Two different polyisoprene synthases have been shown [1,2,3] to share a number of regions of sequence similarities:

• Squalene synthase (EC 2.5.1.21) (farnesyl-diphosphate farnesyltransferase) (SQS), which catalyzes the conversion of two molecules of farnesyl diphosphate (FPP) into squalene. It is the first committed step in the cholesterol biosynthetic pathway. The reaction carried out by SQS is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of FPP to form presqualene diphosphate; this intermediate is then rearranged in a NADP-dependent reduction, to form squalene. SQS is found in eukaryotes. In yeast is is encoded by the ERG9 gene, in mammals by the FDFT1 gene. SQS seems to be membrane-bound.
• Phytoene synthase (EC 2.5.1.-) (PSY), which catalyzes the conversion of two molecules of geranylgeranyl diphosphate (GGPP) into phytoene. It is the second step in the biosynthesis of carotenoids from isopentenyl diphosphate. The reaction carried out by PSY is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of GGPP to form prephytoene diphosphate; this intermediate is then rearranged to form phytoene. PSY is found in all organisms that synthesize carotenoids: plants and photosynthetic bacteria as well as some non- photosynthetic bacteria and fungi. In bacteria PSY is encoded by the gene crtB. In plants PSY is localized in the chloroplast.

As it can be seen from the description above, both SQS and PSY share a number of functional similarities which are also reflected at the level of their primary structure. In particular three well conserved regions are shared by SQS and PSY; they could be involved in substrate binding and/or the catalytic mechanism. We developed signature patterns for the second and third conserved regions; they are localized in the central part of these enzymes.