451
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Zha L, Jiang Y, Henke MT, Wilson MR, Wang JX, Kelleher NL, Balskus EP. Colibactin assembly line enzymes use S-adenosylmethionine to build a cyclopropane ring. Nat Chem Biol 2017; 13:1063-1065. [PMID: 28805802 PMCID: PMC5657534 DOI: 10.1038/nchembio.2448] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 06/23/2017] [Indexed: 01/01/2023]
Abstract
Despite containing an α-amino acid, the versatile cofactor S-adenosylmethionine (SAM) is not a known building block for nonribosomal peptide synthetase (NRPS) assembly lines. Here we report an unusual NRPS module from colibactin biosynthesis that uses SAM for amide bond formation and subsequent cyclopropanation. Our findings showcase a new use for SAM and reveal a novel biosynthetic route to a functional group that likely mediates colibactin's genotoxicity.
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Affiliation(s)
- Li Zha
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Yindi Jiang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Matthew T Henke
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Matthew R Wilson
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jennifer X Wang
- Small Molecule Mass Spectrometry Facility, FAS Division of Science, Cambridge, Massachusetts, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA.,Department of Molecular Biosciences and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
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452
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Joshi S, Mahanta N, Fedoseyenko D, Williams H, Begley TP. Aminofutalosine Synthase: Evidence for Captodative and Aryl Radical Intermediates Using β-Scission and SRN1 Trapping Reactions. J Am Chem Soc 2017; 139:10952-10955. [DOI: 10.1021/jacs.7b04209] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sumedh Joshi
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Nilkamal Mahanta
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Dmytro Fedoseyenko
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Howard Williams
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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453
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Qianzhu H, Ji W, Ji X, Chu L, Guo C, Lu W, Ding W, Gao J, Zhang Q. Reactivity of the nitrogen-centered tryptophanyl radical in the catalysis by the radical SAM enzyme NosL. Chem Commun (Camb) 2017; 53:344-347. [PMID: 27929146 DOI: 10.1039/c6cc08869d] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The radical SAM tryptophan (Trp) lyase NosL involved in nosiheptide biosynthesis catalyzes two parallel reactions, converting l-Trp to 3-methyl-2-indolic acid (MIA) and to dehydroglycine and 3-methylindole, respectively. The two parallel reactions diverge from a nitrogen-centered tryptophanyl radical intermediate. Here we report an investigation on the intrinsic reactivity of the tryptophanyl radical using a chemical model study and DFT calculations. The kinetics of the formation and fragmentation of this nitrogen-centered radical in NosL catalysis were also studied in detail. Our analysis explains the intriguing catalytic promiscuity of NosL and highlights the remarkable role this enzyme plays in achieving an energetically highly unfavorable transformation.
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Affiliation(s)
- Haocheng Qianzhu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. and Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Wenjuan Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Leixia Chu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Chuchu Guo
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Wei Lu
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Wei Ding
- Department of Chemistry, Fudan University, Shanghai, 200433, China. and School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jiangtao Gao
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
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454
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Nelp MT, Young AP, Stepanski BM, Bandarian V. Human Viperin Causes Radical SAM-Dependent Elongation of Escherichia coli, Hinting at Its Physiological Role. Biochemistry 2017; 56:3874-3876. [PMID: 28708394 DOI: 10.1021/acs.biochem.7b00608] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Viperin (virus inhibitory protein, endoplasmic reticulum-associated, interferon-inducible) is a widely distributed protein that is expressed in response to infection and causes antiviral effects against a broad spectrum of viruses. Viperin is a member of the radical S-adenosyl-l-methionine (SAM) superfamily of enzymes, which typically employ a 4Fe-4S cluster to reductively cleave SAM to initiate chemistry. Though the specific reaction catalyzed by viperin remains unknown, it has been shown that expression of viperin causes an increase in the fluidity of lipid membranes, which impedes the budding of nascent viral particles from the membrane inhibiting propagation of the infection. Herein, we show that expression of the human viperin homologue induces a dramatically elongated morphology of the host Escherichia coli cells. Mutation of an essential cysteine that coordinates the radical SAM cluster abrogates this effect. Thus, the native radical SAM activity of viperin is likely occurring in the host bacteria, indicating the elusive substrate is shared between both bacteria and humans, significantly narrowing the range of potential candidate substrates and providing a convenient bacterial platform from which future studies can occur.
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Affiliation(s)
- Micah T Nelp
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Anthony P Young
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Branden M Stepanski
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112, United States
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455
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Abstract
The regulation of the genome relies on the epigenome to instruct, define and restrict the activities of growth and development. Among the cohort of epigenetic instructions, DNA methylation is perhaps the best understood. In most mammals, cycles of the addition and removal of DNA methylation constitute phases of reprogramming when the developing embryo must negotiate lineage defining and developmental commitment events. In these instances, the DNA methylation instruction is often removed, thereby allowing a change in permission for future development and a return to a more plastic and pluripotent state. Because of this, the germ line, upon demethylation, can give rise to gametes that are fully functional across generations and poised for totipotency. This return to a less differentiated state can also be achieved experimentally. The loss of DNA methylation constitutes one of the significant barriers to induced pluripotency and is a prerequisite for the generation of iPS cells. Taking fully differentiated cells, such as skin cells, and turning back the developmental clock heralded a technological breakthrough discovery in 2006 (Takahashi and Yamanaka 2006) with unprecedented promise in regenerative medicine. In this chapter, the mechanistic possibilities for DNA demethylation will be described in the context of natural and experimentally induced epigenetic reprogramming. The balance of the maintenance of this heritable mark together with its timely removal is essential for lifelong health and may be a key in our understanding of ageing.
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Affiliation(s)
- Wendy Dean
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.
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456
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Fenwick MK, Li Y, Cresswell P, Modis Y, Ealick SE. Structural studies of viperin, an antiviral radical SAM enzyme. Proc Natl Acad Sci U S A 2017; 114:6806-6811. [PMID: 28607080 PMCID: PMC5495270 DOI: 10.1073/pnas.1705402114] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viperin is an IFN-inducible radical S-adenosylmethionine (SAM) enzyme that inhibits viral replication. We determined crystal structures of an anaerobically prepared fragment of mouse viperin (residues 45-362) complexed with S-adenosylhomocysteine (SAH) or 5'-deoxyadenosine (5'-dAdo) and l-methionine (l-Met). Viperin contains a partial (βα)6-barrel fold with a disordered N-terminal extension (residues 45-74) and a partially ordered C-terminal extension (residues 285-362) that bridges the partial barrel to form an overall closed barrel structure. Cys84, Cys88, and Cys91 located after the first β-strand bind a [4Fe-4S] cluster. The active site architecture of viperin with bound SAH (a SAM analog) or 5'-dAdo and l-Met (SAM cleavage products) is consistent with the canonical mechanism of 5'-deoxyadenosyl radical generation. The viperin structure, together with sequence alignments, suggests that vertebrate viperins are highly conserved and that fungi contain a viperin-like ortholog. Many bacteria and archaebacteria also express viperin-like enzymes with conserved active site residues. Structural alignments show that viperin is similar to several other radical SAM enzymes, including the molybdenum cofactor biosynthetic enzyme MoaA and the RNA methyltransferase RlmN, which methylates specific nucleotides in rRNA and tRNA. The viperin putative active site contains several conserved positively charged residues, and a portion of the active site shows structural similarity to the GTP-binding site of MoaA, suggesting that the viperin substrate may be a nucleoside triphosphate of some type.
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Affiliation(s)
- Michael K Fenwick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Yue Li
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Peter Cresswell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520;
| | - Yorgo Modis
- Department of Medicine, University of Cambridge, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Steven E Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853;
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457
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Shepard EM, Byer AS, Aggarwal P, Betz JN, Scott AG, Shisler KA, Usselman RJ, Eaton GR, Eaton SS, Broderick JB. Electron Spin Relaxation and Biochemical Characterization of the Hydrogenase Maturase HydF: Insights into [2Fe-2S] and [4Fe-4S] Cluster Communication and Hydrogenase Activation. Biochemistry 2017; 56:3234-3247. [PMID: 28525271 PMCID: PMC5490485 DOI: 10.1021/acs.biochem.7b00169] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nature utilizes [FeFe]-hydrogenase enzymes to catalyze the interconversion between H2 and protons and electrons. Catalysis occurs at the H-cluster, a carbon monoxide-, cyanide-, and dithiomethylamine-coordinated 2Fe subcluster bridged via a cysteine to a [4Fe-4S] cluster. Biosynthesis of this unique metallocofactor is accomplished by three maturase enzymes denoted HydE, HydF, and HydG. HydE and HydG belong to the radical S-adenosylmethionine superfamily of enzymes and synthesize the nonprotein ligands of the H-cluster. These enzymes interact with HydF, a GTPase that acts as a scaffold or carrier protein during 2Fe subcluster assembly. Prior characterization of HydF demonstrated the protein exists in both dimeric and tetrameric states and coordinates both [4Fe-4S]2+/+ and [2Fe-2S]2+/+ clusters [Shepard, E. M., Byer, A. S., Betz, J. N., Peters, J. W., and Broderick, J. B. (2016) Biochemistry 55, 3514-3527]. Herein, electron paramagnetic resonance (EPR) is utilized to characterize the [2Fe-2S]+ and [4Fe-4S]+ clusters bound to HydF. Examination of spin relaxation times using pulsed EPR in HydF samples exhibiting both [4Fe-4S]+ and [2Fe-2S]+ cluster EPR signals supports a model in which the two cluster types either are bound to widely separated sites on HydF or are not simultaneously bound to a single HydF species. Gel filtration chromatographic analyses of HydF spectroscopic samples strongly suggest the [2Fe-2S]+ and [4Fe-4S]+ clusters are coordinated to the dimeric form of the protein. Lastly, we examined the 2Fe subcluster-loaded form of HydF and showed the dimeric state is responsible for [FeFe]-hydrogenase activation. Together, the results indicate a specific role for the HydF dimer in the H-cluster biosynthesis pathway.
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Affiliation(s)
- Eric M Shepard
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Amanda S Byer
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Priyanka Aggarwal
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
| | - Jeremiah N Betz
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Anna G Scott
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Krista A Shisler
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Robert J Usselman
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
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458
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Zhou X, Guo QL, Zhu CG, Xu CB, Wang YN, Shi JG. Gastradefurphenol, a minor 9,9′-neolignan with a new carbon skeleton substituted by two p -hydroxybenzyls from an aqueous extract of “tian ma”. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2017.03.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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459
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Parmeggiani F, Weise NJ, Ahmed ST, Turner NJ. Synthetic and Therapeutic Applications of Ammonia-lyases and Aminomutases. Chem Rev 2017; 118:73-118. [DOI: 10.1021/acs.chemrev.6b00824] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Fabio Parmeggiani
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Weise
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Syed T. Ahmed
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Turner
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
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460
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Benjdia A, Decamps L, Guillot A, Kubiak X, Ruffié P, Sandström C, Berteau O. Insights into the catalysis of a lysine-tryptophan bond in bacterial peptides by a SPASM domain radical S-adenosylmethionine (SAM) peptide cyclase. J Biol Chem 2017; 292:10835-10844. [PMID: 28476884 PMCID: PMC5491770 DOI: 10.1074/jbc.m117.783464] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/26/2017] [Indexed: 11/06/2022] Open
Abstract
Radical S-adenosylmethionine (SAM) enzymes are emerging as a major superfamily of biological catalysts involved in the biosynthesis of the broad family of bioactive peptides called ribosomally synthesized and post-translationally modified peptides (RiPPs). These enzymes have been shown to catalyze unconventional reactions, such as methyl transfer to electrophilic carbon atoms, sulfur to Cα atom thioether bonds, or carbon-carbon bond formation. Recently, a novel radical SAM enzyme catalyzing the formation of a lysine-tryptophan bond has been identified in Streptococcus thermophilus, and a reaction mechanism has been proposed. By combining site-directed mutagenesis, biochemical assays, and spectroscopic analyses, we show here that this enzyme, belonging to the emerging family of SPASM domain radical SAM enzymes, likely contains three [4Fe-4S] clusters. Notably, our data support that the seven conserved cysteine residues, present within the SPASM domain, are critical for enzyme activity. In addition, we uncovered the minimum substrate requirements and demonstrate that KW cyclic peptides are more widespread than anticipated, notably in pathogenic bacteria. Finally, we show a strict specificity of the enzyme for lysine and tryptophan residues and the dependence of an eight-amino acid leader peptide for activity. Altogether, our study suggests novel mechanistic links among SPASM domain radical SAM enzymes and supports the involvement of non-cysteinyl ligands in the coordination of auxiliary clusters.
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Affiliation(s)
- Alhosna Benjdia
- From the Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France and
| | - Laure Decamps
- From the Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France and
| | - Alain Guillot
- From the Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France and
| | - Xavier Kubiak
- From the Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France and
| | - Pauline Ruffié
- From the Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France and
| | - Corine Sandström
- the Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P. O. Box 7015, Uppsala 750-07, Sweden
| | - Olivier Berteau
- From the Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France and
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461
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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.
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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
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462
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Schramma KR, Seyedsayamdost MR. Lysine-Tryptophan-Crosslinked Peptides Produced by Radical SAM Enzymes in Pathogenic Streptococci. ACS Chem Biol 2017; 12:922-927. [PMID: 28191919 DOI: 10.1021/acschembio.6b01069] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Macrocycles represent a common structural framework in many naturally occurring peptides. Several strategies exist for macrocyclization, and the enzymes that incorporate them are of great interest, as they enhance our repertoire for creating complex molecules. We recently discovered a new peptide cyclization reaction involving a crosslink between the side chains of lysine and tryptophan that is installed by a radical SAM enzyme. Herein, we characterize relatives of this metalloenzyme from the pathogens Streptococcus agalactiae and Streptococcus suis. Our results show that the corresponding enzymes, which we call AgaB and SuiB, contain multiple [4Fe-4S] clusters and catalyze Lys-Trp crosslink formation in their respective substrates. Subsequent high-resolution-MS and 2D-NMR analyses located the site of macrocyclization. Moreover, we report that AgaB can accept modified substrates containing natural or unnatural amino acids. Aside from providing insights into the mechanism of this unusual modification, the substrate promiscuity of AgaB may be exploited to create diverse macrocyclic peptides.
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Affiliation(s)
- Kelsey R. Schramma
- Departments
of Chemistry and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R. Seyedsayamdost
- Departments
of Chemistry and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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463
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Dunbar KL, Scharf DH, Litomska A, Hertweck C. Enzymatic Carbon-Sulfur Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5521-5577. [PMID: 28418240 DOI: 10.1021/acs.chemrev.6b00697] [Citation(s) in RCA: 356] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sulfur plays a critical role for the development and maintenance of life on earth, which is reflected by the wealth of primary metabolites, macromolecules, and cofactors bearing this element. Whereas a large body of knowledge has existed for sulfur trafficking in primary metabolism, the secondary metabolism involving sulfur has long been neglected. Yet, diverse sulfur functionalities have a major impact on the biological activities of natural products. Recent research at the genetic, biochemical, and chemical levels has unearthed a broad range of enzymes, sulfur shuttles, and chemical mechanisms for generating carbon-sulfur bonds. This Review will give the first systematic overview on enzymes catalyzing the formation of organosulfur natural products.
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Affiliation(s)
- Kyle L Dunbar
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Daniel H Scharf
- Life Sciences Institute, University of Michigan , 210 Washtenaw Avenue, Ann Arbor, Michigan 48109-2216, United States
| | - Agnieszka Litomska
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany.,Friedrich Schiller University , 07743 Jena, Germany
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464
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Dong M, Horitani M, Dzikovski B, Freed JH, Ealick SE, Hoffman BM, Lin H. Substrate-Dependent Cleavage Site Selection by Unconventional Radical S-Adenosylmethionine Enzymes in Diphthamide Biosynthesis. J Am Chem Soc 2017; 139:5680-5683. [PMID: 28383907 DOI: 10.1021/jacs.7b01712] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
S-Adenosylmethionine (SAM) has a sulfonium ion with three distinct C-S bonds. Conventional radical SAM enzymes use a [4Fe-4S] cluster to cleave homolytically the C5',adenosine-S bond of SAM to generate a 5'-deoxyadenosyl radical, which catalyzes various downstream chemical reactions. Radical SAM enzymes involved in diphthamide biosynthesis, such as Pyrococcus horikoshii Dph2 (PhDph2) and yeast Dph1-Dph2 instead cleave the Cγ,Met-S bond of methionine to generate a 3-amino-3-carboxylpropyl radical. We here show radical SAM enzymes can be tuned to cleave the third C-S bond to the sulfonium sulfur by changing the structure of SAM. With a decarboxyl SAM analogue (dc-SAM), PhDph2 cleaves the Cmethyl-S bond, forming 5'-deoxy-5'-(3-aminopropylthio) adenosine (dAPTA, 1). The methyl cleavage activity, like the cleavage of the other two C-S bonds, is dependent on the presence of a [4Fe-4S]+ cluster. Electron-nuclear double resonance and mass spectroscopy data suggests that mechanistically one of the S atoms in the [4Fe-4S] cluster captures the methyl group from dc-SAM, forming a distinct EPR-active intermediate, which can transfer the methyl group to nucleophiles such as dithiothreitol. This reveals the [4Fe-4S] cluster in a radical SAM enzyme can be tuned to cleave any one of the three bonds to the sulfonium sulfur of SAM or analogues, and is the first demonstration a radical SAM enzyme could switch from an Fe-based one electron transfer reaction to a S-based two electron transfer reaction in a substrate-dependent manner. This study provides an illustration of the versatile reactivity of Fe-S clusters.
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Affiliation(s)
- Min Dong
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Masaki Horitani
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States.,Department of Applied Biochemistry and Food Science, Saga University , Saga 840-8502, Japan
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Steven E Ealick
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
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465
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Remelli W, Santabarbara S, Carbonera D, Bonomi F, Ceriotti A, Casazza AP. Iron Binding Properties of Recombinant Class A Protein Disulfide Isomerase from Arabidopsis thaliana. Biochemistry 2017; 56:2116-2125. [DOI: 10.1021/acs.biochem.6b01257] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- William Remelli
- Istituto
di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via Bassini 15a, 20133 Milano, Italy
- Istituto
di Biofisica, Consiglio Nazionale delle Ricerche, Via Celoria
26, 20133 Milano, Italy
| | - Stefano Santabarbara
- Istituto
di Biofisica, Consiglio Nazionale delle Ricerche, Via Celoria
26, 20133 Milano, Italy
| | - Donatella Carbonera
- Dipartimento
di Scienze Chimiche, Università di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Francesco Bonomi
- Dipartimento
di Scienze per gli Alimenti, la Nutrizione e l’Ambiente, DeFENS, Università di Milano, Via G. Celoria 2, 20133 Milano, Italy
| | - Aldo Ceriotti
- Istituto
di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via Bassini 15a, 20133 Milano, Italy
| | - Anna Paola Casazza
- Istituto
di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via Bassini 15a, 20133 Milano, Italy
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466
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Kumaresan V, Nizam F, Ravichandran G, Viswanathan K, Palanisamy R, Bhatt P, Arasu MV, Al-Dhabi NA, Mala K, Arockiaraj J. Transcriptome changes of blue-green algae, Arthrospira sp. in response to sulfate stress. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.01.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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467
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Mahanta N, Zhang Z, Hudson GA, van der Donk WA, Mitchell DA. Reconstitution and Substrate Specificity of the Radical S-Adenosyl-methionine Thiazole C-Methyltransferase in Thiomuracin Biosynthesis. J Am Chem Soc 2017; 139:4310-4313. [PMID: 28301141 PMCID: PMC5477235 DOI: 10.1021/jacs.7b00693] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Thiomuracin is a thiopeptide antibiotic with potent activity toward Gram-positive drug-resistant bacteria. Thiomuracin is biosynthesized from a precursor peptide, TbtA, by a complex array of posttranslational modifications. One of several intriguing transformations is the C-methylation of thiazole, occurring at an unactivated sp2 carbon. Herein, we report the in vitro reconstitution of TbtI, the responsible radical S-adenosyl-methionine (rSAM) C-methyltransferase, which catalyzes the formation of 5-methylthiazole at a single site. Our studies demonstrate that a linear hexazole-bearing intermediate of TbtA is a substrate for TbtI whereas macrocyclized thiomuracin GZ is not. In determining the minimal substrate for TbtI, we found that the enzyme is functional when most of the leader peptide has been removed. The in vitro reconstitution of TbtI, a class C rSAM methyltransferase, further adds to the chemical versatility of rSAM enzymes, and informs on the complexity of thiomuracin biosynthesis.
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Affiliation(s)
- Nilkamal Mahanta
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
| | - Zhengan Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Graham A. Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
- Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
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468
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Yang L, Li L. Insights into the Activity Change of Spore Photoproduct Lyase Induced by Mutations at a Peripheral Glycine Residue. Front Chem 2017; 5:14. [PMID: 28401144 PMCID: PMC5368176 DOI: 10.3389/fchem.2017.00014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/28/2017] [Indexed: 12/19/2022] Open
Abstract
UV radiation triggers the formation of 5-thyminyl-5,6-dihydrothymine, i.e., the spore photoproduct (SP), in the genomic DNA of bacterial endospores. These SPs, if not repaired in time, may lead to genome instability and cell death. SP is mainly repaired by spore photoproduct lyase (SPL) during spore outgrowth via an unprecedented protein-harbored radical transfer pathway that is composed of at least a cysteine and two tyrosine residues. This mechanism is consistent with the recently solved SPL structure that shows all three residues are located in proximity and thus able to participate in the radical transfer process during the enzyme catalysis. In contrast, an earlier in vivo mutational study identified a glycine to arginine mutation at the position 168 on the B. subtilis SPL that is >15 Å away from the enzyme active site. This mutation appears to abolish the enzyme activity because endospores carrying this mutant were sensitive to UV light. To understand the molecular basis for this rendered enzyme activity, we constructed two SPL mutations G168A and G168R, examined their repair of dinucleotide SP TpT, and found that both mutants exhibit reduced enzyme activity. Comparing with the wildtype (WT) SPL enzyme, the G168A mutant slows down the SP TpT repair by 3~4-fold while the G168R mutant by ~ 80-fold. Both mutants exhibit a smaller apparent (DV) kinetic isotope effect (KIE) but a bigger competitive (DV/K) KIE than that by the WT SPL. Moreover, the G168R mutant also produces a large portion of the abortive repair product TpT-[Formula: see text]; the formation of which indicates that cysteine 141 is no longer well positioned as the H-donor to the thymine allylic radical intermediate. All these data imply that the mutation at the remote glycine 168 residue alters the enzyme 3D structure, subsequently reducing the SPL activity by changing the positions of the essential amino acids involved in the radical transfer process.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University IndianapolisIndianapolis, IN, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University IndianapolisIndianapolis, IN, USA
- Department of Dermatology, Indiana University School of MedicineIndianapolis, IN, USA
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469
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A B 12-dependent radical SAM enzyme involved in oxetanocin A biosynthesis. Nature 2017; 544:322-326. [PMID: 28346939 PMCID: PMC5398914 DOI: 10.1038/nature21689] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 02/03/2017] [Indexed: 11/22/2022]
Abstract
Oxetanocin-A (OXT-A, 1) is a potent antitumor, antiviral, and
antibacterial compound. Biosynthesis of OXT-A has been linked to a
plasmid-borne, Bacillus megaterium gene cluster that contains
four genes, oxsA, oxsB, oxrA,
and oxrB. Here, we show that the oxsA and
oxsB genes are both required for the production of OXT-A.
Biochemical analysis of the encoded proteins, a cobalamin (Cbl)-dependent
S-adenosylmethionine (AdoMet) radical enzyme, OxsB, and an
HD-domain phosphohydrolase, OxsA, revealed that OXT-A is derived from
2′-deoxyadenosine phosphate in an OxsB-catalyzed ring contraction
reaction initiated by H-atom abstraction from C2′. Hence, OxsB
represents the first biochemically characterized non-methylating Cbl-dependent
AdoMet radical enzyme. X-ray analysis of OxsB reveals the fold of a
Cbl-dependent AdoMet radical enzyme for which there are an estimated 7000
members. Overall, this work provides a framework for understanding the interplay
of AdoMet and Cbl cofactors and expands the catalytic repertoire of
Cbl-dependent AdoMet radical enzymes.
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470
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471
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Yang L, Jian Y, Setlow P, Li L. Spore photoproduct within DNA is a surprisingly poor substrate for its designated repair enzyme-The spore photoproduct lyase. DNA Repair (Amst) 2017; 53:31-42. [PMID: 28320593 DOI: 10.1016/j.dnarep.2016.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 05/23/2016] [Accepted: 11/15/2016] [Indexed: 12/15/2022]
Abstract
DNA repair enzymes typically recognize their substrate lesions with high affinity to ensure efficient lesion repair. In UV irradiated endospores, a special thymine dimer, 5-thyminyl-5,6-dihydrothymine, termed the spore photoproduct (SP), is the dominant DNA photolesion, which is rapidly repaired during spore outgrowth mainly by spore photoproduct lyase (SPL) using an unprecedented protein-harbored radical transfer process. Surprisingly, our in vitro studies using SP-containing short oligonucleotides, pUC 18 plasmid DNA, and E. coli genomic DNA found that they are all poor substrates for SPL in general, exhibiting turnover numbers of 0.01-0.2min-1. The faster turnover numbers are reached under single turnover conditions, and SPL activity is low with oligonucleotide substrates at higher concentrations. Moreover, SP-containing oligonucleotides do not go past one turnover. In contrast, the dinucleotide SP TpT exhibits a turnover number of 0.3-0.4min-1, and the reaction may reach up to 10 turnovers. These observations distinguish SPL from other specialized DNA repair enzymes. To the best of our knowledge, SPL represents an unprecedented example of a major DNA repair enzyme that cannot effectively repair its substrate lesion within the normal DNA conformation adopted in growing cells. Factors such as other DNA binding proteins, helicases or an altered DNA conformation may cooperate with SPL to enable efficient SP repair in germinating spores. Therefore, both SP formation and SP repair are likely to be tightly controlled by the unique cellular environment in dormant and outgrowing spore-forming bacteria, and thus SP repair may be extremely slow in non-spore-forming organisms.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, IN 46202, United States
| | - Yajun Jian
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, IN 46202, United States
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, United States
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, IN 46202, United States; Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, United States.
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472
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Burkhart BJ, Schwalen CJ, Mann G, Naismith JH, Mitchell DA. YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function. Chem Rev 2017; 117:5389-5456. [PMID: 28256131 DOI: 10.1021/acs.chemrev.6b00623] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
With advances in sequencing technology, uncharacterized proteins and domains of unknown function (DUFs) are rapidly accumulating in sequence databases and offer an opportunity to discover new protein chemistry and reaction mechanisms. The focus of this review, the formerly enigmatic YcaO superfamily (DUF181), has been found to catalyze a unique phosphorylation of a ribosomal peptide backbone amide upon attack by different nucleophiles. Established nucleophiles are the side chains of Cys, Ser, and Thr which gives rise to azoline/azole biosynthesis in ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products. However, much remains unknown about the potential for YcaO proteins to collaborate with other nucleophiles. Recent work suggests potential in forming thioamides, macroamidines, and possibly additional post-translational modifications. This review covers all knowledge through mid-2016 regarding the biosynthetic gene clusters (BGCs), natural products, functions, mechanisms, and applications of YcaO proteins and outlines likely future research directions for this protein superfamily.
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Affiliation(s)
| | | | - Greg Mann
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom
| | - James H Naismith
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom.,State Key Laboratory of Biotherapy, Sichuan University , Sichuan, China
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473
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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]
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474
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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
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475
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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.
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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
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476
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Turner AG, Ong CLY, Walker MJ, Djoko KY, McEwan AG. Transition Metal Homeostasis in Streptococcus pyogenes and Streptococcus pneumoniae. Adv Microb Physiol 2017; 70:123-191. [PMID: 28528647 DOI: 10.1016/bs.ampbs.2017.01.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Trace metals such as Fe, Mn, Zn and Cu are essential for various biological functions including proper innate immune function. The host immune system has complicated and coordinated mechanisms in place to either starve and/or overload invading pathogens with various metals to combat the infection. Here, we discuss the roles of Fe, Mn and Zn in terms of nutritional immunity, and also the roles of Cu and Zn in metal overload in relation to the physiology and pathogenesis of two human streptococcal species, Streptococcus pneumoniae and Streptococcus pyogenes. S. pneumoniae is a major human pathogen that is carried asymptomatically in the nasopharynx by up to 70% of the population; however, transition to internal sites can cause a range of diseases such as pneumonia, otitis media, meningitis and bacteraemia. S. pyogenes is a human pathogen responsible for diseases ranging from pharyngitis and impetigo, to severe invasive infections. Both species have overlapping capacity with respect to metal acquisition, export and regulation and how metal homeostasis relates to their virulence and ability to invade and survive within the host. It is becoming more apparent that metals have an important role to play in the control of infection, and with further investigations, it could lead to the potential use of metals in novel antimicrobial therapies.
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Affiliation(s)
- Andrew G Turner
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Cheryl-Lynn Y Ong
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Mark J Walker
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Karrera Y Djoko
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Alastair G McEwan
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia.
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477
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Wang Y, Schnell B, Baumann S, Müller R, Begley TP. Biosynthesis of Branched Alkoxy Groups: Iterative Methyl Group Alkylation by a Cobalamin-Dependent Radical SAM Enzyme. J Am Chem Soc 2017; 139:1742-1745. [PMID: 28040895 PMCID: PMC6078419 DOI: 10.1021/jacs.6b10901] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The biosynthesis of branched alkoxy groups, such as the unique t-butyl group found in a variety of natural products, is still poorly understood. Recently, cystobactamids were isolated and identified from Cystobacter sp as novel antibacterials. These metabolites contain an isopropyl group proposed to be formed using CysS, a cobalamin-dependent radical S-adenosylmethionine (SAM) methyltransferase. Here, we reconstitute the CysS-catalyzed reaction, on p-aminobenzoate thioester substrates, and demonstrate that it not only catalyzes sequential methylations of a methyl group to form ethyl and isopropyl groups but remarkably also sec-butyl and t-butyl groups. To our knowledge, this is the first in vitro reconstitution of a cobalamin-dependent radical SAM enzyme catalyzing the conversion of a methyl group to a t-butyl group.
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Affiliation(s)
- Yuanyou Wang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Bastien Schnell
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, Saarland University, Universitätscampus E8.1, D-66123 Saarbrücken, Germany
| | - Sascha Baumann
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, Saarland University, Universitätscampus E8.1, D-66123 Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, Saarland University, Universitätscampus E8.1, D-66123 Saarbrücken, Germany
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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478
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Mordhorst S, Siegrist J, Müller M, Richter M, Andexer JN. Catalytic Alkylation Using a CyclicS-Adenosylmethionine Regeneration System. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611038] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Silja Mordhorst
- Institute of Pharmaceutical Sciences; University of Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Jutta Siegrist
- Institute of Pharmaceutical Sciences; University of Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences; University of Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Michael Richter
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB; Bio, Electro and Chemocatalysis BioCat; Straubing branch; Schulgasse 11a 94315 Straubing Germany
| | - Jennifer N. Andexer
- Institute of Pharmaceutical Sciences; University of Freiburg; Albertstrasse 25 79104 Freiburg Germany
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479
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Mordhorst S, Siegrist J, Müller M, Richter M, Andexer JN. Catalytic Alkylation Using a CyclicS-Adenosylmethionine Regeneration System. Angew Chem Int Ed Engl 2017; 56:4037-4041. [DOI: 10.1002/anie.201611038] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Indexed: 01/28/2023]
Affiliation(s)
- Silja Mordhorst
- Institute of Pharmaceutical Sciences; University of Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Jutta Siegrist
- Institute of Pharmaceutical Sciences; University of Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences; University of Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Michael Richter
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB; Bio, Electro and Chemocatalysis BioCat; Straubing branch; Schulgasse 11a 94315 Straubing Germany
| | - Jennifer N. Andexer
- Institute of Pharmaceutical Sciences; University of Freiburg; Albertstrasse 25 79104 Freiburg Germany
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480
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Post-translational modification of ribosomally synthesized peptides by a radical SAM epimerase in Bacillus subtilis. Nat Chem 2017. [PMID: 28644475 DOI: 10.1038/nchem.2714] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosomally synthesized peptides are built out of L-amino acids, whereas D-amino acids are generally the hallmark of non-ribosomal synthetic processes. Here we show that the model bacterium Bacillus subtilis is able to produce a novel type of ribosomally synthesized and post-translationally modified peptide that contains D-amino acids, and which we propose to call epipeptides. We demonstrate that a two [4Fe-4S]-cluster radical S-adenosyl-L-methionine (SAM) enzyme converts L-amino acids into their D-counterparts by catalysing Cα-hydrogen-atom abstraction and using a critical cysteine residue as the hydrogen-atom donor. Unexpectedly, these D-amino acid residues proved to be essential for the activity of a peptide that induces the expression of LiaRS, a major component of the bacterial cell envelope stress-response system. Present in B. subtilis and in several members of the human microbiome, these epipeptides and radical SAM epimerases broaden the landscape of peptidyl structures accessible to living organisms.
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481
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Berteau O, Benjdia A. DNA Repair by the Radical SAM Enzyme Spore Photoproduct Lyase: From Biochemistry to Structural Investigations. Photochem Photobiol 2017; 93:67-77. [DOI: 10.1111/php.12702] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/19/2016] [Indexed: 10/20/2022]
Affiliation(s)
- Olivier Berteau
- Micalis Institute; INRA; ChemSyBio; AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
| | - Alhosna Benjdia
- Micalis Institute; INRA; ChemSyBio; AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
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482
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Bruender NA, Grell TAJ, Dowling DP, McCarty RM, Drennan CL, Bandarian V. 7-Carboxy-7-deazaguanine Synthase: A Radical S-Adenosyl-l-methionine Enzyme with Polar Tendencies. J Am Chem Soc 2017; 139:1912-1920. [PMID: 28045519 PMCID: PMC5301278 DOI: 10.1021/jacs.6b11381] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Radical S-adenosyl-l-methionine (SAM)
enzymes are widely distributed and catalyze diverse reactions. SAM
binds to the unique iron atom of a site-differentiated [4Fe-4S] cluster
and is reductively cleaved to generate a 5′-deoxyadenosyl radical,
which initiates turnover. 7-Carboxy-7-deazaguanine (CDG) synthase
(QueE) catalyzes a key step in the biosynthesis of 7-deazapurine containing
natural products. 6-Carboxypterin (6-CP), an oxidized analogue of
the natural substrate 6-carboxy-5,6,7,8-tetrahydropterin (CPH4), is shown to be an alternate substrate for CDG synthase.
Under reducing conditions that would promote the reductive cleavage
of SAM, 6-CP is turned over to 6-deoxyadenosylpterin (6-dAP), presumably
by radical addition of the 5′-deoxyadenosine followed by oxidative
decarboxylation to the product. By contrast, in the absence of the
strong reductant, dithionite, the carboxylate of 6-CP is esterified
to generate 6-carboxypterin-5′-deoxyadenosyl ester (6-CP-dAdo
ester). Structural studies with 6-CP and SAM also reveal electron
density consistent with the ester product being formed in crystallo.
The differential reactivity of 6-CP under reducing and nonreducing
conditions highlights the ability of radical SAM enzymes to carry
out both polar and radical transformations in the same active site.
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Affiliation(s)
- Nathan A Bruender
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | | | | | - Reid M McCarty
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | | | - Vahe Bandarian
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
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483
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The Catalytic Mechanism of the Class C Radical S
-Adenosylmethionine Methyltransferase NosN. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609948] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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484
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Ding W, Li Y, Zhao J, Ji X, Mo T, Qianzhu H, Tu T, Deng Z, Yu Y, Chen F, Zhang Q. The Catalytic Mechanism of the Class C Radical S-Adenosylmethionine Methyltransferase NosN. Angew Chem Int Ed Engl 2017; 56:3857-3861. [PMID: 28112859 DOI: 10.1002/anie.201609948] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/15/2016] [Indexed: 12/23/2022]
Abstract
S-Adenosylmethionine (SAM) is one of the most common co-substrates in enzyme-catalyzed methylation reactions. Most SAM-dependent reactions proceed through an SN 2 mechanism, whereas a subset of them involves radical intermediates for methylating non-nucleophilic substrates. Herein, we report the characterization and mechanistic investigation of NosN, a class C radical SAM methyltransferase involved in the biosynthesis of the thiopeptide antibiotic nosiheptide. We show that, in contrast to all known SAM-dependent methyltransferases, NosN does not produce S-adenosylhomocysteine (SAH) as a co-product. Instead, NosN converts SAM into 5'-methylthioadenosine as a direct methyl donor, employing a radical-based mechanism for methylation and releasing 5'-thioadenosine as a co-product. A series of biochemical and computational studies allowed us to propose a comprehensive mechanism for NosN catalysis, which represents a new paradigm for enzyme-catalyzed methylation reactions.
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Affiliation(s)
- Wei Ding
- Department of Chemistry, Fudan University, Shanghai, 200433, China.,School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yongzhen Li
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Junfeng Zhao
- Department of Chemistry, Fudan University, Shanghai, 200433, China.,Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Tianlu Mo
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Haocheng Qianzhu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Tao Tu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Fener Chen
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China
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485
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Jäger CM, Croft AK. Radical Reaction Control in the AdoMet Radical Enzyme CDG Synthase (QueE): Consolidate, Destabilize, Accelerate. Chemistry 2017; 23:953-962. [PMID: 27859789 PMCID: PMC5347944 DOI: 10.1002/chem.201604719] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Indexed: 12/29/2022]
Abstract
Controlling radical intermediates and thus catalysing and directing complex radical reactions is a central feature of S-adensosylmethionine (SAM)-dependent radical enzymes. We report ab initio and DFT calculations highlighting the specific influence of ion complexation, including Mg2+ , identified as a key catalytic component on radical stability and reaction control in 7-carboxy-7-deazaguanine synthase (QueE). Radical stabilisation energies (RSEs) of key intermediates and radical clock-like model systems of the enzyme-catalysed rearrangement of 6-carboxytetrahydropterin (CPH4), reveals a directing role of Mg2+ in destabilising both the substrate-derived radical and corresponding side reactions, with the effect that the experimentally-observed rearrangement becomes dominant over possible alternatives. Importantly, this is achieved with minimal disruption of the thermodynamics of the substrate itself, affording a novel mechanism for an enzyme to both maintain binding potential and accelerate the rearrangement step. Other mono and divalent ions were probed with only dicationic species achieving the necessary radical conformation to facilitate the reaction.
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Affiliation(s)
- Christof M. Jäger
- The University of NottinghamDepartment of Chemical and Environmental EngineeringUniversity ParkNottinghamNG7 2RDUnited Kingdom
| | - Anna K. Croft
- The University of NottinghamDepartment of Chemical and Environmental EngineeringUniversity ParkNottinghamNG7 2RDUnited Kingdom
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486
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Bruender NA, Bandarian V. The Creatininase Homolog MftE from Mycobacterium smegmatis Catalyzes a Peptide Cleavage Reaction in the Biosynthesis of a Novel Ribosomally Synthesized Post-translationally Modified Peptide (RiPP). J Biol Chem 2017; 292:4371-4381. [PMID: 28077628 DOI: 10.1074/jbc.m116.762062] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/03/2017] [Indexed: 11/06/2022] Open
Abstract
Most ribosomally synthesized and post-translationally modified peptide (RiPP) natural products are processed by tailoring enzymes to create complex natural products that are still recognizably peptide-based. However, some tailoring enzymes dismantle the peptide en route to synthesis of small molecules. A small molecule natural product of as yet unknown structure, mycofactocin, is thought to be synthesized in this way via the mft gene cluster found in many strains of mycobacteria. This cluster harbors at least six genes, which appear to be conserved across species. We have previously shown that one enzyme from this cluster, MftC, catalyzes the oxidative decarboxylation of the C-terminal Tyr of the substrate peptide MftA in a reaction that requires the MftB protein. Herein we show that mftE encodes a creatininase homolog that catalyzes cleavage of the oxidatively decarboxylated MftA peptide to liberate its final two residues, including the C-terminal decarboxylated Tyr (VY*). Unlike MftC, which requires MftB for function, MftE catalyzes the cleavage reaction in the absence of MftB. The identification of this novel metabolite, VY*, supports the notion that the mft cluster is involved in generating a small molecule from the MftA peptide. The ability to produce VY* from MftA by in vitro reconstitution of the activities of MftB, MftC, and MftE sets the stage for identification of the novel metabolite that results from the proteins encoded by the mft cluster.
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Affiliation(s)
- Nathan A Bruender
- From the Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
| | - Vahe Bandarian
- From the Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
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487
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Liu L, Ji X, Li Y, Ji W, Mo T, Ding W, Zhang Q. A mechanistic study of the non-oxidative decarboxylation catalyzed by the radical S-adenosyl-l-methionine enzyme BlsE involved in blasticidin S biosynthesis. Chem Commun (Camb) 2017; 53:8952-8955. [DOI: 10.1039/c7cc04286h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BlsE-catalyzed non-oxidative decarboxylation is initiated by a hydrogen abstraction from a sugar carbon of the substrate cytosylglucuronic acid (CGA).
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Affiliation(s)
- Lei Liu
- College of Life Science & Biotechnology
- Mianyang Normal University
- Mianyang 621000
- P. R. China
- Department of Chemistry
| | - Xinjian Ji
- Department of Chemistry
- Fudan University
- Shanghai
- China
| | - Yongzhen Li
- Department of Chemistry
- Fudan University
- Shanghai
- China
- Medical College of Qinghai University
| | - Wenjuan Ji
- Department of Chemistry
- Fudan University
- Shanghai
- China
| | - Tianlu Mo
- Department of Chemistry
- Fudan University
- Shanghai
- China
| | - Wei Ding
- Department of Chemistry
- Fudan University
- Shanghai
- China
| | - Qi Zhang
- Department of Chemistry
- Fudan University
- Shanghai
- China
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488
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He N, Wu P, Lei Y, Xu B, Zhu X, Xu G, Gao Y, Qi J, Deng Z, Tang G, Chen W, Xiao Y. Construction of an octosyl acid backbone catalyzed by a radical S-adenosylmethionine enzyme and a phosphatase in the biosynthesis of high-carbon sugar nucleoside antibiotics. Chem Sci 2017; 8:444-451. [PMID: 28451191 PMCID: PMC5365060 DOI: 10.1039/c6sc01826b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/17/2016] [Indexed: 01/26/2023] Open
Abstract
Unique bicyclic octosyl uronic acid nucleosides include ezomycin, malayamycin, and octosyl acid (OA). They are structurally characterized by OA, an unusual 8-carbon furanosyl nucleoside core proposed to be the precursor to polyoxin and nikkomycin. Despite the well-known bioactivity of these nucleoside antibiotics, the biosynthesis of OA has not been elucidated yet. Here we report the two pivotal enzymatic steps in the polyoxin biosynthetic pathway leading to the identification of OA as a key intermediate. Our data suggest that this intermediate is formed via a free radical reaction catalyzed by the radical S-adenosylmethionine (SAM) enzyme, PolH, and using 3'-enolpyruvyl uridine 5'-monophosphate (3'-EUMP) as a substrate. Subsequent dephosphorylation catalyzed by phosphatase PolJ converts the resulting octosyl acid 5'-phosphate (OAP) to OA. These results provide, for the first time, significant in vitro evidence for the biosynthetic origins of the C8 backbone of OA.
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Affiliation(s)
- Nisha He
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
- CAS Key Laboratory of Synthetic Biology , CAS Center for Excellence in Molecular Plant Sciences , Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , 300 FengLin Road , Shanghai 200032 , China .
- University of Chinese Academy of Sciences , Beijing 100039 , China
| | - Pan Wu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
| | - Yongxing Lei
- CAS Key Laboratory of Synthetic Biology , CAS Center for Excellence in Molecular Plant Sciences , Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , 300 FengLin Road , Shanghai 200032 , China .
- University of Chinese Academy of Sciences , Beijing 100039 , China
| | - Baofu Xu
- CAS Key Laboratory of Synthetic Biology , CAS Center for Excellence in Molecular Plant Sciences , Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , 300 FengLin Road , Shanghai 200032 , China .
- University of Chinese Academy of Sciences , Beijing 100039 , China
| | - Xiaochen Zhu
- CAS Key Laboratory of Synthetic Biology , CAS Center for Excellence in Molecular Plant Sciences , Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , 300 FengLin Road , Shanghai 200032 , China .
| | - Gudan Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
| | - Yaojie Gao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
| | - Jianzhao Qi
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
| | - Gongli Tang
- 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
| | - Wenqing Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery , Ministry of Education , School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , China .
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology , CAS Center for Excellence in Molecular Plant Sciences , Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , 300 FengLin Road , Shanghai 200032 , China .
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489
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Ding W, Wu Y, Ji X, Qianzhu H, Chen F, Deng Z, Yu Y, Zhang Q. Nucleoside-linked shunt products in the reaction catalyzed by the class C radical S-adenosylmethionine methyltransferase NosN. Chem Commun (Camb) 2017; 53:5235-5238. [DOI: 10.1039/c7cc02162c] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A series of nucleoside-linked shunt products have been identified in reactions catalyzed by NosN, a class C radical S-adenosylmethionine (SAM) methyltransferase, providing strong evidence supporting that 5′-methylthioadenosine (MTA) is a direct methyl donor in this reaction.
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Affiliation(s)
- Wei Ding
- School of Life Sciences
- Lanzhou University
- Lanzhou
- China
- Department of Chemistry
| | - Yujie Wu
- School of Life Sciences
- Lanzhou University
- Lanzhou
- China
- Department of Chemistry
| | - Xinjian Ji
- Department of Chemistry
- Fudan University
- Shanghai
- China
| | | | - Fener Chen
- Department of Chemistry
- Fudan University
- Shanghai
- China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education)
- School of Pharmaceutical Sciences
- Wuhan University
- Wuhan
- China
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education)
- School of Pharmaceutical Sciences
- Wuhan University
- Wuhan
- China
| | - Qi Zhang
- Department of Chemistry
- Fudan University
- Shanghai
- China
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490
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Yang L, Adhikari J, Gross ML, Li L. Kinetic Isotope Effects and Hydrogen/Deuterium Exchange Reveal Large Conformational Changes During the Catalysis of the Clostridium acetobutylicum Spore Photoproduct Lyase. Photochem Photobiol 2017; 93:331-342. [PMID: 27992649 PMCID: PMC5315627 DOI: 10.1111/php.12697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/29/2016] [Indexed: 11/30/2022]
Abstract
Spore photoproduct lyase (SPL) catalyzes the direct reversal of a thymine dimer 5-thyminyl-5,6-dihydrothymine (i.e. the spore photoproduct (SP)) to two thymine residues in germinating endospores. Previous studies suggest that SPL from the bacterium Bacillus subtilis (Bs) harbors an unprecedented radical-transfer pathway starting with cysteine 141 proceeding through tyrosine 99. However, in SPL from the bacterium Clostridium acetobutylicum (Ca), the cysteine (at position 74) and the tyrosine are located on the opposite sides of a substrate-binding pocket that has to collapse to bring the two residues into proximity, enabling the C→Y radical passage as implied in SPL(Bs) . To test this hypothesis, we adopted hydrogen/deuterium exchange mass spectrometry (HDX-MS) to show that C74(Ca) is located at a highly flexible region. The repair of dinucleotide SP TpT by SPL(Ca) is eight-fold to 10-fold slower than that by SPL(Bs) ; the process also generates a large portion of the aborted product TpTSO2- . SPL(Ca) exhibits apparent (D V) kinetic isotope effects (KIEs) of ~6 and abnormally large competitive (D V/K) KIEs (~20), both of which are much larger than the KIEs observed for SPL(Bs) . All these observations indicate that SPL(Ca) possesses a flexible active site and readily undergoes conformational changes during catalysis.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
| | - Jagat Adhikari
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO 63130, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
- Department of Biochemistry and Molecular Biology & Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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491
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Characterization of Radical S-adenosylmethionine Enzymes and Intermediates in their Reactions by Continuous Wave and Pulse Electron Paramagnetic Resonance Spectroscopies. FUTURE DIRECTIONS IN METALLOPROTEIN AND METALLOENZYME RESEARCH 2017. [DOI: 10.1007/978-3-319-59100-1_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
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492
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Heidinger L, Kneuttinger AC, Kashiwazaki G, Weber S, Carell T, Schleicher E. Direct observation of a deoxyadenosyl radical in an active enzyme environment. FEBS Lett 2016; 590:4489-4494. [PMID: 27878994 DOI: 10.1002/1873-3468.12498] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 11/11/2022]
Abstract
5'-deoxyadenosyl radicals have been proposed as the first common intermediate in the molecular reaction mechanism of the family of radical S-adenosyl-l-methionine (SAM) enzymes. However, this radical species has not yet been directly observed in a catalytically active enzyme environment. In a reduced and SAM-containing C140A mutant of the spore photoproduct lyase from Geobacillus thermodenitrificans, a mutant with altered catalytic activity, we were able to identify an organic radical with pronounced hyperfine structure using electron paramagnetic resonance spectroscopy. Guided by quantum-chemical computations at the density functional theory level of theory, this radical could be tentatively assigned to a deoxyadenosyl radical, which provides first experimental evidence for this intermediate in the reaction mechanism of radical SAM enzymes.
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Affiliation(s)
- Lorenz Heidinger
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Andrea C Kneuttinger
- Department für Chemie, Ludwig-Maximilians-Universität München, Germany.,Institute of Biophysics and Physical Biochemistry, University of Regensburg, Germany
| | - Gengo Kashiwazaki
- Department für Chemie, Ludwig-Maximilians-Universität München, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Thomas Carell
- Department für Chemie, Ludwig-Maximilians-Universität München, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
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493
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Unjaroen D, Swart M, Browne WR. Electrochemical Polymerization of Iron(III) Polypyridyl Complexes through C–C Coupling of Redox Non-innocent Phenolato Ligands. Inorg Chem 2016; 56:470-479. [DOI: 10.1021/acs.inorgchem.6b02378] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Duenpen Unjaroen
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marcel Swart
- Institut de Química Computacional i Catàlisi (IQCC),
Departament de Química, Universitat de Girona, Campus Montilivi, 17003 Girona, Catalonia, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Wesley R. Browne
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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494
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Bhandari DM, Fedoseyenko D, Begley TP. Tryptophan Lyase (NosL): A Cornucopia of 5′-Deoxyadenosyl Radical Mediated Transformations. J Am Chem Soc 2016; 138:16184-16187. [DOI: 10.1021/jacs.6b06139] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dhananjay M. Bhandari
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Dmytro Fedoseyenko
- 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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495
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Hanson AD, Beaudoin GA, McCarty DR, Gregory JF. Does Abiotic Stress Cause Functional B Vitamin Deficiency in Plants? PLANT PHYSIOLOGY 2016; 172:2082-2097. [PMID: 27807106 PMCID: PMC5129723 DOI: 10.1104/pp.16.01371] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/19/2016] [Indexed: 05/20/2023]
Abstract
B vitamins are the precursors of essential metabolic cofactors but are prone to destruction under stress conditions. It is therefore a priori reasonable that stressed plants suffer B vitamin deficiencies and that certain stress symptoms are metabolic knock-on effects of these deficiencies. Given the logic of these arguments, and the existence of data to support them, it is a shock to realize that the roles of B vitamins in plant abiotic stress have had minimal attention in the literature (100-fold less than hormones) and continue to be overlooked. In this article, we therefore aim to explain the connections among B vitamins, enzyme cofactors, and stress conditions in plants. We first outline the chemistry and biochemistry of B vitamins and explore the concept of vitamin deficiency with the help of information from mammals. We then summarize classical and recent evidence for stress-induced vitamin deficiencies and for plant responses that counter these deficiencies. Lastly, we consider potential implications for agriculture.
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Affiliation(s)
- Andrew D Hanson
- Horticultural Sciences Department (A.D.H., G.A.B., D.R.M) and Food Science and Human Nutrition Department (J.F.G.), University of Florida, Gainesville, Florida 32611-0690
| | - Guillaume A Beaudoin
- Horticultural Sciences Department (A.D.H., G.A.B., D.R.M) and Food Science and Human Nutrition Department (J.F.G.), University of Florida, Gainesville, Florida 32611-0690
| | - Donald R McCarty
- Horticultural Sciences Department (A.D.H., G.A.B., D.R.M) and Food Science and Human Nutrition Department (J.F.G.), University of Florida, Gainesville, Florida 32611-0690
| | - Jesse F Gregory
- Horticultural Sciences Department (A.D.H., G.A.B., D.R.M) and Food Science and Human Nutrition Department (J.F.G.), University of Florida, Gainesville, Florida 32611-0690
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496
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Laurino P, Tawfik DS. Spontaneous Emergence of
S
‐Adenosylmethionine and the Evolution of Methylation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609615] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Paola Laurino
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot 76100 Israel
| | - Dan S. Tawfik
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot 76100 Israel
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497
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Laurino P, Tawfik DS. Spontaneous Emergence of S-Adenosylmethionine and the Evolution of Methylation. Angew Chem Int Ed Engl 2016; 56:343-345. [PMID: 27901309 DOI: 10.1002/anie.201609615] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Indexed: 12/28/2022]
Abstract
S-Adenosylmethionine (SAM) is an essential methylation cofactor. The origins of SAM methylation are complex, seemingly demanding the simultaneous emergence of an enzyme that makes SAM and enzyme(s) that utilize it. We report that both ATP and adenosine spontaneously react with methionine to yield SAM, thus suggesting that SAM could have emerged by chance. SAM methylation thus exemplifies how metabolites and pathways can co-emerge through the gradual recruitment of individual enzymes in reverse order.
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Affiliation(s)
- Paola Laurino
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
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498
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Parent A, Guillot A, Benjdia A, Chartier G, Leprince J, Berteau O. The B 12-Radical SAM Enzyme PoyC Catalyzes Valine C β-Methylation during Polytheonamide Biosynthesis. J Am Chem Soc 2016; 138:15515-15518. [PMID: 27934015 PMCID: PMC5410653 DOI: 10.1021/jacs.6b06697] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Genomic and metagenomic
investigations have recently led to the
delineation of a novel class of natural products called ribosomally
synthesized and post-translationally modified peptides (RiPPs). RiPPs
are ubiquitous among living organisms and include pharmaceutically
relevant compounds such as antibiotics and toxins. A prominent example
is polytheonamide A, which exhibits numerous post-translational modifications,
some of which were unknown in ribosomal peptides until recently. Among
these post-translational modifications, C-methylations have been proposed
to be catalyzed by two putative radical S-adenosylmethionine
(rSAM) enzymes, PoyB and PoyC. Here we report the in vitro activity of PoyC, the first B12-dependent rSAM enzyme
catalyzing peptide Cβ-methylation. We show that PoyC
catalyzes the formation of S-adenosylhomocysteine
and 5′-deoxyadenosine and the transfer of a methyl group to l-valine residue. In addition, we demonstrate for the first
time that B12-rSAM enzymes have a tightly bound MeCbl cofactor
that during catalysis transfers a methyl group originating from S-adenosyl-l-methionine. Collectively, our results
shed new light on polytheonamide biosynthesis and the large and emerging
family of B12-rSAM enzymes.
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Affiliation(s)
- Aubérie Parent
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay , F-78350 Jouy-en-Josas, France
| | - Alain Guillot
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay , F-78350 Jouy-en-Josas, France
| | - Alhosna Benjdia
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay , F-78350 Jouy-en-Josas, France
| | - Gwladys Chartier
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay , F-78350 Jouy-en-Josas, France
| | - Jérôme Leprince
- INSERM U982, Université Rouen-Normandie , F-76821 Mont-Saint-Aignan, France
| | - Olivier Berteau
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay , F-78350 Jouy-en-Josas, France
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499
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An HD domain phosphohydrolase active site tailored for oxetanocin-A biosynthesis. Proc Natl Acad Sci U S A 2016; 113:13750-13755. [PMID: 27849620 DOI: 10.1073/pnas.1613610113] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
HD domain phosphohydrolase enzymes are characterized by a conserved set of histidine and aspartate residues that coordinate an active site metallocenter. Despite the important roles these enzymes play in nucleotide metabolism and signal transduction, few have been both biochemically and structurally characterized. Here, we present X-ray crystal structures and biochemical characterization of the Bacillus megaterium HD domain phosphohydrolase OxsA, involved in the biosynthesis of the antitumor, antiviral, and antibacterial compound oxetanocin-A. These studies reveal a previously uncharacterized reaction for this family; OxsA catalyzes the conversion of a triphosphorylated compound into a nucleoside, releasing one molecule of inorganic phosphate at a time. Remarkably, this functionality is a result of the OxsA active site, which based on structural and kinetic analyses has been tailored to bind the small, four-membered ring of oxetanocin-A over larger substrates. Furthermore, our OxsA structures show an active site that switches from a dinuclear to a mononuclear metal center as phosphates are eliminated from substrate.
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500
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Makins C, Ghosh S, Román-Meléndez GD, Malec PA, Kennedy RT, Marsh ENG. Does Viperin Function as a Radical S-Adenosyl-l-methionine-dependent Enzyme in Regulating Farnesylpyrophosphate Synthase Expression and Activity? J Biol Chem 2016; 291:26806-26815. [PMID: 27834682 DOI: 10.1074/jbc.m116.751040] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/31/2016] [Indexed: 01/09/2023] Open
Abstract
Viperin is an endoplasmic reticulum-associated antiviral responsive protein that is highly up-regulated in eukaryotic cells upon viral infection through both interferon-dependent and independent pathways. Viperin is predicted to be a radical S-adenosyl-l-methionine (SAM) enzyme, but it is unknown whether viperin actually exploits radical SAM chemistry to exert its antiviral activity. We have investigated the interaction of viperin with its most firmly established cellular target, farnesyl pyrophosphate synthase (FPPS). Numerous enveloped viruses utilize cholesterol-rich lipid rafts to bud from the host cell membrane, and it is thought that by inhibiting FPPS activity (and therefore cholesterol synthesis), viperin retards viral budding from infected cells. We demonstrate that, consistent with this hypothesis, overexpression of viperin in human embryonic kidney cells reduces the intracellular rate of accumulation of FPPS but does not inhibit or inactivate FPPS. The endoplasmic reticulum-localizing, N-terminal amphipathic helix of viperin is specifically required for viperin to reduce cellular FPPS levels. However, although viperin reductively cleaves SAM to form 5'-deoxyadenosine in a slow, uncoupled reaction characteristic of radical SAM enzymes, this cleavage reaction is independent of FPPS. Furthermore, mutation of key cysteinyl residues ligating the catalytic [Fe4S4] cluster in the radical SAM domain, surprisingly, does not abolish the inhibitory activity of viperin against FPPS; indeed, some mutations potentiate viperin activity. These observations imply that viperin does not act as a radical SAM enzyme in regulating FPPS.
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Affiliation(s)
- Caitlyn Makins
- From the Departments of Chemistry and.,Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
| | | | | | | | | | - E Neil G Marsh
- From the Departments of Chemistry and .,Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
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