9C7L

Crystal structure of pentalenene synthase variant F76A complexed with 2-fluorofarnesyl diphosphate

Summary for 9C7L

• Entry DOI: 10.2210/pdb9c7l/pdb
• Descriptor: Pentalenene synthase, (2Z,6E)-2-fluoro-3,7,11-trimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: terpene synthase, cyclase, sesquiterpene synthase, complex, inhibitors, fluoro analog, metal binding protein
• Biological source: Streptomyces exfoliatus
• Total number of polymer chains: 2
• Total formula weight: 76421.86

Authors

Prem Kumar, R.,Ellenburg, W.H.,Oprian, D.D. (deposition date: 2024-06-10, release date: 2024-11-06, Last modification date: 2024-11-13)

Primary citation

Kumar, R.P.,Matos, J.O.,Black, B.Y.,Ellenburg, W.H.,Chen, J.,Patterson, M.,Gehtman, J.A.,Theobald, D.L.,Krauss, I.J.,Oprian, D.D.
Crystal Structure of Caryolan-1-ol Synthase, a Sesquiterpene Synthase Catalyzing an Initial Anti-Markovnikov Cyclization Reaction.
Biochemistry, 63:2904-2915, 2024

PubMed Abstract: In a continuing effort to understand reaction mechanisms of terpene synthases catalyzing initial anti-Markovnikov cyclization reactions, we solved the X-ray crystal structure of (+)-caryolan-1-ol synthase (CS) from , with and without an inactive analog of the farnesyl diphosphate (FPP) substrate, 2-fluorofarnesyl diphosphate (2FFPP), bound in the active site of the enzyme. The CS-2FFPP structure was solved to 2.65 Å resolution and showed the ligand in an elongated orientation, incapable of undergoing the initial cyclization event to form a C1-C11 bond. Intriguingly, the apo CS structure (2.2 Å) also had electron density in the active site, in this case, well fit by a curled-up tetraethylene glycol molecule recruited, presumably, from the crystallization medium. The density was also well fit by a molecule of farnesene suggesting that the structure may mimic an intermediate along the reaction coordinate. The curled-up conformation of tetraethylene glycol was accompanied by dramatic rotation of some active-site residues in comparison to the 2FFPP-structure. Most notably, W56 and F183 undergo 90° rotations between the 2FFPP complex and apoenzyme structures, suggesting that these residues provide interactions that help curl the tetraethylene glycol molecule in the active site, and by extension perhaps also a derivative of the FPP substrate in the normal course of the cyclization reaction. In support of this proposal, the CS W56L and F183A variants were observed to be severely restricted in their ability to catalyze C1-C11 cyclization of the FPP substrate and instead produced predominantly acyclic terpene products dominated by farnesol, β-farnesene, and nerolidol.

PubMed: 39400323
DOI: 10.1021/acs.biochem.4c00547

Experimental method

X-RAY DIFFRACTION (2.2 Å)