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TitleStructural and functional investigations of syn-copalyl diphosphate synthase from Oryza sativa.
Journal, issue, pagesCommun Chem, Vol. 6, Issue 1, Page 240, Year 2023
Publish dateNov 6, 2023
AuthorsXiaoli Ma / Haifeng Xu / Yuru Tong / Yunfeng Luo / Qinghua Dong / Tao Jiang /
PubMed AbstractThe 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 ...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.
External linksCommun Chem / PubMed:37932442 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution3.49 - 7.9 Å
Structure data

35202

8i6p

EMDB-35202, PDB-8i6p:
The cryo-EM structure of OsCyc1 tetramer state
Method: EM (single particle) / Resolution: 3.5 Å

35206

8i6t

EMDB-35206, PDB-8i6t:
The cryo-EM structure of OsCyc1 hexamer state
Method: EM (single particle) / Resolution: 3.7 Å

35207

8i6u

EMDB-35207, PDB-8i6u:
The cryo-EM structure of OsCyc1 dimer state
Method: EM (single particle) / Resolution: 7.9 Å

35440

8ih5

EMDB-35440, PDB-8ih5:
The cryo-EM structure of OsCyc1 that complexed with GGPP
Method: EM (single particle) / Resolution: 4.0 Å

PDB-8kbw:
The crystal structure of syn-copalyl diphosphate synthase from Oryza sativa
Method: X-RAY DIFFRACTION / Resolution: 3.49 Å

Chemicals

ChemComp-GRG:
GERANYLGERANYL DIPHOSPHATE

Source
  • oryza sativa japonica group (Japanese rice)
KeywordsISOMERASE / syn-copalyl diphosphate synthase / labdane-related diterpenoids / oligomer cryo-EM structure / plant defense / PLANT PROTEIN / hexamer cryo-EM structure / dimer cryo-EM structure / labdane-related diterpenoid / GGPP complexed cryo-EM structure / apo-state crystal structure

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