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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.

December 2004 / Pattern and text revised.

PROSITE methods (with tools and information) covered by this documentation:

SQUALEN_PHYTOEN_SYN_1, PS01044; Squalene and phytoene synthases signature 1  (PATTERN)

Consensus pattern: Y-[CSAM]-x(2)-[VSG]-A-[GSA]-[LIVAT]-[IV]-G-x(2)-[LMSC]-x(2)-[LIV] Sequences known to belong to this class detected by the pattern: ALL Other sequence(s) detected in Swiss-Prot: 1.

• Retrieve an alignment of Swiss-Prot true positive hits:   Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format • Retrieve the sequence logo from the alignment • Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS01044 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS01044 • Scan Swiss-Prot/TrEMBL entries against PS01044 • view ligand binding statistics

Matching PDB structures: 1EZF 2ZCO 2ZCP 2ZCQ ... [ALL]

SQUALEN_PHYTOEN_SYN_2, PS01045; Squalene and phytoene synthases signature 2  (PATTERN)

Consensus pattern: [LIVM]-G-x(3)-Q-x(2,3)-[ND]-[IFL]-x-[RE]-D-[LIVMFY]-x(2)-[DE]-x(4,7)-R-x-[FY]-x-P Sequences known to belong to this class detected by the pattern: ALL Other sequence(s) detected in Swiss-Prot: NONE.

• Retrieve an alignment of Swiss-Prot true positive hits:   Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format • Retrieve the sequence logo from the alignment • Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS01045 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS01045 • Scan Swiss-Prot/TrEMBL entries against PS01045 • view ligand binding statistics

Matching PDB structures: 1EZF 3ASX 3LEE 3Q2Z ... [ALL]

1	Authors	Summers C., Karst F., Charles A.D.
	Title	Cloning, expression and characterisation of the cDNA encoding human hepatic squalene synthase, and its relationship to phytoene synthase.
	Source	Gene 136:185-192(1993).
	PubMed ID	8294001

2	Authors	Robinson G.W., Tsay Y.H., Kienzle B.K., Smith-Monroy C.A., Bishop R.W.
	Title	Conservation between human and fungal squalene synthetases: similarities in structure, function, and regulation.
	Source	Mol. Cell. Biol. 13:2706-2717(1993).
	PubMed ID	8474436

3	Authors	Roemer S., Hugueney P., Bouvier F., Camara B., Kuntz M.
	Source	Biochem. Biophys. Res. Commun. 196:1414-1421(1993).

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