Molecule of the Month: Isoprene Synthase
Plants release a billion metric tons of isoprene and other organic gases every year.
Exploring the Structure
Terpenoid Synthase Fold
A large collection of enzymes uses DMAPP and IPP to build different isoprenoid molecules. Many of these enzymes, including isoprene synthase, share a common protein fold, termed the “terpenoid synthase fold.” Four examples are shown here. Isoprene synthase breaks off the phosphate and releases isoprene. Farnesyl diphosphate synthase (PDB entry 1fps) connects three of the isoprene units together to create a longer chain. Bornyl diphosphate synthase (PDB entry 1n20) forms rings out of these types of longer chains. Taxadiene synthase (PDB entry 3p5p) fashions a more complicated structure out of isoprene units for use in building taxol. To explore these structures in more detail, click on the image for an interactive JSmol.
Topics for Further Discussion
- Isoprenoid molecules have a distinctive shape, with a zigzag string of carbon atoms and little one-carbon branches along the chain. For representative examples, take a look at the page for farnesyl diphosphate or search for molecules like chlorophyll, retinol or beta-carotene with the Chemical Component Search to explore the chemical structures of these molecules.
- These enzymes often use magnesium enzymes in the active site—based on the structures, can you discover what are these ions doing?
September 2016, Luigi Di Costanzo, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2016_9