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0  structures 2177  species 0  interactions 4976  sequences 98  architectures

Family: SQHop_cyclase_N (PF13249)

Summary: Squalene-hopene cyclase N-terminal domain

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Squalene-hopene cyclase N-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 N-terminal domain.

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


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR032697

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 ]. 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 N-terminal domain of squalene cyclases [ PUBMED:9931258 , PUBMED:12747780 ].

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 29 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 Trehalase

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...

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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.

  Seed
(121)
Full
(4976)
Representative proteomes UniProt
(12496)
RP15
(510)
RP35
(2180)
RP55
(4055)
RP75
(6296)
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PP/heatmap 1 View           

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

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(121)
Full
(4976)
Representative proteomes UniProt
(12496)
RP15
(510)
RP35
(2180)
RP55
(4055)
RP75
(6296)
Alignment:
Format:
Order:
Sequence:
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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
(121)
Full
(4976)
Representative proteomes UniProt
(12496)
RP15
(510)
RP35
(2180)
RP55
(4055)
RP75
(6296)
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 View help on the curation process

Seed source: Jackhmmer:O26856
Previous IDs: Prenyltrans_2;
Type: Repeat
Sequence Ontology: SO:0001068
Author: Coggill P
Number in seed: 121
Number in full: 4976
Average length of the domain: 270.10 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 40.48 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.2 26.2
Trusted cut-off 26.2 26.2
Noise cut-off 26.1 26.1
Model length: 291
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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

Selections

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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
A0A0N7KEN4 View 3D Structure Click here
A0A0R0EDA7 View 3D Structure Click here
A0A0R0G4T9 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
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
A0A1D6KEK0 View 3D Structure Click here
A0A1D6KEK3 View 3D Structure Click here
A0A1D6LG90 View 3D Structure Click here
A0A1D6LG93 View 3D Structure Click here
A0A1D6Q2R1 View 3D Structure Click here
A0A1D6QL70 View 3D Structure Click here
A0A1D6QT72 View 3D Structure Click here
A0A1R3LZ28 View 3D Structure Click here
A4HSV6 View 3D Structure Click here
B0S5M5 View 3D Structure Click here
B6EXY6 View 3D Structure Click here
C0PGA6 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
K7KEK9 View 3D Structure Click here
O23390 View 3D Structure Click here
P0C8Y0 View 3D Structure Click here
P38604 View 3D Structure Click here
P48450 View 3D Structure Click here
Q0IS49 View 3D Structure Click here
Q0IT98 View 3D Structure Click here
Q0J778 View 3D Structure Click here
Q1G1A4 View 3D Structure Click here
Q2R712 View 3D Structure Click here
Q4DZE6 View 3D Structure Click here
Q4E2Y7 View 3D Structure Click here
Q55D85 View 3D Structure Click here
Q6Z2X6 View 3D Structure Click here
Q8BLN5 View 3D Structure Click here
Q8RWT0 View 3D Structure Click here
Q9C5M3 View 3D Structure Click here
Q9FI37 View 3D Structure Click here
Q9FJV8 View 3D Structure Click here
Q9FR95 View 3D Structure Click here
Q9FZI2 View 3D Structure Click here
Q9LS68 View 3D Structure Click here
Q9LVY2 View 3D Structure Click here
Q9SYN1 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;