Summary: Squalene/phytoene synthase

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Wikipedia: Squalene/phytoene synthase family
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This is the Wikipedia entry entitled "Squalene/phytoene synthase family". More...

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Squalene/phytoene synthase family Edit Wikipedia article

SQS_PSY

Identifiers

Symbol

SQS_PSY

1ezf / SCOPe / SUPFAM

Available protein structures:
Pfam Â	structures / ECOD Â
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

Squalene synthase EC (farnesyl-diphosphate farnesyltransferase) (SQS) and Phytoene synthase EC (PSY) are enzymes that share a number of functional similarities. These similarities are also reflected in their primary structure.^[1]^[2]^[3] In particular three well conserved regions are shared by SQS and PSY; they could be involved in substrate binding and/or the catalytic mechanism. SQS 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:

2 FPP -> presqualene diphosphate + NADP -> squalene

SQS is found in eukaryotes. In yeast it is encoded by the ERG9 gene, in mammals by the FDFT1 gene. SQS is membrane-bound.

PSY 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.

2 GGPP -> prephytoene diphosphate -> 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.

References

^ Summers C, Karst F, Charles AD (1993). "Cloning, expression and characterisation of the cDNA encoding human hepatic squalene synthase, and its relationship to phytoene synthase". Gene. 136 (1-2Che): 185â€“92. PMIDÂ 8294001. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
^ Robinson GW, Tsay YH, Kienzle BK, Smith-Monroy CA, Bishop RW (1993). "Conservation between human and fungal squalene synthetases: similarities in structure, function, and regulation". Mol. Cell. Biol. 13 (5): 2706â€“17. PMCÂ 359645. PMIDÂ 8474436. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
^ RÃƒÂ¶mer S, Hugueney P, Bouvier F, Camara B, Kuntz M (1993). "Expression of the genes encoding the early carotenoid biosynthetic enzymes in Capsicum annuum". Biochem. Biophys. Res. Commun. 196 (3): 1414â€“21. doi:10.1006/bbrc.1993.2410. PMIDÂ 8250898. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

This article incorporates text from the public domain Pfam and InterPro: IPR002060

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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No Pfam abstract.

Internal database links

SCOOP:

polyprenyl_synt

External database links

PROSITE:	PDOC00802
SCOP:	1ezf

This tab holds annotation information from the InterPro database.

InterPro entry IPR002060

Squalene synthase EC (farnesyl-diphosphate farnesyltransferase)(SQS) and phytoene synthase EC (PSY) share a number of functional similarities. These similarities are also reflected at the level of their primary structure [ PUBMED:8294001 , PUBMED:8474436 , PUBMED:8250898 ]. In particular three well conserved regions are shared by SQS and PSY; they could be involved in substrate binding and/or the catalytic mechanism. SQS 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:

2 FPP -> presqualene diphosphate + NADP -> squalene

SQS is found in eukaryotes. In yeast it is encoded by the ERG9 gene, in mammals by the FDFT1 gene. SQS seems to be membrane-bound.

PSY 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.

2 GGPP -> prephytoene diphosphate -> 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.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Molecular function	transferase activity (GO:0016740)
Biological process	biosynthetic process (GO:0009058)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Terp_synthase (CL0613), which has the following description:

This superfamily includes a diverse range of terpene synthase enzymes which share an alpha helical core.

The clan contains the following 7 members:

HEPPP_synt_1 polyprenyl_synt SQS_PSY Terpene_syn_C_2 Terpene_synth_C TRI5 UbiA

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
UniProt: alignment generated by searching the UniProtKB sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

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PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.

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Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

	Seed (88)	Full (12127)	Representative proteomes				UniProt (41447)
	Seed (88)	Full (12127)	RP15 (1636)	RP35 (5507)	RP55 (11445)	RP75 (18404)	UniProt (41447)
Jalview	View	View	View	View	View	View	View
HTML	View
PP/heatmap	₁

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (88)	Full (12127)	Representative proteomes				UniProt (41447)
	Seed (88)	Full (12127)	RP15 (1636)	RP35 (5507)	RP55 (11445)	RP75 (18404)	UniProt (41447)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

	Seed (88)	Full (12127)	Representative proteomes				UniProt (41447)
	Seed (88)	Full (12127)	RP15 (1636)	RP35 (5507)	RP55 (11445)	RP75 (18404)	UniProt (41447)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation

Seed source:

Prosite

Previous IDs:

none

Type:

Domain

Sequence Ontology:

SO:0000417

Author:

Finn RD

Number in seed:

88

Number in full:

12127

Average length of the domain:

252.5 aa

Average identity of full alignment:

20 %

Average coverage of the sequence by the domain:

74.36 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	26.0	26.0
Trusted cut-off	26.0	26.0
Noise cut-off	25.8	25.9

Model length:

263

Family (HMM) version:

22

Download:

download the raw HMM for this family

Species distribution

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

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order
family
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Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

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Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

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Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the SQS_PSY domain has been found. There are 154 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein	Predicted structure	External Information
A0A044QL57	View 3D Structure	Click here
A0A0A2UYM1	View 3D Structure	Click here
A0A0D2E8M6	View 3D Structure	Click here
A0A0D2EVB8	View 3D Structure	Click here
A0A0D2GPQ3	View 3D Structure	Click here
A0A0K0EKR3	View 3D Structure	Click here
A0A0R0HM78	View 3D Structure	Click here
A0A0R4IVV5	View 3D Structure	Click here
A0A0R4J4H6	View 3D Structure	Click here
A0A175W7X6	View 3D Structure	Click here
A0A175WHU1	View 3D Structure	Click here
A0A1C1C9J1	View 3D Structure	Click here
A0A1C1CDP1	View 3D Structure	Click here
A0A1C1CZA7	View 3D Structure	Click here
A0A1D6IAQ5	View 3D Structure	Click here
A0A1D6L8A5	View 3D Structure	Click here
A0A1D6LJ95	View 3D Structure	Click here
A0A1D6LKM3	View 3D Structure	Click here
A0A1D8PI71	View 3D Structure	Click here
A0A1D8PJ15	View 3D Structure	Click here
A0A3P7E5P0	View 3D Structure	Click here
A0A3P7PAL1	View 3D Structure	Click here
A0A5K4F4C3	View 3D Structure	Click here
A0A5K4F5S2	View 3D Structure	Click here
A0A5K4F695	View 3D Structure	Click here
A0A5K4F7L0	View 3D Structure	Click here
A2AIL4	View 3D Structure	Click here
A2QM49	View 3D Structure	Click here
A4I799	View 3D Structure	Click here
A4ID42	View 3D Structure	Click here
A7YVD7	View 3D Structure	Click here
B0KZ40	View 3D Structure	Click here
B2ATB0	View 3D Structure	Click here
B2WAQ3	View 3D Structure	Click here
B4FE64	View 3D Structure	Click here
B4FPS7	View 3D Structure	Click here
B6UV92	View 3D Structure	Click here
C0NFH6	View 3D Structure	Click here
C0NVZ9	View 3D Structure	Click here
C1GV53	View 3D Structure	Click here

Showing 40 matches

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Family: SQS_PSY (PF00494)

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