9B99

Crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase

Summary for 9B99

• Entry DOI: 10.2210/pdb9b99/pdb
• Descriptor: Labda-7,13E-dienyl diphosphate synthase (2 entities in total)
• Functional Keywords: terpene synthases class ii diterpene synthases, plant protein
• Biological source: Grindelia hirsutula
• Total number of polymer chains: 1
• Total formula weight: 84727.60

Authors

Pereira, J.H.,Cowie, A.E.,Zerbe, P.,Adams, P.D. (deposition date: 2024-04-01, release date: 2024-11-06)

Primary citation

Cowie, A.E.,Pereira, J.H.,DeGiovanni, A.,McAndrew, R.P.,Palayam, M.,Peek, J.O.,Muchlinski, A.J.,Yoshikuni, Y.,Shabek, N.,Adams, P.D.,Zerbe, P.
The crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase reveals active site features controlling catalytic specificity.
J.Biol.Chem., :107921-107921, 2024

PubMed Abstract: Diterpenoid natural products serve critical functions in plant development and ecological adaptation and many diterpenoids have economic value as bioproducts. The family of class II diterpene synthases catalyzes the committed reactions in diterpenoid biosynthesis, converting a common geranylgeranyl diphosphate precursor into different bicyclic prenyl diphosphate scaffolds. Enzymatic rearrangement and modification of these precursors generates the diversity of bioactive diterpenoids. We report the crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase, GrTPS2, at 2.1 Å of resolution. GrTPS2 catalyzes the committed reaction in the biosynthesis of grindelic acid, which represents the signature metabolite in species of gumweed (Grindelia spp., Asteraceae). Grindelic acid has been explored as a potential source for drug leads and biofuel production. The GrTPS2 crystal structure adopts the conserved three-domain fold of class II diterpene synthases featuring a functional active site in the γβ-domain and a vestigial ɑ-domain. Substrate docking into the active site of the GrTPS2 apo protein structure predicted catalytic amino acids. Biochemical characterization of protein variants identified residues with impact on enzyme activity and catalytic specificity. Specifically, mutagenesis of Y457 provided mechanistic insight into the position-specific deprotonation of the intermediary carbocation to form the characteristic 7,13 double bond of 7,13-copalyl diphosphate.

PubMed: 39454950
DOI: 10.1016/j.jbc.2024.107921

Experimental method

X-RAY DIFFRACTION (2.12 Å)