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* Polyprenyl synthetases signatures *
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A variety of isoprenoid compounds  are synthesized by various organisms.   For
example in eukaryotes the isoprenoid biosynthetic  pathway is  responsible for
the synthesis of a variety  of end products including  cholesterol,  dolichol,
ubiquinone or coenzyme Q.  In  bacteria this pathway leads to the synthesis of
isopentenyl tRNA, isoprenoid quinones, and sugar carrier lipids.    Among  the
enzymes  that  participate  in  that  pathway,  are  a  number  of  polyprenyl
synthetase enzymes which catalyze a 1'4-condensation between 5 carbon isoprene
units.

Currently the sequence of some of these enzymes is known:

 - Eukaryotic farnesyl pyrophosphate synthetase (FPP synthetase) (EC 2.5.1.1 /
   EC 2.5.1.10) which  catalyzes  the  sequential condensation  of isopentenyl
   pyrophosphate (IPP) with dimethylallyl pyrophosphate (DMAPP), and then with
   the resultant  geranyl pyrophosphate  to form farnesyl pyrophosphate.   FPP
   synthetase is a cytoplasmic dimeric enzyme.
 - Prokaryotic farnesyl pyrophosphate synthetase (gene ispA).
 - Eukaryotic  geranylgeranyl  pyrophosphate   synthetase   (GGPP  synthetase)
   (EC 2.5.1.1 / EC 2.5.1.10 / EC 2.5.1.29)  which  catalyzes  the  sequential
   addition of the three molecules  of  IPP  onto DMAPP to form geranylgeranyl
   pyrophosphate.  In plants GGPP synthase is a chloroplast enzyme involved in
   the biosynthesis of terpenoids; in  fungi,  such as Neurospora crassa (gene
   al-3), this enzyme is involved in the biosynthesis of carotenoids.
 - Prokaryotic GGPP synthetase,  which  are  involved  in  the biosynthesis of
   carotenoids (gene crtE). Such  an  enzyme  is  also encoded in the cyanelle
   genome of Cyanophora paradoxa.
 - Eukaryotic hexaprenyl pyrophosphate synthetase,  which  is involved in  the
   biosynthesis of coenzyme Q  and which catalyzes the formation of all trans-
   polyprenyl pyrophosphates generally ranging in  length of  between 6 and 10
   isoprene units depending on the species.   HP synthetase is a mitochondrial
   membrane-associated enzyme.

It has been shown [1 to 5] that  all the above enzymes share some  regions  of
sequence similarity.   Two of these regions are rich in aspartic-acid residues
and could be  involved  in the  catalytic  mechanism and/or the binding of the
substrates. We have developed signature patterns for both regions.

Two possible additional members of this family of proteins are:

 - Escherichia coli hypothetical protein yhbD.
 - Bacillus subtilis spore germination protein C3 (gene gerC3).

We believe [6] that both  proteins  are most probably also enzymes involved in
isoprenoid metabolism.

-Consensus pattern: [LIVM](2)-x-D-D-x(2,4)-D-x(4)-R-R-G
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in SWISS-PROT: NONE.

-Consensus pattern: [LIVMFY]-G-x(2)-[FY]-Q-[LIVM]-x-D-D-[LIVMFY]-x-[DN]
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in SWISS-PROT: NONE.

-Last update: October 1993 / Patterns and text revised.

[ 1] Ashby M.N., Edwards P.A.
     J. Biol. Chem. 265:13157-13164(1990).
[ 2] Fujisaki S., Hara H., Nishimura Y., Horiuchi K., Nishino T.
     J. Biochem. 108:995-1000(1990).
[ 3] Carattoli A., Romano N., Ballario P., Morelli G., Macino G.
     J. Biol. Chem. 266:5854-5859(1991).
[ 4] Kuntz M., Roemer S., Suire C., Hugueney P., Weil J.H., Schantz R.,
     Camara B.
     Plant J. 2:25-34(1992).
[ 5] Math S.K., Hearst J.E., Poulter C.D.
     Proc. Natl. Acad. Sci. U.S.A. 89:6761-6764(1992).
[ 6] Bairoch A.
     Unpublished observations (1993).