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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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.
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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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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.
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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.
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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DOI: https://doi.org/10.1038/s41929-022-00735-0
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