101
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Koehnke J, Bent AF, Zollman D, Smith K, Houssen WE, Zhu X, Mann G, Lebl T, Scharff R, Shirran S, Botting CH, Jaspars M, Schwarz-Linek U, Naismith JH. The Cyanobactin Heterocyclase Enzyme: A Processive Adenylase That Operates with a Defined Order of Reaction. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306302] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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102
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Koehnke J, Bent AF, Zollman D, Smith K, Houssen WE, Zhu X, Mann G, Lebl T, Scharff R, Shirran S, Botting CH, Jaspars M, Schwarz-Linek U, Naismith JH. The cyanobactin heterocyclase enzyme: a processive adenylase that operates with a defined order of reaction. Angew Chem Int Ed Engl 2013; 52:13991-6. [PMID: 24214017 PMCID: PMC3995012 DOI: 10.1002/anie.201306302] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/03/2013] [Indexed: 11/12/2022]
Affiliation(s)
- Jesko Koehnke
- Biomedical Science Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST (UK)
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103
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Genome Mining Expands the Chemical Diversity of the Cyanobactin Family to Include Highly Modified Linear Peptides. ACTA ACUST UNITED AC 2013; 20:1033-43. [DOI: 10.1016/j.chembiol.2013.06.015] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 06/20/2013] [Accepted: 06/30/2013] [Indexed: 11/19/2022]
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104
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Bent AF, Koehnke J, Houssen WE, Smith MCM, Jaspars M, Naismith JH. Structure of PatF from Prochloron didemni. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:618-23. [PMID: 23722837 PMCID: PMC3668578 DOI: 10.1107/s1744309113012931] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 05/12/2013] [Indexed: 11/10/2022]
Abstract
Patellamides are macrocyclic peptides with potent biological effects and are a subset of the cyanobactins. Cyanobactins are natural products that are produced by a series of enzymatic transformations and a common modification is the addition of a prenyl group. Puzzlingly, the pathway for patellamides in Prochloron didemni contains a gene, patF, with homology to prenylases, but patellamides are not themselves prenylated. The structure of the protein PatF was cloned, expressed, purified and determined. Prenylase activity could not be demonstrated for the protein, and examination of the structure revealed changes in side-chain identity at the active site. It is suggested that these changes have inactivated the protein. Attempts to mutate these residues led to unfolded protein.
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Affiliation(s)
- Andrew F. Bent
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland
| | - Jesko Koehnke
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland
| | - Wael E. Houssen
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland
- Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Aberdeen AB25 2ZD, Scotland
| | - Margaret C. M. Smith
- Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Aberdeen AB25 2ZD, Scotland
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, England
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland
| | - James H. Naismith
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland
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105
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McIntosh JA, Lin Z, Tianero MDB, Schmidt EW. Aestuaramides, a natural library of cyanobactin cyclic peptides resulting from isoprene-derived Claisen rearrangements. ACS Chem Biol 2013; 8:877-83. [PMID: 23411099 DOI: 10.1021/cb300614c] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We report 12 cyanobactin cyclic peptides, the aestuaramides, from the cultivated cyanobacterium Lyngbya aestuarii. We show that aestuaramides are synthesized enzymatically as reverse O-prenylated tyrosine ethers that subsequently undergo a Claisen rearrangement to produce forward C-prenylated tyrosine. These results reveal that a nonenzymatic Claisen rearrangement dictates isoprene regiochemistry in a natural system. They also reveal one of the mechanisms that organisms use to generate structurally diverse compound libraries starting from simple ribosomal peptide pathways (RiPPs).
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Affiliation(s)
- John A. McIntosh
- Department of Medicinal
Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United
States
| | - Zhenjian Lin
- Department of Medicinal
Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United
States
| | - Ma. Diarey B. Tianero
- Department of Medicinal
Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United
States
| | - Eric W. Schmidt
- Department of Medicinal
Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United
States
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106
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Yang X, van der Donk WA. Ribosomally synthesized and post-translationally modified peptide natural products: new insights into the role of leader and core peptides during biosynthesis. Chemistry 2013; 19:7662-77. [PMID: 23666908 DOI: 10.1002/chem.201300401] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Indexed: 11/08/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a major class of natural products with a high degree of structural diversity and a wide variety of bioactivities. Understanding the biosynthetic machinery of these RiPPs will benefit the discovery and development of new molecules with potential pharmaceutical applications. In this Concept article, we discuss the features of the biosynthetic pathways to different RiPP classes, and propose mechanisms regarding recognition of the precursor peptide by the post-translational modification enzymes. We propose that the leader peptides function as allosteric regulators that bind the active form of the biosynthetic enzymes in a conformational selection process. We also speculate how enzymes that generate polycyclic products of defined topologies may have been selected for during evolution.
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Affiliation(s)
- Xiao Yang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801, USA
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107
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Koehnke J, Morawitz F, Bent AF, Houssen WE, Shirran SL, Fuszard MA, Smellie IA, Botting CH, Smith MCM, Jaspars M, Naismith JH. An enzymatic route to selenazolines. Chembiochem 2013; 14:564-7. [PMID: 23483642 PMCID: PMC3625746 DOI: 10.1002/cbic.201300037] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Indexed: 11/11/2022]
Abstract
Ringing the changes: Selenazolines have applications in medicinal chemistry, but their synthesis is challenging. We report a new convenient and less toxic route to these heterocycles that starts from commercially available selenocysteine. The new route depends on a heterocyclase enzyme that creates oxazolines and thiazolines from serines/threonines and cysteines.
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Affiliation(s)
- Jesko Koehnke
- Biomedical Science Research Complex, University of St Andrews, North Haugh, St. Andrews, KY16 9ST, UK
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108
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Dunbar KL, Mitchell DA. Revealing nature's synthetic potential through the study of ribosomal natural product biosynthesis. ACS Chem Biol 2013; 8:473-87. [PMID: 23286465 DOI: 10.1021/cb3005325] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribosomally synthesized posttranslationally modified peptides (RiPPs) are a rapidly growing class of natural products with diverse structures and activities. In recent years, a great deal of progress has been made in elucidating the biosynthesis of various RiPP family members. As with the study of nonribosomal peptide and polyketide biosynthetic enzymes, these investigations have led to the discovery of entirely new biological chemistry. With each unique enzyme investigated, a more complex picture of Nature's synthetic potential is revealed. This Review focuses on recent reports (since 2008) that have changed the way that we think about ribosomal natural product biosynthesis and the enzymology of complex bond-forming reactions.
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Affiliation(s)
- Kyle L. Dunbar
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United
States
| | - Douglas A. Mitchell
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United
States
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109
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Barber CJS, Pujara PT, Reed DW, Chiwocha S, Zhang H, Covello PS. The two-step biosynthesis of cyclic peptides from linear precursors in a member of the plant family Caryophyllaceae involves cyclization by a serine protease-like enzyme. J Biol Chem 2013; 288:12500-10. [PMID: 23486480 DOI: 10.1074/jbc.m112.437947] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Caryophyllaceae-type cyclic peptides (CPs) of 5-12 proteinogenic amino acids occur in 10 plant families. In Saponaria vaccaria (Caryophyllaceae), they have been shown to be formed from linear peptide precursors derived from ribosomal translation. There is also evidence for such precursors in other members of the Caryophyllaceae, Rutaceae, and Linaceae families. The biosynthesis of CP in the developing seeds of S. vaccaria was investigated with respect to the enzymes involved in precursor processing. Through biochemical assays with seed extracts and synthetic peptides, an enzyme named oligopeptidase 1 (OLP1) was found that catalyzes the cleavage of intermediates at the N terminus of the incipient CP. A second enzyme, peptide cyclase 1 (PCY1), which was separated chromatographically from OLP1, was found to act on the product of OLP1, giving rise to a cyclic peptide and concomitant removal of a C-terminal flanking sequence. PCY1 was partially purified, and using the methods of proteomics, a full-length cDNA clone encoding an enzyme matching the properties of PCY1 was obtained. The substrate specificity of purified recombinant PCY1, believed to be the first cloned plant enzyme whose function is peptide cyclization, was tested with synthetic peptides. The results are discussed in the light of CP biosynthetic systems of other organisms.
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Affiliation(s)
- Carla J S Barber
- National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
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110
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Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G, Camarero JA, Campopiano DJ, Challis GL, Clardy J, Cotter PD, Craik DJ, Dawson M, Dittmann E, Donadio S, Dorrestein PC, Entian KD, Fischbach MA, Garavelli JS, Göransson U, Gruber CW, Haft DH, Hemscheidt TK, Hertweck C, Hill C, Horswill AR, Jaspars M, Kelly WL, Klinman JP, Kuipers OP, Link AJ, Liu W, Marahiel MA, Mitchell DA, Moll GN, Moore BS, Müller R, Nair SK, Nes IF, Norris GE, Olivera BM, Onaka H, Patchett ML, Piel J, Reaney MJT, Rebuffat S, Ross RP, Sahl HG, Schmidt EW, Selsted ME, Severinov K, Shen B, Sivonen K, Smith L, Stein T, Süssmuth RD, Tagg JR, Tang GL, Truman AW, Vederas JC, Walsh CT, Walton JD, Wenzel SC, Willey JM, van der Donk WA. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep 2013; 30:108-60. [PMID: 23165928 DOI: 10.1039/c2np20085f] [Citation(s) in RCA: 1466] [Impact Index Per Article: 133.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products. The current knowledge regarding the biosynthesis of the >20 distinct compound classes is also reviewed, and commonalities are discussed.
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Affiliation(s)
- Paul G Arnison
- Prairie Plant Systems Inc, Botanical Alternatives Inc, Suite 176, 8B-3110 8th Street E, Saskatoon, SK, S7H 0W2, Canada
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111
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Houssen WE, Koehnke J, Zollman D, Vendome J, Raab A, Smith MCM, Naismith JH, Jaspars M. The Discovery of New Cyanobactins fromCyanothecePCC 7425 Defines a New Signature for Processing of Patellamides. Chembiochem 2012; 13:2683-9. [DOI: 10.1002/cbic.201200661] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Indexed: 11/07/2022]
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112
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Agarwal V, Pierce E, McIntosh J, Schmidt E, Nair S. Structures of Cyanobactin Maturation Enzymes Define a Family of Transamidating Proteases. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.chembiol.2012.09.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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