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54  structures 2435  species 0  interactions 6041  sequences 154  architectures

Family: SQHop_cyclase_C (PF13243)

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.

  1. ^ "Chem Rec. 2006;6(4):194-205."

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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:, 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

  1. 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

  2. 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

  3. 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

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...

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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 Trehalase


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...

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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.

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

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Representative proteomes UniProt

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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...


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 View help on the curation process

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 View help on HMM parameters

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 26.1 26.1
Trusted cut-off 26.1 26.1
Noise cut-off 26.0 26.0
Model length: 319
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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...

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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.

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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
A0A0D2EZI9 View 3D Structure Click here
A0A0R0EDA7 View 3D Structure Click here
A0A0R0G4T9 View 3D Structure Click here
A0A0R0G851 View 3D Structure Click here
A0A0R0IG75 View 3D Structure Click here
A0A0R0IYV7 View 3D Structure Click here
A0A0R0J895 View 3D Structure Click here
A0A0R4J2H1 View 3D Structure Click here
A0A175W263 View 3D Structure Click here
A0A1C1CVG5 View 3D Structure Click here
A0A1D6FEN9 View 3D Structure Click here
A0A1D6FEP1 View 3D Structure Click here
A0A1D6GMB7 View 3D Structure Click here
A0A1D6GVH8 View 3D Structure Click here
A0A1D6H0A5 View 3D Structure Click here
A0A1D6IYU4 View 3D Structure Click here
A0A1D6KEJ9 View 3D Structure Click here
A0A1D6KEK8 View 3D Structure Click here
A0A1D6KEK9 View 3D Structure Click here
A0A1D6LG90 View 3D Structure Click here
A0A1D6Q2R1 View 3D Structure Click here
A0A1D6QL70 View 3D Structure Click here
A0A1D6QT72 View 3D Structure Click here
A1CVK0 View 3D Structure Click here
A4HSV6 View 3D Structure Click here
A9AWD5 View 3D Structure Click here
B0S5M5 View 3D Structure Click here
B6EXY6 View 3D Structure Click here
C0NTW1 View 3D Structure Click here
C0P0D4 View 3D Structure Click here
C0PGA6 View 3D Structure Click here
C1H0A2 View 3D Structure Click here
D5SJ87 View 3D Structure Click here
E4V6I8 View 3D Structure Click here
E7DN63 View 3D Structure Click here
E7DN64 View 3D Structure Click here
H2KWF1 View 3D Structure Click here
I1J4A4 View 3D Structure Click here
I1MFB9 View 3D Structure Click here
K7KEK6 View 3D Structure Click here