
|
35
|
Huang W, Xu H, Li Y, Zhang F, Chen XY, He QL, Igarashi Y, Tang GL. Characterization of yatakemycin gene cluster revealing a radical S-adenosylmethionine dependent methyltransferase and highlighting spirocyclopropane biosynthesis. J Am Chem Soc 2012; 134:8831-40. [PMID: 22612591 DOI: 10.1021/ja211098r] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Yatakemycin (YTM), an antitumor natural product, represents the most potent member of a class of potent anticancer natural products including CC-1065 and duocarmycins. Herein we describe the biosynthetic gene cluster of YTM, which was identified by genome scanning of Streptomyces sp. TP-A0356. This cluster consists of 31 open reading frames (ORFs) and was localized to a 36 kb DNA segment. Moreover, its involvement in YTM biosynthesis was confirmed by cluster deletion, gene replacement, and complementation. Inactivation of ytkT, which encodes a radical S-adenosylmethionine (SAM) protein, created a mutant strain that failed to produce YTM but accumulated a new metabolite, which was structurally elucidated as a precursor that was related to the formation of the cyclopropane ring. More importantly, biochemical characterization of the radical SAM-dependent enzyme YtkT revealed that it is a novel C-methyltransferase and contributes to an advanced intermediate during formation of the cyclopropane ring through a radical mechanism in the YTM biosynthetic pathway. On the basis of in silico analysis, genetic experiments, structure elucidation of the novel intermediate, and biochemical characterization, a biosynthetic pathway for yatakemycin was proposed, which sets the stage to further investigate the novel enzymatic mechanisms and engineer the biosynthetic machinery for the production of novel analogues.
Collapse
Affiliation(s)
- Wei Huang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Affiliation(s)
- Qi Zhang
- Department of Chemistry, Howard Hughes Medical Institute, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
| | - Wilfred A. van der Donk
- Department of Chemistry, Howard Hughes Medical Institute, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
| |
Collapse
|
37
|
Lanz ND, Grove TL, Gogonea CB, Lee KH, Krebs C, Booker SJ. RlmN and AtsB as Models for the Overproduction and Characterization of Radical SAM Proteins. Methods Enzymol 2012; 516:125-52. [DOI: 10.1016/b978-0-12-394291-3.00030-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|