7Y9H

Crystal structure of diterpene synthase VenA from Streptomyces venezuelae ATCC 15439

Summary for 7Y9H

• Entry DOI: 10.2210/pdb7y9h/pdb
• Descriptor: Diterpene synthase VenA, SODIUM ION, 1,2-ETHANEDIOL, ... (5 entities in total)
• Functional Keywords: pyrophosphate, terpenoids, lyase
• Biological source: Streptomyces venezuelae
• Total number of polymer chains: 2
• Total formula weight: 83899.12

Authors

Zhang, L.L.,Xie, Z.Z.,Huang, J.-W.,Hu, Y.C.,Liu, W.D.,Yang, Y.,Chen, C.-C.,Guo, R.-T. (deposition date: 2022-06-24, release date: 2023-06-14, Last modification date: 2023-11-29)

Primary citation

Li, Z.,Zhang, L.,Xu, K.,Jiang, Y.,Du, J.,Zhang, X.,Meng, L.H.,Wu, Q.,Du, L.,Li, X.,Hu, Y.,Xie, Z.,Jiang, X.,Tang, Y.J.,Wu, R.,Guo, R.T.,Li, S.
Molecular insights into the catalytic promiscuity of a bacterial diterpene synthase.
Nat Commun, 14:4001-4001, 2023

PubMed Abstract: Diterpene synthase VenA is responsible for assembling venezuelaene A with a unique 5-5-6-7 tetracyclic skeleton from geranylgeranyl pyrophosphate. VenA also demonstrates substrate promiscuity by accepting geranyl pyrophosphate and farnesyl pyrophosphate as alternative substrates. Herein, we report the crystal structures of VenA in both apo form and holo form in complex with a trinuclear magnesium cluster and pyrophosphate group. Functional and structural investigations on the atypical DSFVSD motif of VenA, versus the canonical Asp-rich motif of DDXX(X)D/E, reveal that the absent second Asp of canonical motif is functionally replaced by Ser116 and Gln83, together with bioinformatics analysis identifying a hidden subclass of type I microbial terpene synthases. Further structural analysis, multiscale computational simulations, and structure-directed mutagenesis provide significant mechanistic insights into the substrate selectivity and catalytic promiscuity of VenA. Finally, VenA is semi-rationally engineered into a sesterterpene synthase to recognize the larger substrate geranylfarnesyl pyrophosphate.

PubMed: 37414771
DOI: 10.1038/s41467-023-39706-9

Experimental method

X-RAY DIFFRACTION (2.03 Å)