Summary: Squalene-hopene cyclase C-terminal domain
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
This is the Wikipedia entry entitled "Prenyltransferase". More...
Prenyltransferase Edit Wikipedia article
Prenyltransferases are a class of enzymes that transfer allylic prenyl groups to acceptor molecules. Prenyl transferases commonly refer to prenyl diphosphate synthases [1].
There are two classes of prenyltransferases, cis (or Z) and trans (or E), depending upon the stereo chemistry of the resulting products. Examples of trans-prenyltranferases include dimethylallyltranstransferase, and geranylgeranyl pyrophosphate synthase. Cis prenyltransferases include dehydrodolichol diphosphate synthase (involved in the production of dolichol precursors.
- ^ "Chem Rec. 2006;6(4):194-205."
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.
Squalene-hopene cyclase C-terminal domain Provide feedback
Squalene-hopene cyclase, EC:5.4.99.17, catalyses the cyclisation of squalene into hopene in bacteria. This reaction is part of a cationic cyclisation cascade, which is homologous to a key step in cholesterol biosynthesis. This family is the C-terminal half of the molecule.
Literature references
-
Wendt KU, Lenhart A, Schulz GE;, J Mol Biol. 1999;286:175-187.: The structure of the membrane protein squalene-hopene cyclase at 2.0 A resolution. PUBMED:9931258 EPMC:9931258
-
Lenhart A, Reinert DJ, Aebi JD, Dehmlow H, Morand OH, Schulz GE;, J Med Chem. 2003;46:2083-2092.: Binding structures and potencies of oxidosqualene cyclase inhibitors with the homologous squalene-hopene cyclase. PUBMED:12747780 EPMC:12747780
-
Milla P, Viola F, Oliaro Bosso S, Rocco F, Cattel L, Joubert BM, LeClair RJ, Matsuda SP, Balliano G;, Lipids. 2002;37:1171-1176.: Subcellular localization of oxidosqualene cyclases from Arabidopsis thaliana, Trypanosoma cruzi, and Pneumocystis carinii expressed in yeast. PUBMED:12617471 EPMC:12617471
Internal database links
SCOOP: | Glyco_hydro_127 Pec_lyase Prenyltrans SQHop_cyclase_N TED_complement |
Similarity to PfamA using HHSearch: | Prenyltrans Prenyltrans TED_complement TED_complement Pec_lyase SQHop_cyclase_N SQHop_cyclase_N |
This tab holds annotation information from the InterPro database.
InterPro entry IPR032696
Several enzymes catalyse mechanistically related reactions which involve the highly complex cyclic rearrangement of squalene or its 2,3 oxide. Squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY) are integral membrane proteins that catalyse a cationic cyclization cascade converting linear triterpenes to fused ring compounds [ PUBMED:11027983 , PUBMED:9295270 ]. Lanosterol synthase ( EC ) (oxidosqualene--lanosterol cyclase) catalyses the cyclization of (S)-2,3-epoxysqualene to lanosterol, the initial precursor of cholesterol, steroid hormones and vitamin D in vertebrates and of ergosterol in fungi (gene ERG7). Cycloartenol synthase ( EC ) (2,3-epoxysqualene--cycloartenol cyclase), is a plant enzyme that catalyses the cyclization of (S)-2,3-epoxysqualene to cycloartenol [ PUBMED:9519404 ], and hopene synthase ( EC ) (squalene--hopene cyclase), is a bacterial enzyme that catalyses the cyclization of squalene into hopene or diplopterol, a key step in hopanoid (triterpenoid) metabolism [ PUBMED:9931258 , PUBMED:2253626 ] also found in Aspergillus fumigatus as part of the gene cluster that mediates the biosynthesis fumihopaside A [ PUBMED:30977375 ]. These enzymes are evolutionary related [ PUBMED:7505443 ] proteins of about 70 to 85kDa and have an alpha 6 - alpha 6 barrel fold. Deletion of a single glycine residue of Alicyclobacillus acidocaldarius SQCY alters its substrate specificity into that of eukaryotic OSQCY [ PUBMED:15593147 ]. Both enzymes have a second minor domain, which forms an alpha-alpha barrel that is inserted into the major domain.
This entry represents the C-terminal domain of squalene cyclases [ PUBMED:9931258 , PUBMED:12747780 , PUBMED:12617471 ].
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
Loading domain graphics...
Pfam Clan
This family is a member of clan 6_Hairpin (CL0059), which has the following description:
This Clan includes CAZy clans GH-L, GH-M and GH-G. The members of this clan share a common structure composed of 6 helical hairpins. Most members of this superfamily are glycosyl hydrolase enzymes.
The clan contains the following 30 members:
Bac_rhamnosid6H C5-epim_C Cobalamin_bind DUF608 GDE_C GlcNAc_2-epim Glyco_hydro81C Glyco_hydro_100 Glyco_hydro_125 Glyco_hydro_127 Glyco_hydro_15 Glyco_hydro_36 Glyco_hydro_47 Glyco_hydro_48 Glyco_hydro_63 Glyco_hydro_65m Glyco_hydro_76 Glyco_hydro_8 Glyco_hydro_88 Glyco_hydro_9 Glycoamylase LANC_like Ldi Pec_lyase Prenyltrans SQHop_cyclase_C SQHop_cyclase_N TED_complement Terpene_synth TrehalaseAlignments
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...
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 (14) |
Full (6041) |
Representative proteomes | UniProt (17111) |
||||
---|---|---|---|---|---|---|---|
RP15 (754) |
RP35 (2736) |
RP55 (5242) |
RP75 (7966) |
||||
Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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 (14) |
Full (6041) |
Representative proteomes | UniProt (17111) |
||||
---|---|---|---|---|---|---|---|
RP15 (754) |
RP35 (2736) |
RP55 (5242) |
RP75 (7966) |
||||
Raw Stockholm | |||||||
Gzipped |
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: | Jackhammer:O27751; manual |
Previous IDs: | Prenyltrans_1; |
Type: | Repeat |
Sequence Ontology: | SO:0001068 |
Author: |
Coggill P |
Number in seed: | 14 |
Number in full: | 6041 |
Average length of the domain: | 282.4 aa |
Average identity of full alignment: | 31 % |
Average coverage of the sequence by the domain: | 44.23 % |
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: |
|
||||||||||||
Model length: | 319 | ||||||||||||
Family (HMM) version: | 9 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
Selections
Align selected sequences to HMM
Generate a FASTA-format file
Clear selection
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...
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
Loading...
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
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 SQHop_cyclase_C domain has been found. There are 54 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.
Loading structure mapping...
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.