Two different polyisoprene synthases have been shown [1,2,3] to share a number
of regions of sequence similarities:
Squalene synthase (EC 188.8.131.52) (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.
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