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Catalytic role of carbonyl oxygens and water in selinadiene synthase

Nature Catalysis volume 5, pages 128–135 (2022)Cite this article

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Abstract

Terpene synthases (TSs) catalyse the most complex cyclization cascades in nature, with generation and taming of reactive carbocations. Although deprotonation–reprotonation sequences are frequently relevant for TS catalysis, little is known how the enzyme acts in these processes. Here we show, through quantum mechanics (density functional theory)/molecular mechanics molecular dynamics simulations that the main-chain carbonyl oxygen of Gly182 of selina-4(15),7(11)-diene synthase (SdS) has a dual role as a base and an acid and acts in synchrony with one water molecule. The computational model is supported by isotopic labelling experiments confirming the predicted stereochemical course associated with the deprotonation–reprotonation sequence. Gly182 is located within the G1/2 helix break of SdS, with all backbone carbonyl oxygens pointing into the active site having functions in recognizing substrate conformation, stabilizing carbocation intermediates and anchoring their poses. The strict conservation of the G1/2 helix break in type I TSs from bacteria, fungi and plants suggests that its functions as described here may be of general importance in TS catalysis.

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Fig. 1: Cyclization mechanism of SdS.
Fig. 2: Key structures for SdS catalysis obtained from QM(DFT)/MM simulations.
Fig. 3: Molecular orbital interactions during C10–C11 bond rotation in (10R)-A+.
Fig. 4: Stereochemical fate of the geminal C12 and C13 methyl groups of FPP.
Fig. 5: Reprotonation of GB in the biosynthesis of SD.
Fig. 6: Stereochemical course of the protonation-induced cyclization of GB to SD.

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Data availability

The authors declare that data supporting the findings of this study are available within the article and its Supplementary Information file. FPP parameters and key structures are given as Supplementary Data files. Data that support the plots within the paper and other findings of this study are available from the corresponding authors on reasonable request.

References

  1. Christianson, D. W. Structural and chemical biology of terpenoid cyclases. Chem. Rev. 117, 11570–11648 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Christianson, D. W. Structural biology and chemistry of the terpenoid cyclases. Chem. Rev. 106, 3412–3442 (2006).

    Article  CAS  PubMed  Google Scholar 

  3. Dickschat, J. S. Bacterial diterpene biosynthesis. Angew. Chem. Int. Ed. 58, 15964–15976 (2019).

    Article  CAS  Google Scholar 

  4. Hong, Y. J. & Tantillo, D. J. Biosynthetic consequences of multiple sequential post-transition-state bifurcations. Nat. Chem. 6, 104–111 (2014).

    Article  CAS  PubMed  Google Scholar 

  5. Tantillo, D. J. Biosynthesis via carbocations: theoretical studies on terpene formation. Nat. Prod. Rep. 28, 1035–1053 (2011).

    Article  CAS  PubMed  Google Scholar 

  6. Hong, Y. J. & Tantillo, D. J. Branching out from the bisabolyl cation. Unifying mechanistic pathways to barbatene, bazzanene, chamigrene, chamipinene, cumacrene, cuprenene, dunniene, isobazzanene, iso-gamma-bisabolene, isochamigrene, laurene, microbiotene, sesquithujene, sesquisabinene, thujopsene, trichodiene, and widdradiene sesquiterpenes. J. Am. Chem. Soc. 136, 2450–2463 (2014).

    Article  CAS  PubMed  Google Scholar 

  7. Hong, Y. J. & Tantillo, D. J. Consequences of conformational preorganization in sesquiterpene biosynthesis: theoretical studies on the formation of the bisabolene, curcumene, acoradiene, zizaene, cedrene, duprezianene, and sesquithuriferol sesquiterpenes. J. Am. Chem. Soc. 131, 7999–8015 (2009).

    Article  CAS  PubMed  Google Scholar 

  8. Mahadevi, A. S. & Sastry, G. N. Cation-pi interaction: its role and relevance in chemistry, biology, and material science. Chem. Rev. 113, 2100–2138 (2013).

    Article  CAS  PubMed  Google Scholar 

  9. Tantillo, D. J. Importance of inherent substrate reactivity in enzyme-promoted carbocation syclization/rearrangements. Angew. Chem. Int. Ed. 56, 10040–10045 (2017).

    Article  CAS  Google Scholar 

  10. Chen, M. et al. Mechanistic insights from the binding of substrate and carbocation intermediate analogues to aristolochene synthase. Biochemistry 52, 5441–5453 (2013).

    Article  CAS  PubMed  Google Scholar 

  11. Noel, J. P. et al. Structural elucidation of cisoid and transoid cyclization pathways of a sesquiterpene synthase using 2-fluorofarnesyl diphosphates. ACS Chem. Biol. 5, 377–392 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Minami, A., Ozaki, T., Liu, C. & Oikawa, H. Cyclopentane-forming di/sesterterpene synthases: widely distributed enzymes in bacteria, fungi, and plants. Nat. Prod. Rep. 35, 1330–1346 (2018).

    Article  CAS  PubMed  Google Scholar 

  13. Rinkel, J. et al. Mechanisms of the diterpene cyclases β-pinacene synthase from Dictyostelium discoideum and hydropyrene synthase from Streptomyces clavuligerus. Chem. Eur. J. 23, 10501–10505 (2017).

    Article  CAS  PubMed  Google Scholar 

  14. Rinkel, J., Lauterbach, L. & Dickschat, J. S. Spata-13,17-diene synthase—an enzyme with sesqui-, di-, and sesterterpene synthase activity from Streptomyces xinghaiensis. Angew. Chem. Int. Ed. 56, 16385–16389 (2017).

    Article  CAS  Google Scholar 

  15. Bian, G. K. et al. A clade II-D fungal chimeric diterpene synthase from Colletotrichum gloeosporioides produces dolasta-1(15),8-diene. Angew. Chem. Int. Ed. 57, 15887–15890 (2018).

    Article  CAS  Google Scholar 

  16. Rinkel, J., Lauterbach, L. & Dickschat, J. S. A branched diterpene cascade: the mechanism of spinodiene synthase from Saccharopolyspora spinosa. Angew. Chem. Int. Ed. 58, 452–455 (2019).

    Article  CAS  Google Scholar 

  17. Zhang, F., Chen, N. H., Zhou, J. W. & Wu, R. B. Protonation-dependent diphosphate cleavage in FPP cyclases and synthases. ACS Catal. 6, 6918–6929 (2016).

    Article  CAS  Google Scholar 

  18. Hong, Y. J. & Tantillo, D. J. Feasibility of intramolecular proton transfers in terpene biosynthesis-guiding principles. J. Am. Chem. Soc. 137, 4134–4140 (2015).

    Article  CAS  PubMed  Google Scholar 

  19. Seemann, M. et al. Pentalenene synthase. Analysis of active site residues by site-directed mutagenesis. J. Am. Chem. Soc. 124, 7681–7689 (2002).

    Article  CAS  PubMed  Google Scholar 

  20. Jiang, J., He, X. & Cane, D. E. Biosynthesis of the earthy odorant geosmin by a bifunctional Streptomyces coelicolor enzyme. Nat. Chem. Biol. 3, 711–715 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Baer, P. et al. Induced-fit mechanism in class I terpene cyclases. Angew. Chem. Int. Ed. 53, 7652–7656 (2014).

    Article  CAS  Google Scholar 

  22. Köksal, M., Chou, W. K. W., Cane, D. E. & Christianson, D. W. Structure of 2-methylisoborneol synthase from Streptomyces coelicolor and implications for the cyclization of a noncanonical C-methylated monoterpenoid substrate. Biochemistry 51, 3011–3020 (2012).

    Article  PubMed  Google Scholar 

  23. Aaron, J. A., Lin, X., Cane, D. E. & Christianson, D. W. Structure of epi-isozizaene synthase from Streptomyces coelicolor A3(2), a platform for new terpenoid cyclization templates. Biochemistry 49, 1787–1797 (2010).

    Article  CAS  PubMed  Google Scholar 

  24. Xu, H., Rinkel, J. R. & Dickschat, J. S. Isoishwarane synthase from Streptomyces lincolnensis. Org. Chem. Front. 8, 1177–1184 (2021).

    Article  CAS  Google Scholar 

  25. Lauterbach, L., Rinkel, J. & Dickschat, J. S. Two bacterial diterpene synthases from Allokutzneria albata for bonnadiene and for phomopsene and allokutznerene. Angew. Chem. Int. Ed. 57, 8280–8283 (2018).

    Article  CAS  Google Scholar 

  26. Tantillo, D. J. Walking in the woods with quantum chemistry—applications of quantum chemical calculations in natural products research. Nat. Prod. Rep. 30, 1079–1086 (2013).

    Article  CAS  PubMed  Google Scholar 

  27. Ganguly, A., Thaplyal, P., Rosta, E., Bevilacqua, P. C. & Hammes-Schiffer, S. Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis Delta virus ribozyme. J. Am. Chem. Soc. 136, 1483–1496 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Rooklin, D. W., Lu, M. & Zhang, Y. Revelation of a catalytic calcium-binding site elucidates unusual metal dependence of a human apyrase. J. Am. Chem. Soc. 134, 15595–15603 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Ke, Z., Smith, G. K., Zhang, Y. & Guo, H. Molecular mechanism for eliminylation, a newly discovered post-translational modification. J. Am. Chem. Soc. 133, 11103–11105 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Wang, Y.-H., Xie, H., Zhou, J., Zhang, F. & Wu, R. Substrate folding modes in trichodiene synthase: a determinant of chemo- and stereoselectivity. ACS Catal. 7, 5841–5846 (2017).

    Article  CAS  Google Scholar 

  31. Diao, H. et al. Biosynthetic mechanism of lanosterol: a completed story. ACS Catal. 10, 2157–2168 (2020).

    Article  CAS  Google Scholar 

  32. Chen, N., Wang, S., Smentek, L., Hess, B. A. & Wu, R. Biosynthetic mechanism of lanosterol: cyclization. Angew. Chem. Int. Ed. 54, 8693–8696 (2015).

    Article  CAS  Google Scholar 

  33. Das, S., Dixit, M. & Major, D. T. First principles model calculations of the biosynthetic pathway in selinadiene synthase. Bioorg. Med. Chem. 24, 4867–4870 (2016).

    Article  PubMed  Google Scholar 

  34. Rabe, P. et al. Terpene cyclases from social Amoebae. Angew. Chem. Int. Ed. 55, 15420–15423 (2016).

    Article  CAS  Google Scholar 

  35. Rinkel, J. & Dickschat, J. S. Addressing the chemistry of germacrene A by isotope labeling experiments. Org. Lett. 21, 2426–2429 (2019).

    Article  CAS  PubMed  Google Scholar 

  36. Hahn, F. M., Hurlburt, A. P. & Poulter, C. D. Escherichia coli open reading frame 696 is idi, a nonessential gene encoding isopentenyl diphosphate isomerase. J. Bacteriol. 181, 4499–4504 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Cornforth, J. W., Cornforth, R. H., Popjak, G. & Yengoyan, L. Sudies on the biosynthesis of cholesterol XX. Steric course of decarboxylation of 5-pyrophosphomevalonate and of the carbon to carbon bond formation in the biosynthesis of farnesyl pyrophosphate. J. Biol. Chem. 241, 3970–3987 (1966).

    Article  CAS  PubMed  Google Scholar 

  38. Zhou, J. et al. Protonation-triggered carbon-chain elongation in geranyl pyrophosphate synthase (GPPS). ACS Catal. 5, 4466–4478 (2015).

    Article  CAS  Google Scholar 

  39. Rabe, P. et al. Conformational analysis, thermal rearrangement and EI-MS-fragmentation mechanism of (1(10)E,4E,6S,7R)-germacradien-6-ol by 13C-labeling experiments. Angew. Chem. Int. Ed. 54, 13448–13451 (2015).

    Article  CAS  Google Scholar 

  40. Lin, F.-L. et al. Mechanistic characterization of the fusicoccane-type diterpene synthase for myrothec-15(17)-en-7-ol. ACS Catal. 10, 4306–4312 (2020).

    Article  CAS  Google Scholar 

  41. Dereka, B. et al. Crossover from hydrogen to chemical bonding. Science 371, 160–164 (2021).

    Article  CAS  PubMed  Google Scholar 

  42. Rabe, P., Pahirulzaman, K. A. K. & Dickschat, J. S. Structures and biosynthesis of corvol ethers—sesquiterpenes from the actinomycete Kitasatospora setae. Angew. Chem. Int. Ed. 54, 6041–6045 (2015).

    Article  CAS  Google Scholar 

  43. Rabe, P., Rinkel, J., Klapschinski, T. A., Barra, L. & Dickschat, J. S. A method for investigating the stereochemical course of terpene cyclisations. Org. Biomol. Chem. 14, 158–164 (2016).

    Article  CAS  PubMed  Google Scholar 

  44. Xu, H. & Dickschat, J. S. Germacrene A–a central intermediate in sesquiterpene biosynthesis. Chem. Eur. J. 26, 17318–17341 (2020).

  45. Potter, K., Criswell, J., Zi, J., Stubbs, A. & Peters, R. J. Novel product chemistry from mechanistic analysis of ent-copalyl diphosphate synthases from plant hormone biosynthesis. Angew. Chem. Int. Ed. 53, 7198–7202 (2014).

    Article  CAS  Google Scholar 

  46. Potter, K. C. et al. Blocking deprotonation with retention of aromaticity in a plant ent-copalyl diphosphate synthase leads to product rearrangement. Angew. Chem. Int. Ed. 55, 634–638 (2016).

    Article  CAS  Google Scholar 

  47. Srivastava, P. L. et al. Redesigning the molecular choreography to prevent hydroxylation in germacradien-11-ol synthase catalysis. ACS Catal. 11, 1033–1041 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was supported by the German Research Foundation DFG (no. DI1536/7-2 to J.S.D.); the National Key Research and Development Program of China (nos. 2018YFA0903200 and 2018YFA0903201 to H.G.); the National Natural Science Foundation of China (nos. 21803080 and 32070042 to Y.-H.W., 81925037 to H.G., 81872759 to P.-H.S. and 21773313 to R.W.); the National High-level Personnel of Special Support Program (no. 2017RA2259 to H.G.); the Chang Jiang Scholars Program (Young Scholar) from the Ministry of Education of China (to H.G.); and the K. C. Wong Education Foundation (to H.G.). We thank X.-S. Yao (Guangzhou) for his support of this study through the 111 Project of the Ministry of Education of the People’s Republic of China (no. B13038), and the Guangzhou and Shenzhen Supercomputer Center for providing the computational source.

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Author notes

  1. These authors contributed equally: Yong-Heng Wang, Houchao Xu, Jian Zou.

Authors and Affiliations

  1. College of Pharmacy, Jinan University, Guangzhou, P. R. China

    Yong-Heng Wang, Jian Zou, Xian-Bo Chen, Yu-Qing Zhuang, Wei-Liang Liu, Guo-Dong Chen, Dan Hu, Hao Gao & Ping-Hua Sun

  2. School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, P. R. China

    Yong-Heng Wang & Ruibo Wu

  3. Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Bonn, Germany

    Houchao Xu, Ersin Celik & Jeroen S. Dickschat

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Contributions

J.S.D., R.W. and Y.-H.W. designed the research. J.S.D. supervised the experimental procedures. R.W. and P.-H.S. supervised the computational work. R.W. provided the Qchem–Tinker software package. Y.-H.W. and J.Z. performed the QM/MM MD simulations. H.X. and E.C. carried out the experimental work. Y.-H.W., J.Z., X.-B.C., Y.-Q.Z., W.-L.L., G.-D.C., D.H., H.G. and P.-H.S. analysed computational data. Y.-H.W., J.S.D., J.Z. and H.X. wrote the manuscript.

Corresponding authors

Correspondence to Ruibo Wu, Ping-Hua Sun or Jeroen S. Dickschat.

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The authors declare no competing interests.

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Nature Catalysis thanks Hideaki Oikawa, Per-Olof Syren and Marc van der Kamp for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Methods, Tables 1 and 2 and Figs. 1–26.

Reporting Summary

Supplementary Data 1

Computed structure FPP-exo.

Supplementary Data 2

Computed structure FPP-endo.

Supplementary Data 3

Computed structure I-endo.

Supplementary Data 4

Computed structure I-exo.

Supplementary Data 5

Computed structure TS II.

Supplementary Data 6

Computed structure II.

Supplementary Data 7

Computed structure TS II–III.

Supplementary Data 8

Computed structure III.

Supplementary Data 9

Computed structure TS III–IV.

Supplementary Data 10

Computed structure IV.

Supplementary Data 11

Computed structure TS IV–V.

Supplementary Data 12

Computed structure V.

Supplementary Data 13

Computed structure TS V–VI.

Supplementary Data 14

Computed structure VI.

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Wang, YH., Xu, H., Zou, J. et al. Catalytic role of carbonyl oxygens and water in selinadiene synthase. Nat Catal 5, 128–135 (2022). https://doi.org/10.1038/s41929-022-00735-0

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