 Dimethylallyl diphosphate

Dimethylallyl diphosphate is a five-carbon isoprenoid building block carrying an activated diphosphate group. Its carbon skeleton is $(\mathrm{C}{\mathrm{H}}_3{)}_2\mathrm{C}=\mathrm{CH}-\mathrm{C}{\mathrm{H}}_2-$, attached through oxygen to diphosphate. The neutral-acid molecular formula is ${\mathrm{C}}_5{\mathrm{H}}_{12}{\mathrm{O}}_7{\mathrm{P}}_2$. ChEBI calls this specific compound prenyl diphosphate; the title here distinguishes it from longer prenyl diphosphates.^[ref]

The placement of its double bond differs from that in isopentenyl diphosphate. Matching molecular formulas therefore does not make these substrates interchangeable: an enzyme encounters a specific arrangement of bonds, not just five carbons and two phosphorus atoms.

In the reaction catalysed by dimethylallyltranstransferase, dimethylallyl diphosphate supplies the donor group, isopentenyl diphosphate is the other substrate, and ten-carbon geranyl diphosphate is produced with release of diphosphate.^[ref] Mixing $1\mu \mathrm{mol}$ of each substrate can produce at most $1\mu \mathrm{mol}$ of geranyl product in the ideal isolated reaction. Summing both substrate amounts and predicting two micromoles of product would count molecules without respecting the two-substrate reaction stoichiometry.