8IH5

The cryo-EM structure of OsCyc1 that complexed with GGPP

Summary for 8IH5

• Entry DOI: 10.2210/pdb8ih5/pdb
• EMDB information: 35440
• Descriptor: Syn-copalyl diphosphate synthase, chloroplastic, GERANYLGERANYL DIPHOSPHATE (2 entities in total)
• Functional Keywords: syn-copalyl diphosphate synthase, labdane-related diterpenoid, ggpp complexed cryo-em structure, plant defense, plant protein
• Biological source: Oryza sativa Japonica Group (Japanese rice)
• Total number of polymer chains: 6
• Total formula weight: 533003.29

Authors

Ma, X.L.,Xu, H.F.,Jiang, T. (deposition date: 2023-02-22, release date: 2023-12-06, Last modification date: 2025-07-02)

Primary citation

Ma, X.,Xu, H.,Tong, Y.,Luo, Y.,Dong, Q.,Jiang, T.
Structural and functional investigations of syn-copalyl diphosphate synthase from Oryza sativa.
Commun Chem, 6:240-240, 2023

PubMed Abstract: The large superfamily of labdane-related diterpenoids is defined by the cyclization of linear geranylgeranyl pyrophosphate (GGPP), catalyzed by copalyl diphosphate synthases (CPSs) to form the basic decalin core, the copalyl diphosphates (CPPs). Three stereochemically distinct CPPs have been found in plants, namely (+)-CPP, ent-CPP and syn-CPP. Here, we used X-ray crystallography and cryo-EM methods to describe different oligomeric structures of a syn-copalyl diphosphate synthase from Oryza sativa (OsCyc1), and provided a cryo-EM structure of OsCyc1 mutant in complex with the substrate GGPP. Further analysis showed that tetramers are the dominant form of OsCyc1 in solution and are not necessary for enzyme activity in vitro. Through rational design, we identified an OsCyc1 mutant that can generate ent-CPP in addition to syn-CPP. Our work provides a structural and mechanistic basis for comparing different CPSs and paves the way for further enzyme design to obtain diterpene derivatives with specific chirality.

PubMed: 37932442
DOI: 10.1038/s42004-023-01042-w

Experimental method

ELECTRON MICROSCOPY (4 Å)