In vertebrates there are two isozymes located in different subcellular compartments: a cytosolic form which is the starting point of the mevalonate pathway which leads to cholesterol and other sterolic and isoprenoid compounds and a mitochondrial form responsible for ketone body biosynthesis. HMG-CoA is also found in other eukaryotes such as insect, plants and fungi.

A cysteine is known to act as the catalytic nucleophile in the first step of the reaction, the acetylation of the enzyme by acetyl-CoA. The conserved region around this active site residue has been used as a signature pattern.
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