3P5R

Crystal Structure of Taxadiene Synthase from Pacific Yew (Taxus brevifolia) in complex with Mg2+ and 2-fluorogeranylgeranyl diphosphate

Summary for 3P5R

• Entry DOI: 10.2210/pdb3p5r/pdb
• Related: 3P5P
• Descriptor: Taxadiene synthase, MAGNESIUM ION, (2Z,6E,10E)-2-fluoro-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl trihydrogen diphosphate, ... (4 entities in total)
• Functional Keywords: class i and ii terpene cyclase fold, diterpene cyclase, ddxxd motif, nse/dte motif, 2-fluoro-geranylgeranyl diphosphate, biosynthesis of paclitaxel, lyase
• Biological source: Taxus brevifolia (Pacific yew)
• Total number of polymer chains: 2
• Total formula weight: 176685.95

Authors

Koksal, M.,Christianson, D.W. (deposition date: 2010-10-10, release date: 2010-12-29, Last modification date: 2023-09-06)

Primary citation

Koksal, M.,Jin, Y.,Coates, R.M.,Croteau, R.,Christianson, D.W.
Taxadiene synthase structure and evolution of modular architecture in terpene biosynthesis.
Nature, 469:116-120, 2011

PubMed Abstract: With more than 55,000 members identified so far in all forms of life, the family of terpene or terpenoid natural products represents the epitome of molecular biodiversity. A well-known and important member of this family is the polycyclic diterpenoid Taxol (paclitaxel), which promotes tubulin polymerization and shows remarkable efficacy in cancer chemotherapy. The first committed step of Taxol biosynthesis in the Pacific yew (Taxus brevifolia) is the cyclization of the linear isoprenoid substrate geranylgeranyl diphosphate (GGPP) to form taxa-4(5),11(12)diene, which is catalysed by taxadiene synthase. The full-length form of this diterpene cyclase contains 862 residues, but a roughly 80-residue amino-terminal transit sequence is cleaved on maturation in plastids. We now report the X-ray crystal structure of a truncation variant lacking the transit sequence and an additional 27 residues at the N terminus, hereafter designated TXS. Specifically, we have determined structures of TXS complexed with 13-aza-13,14-dihydrocopalyl diphosphate (1.82 Å resolution) and 2-fluorogeranylgeranyl diphosphate (2.25 Å resolution). The TXS structure reveals a modular assembly of three α-helical domains. The carboxy-terminal catalytic domain is a class I terpenoid cyclase, which binds and activates substrate GGPP with a three-metal ion cluster. The N-terminal domain and a third 'insertion' domain together adopt the fold of a vestigial class II terpenoid cyclase. A class II cyclase activates the isoprenoid substrate by protonation instead of ionization, and the TXS structure reveals a definitive connection between the two distinct cyclase classes in the evolution of terpenoid biosynthesis.

PubMed: 21160477
DOI: 10.1038/nature09628

Experimental method

X-RAY DIFFRACTION (2.247 Å)