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Trapping biosynthetic acyl-enzyme intermediates with encoded 2,3-diaminopropionic acid.

Huguenin-Dezot N, Alonzo DA, Heberlig GW, Mahesh M, Nguyen DP, Dornan MH, Boddy CN, Schmeing TM, Chin JW
Nature 565 112-117 (2019)
Related entries: 6ecc, 6ecd, 6ece, 6ecf

Cited: 32 times
EuropePMC logo PMID: 30542153

Abstract

Many enzymes catalyse reactions that proceed through covalent acyl-enzyme (ester or thioester) intermediates1. These enzymes include serine hydrolases2,3 (encoded by one per cent of human genes, and including serine proteases and thioesterases), cysteine proteases (including caspases), and many components of the ubiquitination machinery4,5. Their important acyl-enzyme intermediates are unstable, commonly having half-lives of minutes to hours6. In some cases, acyl-enzyme complexes can be stabilized using substrate analogues or active-site mutations but, although these approaches can provide valuable insight7-10, they often result in complexes that are substantially non-native. Here we develop a strategy for incorporating 2,3-diaminopropionic acid (DAP) into recombinant proteins, via expansion of the genetic code11. We show that replacing catalytic cysteine or serine residues of enzymes with DAP permits their first-step reaction with native substrates, allowing the efficient capture of acyl-enzyme complexes that are linked through a stable amide bond. For one of these enzymes, the thioesterase domain of valinomycin synthetase12, we elucidate the biosynthetic pathway by which it progressively oligomerizes tetradepsipeptidyl substrates to a dodecadepsipeptidyl intermediate, which it then cyclizes to produce valinomycin. By trapping the first and last acyl-thioesterase intermediates in the catalytic cycle as DAP conjugates, we provide structural insight into how conformational changes in thioesterase domains of such nonribosomal peptide synthetases control the oligomerization and cyclization of linear substrates. The encoding of DAP will facilitate the characterization of diverse acyl-enzyme complexes, and may be extended to capturing the native substrates of transiently acylated proteins of unknown function.

Reviews - 6ecb mentioned but not cited (1)

  1. Structural advances toward understanding the catalytic activity and conformational dynamics of modular nonribosomal peptide synthetases. Patel KD, MacDonald MR, Ahmed SF, Singh J, Gulick AM. Nat Prod Rep 40 1550-1582 (2023)

Articles - 6ecb mentioned but not cited (1)

  1. Trapping biosynthetic acyl-enzyme intermediates with encoded 2,3-diaminopropionic acid. Huguenin-Dezot N, Alonzo DA, Heberlig GW, Mahesh M, Nguyen DP, Dornan MH, Boddy CN, Schmeing TM, Chin JW. Nature 565 112-117 (2019)


Reviews citing this publication (6)

  1. Reprogramming the genetic code. de la Torre D, Chin JW. Nat Rev Genet 22 169-184 (2021)
  2. Biosynthesis of depsipeptides, or Depsi: The peptides with varied generations. Alonzo DA, Schmeing TM. Protein Sci 29 2316-2347 (2020)
  3. Bioorthogonal Ligations and Cleavages in Chemical Biology. Li Y, Fu H. ChemistryOpen 9 835-853 (2020)
  4. The Nonribosomal Peptide Valinomycin: From Discovery to Bioactivity and Biosynthesis. Huang S, Liu Y, Liu WQ, Neubauer P, Li J. Microorganisms 9 780 (2021)
  5. Introducing noncanonical amino acids for studying and engineering bacterial microcompartments. Chen H, Wilson J, Ottinger S, Gan Q, Fan C. Curr Opin Microbiol 61 67-72 (2021)
  6. Update of the Pyrrolysyl-tRNA Synthetase/tRNAPyl Pair and Derivatives for Genetic Code Expansion. Gong X, Zhang H, Shen Y, Fu X. J Bacteriol 205 e0038522 (2023)

Articles citing this publication (24)

  1. The structural basis of N-acyl-α-amino-β-lactone formation catalyzed by a nonribosomal peptide synthetase. Kreitler DF, Gemmell EM, Schaffer JE, Wencewicz TA, Gulick AM. Nat Commun 10 3432 (2019)
  2. Systematic Review Cell-Free Approach for Non-canonical Amino Acids Incorporation Into Polypeptides. Cui Z, Johnston WA, Alexandrov K. Front Bioeng Biotechnol 8 1031 (2020)
  3. Structural basis of keto acid utilization in nonribosomal depsipeptide synthesis. Alonzo DA, Chiche-Lapierre C, Tarry MJ, Wang J, Schmeing TM. Nat Chem Biol 16 493-496 (2020)
  4. Biosynthetic Cyclization Catalysts for the Assembly of Peptide and Polyketide Natural Products. Adrover-Castellano ML, Schmidt JJ, Sherman DH. ChemCatChem 13 2095-2116 (2021)
  5. Structure of a bound peptide phosphonate reveals the mechanism of nocardicin bifunctional thioesterase epimerase-hydrolase half-reactions. Patel KD, d'Andrea FB, Gaudelli NM, Buller AR, Townsend CA, Gulick AM. Nat Commun 10 3868 (2019)
  6. The physical basis and practical consequences of biological promiscuity. Copley SD. Phys Biol (2020)
  7. Elastase Inhibitor Cyclotheonellazole A: Total Synthesis and In Vivo Biological Evaluation for Acute Lung Injury. Cui Y, Zhang M, Xu H, Zhang T, Zhang S, Zhao X, Jiang P, Li J, Ye B, Sun Y, Wang M, Deng Y, Meng Q, Liu Y, Fu Q, Lin J, Wang L, Chen Y. J Med Chem 65 2971-2987 (2022)
  8. Mechanism-based traps enable protease and hydrolase substrate discovery. Tang S, Beattie AT, Kafkova L, Petris G, Huguenin-Dezot N, Fiedler M, Freeman M, Chin JW. Nature 602 701-707 (2022)
  9. Novel Modifications of Nonribosomal Peptides from Brevibacillus laterosporus MG64 and Investigation of Their Mode of Action. Li Z, de Vries RH, Chakraborty P, Song C, Zhao X, Scheffers DJ, Roelfes G, Kuipers OP. Appl Environ Microbiol 86 e01981-20 (2020)
  10. Introductory Journal Article Plant proteases and programmed cell death. Stael S, Van Breusegem F, Gevaert K, Nowack MK. J Exp Bot 70 1991-1995 (2019)
  11. Discovery and Genetic Code Expansion of a Polyethylene Terephthalate (PET) Hydrolase from the Human Saliva Metagenome for the Degradation and Bio-Functionalization of PET. Eiamthong B, Meesawat P, Wongsatit T, Jitdee J, Sangsri R, Patchsung M, Aphicho K, Suraritdechachai S, Huguenin-Dezot N, Tang S, Suginta W, Paosawatyanyong B, Babu MM, Chin JW, Pakotiprapha D, Bhanthumnavin W, Uttamapinant C. Angew Chem Int Ed Engl 61 e202203061 (2022)
  12. Genetically programmed cell-based synthesis of non-natural peptide and depsipeptide macrocycles. Spinck M, Piedrafita C, Robertson WE, Elliott TS, Cervettini D, de la Torre D, Chin JW. Nat Chem 15 61-69 (2023)
  13. Enhancing the incorporation of lysine derivatives into proteins with methylester forms of unnatural amino acids. Zhou H, Cheung JW, Carpenter T, Jones SK, Luong NH, Tran NC, Jacobs SE, Galbada Liyanage SA, Cropp TA, Yin J. Bioorg Med Chem Lett 30 126876 (2020)
  14. Structure Revision of Isocereulide A, an Isoform of the Food Poisoning Emetic Bacillus cereus Toxin Cereulide. Walser V, Kranzler M, Ehling-Schulz M, Stark TD, Hofmann TF. Molecules 26 1360 (2021)
  15. A Light-Activated Acyl Carrier Protein "Trap" for Intermediate Capture in Type II Iterative Polyketide Biocatalysis. Kilgour SL, Kilgour DPA, Prasongpholchai P, O'Connor PB, Tosin M. Chemistry 25 16515-16518 (2019)
  16. 2,3-Diaminopropanols Obtained from d-Serine as Intermediates in the Synthesis of Protected 2,3-l-Diaminopropanoic Acid (l-Dap) Methyl Esters. Temperini A, Aiello D, Mazzotti F, Athanassopoulos CM, De Luca P, Siciliano C. Molecules 25 E1313 (2020)
  17. A Photoactivatable Small-Molecule Probe for the In Vivo Capture of Polyketide Intermediates. Kilgour SL, Jenkins R, Tosin M. Chemistry 25 16511-16514 (2019)
  18. Bacillus cereus Toxin Repertoire: Diversity of (Iso)cereulide(s). Walser V, Kranzler M, Dawid C, Ehling-Schulz M, Stark TD, Hofmann TF. Molecules 27 872 (2022)
  19. Engineering enzyme activity using an expanded amino acid alphabet. Birch-Price Z, Taylor CJ, Ortmayer M, Green AP. Protein Eng Des Sel 36 gzac013 (2023)
  20. Site-specific encoding of photoactivity and photoreactivity into antibody fragments. Bridge T, Wegmann U, Crack JC, Orman K, Shaikh SA, Farndon W, Martins C, Saalbach G, Sachdeva A. Nat Chem Biol 19 740-749 (2023)
  21. Comment Enzymes engineered to trap reaction intermediates. Gulick AM. Nature 565 28-29 (2019)
  22. In Vitro Biochemical Characterization of Excised Macrocyclizing Thioesterase Domains from Non-ribosomal Peptide Synthetases. Brazeau-Henrie JT, Paquette AR, Boddy CN. Methods Mol Biol 2670 101-125 (2023)
  23. Mechanism of D-alanine transfer to teichoic acids shows how bacteria acylate cell envelope polymers. Schultz BJ, Snow ED, Walker S. Nat Microbiol 8 1318-1329 (2023)
  24. Selective Synthesis of Lysine Peptides and the Prebiotically Plausible Synthesis of Catalytically Active Diaminopropionic Acid Peptide Nitriles in Water. Thoma B, Powner MW. J Am Chem Soc 145 3121-3130 (2023)


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